diff --git a/.classpath b/.classpath index e43402fa..aa6ee384 100644 --- a/.classpath +++ b/.classpath @@ -1,36 +1,5 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff --git a/.gitignore b/.gitignore index 2f7896d1..d2b96f9e 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ target/ +/.DS_Store diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/minerva-cli/.classpath b/minerva-cli/.classpath new file mode 100644 index 00000000..f619a536 --- /dev/null +++ b/minerva-cli/.classpath @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/minerva-cli/.gitignore b/minerva-cli/.gitignore new file mode 100644 index 00000000..2f7896d1 --- /dev/null +++ b/minerva-cli/.gitignore @@ -0,0 +1 @@ +target/ diff --git a/minerva-cli/.project b/minerva-cli/.project new file mode 100644 index 00000000..6ffc9639 --- /dev/null +++ b/minerva-cli/.project @@ -0,0 +1,23 @@ + + + minerva-cli + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/minerva-cli/.settings/org.eclipse.core.resources.prefs b/minerva-cli/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 00000000..e9441bb1 --- /dev/null +++ b/minerva-cli/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,3 @@ +eclipse.preferences.version=1 +encoding//src/main/java=UTF-8 +encoding/=UTF-8 diff --git a/minerva-cli/.settings/org.eclipse.jdt.core.prefs b/minerva-cli/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 00000000..ec4300d5 --- /dev/null +++ b/minerva-cli/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7 +org.eclipse.jdt.core.compiler.compliance=1.7 +org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning +org.eclipse.jdt.core.compiler.source=1.7 diff --git a/minerva-cli/.settings/org.eclipse.m2e.core.prefs b/minerva-cli/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/minerva-cli/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/minerva-cli/pom.xml b/minerva-cli/pom.xml new file mode 100644 index 00000000..c45028b2 --- /dev/null +++ b/minerva-cli/pom.xml @@ -0,0 +1,24 @@ + + 4.0.0 + + minerva + org.geneontology + 0.2.2-SNAPSHOT + + minerva-cli + Minerva-CommandLineInterface + + + + org.geneontology + minerva-converter + ${project.parent.version} + + + org.bbop + OWLTools-Runner + + + + diff --git a/minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java b/minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java new file mode 100644 index 00000000..c5d59002 --- /dev/null +++ b/minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java @@ -0,0 +1,11 @@ +package org.geneontology.minerva.cli; + + +public class CommandLineInterface { + + public static void main(String[] args) throws Exception { + MinervaCommandRunner cr = new MinervaCommandRunner(); + cr.run(args); + } + +} diff --git a/minerva-cli/src/main/java/org/geneontology/minerva/cli/MinervaCommandRunner.java b/minerva-cli/src/main/java/org/geneontology/minerva/cli/MinervaCommandRunner.java new file mode 100644 index 00000000..3aa60ac2 --- /dev/null +++ b/minerva-cli/src/main/java/org/geneontology/minerva/cli/MinervaCommandRunner.java @@ -0,0 +1,646 @@ +package org.geneontology.minerva.cli; + +import java.io.File; +import java.io.FileOutputStream; +import java.io.FilenameFilter; +import java.io.OutputStream; +import java.io.PrintWriter; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat; +import org.geneontology.minerva.GafToLegoIndividualTranslator; +import org.geneontology.minerva.GafToLegoTranslator; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.generate.LegoModelGenerator; +import org.geneontology.minerva.legacy.LegoToGeneAnnotationTranslator; +import org.geneontology.minerva.util.MinimalModelGenerator; +import org.semanticweb.elk.owlapi.ElkReasonerFactory; +import org.semanticweb.owlapi.io.OWLFunctionalSyntaxOntologyFormat; +import org.semanticweb.owlapi.io.RDFXMLOntologyFormat; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLEntity; +import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectIntersectionOf; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyFormat; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; + +import owltools.cli.JsCommandRunner; +import owltools.cli.Opts; +import owltools.cli.tools.CLIMethod; +import owltools.gaf.BioentityDocument; +import owltools.gaf.GafDocument; +import owltools.gaf.eco.EcoMapperFactory; +import owltools.gaf.eco.SimpleEcoMapper; +import owltools.gaf.io.GpadWriter; +import owltools.graph.OWLGraphWrapper; +import owltools.io.OWLPrettyPrinter; +import owltools.vocab.OBOUpperVocabulary; +import uk.ac.manchester.cs.owlapi.modularity.ModuleType; +import uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor; + +public class MinervaCommandRunner extends JsCommandRunner { + + private volatile MinimalModelGenerator mmg = null; + + + private synchronized MinimalModelGenerator getMinimalModelGenerator(boolean isCreateNewAbox) throws OWLOntologyCreationException { + + if (mmg == null) { + OWLReasonerFactory rf = new ElkReasonerFactory(); + if (isCreateNewAbox) { + ModelContainer model = new ModelContainer(g.getSourceOntology(), rf); + mmg = new MinimalModelGenerator(model); + } + else { + ModelContainer model = new ModelContainer(g.getSourceOntology(), g.getSourceOntology(), rf); + mmg = new MinimalModelGenerator(model); + } + } + return mmg; + } + + @CLIMethod("--generate-minimal-model") + public void generateMinimalModel(Opts opts) throws Exception { + opts.info("[--no-collapse] [--no-reduce] [--reuse-tblox] [-x] [-a] [-s] CLASS", "Generates default/proto individuals for a class"); + boolean isCollapse = true; + boolean isReduce = true; + boolean isExtractModule = false; + boolean isPrecomputePropertyClassCombinations = true; + boolean isCreateNewAbox = true; + boolean isAllIndividuals = false; + boolean isStrict = true; + Set normProps = new HashSet(); + Set preservedClassSet = null; + OWLClass c; + while (opts.hasOpts()) { + if (opts.nextEq("--no-collapse")) { + opts.info("", "if set, do not heuristically collapse individuals"); + isCollapse = false; + } + else if (opts.nextEq("--no-reduce")) { + opts.info("", "if set, do not perform transitive reduction"); + isReduce = false; + } + else if (opts.nextEq("--reuse-tbox")) { + opts.info("", "if set, place new individuals in the ontology"); + isCreateNewAbox = false; + } + else if (opts.nextEq("-a|--all-individuals")) { + isAllIndividuals = true; + } + else if (opts.nextEq("-s|--is-strict")) { + isStrict = true; + } + else if (opts.nextEq("-x|--extract-module")) { + isExtractModule = true; + } + else if (opts.nextEq("-q|--quick")) { + isPrecomputePropertyClassCombinations = false; + } + else if (opts.nextEq("-p|--property")) { + normProps.add(this.resolveObjectProperty(opts.nextOpt())); + } + else if (opts.nextEq("-l|--plist")) { + normProps.addAll(this.resolveObjectPropertyList(opts)); + } + else if (opts.nextEq("--lego")) { + preservedClassSet = new HashSet(); + preservedClassSet.add(g.getDataFactory().getOWLClass(OBOUpperVocabulary.GO_biological_process.getIRI())); + preservedClassSet.add(g.getDataFactory().getOWLClass(OBOUpperVocabulary.GO_molecular_function.getIRI())); + } + + else { + break; + } + } + mmg = getMinimalModelGenerator(isCreateNewAbox); + if (isStrict) { + mmg.isStrict = true; + } + mmg.setPrecomputePropertyClassCombinations(isPrecomputePropertyClassCombinations); + + if (isAllIndividuals) { + mmg.generateAllNecessaryIndividuals(isCollapse, isReduce); + } + else { + c = this.resolveClass(opts.nextOpt()); + mmg.generateNecessaryIndividuals(c, isCollapse, isReduce); + } + for (OWLObjectProperty p : normProps) { + mmg.normalizeDirections(p); + } + if (preservedClassSet != null && preservedClassSet.size() > 0) { + mmg.anonymizeIndividualsNotIn(preservedClassSet); + } + if (isExtractModule) { + mmg.extractModule(); + } + g.setSourceOntology(mmg.getModel().getAboxOntology()); + } + + @CLIMethod("--most-specific-class-expression|--msce") + public void msce(Opts opts) throws Exception { + opts.info("[-c CLASS] INDIVIDUAL", "Generates MSCE for an individual using MinimalModelGenerator"); + mmg = getMinimalModelGenerator(false); + OWLNamedIndividual ind; + OWLClass c = null; + while (opts.hasOpts()) { + if (opts.nextEq("-c|--class")) { + opts.info("CLASS", "if set will add equivalence axioms to CLASS"); + c = this.resolveClass(opts.nextOpt()); + } + else { + break; + } + } + ind = (OWLNamedIndividual) this.resolveEntity(opts); + OWLClassExpression ce = mmg.getMostSpecificClassExpression(ind); + + System.out.println(getPrettyPrinter().render(ce)); + System.out.println(ce); + + if (c != null) { + OWLEquivalentClassesAxiom ax = g.getDataFactory().getOWLEquivalentClassesAxiom(c, ce); + g.getManager().addAxiom(g.getSourceOntology(), ax); + } + } + + @CLIMethod("--modalize") + public void modalize(Opts opts) throws Exception { + opts.info("CLASS", "Take all instances of CLASS and make a generalized statement about them"); + mmg = getMinimalModelGenerator(false); + OWLClass qc = null; + OWLObjectProperty p = null; + OWLDataFactory df = g.getDataFactory(); + while (opts.hasOpts()) { + if (opts.nextEq("-p|--modal-property")) { + p = resolveObjectProperty(opts.nextOpt()); + opts.info("CLASS", "if set will add equivalence axioms to CLASS"); + //c = this.resolveClass(opts.nextOpt()); + } + else { + break; + } + } + qc = this.resolveClass(opts.nextOpt()); + Set inds = mmg.getModel().getReasoner().getInstances(qc, false).getFlattened(); + for (OWLNamedIndividual ind : inds) { + OWLClassExpression ce = mmg.getMostSpecificClassExpression(ind); + if (ce instanceof OWLObjectIntersectionOf) { + for (OWLClassExpression x : ((OWLObjectIntersectionOf)ce).getOperands()) { + if (x instanceof OWLObjectSomeValuesFrom) { + OWLObjectSomeValuesFrom svf = ((OWLObjectSomeValuesFrom)x); + + } + } + } + Set types = mmg.getModel().getReasoner().getTypes(ind, true).getFlattened(); + + System.out.println(getPrettyPrinter().render(ce)); + System.out.println(ce); + for (OWLClass c : types) { + df.getOWLSubClassOfAxiom(c, df.getOWLObjectSomeValuesFrom(p, ce)); + } + } + } + + @CLIMethod("--gaf2lego") + @Deprecated + public void gaf2Lego(Opts opts) throws Exception { + String output = null; + boolean minimize = false; + OWLOntologyFormat format = new RDFXMLOntologyFormat(); + while (opts.hasOpts()) { + if (opts.nextEq("-m|--minimize")) { + opts.info("", "If set, combine into one model"); + minimize = true; + } + else if (opts.nextEq("-o|--output")) { + output = opts.nextOpt(); + } + else if (opts.nextEq("--format")) { + String formatString = opts.nextOpt(); + if ("manchester".equalsIgnoreCase(formatString)) { + format = new ManchesterOWLSyntaxOntologyFormat(); + } + } + else { + break; + } + } + if (g != null && gafdoc != null && output != null) { + GafToLegoTranslator translator = new GafToLegoTranslator(g, null); + OWLOntology lego; + if (minimize) { + lego = translator.minimizedTranslate(gafdoc); + } + else { + lego = translator.translate(gafdoc); + } + + OWLOntologyManager manager = lego.getOWLOntologyManager(); + OutputStream outputStream = null; + try { + outputStream = new FileOutputStream(output); + manager.saveOntology(lego, format, outputStream); + } + finally { + IOUtils.closeQuietly(outputStream); + } + } + else { + if (output == null) { + System.err.println("No output file was specified."); + } + if (g == null) { + System.err.println("No graph available for gaf-run-check."); + } + if (gafdoc == null) { + System.err.println("No loaded gaf available for gaf-run-check."); + } + exit(-1); + return; + } + } + + /** + * Translate the GeneAnnotations into a lego all individual OWL representation. + * + * Will merge the source ontology into the graph by default + * + * @param opts + * @throws Exception + */ + @CLIMethod("--gaf-lego-indivduals") + public void gaf2LegoIndivduals(Opts opts) throws Exception { + boolean addLineNumber = false; + boolean merge = true; + boolean minimize = false; + String output = null; + OWLOntologyFormat format = new RDFXMLOntologyFormat(); + while (opts.hasOpts()) { + if (opts.nextEq("-o|--output")) { + output = opts.nextOpt(); + } + else if (opts.nextEq("--format")) { + String formatString = opts.nextOpt(); + if ("manchester".equalsIgnoreCase(formatString)) { + format = new ManchesterOWLSyntaxOntologyFormat(); + } + else if ("functional".equalsIgnoreCase(formatString)) { + format = new OWLFunctionalSyntaxOntologyFormat(); + } + } + else if (opts.nextEq("--add-line-number")) { + addLineNumber = true; + } + else if (opts.nextEq("--skip-merge")) { + merge = false; + } + else if (opts.nextEq("-m|--minimize")) { + minimize = true; + } + else { + break; + } + } + if (g != null && gafdoc != null && output != null) { + GafToLegoIndividualTranslator tr = new GafToLegoIndividualTranslator(g, addLineNumber); + OWLOntology lego = tr.translate(gafdoc); + + if (merge) { + new OWLGraphWrapper(lego).mergeImportClosure(true); + } + if (minimize) { + final OWLOntologyManager m = lego.getOWLOntologyManager(); + + SyntacticLocalityModuleExtractor sme = new SyntacticLocalityModuleExtractor(m, lego, ModuleType.BOT); + Set sig = new HashSet(lego.getIndividualsInSignature()); + Set moduleAxioms = sme.extract(sig); + + OWLOntology module = m.createOntology(IRI.generateDocumentIRI()); + m.addAxioms(module, moduleAxioms); + lego = module; + } + + OWLOntologyManager manager = lego.getOWLOntologyManager(); + OutputStream outputStream = null; + try { + outputStream = new FileOutputStream(output); + manager.saveOntology(lego, format, outputStream); + } + finally { + IOUtils.closeQuietly(outputStream); + } + } + else { + if (output == null) { + System.err.println("No output file was specified."); + } + if (g == null) { + System.err.println("No graph available for gaf-run-check."); + } + if (gafdoc == null) { + System.err.println("No loaded gaf available for gaf-run-check."); + } + exit(-1); + return; + } + } + + @CLIMethod("--generate-molecular-model") + @Deprecated + public void generateMolecularModel(Opts opts) throws Exception { + opts.info("[--owl FILE] [-s SEED-GENE-LIST] [-a] [-r] -p PROCESS", "Generates an activity network (aka lego) from existing GAF and ontology"); + OWLClass processCls = null; + File owlOutputFile = null; + boolean isReplaceSourceOntology = false; + boolean isPrecomputePropertyClassCombinations = false; + boolean isExtractModule = false; + List seedGenes = new ArrayList(); + while (opts.hasOpts()) { + if (opts.nextEq("-p")) { + processCls = this.resolveClass(opts.nextOpt()); + } + else if (opts.nextEq("-r|--replace")) { + isReplaceSourceOntology = true; + } + else if (opts.nextEq("-q|--quick")) { + isPrecomputePropertyClassCombinations = false; + } + else if (opts.nextEq("-x|--extract-module")) { + isExtractModule = true; + } + else if (opts.nextEq("-a|--all-relation-class-pairs")) { + isPrecomputePropertyClassCombinations = true; + } + else if (opts.nextEq("-s|--seed")) { + seedGenes = opts.nextList(); + } + else if (opts.nextEq("--owl")) { + owlOutputFile = opts.nextFile(); + } + else { + break; + } + } + ModelContainer model = new ModelContainer(g.getSourceOntology(), new ElkReasonerFactory()); + LegoModelGenerator ni = new LegoModelGenerator(model); + ni.setPrecomputePropertyClassCombinations(isPrecomputePropertyClassCombinations); + ni.initialize(gafdoc, g); + + String p = g.getIdentifier(processCls); + seedGenes.addAll(ni.getGenes(processCls)); + + ni.buildNetwork(p, seedGenes); + + + OWLOntology ont = model.getAboxOntology(); + if (isExtractModule) { + ni.extractModule(); + } + if (owlOutputFile != null) { + FileOutputStream os = new FileOutputStream(owlOutputFile); + g.getManager().saveOntology(ont, os); + } + if (isReplaceSourceOntology) { + g.setSourceOntology(model.getAboxOntology()); + } + } + + @SuppressWarnings("unused") + @CLIMethod("--fetch-candidate-process") + @Deprecated + public void fetchCandidateProcess(Opts opts) throws Exception { + Double pvalThresh = 0.05; + Double pvalCorrectedThresh = 0.05; + Integer popSize = null; + boolean isDirect = false; + boolean isReflexive = false; + while (opts.hasOpts()) { + if (opts.nextEq("-p")) { + pvalCorrectedThresh = Double.valueOf(opts.nextOpt()); + } + else if (opts.nextEq("--pval-uncorrected")) { + pvalThresh = Double.valueOf(opts.nextOpt()); + } + else if (opts.nextEq("--pop-size")) { + popSize = Integer.valueOf(opts.nextOpt()); + } + else if (opts.nextEq("-d")) { + isDirect = true; + } + else if (opts.nextEq("-r")) { + isReflexive = true; + } + else { + break; + } + } + OWLClass disease = this.resolveClass(opts.nextOpt()); + + OWLPrettyPrinter owlpp = new OWLPrettyPrinter(g); + ModelContainer model = new ModelContainer(g.getSourceOntology(), new ElkReasonerFactory()); + LegoModelGenerator ni = new LegoModelGenerator(model); + ni.setPrecomputePropertyClassCombinations(false); + + ni.initialize(gafdoc, g); + OWLClass nothing = g.getDataFactory().getOWLNothing(); + Map smap = ni.fetchScoredCandidateProcesses(disease, popSize); + int MAX = 500; + int n=0; + for (Map.Entry e : smap.entrySet()) { + n++; + if (n > MAX) { + break; + } + Double score = e.getValue(); + OWLClass c = e .getKey(); + System.out.println("PROC\t"+owlpp.render(c)+"\t"+score); + } + } + + @CLIMethod("--go-multi-enrichment") + @Deprecated + public void goMultiEnrichment(Opts opts) throws Exception { + opts.info("P1 P2", "Generates an activity network (aka lego) from existing GAF and ontology"); + Double pvalThresh = 0.05; + Double pvalCorrectedThresh = 0.05; + Integer popSize = null; + boolean isDirect = false; + boolean isReflexive = false; + while (opts.hasOpts()) { + if (opts.nextEq("-p")) { + pvalCorrectedThresh = Double.valueOf(opts.nextOpt()); + } + else if (opts.nextEq("--pval-uncorrected")) { + pvalThresh = Double.valueOf(opts.nextOpt()); + } + else if (opts.nextEq("--pop-size")) { + popSize = Integer.valueOf(opts.nextOpt()); + } + else if (opts.nextEq("-d")) { + isDirect = true; + } + else if (opts.nextEq("-r")) { + isReflexive = true; + } + else { + break; + } + } + OWLClass rc1 = this.resolveClass(opts.nextOpt()); + OWLClass rc2 = this.resolveClass(opts.nextOpt()); + ModelContainer model = new ModelContainer(g.getSourceOntology(), new ElkReasonerFactory()); + LegoModelGenerator ni = new LegoModelGenerator(model); + + ni.initialize(gafdoc, g); + OWLPrettyPrinter owlpp = new OWLPrettyPrinter(g); + OWLClass nothing = g.getDataFactory().getOWLNothing(); + Set sampleSet = model.getReasoner().getSubClasses(rc2, false).getFlattened(); + sampleSet.remove(nothing); + if (isDirect) { + sampleSet = Collections.singleton(rc2); + } + if (isReflexive) { + sampleSet.add(rc2); + } + + // calc correction factor + int numHypotheses = 0; + for (OWLClass c1 : model.getReasoner().getSubClasses(rc1, false).getFlattened()) { + if (c1.equals(nothing)) + continue; + if (ni.getGenes(c1).size() < 2) { + continue; + } + for (OWLClass c2 : sampleSet) { + if (ni.getGenes(c2).size() < 2) { + continue; + } + numHypotheses++; + } + } + + + for (OWLClass c1 : model.getReasoner().getSubClasses(rc1, false).getFlattened()) { + if (c1.equals(nothing)) + continue; + System.out.println("Sample: "+c1); + for (OWLClass c2 : sampleSet) { + if (c2.equals(nothing)) + continue; + Double pval = ni.calculatePairwiseEnrichment(c1, c2, popSize); + if (pval == null || pval > pvalThresh) + continue; + Double pvalCorrected = pval * numHypotheses; + if (pvalCorrected == null || pvalCorrected > pvalCorrectedThresh) + continue; + System.out.println("enrich\t"+owlpp.render(c1)+"\t"+owlpp.render(c2)+"\t"+pval+"\t"+pvalCorrected); + } + } + } + + @CLIMethod("--lego-to-gpad") + public void legoToAnnotations(Opts opts) throws Exception { + String inputName = null; + String outputFileName = null; + List defaultRefs = null; + boolean addLegoModelId = true; + while (opts.hasOpts()) { + if (opts.nextEq("-i|--input")) { + inputName = opts.nextOpt(); + } + else if (opts.nextEq("-o|--output")) { + outputFileName = opts.nextOpt(); + } + else if (opts.nextEq("--add-default-ref")) { + if (defaultRefs == null) { + defaultRefs = new ArrayList(); + } + defaultRefs.add(opts.nextOpt()); + } + else if (opts.nextEq("--remove-lego-model-ids")) { + addLegoModelId = false; + } + else { + break; + } + } + + SimpleEcoMapper mapper = EcoMapperFactory.createSimple(); + LegoToGeneAnnotationTranslator translator = new LegoToGeneAnnotationTranslator(g, reasoner, mapper); + GafDocument annotations = new GafDocument(null, null); + BioentityDocument entities = new BioentityDocument(null); + + File inputFile = new File(inputName).getCanonicalFile(); + OWLOntologyManager m = g.getManager(); + if (inputFile.isFile()) { + OWLOntology model = m.loadOntology(IRI.create(inputFile)); + String modelId = StringUtils.stripEnd(inputFile.getName(), ".owl"); + List addtitionalRefs = handleRefs(defaultRefs, addLegoModelId, modelId); + translator.translate(model, annotations, entities, addtitionalRefs); + } + else if (inputFile.isDirectory()) { + File[] files = inputFile.listFiles(new FilenameFilter() { + + @Override + public boolean accept(File dir, String name) { + return StringUtils.trimToEmpty(name).toLowerCase().endsWith(".owl"); + } + }); + for (File file : files) { + String modelId = StringUtils.stripEnd(file.getName(), ".owl"); + List addtitionalRefs = handleRefs(defaultRefs, addLegoModelId, modelId); + OWLOntology model = m.loadOntology(IRI.create(file)); + translator.translate(model, annotations, entities, addtitionalRefs); + } + } + + // write GPAD to avoid bioentity data issues + PrintWriter fileWriter = null; + try { + fileWriter = new PrintWriter(new File(outputFileName)); + GpadWriter writer = new GpadWriter(fileWriter, 1.2d); + writer.write(annotations); + } + finally { + IOUtils.closeQuietly(fileWriter); + } + } + + List handleRefs(List defaultRefs, boolean addLegoModelId, String modelId) { + List addtitionalRefs; + if (addLegoModelId) { + if (defaultRefs == null) { + addtitionalRefs = Collections.singletonList(modelId); + } + else { + addtitionalRefs = new ArrayList(defaultRefs.size() + 1); + addtitionalRefs.addAll(defaultRefs); + addtitionalRefs.add(modelId); + } + } + else { + addtitionalRefs = defaultRefs; + } + return addtitionalRefs; + } +} diff --git a/minerva-converter/.classpath b/minerva-converter/.classpath new file mode 100644 index 00000000..b2acffc9 --- /dev/null +++ b/minerva-converter/.classpath @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/minerva-converter/.gitignore b/minerva-converter/.gitignore new file mode 100644 index 00000000..2f7896d1 --- /dev/null +++ b/minerva-converter/.gitignore @@ -0,0 +1 @@ +target/ diff --git a/minerva-converter/.project b/minerva-converter/.project new file mode 100644 index 00000000..249b612b --- /dev/null +++ b/minerva-converter/.project @@ -0,0 +1,23 @@ + + + minerva-converter + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/minerva-converter/.settings/org.eclipse.core.resources.prefs b/minerva-converter/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 00000000..e9441bb1 --- /dev/null +++ b/minerva-converter/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,3 @@ +eclipse.preferences.version=1 +encoding//src/main/java=UTF-8 +encoding/=UTF-8 diff --git a/minerva-converter/.settings/org.eclipse.jdt.core.prefs b/minerva-converter/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 00000000..ec4300d5 --- /dev/null +++ b/minerva-converter/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7 +org.eclipse.jdt.core.compiler.compliance=1.7 +org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning +org.eclipse.jdt.core.compiler.source=1.7 diff --git a/minerva-converter/.settings/org.eclipse.m2e.core.prefs b/minerva-converter/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/minerva-converter/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/minerva-converter/pom.xml b/minerva-converter/pom.xml new file mode 100644 index 00000000..6234f813 --- /dev/null +++ b/minerva-converter/pom.xml @@ -0,0 +1,32 @@ + + 4.0.0 + + minerva + org.geneontology + 0.2.2-SNAPSHOT + + minerva-converter + Minerva-Converter + + + + org.geneontology + minerva-core + ${project.parent.version} + + + org.geneontology + minerva-json + ${project.parent.version} + test + + + org.bbop + OWLTools-Core + test-jar + test + + + + diff --git a/minerva-converter/src/main/java/org/geneontology/minerva/GafToLegoIndividualTranslator.java b/minerva-converter/src/main/java/org/geneontology/minerva/GafToLegoIndividualTranslator.java new file mode 100644 index 00000000..797233d4 --- /dev/null +++ b/minerva-converter/src/main/java/org/geneontology/minerva/GafToLegoIndividualTranslator.java @@ -0,0 +1,365 @@ +package org.geneontology.minerva; + +import java.util.Collection; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.UUID; + +import org.apache.commons.lang3.StringUtils; +import org.apache.log4j.Logger; +import org.geneontology.minerva.util.IdStringManager; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLException; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObject; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyID; +import org.semanticweb.owlapi.model.OWLOntologyManager; + +import owltools.gaf.Bioentity; +import owltools.gaf.ExtensionExpression; +import owltools.gaf.GafDocument; +import owltools.gaf.GeneAnnotation; +import owltools.graph.OWLGraphWrapper; +import owltools.vocab.OBOUpperVocabulary; + + +/** + * Simple translation of {@link GeneAnnotation} to the all individual lego annotation model. + * + */ +public class GafToLegoIndividualTranslator { + + private static Logger logger = Logger.getLogger(GafToLegoIndividualTranslator.class); + + private final OWLGraphWrapper graph; + private final OWLObjectProperty partOf; + private final OWLObjectProperty occursIn; + private final OWLObjectProperty inTaxon; + private OWLClass mf; + private OWLObjectProperty enabledBy; + + private Map allOWLObjectsByAltId; + + private final boolean addLineNumber; + + public GafToLegoIndividualTranslator(OWLGraphWrapper graph, boolean addLineNumber) { + this.graph = graph; + this.addLineNumber = addLineNumber; + allOWLObjectsByAltId = graph.getAllOWLObjectsByAltId(); + OWLDataFactory df = graph.getDataFactory(); + partOf = OBOUpperVocabulary.BFO_part_of.getObjectProperty(df); + occursIn = OBOUpperVocabulary.BFO_occurs_in.getObjectProperty(df); + + mf = OBOUpperVocabulary.GO_molecular_function.getOWLClass(df); + enabledBy = OBOUpperVocabulary.GOREL_enabled_by.getObjectProperty(df); + inTaxon = graph.getOWLObjectPropertyByIdentifier("RO:0002162"); // in taxon + } + + protected void reportError(String error, GeneAnnotation annotation) { + logger.error(error+" \t Annotation: "+annotation.toString()); + } + + protected void reportWarn(String warning, GeneAnnotation annotation) { + logger.warn(warning+" \t Annotation: "+annotation.toString()); + } + + /** + * Translate the given {@link GafDocument} into an OWL representation of the LEGO model. + * + * @param gaf + * @return lego ontology + * @throws OWLException + */ + public OWLOntology translate(GafDocument gaf) throws OWLException { + final OWLOntologyManager m = graph.getManager(); + OWLOntology lego = m.createOntology(IRI.generateDocumentIRI()); + OWLOntology sourceOntology = graph.getSourceOntology(); + OWLOntologyID ontologyID = sourceOntology.getOntologyID(); + if (ontologyID != null) { + IRI ontologyIRI = ontologyID.getOntologyIRI(); + if (ontologyIRI != null) { + OWLDataFactory f = m.getOWLDataFactory(); + OWLImportsDeclaration importDeclaration = f.getOWLImportsDeclaration(ontologyIRI); + m.applyChange(new AddImport(lego, importDeclaration )); + } + } + translate(gaf.getGeneAnnotations(), lego); + return lego; + } + + /** + * Translate the given annotations ({@link GeneAnnotation}) into an OWL representation of the LEGO model. + * + * @param annotations + * @param lego + * @throws OWLException + */ + public void translate(Collection annotations, final OWLOntology lego) throws OWLException { + final OWLOntologyManager m = graph.getManager(); + + Set axioms = new HashSet(); + for(GeneAnnotation annotation : annotations) { + translate(annotation, axioms); + } + m.addAxioms(lego, axioms); + } + + /** + * Translate theGeneAnnotation into an OWL representation of the LEGO model. + * + * @param annotation + * @param axioms + * @throws OWLException + */ + public void translate(GeneAnnotation annotation, Set axioms) throws OWLException { + // skip ND annotations + if ("ND".equals(annotation.getShortEvidence())) { + reportWarn("Skipping ND annotation", annotation); + return; + } + // skip annotation using a qualifier + String rel = StringUtils.trimToNull(annotation.getRelation()); + if (rel != null) { + if ("enables".equals(rel) == false && "part_of".equals(rel) == false && "involved_in".equals(rel) == false) { + reportWarn("Skipping annotation with unsupported relation: "+annotation.getRelation(), annotation); + return; + } + } + + final OWLDataFactory f = graph.getDataFactory(); + + + final String annotationClsString = annotation.getCls(); + final OWLClass c = getOwlClass(annotationClsString); + if (c == null) { + reportError("Could not find a class for the given identifier: "+annotationClsString, annotation); + return; + } + + List> extensionExpressionGroups = annotation.getExtensionExpressions(); + if (extensionExpressionGroups != null && !extensionExpressionGroups.isEmpty()) { + Set parsedGroups = new HashSet(); + for(List group : extensionExpressionGroups) { + Set operands = new HashSet(); + for(ExtensionExpression extension : group) { + final String extensionClsString = extension.getCls(); + final String extensionRelationString = extension.getRelation(); + OWLClass extensionCls = getOwlClass(extensionClsString); + if (extensionCls == null) { + IRI extensionIRI = IdStringManager.getIRI(extensionClsString); + extensionCls = f.getOWLClass(extensionIRI); + } + final OWLObjectProperty extensionRelation = graph.getOWLObjectPropertyByIdentifier(extensionRelationString); + if (extensionRelation == null) { + reportError("Could not find a class for the given extension relation identifier: "+extensionRelationString, annotation); + continue; + } + operands.add(f.getOWLObjectSomeValuesFrom(extensionRelation, extensionCls)); + } + operands.add(c); + parsedGroups.add(f.getOWLObjectIntersectionOf(operands)); + } + if (annotation.isNegated()) { + OWLClassExpression union = f.getOWLObjectUnionOf(parsedGroups); + translate(annotation, union, axioms); + } + else { + for(OWLClassExpression ce : parsedGroups) { + translate(annotation, ce, axioms); + } + } + } + else { + translate(annotation, c, axioms); + } + } + + + private void translate(GeneAnnotation annotation, OWLClassExpression ce, Set axioms) throws OWLException { + final OWLDataFactory f = graph.getDataFactory(); + + // # STEP 1 - Bioentity instance + final Bioentity bioentity = annotation.getBioentityObject(); + final String isoForm = StringUtils.trimToNull(annotation.getGeneProductForm()); + + final OWLClass bioentityClass; + if (isoForm == null) { + // option #1: default bioentity id + bioentityClass = addBioentityCls(bioentity.getId(), bioentity.getSymbol(), bioentity.getNcbiTaxonId(), axioms, f); + } + else { + // option #2: ISO-form as subclass of bioentity + bioentityClass = addBioentityCls(isoForm, bioentity.getSymbol()+" ISO Form "+isoForm, bioentity.getNcbiTaxonId(), axioms, f); + OWLClass bioentityClassSuper = addBioentityCls(bioentity.getId(), bioentity.getSymbol(), bioentity.getNcbiTaxonId(), axioms, f); + axioms.add(f.getOWLDeclarationAxiom(bioentityClassSuper)); + axioms.add(f.getOWLSubClassOfAxiom(bioentityClass, bioentityClassSuper)); + } + + IRI bioentityInstanceIRI = generateNewIRI("bioentity", bioentityClass); + OWLNamedIndividual bioentityInstance = f.getOWLNamedIndividual(bioentityInstanceIRI); + axioms.add(f.getOWLDeclarationAxiom(bioentityInstance)); + axioms.add(f.getOWLClassAssertionAxiom(bioentityClass, bioentityInstance)); + + // # STEP 2 - create instance: + + // use Aspect to switch between the three options: P == BP, C == CC, F = MF + String aspect = annotation.getAspect(); + if (aspect == null) { + reportError("Error, no aspect defined.", annotation); + return; + } + + // TODO evidence + Set annotations = Collections.emptySet(); + if (addLineNumber) { + int lineNumber = annotation.getSource().getLineNumber(); + OWLAnnotation source = f.getOWLAnnotation(getLineNumberProperty(axioms, f), f.getOWLLiteral(lineNumber)); + annotations = Collections.singleton(source); + } + boolean negated = annotation.isNegated(); + if (negated) { + handleNegated(bioentityClass, aspect, annotations, ce, axioms, f); + return; + } + + //List sources = annotation.getReferenceIds(); + if ("F".equals(aspect)) { + // create individual + OWLNamedIndividual individual = f.getOWLNamedIndividual(generateNewIRI("mf", ce)); + axioms.add(f.getOWLDeclarationAxiom(individual)); + + // types + axioms.add(f.getOWLClassAssertionAxiom(ce, individual)); + + // link instances + + axioms.add(f.getOWLObjectPropertyAssertionAxiom(enabledBy, individual, bioentityInstance, annotations)); + } + else if ("C".equals(aspect)) { + // generic mf instance + OWLNamedIndividual mfIndividual = f.getOWLNamedIndividual(generateNewIRI("mf", mf)); + axioms.add(f.getOWLDeclarationAxiom(mfIndividual)); + + // generic mf type + axioms.add(f.getOWLClassAssertionAxiom(mf, mfIndividual)); + + // link mf to bioentity + axioms.add(f.getOWLObjectPropertyAssertionAxiom(enabledBy, mfIndividual, bioentityInstance)); + + // cc instance + OWLNamedIndividual ccIndividual = f.getOWLNamedIndividual(generateNewIRI("cc", ce)); + axioms.add(f.getOWLDeclarationAxiom(ccIndividual)); + + // cc type + axioms.add(f.getOWLClassAssertionAxiom(ce, ccIndividual)); + + // link cc and mf + axioms.add(f.getOWLObjectPropertyAssertionAxiom(occursIn, ccIndividual, mfIndividual, annotations)); + + + } + else if ("P".equals(aspect)) { + // generic mf instance + OWLNamedIndividual mfIndividual = f.getOWLNamedIndividual(generateNewIRI("mf", mf)); + axioms.add(f.getOWLDeclarationAxiom(mfIndividual)); + + // generic mf type + axioms.add(f.getOWLClassAssertionAxiom(mf, mfIndividual)); + + // link mf to bioentity + axioms.add(f.getOWLObjectPropertyAssertionAxiom(enabledBy, mfIndividual, bioentityInstance)); + + // cc instance + OWLNamedIndividual bpIndividual = f.getOWLNamedIndividual(generateNewIRI("bp", ce)); + axioms.add(f.getOWLDeclarationAxiom(bpIndividual)); + + // cc type + axioms.add(f.getOWLClassAssertionAxiom(ce, bpIndividual)); + + // link cc and mf + axioms.add(f.getOWLObjectPropertyAssertionAxiom(partOf, bpIndividual, mfIndividual, annotations)); + } + } + + private void handleNegated(OWLClass bioentityClass, String aspect, Set annotations, + OWLClassExpression ce, Set axioms, OWLDataFactory f) { + if ("F".equals(aspect)) { + OWLClassExpression notCE = f.getOWLObjectComplementOf(f.getOWLObjectSomeValuesFrom(enabledBy, ce)); + axioms.add(f.getOWLSubClassOfAxiom(bioentityClass, notCE, annotations)); + } + else if ("C".equals(aspect)) { + OWLClassExpression notCE = f.getOWLObjectComplementOf(f.getOWLObjectSomeValuesFrom(occursIn, ce)); + axioms.add(f.getOWLSubClassOfAxiom(bioentityClass, notCE, annotations)); + } + else if ("P".equals(aspect)) { + OWLClassExpression notCE = f.getOWLObjectComplementOf(f.getOWLObjectSomeValuesFrom(partOf, ce)); + axioms.add(f.getOWLSubClassOfAxiom(bioentityClass, notCE, annotations)); + } + } + + private OWLClass addBioentityCls(String id, String lbl, String taxon, Set axioms, OWLDataFactory f) { + IRI iri = IdStringManager.getIRI(id); + OWLClass cls = f.getOWLClass(iri); + boolean add = axioms.add(f.getOWLDeclarationAxiom(cls)); + if (add) { + OWLAnnotation annotation = f.getOWLAnnotation(f.getRDFSLabel(), f.getOWLLiteral(lbl)); + axioms.add(f.getOWLAnnotationAssertionAxiom(iri, annotation)); + if (taxon != null) { + OWLClass taxonClass = f.getOWLClass(IdStringManager.getIRI(taxon)); + axioms.add(f.getOWLDeclarationAxiom(taxonClass)); + axioms.add(f.getOWLSubClassOfAxiom(cls, + f.getOWLObjectSomeValuesFrom(inTaxon, taxonClass))); + } + } + return cls; + } + + /** + * @param id + * @return cls or null + */ + private OWLClass getOwlClass(String id) { + OWLClass cls = graph.getOWLClassByIdentifier(id); + if (cls == null) { + // check alt ids + OWLObject owlObject = allOWLObjectsByAltId.get(id); + if (owlObject != null && owlObject instanceof OWLClass) { + cls = (OWLClass) owlObject; + } + } + return cls; + } + + + private static final IRI GAF_LINE_NUMBER = IRI.create("http://gaf/line_number"); + + private OWLAnnotationProperty getLineNumberProperty(Set axioms, OWLDataFactory f) { + OWLAnnotationProperty p = f.getOWLAnnotationProperty(GAF_LINE_NUMBER); + axioms.add(f.getOWLDeclarationAxiom(p)); + return p; + } + + private IRI generateNewIRI(String type, OWLClassExpression ce) { + if( ce.isAnonymous() == false) { + OWLClass c = ce.asOWLClass(); + String id = StringUtils.replaceOnce(IdStringManager.getId(c.getIRI()), ":", "_"); + type = type + "-" + id; + } + return IRI.create("http://geneontology.org/lego/"+type+"-"+UUID.randomUUID().toString()); + + } + +} diff --git a/minerva-converter/src/main/java/org/geneontology/minerva/GafToLegoTranslator.java b/minerva-converter/src/main/java/org/geneontology/minerva/GafToLegoTranslator.java new file mode 100644 index 00000000..65da637a --- /dev/null +++ b/minerva-converter/src/main/java/org/geneontology/minerva/GafToLegoTranslator.java @@ -0,0 +1,492 @@ +package org.geneontology.minerva; + +import java.util.Collection; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.UUID; + +import org.apache.log4j.Logger; +import org.obolibrary.obo2owl.Obo2OWLConstants; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLDeclarationAxiom; +import org.semanticweb.owlapi.model.OWLEntity; +import org.semanticweb.owlapi.model.OWLException; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObject; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.vocab.OWLRDFVocabulary; + +import owltools.gaf.Bioentity; +import owltools.gaf.ExtensionExpression; +import owltools.gaf.GafDocument; +import owltools.gaf.GeneAnnotation; +import owltools.graph.OWLGraphWrapper; +import owltools.vocab.OBOUpperVocabulary; +import uk.ac.manchester.cs.owlapi.modularity.ModuleType; +import uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor; + +/** + * 
+Given a set of gene associations, this procedure will generate LEGO individuals.
+
+The set of associations can be specified by a user query. Includes:
+
+ * grepping a GAF and feeding results
+ * selecting all associations for all genes that are involved with some process
+
+# STEP 0 - map GeneAssociation in GAF model
+
+GeneAssociation(
+ bioentity:
+ class:
+ ext:
+ reference:
+ evidence: # TODO
+)
+
+==>
+
+# STEP 1 - calculate class expression
+
+IF 
+ THEN let  = IntersectionOf( )
+ ELSE let  = 
+
+# STEP 2 - map to protein ID
+
+IF .IRI startsWith "uniProtKB"
+ THEN let  = 
+ ELSE let  = SELECT  WHERE  SubClassOf encoded_by some   ### requires Omeo
+
+# STEP 3 - create instance:
+
+IF  SubClassOf MF THEN:
+
+ NamedIndividual( 
+   Types: 
+     ,
+     enabled_by SOME 
+   Facts:
+     source 
+
+ELSE IF  SubClassOf CC THEN:
+
+ NamedIndividual( 
+   Types: 
+     'molecular_function', occurs_in some  
+     enabled_by SOME 
+   Facts:
+     source 
+
+ELSE IF  SubClassOf BP THEN:
+
+  # note we create two individuals here
+
+ NamedIndividual( 
+   Types: 
+     
+   Facts:
+     source 
+
+
+ NamedIndividual( 
+   Types: 
+     'molecular_function'
+     enabled_by SOME 
+  Facts:
+    part_of ,
+    source 
+
+
+# VARIANT OF ABOVE STEP
+
+(optional)
+
+keep a map of Refs -> generated Ids 
+
+when performing , first check map. If an individual Id has already been generated for this , then re-use the existing id from the map.
+
+Note this may result in multiple classification of individuals (MCI). The user can rectify these in Protege.
+
+One variant of this strategy may be to retain the original Id,
+generate new Ids for the collapsed aggregate MF individual, and
+include evidence links back to the atomic MF individuals.
+
+
+ +@see lego-from-gaf.txt + */ +@Deprecated +public class GafToLegoTranslator { + + private static Logger logger = Logger.getLogger(GafToLegoTranslator.class); + + private final OWLGraphWrapper graph; + private final Map gp2protein; + private OWLObjectProperty partOf; + private OWLObjectProperty occursIn; + private OWLClass mf; + private OWLObjectProperty enabledBy; + private OWLObjectProperty geneProductOf; + + private Map allOWLObjectsByAltId; + + public GafToLegoTranslator(OWLGraphWrapper graph, Map gp2protein) { + this.graph = graph; + allOWLObjectsByAltId = graph.getAllOWLObjectsByAltId(); + this.gp2protein = gp2protein; + OWLDataFactory df = graph.getDataFactory(); + partOf = OBOUpperVocabulary.BFO_part_of.getObjectProperty(df); + occursIn = OBOUpperVocabulary.BFO_occurs_in.getObjectProperty(df); + + mf = OBOUpperVocabulary.GO_molecular_function.getOWLClass(df); + enabledBy = OBOUpperVocabulary.GOREL_enabled_by.getObjectProperty(df); + geneProductOf = OBOUpperVocabulary.RO_gene_product_of.getObjectProperty(df); + } + + protected void reportError(String error, GeneAnnotation annotation) { + logger.error(error+" \t Annotation: "+annotation.toString()); + } + + protected void reportWarn(String warning, GeneAnnotation annotation) { + logger.warn(warning+" \t Annotation: "+annotation.toString()); + } + + /** + * Translate the given {@link GafDocument} into an OWL representation of the LEGO model. + * + * @param gaf + * @return lego ontology + */ + public OWLOntology translate(GafDocument gaf) { + return translate(gaf.getGeneAnnotations()); + } + + /** + * Translate the given annotations ({@link GeneAnnotation}) into an OWL representation of the LEGO model. + * + * @param annotations + * @return lego ontology + */ + public OWLOntology translate(Collection annotations) { + final OWLDataFactory f = graph.getDataFactory(); + final OWLOntologyManager m = graph.getManager(); + try { + OWLOntology lego = m.createOntology(IRI.generateDocumentIRI()); + // add all ontologies from the graph wrapper as import to the new ontology + Set allOntologies = graph.getAllOntologies(); + for (OWLOntology importOntology : allOntologies) { + IRI importIRI = importOntology.getOntologyID().getOntologyIRI(); + OWLImportsDeclaration importDeclaration = f.getOWLImportsDeclaration(importIRI); + m.applyChange(new AddImport(lego, importDeclaration)); + } + + for(GeneAnnotation annotation : annotations) { + /* + * GeneAssociation( + * bioentity: + * class: + * ext: + * reference: + * evidence: # TODO + * ) + */ + final String annotationClsString = annotation.getCls(); + final OWLClass c = getOwlClass(annotationClsString); + String classLabel = graph.getLabel(c); + if (c == null) { + reportError("Could not find a class for the given identifier: "+annotationClsString, annotation); + continue; + } + + // STEP 1 - calculate class expression + // + // IF + // THEN let = IntersectionOf( ) + // ELSE let = + + final Set ceSet; + List> extensionExpressionGroups = annotation.getExtensionExpressions(); + if (extensionExpressionGroups != null && !extensionExpressionGroups.isEmpty()) { + ceSet = new HashSet(); + for(List group : extensionExpressionGroups) { + Set operands = new HashSet(); + for(ExtensionExpression extension : group) { + final String extensionClsString = extension.getCls(); + final String extensionRelationString = extension.getRelation(); + OWLClass extensionCls = getOwlClass(extensionClsString); + if (extensionCls == null && extensionClsString.startsWith("UniProtKB:")) { + IRI iri = IRI.create(Obo2OWLConstants.DEFAULT_IRI_PREFIX+"pr/"+extensionClsString.substring(10)); + extensionCls = f.getOWLClass(iri); + } + if (extensionCls == null) { + reportError("Could not find a class for the given extension cls identifier: "+extensionClsString, annotation); + continue; + } + final OWLObjectProperty extensionRelation = graph.getOWLObjectPropertyByIdentifier(extensionRelationString); + if (extensionRelation == null) { + reportError("Could not find a class for the given extension relation identifier: "+extensionRelationString, annotation); + continue; + } + operands.add(f.getOWLObjectSomeValuesFrom(extensionRelation, extensionCls)); + } + // if (operands.size() != extensionExpressions.size()) { + // reportError("Problems during the translation of the annotation extensions.", annotation); + // continue; + // } + operands.add(c); + ceSet.add(f.getOWLObjectIntersectionOf(operands)); + } + } + else { + ceSet = Collections.singleton(c); + } + + // # STEP 2 - map to protein ID + Bioentity bioentity = annotation.getBioentityObject(); + String dbprefix = bioentity.getDb(); + String annLabel = bioentity.getSymbol() + " " + classLabel; + + // TODO use ISO form information + // IF .IRI startsWith "uniProtKB" + // THEN let = + OWLClassExpression enabler; + if (dbprefix.equalsIgnoreCase("uniProtKB")) { + OWLClass pr = f.getOWLClass(IRI.create(Obo2OWLConstants.DEFAULT_IRI_PREFIX+"pr/"+bioentity.getDBID())); + addBioEntity(pr, lego, bioentity); + enabler = pr; + } + else { + // TODO use gp2protein + OWLClass gene = f.getOWLClass(graph.getIRIByIdentifier(bioentity.getId())); + OWLClassExpression pr = f.getOWLObjectSomeValuesFrom(geneProductOf, gene); + addBioEntity(gene, lego, bioentity); + enabler = pr; + //reportWarn("Skipping non-uniProtKB bioentity: "+bioentity.getId(), annotation); + //continue; + } + + // # STEP 3 - create instance: + + // use Aspect to switch between the three options: P == BP, C == CC, F = MF + String aspect = annotation.getAspect(); + if (aspect == null) { + reportError("Error, no aspect defined.", annotation); + continue; + } + + Set axioms = new HashSet(); + List sources = annotation.getReferenceIds(); + OWLNamedIndividual annIndividual = null; + // IF SubClassOf MF THEN: + if ("F".equals(aspect)) { + // NamedIndividual( + // Types: + // , + // enabled_by SOME + // Facts: + // source + + for(OWLClassExpression ce : ceSet) { + // create individual + OWLNamedIndividual individual = f.getOWLNamedIndividual(generateNewIRI(lego, "mf")); + axioms.add(f.getOWLDeclarationAxiom(individual)); + + // facts + OWLAnnotationProperty dcsource = getDcSourceProperty(lego, f); + for(String source : sources) { + axioms.add(f.getOWLAnnotationAssertionAxiom(dcsource, individual.getIRI(), f.getOWLLiteral(source))); + } + + // types + axioms.add(f.getOWLClassAssertionAxiom(ce, individual)); + axioms.add(f.getOWLClassAssertionAxiom(f.getOWLObjectSomeValuesFrom(enabledBy, enabler), individual)); + + axioms.add(labelAxiom(f, individual, annLabel)); + } + } + // ELSE IF SubClassOf CC THEN: + else if ("C".equals(aspect)) { + // NamedIndividual( + // Types: + // 'molecular_function', occurs_in some + // enabled_by SOME + // Facts: + // source + + for(OWLClassExpression ce : ceSet) { + OWLNamedIndividual individual = f.getOWLNamedIndividual(generateNewIRI(lego, "cc")); + axioms.add(f.getOWLDeclarationAxiom(individual)); + + // facts + OWLAnnotationProperty dcsource = getDcSourceProperty(lego, f); + for(String source : sources) { + axioms.add(f.getOWLAnnotationAssertionAxiom(dcsource, individual.getIRI(), f.getOWLLiteral(source))); + } + + // types + axioms.add(f.getOWLClassAssertionAxiom(mf, individual)); + axioms.add(f.getOWLClassAssertionAxiom(f.getOWLObjectSomeValuesFrom(occursIn, ce), individual)); + axioms.add(f.getOWLClassAssertionAxiom(f.getOWLObjectSomeValuesFrom(enabledBy, enabler), individual)); + + axioms.add(labelAxiom(f, individual, annLabel)); + + } + } + //ELSE IF SubClassOf BP THEN: + else if ("P".equals(aspect)) { + // # note we create two individuals here + + for(OWLClassExpression ce : ceSet) { + // NamedIndividual( + // Types: + // + // Facts: + // source + // create individual + OWLNamedIndividual individualX = f.getOWLNamedIndividual(generateNewIRI(lego, "bp")); + axioms.add(f.getOWLDeclarationAxiom(individualX)); + + // facts + OWLAnnotationProperty dcsource = getDcSourceProperty(lego, f); + for(String source : sources) { + axioms.add(f.getOWLAnnotationAssertionAxiom(dcsource, individualX.getIRI(), f.getOWLLiteral(source))); + } + + // types + axioms.add(f.getOWLClassAssertionAxiom(ce, individualX)); + axioms.add(labelAxiom(f, individualX, classLabel+" "+individualX.getIRI().getFragment())); + + + // NamedIndividual( + // Types: + // 'molecular_function' + // enabled_by SOME + // Facts: + // part_of , + // source + OWLNamedIndividual individual = f.getOWLNamedIndividual(generateNewIRI(lego, "bp")); + axioms.add(f.getOWLDeclarationAxiom(individual)); + + axioms.add(labelAxiom(f, individual, annLabel)); + + // facts + for(String source : sources) { + axioms.add(f.getOWLAnnotationAssertionAxiom(dcsource, individual.getIRI(), f.getOWLLiteral(source))); + } + axioms.add(f.getOWLObjectPropertyAssertionAxiom(partOf, individual, individualX)); + + // types + axioms.add(f.getOWLClassAssertionAxiom(mf, individual)); + axioms.add(f.getOWLClassAssertionAxiom(f.getOWLObjectSomeValuesFrom(enabledBy, enabler), individual)); + } + } + else { + reportError("Error, unknown aspect: "+aspect, annotation); + continue; + } + + m.addAxioms(lego, axioms); + } + + return lego; + } + catch (OWLException e) { + throw new RuntimeException("Could not create lego model.", e); + } + } + + private OWLAxiom labelAxiom(OWLDataFactory f, OWLNamedIndividual individual, String annLabel) { + return + f.getOWLAnnotationAssertionAxiom( + f.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()), + individual.getIRI(), + f.getOWLLiteral(annLabel)); + } + + /** + * @param id + * @return cls or null + */ + private OWLClass getOwlClass(String id) { + OWLClass cls = graph.getOWLClassByIdentifier(id); + if (cls == null) { + // check alt ids + OWLObject owlObject = allOWLObjectsByAltId.get(id); + if (owlObject != null && owlObject instanceof OWLClass) { + cls = (OWLClass) owlObject; + } + } + return cls; + } + + private void addBioEntity(OWLClass pr, OWLOntology lego, Bioentity bioentity) { + Set declarationAxioms = lego.getDeclarationAxioms(pr); + if (declarationAxioms == null || declarationAxioms.isEmpty()) { + // add class declaration and add label + OWLOntologyManager m = lego.getOWLOntologyManager(); + OWLDataFactory f = m.getOWLDataFactory(); + + Set axioms = new HashSet(); + axioms.add(f.getOWLDeclarationAxiom(pr)); + + String label = bioentity.getSymbol()+" - "+bioentity.getFullName(); + + axioms.add(f.getOWLAnnotationAssertionAxiom(f.getRDFSLabel(), pr.getIRI(), f.getOWLLiteral(label))); + + m.addAxioms(lego, axioms); + } + } + + private static final IRI DC_SOURCE = IRI.create("http://purl.org/dc/terms/source"); + + private OWLAnnotationProperty getDcSourceProperty(OWLOntology lego, OWLDataFactory f) { + OWLAnnotationProperty p = f.getOWLAnnotationProperty(DC_SOURCE); + Set declarationAxioms = lego.getDeclarationAxioms(p); + if (declarationAxioms == null || declarationAxioms.isEmpty()) { + OWLOntologyManager m = lego.getOWLOntologyManager(); + m.addAxiom(lego, f.getOWLDeclarationAxiom(p)); + } + return p; + } + + private IRI generateNewIRI(OWLOntology ont, String type) { + return IRI.create("http://geneontology.org/lego/"+type+"/"+UUID.randomUUID().toString()); + } + + /** + * Translate the given {@link GafDocument} into an OWL representation of the LEGO model. + * Additionally minimize the lego model and imports into one ontology module. + * + * @param gaf + * @return minimized lego ontology + */ + public OWLOntology minimizedTranslate(GafDocument gaf) { + OWLOntology all = translate(gaf); + final OWLOntologyManager m = all.getOWLOntologyManager(); + + SyntacticLocalityModuleExtractor sme = new SyntacticLocalityModuleExtractor(m, all, ModuleType.BOT); + Set sig = new HashSet(all.getIndividualsInSignature()); + Set moduleAxioms = sme.extract(sig); + + try { + OWLOntology module = m.createOntology(IRI.generateDocumentIRI()); + m.addAxioms(module, moduleAxioms); + return module; + } catch (OWLException e) { + throw new RuntimeException("Could not create minimized lego model.", e); + } + } +} diff --git a/minerva-converter/src/main/java/org/geneontology/minerva/format/LegeModelVersionConverterMain.java b/minerva-converter/src/main/java/org/geneontology/minerva/format/LegeModelVersionConverterMain.java new file mode 100644 index 00000000..0877c560 --- /dev/null +++ b/minerva-converter/src/main/java/org/geneontology/minerva/format/LegeModelVersionConverterMain.java @@ -0,0 +1,72 @@ +package org.geneontology.minerva.format; + +import java.io.File; +import java.io.FileFilter; + +import org.apache.commons.io.FilenameUtils; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLOntology; + +import owltools.cli.Opts; +import owltools.io.CatalogXmlIRIMapper; +import owltools.io.ParserWrapper; + +public class LegeModelVersionConverterMain { + + public static void main(String[] args) throws Exception { + ParserWrapper pw = new ParserWrapper(); + String inputFolder = null; + String outputFolder = null; + Opts opts = new Opts(args); + while (opts.hasOpts()) { + if (opts.nextEq("--use-catalog|--use-catalog-xml")) + pw.addIRIMapper(new CatalogXmlIRIMapper(new File("catalog-v001.xml").getAbsoluteFile())); + else if (opts.nextEq("--catalog-xml")) + pw.addIRIMapper(new CatalogXmlIRIMapper(opts.nextOpt())); + else if (opts.nextEq("-i|--input-folder")) { + inputFolder = opts.nextOpt(); + } + else if (opts.nextEq("-o|--output-folder")) { + outputFolder = opts.nextOpt(); + } + else + break; + } + if (inputFolder == null) { + throw new Exception("No input folder specified"); + } + if (outputFolder == null) { + throw new Exception("No output folder specified"); + } + + File input = new File(inputFolder).getCanonicalFile(); + File output = new File(outputFolder).getCanonicalFile(); + + File[] owlFiles = input.listFiles(new FileFilter() { + + @Override + public boolean accept(File pathname) { + String extension = FilenameUtils.getExtension(pathname.getName()); + if (extension != null) { + return "owl".equalsIgnoreCase(extension); + } + return false; + } + }); + if (owlFiles.length == 0) { + throw new Exception("No owl files found in input folder: "+inputFolder); + } + + LegoModelVersionConverter converter = new LegoModelVersionConverter(); + for (File owlFile : owlFiles) { + final OWLOntology abox = pw.parseOWL(IRI.create(owlFile)); + final String modelId = FilenameUtils.removeExtension(owlFile.getName()); + converter.convertLegoModelToAllIndividuals(abox, modelId); + + final File outputFile = new File(output, owlFile.getName()); + abox.getOWLOntologyManager().saveOntology(abox, IRI.create(outputFile)); + } + + } + +} diff --git a/minerva-converter/src/main/java/org/geneontology/minerva/format/LegoModelVersionConverter.java b/minerva-converter/src/main/java/org/geneontology/minerva/format/LegoModelVersionConverter.java new file mode 100644 index 00000000..d5fb8ad7 --- /dev/null +++ b/minerva-converter/src/main/java/org/geneontology/minerva/format/LegoModelVersionConverter.java @@ -0,0 +1,256 @@ +package org.geneontology.minerva.format; + +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.CoreMolecularModelManager; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; +import org.semanticweb.owlapi.model.AddAxiom; +import org.semanticweb.owlapi.model.AxiomType; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAnnotationSubject; +import org.semanticweb.owlapi.model.OWLAnnotationValue; +import org.semanticweb.owlapi.model.OWLAnnotationValueVisitor; +import org.semanticweb.owlapi.model.OWLAnonymousIndividual; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLIndividualAxiom; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyChange; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.RemoveAxiom; +import org.semanticweb.owlapi.util.OWLAxiomVisitorAdapter; + +public class LegoModelVersionConverter { + + static class EvidenceTriple { + final Set ecoIRIs = new HashSet(); + final Set evidenceAnnotations = new HashSet(); + final Set contributors = new HashSet(); + + public static EvidenceTriple createEvidenceTriple(Set axioms, OWLOntology abox, List changes) { + final EvidenceTriple triple = new EvidenceTriple(); + for(OWLAnnotationAssertionAxiom axiom : axioms) { + OWLAnnotationProperty property = axiom.getProperty(); + if (AnnotationShorthand.evidence.getAnnotationProperty().equals(property.getIRI())) { + OWLAnnotationValue value = axiom.getValue(); + value.accept(new OWLAnnotationValueVisitor() { + + @Override + public void visit(OWLLiteral literal) { + // ignore + } + + @Override + public void visit(OWLAnonymousIndividual individual) { + // ignore + } + + @Override + public void visit(IRI iri) { + triple.ecoIRIs.add(iri); + } + }); + changes.add(new RemoveAxiom(abox, axiom)); + } + else if(AnnotationShorthand.contributor.getAnnotationProperty().equals(property.getIRI())) { + // keep and propagate + triple.contributors.add(axiom.getAnnotation()); + } + else if(AnnotationShorthand.date.getAnnotationProperty().equals(property.getIRI())) { + // keep and propagate + triple.contributors.add(axiom.getAnnotation()); + } + else if(AnnotationShorthand.comment.getAnnotationProperty().equals(property.getIRI())) { + // keep only + } + else { + // remove and move to evidence individual + changes.add(new RemoveAxiom(abox, axiom)); + triple.evidenceAnnotations.add(axiom.getAnnotation()); + } + } + return triple; + } + + public static EvidenceTriple createEvidenceTriple(Set annotations) { + final EvidenceTriple triple = new EvidenceTriple(); + for (OWLAnnotation annotation : annotations) { + OWLAnnotationProperty property = annotation.getProperty(); + if (AnnotationShorthand.evidence.getAnnotationProperty().equals(property.getIRI())) { + OWLAnnotationValue value = annotation.getValue(); + value.accept(new OWLAnnotationValueVisitor() { + + @Override + public void visit(OWLLiteral literal) { + // ignore + } + + @Override + public void visit(OWLAnonymousIndividual individual) { + // ignore + } + + @Override + public void visit(IRI iri) { + triple.ecoIRIs.add(iri); + } + }); + } + else if(AnnotationShorthand.contributor.getAnnotationProperty().equals(property.getIRI())) { + triple.contributors.add(annotation); + } + else if(AnnotationShorthand.date.getAnnotationProperty().equals(property.getIRI())) { + triple.contributors.add(annotation); + } + else if(AnnotationShorthand.comment.getAnnotationProperty().equals(property.getIRI())) { + triple.contributors.add(annotation); + } + else { + triple.evidenceAnnotations.add(annotation); + } + } + return triple; + } + } + + public void convertLegoModelToAllIndividuals(final OWLOntology abox, final String modelId) { + final OWLOntologyManager m = abox.getOWLOntologyManager(); + final OWLDataFactory f = m.getOWLDataFactory(); + final List changes = new ArrayList(); + final Set individuals = abox.getIndividualsInSignature(); + final Set propertyAssertionAxioms = abox.getAxioms(AxiomType.OBJECT_PROPERTY_ASSERTION); + + // update all relevant axioms pertaining to only one individual + for (final OWLNamedIndividual individual : individuals) { + Set annotationAssertionAxioms = getAnnotationAssertionAxioms(abox, individual); + // convert evidence into individual(s) + // split into ECO IRI and annotations + EvidenceTriple triple = EvidenceTriple.createEvidenceTriple(annotationAssertionAxioms, abox, changes); + + // create individuals for ECO IRIs and link to existing individual + Set evidenceIndividuals = new HashSet(); + for(IRI ecoIRI : triple.ecoIRIs) { + OWLNamedIndividual evidenceIndividual = createEvidenceIndividual(ecoIRI, triple.evidenceAnnotations, modelId, abox, changes); + evidenceIndividuals.add(evidenceIndividual.getIRI()); + OWLAnnotationValue value = evidenceIndividual.getIRI(); + OWLAnnotation a = f.getOWLAnnotation( + f.getOWLAnnotationProperty(AnnotationShorthand.evidence.getAnnotationProperty()), + value); + changes.add(new AddAxiom(abox, f.getOWLAnnotationAssertionAxiom(individual.getIRI(), a))); + } + + // convert svf types into individuals + final Set classAssertionAxioms = getClassAssertionAxioms(abox, individual); + for(OWLClassAssertionAxiom axiom : classAssertionAxioms) { + OWLClassExpression ce = axiom.getClassExpression(); + if (ce instanceof OWLObjectSomeValuesFrom) { + OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom) ce; + OWLClassExpression filler = svf.getFiller(); + OWLObjectPropertyExpression property = svf.getProperty(); + + Pair> pair = CoreMolecularModelManager.createIndividual(modelId, abox, filler, triple.contributors); + OWLNamedIndividual newIndividual = pair.getLeft(); + for(OWLAxiom newAxiom : pair.getRight()) { + changes.add(new AddAxiom(abox, newAxiom)); + } + changes.add(new AddAxiom(abox, CoreMolecularModelManager.createFact(f, property, individual, newIndividual, triple.contributors))); + changes.add(new RemoveAxiom(abox, axiom)); + } + } + } + + // update all (old) axioms for two individuals + for(OWLObjectPropertyAssertionAxiom oldAxiom : propertyAssertionAxioms) { + Set annotations = oldAxiom.getAnnotations(); + EvidenceTriple triple = EvidenceTriple.createEvidenceTriple(annotations); + if (triple.ecoIRIs.isEmpty() == false) { + // clean up axiom annotations + changes.add(new RemoveAxiom(abox, oldAxiom)); + // add annotations for new evidence individuals + Set newAnnotations = new HashSet(triple.contributors); + for(IRI ecoIRI : triple.ecoIRIs) { + OWLNamedIndividual evidenceIndividual = createEvidenceIndividual(ecoIRI, triple.evidenceAnnotations, modelId, abox, changes); + newAnnotations.add(f.getOWLAnnotation( + f.getOWLAnnotationProperty(AnnotationShorthand.evidence.getAnnotationProperty()), + evidenceIndividual.getIRI())); + } + // create new axiom + changes.add(new AddAxiom(abox, + f.getOWLObjectPropertyAssertionAxiom( + oldAxiom.getProperty(), + oldAxiom.getSubject(), + oldAxiom.getObject(), + newAnnotations))); + } + } + + if (changes.isEmpty() == false) { + m.applyChanges(changes); + } + } + + static OWLNamedIndividual createEvidenceIndividual(IRI ecoIRI, Set evidenceAnnotations, String modelId, OWLOntology abox, List changes) { + OWLDataFactory f = abox.getOWLOntologyManager().getOWLDataFactory(); + OWLClass c = f.getOWLClass(ecoIRI); + Pair> evidenceIndividualPair = CoreMolecularModelManager.createIndividual(modelId, abox, c, null); + OWLNamedIndividual individual = evidenceIndividualPair.getLeft(); + for(OWLAxiom newAxiom : evidenceIndividualPair.getRight()) { + changes.add(new AddAxiom(abox, newAxiom)); + } + IRI individualIRI = individual.getIRI(); + for(OWLAnnotation evidenceAnnotation : evidenceAnnotations) { + changes.add(new AddAxiom(abox, f.getOWLAnnotationAssertionAxiom(individualIRI, evidenceAnnotation))); + } + return individual; + } + + private Set getAnnotationAssertionAxioms(OWLOntology abox, OWLNamedIndividual individual) { + Set all = abox.getAxioms(AxiomType.ANNOTATION_ASSERTION); + Set relevant = new HashSet(); + IRI individualIRI = individual.getIRI(); + for (OWLAnnotationAssertionAxiom axiom : all) { + OWLAnnotationSubject subject = axiom.getSubject(); + if (individualIRI.equals(subject)) { + relevant.add(axiom); + } + } + return relevant; + } + + /** + * @param abox + * @param individual + * @return axioms + */ + private Set getClassAssertionAxioms(OWLOntology abox, OWLNamedIndividual individual) { + Set axioms = abox.getAxioms(individual); + final Set classAssertionAxioms = new HashSet(); + + for (final OWLIndividualAxiom owlIndividualAxiom : axioms) { + owlIndividualAxiom.accept(new OWLAxiomVisitorAdapter(){ + + @Override + public void visit(OWLClassAssertionAxiom axiom) { + classAssertionAxioms.add(axiom); + } + }); + } + return classAssertionAxioms; + } + +} diff --git a/minerva-converter/src/main/java/org/geneontology/minerva/legacy/AbstractLegoTranslator.java b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/AbstractLegoTranslator.java new file mode 100644 index 00000000..e48e042b --- /dev/null +++ b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/AbstractLegoTranslator.java @@ -0,0 +1,425 @@ +package org.geneontology.minerva.legacy; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashSet; +import java.util.Iterator; +import java.util.List; +import java.util.Set; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; +import org.obolibrary.obo2owl.Owl2Obo; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.reasoner.OWLReasoner; + +import owltools.gaf.Bioentity; +import owltools.gaf.BioentityDocument; +import owltools.gaf.ExtensionExpression; +import owltools.gaf.GafDocument; +import owltools.gaf.GeneAnnotation; +import owltools.gaf.eco.SimpleEcoMapper; +import owltools.graph.OWLGraphWrapper; +import owltools.vocab.OBOUpperVocabulary; + +abstract class AbstractLegoTranslator { + + protected final OWLObjectProperty partOf; + protected final OWLObjectProperty occursIn; + protected final OWLObjectProperty enabledBy; + + protected final OWLAnnotationProperty source; + protected final OWLAnnotationProperty contributor; + protected final OWLAnnotationProperty date; + protected final OWLAnnotationProperty evidence; + + protected final OWLClass mf; + protected final Set mfSet; + + protected final OWLClass cc; + protected final Set ccSet; + + protected final OWLClass bp; + protected final Set bpSet; + + protected final SimpleEcoMapper mapper; + + protected AbstractLegoTranslator(OWLGraphWrapper graph, OWLReasoner reasoner, SimpleEcoMapper mapper) { + this.mapper = mapper; + OWLDataFactory df = graph.getDataFactory(); + partOf = OBOUpperVocabulary.BFO_part_of.getObjectProperty(df); + occursIn = OBOUpperVocabulary.BFO_occurs_in.getObjectProperty(df); + + mf = OBOUpperVocabulary.GO_molecular_function.getOWLClass(df); + cc = graph.getOWLClassByIdentifier("GO:0005575"); + bp = OBOUpperVocabulary.GO_biological_process.getOWLClass(df); + + enabledBy = OBOUpperVocabulary.GOREL_enabled_by.getObjectProperty(df); + + source = df.getOWLAnnotationProperty(AnnotationShorthand.source.getAnnotationProperty()); + contributor = df.getOWLAnnotationProperty(AnnotationShorthand.contributor.getAnnotationProperty()); + date = df.getOWLAnnotationProperty(AnnotationShorthand.date.getAnnotationProperty()); + evidence = df.getOWLAnnotationProperty(AnnotationShorthand.evidence.getAnnotationProperty()); + + bpSet = getAllSubClasses(bp, graph, reasoner, true); + mfSet = getAllSubClasses(mf, graph, reasoner, true); + ccSet = getAllSubClasses(cc, graph, reasoner, false); + } + + protected static Set getAllSubClasses(OWLClass cls, OWLGraphWrapper g, OWLReasoner r, boolean reflexive) { + Set allSubClasses = r.getSubClasses(cls, false).getFlattened(); + Iterator it = allSubClasses.iterator(); + while (it.hasNext()) { + OWLClass current = it.next(); + if (current.isBuiltIn()) { + it.remove(); + } + } + if (reflexive) { + allSubClasses.add(cls); + } + return allSubClasses; + } + + + protected static class Entry { + T value; + Metadata metadata; + // TODO multi-species interactions + } + + protected static class Metadata { + OWLClass evidence = null; + String assignedBy = null; + String date = null; + Set sources = null; + + Metadata copy() { + Metadata metadata = new Metadata(); + metadata.evidence = this.evidence; + metadata.assignedBy = this.assignedBy; + metadata.date = this.date; + metadata.sources = copy(this.sources); + return metadata; + } + + private static Set copy(Set c) { + if (c == null) { + return null; + } + return new HashSet(c); + } + + private static Metadata combine(Metadata primary, Metadata secondary) { + if (primary.evidence != null) { + return primary.copy(); + } + if (secondary.evidence != null) { + return secondary.copy(); + } + if (primary.sources != null && !primary.sources.isEmpty()) { + return primary.copy(); + } + return secondary.copy(); + } + } + + protected class Summary { + + Set> activities = null; + Set> activityExpressions = null; + Set> locations = null; + Set> processes = null; + OWLClass entity = null; + String entityType = null; + String entityTaxon = null; + + void addMfOrBp(OWLClass cls, Metadata metadata) { + if (isMf(cls)) { + activities = addAnnotation(cls, metadata , activities); + } + else if (isBp(cls)) { + processes = addAnnotation(cls, metadata, processes); + } + } + + void addMf(OWLClass cls, Metadata metadata) { + if (isMf(cls)) { + activities = addAnnotation(cls, metadata , activities); + } + } + + void addBp(OWLClass cls, Metadata metadata) { + if (isBp(cls)) { + processes = addAnnotation(cls, metadata, processes); + } + } + + void addCc(OWLClassExpression ce, Metadata metadata) { + if (ce instanceof OWLClass) { + OWLClass cls = ce.asOWLClass(); + locations = addAnnotation(cls, metadata, locations); + } + } + + private Set> addAnnotation(T cls, Metadata metadata, Set> set) { + if (set == null) { + set = new HashSet>(); + } + Entry entry = new Entry(); + entry.value = cls; + entry.metadata = metadata.copy(); + set.add(entry); + return set; + } + + void addProcesses(Set> processes, Metadata metadata) { + if (processes != null) { + if (this.processes == null) { + this.processes = new HashSet>(); + } + for(Entry process : processes) { + Entry newEntry = new Entry(); + newEntry.value = process.value; + newEntry.metadata = Metadata.combine(metadata, process.metadata); + this.processes.add(newEntry); + } + } + } + + void addLocations(Set> locations) { + if (locations != null) { + if (this.locations == null) { + this.locations = new HashSet>(locations); + } + else { + this.locations.addAll(locations); + } + } + } + + void addExpression(OWLObjectPropertyExpression p, Collection> entries, OWLDataFactory f) { + if (entries != null && !entries.isEmpty()) { + for (Entry entry : entries) { + OWLObjectSomeValuesFrom svf = f.getOWLObjectSomeValuesFrom(p, entry.value); + activityExpressions = addAnnotation(svf, entry.metadata, activityExpressions); + } + } + } + + void addExpression(OWLObjectPropertyExpression p, OWLClass cls, Metadata metadata, OWLDataFactory f) { + OWLObjectSomeValuesFrom svf = f.getOWLObjectSomeValuesFrom(p, cls); + activityExpressions = addAnnotation(svf, metadata, activityExpressions); + } + } + + protected boolean isMf(OWLClass cls) { + return mfSet.contains(cls); + } + + protected boolean isBp(OWLClass cls) { + return bpSet.contains(cls); + } + + protected boolean isCc(OWLClass cls) { + return ccSet.contains(cls); + } + + public abstract void translate(OWLOntology modelAbox, GafDocument annotations, BioentityDocument entities, List additionalRefs); + + /** + * Get the type of an enabled by entity, e.g. gene, protein + * + * @param modelGraph + * @param entity + * @return type + */ + protected String getEntityType(OWLClass entity, OWLGraphWrapper modelGraph) { + String id = modelGraph.getIdentifier(entity); + if (id.startsWith("UniProtKB")) { + return "protein"; // TODO + } + return "gene"; + } + + protected String getEntityTaxon(OWLClass entity, OWLNamedIndividual individual, OWLGraphWrapper modelGraph) { + return null; // TODO + } + + public Pair translate(String id, OWLOntology modelAbox, List additionalReferences) { + final GafDocument annotations = new GafDocument(id, null); + final BioentityDocument entities = new BioentityDocument(id); + translate(modelAbox, annotations, entities, additionalReferences); + return Pair.of(annotations, entities); + } + + protected GeneAnnotation createAnnotation(Entry e, Bioentity entity, String Aspect, OWLGraphWrapper g, Collection c16) { + GeneAnnotation annotation = new GeneAnnotation(); + annotation.setBioentityObject(entity); + annotation.setBioentity(entity.getId()); + annotation.setAspect(Aspect); + + //annotation.setActsOnTaxonId(taxonRelPair) // TODO? + + if (e.metadata.assignedBy != null) { + annotation.setAssignedBy(e.metadata.assignedBy); + } + + annotation.setCls(g.getIdentifier(e.value)); + + if (e.metadata.evidence != null) { + String ecoId = g.getIdentifier(e.metadata.evidence); + if (ecoId != null) { + String goCode = null; + Pair pair = mapper.getGoCode(ecoId); + if (pair != null) { + goCode = pair.getLeft(); + } + annotation.setEvidence(goCode, ecoId); + } + } + annotation.setLastUpdateDate(e.metadata.date); + //annotation.setRelation(relation); // TODO + if (e.metadata.sources != null) { + annotation.addReferenceIds(e.metadata.sources); + } + + if (c16 != null && !c16.isEmpty()) { + List expressions = new ArrayList(); + for (OWLObjectSomeValuesFrom svf : c16) { + OWLObjectPropertyExpression property = svf.getProperty(); + OWLClassExpression filler = svf.getFiller(); + if (property instanceof OWLObjectProperty && filler instanceof OWLClass) { + String rel = getRelId(property, g); + String objectId = g.getIdentifier(filler); + ExtensionExpression expr = new ExtensionExpression(rel, objectId); + expressions.add(expr); + } + } + annotation.setExtensionExpressions(Collections.singletonList(expressions)); + } + + return annotation; + } + + protected String getRelId(OWLObjectPropertyExpression p, OWLGraphWrapper graph) { + String relId = null; + for(OWLOntology ont : graph.getAllOntologies()) { + relId = Owl2Obo.getIdentifierFromObject(p, ont, null); + if (relId != null && relId.indexOf(':') < 0) { + return relId; + } + } + return relId; + } + + protected Bioentity createBioentity(OWLClass entityCls, String entityType, String taxon, OWLGraphWrapper g) { + Bioentity bioentity = new Bioentity(); + BioentityStrings strings = getBioentityStrings(entityCls, entityType, taxon, g); + String id = strings.id; + bioentity.setId(id); + if (strings.db != null) { + bioentity.setDb(strings.db); + } + bioentity.setSymbol(strings.symbol); + bioentity.setTypeCls(strings.type); + bioentity.setNcbiTaxonId(taxon); + // TODO more bioentity content + return bioentity; + } + + protected static class BioentityStrings { + String id; + String db; + String symbol; + String type; + } + + protected BioentityStrings getBioentityStrings(OWLClass entityCls, String entityType, String taxon, OWLGraphWrapper g) { + BioentityStrings strings = new BioentityStrings(); + strings.id = g.getIdentifier(entityCls); + strings.db = null; + String[] split = StringUtils.split(strings.id, ":", 2); + if (split.length == 2) { + strings.db = split[0]; + } + strings.symbol = g.getLabel(entityCls); + strings.type = entityType; + return strings; + } + + protected void addAnnotations(OWLGraphWrapper modelGraph, + Summary summary, + GafDocument annotations, BioentityDocument entities) + { + final OWLDataFactory f = modelGraph.getDataFactory(); + Bioentity entity = createBioentity(summary.entity, summary.entityType, summary.entityTaxon , modelGraph); + entities.addBioentity(entity); + annotations.addBioentity(entity); + + if (summary.activities != null) { + for (Entry e: summary.activities) { + List c16 = new ArrayList(); + boolean renderActivity = true; + if (mf.equals(e.value)) { + // special handling for top level molecular functions + // only add as annotation, if there is more than one annotation + // otherwise they tend to be redundant with the bp or cc annotation + int count = 0; + if (summary.processes != null) { + count += summary.processes.size(); + } + if (summary.locations != null) { + count += summary.locations.size(); + } + if (count <= 1 && (summary.activityExpressions == null || summary.activityExpressions.isEmpty())) { + renderActivity = false; + } + } + if (renderActivity) { + if (summary.processes != null) { + for (Entry processEntry : summary.processes) { + c16.add(f.getOWLObjectSomeValuesFrom(partOf, processEntry.value)); + } + } + if (summary.locations != null) { + for (Entry locationEntry : summary.locations) { + c16.add(f.getOWLObjectSomeValuesFrom(occursIn, locationEntry.value)); + } + } + if (summary.activityExpressions != null) { + for(Entry expressionEntry : summary.activityExpressions) { + c16.add(expressionEntry.value); + } + } + GeneAnnotation annotation = createAnnotation(e, entity, "F", modelGraph, c16); + annotations.addGeneAnnotation(annotation); + } + } + } + if (summary.processes != null) { + for (Entry e : summary.processes) { + GeneAnnotation annotation = createAnnotation(e, entity, "P", modelGraph, null); + annotations.addGeneAnnotation(annotation); + } + } + if (summary.locations != null) { + for (Entry e : summary.locations) { + if (isCc(e.value)) { + GeneAnnotation annotation = createAnnotation(e, entity, "C", modelGraph, null); + annotations.addGeneAnnotation(annotation); + } + } + } + } +} diff --git a/minerva-converter/src/main/java/org/geneontology/minerva/legacy/GafExportTool.java b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/GafExportTool.java new file mode 100644 index 00000000..1e2f6591 --- /dev/null +++ b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/GafExportTool.java @@ -0,0 +1,81 @@ +package org.geneontology.minerva.legacy; + +import java.io.ByteArrayOutputStream; +import java.io.IOException; +import java.io.PrintStream; +import java.io.PrintWriter; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.ModelContainer; +import org.semanticweb.owlapi.model.OWLOntology; + +import owltools.gaf.BioentityDocument; +import owltools.gaf.GafDocument; +import owltools.gaf.eco.EcoMapperFactory; +import owltools.gaf.eco.SimpleEcoMapper; +import owltools.gaf.io.GafWriter; +import owltools.gaf.io.GpadWriter; +import owltools.graph.OWLGraphWrapper; + +public class GafExportTool { + + private static volatile GafExportTool INSTANCE = null; + + private final SimpleEcoMapper ecoMapper; + + private GafExportTool(SimpleEcoMapper mapper) { + this.ecoMapper = mapper; + } + + public static synchronized GafExportTool getInstance() throws IOException { + if (INSTANCE == null) { + INSTANCE = new GafExportTool(EcoMapperFactory.createSimple()); + } + return INSTANCE; + } + + /** + * Export the model (ABox) in a legacy format, such as GAF or GPAD. + * + * @param modelId + * @param model + * @param format format name or null for default + * @return modelContent + * @throws IOException + */ + public String exportModelLegacy(String modelId, ModelContainer model, String format) throws IOException { + final OWLOntology aBox = model.getAboxOntology(); + LegoToGeneAnnotationTranslator translator = new LegoToGeneAnnotationTranslator(new OWLGraphWrapper(model.getTboxOntology()), model.getReasoner(), ecoMapper); + Pair pair = translator.translate(modelId, aBox, null); + ByteArrayOutputStream outputStream = null; + try { + outputStream = new ByteArrayOutputStream(); + if (format == null || "gaf".equalsIgnoreCase(format)) { + // GAF + GafWriter writer = new GafWriter(); + try { + writer.setStream(new PrintStream(outputStream)); + GafDocument gafdoc = pair.getLeft(); + writer.write(gafdoc); + } + finally { + writer.close(); + } + + } + else if ("gpad".equalsIgnoreCase(format)) { + // GPAD version 1.2 + GpadWriter writer = new GpadWriter(new PrintWriter(outputStream) , 1.2); + writer.write(pair.getLeft()); + } + else { + throw new IOException("Unknown legacy format: "+format); + } + return outputStream.toString(); + } + finally { + IOUtils.closeQuietly(outputStream); + } + } +} diff --git a/minerva-converter/src/main/java/org/geneontology/minerva/legacy/LegoAllIndividualToGeneAnnotationTranslator.java b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/LegoAllIndividualToGeneAnnotationTranslator.java new file mode 100644 index 00000000..743e9de6 --- /dev/null +++ b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/LegoAllIndividualToGeneAnnotationTranslator.java @@ -0,0 +1,290 @@ +package org.geneontology.minerva.legacy; + +import java.util.Collection; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.semanticweb.owlapi.model.AxiomType; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAnnotationValue; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.reasoner.OWLReasoner; + +import owltools.gaf.BioentityDocument; +import owltools.gaf.GafDocument; +import owltools.gaf.eco.SimpleEcoMapper; +import owltools.graph.OWLGraphWrapper; + +import com.google.common.collect.Sets; + +public class LegoAllIndividualToGeneAnnotationTranslator extends AbstractLegoTranslator { + + private OWLGraphWrapper graph; + + public LegoAllIndividualToGeneAnnotationTranslator(OWLGraphWrapper graph, OWLReasoner reasoner, SimpleEcoMapper mapper) { + super(graph, reasoner, mapper); + this.graph = graph; + } + + private boolean isEco(OWLClass cls) { + String identifier = graph.getIdentifier(cls); + return identifier != null && identifier.startsWith("ECO:"); + } + + private OWLClass getEco(Set set) { + for (OWLClass cls : set) { + if (isEco(cls)) { + return cls; + } + } + return null; + } + + private boolean isTaxon(OWLClass cls) { + String identifier = graph.getIdentifier(cls); + return identifier != null && identifier.startsWith("NCBITaxon:"); + } + + private OWLClass getTaxon(Set set) { + for (OWLClass cls : set) { + if (isTaxon(cls)) { + return cls; + } + } + return null; + } + + private Set getTypes(OWLNamedIndividual i, OWLOntology modelAbox) { + Set axioms = modelAbox.getClassAssertionAxioms(i); + Set types = new HashSet(); + for (OWLClassAssertionAxiom axiom : axioms) { + OWLClassExpression ce = axiom.getClassExpression(); + if (ce instanceof OWLClass) { + OWLClass cls = ce.asOWLClass(); + if (cls.isBuiltIn() == false) { + types.add(cls); + } + } + } + return types; + } + + private Metadata mergeMetadata(Metadata...data) { + Metadata result = null; + for (Metadata metadata : data) { + if (metadata != null) { + if (result == null) { + result = metadata.copy(); + } + else { + if (result.evidence == null && metadata.evidence != null) { + Metadata oldResult = result; + result = metadata.copy(); + if (oldResult.sources != null && !oldResult.sources.isEmpty()) { + if (result.sources == null) { + result.sources = Sets.newHashSet(oldResult.sources); + } + else { + result.sources.addAll(oldResult.sources); + } + } + } + } + } + } + return result; + } + + public void translate(OWLOntology modelAbox, GafDocument annotations, BioentityDocument entities, List additionalRefs) { + final OWLGraphWrapper modelGraph = new OWLGraphWrapper(modelAbox); + final OWLDataFactory f = modelGraph.getDataFactory(); + + final Set annotationIndividuals = new HashSet(); + final Map evidenceIndividuals = new HashMap(); + final Map taxonIndividuals = new HashMap(); + + for(OWLNamedIndividual individual : modelAbox.getIndividualsInSignature()) { + Set individualTypes = getTypes(individual, modelAbox); + OWLClass eco = getEco(individualTypes); + OWLClass taxon = getTaxon(individualTypes); + if (eco != null) { + // is eco + Metadata metadata = extractMetadata(individual, modelGraph, null); + metadata.evidence = eco; + evidenceIndividuals.put(individual.getIRI(), metadata); + } + else if(taxon != null) { + // is taxon (in future, currently not used) + taxonIndividuals.put(individual, taxon); + } + else { + // assume annotation + annotationIndividuals.add(individual); + } + } + + final Map allMetadata = new HashMap(); + for(OWLNamedIndividual individual : annotationIndividuals) { + Metadata metadata = extractMetadata(individual, modelGraph, evidenceIndividuals); + allMetadata.put(individual, metadata); + } + + Set summaries = new HashSet(); + for (OWLObjectPropertyAssertionAxiom axiom : modelAbox.getAxioms(AxiomType.OBJECT_PROPERTY_ASSERTION)) { + final OWLObjectPropertyExpression p = axiom.getProperty(); + if (enabledBy.equals(p)) { + + // gene/protein/complex + final OWLNamedIndividual object = axiom.getObject().asOWLNamedIndividual(); + Set objectTypes = getTypes(object, modelAbox); + for (OWLClass objectType : objectTypes) { + final Summary summary = new Summary(); + summary.entity = objectType; + summary.entityTaxon = getEntityTaxon(objectType, object, modelGraph); + summary.entityType = getEntityType(objectType, modelGraph); + summaries.add(summary); + + final OWLNamedIndividual subject = axiom.getSubject().asOWLNamedIndividual(); + + // get associated meta data + final Metadata linkMetadata = extractMetadata(axiom.getAnnotations(), modelGraph, evidenceIndividuals); + final Metadata objectMetadata = allMetadata.get(object); + final Metadata subjectMetadata = allMetadata.get(subject); + final Metadata mfMetadata = mergeMetadata(linkMetadata, objectMetadata, subjectMetadata); + + // handle types + for(OWLClass cls : getTypes(subject, modelAbox)) { + if (isMf(cls)) { + summary.addMf(cls, mfMetadata); + } + else { + // TODO how do we record that in a GAF? + } + } + + // get all OWLObjectPropertyAssertionAxiom for subject + Set subjectAxioms = modelAbox.getObjectPropertyAssertionAxioms(subject); + for(OWLObjectPropertyAssertionAxiom current : subjectAxioms) { + final Metadata currentLinkMetadata = extractMetadata(current.getAnnotations(), modelGraph, evidenceIndividuals); + final OWLObjectPropertyExpression currentP = current.getProperty(); + final OWLNamedIndividual currentObj = current.getObject().asOWLNamedIndividual(); + final Metadata currentObjMetadata = allMetadata.get(currentObj); + if (occursIn.equals(currentP)) { + // check for cc for subject (occurs in) + final Metadata metadata = mergeMetadata(currentObjMetadata, currentLinkMetadata); + for(OWLClass cls : getTypes(currentObj, modelAbox)) { + if (isCc(cls)) { + summary.addCc(cls, metadata); + } + else { + summary.addExpression(occursIn, cls, metadata, f); + } + } + } + else if (partOf.equals(currentP)) { + // check for bp for subject (part_of) + final Metadata metadata = mergeMetadata(currentObjMetadata, currentLinkMetadata); + for(OWLClass cls : getTypes(currentObj, modelAbox)) { + if (isBp(cls)) { + summary.addBp(cls, metadata); + } + else { + summary.addExpression(currentP, cls, metadata, f); + } + } + + }else if (enabledBy.equals(currentP)) { + // do nothing + } +// else if (taxon.equals(currentP)) { +// // do nothing +// } + else { + Set types = getTypes(currentObj, modelAbox); + final Metadata miscMetadata = mergeMetadata(currentObjMetadata, currentLinkMetadata); + for (OWLClass cls : types) { + summary.addExpression(currentP, cls, miscMetadata, f); + } + } + } + } + } + } + + for(Summary summary : summaries) { + if (summary.entity != null) { + addAnnotations(modelGraph, summary, annotations, entities); + } + } + } + + + private Metadata extractMetadata(OWLNamedIndividual individual, OWLGraphWrapper modelGraph, Map allEvidences) { + Metadata metadata = new Metadata(); + Set assertionAxioms = modelGraph.getSourceOntology().getAnnotationAssertionAxioms(individual.getIRI()); + for (OWLAnnotationAssertionAxiom axiom : assertionAxioms) { + OWLAnnotationProperty currentProperty = axiom.getProperty(); + OWLAnnotationValue value = axiom.getValue(); + extractMetadata(currentProperty, value, metadata, allEvidences); + } + return metadata; + } + + private void extractMetadata(OWLAnnotationProperty p, OWLAnnotationValue v, final Metadata metadata, Map allEvidences) + { + if (this.evidence.equals(p) && allEvidences != null && metadata.evidence == null) { + Metadata evidenceMetadata = allEvidences.get(v); + if (evidenceMetadata != null) { + metadata.evidence = evidenceMetadata.evidence; + metadata.sources = evidenceMetadata.sources; + } + } + else if (this.contributor.equals(p)) { + if (v instanceof OWLLiteral) { + metadata.assignedBy = ((OWLLiteral) v).getLiteral(); + } + } + else if (this.date.equals(p)) { + if (v instanceof OWLLiteral) { + metadata.date = ((OWLLiteral) v).getLiteral(); + } + } + else if (this.source.equals(p)) { + if (v instanceof OWLLiteral) { + String source = ((OWLLiteral) v).getLiteral(); + if (metadata.sources == null) { + metadata.sources = new HashSet(); + } + metadata.sources.add(source); + } + } + + } + + private Metadata extractMetadata(Collection annotations, OWLGraphWrapper modelGraph, Map allEvidences) { + Metadata metadata = new Metadata(); + if (annotations != null && !annotations.isEmpty()) { + for (OWLAnnotation owlAnnotation : annotations) { + OWLAnnotationProperty currentProperty = owlAnnotation.getProperty(); + OWLAnnotationValue value = owlAnnotation.getValue(); + extractMetadata(currentProperty, value, metadata, allEvidences); + } + } + return metadata; + } + +} diff --git a/minerva-converter/src/main/java/org/geneontology/minerva/legacy/LegoToGeneAnnotationTranslator.java b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/LegoToGeneAnnotationTranslator.java new file mode 100644 index 00000000..69912460 --- /dev/null +++ b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/LegoToGeneAnnotationTranslator.java @@ -0,0 +1,209 @@ +package org.geneontology.minerva.legacy; + +import java.util.Collection; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.apache.commons.lang3.StringUtils; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAnnotationValue; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLIndividual; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.reasoner.OWLReasoner; + +import owltools.gaf.BioentityDocument; +import owltools.gaf.GafDocument; +import owltools.gaf.eco.SimpleEcoMapper; +import owltools.graph.OWLGraphWrapper; +import owltools.vocab.OBOUpperVocabulary; + +public class LegoToGeneAnnotationTranslator extends AbstractLegoTranslator { + + public LegoToGeneAnnotationTranslator(OWLGraphWrapper graph, OWLReasoner reasoner, SimpleEcoMapper mapper) { + super(graph, reasoner, mapper); + } + + public void translate(OWLOntology modelAbox, GafDocument annotations, BioentityDocument entities, List additionalRefs) { + final OWLGraphWrapper modelGraph = new OWLGraphWrapper(modelAbox); + final OWLDataFactory f = modelGraph.getDataFactory(); + Set individuals = modelAbox.getIndividualsInSignature(); + + // create initial summaries + Map summaries = new HashMap(); + for (OWLNamedIndividual individual : individuals) { + Summary summary = new Summary(); + summaries.put(individual, summary); + + Metadata metadata = extractMetadata(individual, modelGraph, additionalRefs); + + Set assertionAxioms = modelAbox.getClassAssertionAxioms(individual); + for (OWLClassAssertionAxiom axiom : assertionAxioms) { + OWLClassExpression ce = axiom.getClassExpression(); + if (!ce.isAnonymous()) { + if (!ce.isBottomEntity() && !ce.isOWLNothing() && !ce.isOWLThing() && !ce.isTopEntity()) { + summary.addMfOrBp(ce.asOWLClass(), metadata); + } + } + else if (ce instanceof OWLObjectSomeValuesFrom) { + OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom) ce; + OWLObjectPropertyExpression p = svf.getProperty(); + OWLClassExpression filler = svf.getFiller(); + if (occursIn.equals(p)) { + summary.addCc(filler, metadata); + } + else if (enabledBy.equals(p)) { + if (filler instanceof OWLClass) { + summary.entity = (OWLClass) filler; + summary.entityType = getEntityType(summary.entity, modelGraph); + summary.entityTaxon = getEntityTaxon(summary.entity, individual, modelGraph); + // TODO multi-species + } + } + else { + if (filler instanceof OWLClass) { + OWLClass cls = (OWLClass) filler; + summary.addExpression(p, cls, metadata, f); + } + } + } + } + } + + + // extract process and other infos + for(OWLNamedIndividual individual : summaries.keySet()) { + Summary summary = summaries.get(individual); + if (summary.entity != null) { + Set axioms = modelAbox.getObjectPropertyAssertionAxioms(individual); + for (OWLObjectPropertyAssertionAxiom axiom : axioms) { + Metadata metadata = extractMetadata(axiom.getAnnotations(), modelGraph, additionalRefs); + OWLIndividual object = axiom.getObject(); + OWLObjectPropertyExpression property = axiom.getProperty(); + if (partOf.equals(property)) { + Summary objectSummary = summaries.get(object); + if (objectSummary != null) { + summary.addProcesses(objectSummary.processes, metadata); + // only add locations from the process, if there are no ones already present. + if (summary.locations == null || summary.locations.isEmpty()) { + summary.addLocations(objectSummary.locations); + } + } + } + else if (property instanceof OWLObjectProperty) { + Summary objectSummary = summaries.get(object); + if (objectSummary != null) { + // handle as additional information + if (objectSummary.activities != null) { + summary.addExpression(property, objectSummary.activities, f); + } + else { + summary.addExpression(property, objectSummary.processes, f); + } + } + } + } + } + } + + // report + for(OWLNamedIndividual individual : summaries.keySet()) { + Summary summary = summaries.get(individual); + if (summary.entity != null) { + addAnnotations(modelGraph, summary, annotations, entities); + } + } + } + + + private Metadata extractMetadata(OWLNamedIndividual individual, OWLGraphWrapper modelGraph, List additionalRefs) { + Metadata metadata = new Metadata(); + Set assertionAxioms = modelGraph.getSourceOntology().getAnnotationAssertionAxioms(individual.getIRI()); + for (OWLAnnotationAssertionAxiom axiom : assertionAxioms) { + OWLAnnotationProperty currentProperty = axiom.getProperty(); + OWLAnnotationValue value = axiom.getValue(); + extractMetadata(currentProperty, value, metadata, modelGraph, additionalRefs); + } + if (metadata.sources == null && additionalRefs != null) { + metadata.sources = new HashSet(additionalRefs); + } + return metadata; + } + + private void extractMetadata(OWLAnnotationProperty p, OWLAnnotationValue v, Metadata metadata, + OWLGraphWrapper modelGraph, List additionalRefs) + { + if (this.evidence.equals(p)) { + if (v instanceof IRI) { + IRI iri = (IRI) v; + metadata.evidence = modelGraph.getOWLClass(iri); + } + else if (v instanceof OWLLiteral) { + String literal = ((OWLLiteral) v).getLiteral(); + if (StringUtils.startsWith(literal, OBOUpperVocabulary.OBO)) { + IRI iri = IRI.create(literal); + metadata.evidence = modelGraph.getOWLClass(iri); + } + else { + metadata.evidence = modelGraph.getOWLClassByIdentifier(literal); + } + } + } + else if (this.contributor.equals(p)) { + if (v instanceof OWLLiteral) { + metadata.assignedBy = ((OWLLiteral) v).getLiteral(); + } + } + else if (this.date.equals(p)) { + if (v instanceof OWLLiteral) { + metadata.date = ((OWLLiteral) v).getLiteral(); + } + } + else if (this.source.equals(p)) { + if (v instanceof OWLLiteral) { + String sourceValue = ((OWLLiteral) v).getLiteral(); + if (metadata.sources == null) { + metadata.sources = new HashSet(); + } + metadata.sources.add(sourceValue); + } + } + if (additionalRefs != null) { + if (metadata.sources == null) { + metadata.sources = new HashSet(); + } + metadata.sources.addAll(additionalRefs); + } + } + + private Metadata extractMetadata(Collection annotations, OWLGraphWrapper modelGraph, List additionalRefs) { + Metadata metadata = new Metadata(); + if (annotations != null && !annotations.isEmpty()) { + for (OWLAnnotation owlAnnotation : annotations) { + OWLAnnotationProperty currentProperty = owlAnnotation.getProperty(); + OWLAnnotationValue value = owlAnnotation.getValue(); + extractMetadata(currentProperty, value, metadata, modelGraph, additionalRefs); + } + } + if (metadata.sources == null && additionalRefs != null) { + metadata.sources = new HashSet(additionalRefs); + } + return metadata; + } + +} diff --git a/minerva-converter/src/test/java/org/geneontology/minerva/format/LegoModelVersionConverterTest.java b/minerva-converter/src/test/java/org/geneontology/minerva/format/LegoModelVersionConverterTest.java new file mode 100644 index 00000000..b33d2f1c --- /dev/null +++ b/minerva-converter/src/test/java/org/geneontology/minerva/format/LegoModelVersionConverterTest.java @@ -0,0 +1,85 @@ +package org.geneontology.minerva.format; + +import static org.junit.Assert.*; + +import java.io.ByteArrayOutputStream; +import java.util.HashSet; +import java.util.Set; + +import org.apache.commons.io.IOUtils; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.MolecularModelManager; +import org.geneontology.minerva.format.LegoModelVersionConverter; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.junit.Test; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyManager; + +import owltools.graph.OWLGraphWrapper; +import owltools.io.ParserWrapper; + +import com.google.common.collect.Sets; + +public class LegoModelVersionConverterTest { + + @Test + public void testConvertLegoModelToAllIndividuals() throws Exception { + ParserWrapper pw = new ParserWrapper(); + OWLGraphWrapper graph = new OWLGraphWrapper(pw.parse("http://purl.obolibrary.org/obo/go.owl")); + MolecularModelManager m3 = new MolecularModelManager(graph); + m3.setPathToOWLFiles("src/test/resources/lego-conversion"); + Set modelIds = m3.getAvailableModelIds(); + assertEquals(1, modelIds.size()); + + final String modelId = modelIds.iterator().next(); + final ModelContainer model = m3.getModel(modelId); + assertNotNull(model); + OWLOntology aboxOntology = model.getAboxOntology(); + Set allIndividualsOld = aboxOntology.getIndividualsInSignature(); + + LegoModelVersionConverter converter = new LegoModelVersionConverter(); + converter.convertLegoModelToAllIndividuals(model.getAboxOntology(), modelId); + + + Set allIndividualsNew = aboxOntology.getIndividualsInSignature(); + assertTrue(allIndividualsNew.size() >= allIndividualsOld.size()); + assertTrue(allIndividualsNew.containsAll(allIndividualsOld)); + Set newIndividuals = Sets.difference(allIndividualsNew, allIndividualsOld); + Set ecoIndividuals = new HashSet(); + for (OWLNamedIndividual newIndividual : newIndividuals) { + IRI iri = newIndividual.getIRI(); + if (iri.toString().contains("-ECO-")) { + ecoIndividuals.add(newIndividual); + } + } + //assertEquals(3, ecoIndividuals.size()); + + System.out.println("---------"); + System.out.println(renderModel(model)); + System.out.println("---------"); + + System.out.println("----------"); + System.out.println(rendertoJson(model)); + System.out.println("----------"); + + } + + static String rendertoJson(ModelContainer model) { + return MolecularModelJsonRenderer.renderToJson(model.getAboxOntology(), true, true); + } + + static String renderModel(ModelContainer model) throws Exception { + OWLOntology aboxOntology = model.getAboxOntology(); + OWLOntologyManager m = aboxOntology.getOWLOntologyManager(); + ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); + try { + m.saveOntology(aboxOntology, outputStream); + return outputStream.toString(); + } + finally { + IOUtils.closeQuietly(outputStream); + } + } +} diff --git a/minerva-converter/src/test/java/org/geneontology/minerva/legacy/LegoAllIndividualToGeneAnnotationTranslatorTest.java b/minerva-converter/src/test/java/org/geneontology/minerva/legacy/LegoAllIndividualToGeneAnnotationTranslatorTest.java new file mode 100644 index 00000000..f9d28d3f --- /dev/null +++ b/minerva-converter/src/test/java/org/geneontology/minerva/legacy/LegoAllIndividualToGeneAnnotationTranslatorTest.java @@ -0,0 +1,129 @@ +package org.geneontology.minerva.legacy; + +import static org.junit.Assert.*; + +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.IOException; +import java.io.PrintStream; +import java.util.List; +import java.util.Set; + +import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.MolecularModelManager; +import org.geneontology.minerva.format.LegoModelVersionConverter; +import org.geneontology.minerva.legacy.LegoAllIndividualToGeneAnnotationTranslator; +import org.geneontology.minerva.legacy.LegoToGeneAnnotationTranslator; +import org.junit.AfterClass; +import org.junit.BeforeClass; +import org.junit.Test; + +import owltools.OWLToolsTestBasics; +import owltools.gaf.BioentityDocument; +import owltools.gaf.GafDocument; +import owltools.gaf.GeneAnnotation; +import owltools.gaf.eco.EcoMapperFactory; +import owltools.gaf.eco.SimpleEcoMapper; +import owltools.gaf.io.GafWriter; +import owltools.graph.OWLGraphWrapper; +import owltools.io.ParserWrapper; + +public class LegoAllIndividualToGeneAnnotationTranslatorTest extends OWLToolsTestBasics { + + static SimpleEcoMapper mapper = null; + static ModelContainer model = null; + static String modelId = null; + static MolecularModelManager m3 = null; + + @BeforeClass + public static void setUpBeforeClass() throws Exception { + ParserWrapper pw = new ParserWrapper(); + OWLGraphWrapper go = pw.parseToOWLGraph("http://purl.obolibrary.org/obo/go.owl"); + MolecularModelManager m3 = new MolecularModelManager(go); + m3.setPathToOWLFiles(new File("src/test/resources/lego-conversion").getCanonicalPath()); + + Set modelIds = m3.getAvailableModelIds(); + assertEquals(1, modelIds.size()); + modelId = modelIds.iterator().next(); + model = m3.getModel(modelId); + mapper = EcoMapperFactory.createSimple(); + } + + @AfterClass + public static void afterClass() throws Exception { + if (m3 != null) { + m3.dispose(); + } + } + + @Test + public void test() throws Exception { + // old conversion + LegoToGeneAnnotationTranslator oldTranslator = + new LegoToGeneAnnotationTranslator(new OWLGraphWrapper(model.getAboxOntology()), model.getReasoner(), mapper); + + Pair oldPair = oldTranslator.translate(modelId, model.getAboxOntology(), null); + GafDocument oldGaf = oldPair.getLeft(); + BioentityDocument oldBioentityDocument = oldPair.getRight(); +// System.out.println("-----"); +// System.out.println(renderGaf(oldGaf, oldBioentityDocument)); +// System.out.println("-----"); + + // new conversion + // #1 convert model to all individuals + LegoModelVersionConverter converter = new LegoModelVersionConverter(); + converter.convertLegoModelToAllIndividuals(model.getAboxOntology(), modelId); + + // #2 translate to legacy + LegoAllIndividualToGeneAnnotationTranslator newTranslator = + new LegoAllIndividualToGeneAnnotationTranslator(new OWLGraphWrapper(model.getAboxOntology()), model.getReasoner(), mapper); + + Pair newPair = newTranslator.translate(modelId, model.getAboxOntology(), null); + GafDocument newGaf = newPair.getLeft(); + BioentityDocument newBioentityDocument = newPair.getRight(); +// System.out.println("-------------"); +// System.out.println(renderGaf(newGaf, newBioentityDocument)); +// System.out.println("-------------"); + + // assert same amount of bioentities + assertEquals(oldBioentityDocument.getBioentities().size(), newBioentityDocument.getBioentities().size()); + + // assert same amount of annotations + List oldAnnotations = oldGaf.getGeneAnnotations(); + List newAnnotations = newGaf.getGeneAnnotations(); + assertEquals(oldAnnotations.size(), newAnnotations.size()); + + // assert that the one mf annotation has the same amount of c16 + GeneAnnotation oldMf = findMfAnnotation(oldAnnotations); + GeneAnnotation newMf = findMfAnnotation(newAnnotations); + assertNotNull(oldMf); + assertNotNull(newMf); + assertEquals(oldMf.getExtensionExpressions().size(), newMf.getExtensionExpressions().size()); + + } + + private GeneAnnotation findMfAnnotation(List annotations) { + for (GeneAnnotation annotation : annotations) { + if ("F".equals(annotation.getAspect())) { + return annotation; + } + } + return null; + } + + static String renderGaf(GafDocument gaf, BioentityDocument bioentities) throws IOException { + GafWriter gafWriter = new GafWriter(); + ByteArrayOutputStream out = new ByteArrayOutputStream(); + try { + gafWriter.setStream(new PrintStream(out)); + gafWriter.write(gaf); + } + finally { + gafWriter.close(); + out.close(); + } + String s = out.toString(); + return s; + } +} diff --git a/minerva-converter/src/test/resources/lego-conversion/gomodel:tair-5362b2ed0000015.owl b/minerva-converter/src/test/resources/lego-conversion/gomodel:tair-5362b2ed0000015.owl new file mode 100644 index 00000000..3d5e253d --- /dev/null +++ b/minerva-converter/src/test/resources/lego-conversion/gomodel:tair-5362b2ed0000015.owl @@ -0,0 +1,127 @@ +Prefix: owl: +Prefix: rdf: +Prefix: xml: +Prefix: xsd: +Prefix: rdfs: + + + +Ontology: + +Import: +Import: +Import: +Import: + +Annotations: + "PMID:24368792"^^xsd:string, + "GOC:tb"^^xsd:string + +AnnotationProperty: + + +AnnotationProperty: + + +AnnotationProperty: + + +Datatype: xsd:string + + +ObjectProperty: + + +ObjectProperty: + + +ObjectProperty: + + +Class: + + +Class: + + +Class: + + +Class: + + +Class: + + +Class: + + +Individual: + + Annotations: + , + "PMID:24368792"^^xsd:string, + "GOC:tb"^^xsd:string + + Types: + , + some + + +Individual: + + Annotations: + , + "PMID:24368792"^^xsd:string, + "GOC:tb"^^xsd:string + + Types: + some , + some , + , + some + + Facts: + + Annotations: , + "PMID:24368792"^^xsd:string, + "GOC:tb"^^xsd:string + + + + +Individual: + + Annotations: + , + "PMID:24368792"^^xsd:string, + "GOC:tb"^^xsd:string + + Types: + + + Facts: + + + +Individual: + + Annotations: + , + "PMID:24368792"^^xsd:string, + "GOC:tb"^^xsd:string + + Types: + + + +Individual: + + Types: + , + some + + Facts: + + + diff --git a/minerva-core/.classpath b/minerva-core/.classpath new file mode 100644 index 00000000..b2acffc9 --- /dev/null +++ b/minerva-core/.classpath @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/minerva-core/.gitignore b/minerva-core/.gitignore new file mode 100644 index 00000000..2f7896d1 --- /dev/null +++ b/minerva-core/.gitignore @@ -0,0 +1 @@ +target/ diff --git a/minerva-core/.project b/minerva-core/.project new file mode 100644 index 00000000..b8740ce4 --- /dev/null +++ b/minerva-core/.project @@ -0,0 +1,23 @@ + + + minerva-core + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/minerva-core/.settings/org.eclipse.core.resources.prefs b/minerva-core/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 00000000..cdfe4f1b --- /dev/null +++ b/minerva-core/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +encoding//src/main/java=UTF-8 +encoding//src/test/java=UTF-8 +encoding//src/test/resources=UTF-8 +encoding/=UTF-8 diff --git a/minerva-core/.settings/org.eclipse.jdt.core.prefs b/minerva-core/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 00000000..ec4300d5 --- /dev/null +++ b/minerva-core/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7 +org.eclipse.jdt.core.compiler.compliance=1.7 +org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning +org.eclipse.jdt.core.compiler.source=1.7 diff --git a/minerva-core/.settings/org.eclipse.m2e.core.prefs b/minerva-core/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/minerva-core/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/minerva-core/pom.xml b/minerva-core/pom.xml new file mode 100644 index 00000000..dc338d0c --- /dev/null +++ b/minerva-core/pom.xml @@ -0,0 +1,43 @@ + + 4.0.0 + + minerva + org.geneontology + 0.2.2-SNAPSHOT + + minerva-core + Minerva-Core + + + + + org.apache.maven.plugins + maven-surefire-plugin + + + **/FooTest.java + + + + + + + + + org.geneontology + minerva-json + ${project.parent.version} + + + org.bbop + OWLTools-Annotation + + + org.bbop + OWLTools-Core + test-jar + test + + + diff --git a/minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java new file mode 100644 index 00000000..911c114c --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java @@ -0,0 +1,1377 @@ +package org.geneontology.minerva; + +import java.io.ByteArrayOutputStream; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.apache.commons.lang3.tuple.Pair; +import org.apache.log4j.Logger; +import org.geneontology.minerva.util.IdStringManager; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.io.IRIDocumentSource; +import org.semanticweb.owlapi.io.OWLOntologyDocumentSource; +import org.semanticweb.owlapi.io.StringDocumentSource; +import org.semanticweb.owlapi.model.AddAxiom; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.AddOntologyAnnotation; +import org.semanticweb.owlapi.model.AxiomType; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAnnotationSubject; +import org.semanticweb.owlapi.model.OWLAnnotationSubjectVisitor; +import org.semanticweb.owlapi.model.OWLAnnotationValueVisitor; +import org.semanticweb.owlapi.model.OWLAnonymousIndividual; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLDataProperty; +import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; +import org.semanticweb.owlapi.model.OWLIndividual; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException; +import org.semanticweb.owlapi.model.OWLOntologyChange; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyFormat; +import org.semanticweb.owlapi.model.OWLOntologyID; +import org.semanticweb.owlapi.model.OWLOntologyIRIMapper; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; +import org.semanticweb.owlapi.model.RemoveAxiom; +import org.semanticweb.owlapi.model.RemoveImport; +import org.semanticweb.owlapi.model.RemoveOntologyAnnotation; +import org.semanticweb.owlapi.model.SetOntologyID; + +import owltools.graph.OWLGraphWrapper; +import owltools.vocab.OBOUpperVocabulary; + +/** + * Manager and core operations for in memory MolecularModels (aka lego diagrams). + * + * Any number of models can be loaded at any time
+ * TODO - impose some limit to avoid using too much memory + * + * each model has a generator, an OWLOntology (containing the set of class assertions) + * and a reasoner associated with it
+ * TODO - test memory requirements + * + * @param object for holding meta data associated with each operation + */ +public abstract class CoreMolecularModelManager { + + private static Logger LOG = Logger.getLogger(CoreMolecularModelManager.class); + + final OWLGraphWrapper graph; + private final IRI tboxIRI; + final Map modelMap = new HashMap(); + Set additionalImports; + final Map obsoleteOntologies = new HashMap(); + final Set obsoleteImports = new HashSet(); + + + // TODO: Temporarily for keeping instances unique (search for "unique" below). + static String uniqueTop = Long.toHexString((System.currentTimeMillis()/1000)); + static long instanceCounter = 0; + + private static String localUnique(){ + instanceCounter++; + String unique = uniqueTop + String.format("%07d", instanceCounter); + return unique; + } + + static String generateId(CharSequence...prefixes) { + StringBuilder sb = new StringBuilder(); + for (CharSequence prefix : prefixes) { + sb.append(prefix); + } + /* + * TODO finalize identifier policy + */ + sb.append(localUnique()); + return sb.toString(); + } + + /** + * @param graph + * @throws OWLOntologyCreationException + */ + public CoreMolecularModelManager(OWLGraphWrapper graph) throws OWLOntologyCreationException { + super(); + this.graph = graph; + tboxIRI = getTboxIRI(graph); + init(); + } + + /** + * Executed before the init call {@link #init()}. + * + * @param graph + * @return IRI, never null + * @throws OWLOntologyCreationException + */ + protected IRI getTboxIRI(OWLGraphWrapper graph) throws OWLOntologyCreationException { + OWLOntology tbox = graph.getSourceOntology(); + OWLOntologyID ontologyID = tbox.getOntologyID(); + if (ontologyID != null) { + IRI ontologyIRI = ontologyID.getOntologyIRI(); + if (ontologyIRI != null) { + return ontologyIRI; + } + } + throw new OWLOntologyCreationException("No ontology id available for tbox. An ontology IRI is required for the import into the abox."); + } + + /** + * @throws OWLOntologyCreationException + */ + protected void init() throws OWLOntologyCreationException { + // set default imports + additionalImports = new HashSet(); + } + + + /** + * @return graph wrapper for core/source ontology + */ + public OWLGraphWrapper getGraph() { + return graph; + } + + /** + * @return core/source ontology + */ + public OWLOntology getOntology() { + return graph.getSourceOntology(); + } + + + /** + * Add additional import declarations for any newly generated model. + * + * @param imports + */ + public void addImports(Iterable imports) { + if (imports != null) { + for (String importIRIString : imports) { + additionalImports.add(IRI.create(importIRIString)); + } + } + } + + /** + * Mark the given imports as obsolete. + * + * @param obsoletes + */ + public void addObsoleteImports(Iterable obsoletes) { + if (obsoletes != null) { + for (String obsolete : obsoletes) { + addObsoleteImport(IRI.create(obsolete)); + } + } + } + + /** + * Mark the given imports as obsolete. + * + * @param obsoleteImports + */ + public void addObsoleteImportIRIs(Collection obsoleteImports) { + if (obsoleteImports != null) { + for (IRI obsoleteImport : obsoleteImports) { + addObsoleteImport(obsoleteImport); + } + } + } + + private void addObsoleteImport(IRI obsoleteImport) { + // complete list + obsoleteImports.add(obsoleteImport); + + // check if we need to create an empty importer + final OWLOntologyManager m = graph.getManager(); + OWLOntology obsoleteOntology = m.getOntology(obsoleteImport); + if (obsoleteOntology == null) { + try { + // add mapper to provide empty ontologies for obsolete imports + OWLOntology empty = m.createOntology(obsoleteImport); + obsoleteOntologies.put(obsoleteImport, empty); + } catch (OWLOntologyCreationException e) { + // ignore for now, just log as warning + LOG.warn("Could not create empty dummy ontology for obsolete import: "+obsoleteImport, e); + } + } + } + + public Collection getImports() { + Set allImports = new HashSet(); + allImports.add(tboxIRI); + allImports.addAll(additionalImports); + return allImports; + } + + /** + * + * @param modelId + * @return all individuals in the model + */ + public Set getIndividuals(String modelId) { + ModelContainer mod = getModel(modelId); + return mod.getAboxOntology().getIndividualsInSignature(); + } + + + /** + * @param modelId + * @param q + * @return all individuals in the model that satisfy q + */ + public Set getIndividualsByQuery(String modelId, OWLClassExpression q) { + ModelContainer mod = getModel(modelId); + return mod.getReasoner().getInstances(q, false).getFlattened(); + } + + /** + * @param modelId + * @param model + * @param ce + * @param metadata + * @return individual + */ + public OWLNamedIndividual createIndividual(String modelId, ModelContainer model, OWLClassExpression ce, METADATA metadata) { + OWLNamedIndividual individual = createIndividual(modelId, model, ce, null, true, metadata); + return individual; + } + + OWLNamedIndividual createIndividual(String modelId, ModelContainer model, OWLClassExpression ce, Set annotations, boolean flushReasoner, METADATA metadata) { + LOG.info("Creating individual of type: "+ce); + Pair> pair = createIndividual(modelId, model.getAboxOntology(), ce, annotations); + addAxioms(modelId, model, pair.getRight(), flushReasoner, metadata); + return pair.getLeft(); + } + + public static Pair> createIndividual(String modelId, OWLOntology abox, OWLClassExpression ce, Set annotations) { + OWLGraphWrapper graph = new OWLGraphWrapper(abox); + String iid; + if (ce instanceof OWLClass) { + String cid = graph.getIdentifier(ce).replaceAll(":","-"); // e.g. GO-0123456 + // Make something unique to tag onto the generated IDs. + iid = generateId(modelId, "-", cid, "-"); + } + else { + iid = generateId(modelId, "-"); + } + + IRI iri = IdStringManager.getIRI(iid, graph); + OWLDataFactory f = graph.getDataFactory(); + OWLNamedIndividual i = f.getOWLNamedIndividual(iri); + + // create axioms + Set axioms = new HashSet(); + // declaration + axioms.add(f.getOWLDeclarationAxiom(i)); + // annotation assertions + if(annotations != null) { + for(OWLAnnotation annotation : annotations) { + axioms.add(f.getOWLAnnotationAssertionAxiom(iri, annotation)); + } + } + + OWLClassAssertionAxiom typeAxiom = createType(f, i, ce); + if (typeAxiom != null) { + axioms.add(typeAxiom); + } + + return Pair.of(i, axioms); + } + + /** + * Deletes an individual and return all IRIs used as an annotation value + * + * @param modelId + * @param model + * @param i + * @param metadata + * @return set of IRIs used in annotations + */ + public DeleteInformation deleteIndividual(String modelId, ModelContainer model, OWLNamedIndividual i, METADATA metadata) { + return deleteIndividual(modelId, model, i, true, metadata); + } + + public static class DeleteInformation { + public final Set usedIRIs = new HashSet(); + public final Set updated = new HashSet(); + public final Set touched = new HashSet(); + } + + /** + * Deletes an individual and return all IRIs used as an annotation value. + * Also tries to delete all annotations (OWLObjectPropertyAssertionAxiom + * annotations and OWLAnnotationAssertionAxiom) with the individual IRI as + * value. + * + * @param modelId + * @param model + * @param i + * @param flushReasoner + * @param metadata + * @return set of IRIs used in annotations + */ + DeleteInformation deleteIndividual(String modelId, ModelContainer model, OWLNamedIndividual i, boolean flushReasoner, METADATA metadata) { + Set toRemoveAxioms = new HashSet(); + final DeleteInformation deleteInformation = new DeleteInformation(); + + final OWLOntology ont = model.getAboxOntology(); + final OWLDataFactory f = model.getOWLDataFactory(); + + // Declaration axiom + toRemoveAxioms.add(model.getOWLDataFactory().getOWLDeclarationAxiom(i)); + + // Logic axiom + for (OWLAxiom ax : ont.getAxioms(i)) { + extractIRIValues(ax.getAnnotations(), deleteInformation.usedIRIs); + toRemoveAxioms.add(ax); + } + + // OWLObjectPropertyAssertionAxiom + Set allAssertions = ont.getAxioms(AxiomType.OBJECT_PROPERTY_ASSERTION); + final IRI iIRI = i.getIRI(); + for (OWLObjectPropertyAssertionAxiom ax : allAssertions) { + if (toRemoveAxioms.contains(ax) == false) { + Set currentIndividuals = ax.getIndividualsInSignature(); + if (currentIndividuals.contains(i)) { + extractIRIValues(ax.getAnnotations(), deleteInformation.usedIRIs); + toRemoveAxioms.add(ax); + continue; + } + // check annotations for deleted individual IRI + Set annotations = ax.getAnnotations(); + Set removeAnnotations = new HashSet(); + for (OWLAnnotation annotation : annotations) { + if (iIRI.equals(annotation.getValue())) { + removeAnnotations.add(annotation); + } + } + // if there is an annotations that needs to be removed, + // recreate axiom with cleaned annotation set + if (removeAnnotations.isEmpty() == false) { + annotations.removeAll(removeAnnotations); + toRemoveAxioms.add(ax); + deleteInformation.updated.add(f. + getOWLObjectPropertyAssertionAxiom( + ax.getProperty(), ax.getSubject(), ax.getObject(), annotations)); + } + } + } + // OWLAnnotationAssertionAxiom + Set annotationAssertionAxioms = ont.getAnnotationAssertionAxioms(i.getIRI()); + for (OWLAnnotationAssertionAxiom axiom : annotationAssertionAxioms) { + extractIRIValues(axiom.getAnnotation(), deleteInformation.usedIRIs); + toRemoveAxioms.add(axiom); + } + + // search for all annotations which use individual IRI as value + Set axioms = ont.getAxioms(AxiomType.ANNOTATION_ASSERTION); + for (OWLAnnotationAssertionAxiom ax : axioms) { + if (toRemoveAxioms.contains(ax) == false) { + if (iIRI.equals(ax.getValue())) { + toRemoveAxioms.add(ax); + OWLAnnotationSubject subject = ax.getSubject(); + subject.accept(new OWLAnnotationSubjectVisitor() { + + @Override + public void visit(OWLAnonymousIndividual individual) { + // do nothing + } + + @Override + public void visit(IRI iri) { + // check if they subject is a declared named individual + if (ont.containsIndividualInSignature(iri)) { + deleteInformation.touched.add(iri); + } + } + }); + } + } + } + + removeAxioms(modelId, model, toRemoveAxioms, flushReasoner, metadata); + if (deleteInformation.updated.isEmpty() == false) { + addAxioms(modelId, model, deleteInformation.updated, flushReasoner, metadata); + } + + return deleteInformation; + } + + public static Set extractIRIValues(Set annotations) { + if (annotations == null || annotations.isEmpty()) { + return Collections.emptySet(); + } + Set iriSet = new HashSet(); + extractIRIValues(annotations, iriSet); + return iriSet; + } + + private static void extractIRIValues(Set annotations, final Set iriSet) { + if (annotations != null) { + for (OWLAnnotation annotation : annotations) { + extractIRIValues(annotation, iriSet); + } + } + } + + private static void extractIRIValues(OWLAnnotation annotation, final Set iriSet) { + if (annotation != null) { + annotation.getValue().accept(new OWLAnnotationValueVisitor() { + + @Override + public void visit(OWLLiteral literal) { + // ignore + } + + @Override + public void visit(OWLAnonymousIndividual individual) { + // ignore + } + + @Override + public void visit(IRI iri) { + iriSet.add(iri); + } + }); + } + } + + public void addAnnotations(String modelId, ModelContainer model, OWLNamedIndividual i, Collection annotations, METADATA metadata) { + addAnnotations(modelId, model, i.getIRI(), annotations, metadata); + } + + void addAnnotations(String modelId, ModelContainer model, IRI subject, Collection annotations, METADATA metadata) { + Set axioms = new HashSet(); + OWLDataFactory f = model.getOWLDataFactory(); + for (OWLAnnotation annotation : annotations) { + axioms.add(f.getOWLAnnotationAssertionAxiom(subject, annotation)); + } + addAxioms(modelId, model, axioms, false, metadata); + } + + void updateAnnotation(String modelId, ModelContainer model, IRI subject, OWLAnnotation update, METADATA metadata) { + Set removeAxioms = new HashSet(); + OWLDataFactory f = model.getOWLDataFactory(); + Set existing = model.getAboxOntology().getAnnotationAssertionAxioms(subject); + OWLAnnotationProperty target = update.getProperty(); + for (OWLAnnotationAssertionAxiom axiom : existing) { + if (target.equals(axiom.getProperty())) { + removeAxioms.add(axiom); + } + } + removeAxioms(modelId, model, removeAxioms, false, metadata); + addAxiom(modelId, model, f.getOWLAnnotationAssertionAxiom(subject, update), false, metadata); + } + + void addAnnotations(String modelId, ModelContainer model, Collection annotations, METADATA metadata) { + OWLOntology aBox = model.getAboxOntology(); + List changes = new ArrayList(); + for (OWLAnnotation annotation : annotations) { + changes.add(new AddOntologyAnnotation(aBox, annotation)); + } + applyChanges(modelId, model, changes, false, metadata); + } + + void updateAnnotation(String modelId, ModelContainer model, OWLAnnotation update, METADATA metadata) { + OWLOntology aBox = model.getAboxOntology(); + List changes = new ArrayList(); + Set existing = model.getAboxOntology().getAnnotations(); + OWLAnnotationProperty target = update.getProperty(); + for (OWLAnnotation annotation : existing) { + if (target.equals(annotation.getProperty())) { + changes.add(new RemoveOntologyAnnotation(aBox, annotation)); + } + } + changes.add(new AddOntologyAnnotation(aBox, update)); + applyChanges(modelId, model, changes, false, metadata); + } + + public void removeAnnotations(String modelId, ModelContainer model, OWLNamedIndividual i, Collection annotations, METADATA metadata) { + removeAnnotations(modelId, model, i.getIRI(), annotations, metadata); + } + + void removeAnnotations(String modelId, ModelContainer model, IRI subject, Collection annotations, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + Set toRemove = new HashSet(); + Set candidates = ont.getAnnotationAssertionAxioms(subject); + for (OWLAnnotationAssertionAxiom axiom : candidates) { + OWLAnnotation annotation = axiom.getAnnotation(); + if (annotations.contains(annotation)) { + toRemove.add(axiom); + } + } + removeAxioms(modelId, model, toRemove, false, metadata); + } + + void removeAnnotations(String modelId, ModelContainer model, Collection annotations, METADATA metadata) { + OWLOntology aBox = model.getAboxOntology(); + List changes = new ArrayList(); + for (OWLAnnotation annotation : annotations) { + changes.add(new RemoveOntologyAnnotation(aBox, annotation)); + } + applyChanges(modelId, model, changes, false, metadata); + } + + public void addDataProperty(String modelId, ModelContainer model, + OWLNamedIndividual i, OWLDataProperty prop, OWLLiteral literal, + boolean flushReasoner, METADATA metadata) { + OWLAxiom axiom = model.getOWLDataFactory().getOWLDataPropertyAssertionAxiom(prop, i, literal); + addAxiom(modelId, model, axiom, flushReasoner, metadata); + } + + public void removeDataProperty(String modelId, ModelContainer model, + OWLNamedIndividual i, OWLDataProperty prop, OWLLiteral literal, + boolean flushReasoner, METADATA metadata) { + OWLAxiom toRemove = null; + Set existing = model.getAboxOntology().getDataPropertyAssertionAxioms(i); + for (OWLDataPropertyAssertionAxiom ax : existing) { + if (prop.equals(ax.getProperty()) && literal.equals(ax.getObject())) { + toRemove = ax; + break; + } + } + + if (toRemove != null) { + removeAxiom(modelId, model, toRemove, flushReasoner, metadata); + } + } + + /** + * Fetches a model by its Id + * + * @param id + * @return wrapped model + */ + public ModelContainer getModel(String id) { + if (!modelMap.containsKey(id)) { + try { + loadModel(id, false); + } catch (OWLOntologyCreationException e) { + LOG.info("Could not load model with id: "+id, e); + } + } + return modelMap.get(id); + } + + /** + * Retrieve the abox ontology. May skip loading the imports. + * This method is mostly intended to read metadata from a model. + * + * @param id + * @return abox, maybe without any imports loaded + */ + public OWLOntology getModelAbox(String id) { + ModelContainer model = modelMap.get(id); + if (model != null) { + return model.getAboxOntology(); + } + OWLOntology abox = null; + try { + abox = loadModelABox(id); + } catch (OWLOntologyCreationException e) { + LOG.info("Could not load model with id: "+id, e); + } + return abox; + } + + /** + * @param modelId + * @return ontology + * @throws OWLOntologyCreationException + */ + protected abstract OWLOntology loadModelABox(String modelId) throws OWLOntologyCreationException; + + /** + * @param id + */ + public void unlinkModel(String id) { + ModelContainer model = modelMap.get(id); + model.dispose(); + modelMap.remove(id); + } + + /** + * @return ids for all loaded models + */ + public Set getModelIds() { + return modelMap.keySet(); + } + + /** + * internal method to cleanup this instance + */ + public void dispose() { + Set ids = new HashSet(getModelIds()); + for (String id : ids) { + unlinkModel(id); + } + } + +// private synchronized SimpleEcoMapper getSimpleEcoMapper() throws IOException { +// if (simpleEcoMapper == null) { +// simpleEcoMapper = EcoMapperFactory.createSimple(); +// } +// return simpleEcoMapper; +// } +// +// /** +// * Export the model (ABox) in a legacy format, such as GAF or GPAD. +// * +// * @param modelId +// * @param model +// * @param format format name or null for default +// * @return modelContent +// * @throws IOException +// */ +// public String exportModelLegacy(String modelId, ModelContainer model, String format) throws IOException { +// final OWLOntology aBox = model.getAboxOntology(); +// SimpleEcoMapper ecoMapper = getSimpleEcoMapper(); +// LegoToGeneAnnotationTranslator translator = new LegoToGeneAnnotationTranslator(graph, model.getReasoner(), ecoMapper); +// Pair pair = translator.translate(modelId, aBox, null); +// ByteArrayOutputStream outputStream = null; +// try { +// outputStream = new ByteArrayOutputStream(); +// if (format == null || "gaf".equalsIgnoreCase(format)) { +// // GAF +// GafWriter writer = new GafWriter(); +// try { +// writer.setStream(new PrintStream(outputStream)); +// GafDocument gafdoc = pair.getLeft(); +// writer.write(gafdoc); +// } +// finally { +// writer.close(); +// } +// +// } +// else if ("gpad".equalsIgnoreCase(format)) { +// // GPAD version 1.2 +// GpadWriter writer = new GpadWriter(new PrintWriter(outputStream) , 1.2); +// writer.write(pair.getLeft()); +// } +// else { +// throw new IOException("Unknown legacy format: "+format); +// } +// return outputStream.toString(); +// } +// finally { +// IOUtils.closeQuietly(outputStream); +// } +// } + + /** + * Export the ABox, will try to set the ontologyID to the given modelId (to + * ensure import assumptions are met) + * + * @param modelId + * @param model + * @param ontologyFormat + * @return modelContent + * @throws OWLOntologyStorageException + */ + public String exportModel(String modelId, ModelContainer model, OWLOntologyFormat ontologyFormat) throws OWLOntologyStorageException { + final OWLOntology aBox = model.getAboxOntology(); + final OWLOntologyManager manager = aBox.getOWLOntologyManager(); + + // make sure the exported ontology has an ontologyId and that it maps to the modelId + final IRI expectedABoxIRI = IdStringManager.getIRI(modelId, graph); + OWLOntologyID ontologyID = aBox.getOntologyID(); + if (ontologyID == null) { + manager.applyChange(new SetOntologyID(aBox, expectedABoxIRI)); + } + else { + IRI currentABoxIRI = ontologyID.getOntologyIRI(); + if (expectedABoxIRI.equals(currentABoxIRI) == false) { + ontologyID = new OWLOntologyID(expectedABoxIRI, ontologyID.getVersionIRI()); + manager.applyChange(new SetOntologyID(aBox, ontologyID)); + } + } + + // write the model into a buffer + ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); + if (ontologyFormat != null) { + manager.saveOntology(aBox, ontologyFormat, outputStream); + } + else { + manager.saveOntology(aBox, outputStream); + } + + // extract the string from the buffer + String modelString = outputStream.toString(); + return modelString; + } + + /** + * Try to load (or replace) a model with the given ontology. It is expected + * that the content is an A-Box ontology, which imports the T-BOX. Also the + * ontology ID is used to extract the modelId.
+ *
+ * This method will currently NOT work due to a bug in the OWL-API. + * The functional syntax parser does not properly report the exceptions and + * will return an ontology with an wrong ontology ID! + * + * @param modelData + * @return modelId + * @throws OWLOntologyCreationException + */ + public String importModel(String modelData) throws OWLOntologyCreationException { + // load data from String + final OWLOntologyManager manager = graph.getManager(); + final OWLOntologyDocumentSource documentSource = new StringDocumentSource(modelData); + OWLOntology modelOntology; + try { + modelOntology = manager.loadOntologyFromOntologyDocument(documentSource); + } + catch (OWLOntologyAlreadyExistsException e) { + // exception is thrown if there is an ontology with the same ID already in memory + OWLOntologyID id = e.getOntologyID(); + String existingModelId = IdStringManager.getId(id.getOntologyIRI()); + + // remove the existing memory model + unlinkModel(existingModelId); + + // try loading the import version (again) + modelOntology = manager.loadOntologyFromOntologyDocument(documentSource); + } + + // try to extract modelId + String modelId = null; + OWLOntologyID ontologyId = modelOntology.getOntologyID(); + if (ontologyId != null) { + IRI iri = ontologyId.getOntologyIRI(); + if (iri != null) { + modelId = IdStringManager.getId(iri); + } + } + if (modelId == null) { + throw new OWLOntologyCreationException("Could not extract the modelId from the given model"); + } + // paranoia check + ModelContainer existingModel = modelMap.get(modelId); + if (existingModel != null) { + unlinkModel(modelId); + } + + // add to internal model + ModelContainer newModel = addModel(modelId, modelOntology); + + // update imports + updateImports(newModel); + + return modelId; + } + + /** + * Retrieve a collection of all model ids currently in memory.
+ * + * @return set of modelids. + * @throws IOException + */ + public Set getCurrentModelIds() throws IOException { + Set allModelIds = new HashSet(); + // add all model ids currently in memory + allModelIds.addAll(modelMap.keySet()); + return allModelIds; + } + + protected abstract void loadModel(String modelId, boolean isOverride) throws OWLOntologyCreationException; + + ModelContainer addModel(String modelId, OWLOntology abox) throws OWLOntologyCreationException { + OWLOntology tbox = graph.getSourceOntology(); + ModelContainer m = new ModelContainer(tbox, abox); + modelMap.put(modelId, m); + return m; + } + + + /** + * + * @param modelId + * @return true if the ontology formed by the specified model is inconsistent + */ + public boolean isConsistent(String modelId) { + ModelContainer model = getModel(modelId); + // TODO - is it scalable to have each model have its own reasoner? + // may make more sense to have a single reasoner instance operating over entire kb; + // this would mean the entire kb should be kept consistent - an inconsistency in one + // model would mean the entire kb is inconsistent + return model.getReasoner().isConsistent(); + } + + /** + * @param modelId + * @return data factory for the specified model + */ + public OWLDataFactory getOWLDataFactory(String modelId) { + ModelContainer model = getModel(modelId); + return model.getOWLDataFactory(); + } + + protected OWLOntologyManager getOWLOntologyManager(String modelId) { + ModelContainer model = getModel(modelId); + return model.getAboxOntology().getOWLOntologyManager(); + } + + /** + * Adds ClassAssertion(c,i) to specified model + * + * @param modelId + * @param i + * @param c + * @param metadata + */ + public void addType(String modelId, OWLNamedIndividual i, OWLClass c, METADATA metadata) { + ModelContainer model = getModel(modelId); + addType(modelId, model, i, c, true, metadata); + } + + /** + * Adds ClassAssertion(c,i) to specified model + * + * @param modelId + * @param model + * @param i + * @param c + * @param flushReasoner + * @param metadata + */ + void addType(String modelId, ModelContainer model, OWLIndividual i, + OWLClassExpression c, boolean flushReasoner, METADATA metadata) { + OWLClassAssertionAxiom axiom = createType(model.getOWLDataFactory(), i, c); + addAxiom(modelId, model, axiom, flushReasoner, metadata); + } + + /** + * @param f + * @param i + * @param c + * @return axiom + */ + public static OWLClassAssertionAxiom createType(OWLDataFactory f, OWLIndividual i, OWLClassExpression c) { + OWLClassAssertionAxiom axiom = f.getOWLClassAssertionAxiom(c,i); + return axiom; + } + + /** + * Adds a ClassAssertion, where the class expression instantiated is an + * ObjectSomeValuesFrom expression + * + * Example: Individual: i Type: enabledBy some PRO_123 + * + * @param modelId + * @param i + * @param p + * @param filler + * @param metadata + */ + public void addType(String modelId, + OWLNamedIndividual i, + OWLObjectPropertyExpression p, + OWLClassExpression filler, + METADATA metadata) { + ModelContainer model = getModel(modelId); + addType(modelId, model, i, p, filler, true, metadata); + } + + /** + * Adds a ClassAssertion, where the class expression instantiated is an + * ObjectSomeValuesFrom expression + * + * Example: Individual: i Type: enabledBy some PRO_123 + * + * @param modelId + * @param model + * @param i + * @param p + * @param filler + * @param flushReasoner + * @param metadata + */ + void addType(String modelId, + ModelContainer model, + OWLIndividual i, + OWLObjectPropertyExpression p, + OWLClassExpression filler, + boolean flushReasoner, + METADATA metadata) { + if (LOG.isDebugEnabled()) { + LOG.debug("Adding "+i+ " type "+p+" some "+filler); + } + OWLDataFactory f = model.getOWLDataFactory(); + OWLObjectSomeValuesFrom c = f.getOWLObjectSomeValuesFrom(p, filler); + OWLClassAssertionAxiom axiom = f.getOWLClassAssertionAxiom(c, i); + addAxiom(modelId, model, axiom, flushReasoner, metadata); + } + + /** + * remove ClassAssertion(c,i) to specified model + * + * @param modelId + * @param i + * @param c + * @param metadata + */ + public void removeType(String modelId, OWLNamedIndividual i, OWLClass c, METADATA metadata) { + ModelContainer model = getModel(modelId); + removeType(modelId, model, i, c, true, metadata); + } + + /** + * remove ClassAssertion(c,i) from the model + * + * @param modelId + * @param model + * @param i + * @param ce + * @param flushReasoner + * @param metadata + */ + void removeType(String modelId, ModelContainer model, OWLIndividual i, + OWLClassExpression ce, boolean flushReasoner, METADATA metadata) { + Set allAxioms = model.getAboxOntology().getClassAssertionAxioms(i); + // use search to remove also axioms with annotations + for (OWLClassAssertionAxiom ax : allAxioms) { + if (ce.equals(ax.getClassExpression())) { + removeAxiom(modelId, model, ax, flushReasoner, metadata); + } + } + + } + + /** + * Removes a ClassAssertion, where the class expression instantiated is an + * ObjectSomeValuesFrom expression + * + * @param modelId + * @param i + * @param p + * @param filler + * @param metadata + */ + public void removeType(String modelId, + OWLNamedIndividual i, + OWLObjectPropertyExpression p, + OWLClassExpression filler, + METADATA metadata) { + ModelContainer model = getModel(modelId); + removeType(modelId, model, i, p, filler, true, metadata); + } + + + void removeType(String modelId, + ModelContainer model, + OWLIndividual i, + OWLObjectPropertyExpression p, + OWLClassExpression filler, + boolean flushReasoner, + METADATA metadata) { + OWLDataFactory f = model.getOWLDataFactory(); + OWLClassAssertionAxiom axiom = f.getOWLClassAssertionAxiom(f.getOWLObjectSomeValuesFrom(p, filler), i); + removeAxiom(modelId, model, axiom, flushReasoner, metadata); + } + + /** + * Adds triple (i,p,j) to specified model + * + * @param modelId + * @param p + * @param i + * @param j + * @param annotations + * @param metadata + */ + public void addFact(String modelId, OWLObjectPropertyExpression p, + OWLNamedIndividual i, OWLNamedIndividual j, Set annotations, METADATA metadata) { + ModelContainer model = getModel(modelId); + addFact(modelId, model, p, i, j, annotations, true, metadata); + } + + /** + * Convenience wrapper for {@link #addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set, Object)} + * + * @param modelId + * @param vocabElement + * @param i + * @param j + * @param annotations + * @param metadata + */ + public void addFact(String modelId, OBOUpperVocabulary vocabElement, + OWLNamedIndividual i, OWLNamedIndividual j, Set annotations, METADATA metadata) { + ModelContainer model = getModel(modelId); + OWLObjectProperty p = vocabElement.getObjectProperty(model.getAboxOntology()); + addFact(modelId, model, p, i, j, annotations, true, metadata); + } + + void addFact(String modelId, ModelContainer model, OWLObjectPropertyExpression p, + OWLIndividual i, OWLIndividual j, Set annotations, boolean flushReasoner, METADATA metadata) { + OWLObjectPropertyAssertionAxiom axiom = createFact(model.getOWLDataFactory(), p, i, j, annotations); + addAxiom(modelId, model, axiom, flushReasoner, metadata); + } + + /** + * @param f + * @param p + * @param i + * @param j + * @param annotations + * @return axiom + */ + public static OWLObjectPropertyAssertionAxiom createFact(OWLDataFactory f, + OWLObjectPropertyExpression p, OWLIndividual i, OWLIndividual j, + Set annotations) { + final OWLObjectPropertyAssertionAxiom axiom; + if (annotations != null && !annotations.isEmpty()) { + axiom = f.getOWLObjectPropertyAssertionAxiom(p, i, j, annotations); + } + else { + axiom = f.getOWLObjectPropertyAssertionAxiom(p, i, j); + } + return axiom; + } + + public void removeFact(String modelId, OWLObjectPropertyExpression p, + OWLNamedIndividual i, OWLNamedIndividual j, METADATA metadata) { + ModelContainer model = getModel(modelId); + removeFact(modelId, model, p, i, j, true, metadata); + } + + Set removeFact(String modelId, ModelContainer model, OWLObjectPropertyExpression p, + OWLIndividual i, OWLIndividual j, boolean flushReasoner, METADATA metadata) { + OWLDataFactory f = model.getOWLDataFactory(); + + OWLOntology ont = model.getAboxOntology(); + OWLAxiom toRemove = null; + Set iriSet = new HashSet(); + Set candidates = ont.getObjectPropertyAssertionAxioms(i); + for (OWLObjectPropertyAssertionAxiom axiom : candidates) { + if (p.equals(axiom.getProperty()) && j.equals(axiom.getObject())) { + toRemove = axiom; + extractIRIValues(axiom.getAnnotations(), iriSet); + break; + } + } + if (toRemove == null) { + // fall back solution + toRemove = f.getOWLObjectPropertyAssertionAxiom(p, i, j); + } + removeAxiom(modelId, model, toRemove, flushReasoner, metadata); + return iriSet; + } + + public void addAnnotations(String modelId, OWLObjectPropertyExpression p, + OWLNamedIndividual i, OWLNamedIndividual j, Set annotations, METADATA metadata) { + ModelContainer model = getModel(modelId); + addAnnotations(modelId, model, p, i, j, annotations, true, metadata); + } + + void addAnnotations(String modelId, ModelContainer model, OWLObjectPropertyExpression p, + OWLNamedIndividual i, OWLNamedIndividual j, Set annotations, + boolean flushReasoner, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + Set axioms = ont.getObjectPropertyAssertionAxioms(i); + OWLObjectPropertyAssertionAxiom toModify = null; + for (OWLObjectPropertyAssertionAxiom axiom : axioms) { + if (p.equals(axiom.getProperty()) && j.equals(axiom.getObject())) { + toModify = axiom; + break; + } + } + addAnnotations(modelId, model, toModify, annotations, flushReasoner, metadata); + } + + void addAnnotations(String modelId, ModelContainer model, OWLObjectPropertyAssertionAxiom toModify, + Set annotations, boolean flushReasoner, METADATA metadata) { + if (toModify != null) { + Set combindedAnnotations = new HashSet(annotations); + combindedAnnotations.addAll(toModify.getAnnotations()); + modifyAnnotations(toModify, combindedAnnotations, modelId, model, flushReasoner, metadata); + } + } + + void updateAnnotation(String modelId, ModelContainer model, OWLObjectPropertyExpression p, + OWLNamedIndividual i, OWLNamedIndividual j, OWLAnnotation update, + boolean flushReasoner, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + Set axioms = ont.getObjectPropertyAssertionAxioms(i); + OWLObjectPropertyAssertionAxiom toModify = null; + for (OWLObjectPropertyAssertionAxiom axiom : axioms) { + if (p.equals(axiom.getProperty()) && j.equals(axiom.getObject())) { + toModify = axiom; + break; + } + } + updateAnnotation(modelId, model, toModify, update, flushReasoner, metadata); + } + + OWLObjectPropertyAssertionAxiom updateAnnotation(String modelId, ModelContainer model, + OWLObjectPropertyAssertionAxiom toModify, OWLAnnotation update, + boolean flushReasoner, METADATA metadata) { + OWLObjectPropertyAssertionAxiom newAxiom = null; + if (toModify != null) { + Set combindedAnnotations = new HashSet(); + OWLAnnotationProperty target = update.getProperty(); + for(OWLAnnotation existing : toModify.getAnnotations()) { + if (target.equals(existing.getProperty()) == false) { + combindedAnnotations.add(existing); + } + } + combindedAnnotations.add(update); + newAxiom = modifyAnnotations(toModify, combindedAnnotations, modelId, model, flushReasoner, metadata); + } + return newAxiom; + } + + OWLObjectPropertyAssertionAxiom removeAnnotations(String modelId, ModelContainer model, OWLObjectPropertyExpression p, + OWLNamedIndividual i, OWLNamedIndividual j, Set annotations, + boolean flushReasoner, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + Set axioms = ont.getObjectPropertyAssertionAxioms(i); + OWLObjectPropertyAssertionAxiom toModify = null; + for (OWLObjectPropertyAssertionAxiom axiom : axioms) { + if (p.equals(axiom.getProperty()) && j.equals(axiom.getObject())) { + toModify = axiom; + break; + } + } + OWLObjectPropertyAssertionAxiom newAxiom = null; + if (toModify != null) { + Set combindedAnnotations = new HashSet(toModify.getAnnotations()); + combindedAnnotations.removeAll(annotations); + newAxiom = modifyAnnotations(toModify, combindedAnnotations, modelId, model, flushReasoner, metadata); + } + return newAxiom; + } + + private OWLObjectPropertyAssertionAxiom modifyAnnotations(OWLObjectPropertyAssertionAxiom axiom, + Set replacement, + String modelId, ModelContainer model, boolean flushReasoner, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + OWLDataFactory f = model.getOWLDataFactory(); + List changes = new ArrayList(2); + changes.add(new RemoveAxiom(ont, axiom)); + OWLObjectPropertyAssertionAxiom newAxiom = + f.getOWLObjectPropertyAssertionAxiom(axiom.getProperty(), axiom.getSubject(), axiom.getObject(), replacement); + changes.add(new AddAxiom(ont, newAxiom)); + applyChanges(modelId, model, changes, flushReasoner, metadata); + return newAxiom; + } + + public void addAxiom(String modelId, ModelContainer model, OWLAxiom axiom, + boolean flushReasoner, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + List changes = Collections.singletonList(new AddAxiom(ont, axiom)); + synchronized (ont) { + /* + * all changes to the ontology are synchronized via the ontology object + */ + applyChanges(modelId, model, ont.getOWLOntologyManager(), changes, metadata); + } + if (flushReasoner) { + model.getReasoner().flush(); + } + } + + void addAxioms(String modelId, ModelContainer model, Set axioms, + boolean flushReasoner, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + List changes = new ArrayList(axioms.size()); + for(OWLAxiom axiom : axioms) { + changes.add(new AddAxiom(ont, axiom)); + } + synchronized (ont) { + /* + * all changes to the ontology are synchronized via the ontology object + */ + applyChanges(modelId, model, ont.getOWLOntologyManager(), changes, metadata); + } + if (flushReasoner) { + model.getReasoner().flush(); + } + } + + void removeAxiom(String modelId, ModelContainer model, OWLAxiom axiom, + boolean flushReasoner, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + List changes = Collections.singletonList(new RemoveAxiom(ont, axiom)); + synchronized (ont) { + /* + * all changes to the ontology are synchronized via the ontology object + */ + applyChanges(modelId, model, ont.getOWLOntologyManager(), changes, metadata); + } + if (flushReasoner) { + model.getReasoner().flush(); + } + } + + void removeAxioms(String modelId, Set axioms, boolean flushReasoner, METADATA metadata) { + ModelContainer model = getModel(modelId); + removeAxioms(modelId, model, axioms, flushReasoner, metadata); + } + + void removeAxioms(String modelId, ModelContainer model, Set axioms, + boolean flushReasoner, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + List changes = new ArrayList(axioms.size()); + for(OWLAxiom axiom : axioms) { + changes.add(new RemoveAxiom(ont, axiom)); + } + synchronized (ont) { + /* + * all changes to the ontology are synchronized via the ontology object + */ + applyChanges(modelId, model, ont.getOWLOntologyManager(), changes, metadata); + } + if (flushReasoner) { + model.getReasoner().flush(); + } + } + + private void applyChanges(String modelId, ModelContainer model, + List changes, boolean flushReasoner, METADATA metadata) { + OWLOntology ont = model.getAboxOntology(); + synchronized (ont) { + /* + * all changes to the ontology are synchronized via the ontology object + */ + applyChanges(modelId, model, ont.getOWLOntologyManager(), changes, metadata); + } + if (flushReasoner) { + model.getReasoner().flush(); + } + } + + private void applyChanges(String modelId, ModelContainer model, OWLOntologyManager m, + List changes, METADATA metadata) { + List appliedChanges = m.applyChanges(changes); + addToHistory(modelId, model, appliedChanges, metadata); + } + + /** + * Hook for implementing an undo and redo. + * + * @param modelId + * @param model + * @param appliedChanges + * @param metadata + */ + protected void addToHistory(String modelId, ModelContainer model, + List appliedChanges, METADATA metadata) { + // do nothing, for now + } + + protected OWLOntology loadOntologyIRI(final IRI sourceIRI, boolean minimal) throws OWLOntologyCreationException { + // silence the OBO parser in the OWL-API + java.util.logging.Logger.getLogger("org.obolibrary").setLevel(java.util.logging.Level.SEVERE); + + // load model from source + OWLOntologyDocumentSource source = new IRIDocumentSource(sourceIRI); + if (minimal == false) { + // add the obsolete imports to the ignored imports + OWLOntology abox = graph.getManager().loadOntologyFromOntologyDocument(source); + return abox; + } + else { + // only load the model, skip imports + // approach: return an empty ontology IRI for any IRI mapping request using. + final OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + final Set emptyOntologies = new HashSet(); + m.addIRIMapper(new OWLOntologyIRIMapper() { + + @Override + public IRI getDocumentIRI(IRI ontologyIRI) { + + // quick check: + // do nothing for the original IRI and known empty ontologies + if (sourceIRI.equals(ontologyIRI) || emptyOntologies.contains(ontologyIRI)) { + return null; + } + emptyOntologies.add(ontologyIRI); + try { + OWLOntology emptyOntology = m.createOntology(ontologyIRI); + return emptyOntology.getOntologyID().getDefaultDocumentIRI(); + } catch (OWLOntologyCreationException e) { + throw new RuntimeException(e); + } + } + }); + OWLOntology minimalAbox = m.loadOntologyFromOntologyDocument(source); + return minimalAbox; + } + } + + /** + * This method will check the given model and update the import declarations. + * It will add missing IRIs and remove obsolete ones. + * + * @param modelId + * @param model + * @see #additionalImports + * @see #addImports(Iterable) + * @see #obsoleteOntologies + * @see #addObsoleteImports(Iterable) + */ + public void updateImports(String modelId, ModelContainer model) { + updateImports(model); + } + + private void updateImports(ModelContainer model) { + updateImports(model.getAboxOntology(), tboxIRI, additionalImports, obsoleteImports); + } + + static void updateImports(final OWLOntology aboxOntology, IRI tboxIRI, Set additionalImports, Set obsoleteImports) { + List changes = new ArrayList(); + + Set missingImports = new HashSet(); + missingImports.add(tboxIRI); + missingImports.addAll(additionalImports); + Set importsDeclarations = aboxOntology.getImportsDeclarations(); + for (OWLImportsDeclaration decl : importsDeclarations) { + IRI iri = decl.getIRI(); + if (obsoleteImports.contains(iri)) { + changes.add(new RemoveImport(aboxOntology, decl)); + } + else { + missingImports.remove(iri); + } + } + final OWLOntologyManager m = aboxOntology.getOWLOntologyManager(); + if (!missingImports.isEmpty()) { + OWLDataFactory f = m.getOWLDataFactory(); + for(IRI missingImport : missingImports) { + OWLImportsDeclaration decl = f.getOWLImportsDeclaration(missingImport); + changes.add(new AddImport(aboxOntology, decl)); + } + } + + if (!changes.isEmpty()) { + m.applyChanges(changes); + } + } + +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/FileBasedMolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/FileBasedMolecularModelManager.java new file mode 100644 index 00000000..b53083c5 --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/FileBasedMolecularModelManager.java @@ -0,0 +1,631 @@ +package org.geneontology.minerva; + +import java.io.File; +import java.io.FilenameFilter; +import java.io.IOException; +import java.net.URISyntaxException; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.Set; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.FilenameUtils; +import org.apache.log4j.Logger; +import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat; +import org.geneontology.minerva.generate.LegoModelGenerator; +import org.geneontology.minerva.util.IdStringManager; +import org.geneontology.minerva.util.ReverseChangeGenerator; +import org.semanticweb.owlapi.io.OWLFunctionalSyntaxOntologyFormat; +import org.semanticweb.owlapi.io.OWLXMLOntologyFormat; +import org.semanticweb.owlapi.io.RDFXMLOntologyFormat; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException; +import org.semanticweb.owlapi.model.OWLOntologyChange; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyDocumentAlreadyExistsException; +import org.semanticweb.owlapi.model.OWLOntologyFormat; +import org.semanticweb.owlapi.model.OWLOntologyID; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; + +import owltools.gaf.GafDocument; +import owltools.gaf.parser.GafObjectsBuilder; +import owltools.graph.OWLGraphWrapper; + +/** + * Layer for retrieving and storing models as OWL files. + * + * @param + * @see CoreMolecularModelManager + */ +public class FileBasedMolecularModelManager extends CoreMolecularModelManager { + + private static Logger LOG = Logger.getLogger(FileBasedMolecularModelManager.class); + + boolean isPrecomputePropertyClassCombinations = false; + + @Deprecated + Map dbToGafdoc = new HashMap(); + + @Deprecated + String pathToGafs = "gene-associations"; + + String pathToOWLFiles = "owl-models"; + + GafObjectsBuilder builder = new GafObjectsBuilder(); + // WARNING: Do *NOT* switch to functional syntax until the OWL-API has fixed a bug. + OWLOntologyFormat ontologyFormat = new ManchesterOWLSyntaxOntologyFormat(); + + /** + * @param graph + * @throws OWLOntologyCreationException + */ + public FileBasedMolecularModelManager(OWLGraphWrapper graph) throws OWLOntologyCreationException { + super(graph); + } + + /** + * @return path to gafs direcory + */ + @Deprecated + public String getPathToGafs() { + return pathToGafs; + } + /** + * Can either be an HTTP prefix, or an absolute file path + * + * @param pathToGafs + */ + @Deprecated + public void setPathToGafs(String pathToGafs) { + this.pathToGafs = pathToGafs; + } + + /** + * Note this may move to an implementation-specific subclass in future + * + * @return path to owl on server + */ + public String getPathToOWLFiles() { + return pathToOWLFiles; + } + /** + * @param pathToOWLFiles + */ + public void setPathToOWLFiles(String pathToOWLFiles) { + this.pathToOWLFiles = pathToOWLFiles; + } + + /** + * loads/register a Gaf document + * + * @param db + * @return Gaf document + * @throws IOException + * @throws URISyntaxException + */ + @Deprecated + public GafDocument loadGaf(String db) throws IOException, URISyntaxException { + if (!dbToGafdoc.containsKey(db)) { + LOG.info("Loading GAF for db: "+db); + GafDocument gafdoc = builder.buildDocument(pathToGafs + "/gene_association." + db + ".gz"); + dbToGafdoc.put(db, gafdoc); + } + return dbToGafdoc.get(db); + } + + /** + * Loads and caches a GAF document from a specified location + * + * @param db + * @param gafFile + * @return Gaf document + * @throws IOException + * @throws URISyntaxException + */ + @Deprecated + public GafDocument loadGaf(String db, File gafFile) throws IOException, URISyntaxException { + if (!dbToGafdoc.containsKey(db)) { + + GafDocument gafdoc = builder.buildDocument(gafFile); + dbToGafdoc.put(db, gafdoc); + } + return dbToGafdoc.get(db); + } + + + /** + * @param db + * @return Gaf document for db + * @throws IOException + * @throws URISyntaxException + */ + @Deprecated + public GafDocument getGaf(String db) throws IOException, URISyntaxException { + return loadGaf(db); + } + + /** + * Generates a new model taking as input a biological process P and a database D. + * The axioms from P and annotations to P from D are used to seed a new model + * + * See {@link LegoModelGenerator#buildNetwork(OWLClass, java.util.Collection)} + * And also https://docs.google.com/document/d/1TV8Eb9sSvFY-weVZaIfzCxF1qbnmkUaiUhTm9Bs3gRE/edit + * + * Note the resulting model is uniquely identified by the modeId, which is currently constructed + * as a concatenation of the db and the P id. This means that if there is an existing model by + * this ID it will be overwritten + * + * @param processCls + * @param db + * @param metadata + * @return modelId + * @throws OWLOntologyCreationException + * @throws URISyntaxException + * @throws IOException + */ + @Deprecated + public String generateModel(OWLClass processCls, String db, METADATA metadata) throws OWLOntologyCreationException, IOException, URISyntaxException { + // quick check, only generate a model if it does not already exists. + final String p = graph.getIdentifier(processCls); + String modelId = getModelId(p, db); + if (modelMap.containsKey(modelId)) { + throw new OWLOntologyCreationException("A model already exists for this process and db: "+modelId); + } + LOG.info("Generating model for Class: "+p+" and db: "+db); + OWLOntology tbox = graph.getSourceOntology(); + OWLOntology abox = null; + ModelContainer model = null; + + // create empty ontology + // use model id as ontology IRI + OWLOntologyManager m = graph.getManager(); + IRI iri = IdStringManager.getIRI(modelId, graph); + try { + abox = m.createOntology(iri); + + // setup model ontology to import the source ontology and other imports + createImports(abox, tbox.getOntologyID(), metadata); + + // create generator + model = new ModelContainer(tbox, abox); + LegoModelGenerator generator = new LegoModelGenerator(model); + + generator.setPrecomputePropertyClassCombinations(isPrecomputePropertyClassCombinations); + Set seedGenes = new HashSet(); + // only look for genes if a GAF is available + if (db != null) { + GafDocument gafdoc = getGaf(db); + generator.initialize(gafdoc, graph); + seedGenes.addAll(generator.getGenes(processCls)); + } + generator.setContextualizingSuffix(db); + generator.buildNetwork(p, seedGenes); + } + catch (OWLOntologyCreationException exception) { + if (model != null) { + model.dispose(); + } else if (abox != null) { + m.removeOntology(abox); + } + throw exception; + } + catch (IOException exception) { + if (model != null) { + model.dispose(); + } + throw exception; + } + catch (URISyntaxException exception) { + if (model != null) { + model.dispose(); + } + throw exception; + } + modelMap.put(modelId, model); + return modelId; + } + + private void createImports(OWLOntology ont, OWLOntologyID tboxId, METADATA metadata) throws OWLOntologyCreationException { + OWLOntologyManager m = ont.getOWLOntologyManager(); + OWLDataFactory f = m.getOWLDataFactory(); + + // import T-Box + OWLImportsDeclaration tBoxImportDeclaration = f.getOWLImportsDeclaration(tboxId.getOntologyIRI()); + m.applyChange(new AddImport(ont, tBoxImportDeclaration)); + + // import additional ontologies via IRI + for (IRI importIRI : additionalImports) { + OWLImportsDeclaration importDeclaration = f.getOWLImportsDeclaration(importIRI); + // check that the import ontology is available + OWLOntology importOntology = m.getOntology(importIRI); + if (importOntology == null) { + // only try to load it, if it isn't already loaded + try { + m.loadOntology(importIRI); + } catch (OWLOntologyDocumentAlreadyExistsException e) { + // ignore + } catch (OWLOntologyAlreadyExistsException e) { + // ignore + } + } + m.applyChange(new AddImport(ont, importDeclaration)); + } + } + + /** + * Generates a new model taking as input a database D. + * + * Note that the resulting model is uniquely identified by the modeId, which is currently constructed + * as a concatenation of the db and a hidden UUID state. This means that in the unlikely case that + * there is an existing model by this ID, it will be overwritten, + * + * @param db + * @param metadata + * @return modelId + * @throws OWLOntologyCreationException + * @throws URISyntaxException + * @throws IOException + */ + public String generateBlankModel(String db, METADATA metadata) throws OWLOntologyCreationException, IOException, URISyntaxException { + + // Create an arbitrary unique ID and add it to the system. + String modelId; + if (db != null) { + modelId = generateId("gomodel:", db, "-"); + } + else{ + modelId = generateId("gomodel:"); + } + if (modelMap.containsKey(modelId)) { + throw new OWLOntologyCreationException("A model already exists for this db: "+modelId); + } + LOG.info("Generating blank model for new modelId: "+modelId); + + // create empty ontology, use model id as ontology IRI + final OWLOntologyManager m = graph.getManager(); + IRI aBoxIRI = IdStringManager.getIRI(modelId, graph); + final OWLOntology tbox = graph.getSourceOntology(); + OWLOntology abox = null; + ModelContainer model = null; + try { + abox = m.createOntology(aBoxIRI); + + // add imports to T-Box and additional ontologies via IRI + createImports(abox, tbox.getOntologyID(), metadata); + + // generate model + model = new ModelContainer(tbox, abox); + } + catch (OWLOntologyCreationException exception) { + if (abox != null) { + m.removeOntology(abox); + } + throw exception; + } + // add to internal map + modelMap.put(modelId, model); + return modelId; + } + + /** + * Generates a new blank model, add protein label for the given as import. + * + * @param taxonId + * @param metadata + * @return modelId + * @throws OWLOntologyCreationException + * @throws URISyntaxException + * @throws IOException + */ + public String generateBlankModelWithTaxon(String taxonId, METADATA metadata) throws OWLOntologyCreationException, IOException, URISyntaxException { + + // Create an arbitrary unique ID and add it to the system. + String modelId; + if (taxonId != null) { + taxonId = normalizeTaxonId(taxonId); + modelId = generateId("gomodel:taxon_", taxonId, "-"); + } + else{ + modelId = generateId("gomodel:"); + } + if (modelMap.containsKey(modelId)) { + throw new OWLOntologyCreationException("A model already exists for this db: "+modelId); + } + LOG.info("Generating blank model for new modelId: "+modelId); + + // create empty ontology, use model id as ontology IRI + final OWLOntologyManager m = graph.getManager(); + IRI aBoxIRI = IdStringManager.getIRI(modelId, graph); + final OWLOntology tbox = graph.getSourceOntology(); + OWLOntology abox = null; + ModelContainer model = null; + try { + abox = m.createOntology(aBoxIRI); + + // add imports to T-Box and additional ontologies via IRI + createImports(abox, tbox.getOntologyID(), metadata); + + // generate model + model = new ModelContainer(tbox, abox); + } + catch (OWLOntologyCreationException exception) { + if (abox != null) { + m.removeOntology(abox); + } + throw exception; + } + // add to internal map + modelMap.put(modelId, model); + return modelId; + } + + private String normalizeTaxonId(String taxonId) { + // only take the numeric part + StringBuilder sb = new StringBuilder(); + for (int i = 0; i < taxonId.length(); i++) { + char c = taxonId.charAt(i); + if (Character.isDigit(c)) { + sb.append(c); + } + } + return sb.toString(); + } + + /** + * Save all models to disk. The optional annotations may be used to set saved_by and other meta data. + * + * @param annotations + * @param metadata + * + * @throws OWLOntologyStorageException + * @throws OWLOntologyCreationException + * @throws IOException + */ + public void saveAllModels(Set annotations, METADATA metadata) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException { + for (Entry entry : modelMap.entrySet()) { + saveModel(entry.getKey(), entry.getValue(), annotations, metadata); + } + } + + /** + * Save a model to disk. + * + * @param modelId + * @param m + * @param annotations + * @param metadata + * + * @throws OWLOntologyStorageException + * @throws OWLOntologyCreationException + * @throws IOException + */ + public void saveModel(String modelId, ModelContainer m, Set annotations, METADATA metadata) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException { + final OWLOntology ont = m.getAboxOntology(); + final OWLOntologyManager manager = ont.getOWLOntologyManager(); + + // prelimiary checks for the target file + File targetFile = getOwlModelFile(modelId).getCanonicalFile(); + if (targetFile.exists()) { + if (targetFile.isFile() == false) { + throw new IOException("For modelId: '"+modelId+"', the resulting path is not a file: "+targetFile.getAbsolutePath()); + } + if (targetFile.canWrite() == false) { + throw new IOException("For modelId: '"+modelId+"', Cannot write to the file: "+targetFile.getAbsolutePath()); + } + } + else { + File targetFolder = targetFile.getParentFile(); + FileUtils.forceMkdir(targetFolder); + } + File tempFile = null; + try { + // create tempFile + tempFile = File.createTempFile(modelId, ".owl"); + + // write to a temp file + synchronized (ont) { + saveToFile(ont, manager, tempFile, annotations, metadata); + } + + // copy temp file to the finalFile + FileUtils.copyFile(tempFile, targetFile); + } + finally { + // delete temp file + FileUtils.deleteQuietly(tempFile); + } + } + + private void saveToFile(final OWLOntology ont, final OWLOntologyManager manager, + final File outfile, final Set annotations, METADATA metadata) + throws OWLOntologyStorageException { + // check that the annotations contain relevant meta data + final Set metadataAxioms = new HashSet(); + if (annotations != null) { +// for (Pair pair : annotations) { + // TODO saved by +// } + } + // TODO save date? + + List changes = null; + final IRI outfileIRI = IRI.create(outfile); + try { + if (metadataAxioms.isEmpty() == false) { + changes = manager.addAxioms(ont, metadataAxioms); + } + manager.saveOntology(ont, ontologyFormat, outfileIRI); + } + finally { + if (changes != null) { + List invertedChanges = ReverseChangeGenerator.invertChanges(changes); + if (invertedChanges != null && !invertedChanges.isEmpty()) { + manager.applyChanges(invertedChanges); + } + } + } + } + + /** + * Export the ABox for the given modelId in the default {@link OWLOntologyFormat}. + * + * @param modelId + * @param model + * @return modelContent + * @throws OWLOntologyStorageException + */ + public String exportModel(String modelId, ModelContainer model) throws OWLOntologyStorageException { + return exportModel(modelId, model, ontologyFormat); + } + + /** + * Export the ABox for the given modelId in the given ontology format.
+ * Warning: The mapping from String to {@link OWLOntologyFormat} does not map every format! + * + * @param modelId + * @param model + * @param format + * @return modelContent + * @throws OWLOntologyStorageException + */ + public String exportModel(String modelId, ModelContainer model, String format) throws OWLOntologyStorageException { + OWLOntologyFormat ontologyFormat = getOWLOntologyFormat(format); + if (ontologyFormat == null) { + ontologyFormat = this.ontologyFormat; + } + return exportModel(modelId, model, ontologyFormat); + } + + private OWLOntologyFormat getOWLOntologyFormat(String fmt) { + OWLOntologyFormat ofmt = null; + if (fmt != null) { + fmt = fmt.toLowerCase(); + if (fmt.equals("rdfxml")) + ofmt = new RDFXMLOntologyFormat(); + else if (fmt.equals("owl")) + ofmt = new RDFXMLOntologyFormat(); + else if (fmt.equals("rdf")) + ofmt = new RDFXMLOntologyFormat(); + else if (fmt.equals("owx")) + ofmt = new OWLXMLOntologyFormat(); + else if (fmt.equals("owf")) + ofmt = new OWLFunctionalSyntaxOntologyFormat(); + else if (fmt.equals("owm")) + ofmt = new ManchesterOWLSyntaxOntologyFormat(); + } + return ofmt; + } + + /* + * look for all owl files in the give model folder. + */ + private Set getOWLFilesFromPath(String pathTo) { + Set allModelIds = new HashSet(); + File modelFolder = new File(pathTo); + File[] modelFiles = modelFolder.listFiles(new FilenameFilter() { + + @Override + public boolean accept(File dir, String name) { + if (name.endsWith(".owl")) { + return true; + } + return false; + } + }); + for (File modelFile : modelFiles) { + String modelFileName = modelFile.getName(); + String modelId = FilenameUtils.removeExtension(modelFileName); + allModelIds.add(modelId); + } + return allModelIds; + } + + /** + * Retrieve a collection of all file/stored model ids found in the repo.
+ * Note: Models may not be loaded at this point. + * + * @return set of modelids. + * @throws IOException + */ + public Set getStoredModelIds() throws IOException { + return getOWLFilesFromPath(this.pathToOWLFiles); + } + + /** + * Retrieve a collection of all model ids currently in memory.
+ * + * @return set of modelids. + * @throws IOException + */ + public Set getCurrentModelIds() throws IOException { + Set allModelIds = new HashSet(); + // add all model ids currently in memory + allModelIds.addAll(modelMap.keySet()); + return allModelIds; + } + + /** + * Retrieve a collection of all available model ids.
+ * Note: Models may not be loaded at this point. + * + * @return set of modelids. + * @throws IOException + */ + public Set getAvailableModelIds() throws IOException { + Set allModelIds = new HashSet(); + allModelIds.addAll(this.getStoredModelIds()); + allModelIds.addAll(this.getCurrentModelIds()); + return allModelIds; + } + + @Override + protected void loadModel(String modelId, boolean isOverride) throws OWLOntologyCreationException { + LOG.info("Load model: "+modelId+" from file"); + if (modelMap.containsKey(modelId)) { + if (!isOverride) { + throw new OWLOntologyCreationException("Model already exists: "+modelId); + } + unlinkModel(modelId); + } + File modelFile = getOwlModelFile(modelId); + IRI sourceIRI = IRI.create(modelFile); + OWLOntology abox = loadOntologyIRI(sourceIRI, false); + ModelContainer model = addModel(modelId, abox); + updateImports(modelId, model); + } + + @Override + protected OWLOntology loadModelABox(String modelId) throws OWLOntologyCreationException { + File modelFile = getOwlModelFile(modelId); + IRI sourceIRI = IRI.create(modelFile); + OWLOntology abox = loadOntologyIRI(sourceIRI, true); + return abox; + } + + private File getOwlModelFile(String modelId) { + return new File(pathToOWLFiles, modelId + ".owl").getAbsoluteFile(); + } + + /** + * TODO decide identifier policy for models + * + * @param p + * @param db + * @return identifier + */ + String getModelId(String p, String db) { + return "gomodel:" + db + "-"+ p.replaceAll(":", "-"); + } + +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/ModelContainer.java b/minerva-core/src/main/java/org/geneontology/minerva/ModelContainer.java new file mode 100644 index 00000000..f7ce4c27 --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/ModelContainer.java @@ -0,0 +1,442 @@ +package org.geneontology.minerva; + +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.UUID; + +import org.apache.log4j.Logger; +import org.semanticweb.elk.owlapi.ElkReasonerFactory; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLEntity; +import org.semanticweb.owlapi.model.OWLNamedObject; +import org.semanticweb.owlapi.model.OWLObject; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyChange; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.reasoner.OWLReasoner; +import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; + +public class ModelContainer { + + private static Logger LOG = Logger.getLogger(ModelContainer.class); + + private OWLReasonerFactory reasonerFactory = null; + private OWLReasoner reasoner = null; + private OWLOntology aboxOntology = null; + private OWLOntology tboxOntology = null; + private OWLOntology queryOntology = null; + private Map queryClassMap = null; + Map> collectedAxioms = new HashMap>(); + + /** + * The container is seeded with a tbox (i.e. ontology). An abox will be created + * automatically. + * + * A default reasoner factory will be selected (Elk) + * + * @param tbox + * @throws OWLOntologyCreationException + */ + public ModelContainer(OWLOntology tbox) throws OWLOntologyCreationException { + tboxOntology = tbox; + reasonerFactory = new ElkReasonerFactory(); + init(); + } + /** + * Creates a container with a pre-defined tbox (ontology) and abox (instance store). + * Note the abox should import the tbox (directly or indirectly). + * + * The abox may be identical to the tbox, in which case individuals are added to + * the same ontology + * + * @param tbox + * @param abox + * @throws OWLOntologyCreationException + */ + public ModelContainer(OWLOntology tbox, OWLOntology abox) throws OWLOntologyCreationException { + tboxOntology = tbox; + aboxOntology = abox; + reasonerFactory = new ElkReasonerFactory(); + init(); + } + + /** + * The container is seeded with a tbox (i.e. ontology). An abox will be created + * automatically. + * + * @param tbox + * @param reasonerFactory + * @throws OWLOntologyCreationException + */ + public ModelContainer(OWLOntology tbox, + OWLReasonerFactory reasonerFactory) throws OWLOntologyCreationException { + tboxOntology = tbox; + this.reasonerFactory = reasonerFactory; + init(); + } + + /** + * Creates a container with a pre-defined tbox (ontology) and abox (instance store). + * Note the abox should import the tbox (directly or indirectly). + * + * The abox may be identical to the tbox, in which case individuals are added to + * the same ontology + * + * @param tbox + * @param abox + * @param rf + * @throws OWLOntologyCreationException + */ + public ModelContainer(OWLOntology tbox, OWLOntology abox, + OWLReasonerFactory rf) throws OWLOntologyCreationException { + tboxOntology = tbox; + aboxOntology = abox; + reasonerFactory = rf; + init(); + } + + /** + * Initialization consists of: + * + *
    + *
  • Setting aboxOntology, if not set - defaults to a new ontology using tbox.IRI as base. + * Adds import to tbox. + *
  • Setting queryOntology, if not set. Adds abox imports queryOntology declaration + *
+ * + * @throws OWLOntologyCreationException + */ + private void init() throws OWLOntologyCreationException { + // reasoner -> query -> abox -> tbox + if (aboxOntology == null) { + LOG.debug("Creating abox ontology. mgr = "+getOWLOntologyManager()); + IRI ontologyIRI = IRI.create(tboxOntology.getOntologyID().getOntologyIRI()+"__abox"); + aboxOntology = getOWLOntologyManager().getOntology(ontologyIRI); + if (aboxOntology != null) { + LOG.warn("Clearing existing abox ontology"); + getOWLOntologyManager().removeOntology(aboxOntology); + } + aboxOntology = getOWLOntologyManager().createOntology(ontologyIRI); + AddImport ai = new AddImport(aboxOntology, + getOWLDataFactory().getOWLImportsDeclaration(tboxOntology.getOntologyID().getOntologyIRI())); + getOWLOntologyManager().applyChange(ai); + } + if (queryOntology == null) { + // Imports: {q imports a, a imports t} + LOG.debug("Creating query ontology"); + + IRI ontologyIRI = IRI.create(tboxOntology.getOntologyID().getOntologyIRI()+"__query"); + queryOntology = getOWLOntologyManager().getOntology(ontologyIRI); + if (queryOntology == null) { + queryOntology = getOWLOntologyManager().createOntology(ontologyIRI); + } + AddImport ai = new AddImport(queryOntology, + getOWLDataFactory().getOWLImportsDeclaration(aboxOntology.getOntologyID().getOntologyIRI())); + getOWLOntologyManager().applyChange(ai); + } + if (LOG.isDebugEnabled()) { + LOG.debug("manager(T) = "+tboxOntology.getOWLOntologyManager()); + LOG.debug("manager(A) = "+aboxOntology.getOWLOntologyManager()); + LOG.debug("manager(Q) = "+queryOntology.getOWLOntologyManager()); + LOG.debug("id(T) = "+tboxOntology.getOntologyID().getOntologyIRI()); + LOG.debug("id(A) = "+aboxOntology.getOntologyID().getOntologyIRI()); + LOG.debug("id(Q) = "+queryOntology.getOntologyID().getOntologyIRI()); + } + } + + /** + * @return ontology manager for tbox + */ + public OWLOntologyManager getOWLOntologyManager() { + return tboxOntology.getOWLOntologyManager(); + } + + /** + * @return data factory for tbox + */ + public OWLDataFactory getOWLDataFactory() { + return getOWLOntologyManager().getOWLDataFactory(); + } + + /** + * Release the reasoner + * + */ + public void disposeReasoner() { + if (reasoner != null) { + reasoner.dispose(); + reasoner = null; + } + } + + public void dispose() { + disposeReasoner(); + final OWLOntologyManager m = getOWLOntologyManager(); + if (queryOntology != null) { + m.removeOntology(queryOntology); + } + if (aboxOntology != null) { + m.removeOntology(aboxOntology); + } + } + + /** + * The reasoner factory is used during initialization to + * generate a reasoner object using abox as ontology + * + * @param reasonerFactory + */ + public void setReasonerFactory(OWLReasonerFactory reasonerFactory) { + this.reasonerFactory = reasonerFactory; + } + + /** + * @return current reasoner, operating over abox + */ + public synchronized OWLReasoner getReasoner() { + if (reasoner == null) { + // reasoner -> query -> abox -> tbox + if (LOG.isDebugEnabled()) { + LOG.debug("Creating reasoner on "+queryOntology+" ImportsClosure="+ + queryOntology.getImportsClosure()); + } + reasoner = reasonerFactory.createReasoner(queryOntology); + } + return reasoner; + } + /** + * @param reasoner + */ + public void setReasoner(OWLReasoner reasoner) { + this.reasoner = reasoner; + } + /** + * The tbox ontology should contain class axioms used to generate minimal models in the + * abox ontology. + * + * May be the same as abox, in which case generated abox axioms go in the same ontology + * + * @return tbox + */ + public OWLOntology getTboxOntology() { + return tboxOntology; + } + /** + * @param tboxOntology + */ + public void setTboxOntology(OWLOntology tboxOntology) { + this.tboxOntology = tboxOntology; + } + /** + * Note: ABox ontology should import TBox ontology + * @return abox + */ + public OWLOntology getAboxOntology() { + return aboxOntology; + } + + /** + * Note: ABox ontology should import TBox ontology + * @param aboxOntology + */ + public void setAboxOntology(OWLOntology aboxOntology) { + this.aboxOntology = aboxOntology; + } + /** + * You should not need to use this directly - exposed for debugging + * + * @return auxiliary ontology to support queries + */ + public OWLOntology getQueryOntology() { + return queryOntology; + } + + public boolean isQueryClass(OWLClass c) { + if (queryClassMap != null && queryClassMap.containsKey(c)) { + return true; + } + return false; + } + + public Set getQueryClasses() { + if (queryClassMap != null) { + return queryClassMap.keySet(); + } + return Collections.emptySet(); + } + + public void addAxiom(OWLAxiom ax) { + addAxiom(ax, aboxOntology); + } + public void addAxiom(OWLAxiom ax, OWLOntology ont) { + if (LOG.isDebugEnabled()) { + LOG.debug("Adding: "+ax+" to "+ont); + } + getOWLOntologyManager().addAxiom(ont, ax); + } + public void addAxioms(Set axs) { + addAxioms(axs, aboxOntology); + } + public void addAxioms(Set axs, OWLOntology ont) { + if (LOG.isDebugEnabled()) { + LOG.debug("Adding: "+axs+" to "+ont); + } + getOWLOntologyManager().addAxioms(ont, axs); + } + + public void applyChanges(List changeIRI) { + getOWLOntologyManager().applyChanges(changeIRI); + } + + public synchronized Map getQueryClassMap(boolean precomputePropertyClassCombinations) { + if (queryClassMap == null) { + generateQueryOntology(precomputePropertyClassCombinations); + } + return queryClassMap; + } + + /** + * Motivation: OWL reasoners do not return superclass expressions + * If we want to find all class expressions that may hold for a class + * then we must pre-coordinate + * all possible expressions within the subset of OWL we care about. + *
+ * This class generates all satisfiable class expressions of the form + * r some c (for the cross-product of R x C), as well as all + * class expressions that have been used (which may include nested expressions) + * + * The results are stored in queryClassMap + * + * @param precomputePropertyClassCombinations + */ + private void generateQueryOntology(boolean precomputePropertyClassCombinations) { + queryClassMap = new HashMap(); + + getReasoner().flush(); + + if (precomputePropertyClassCombinations) { + LOG.debug("Precomputing all OP x Class combos"); + // cross-product of P x C + // TODO - reflexivity and local reflexivity? + for (OWLObjectProperty p : tboxOntology.getObjectPropertiesInSignature(true)) { + LOG.debug(" materializing P some C for P=:"+p); + for (OWLClass c : tboxOntology.getClassesInSignature(true)) { + OWLObjectSomeValuesFrom r = getOWLDataFactory().getOWLObjectSomeValuesFrom(p, c); + //LOG.debug(" QMAP:"+r); + addClassExpressionToQueryMap(r); + } + } + } + + // all expressions used in ontology + for (OWLOntology ont : tboxOntology.getImportsClosure()) { + LOG.debug("Finding all nested anonymous expressions"); + for (OWLAxiom ax : ont.getAxioms()) { + // TODO - check if this is the nest closure. ie (r some (r2 some (r3 some ...))) + for (OWLClassExpression x : ax.getNestedClassExpressions()) { + if (x.isAnonymous()) { + //LOG.debug(" QMAP+:"+x); + addClassExpressionToQueryMap(x); + } + } + } + } + if (LOG.isDebugEnabled()) { + for (OWLOntology ont : collectedAxioms.keySet()) { + LOG.debug("TOTAL axioms in QMAP: "+collectedAxioms.get(ont).size()); + } + } + LOG.debug("Adding collected axioms"); + addCollectedAxioms(); + LOG.debug("Flushing reasoner..."); + reasoner.flush(); + LOG.debug("Flushed reasoner"); + } + + /** + * Note that this collects axioms but does not change the ontology. Call {@link #addCollectedAxioms()} to add these + * + * @param x + */ + private void addClassExpressionToQueryMap(OWLClassExpression x) { + if (!(x instanceof OWLObjectSomeValuesFrom)) { + // in future we may support a wider variety of expressions - e.g. cardinality + return; + } + // this makes things too slow + //if (!reasoner.isSatisfiable(x)) { + // LOG.debug("Not adding unsatisfiable query expression:" +x); + // return; + //} + IRI nxIRI = getSkolemIRI(x.getSignature()); + OWLClass nx = getOWLDataFactory().getOWLClass(nxIRI); + OWLAxiom ax = getOWLDataFactory().getOWLEquivalentClassesAxiom(nx, x); + collectAxiom(ax, queryOntology); + queryClassMap.put(nx, x); + } + + private IRI getSkolemIRI(Set objs) { + // TODO Auto-generated method stub + IRI iri; + StringBuffer sb = new StringBuffer(); + for (OWLEntity obj : objs) { + sb.append("/"+getFragmentID(obj)); + } + iri = IRI.create("http://x.org"+sb.toString()); + return iri; + } + + private String getFragmentID(OWLObject obj) { + if (obj instanceof OWLNamedObject) { + return ((OWLNamedObject) obj).getIRI().toString().replaceAll(".*/", ""); + } + return UUID.randomUUID().toString(); + } + + + /** + * Collects an axiom to be added to ont at some later time. + * Cal {@link #addCollectedAxioms()} to add these + * + * @param ax + * @param ont + */ + private void collectAxiom(OWLAxiom ax, OWLOntology ont) { + //LOG.debug("Collecting: "+ax+" to "+ont); + if (!collectedAxioms.containsKey(ont)) + collectedAxioms.put(ont, new HashSet()); + collectedAxioms.get(ont).add(ax); + } + + /** + * Adds all collected axioms to their specified destination + */ + private void addCollectedAxioms() { + for (OWLOntology ont : collectedAxioms.keySet()) + addCollectedAxioms(ont); + } + + /** + * Adds all collected axioms to ont + * @param ont + */ + private void addCollectedAxioms(OWLOntology ont) { + if (collectedAxioms.containsKey(ont)) { + getOWLOntologyManager().addAxioms(ont, collectedAxioms.get(ont)); + collectedAxioms.remove(ont); + } + + } +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/MolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/MolecularModelManager.java new file mode 100644 index 00000000..966c5754 --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/MolecularModelManager.java @@ -0,0 +1,997 @@ +package org.geneontology.minerva; + +import java.io.IOException; +import java.net.URISyntaxException; +import java.util.Arrays; +import java.util.Collection; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.Set; + +import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.util.IdStringManager; +import org.geneontology.minerva.util.ManchesterSyntaxTool; +import org.semanticweb.owlapi.expression.ParserException; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataProperty; +import org.semanticweb.owlapi.model.OWLEntity; +import org.semanticweb.owlapi.model.OWLException; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyFormat; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; + +import owltools.graph.OWLGraphWrapper; +import owltools.vocab.OBOUpperVocabulary; + +/** + * Convenience layer for operations on collections of MolecularModels (aka lego diagrams) + * + * This manager is intended to be used within a web server. Multiple clients can + * contact the same manager instance through services + * + * @param + * @see CoreMolecularModelManager + * @see FileBasedMolecularModelManager + */ +public class MolecularModelManager extends FileBasedMolecularModelManager { + + public static class UnknownIdentifierException extends Exception { + + // generated + private static final long serialVersionUID = -847970910712518838L; + + /** + * @param message + * @param cause + */ + public UnknownIdentifierException(String message, Throwable cause) { + super(message, cause); + } + + /** + * @param message + */ + public UnknownIdentifierException(String message) { + super(message); + } + + } + + /** + * @param graph + * @throws OWLOntologyCreationException + */ + public MolecularModelManager(OWLGraphWrapper graph) throws OWLOntologyCreationException { + super(graph); + } + + /** + * wrapper for {@link #generateModel(OWLClass, String, Object)} + * + * @param pid + * @param db + * @param metadata + * @return modelId + * @throws OWLOntologyCreationException + * @throws IOException + * @throws URISyntaxException + * @throws UnknownIdentifierException + */ + @Deprecated + public String generateModel(String pid, String db, METADATA metadata) throws OWLOntologyCreationException, IOException, URISyntaxException, UnknownIdentifierException { + OWLClass cls = getClass(pid, graph); + if (cls == null) { + throw new UnknownIdentifierException("Could not find a class for id: "+pid); + } + return generateModel(cls, db, metadata); + } + + /** + * @param modelId + * @param qs + * @return all individuals in the model that satisfy q + * @throws UnknownIdentifierException + */ + public Set getIndividualsByQuery(String modelId, String qs) throws UnknownIdentifierException { + ModelContainer mod = checkModelId(modelId); + ManchesterSyntaxTool mst = new ManchesterSyntaxTool(new OWLGraphWrapper(mod.getAboxOntology()), false); + OWLClassExpression q = mst.parseManchesterExpression(qs); + return getIndividualsByQuery(modelId, q); + } + + /** + * Shortcut for {@link CoreMolecularModelManager#createIndividual} + * + * @param modelId + * @param cid + * @param annotations + * @param metadata + * @return id and individual + * @throws UnknownIdentifierException + */ + public Pair createIndividual(String modelId, String cid, Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLClass cls = getClass(cid, model); + if (cls == null) { + throw new UnknownIdentifierException("Could not find a class for id: "+cid); + } + OWLNamedIndividual individual = createIndividual(modelId, model, cls, annotations , true, metadata); + return Pair.of(IdStringManager.getId(individual.getIRI()), individual); + } + + + /** + * Shortcut for {@link CoreMolecularModelManager#createIndividual}. + * + * @param modelId + * @param cid + * @param annotations + * @param metadata + * @return id and created individual + * @throws UnknownIdentifierException + */ + public Pair createIndividualNonReasoning(String modelId, String cid, Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLClass cls = getClass(cid, model); + if (cls == null) { + throw new UnknownIdentifierException("Could not find a class for id: "+cid); + } + return createIndividualNonReasoning(modelId, cls, annotations, metadata); + } + + /** + * Shortcut for {@link CoreMolecularModelManager#createIndividual}. + * + * @param modelId + * @param ce + * @param annotations + * @param metadata + * @return id and created individual + * @throws UnknownIdentifierException + */ + public Pair createIndividualNonReasoning(String modelId, OWLClassExpression ce, Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = createIndividual(modelId, model, ce, annotations, false, metadata); + return Pair.of(IdStringManager.getId(i.getIRI()), i); + } + + public OWLNamedIndividual getNamedIndividual(String modelId, String iid) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = getIndividual(iid, model); + if (i == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + return i; + } + + /** + * Deletes an individual and return all IRIs used as an annotation value + * + * @param modelId + * @param iid + * @param metadata + * @return delete information + * @throws UnknownIdentifierException + */ + public DeleteInformation deleteIndividual(String modelId, String iid, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = getIndividual(iid, model); + if (i == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + return deleteIndividual(modelId, model, i, true, metadata); + } + /** + * Deletes an individual and return all IRIs used as an annotation value + * + * @param modelId + * @param iid + * @param metadata + * @return delete information + * @throws UnknownIdentifierException + */ + public DeleteInformation deleteIndividualNonReasoning(String modelId, String iid, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = getIndividual(iid, model); + if (i == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + return deleteIndividual(modelId, model, i, false, metadata); + } + + /** + * Deletes an individual + * + * @param modelId + * @param iri + * @param metadata + * @throws UnknownIdentifierException + */ + public void deleteIndividualNonReasoning(String modelId, IRI iri, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = getIndividual(iri, model); + if (i == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iri); + } + deleteIndividual(modelId, model, i, false, metadata); + } + + public void addAnnotations(String modelId, Set annotations, METADATA metadata) + throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + if (annotations != null && !annotations.isEmpty()) { + addAnnotations(modelId, model, annotations, metadata); + } + } + + public void updateAnnotation(String modelId, OWLAnnotation annotation, METADATA metadata) + throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + if (annotation != null) { + updateAnnotation(modelId, model, annotation, metadata); + } + } + + public OWLNamedIndividual addAnnotations(String modelId, String iid, + Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = getIndividual(iid, model); + if (i == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + if (annotations != null && !annotations.isEmpty()) { + addAnnotations(modelId, model, i.getIRI(), annotations, metadata); + } + return i; + } + + public void addAnnotations(String modelId, IRI subject, + Set annotations, METADATA metadata) throws UnknownIdentifierException { + if (annotations != null && !annotations.isEmpty()) { + ModelContainer model = checkModelId(modelId); + addAnnotations(modelId, model, subject, annotations, metadata); + } + } + + public OWLNamedIndividual updateAnnotation(String modelId, String iid, + OWLAnnotation annotation, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = getIndividual(iid, model); + if (i == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + if (annotation != null) { + updateAnnotation(modelId, model, i.getIRI(), annotation, metadata); + } + return i; + } + + public void updateAnnotation(String modelId, IRI subject, + OWLAnnotation annotation, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + if (annotation != null) { + updateAnnotation(modelId, model, subject, annotation, metadata); + } + } + + public OWLNamedIndividual removeAnnotations(String modelId, String iid, + Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = getIndividual(iid, model); + if (i == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + if (annotations != null && !annotations.isEmpty()) { + removeAnnotations(modelId, model, i.getIRI(), annotations, metadata); + } + return i; + } + + public void removeAnnotations(String modelId, Set annotations, METADATA metadata) + throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + if (annotations != null && !annotations.isEmpty()) { + removeAnnotations(modelId, model, annotations, metadata); + } + } + + /** + * @param id + */ + public void deleteModel(String id) { + // TODO - retrieve from persistent store + modelMap.remove(id); + } + + public Set searchModels(Collection ids) throws IOException { + final Set resultSet = new HashSet(); + // create IRIs + Set searchIRIs = new HashSet(); + for(String id : ids) { + searchIRIs.add(graph.getIRIByIdentifier(id)); + } + + if (!searchIRIs.isEmpty()) { + // search for IRI usage in models + final Set allModelIds = getAvailableModelIds(); + for (final String modelId : allModelIds) { + final ModelContainer model = getModel(modelId); + final OWLOntology aboxOntology = model.getAboxOntology(); + Set signature = aboxOntology.getSignature(); + for (OWLEntity entity : signature) { + if (searchIRIs.contains(entity.getIRI())) { + resultSet.add(modelId); + break; + } + } + } + } + // return results + return resultSet; + } + + /** + * Save a model to disk. + * + * @param modelId + * @param annotations + * @param metadata + * + * @throws OWLOntologyStorageException + * @throws OWLOntologyCreationException + * @throws IOException + * @throws UnknownIdentifierException + */ + public void saveModel(String modelId, Set annotations, METADATA metadata) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException, UnknownIdentifierException { + ModelContainer m = checkModelId(modelId); + saveModel(modelId, m , annotations, metadata); + } + + /** + * Export the ABox for the given modelId in the default {@link OWLOntologyFormat}. + * + * @param modelId + * @return modelContent + * @throws OWLOntologyStorageException + * @throws UnknownIdentifierException + */ + public String exportModel(String modelId) throws OWLOntologyStorageException, UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + return exportModel(modelId, model); + } + + private OWLNamedIndividual getIndividual(String indId, ModelContainer model) { + OWLGraphWrapper graph = new OWLGraphWrapper(model.getAboxOntology()); + IRI iri = IdStringManager.getIRI(indId, graph); + return getIndividual(iri, model); + } + private OWLNamedIndividual getIndividual(IRI iri, ModelContainer model) { + // check that individual is actually declared + boolean containsIRI = model.getAboxOntology().containsEntityInSignature(iri); + if (containsIRI == false) { + return null; + } + OWLNamedIndividual individual = model.getOWLDataFactory().getOWLNamedIndividual(iri); + return individual; + } + private OWLClass getClass(String cid, ModelContainer model) { + OWLGraphWrapper graph = new OWLGraphWrapper(model.getAboxOntology()); + return getClass(cid, graph); + } + private OWLClass getClass(String cid, OWLGraphWrapper graph) { + IRI iri = IdStringManager.getIRI(cid, graph); + return graph.getOWLClass(iri); + } + @Deprecated + private OWLClass getGeneClass(String cid, ModelContainer model) { + OWLGraphWrapper graph = new OWLGraphWrapper(model.getAboxOntology()); + IRI iri = IdStringManager.getIRI(cid, graph); + return model.getOWLDataFactory().getOWLClass(iri); + } + private OWLObjectProperty getObjectProperty(String pid, ModelContainer model) { + OWLGraphWrapper graph = new OWLGraphWrapper(model.getAboxOntology()); + IRI iri = IdStringManager.getIRI(pid, graph); + return graph.getOWLObjectProperty(iri); + } + + public ModelContainer checkModelId(String modelId) throws UnknownIdentifierException { + ModelContainer model = getModel(modelId); + if (model == null) { + throw new UnknownIdentifierException("Could not find a model for id: "+modelId); + } + return model; + } + + private OWLObjectPropertyExpression getObjectProperty(OBOUpperVocabulary vocabElement, + ModelContainer model) { + return vocabElement.getObjectProperty(model.getAboxOntology()); + } + + /** + * Convenience wrapper for {@link CoreMolecularModelManager#addType} + * + * @param modelId + * @param iid + * @param cid + * @param metadata + * @throws UnknownIdentifierException + */ + public void addType(String modelId, String iid, String cid, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual individual = getIndividual(iid, model); + if (individual == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLClass cls = getClass(cid, model); + if (cls == null) { + throw new UnknownIdentifierException("Could not find a class for id: "+cid); + } + addType(modelId, model, individual, cls, true, metadata); + } + + /** + * @param modelId + * @param iid + * @param clsExp + * @param metadata + * @return individual + * @throws UnknownIdentifierException + */ + public OWLNamedIndividual addTypeNonReasoning(String modelId, String iid, OWLClassExpression clsExp, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual individual = getIndividual(iid, model); + if (individual == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + addType(modelId, model, individual, clsExp, false, metadata); + return individual; + } + + /** + * Convenience wrapper for {@link CoreMolecularModelManager#addType}. + * + * @param modelId + * @param iid + * @param pid + * @param cid + * @param metadata + * @throws UnknownIdentifierException + */ + public void addType(String modelId, + String iid, String pid, String cid, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual individual = getIndividual(iid, model); + if (individual == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLObjectProperty property = getObjectProperty(pid, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a property for id: "+pid); + } + OWLClass cls = getClass(cid, model); + if (cls == null) { + throw new UnknownIdentifierException("Could not find a class for id: "+cid); + } + addType(modelId, model, individual, property, cls, true, metadata); + } + + public OWLNamedIndividual addTypeNonReasoning(String modelId, + String iid, String pid, OWLClassExpression ce, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual individual = getIndividual(iid, model); + if (individual == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLObjectProperty property = getObjectProperty(pid, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a property for id: "+pid); + } + addType(modelId, model, individual, property, ce, false, metadata); + return individual; + } + + /** + * Convenience wrapper for {@link CoreMolecularModelManager#removeType} + * + * @param modelId + * @param iid + * @param cid + * @param metadata + * @throws UnknownIdentifierException + */ + public void removeType(String modelId, String iid, String cid, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual individual = getIndividual(iid, model); + if (individual == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLClass cls = getClass(cid, model); + if (cls == null) { + throw new UnknownIdentifierException("Could not find a class for id: "+cid); + } + removeType(modelId, model, individual, cls, true, metadata); + } + + public OWLNamedIndividual removeTypeNonReasoning(String modelId, String iid, OWLClassExpression clsExp, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual individual = getIndividual(iid, model); + if (individual == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + removeType(modelId, model, individual, clsExp, false, metadata); + return individual; + } + + /** + * Convenience wrapper for {@link #addOccursIn(String, OWLNamedIndividual, OWLClassExpression)} + * + * @param modelId + * @param iid + * @param eid - e.g. PR:P12345 + * @throws UnknownIdentifierException + */ + @Deprecated + public void addOccursIn(String modelId, + String iid, String eid) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual individual = getIndividual(iid, model); + if (individual == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLClass cls = getClass(eid, model); + if (cls == null) { + throw new UnknownIdentifierException("Could not find a class for id: "+eid); + } + addOccursIn(modelId, model, individual, cls); + } + + /** + * Adds a ClassAssertion to the model, connecting an activity instance to the class of molecule + * that enables the activity. + * + * Example: FGFR receptor activity occursIn some UniProtKB:FGF + * + * The reasoner may detect an inconsistency under different scenarios: + * - i may be an instance of a class that is disjoint with a bfo process + * - the enabled may be an instance of a class that is disjoint with molecular entity + * + * Under these circumstances, no error is thrown, but the response code indicates that no operation + * was performed on the kb, and the response object indicates the operation caused an inconsistency + * + * @param modelId + * @param i + * @param enabler + * @throws UnknownIdentifierException + */ + @Deprecated + public void addOccursIn(String modelId, + OWLNamedIndividual i, + OWLClassExpression enabler) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + addOccursIn(modelId, model, i, enabler); + } + + @Deprecated + private void addOccursIn(String modelId, ModelContainer model, + OWLNamedIndividual i, + OWLClassExpression enabler) { + addType(modelId, model, i, OBOUpperVocabulary.BFO_occurs_in.getObjectProperty(getOntology()), enabler, true, null); + } + + /** + * Convenience wrapper for {@link #addEnabledBy(String, OWLNamedIndividual, OWLClassExpression)} + * + * @param modelId + * @param iid + * @param eid - e.g. PR:P12345 + * @throws UnknownIdentifierException + * @throws OWLException + */ + @Deprecated + public void addEnabledBy(String modelId, + String iid, String eid) throws UnknownIdentifierException, + OWLException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual individual = getIndividual(iid, model); + if (individual == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLClassExpression clsExpr; + if (eid.contains(" ")) { + clsExpr = parseClassExpression(eid, model); + } + else { + clsExpr = getGeneClass(eid, model); + if (clsExpr == null) { + throw new UnknownIdentifierException("Could not find a class for id: "+eid); + } + } + addEnabledBy(modelId, model, individual, clsExpr); + } + + @Deprecated + private OWLClassExpression parseClassExpression(String expression, ModelContainer model) throws OWLException { + OWLGraphWrapper g = new OWLGraphWrapper(model.getAboxOntology()); + return parseClassExpression(expression, g); + } + + @Deprecated + public static OWLClassExpression parseClassExpression(String expression, OWLGraphWrapper g) throws OWLException { + try { + ManchesterSyntaxTool syntaxTool = new ManchesterSyntaxTool(g, true); + OWLClassExpression clsExpr = syntaxTool.parseManchesterExpression(expression); + return clsExpr; + } + catch (ParserException e) { + // wrap in an Exception (not RuntimeException) to enable proper error handling + throw new OWLException("Could not parse expression: \""+expression+"\"", e) { + + private static final long serialVersionUID = -9158071212925724138L; + }; + } + } + + /** + * Adds a ClassAssertion to the model, connecting an activity instance to the class of molecule + * that enables the activity. + * + * Example: FGFR receptor activity enabledBy some UniProtKB:FGF + * + * The reasoner may detect an inconsistency under different scenarios: + * - i may be an instance of a class that is disjoint with a bfo process + * - the enabled may be an instance of a class that is disjoint with molecular entity + * + * Under these circumstances, no error is thrown, but the response code indicates that no operation + * was performed on the kb, and the response object indicates the operation caused an inconsistency + * + * @param modelId + * @param i + * @param enabler + * @throws UnknownIdentifierException + */ + @Deprecated + public void addEnabledBy(String modelId, + OWLNamedIndividual i, + OWLClassExpression enabler) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + addEnabledBy(modelId, model, i, enabler); + } + + @Deprecated + private void addEnabledBy(String modelId, ModelContainer model, + OWLNamedIndividual i, + OWLClassExpression enabler) { + OWLObjectProperty p = OBOUpperVocabulary.GOREL_enabled_by.getObjectProperty(model.getAboxOntology()); + addType(modelId, model, i, p, enabler, true, null); + } + + /** + * Convenience wrapper for {@link CoreMolecularModelManager#addFact} + * + * @param modelId + * @param pid + * @param iid + * @param jid + * @param annotations + * @param metadata + * @return relevant individuals + * @throws UnknownIdentifierException + */ + public List addFact(String modelId, String pid, String iid, String jid, + Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLObjectProperty property = getObjectProperty(pid, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a property for id: "+pid); + } + OWLNamedIndividual individual1 = getIndividual(iid, model); + if (individual1 == null) { + throw new UnknownIdentifierException("Could not find a individual (1) for id: "+iid); + } + OWLNamedIndividual individual2 = getIndividual(jid, model); + if (individual2 == null) { + throw new UnknownIdentifierException("Could not find a individual (2) for id: "+jid); + } + addFact(modelId, model, property, individual1, individual2, annotations, true, metadata); + return Arrays.asList(individual1, individual2); + } + + /** + * Convenience wrapper for {@link CoreMolecularModelManager#addFact} + * + * @param modelId + * @param pid + * @param iid + * @param jid + * @param annotations + * @param metadata + * @return relevant individuals + * @throws UnknownIdentifierException + */ + public List addFactNonReasoning(String modelId, String pid, String iid, String jid, + Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLObjectProperty property = getObjectProperty(pid, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a property for id: "+pid); + } + OWLNamedIndividual individual1 = getIndividual(iid, model); + if (individual1 == null) { + throw new UnknownIdentifierException("Could not find a individual (1) for id: "+iid); + } + OWLNamedIndividual individual2 = getIndividual(jid, model); + if (individual2 == null) { + throw new UnknownIdentifierException("Could not find a individual (2) for id: "+jid); + } + addFact(modelId, model, property, individual1, individual2, annotations, false, metadata); + return Arrays.asList(individual1, individual2); + } + + /** + * Convenience wrapper for {@link CoreMolecularModelManager#addFact} + * + * @param modelId + * @param vocabElement + * @param iid + * @param jid + * @param annotations + * @param metadata + * @return relevant individuals + * @throws UnknownIdentifierException + */ + public List addFact(String modelId, OBOUpperVocabulary vocabElement, + String iid, String jid, Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLObjectPropertyExpression property = getObjectProperty(vocabElement, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+vocabElement); + } + OWLNamedIndividual individual1 = getIndividual(iid, model); + if (individual1 == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLNamedIndividual individual2 = getIndividual(jid, model); + if (individual2 == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+jid); + } + addFact(modelId, model, property, individual1, individual2, annotations, true, metadata); + return Arrays.asList(individual1, individual2); + } + + /** + * @param modelId + * @param pid + * @param iid + * @param jid + * @param metadata + * @return response info + * @throws UnknownIdentifierException + */ + public List removeFact(String modelId, String pid, + String iid, String jid, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLObjectProperty property = getObjectProperty(pid, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+pid); + } + OWLNamedIndividual individual1 = getIndividual(iid, model); + if (individual1 == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLNamedIndividual individual2 = getIndividual(jid, model); + if (individual2 == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+jid); + } + removeFact(modelId, model, property, individual1, individual2, true, metadata); + return Arrays.asList(individual1, individual2); + } + + public Pair, Set> removeFactNonReasoning(String modelId, String pid, + String iid, String jid, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLObjectProperty property = getObjectProperty(pid, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+pid); + } + OWLNamedIndividual individual1 = getIndividual(iid, model); + if (individual1 == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLNamedIndividual individual2 = getIndividual(jid, model); + if (individual2 == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+jid); + } + Set iriSet = removeFact(modelId, model, property, individual1, individual2, false, metadata); + return Pair.of(Arrays.asList(individual1, individual2), iriSet); + } + + public List addAnnotations(String modelId, String pid, + String iid, String jid, Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLObjectProperty property = getObjectProperty(pid, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a property for id: "+pid); + } + OWLNamedIndividual individual1 = getIndividual(iid, model); + if (individual1 == null) { + throw new UnknownIdentifierException("Could not find a individual (1) for id: "+iid); + } + OWLNamedIndividual individual2 = getIndividual(jid, model); + if (individual2 == null) { + throw new UnknownIdentifierException("Could not find a individual (2) for id: "+jid); + } + addAnnotations(modelId, model, property, individual1, individual2, annotations, false, metadata); + + return Arrays.asList(individual1, individual2); + } + + public void addAnnotations(String modelId, Set axioms, Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + for (OWLObjectPropertyAssertionAxiom axiom : axioms) { + addAnnotations(modelId, model, axiom, annotations, false, metadata); + } + } + + public List updateAnnotation(String modelId, String pid, + String iid, String jid, OWLAnnotation annotation, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLObjectProperty property = getObjectProperty(pid, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a property for id: "+pid); + } + OWLNamedIndividual individual1 = getIndividual(iid, model); + if (individual1 == null) { + throw new UnknownIdentifierException("Could not find a individual (1) for id: "+iid); + } + OWLNamedIndividual individual2 = getIndividual(jid, model); + if (individual2 == null) { + throw new UnknownIdentifierException("Could not find a individual (2) for id: "+jid); + } + updateAnnotation(modelId, model, property, individual1, individual2, annotation, false, metadata); + + return Arrays.asList(individual1, individual2); + } + + public Set updateAnnotation(String modelId, Set axioms, OWLAnnotation annotation, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + Set newAxioms = new HashSet(); + for (OWLObjectPropertyAssertionAxiom axiom : axioms) { + OWLObjectPropertyAssertionAxiom newAxiom = + updateAnnotation(modelId, model, axiom, annotation, false, metadata); + if (newAxiom != null) { + newAxioms.add(newAxiom); + } + } + return newAxioms; + } + + public List removeAnnotations(String modelId, String pid, + String iid, String jid, Set annotations, METADATA metadata) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLObjectProperty property = getObjectProperty(pid, model); + if (property == null) { + throw new UnknownIdentifierException("Could not find a property for id: "+pid); + } + OWLNamedIndividual individual1 = getIndividual(iid, model); + if (individual1 == null) { + throw new UnknownIdentifierException("Could not find a individual (1) for id: "+iid); + } + OWLNamedIndividual individual2 = getIndividual(jid, model); + if (individual2 == null) { + throw new UnknownIdentifierException("Could not find a individual (2) for id: "+jid); + } + removeAnnotations(modelId, model, property, individual1, individual2, annotations, false, metadata); + + return Arrays.asList(individual1, individual2); + } + + public OWLNamedIndividual addDataProperties(String modelId, String iid, + Map> dataProperties, METADATA token) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = getIndividual(iid, model); + if (i == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + if (dataProperties != null && !dataProperties.isEmpty()) { + for(Entry> entry : dataProperties.entrySet()) { + for(OWLLiteral literal : entry.getValue()) { + addDataProperty(modelId, model, i, entry.getKey(), literal, false, token); + } + } + } + return i; + } + + public OWLNamedIndividual removeDataProperties(String modelId, String iid, + Map> dataProperties, METADATA token) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual i = getIndividual(iid, model); + if (i == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + if (dataProperties != null && !dataProperties.isEmpty()) { + for(Entry> entry : dataProperties.entrySet()) { + for(OWLLiteral literal : entry.getValue()) { + removeDataProperty(modelId, model, i, entry.getKey(), literal, false, token); + } + } + } + return i; + } + + /** + * Convenience wrapper for {@link #addPartOf(String, OWLNamedIndividual, OWLNamedIndividual, Set)} + * + * @param modelId + * @param iid + * @param jid + * @param annotations + * @throws UnknownIdentifierException + */ + @Deprecated + public void addPartOf(String modelId, String iid, + String jid, Set annotations) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + OWLNamedIndividual individual1 = getIndividual(iid, model); + if (individual1 == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+iid); + } + OWLNamedIndividual individual2 = getIndividual(jid, model); + if (individual2 == null) { + throw new UnknownIdentifierException("Could not find a individual for id: "+jid); + } + addPartOf(modelId, individual1, individual2, annotations); + } + + /** + * Adds an OWL ObjectPropertyAssertion connecting i to j via part_of + * + * Note that the inverse assertion is entailed, but not asserted + * + * @param modelId + * @param i + * @param j + * @param annotations + * @throws UnknownIdentifierException + */ + @Deprecated + public void addPartOf(String modelId, OWLNamedIndividual i, + OWLNamedIndividual j, Set annotations) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + addPartOf(modelId, model, i, j, annotations, true); + } + + @Deprecated + private void addPartOf(String modelId, ModelContainer model, OWLNamedIndividual i, + OWLNamedIndividual j, Set annotations, boolean flushReasoner) { + addFact(modelId, model, getObjectProperty(OBOUpperVocabulary.BFO_part_of, model), i, j, annotations, flushReasoner, null); + } + + /** + * This method will check the given model and update the import declarations. + * It will add missing IRIs and remove obsolete ones. + * + * @param modelId + * @throws UnknownIdentifierException + * @see #additionalImports + * @see #addImports(Iterable) + * @see #obsoleteImports + * @see #addObsoleteImports(Iterable) + */ + public void updateImports(String modelId) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + updateImports(modelId, model); + } + +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/UndoAwareMolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/UndoAwareMolecularModelManager.java new file mode 100644 index 00000000..5b843b05 --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/UndoAwareMolecularModelManager.java @@ -0,0 +1,327 @@ +package org.geneontology.minerva; + +import java.util.ArrayList; +import java.util.Collections; +import java.util.Deque; +import java.util.HashMap; +import java.util.LinkedList; +import java.util.List; +import java.util.Map; + +import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.UndoAwareMolecularModelManager.UndoMetadata; +import org.geneontology.minerva.util.ReverseChangeGenerator; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyChange; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; + +import owltools.graph.OWLGraphWrapper; + +/** + * Provide undo and redo operations for the {@link MolecularModelManager}. + */ +public class UndoAwareMolecularModelManager extends MolecularModelManager { + + private final Map allChanges = new HashMap(); + + private static class UndoRedo { + final Deque undoBuffer = new LinkedList(); + final Deque redoBuffer = new LinkedList(); + private UndoMetadata token = null; + + void addUndo(List changes, UndoMetadata metadata) { + addUndo(new ChangeEvent(metadata.userId, changes, System.currentTimeMillis()), metadata); + } + + void addUndo(List changes, String userId) { + token = null; + undoBuffer.push(new ChangeEvent(userId, changes, System.currentTimeMillis())); + } + + void addUndo(ChangeEvent changes, UndoMetadata token) { + if (this.token == null || this.token.equals(token) == false) { + // new event or different event + undoBuffer.push(changes); + this.token = token; + } + else { + // append to last event + ChangeEvent current = undoBuffer.peek(); + if (current != null) { + current.getChanges().addAll(changes.getChanges()); + } + else { + undoBuffer.push(changes); + } + } + } + + ChangeEvent getUndo() { + if (undoBuffer.peek() != null) { + return undoBuffer.pop(); + } + return null; + } + + void addRedo(List changes, String userId) { + addRedo(new ChangeEvent(userId, changes, System.currentTimeMillis())); + } + + void addRedo(ChangeEvent changes) { + redoBuffer.push(changes); + this.token = null; + } + + ChangeEvent getRedo() { + if (redoBuffer.peek() != null) { + return redoBuffer.pop(); + } + return null; + } + + void clearRedo() { + redoBuffer.clear(); + } + } + + public static class UndoMetadata { + public final String userId; + public final long requestToken; + + /** + * @param userId + */ + public UndoMetadata(String userId) { + this.userId = userId; + this.requestToken = System.currentTimeMillis(); + } + + @Override + public int hashCode() { + final int prime = 31; + int result = 1; + result = prime * result + + (int) (requestToken ^ (requestToken >>> 32)); + result = prime * result + + ((userId == null) ? 0 : userId.hashCode()); + return result; + } + + @Override + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + if (obj == null) { + return false; + } + if (getClass() != obj.getClass()) { + return false; + } + UndoMetadata other = (UndoMetadata) obj; + if (requestToken != other.requestToken) { + return false; + } + if (userId == null) { + if (other.userId != null) { + return false; + } + } else if (!userId.equals(other.userId)) { + return false; + } + return true; + } + } + + /** + * Details for a change in a model. + */ + public static class ChangeEvent { + final String userId; + final List changes; + final long time; + + /** + * @param userId + * @param changes + * @param time + */ + public ChangeEvent(String userId, List changes, long time) { + this.userId = userId; + this.changes = new ArrayList(changes); + this.time = time; + } + + public String getUserId() { + return userId; + } + + public List getChanges() { + return changes; + } + + public long getTime() { + return time; + } + } + + public UndoAwareMolecularModelManager(OWLGraphWrapper graph) throws OWLOntologyCreationException { + super(graph); + } + + @Override + protected void addToHistory(String modelId, ModelContainer model, List appliedChanges, UndoMetadata metadata) { + if (appliedChanges == null || appliedChanges.isEmpty()) { + // do nothing + return; + } + UndoRedo undoRedo; + synchronized (allChanges) { + undoRedo = allChanges.get(modelId); + if (undoRedo == null) { + undoRedo = new UndoRedo(); + allChanges.put(modelId, undoRedo); + } + } + synchronized (undoRedo) { + // append to undo + undoRedo.addUndo(appliedChanges, metadata); + // clear redo + undoRedo.clearRedo(); + } + } + + /** + * Undo latest change for the given model. + * + * @param modelId + * @param userId + * @return true if the undo was successful + * @throws UnknownIdentifierException + */ + public boolean undo(String modelId, String userId) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + return undo(modelId, model, userId); + } + + /** + * Undo latest change for the given model. + * + * @param modelId + * @param model + * @param userId + * @return true if the undo was successful + */ + public boolean undo(String modelId, ModelContainer model, String userId) { + UndoRedo undoRedo; + synchronized (allChanges) { + undoRedo = allChanges.get(modelId); + } + if (undoRedo != null) { + final OWLOntology abox = model.getAboxOntology(); + synchronized (abox) { + /* + * WARNING multiple locks (undoRedo and abox) always lock ontology first + * to avoid deadlocks! + */ + synchronized (undoRedo) { + // pop from undo + ChangeEvent event = undoRedo.getUndo(); + if (event == null) { + return false; + } + + // invert and apply changes + List invertedChanges = ReverseChangeGenerator.invertChanges(event.getChanges()); + applyChanges(invertedChanges, abox.getOWLOntologyManager()); + + // push to redo + undoRedo.addRedo(event.changes, userId); + return true; + } + } + } + return false; + } + + /** + * Redo latest change for the given model. + * + * @param modelId + * @param userId + * @return true if the redo was successful + * @throws UnknownIdentifierException + */ + public boolean redo(String modelId, String userId) throws UnknownIdentifierException { + ModelContainer model = checkModelId(modelId); + return redo(modelId, model, userId); + } + + /** + * Redo latest change for the given model. + * + * @param modelId + * @param model + * @param userId + * @return true if the redo was successful + */ + public boolean redo(String modelId, ModelContainer model, String userId) { + UndoRedo undoRedo; + synchronized (allChanges) { + undoRedo = allChanges.get(modelId); + } + if (undoRedo != null) { + final OWLOntology abox = model.getAboxOntology(); + synchronized (abox) { + /* + * WARNING multiple locks (undoRedo and abox) always lock ontology first + * to avoid deadlocks! + */ + synchronized (undoRedo) { + // pop() from redo + ChangeEvent event = undoRedo.getRedo(); + if (event == null) { + return false; + } + + // apply changes + applyChanges(event.getChanges(), abox.getOWLOntologyManager()); + + // push() to undo + undoRedo.addUndo(event.getChanges(), userId); + return true; + } + } + } + return false; + } + + /** + * Retrieve the current available undo and redo events. + * + * @param modelId + * @return pair of undo (left) and redo (right) events + */ + public Pair, List> getUndoRedoEvents(String modelId) { + UndoRedo undoRedo = null; + synchronized (allChanges) { + undoRedo = allChanges.get(modelId); + } + if (undoRedo == null) { + // return empty of no data is available + return Pair.of(Collections.emptyList(), Collections.emptyList()); + } + synchronized (undoRedo) { + // copy the current lists + List undoList = new ArrayList(undoRedo.undoBuffer); + List redoList = new ArrayList(undoRedo.redoBuffer); + return Pair.of(undoList, redoList); + } + } + + protected void applyChanges(List changes, OWLOntologyManager manager) { + manager.applyChanges(changes); + } + +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/generate/LegoModelGenerator.java b/minerva-core/src/main/java/org/geneontology/minerva/generate/LegoModelGenerator.java new file mode 100644 index 00000000..0e040449 --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/generate/LegoModelGenerator.java @@ -0,0 +1,1007 @@ +package org.geneontology.minerva.generate; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.Comparator; +import java.util.HashMap; +import java.util.HashSet; +import java.util.LinkedHashMap; +import java.util.LinkedList; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.apache.commons.math.MathException; +import org.apache.commons.math.distribution.HypergeometricDistributionImpl; +import org.apache.log4j.Logger; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.util.MinimalModelGenerator; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLIndividual; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLNamedObject; +import org.semanticweb.owlapi.model.OWLObject; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLPropertyExpression; +import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; +import org.semanticweb.owlapi.vocab.OWLRDFVocabulary; + +import owltools.gaf.ExtensionExpression; +import owltools.gaf.GafDocument; +import owltools.gaf.GeneAnnotation; +import owltools.graph.OWLGraphEdge; +import owltools.graph.OWLGraphWrapper; +import owltools.vocab.OBOUpperVocabulary; + +/** + * Generates an augmented Minimal Model (aka LEGO) graph for a given process, + * given an ontology and a set of annotations. + * + * A process can be a 'normal' biological process (e.g. from GO) or a pathological process + * (we can treat MP as abnormal processes for the purposes of this analysis, + * or make a parallel ontology) + * + * The input is a process class and a set of genes (e.g. all genes involved in that BP), construct the most likely + * set of gene + activity-type (i.e. MF) pairs that are likely to be executed during this process. + * Also infer causal relationships between gene-activity pairs based on PPI networks, annotation extensions. + * + * The network generation is broken into two steps + * + *
  • Minimal Model Generation, which generates a minimal set of individuals inferred to exist given the existence of the process class. + *
  • Model AugmentationDefinitions + * + *
      + *
    • G : set of genes/products (for a whole genome/organism) + *
    • T : set of all ontology classes and object properties (OWL TBox and RBox) + *
    • TA : all ontology classes representing atomic processes, e.g. in MF (activity) + *
    • TP : all ontology classes representing non-atomic processes, e.g. in BP ontology + *
    • A : set of all activity instances in a functional network. Each activity is a gene / activity-class pair. ie A ⊆ G x TA + *
    • E : Optionally typed connections between activity instances. ie E ⊆ A x A x TRel + *
    • P : Set of all process instances. P ⊆ TP + *
    • M : Merelogy (partonomy), from activity instances to process instances, and between process instances. ie M ⊆ A ∪ P x P + *
    + * + *

    Algorithm - TODO - REDOCUMENT

    + * + *

    Inputs

    + *
      + *
    • {@link #seedGraph} - seed initial A + *
    • {@link #createPartonomy} - create partonomy P + *
    • {@link #connectGraph} - created activity network E + *
    + * + *

    Mapping to OWL

    + *
      + *
    • a = g x t ∈ A → a ∈ OWLNamedIndividual, a.iri = genIRI(g, t), a rdf:type t, a rdf:type (enabled_by some g) + *
    • g ∈ G → g ∈ OWLClass, g SubClassOf Protein + *
    • t ∈ T → t ∈ OWLClass + *
    • e = a1 x a2 x t ∈ E → e ∈ OWLObjectPropertyAssertion, e.subject = a1, e.object = a2, e.property = t + *
    • p ∈ P → p ∈ OWLNamedIndividual + *
    • m = p1 x p2 & ∈ M → m ∈ OWLObjectPropertyAssertion, m.subject = p1, m.object = p2, m.property = part_of + *
    • + *
    + * Notes: we treat all members of G as proteins, but these may be other kinds of gene product. Note also the source ID may be a gene ID. + * In this case we can substitute "enabled_by some g" with "enabled_by some (product_of some g)" + * + * In some cases the edge type is not known - here we can use a generic owlTopProperty - or we can assume an activates relation, and leave the user to prune/modify + + *

    TODO

    + * + *
      + *
    • Convert to LEGO + *
    • Rules for inferring occurs_in (requires extending A to be A ⊆ G x TA x TC) + *
    + * + * {@link https://docs.google.com/document/d/1TV8Eb9sSvFY-weVZaIfzCxF1qbnmkUaiUhTm9Bs3gRE/edit} + * + */ +@Deprecated +public class LegoModelGenerator extends MinimalModelGenerator { + + + private static Logger LOG = Logger.getLogger(LegoModelGenerator.class); + + /** + * EA ⊆ A x A x TA + */ + //public ActivityNetwork activityNetwork; + Map> proteinInteractionMap; + Set populationGeneSet; + Map labelMap; + Map> geneByInferredClsMap; + Map> anctesorMap; + HashMap> clsByGeneMap; + Set activityClassSet; + public Set processClassSet; + private Map> activityByGene; + Double ccp = null; // cumulative + + + /** + * M ⊆ N x N, N = A ∪ P + */ + //public Partonomy partonomy; + //Set processSet; // P : process *instances* + + // this should only be used for the generation of candidates/seeds from GAF and/or ontology + // the proper model is the Abox ontology + private OWLGraphWrapper ogw; + + + /** + * @param model + * @throws OWLOntologyCreationException + */ + public LegoModelGenerator(ModelContainer model) throws OWLOntologyCreationException { + super(model); + } + + /** + * @param gafdoc (optional) + * @param g + */ + public void initialize(GafDocument gafdoc, OWLGraphWrapper g) { + ogw = g; + geneByInferredClsMap = new HashMap>(); + populationGeneSet = new HashSet(); + clsByGeneMap = new HashMap>(); + labelMap = new HashMap(); + proteinInteractionMap = new HashMap>(); + activityByGene = new HashMap>(); + + setRemoveAmbiguousIndividuals(false); + + //this.setPrecomputePropertyClassCombinations(true); + Set rels = + new HashSet(getInvolvedInRelations()); + + List anns = new ArrayList(); + if (gafdoc != null) { + anns = gafdoc.getGeneAnnotations(); + } + for (GeneAnnotation ann : anns) { + String c = ann.getCls(); + OWLClass cls = ogw.getOWLClassByIdentifier(c); + String gene = ann.getBioentity(); + + // special case : protein binding - we build a PPI + // using the WITH/FROM column + if (c.equals("GO:0005515")) { + for (String b : ann.getWithInfos()) { + //LOG.debug("Adding PPI based on WITH col"); + addPPI(gene, b); + } + continue; + } + + for (List eel : ann.getExtensionExpressions()) { + for (ExtensionExpression ee : eel) { + // temporary measure - treat all ext expressions as PPIs + addPPI(gene, ee.getCls()); + } + } + + populationGeneSet.add(gene); + String sym = ann.getBioentityObject().getSymbol(); + if (sym != null && !sym.equals("")) + labelMap.put(gene, sym); + + + if (!clsByGeneMap.containsKey(gene)) + clsByGeneMap.put(gene, new HashSet()); + clsByGeneMap.get(gene).add(cls); + + //LOG.debug("Finding ancestors of "+cls+" over "+rels); + for (OWLObject ancCls : g.getAncestorsReflexive(cls, rels)) { // TODO-use reasoner + if (ancCls instanceof OWLClass) { + OWLClass anc = (OWLClass) ancCls; + if (!model.isQueryClass(anc)) { + //LOG.debug(" "+gene + " => "+c+" => "+anc + " // "+ancCls); + if (!geneByInferredClsMap.containsKey(anc)) + geneByInferredClsMap.put(anc, new HashSet()); + geneByInferredClsMap.get(anc).add(gene); + } + } + } + } + + OWLClass MF = getOWLClass(OBOUpperVocabulary.GO_molecular_function); + OWLClass BP = getOWLClass(OBOUpperVocabulary.GO_biological_process); + + activityClassSet = model.getReasoner().getSubClasses(MF, false).getFlattened(); + LOG.debug("# subclasses of "+MF+" = "+activityClassSet.size()); + processClassSet = model.getReasoner().getSubClasses(BP, false).getFlattened(); + LOG.debug("# subclasses of "+BP+" "+processClassSet.size()); + + for (OWLClass cls : model.getTboxOntology().getClassesInSignature(true)) { + String label = g.getLabel(cls); + if (label != "" && label != null) + labelMap.put(cls, label); + } + + } + + + /** + * Performs all steps to seed activation network. + * + * See: https://docs.google.com/document/d/1TV8Eb9sSvFY-weVZaIfzCxF1qbnmkUaiUhTm9Bs3gRE/edit + * + * @param processCls + * @param seedGenes + * @throws OWLOntologyCreationException + */ + public void buildNetwork(OWLClass processCls, Collection seedGenes) throws OWLOntologyCreationException { + generateNecessaryIndividuals(processCls, true); + addGenes(processCls, seedGenes); + //inferLocations(); + connectGraph(); + normalizeDirections(); + combineMultipleEnablers(); + anonymizeMaterialEntities(); + } + + /** + * Example: if we have triples: + * + * + * + * This will generate: + * ClassAssertion( occurs_in some Nucleus, p123) + * + */ + public void anonymizeMaterialEntities() { + Set occs = new HashSet(); + occs.add(getOWLClass(OBOUpperVocabulary.GO_molecular_function)); + occs.add(getOWLClass(OBOUpperVocabulary.GO_biological_process)); + anonymizeIndividualsNotIn(occs); + } + + /** + * Wraps {@link #buildNetwork(OWLClass, Collection)} + * + * @param processClsId + * @param seedGenes + * @throws OWLOntologyCreationException + */ + public void buildNetwork(String processClsId, Collection seedGenes) throws OWLOntologyCreationException { + OWLClass processCls = ogw.getOWLClassByIdentifier(processClsId); + buildNetwork(processCls, seedGenes); + } + + public void addGenes(String processClsId, Collection seedGenes) throws OWLOntologyCreationException { + OWLClass processCls = ogw.getOWLClassByIdentifier(processClsId); + addGenes(processCls, seedGenes); + } + + + /** + * @see seedGraph(String p, Set seed) + * @param processCls + * @throws OWLOntologyCreationException + */ + public void addGenes(OWLClass processCls) throws OWLOntologyCreationException { + addGenes(processCls, getGenes(processCls)); + } + + + /** + * Create initial activation node set A for a process P and a set of seed genes + * + * for all g ∈ Gseed, add a = to A where f = argmax(p) { t : t ∈ TA, p=Prob( t | g) } + * + * @param processCls + * @param seedGenes + * @throws OWLOntologyCreationException + * @throws MathException + */ + public void addGenes(OWLClass processCls, Collection seedGenes) throws OWLOntologyCreationException { + + LOG.debug("Adding seed genes, #=" + seedGenes.size()); + // TODO - use only instance-level parts and regulators + + // Set of all individuals that necessarily exists given P exist; + // (MFs and BPs) + Collection leafNodes = + new HashSet(); + + Set props = getInvolvedInRelations(); + + // loop through all individuals generated so far; this includes the input process class P, + // plus other necessary individuals. For example, if P has_part some P2, and P2 has_part some F, + // then a prototypical instance of is also included + for (OWLNamedIndividual i : getGeneratedIndividuals()) { + boolean isOccurrent = false; + for (OWLClass c : model.getReasoner().getTypes(i, false).getFlattened()) { + if (c.getIRI().equals(OBOUpperVocabulary.GO_biological_process.getIRI())) { + isOccurrent = true; + break; + } + if (c.getIRI().equals(OBOUpperVocabulary.GO_molecular_function.getIRI())) { + isOccurrent = true; + break; + } + } + if (!isOccurrent) { + continue; + } + + // note this has the potential to include individuals which p + // is part of - need to contain the scope here. For now, go liberal + //leafNodes.add(i); + + boolean isInValidPath = false; + Set path = getIndividualsInProperPath(i, props); + path.add(i); // reflexive + for (OWLIndividual m : path) { + if (m instanceof OWLNamedIndividual && getPrototypeClass((OWLNamedIndividual) m) != null) { + if (getPrototypeClass((OWLNamedIndividual) m).equals(processCls)) { + isInValidPath = true; + break; + } + } + } + LOG.debug(" PPATH "+getIdLabelPair(i)+" "+path); + if (isInValidPath) { + LOG.debug(" **VALID: "+getIdLabelPair(i)); + leafNodes.add(i); + } + + } + + + //contextId = ogw.getIdentifier(processCls); // TODO + ccp = 1.0; // cumulative + // generatedIndividuals = new HashSet(); + // // note: here ancestors may be sub-parts + // for (OWLObject obj : ogw.getAncestorsReflexive(prototypeIndividualMap.get(processCls))) { + // LOG.debug(" ANCI="+getIdLabelPair(obj)); + // generatedIndividuals.add((OWLNamedIndividual) obj); + // } + + for (String g : seedGenes) { + + LOG.debug(" Seed gene="+getIdLabelPair(g)); + + // each gene, find it's most likely function F and most direct process class P. + // Note each gene can have multiple functions, but here we select one. + // In addition, a gene may be annotated to different parts of processCls; + // we aim to select one as a "join point" + + Set geneActivityTypes = getMostSpecificActivityTypes(g); // candidate functions + Set geneInferredTypes = getInferredTypes(g); // all annotations + + LOG.debug(" num activity types = "+geneActivityTypes.size()); + LOG.debug(" num inferred types = "+geneInferredTypes.size()); + + + // TODO - first find all other annotations for each gene + // and add these if relevant. + // E.g. in nodal pathway, Dand5 has 'sequestering of nodal from receptor via nodal binding' + + Collection joinPoints = + new HashSet(); + + // g is also annotated to multiple other processes; find the more specific ones + Set alternateProcesses = getMostSpecificProcessTypes(g); + LOG.debug(" alt processes = "+alternateProcesses.size()); + boolean isReset = false; + for (OWLClass alternateProcessCls : alternateProcesses) { + boolean isCandidate = false; + for (OWLGraphEdge edge : ogw.getOutgoingEdgesClosure(alternateProcessCls)) { + if (edge.getTarget().equals(processCls)) { + // alternateProcessCls is more specific + isCandidate = true; + for (OWLObjectSomeValuesFrom r : getExistentialRelationships(alternateProcessCls)) { + if (model.getReasoner().getSuperClasses(r.getFiller(), false).getFlattened().contains(processCls)) { + // should not cause a deepening + isCandidate = false; + } + } + } + } + if (isCandidate) { + if (model.getReasoner().getSuperClasses(alternateProcessCls, false).getFlattened().contains(processCls)) { + // skip + // todo - keep the information somehow that g is annotated to specific + // subtypes of c + } + else { + // experimenting with aggressive approach + OWLNamedIndividual newp = generateNecessaryIndividuals(alternateProcessCls); + if (!isReset) { + LOG.debug("Resetting join points"); + isReset = true; + joinPoints = new HashSet(); + //generatedIndividuals = new HashSet(); + } + LOG.debug(" Using more specific annotation: "+getIdLabelPair(alternateProcessCls)); + joinPoints.add(newp); + } + } + } + if (joinPoints.size() == 0) { + // TODO - use process instance + LOG.debug("No more specific process annotations found; using leafNodes, #="+leafNodes.size()); + joinPoints.addAll(leafNodes); + } + + + Double best = null; + Double cp = 1.0; + OWLClass bestActivityClass = null; + OWLClass bestParentClass = null; + OWLNamedIndividual bestParent = null; + for (OWLNamedIndividual joinPoint : joinPoints) { + //OWLClass joinPointClass = getPrototypeClass(joinPoint); + + //this seemed to be producing redundant types: + Set jpcs = model.getReasoner().getTypes(joinPoint, true).getFlattened(); + LOG.debug(" candidate join point="+getIdLabelPair(joinPoint)+" directTypes: "+jpcs); + Set rd = new HashSet(); // redundant + for (OWLClass jpc : jpcs) { + rd.addAll(model.getReasoner().getSuperClasses(jpc, false).getFlattened()); + } + jpcs.removeAll(rd); + LOG.debug(" Post redundancy filter: "+getIdLabelPair(joinPoint)+" directTypes: "+jpcs); + + for (OWLClass joinPointClass : jpcs) { + + LOG.debug(" Testing JPC: "+getIdLabelPair(joinPointClass)); + + // a gene must have been annotated to some descendant of generatedCls to be considered. + if (true || geneInferredTypes.contains(joinPointClass)) { + for (OWLClass activityCls : geneActivityTypes ) { + // note that generatedCls may be a MF, and may be a subclass, + // which case this would be 1.0 + Double pval; + try { + pval = calculatePairwiseEnrichment(activityCls, joinPointClass); + LOG.debug(" enrichment of "+getIdLabelPair(activityCls)+" IN: "+getIdLabelPair(joinPointClass)+ + " = "+pval); + // temp hack - e.g. frp1 ferric-chelate reductase in iron assimilation by reduction and transport + if (activityCls.equals(joinPointClass)) { + pval = 0.0; + } + + if (best == null || pval < best) { + cp = this.calculateConditionalProbaility(joinPointClass, activityCls); + best = pval; + bestActivityClass = activityCls; + bestParentClass = joinPointClass; + bestParent = joinPoint; + } + } catch (MathException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } + } + else { + LOG.debug(" Skpping: "+getIdLabelPair(joinPointClass)+" -- not in geneInferredTypes"); + } + } + //LOG.debug(" DONE testIndivid="+getIdLabelPair(gi)); + } + + OWLNamedIndividual ai = addActivity(bestActivityClass, g, best, cp); + ccp *= cp; + OWLObjectPropertyExpression relation = getObjectProperty(OBOUpperVocabulary.BFO_part_of); + LOG.debug("Testing if "+getIdLabelPair(bestActivityClass) + + " is under/equiv to "+getIdLabelPair(bestParentClass) + + " for gene: "+g); + if (bestActivityClass != null) { + if (model.getReasoner().getSubClasses(bestActivityClass, false).getFlattened().contains(bestParentClass) || + model.getReasoner().getEquivalentClasses(bestActivityClass).getEntities().contains(bestParentClass)) { + LOG.debug("Merging "+bestParent+" --> "+ai); + mergeInto(bestParent, ai); + } + else { + addEdge(ai, relation, bestParent); + } + } + } + collapseIndividuals(); + } + + + + private void addEdge(OWLNamedIndividual p, OWLObjectPropertyExpression rel, OWLNamedIndividual w) { + if (ogw.getAncestorsReflexive(p).contains(w)) { + LOG.debug("ALREADY CONNECTED TO "+w); + return; + } + if (w != null) { + + OWLAxiom owlObject = + model.getOWLDataFactory().getOWLObjectPropertyAssertionAxiom( + rel, + p, + w); + model.addAxiom(owlObject); + } + else { + LOG.warn("Parent of "+p+" is null"); + } + } + + private OWLNamedIndividual addActivity(OWLClass bestActivityClass, String gene, Double pval, Double cp) { + if (bestActivityClass == null) { + bestActivityClass = model.getOWLDataFactory().getOWLClass(OBOUpperVocabulary.GO_molecular_function.getIRI()); + } + OWLNamedIndividual ai = this.generateNecessaryIndividuals(bestActivityClass); + //this.collapseIndividuals(); + + String label = getLabel(bestActivityClass); + OWLClass geneProductClass = null; + if (gene != null) { + geneProductClass = getOWLClassByIdentifier(gene); + } + else { + //geneProductClass = getOWLClass("PR:00000001"); + } + if (geneProductClass != null) { + OWLClassExpression x = model.getOWLDataFactory().getOWLObjectSomeValuesFrom( + getObjectProperty(OBOUpperVocabulary.GOREL_enabled_by), + geneProductClass); // TODO <-- protein IRI should be here + model.addAxiom(model.getOWLDataFactory().getOWLClassAssertionAxiom( + x, + ai)); + String geneLabel = getLabel(gene); + addOwlLabel(geneProductClass, geneLabel); + label = label + " enabled by " + geneLabel; + if (!activityByGene.containsKey(gene)) { + activityByGene.put(gene, new HashSet()); + } + activityByGene.get(gene).add(ai); + } + label = label + " (pVal_uncorrected="+pval+", p(F|P)="+cp+")"; + addOwlLabel(ai, label); + + return ai; + } + + + + /** + * Add default edges based on PPI network + * + * add ( a1 , a2 ) to E + * where ( g1 , g2 ) is in PPI, and + * a = (g, _) is in A + * + */ + public void connectGraph() { + + // PPI Method + for (String p1 : proteinInteractionMap.keySet()) { + Set aset = lookupActivityByGene(p1); + if (aset == null || aset.size() == 0) + continue; + //LOG.debug("P1="+getIdLabelPair(p1)); + for (String p2 : proteinInteractionMap.get(p1)) { + //LOG.debug(" P2="+getIdLabelPair(p2)); + Set aset2 = lookupActivityByGene(p2); + if (aset2 != null) { + // assumption: if P1 and P2 interact then their activities also interact + for (OWLNamedIndividual a1 : aset) { + for (OWLNamedIndividual a2 : aset2) { + LOG.debug(" PPI-based edge: "+a1+" => "+a2); + addEdge(a1, getObjectProperty(OBOUpperVocabulary.GOREL_directly_provides_input_for), a2); // TODO + } + } + } + } + } + + // Using ontology knowledge (e.g. connected_to relationships; has_input = has_output) + + //for (OWLNamedIndividual a : activityNetwork.activitySet) { + // + //} + + // Annotation extension method + // TODO: e.g. PomBase SPCC645.07 rgf1 GO:0032319-regulation of Rho GTPase activity PMID:16324155 IGI PomBase:SPAC1F7.04 P RhoGEF for Rho1, Rgf1 protein taxon:4896 20100429 PomBase + // in: =GO:0051666 ! actin cortical patch localization + } + + private Set lookupActivityByGene(String g) { + if (activityByGene.containsKey(g)) + return activityByGene.get(g); + else + return null; + + } + + private void combineMultipleEnablers() { + + OWLObjectPropertyExpression enabledBy = this.getObjectProperty(OBOUpperVocabulary.GOREL_enabled_by); + for (OWLNamedIndividual i : model.getAboxOntology().getIndividualsInSignature(false)) { + Set rmAxioms = new HashSet(); + Set xs = new HashSet(); + for (OWLAxiom ax : model.getAboxOntology().getAxioms(i)) { + + if (ax instanceof OWLClassAssertionAxiom) { + //LOG.debug("TESTING:"+ax); + OWLClassAssertionAxiom caa = (OWLClassAssertionAxiom)ax; + if (caa.getClassExpression().getObjectPropertiesInSignature().contains(enabledBy)) { + rmAxioms.add(ax); + if (caa.getClassExpression() instanceof OWLObjectSomeValuesFrom) { + xs.add(((OWLObjectSomeValuesFrom)caa.getClassExpression()).getFiller()); + } + else { + LOG.warn("Hmmmm"+caa); + //xs.add(caa.getClassExpression()); + } + } + } + } + if (xs.size() > 1) { + LOG.debug("Concatenating enables for "+getIdLabelPair(i)); + model.getOWLOntologyManager().removeAxioms(model.getAboxOntology(), rmAxioms); + model.addAxiom( + model.getOWLDataFactory().getOWLClassAssertionAxiom( + model.getOWLDataFactory().getOWLObjectSomeValuesFrom( + enabledBy, + model.getOWLDataFactory().getOWLObjectUnionOf(xs) + ), + i)); + } + } + } + + + + /** + * Reroute all has_parts to part_ofs + * + */ + public void normalizeDirections() { + normalizeDirections(getObjectProperty(OBOUpperVocabulary.BFO_part_of)); + normalizeDirections(getObjectProperty(OBOUpperVocabulary.BFO_occurs_in)); + normalizeDirections(getObjectProperty(OBOUpperVocabulary.RO_starts)); + normalizeDirections(getObjectProperty(OBOUpperVocabulary.RO_ends)); + normalizeDirections(getObjectProperty(OBOUpperVocabulary.RO_regulates)); + normalizeDirections(getObjectProperty(OBOUpperVocabulary.RO_negatively_regulates)); + normalizeDirections(getObjectProperty(OBOUpperVocabulary.RO_positively_regulates)); + } + + /////////////////// + // + // Experimental + + public Map fetchScoredCandidateProcesses(OWLClass disease, Integer populationClassSize) { + OWLNamedIndividual ind = this.generateNecessaryIndividuals(disease); + Set phenotypes = new HashSet(); + for (OWLNamedIndividual j : getGeneratedIndividuals()) { + phenotypes.addAll(model.getReasoner().getTypes(j, true).getFlattened()); + } + OWLClass CELLULAR_PROCESS = model.getOWLDataFactory().getOWLClass(OBOUpperVocabulary.GO_cellular_process.getIRI()); + + Map smap = new HashMap(); + for (OWLClass gc : model.getReasoner().getSubClasses(CELLULAR_PROCESS, false).getFlattened()) { + double cumLogScore = 0.0; + + int n=0; + for (OWLClass pc : phenotypes) { + try { + Double pval = calculatePairwiseEnrichment(pc, gc, populationClassSize); + double logScore = -Math.log(pval)/Math.log(2); + //LOG.debug(" PSCORE: "+getIdLabelPair(gc)+ " = "+logScore+" for: "+getIdLabelPair(pc)+ " pval="+pval); + if (pval >= 0.0) { + cumLogScore += logScore; + n++; + } + + } catch (MathException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } + if (n>0) { + smap.put(gc, cumLogScore); + LOG.debug("SCORE: "+getIdLabelPair(gc)+ " = "+cumLogScore); + } + else { + //smap.remove(key) + } + } + Map osmap = sortByValue(smap); + return osmap; + } + + public static > Map sortByValue( Map map ) { + List> list = + new LinkedList>( map.entrySet() ); + Collections.sort( list, new Comparator>() { + + public int compare( Map.Entry o1, Map.Entry o2 ) { + + return (o1.getValue()).compareTo( o2.getValue() ); + } + } ); + Collections.reverse(list); + Map result = new LinkedHashMap(); + for (Map.Entry entry : list) { + + result.put( entry.getKey(), entry.getValue() ); + } + return result; + } + + + + + /////////////////// + // + // Calculation of gene-class relationships and probabilities + + public Double calculatePairwiseEnrichment(OWLClass sampleSetClass, OWLClass enrichedClass) throws MathException { + return calculatePairwiseEnrichment(sampleSetClass, enrichedClass, populationGeneSet.size()); + } + + public Double calculatePairwiseEnrichment( + OWLClass sampleSetClass, OWLClass enrichedClass, int populationClassSize) throws MathException { + + // LOG.debug("Hyper :"+populationClass + // +" "+sampleSetClass+" "+enrichedClass); + int sampleSetClassSize = getGenes(sampleSetClass).size(); + int enrichedClassSize = getGenes(enrichedClass).size(); + // LOG.debug("Hyper :"+populationClassSize + // +" "+sampleSetClassSize+" "+enrichedClassSize); + HypergeometricDistributionImpl hg = new HypergeometricDistributionImpl( + populationClassSize, sampleSetClassSize, enrichedClassSize); + /* + * LOG.debug("popsize="+getNumElementsForAttribute(populationClass)); + * LOG.debug("sampleSetSize="+getNumElementsForAttribute(sampleSetClass)); + * LOG.debug("enrichedClass="+getNumElementsForAttribute(enrichedClass)); + */ + Set eiSet = getGenes(sampleSetClass); + eiSet.retainAll(getGenes(enrichedClass)); + // LOG.debug("both="+eiSet.size()); + double p = hg.cumulativeProbability(eiSet.size(), + Math.min(sampleSetClassSize, enrichedClassSize)); + //double pCorrected = p * getCorrectionFactor(populationClass); + return p; + } + + /** + * + * Pr( F | P ) = Pr(F,P) / Pr(P) + * + */ + + public Double calculateConditionalProbaility(OWLClass wholeCls, OWLClass partCls) { + Set wgs = getGenes(wholeCls); + Set cgs = getGenes(partCls); + cgs.retainAll(wgs); + double n = getNumberOfGenes(); + Double pr = (cgs.size() / n) / ( wgs.size() / n); + return pr; + } + + + /** + * Get all activity types a gene enables (i.e. direct MF annotations) + * + * always returns a fresh set + * + * @param g + * @return { t : t ∈ TA, g x t ∈ Enables } + */ + public Set getActivityTypes(String g) { + HashSet cset = new HashSet(clsByGeneMap.get(g)); + cset.retainAll(activityClassSet); + return cset; + } + + + /** + * @param g + * @return { t : t ∈ getActivityTypes(g), ¬ ∃ t' : t' ∈ getActivityTypes(g), t' ProperInferredßSubClassOf t } + */ + public Set getMostSpecificActivityTypes(String g) { + Set cset = getActivityTypes(g); + LOG.debug("# activity types for "+g+" = "+cset.size()); + removeRedundantOrHelper(cset, getInvolvedInRelationsAsPEs()); + LOG.debug("# post-NR activity types for "+g+" = "+cset.size()); + return cset; + } + + public Set getMostSpecificProcessTypes(String g) { + Set cset = getProcessTypes(g); + removeRedundantOrHelper(cset, getInvolvedInRelationsAsPEs()); + return cset; + } + + public Set getProcessTypes(String g) { + HashSet cset = new HashSet(clsByGeneMap.get(g)); + cset.retainAll(processClassSet); + return cset; + } + + public Set getInferredTypes(String g) { + HashSet cset = new HashSet(); + Set rels = + new HashSet(getInvolvedInRelations()); + for (OWLClass c : clsByGeneMap.get(g)) { + for (OWLObject a : ogw.getAncestorsReflexive(c, rels)) { // TODO-rel + if (a instanceof OWLClass && !model.isQueryClass((OWLClass) a)) { + cset.add((OWLClass) a); + } + } + } + return cset; + } + + public Set getInferredRelationshipsForGene(String g) { + Set results = new HashSet(); + HashSet cset = new HashSet(clsByGeneMap.get(g)); + for (OWLClass c : cset) { + results.addAll(getExistentialRelationships(c)); + } + return results; + } + + private void removeRedundantOrHelper(Set cset, Set props) { + Set allAncs = new HashSet(); + for (OWLClass c : cset) { + if (model.isQueryClass(c)) { + allAncs.add(c); + continue; + } + Set ancClsSet = ogw.getAncestors(c, props); + for (OWLObject obj : ancClsSet) { + if (obj instanceof OWLClass) { + // named ancestors only + allAncs.add((OWLClass) obj); + } + + } + } + cset.removeAll(allAncs); + } + + /** + * Gets all genes annotated to cls or descendant via involved-in relations + * @param t + * @return { g : g x t ∈ InferredInvolvedIn } + */ + public Set getGenes(OWLClass wholeCls) { + if (!geneByInferredClsMap.containsKey(wholeCls)) { + //LOG.debug("Nothing known about "+wholeCls); + return new HashSet(); + } + return new HashSet(geneByInferredClsMap.get(wholeCls)); + } + + /** + * @return |G| + */ + public int getNumberOfGenes() { + return populationGeneSet.size(); + } + + // adds an (external) protein-protein interaction + private void addPPI(String a, String b) { + if (!proteinInteractionMap.containsKey(a)) + proteinInteractionMap.put(a, new HashSet()); + proteinInteractionMap.get(a).add(b); + + } + + /** + * @param id + * @return label for any class or entity in the graph + */ + public String getLabel(Object k) { + if (k == null) + return "Null"; + if (labelMap.containsKey(k)) + return this.labelMap.get(k); + return k.toString(); + } + + public String getIdLabelPair(Object k) { + if (k == null) + return "Null"; + if (labelMap.containsKey(k)) + return k+" '"+this.labelMap.get(k)+"'"; + return k.toString(); + } + + + public Map getGraphStatistics() { + Map sm = new HashMap(); + //sm.put("activity_node_count", activityNetwork.activitySet.size()); + //sm.put("activity_edge_count", activityNetwork.activityEdgeSet.size()); + //sm.put("process_count", processSet.size()); + return sm; + } + + + + private IRI getIRI(String id) { + return ogw.getIRIByIdentifier(id); + } + + private OWLNamedIndividual getIndividual(String id) { + return model.getOWLDataFactory().getOWLNamedIndividual(getIRI(id)); + } + + + + private OWLClass getOWLClassByIdentifier(String id) { + return model.getOWLDataFactory().getOWLClass(ogw.getIRIByIdentifier(id)); + } + private OWLClass getOWLClass(OBOUpperVocabulary v) { + return model.getOWLDataFactory().getOWLClass(v.getIRI()); + } + + + private Set getInvolvedInRelations() { + Set rels = new HashSet(); + rels.add(getObjectProperty(OBOUpperVocabulary.BFO_part_of)); + rels.add(getObjectProperty(OBOUpperVocabulary.RO_regulates)); + + // these should be inferred in the future: + rels.add(getObjectProperty(OBOUpperVocabulary.RO_negatively_regulates)); + rels.add(getObjectProperty(OBOUpperVocabulary.RO_positively_regulates)); + rels.add(getObjectProperty(OBOUpperVocabulary.RO_starts)); // sub of part_of + rels.add(getObjectProperty(OBOUpperVocabulary.BFO_occurs_in)); + return rels; + } + + private Set getInvolvedInRelationsAsPEs() { + return new HashSet(getInvolvedInRelations()); + } + + + + private OWLObjectPropertyExpression getObjectProperty( + OBOUpperVocabulary vocab) { + // TODO Auto-generated method stub + return getObjectProperty(vocab.getIRI()); + } + private OWLObjectPropertyExpression getObjectProperty( + IRI iri) { + // TODO Auto-generated method stub + return model.getOWLDataFactory().getOWLObjectProperty(iri); + } + + + + + + private void addOwlData(OWLObject subj, OWLAnnotationProperty p, String val) { + OWLLiteral lit = model.getOWLDataFactory().getOWLLiteral(val); + model.addAxiom(model.getOWLDataFactory().getOWLAnnotationAssertionAxiom( + p, + ((OWLNamedObject) subj).getIRI(), + lit)); + } + + private void addOwlLabel(OWLObject owlObject, String val) { + addOwlData(owlObject, + model.getOWLDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()), + val); + labelMap.put(owlObject, val); + } + + + + +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/generate/NetworkInferenceEngine.java b/minerva-core/src/main/java/org/geneontology/minerva/generate/NetworkInferenceEngine.java new file mode 100644 index 00000000..09f7362c --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/generate/NetworkInferenceEngine.java @@ -0,0 +1,938 @@ +package org.geneontology.minerva.generate; + +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.apache.log4j.Logger; +import org.geneontology.minerva.util.MinimalModelGenerator; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLIndividual; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLNamedObject; +import org.semanticweb.owlapi.model.OWLObject; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLPropertyExpression; +import org.semanticweb.owlapi.vocab.OWLRDFVocabulary; + +import owltools.gaf.ExtensionExpression; +import owltools.gaf.GafDocument; +import owltools.gaf.GeneAnnotation; +import owltools.graph.OWLGraphEdge; +import owltools.graph.OWLGraphWrapper; + +/** + * Generates a Ontological Functional Network (aka LEGO graph) for a process given an ontology and a set of annotations + * + * The input is a GO BP class and a set of genes (e.g. all genes involved in that BP), construct the most likely + * set of gene + activity-type (i.e. MF) pairs that are likely to be executed during this process. + * Also infer causal relationships between gene-activity pairs based on PPI networks, annotation extensions. + * + * Finally, break the process into chunks, e.g. using has_part links. + * + *

    Definitions

    + * + *
      + *
    • G : set of genes/products (for a whole genome/organism) + *
    • T : set of all ontology classes and object properties + *
    • TA : all ontology classes in MF (activity) ontology + *
    • TP : all ontology classes in BP ontology + *
    • A : set of all activity instances in a functional network. Each activity is a gene / activity-class pair. ie A ⊆ G x TA + *
    • E : Optionally typed connections between activity instances. ie E ⊆ A x A x TRel + *
    • P : Set of all process instances. P ⊆ TP + *
    • M : Merelogy (partonomy), from activity instances to process instances, and between process instances. ie M ⊆ A ∪ P x P + *
    + * + *

    Algorithm

    + * + *
      + *
    • {@link #seedGraph} - seed initial A + *
    • {@link #createPartonomy} - create partonomy P + *
    • {@link #connectGraph} - created activity network E + *
    + * + *

    TODO

    + * + *
      + *
    • Convert to LEGO + *
    • Rules for inferring occurs_in (requires extending A to be A ⊆ G x TA x TC) + *
    + * + * + */ +@Deprecated +public class NetworkInferenceEngine { + + private static Logger LOG = Logger.getLogger(NetworkInferenceEngine.class); + + /** + * EA ⊆ A x A x TA + */ + public ActivityNetwork activityNetwork; + Map> proteinInteractionMap; + Set populationGeneSet; + Map labelMap; + Map> geneByInferredClsMap; + HashMap> clsByGeneMap; + Set activityClassSet; + public Set processClassSet; + /** + * M ⊆ N x N, N = A ∪ P + */ + public Partonomy partonomy; + Set processSet; // P : process *instances* + OWLGraphWrapper ogw; + OWLOntology exportOntology; // destination for OWL/lego. may be refactored into separate class + public OWLOntologyManager owlOntologyManager; + public MinimalModelGenerator mmg; + + String contextId = ""; // TODO + + private IRI createIRI(String... toks) { + StringBuffer id = new StringBuffer(); + for (String tok : toks) { + //if (tok instanceof OWLObject) + // tok = ogw.getIdentifier(tok); + if (tok.contains(":")) + tok = tok.replaceAll(":", "_"); + id.append("-"+tok); + } + return IRI.create("http://x.org"+id); + } + + // N = A ∪ P + // note: each node wraps an OWLObject + public abstract class InstanceNode { + public OWLIndividual owlObject; + public OWLClassExpression typeOf; + public Set locations = new HashSet(); + public String label; + public int numParents; + public void setLocation(OWLClass c) { + locations.add(c); + OWLClassExpression x = getOWLDataFactory().getOWLObjectSomeValuesFrom( + getObjectProperty("occurs_in"), + c); // TODO <-- protein IRI should be here + addAxiom(getOWLDataFactory().getOWLClassAssertionAxiom( + x, + owlObject)); + } + private void addAxioms() { + } + } + + /** + * A ⊆ G x TA + *
    + * An instance of an activity that is enabled by some gene/product + */ + public class Activity extends InstanceNode { + public final String gene; + public Double strength; + + public Activity(OWLClassExpression a, String g, String context) { + typeOf = a; + gene = g; + String acid = ""; + if (a != null) { + acid = ogw.getIdentifier(a); + label = ogw.getLabelOrDisplayId(a) + " enabled by "+getLabel(g); + } + else { + label = getLabel(g); + } + IRI iri = createIRI(context, acid, g); + owlObject = getOWLDataFactory().getOWLNamedIndividual(iri); + + } + private void addAxioms() { + super.addAxioms(); + OWLClassExpression c = typeOf; + if (c == null) + c = ogw.getOWLClassByIdentifier("GO:0003674"); // TODO - use vocab + addAxiom(getOWLDataFactory().getOWLClassAssertionAxiom( + c, owlObject)); + OWLClass geneProductClass = null; + if (gene != null) { + geneProductClass = getOWLClass(gene); + } + else { + //geneProductClass = getOWLClass("PR:00000001"); + } + if (geneProductClass != null) { + OWLClassExpression x = getOWLDataFactory().getOWLObjectSomeValuesFrom( + getObjectProperty("enabled_by"), + geneProductClass); // TODO <-- protein IRI should be here + addAxiom(getOWLDataFactory().getOWLClassAssertionAxiom( + x, + owlObject)); + addOwlLabel(geneProductClass, getLabel(gene)); + } + addOwlLabel(owlObject, label); + } + } + + public class Process extends InstanceNode { + public Process(OWLClassExpression pc, String context) { + typeOf = pc; + String pid = pc.toString(); + if (pc instanceof OWLClass) + pid = ogw.getIdentifier((OWLClass)pc); + IRI iri = createIRI(context, pid); // TODO + //LOG.info("Creating process: "+iri); + owlObject = getOWLDataFactory().getOWLNamedIndividual(iri); + label = ogw.getLabelOrDisplayId(pc); + } + private void addAxioms() { + super.addAxioms(); + addAxiom(getOWLDataFactory().getOWLClassAssertionAxiom( + typeOf, + owlObject)); + addOwlLabel(owlObject, label); + } + + } + + /** + * + *
    + * EdgeType can be null for unknown (i.e. those derived from + * PPIs) + * @param + * + */ + public class Edge { + public final T subject; + public final U object; + public final OWLObjectPropertyExpression type; + public OWLObjectPropertyAssertionAxiom owlObject; + + /** + * @param subject + * @param object + * @param type + */ + public Edge(T subject, U object, OWLObjectPropertyExpression type) { + super(); + this.subject = subject; + this.object = object; + this.type = type; + // todo - add to owl ontology + } + public Edge(T subject, U object, String type) { + super(); + this.subject = subject; + this.object = object; + this.type = getObjectProperty(type); + // todo - add to owl ontology + } + private void addAxioms() { + // note: type may change with time so we may want to defer...? + owlObject = + getOWLDataFactory().getOWLObjectPropertyAssertionAxiom( + type, + subject.owlObject, + object.owlObject); + addAxiom(owlObject); + + } + } + /* + public class ActivityEdge extends Edge { + public ActivityEdge(Activity subject, Activity object, String type) { + super(subject, object, type); + } + } + */ + + /** + * NA = (A, EA) + *
    + * A network/graph of activity nodes + */ + public class ActivityNetwork { + public Set activitySet = new HashSet(); + public Set> activityEdgeSet = new HashSet>(); + public void add(Activity a) { + activitySet.add(a); + a.addAxioms(); + } + public void addEdge(Activity s, Activity o, OWLObjectPropertyExpression owlObjectPropertyExpression) { + Edge e = new Edge(s, o, owlObjectPropertyExpression); + activityEdgeSet.add(e); + e.addAxioms(); + } + public Set lookupByGene(String g) { + Set activitySubset = new HashSet(); + for (Activity a : activitySet) { + if (a.gene == null) + continue; + if (a.gene.equals(g)) { + activitySubset.add(a); + } + } + return activitySubset; + } + public Set lookupByActivityType(OWLClassExpression t) { + Set activitySubset = new HashSet(); + for (Activity a : activitySet) { + if (a.typeOf == null) + continue; + if (a.typeOf.equals(t)) { + activitySubset.add(a); + } + } + return activitySubset; + } + } + + /** + * M : Merelogy (partonomy), from activity instances to process instances, and between process instances. ie M ⊆ A ∪ P x P + */ + public class Partonomy { + public Set> edgeSet = new HashSet>(); + public void addEdge(InstanceNode s, InstanceNode o) { + Edge e = new Edge(s, o, "part_of"); + edgeSet.add(e); // TODO - use vocab + e.addAxioms(); + } + + } + + /** + * Performs all steps to build activation network + * + * @param processCls + * @param seedGenes + * @throws OWLOntologyCreationException + */ + public void buildNetwork(OWLClass processCls, Set seedGenes) throws OWLOntologyCreationException { + seedGraph(processCls, seedGenes); + createPartonomy(processCls); + inferLocations(); + connectGraph(); + } + public void buildNetwork(String processClsId, Set seedGenes) throws OWLOntologyCreationException { + OWLClass processCls = ogw.getOWLClassByIdentifier(processClsId); + buildNetwork(processCls, seedGenes); + } + + /** + * Create initial activation node set A for a process P and a set of seed genes + * + * for all g ∈ Gseed, add a = to A where f = argmax(p) { t : t ∈ TA, p=Prob( t | g) } + * + * @param processCls + * @param seedGenes + * @throws OWLOntologyCreationException + */ + public void seedGraph(OWLClass processCls, Set seedGenes) throws OWLOntologyCreationException { + + contextId = ogw.getIdentifier(processCls); // TODO + + IRI ontIRI = this.getIRI("TEMP:" + contextId); + //LOG.info("ONT IRI = "+ontIRI); + exportOntology = getOWLOntologyManager().createOntology(ontIRI); + + activityNetwork = new ActivityNetwork(); + for (String g : seedGenes) { + Activity a = getMostLikelyActivityForGene(g, processCls); + activityNetwork.add(a); + } + } + public void seedGraph(String processClsId, Set seedGenes) throws OWLOntologyCreationException { + OWLClass processCls = ogw.getOWLClassByIdentifier(processClsId); + seedGraph(processCls, seedGenes); + } + + /** + * @see seedGraph(String p, Set seed) + * @param processCls + * @throws OWLOntologyCreationException + */ + public void seedGraph(OWLClass processCls) throws OWLOntologyCreationException { + seedGraph(processCls, getGenes(processCls)); + } + + /** + * Generate M = N x N where N ∈ P or N ∈ A + * + * Basic idea: we want to create a partonomy that breaks down a large process into smaller chunks and ultimately partonomic leaves - activities. + * This partonomy may not be identical to the GO partonomy - each node is an instance in the context of the larger process. + * + * As a starting point we have a set of leaves - candidate activations we suspect to be involved somehow in the larger process. + * We also have knowledge in the ontology - both top-down (e.g. W has_part some P) and bottom-up (e.g. P part_of some W). We want to + * connect the leaves to the roots through intermediates. + * + * TODO: MAPKK activity part_of activation of MAPK +reg MAPK activity + * + * @param processCls + */ + public void createPartonomy(OWLClass processCls) { + processSet = new HashSet(); + partonomy = new Partonomy(); + String contextId = ogw.getIdentifier(processCls); // TODO + + // ROOT + Process rootProcess = new Process(processCls, contextId); + rootProcess.addAxioms(); + + // TOP-DOWN : find all necessary parts of an instance of this process + OWLPropertyExpression HP = ogw.getOWLObjectPropertyByIdentifier("BFO:0000051"); + Set downSet = Collections.singleton(HP); + + //ps = new HashSet(); + // note that "ancestors" is potetially confusing here - ancestors of has_part yields necessary parts + Set partClasses = ogw.getAncestors(processCls, downSet, true); + partClasses.add(processCls); // reflexive + + //LOG.info("NECESSARY PARTS: "+partClasses); + //for (OWLObject c : partClasses) { + //LOG.info(" NECPART="+ogw.getIdentifier(c)+ogw.getLabelOrDisplayId(c)); + //} + //Set activitiesWithoutParents = new HashSet(activityNetwork.activitySet); + + /* + Set partClassesRedundant = new HashSet(); + for (OWLObject part : partClasses) { + // loose redundancy - superclasses only + partClassesRedundant.addAll(ogw.getAncestors(part, new HashSet())); + } + // must have has_part in chain; TODO - more elegant way of doing this + partClassesRedundant.addAll(ogw.getAncestors(processCls, Collections.EMPTY_SET)); + */ + + // BOTTOM-UP : define path used to find larger processes a smaller process/acitivity is part of (or regulates) + HashSet upSet = new HashSet(); + OWLPropertyExpression PO = ogw.getOWLObjectPropertyByIdentifier("BFO:0000050"); + OWLPropertyExpression REGULATES = ogw.getOWLObjectPropertyByIdentifier("RO:0002211"); + OWLPropertyExpression NEGATIVELY_REGULATES = ogw.getOWLObjectPropertyByIdentifier("RO:0002212"); + OWLPropertyExpression POSITIVELY_REGULATES = ogw.getOWLObjectPropertyByIdentifier("RO:0002213"); + upSet.add(REGULATES); + upSet.add(NEGATIVELY_REGULATES); + upSet.add(POSITIVELY_REGULATES); + upSet.add(PO); + + // the activity set is already seeded based on this process. + // we find the most likely parent for each activity + for (Activity a : activityNetwork.activitySet) { + // TODO - handdle regulates + Set activityParentClasses = ogw.getAncestors(a.typeOf, upSet, true); + Set directParentClasses = makeClasses(activityParentClasses); + directParentClasses.retainAll(partClasses); + + // also include process annotations that have a path to any part + // ** this may be too liberal ** + for (OWLClass apc : this.getProcessTypes(a.gene)) { + Set pAncs = makeClasses(ogw.getAncestors(apc, upSet, true)); + //pAncs.retainAll(partClasses); <-- todo - only NR partClasses + pAncs.retainAll(Collections.singleton(processCls)); + if (pAncs.size() > 0) { + removeRedundant(pAncs, upSet); + Process partProcess = new Process(apc, contextId); // TODO - reuse if exists + partProcess.addAxioms(); + partonomy.addEdge(a, partProcess); + for (OWLClass pa : pAncs) { + Process pap = new Process(pa, contextId); + pap.addAxioms(); + partonomy.addEdge(partProcess, pap); + partonomy.addEdge(pap, rootProcess); + } + } + } + + + //LOG.info(" ALL INTERMEDIATES FOR "+a.activityClass + " ==> "+directParentClasses); + //for (OWLClass dpc : directParentClasses) { + // LOG.info(" DPC="+ogw.getIdentifier(dpc)+ogw.getLabelOrDisplayId(dpc)); + //} + removeRedundant(directParentClasses, upSet); + //LOG.info(" NR INTERMEDIATES FOR "+a.activityClass + " ==> "+directParentClasses); + if (directParentClasses.size() > 1) { + //LOG.warn("TODO - find best parent"); + } + if (directParentClasses.size() == 0) { + //LOG.warn("No intermediate parent found for "+a.activityClass); + } + for (OWLClass partClass : directParentClasses) { + Process partProcess = new Process(partClass, contextId); // TODO - reuse if exists + partProcess.addAxioms(); + partonomy.addEdge(a, partProcess); + partonomy.addEdge(partProcess, rootProcess); + processSet.add(partProcess); + } + a.numParents = directParentClasses.size(); + } + + /* + + // TODO - for now we leave it as implicit that every member a of A is in P = a x pseed + for (Activity a : activitiesWithoutParents) { + if (a.activityClass != null) + partonomy.addEdge(a, rootProcess); + } + */ + + } + + public void inferLocations() { + for (Process p : processSet) { + inferLocation(p); + } + for (Activity a : activityNetwork.activitySet) { + inferLocation(a); + } + } + + // TODO - use reasoner + private void inferLocation(InstanceNode n) { + OWLPropertyExpression PO = ogw.getOWLObjectPropertyByIdentifier("BFO:0000050"); + OWLPropertyExpression OCCURS_IN = ogw.getOWLObjectPropertyByIdentifier("BFO:0000066"); + Set overProps = Collections.singleton(PO); + // TODO - traverse instance too + Set ancs = ogw.getAncestorsReflexive(n.typeOf, overProps); + //LOG.info("Ancs for "+n.owlObject+" == "+ancs.size()); + for (OWLObject anc : ancs) { + for (OWLGraphEdge e : ogw.getPrimitiveOutgoingEdges(anc)) { + if (e.getSingleQuantifiedProperty().getProperty() != null && + e.getSingleQuantifiedProperty().getProperty().equals(OCCURS_IN)) { + if (e.getTarget() instanceof OWLClass) { + LOG.info("Adding location "+n+" --> "+e.getTarget()); + n.setLocation((OWLClass)e.getTarget()); + } + } + } + } + } + + private Set makeClasses(Set objs) { + Set s = new HashSet(); + for (OWLObject obj : objs) { + if (!(obj instanceof OWLClass)) { + //LOG.warn(""); + continue; + } + s.add((OWLClass) obj); + } + return s; + } + /** + * Add default edges based on PPI network + * + * add ( a1 , a2 ) to E + * where ( g1 , g2 ) is in PPI, and + * a = (g, _) is in A + * + */ + public void connectGraph() { + + // PPI Method + for (String p1 : proteinInteractionMap.keySet()) { + Set aset = activityNetwork.lookupByGene(p1); + if (aset.size() == 0) + continue; + for (String p2 : proteinInteractionMap.get(p1)) { + Set aset2 = activityNetwork.lookupByGene(p2); + for (Activity a1 : aset) { + for (Activity a2 : aset2) { + activityNetwork.addEdge(a1, a2, getObjectProperty("directly_activates")); // TODO + } + } + } + } + + // Using ontology knowledge (e.g. connected_to relationships; has_input = has_output) + + for (Activity a : activityNetwork.activitySet) { + // + } + + // Annotation extension method + // TODO: e.g. PomBase SPCC645.07 rgf1 GO:0032319-regulation of Rho GTPase activity PMID:16324155 IGI PomBase:SPAC1F7.04 P RhoGEF for Rho1, Rgf1 protein taxon:4896 20100429 PomBase + // in: =GO:0051666 ! actin cortical patch localization + } + + + /** + * @param g + * @param processCls + * @return + */ + public Activity getMostLikelyActivityForGene(String g, OWLClass processCls) { + Double bestPr = null; + Activity bestActivity = new Activity(null, g, contextId); // todo + for (OWLClass activityCls : getMostSpecificActivityTypes(g)) { + //Double pr = this.calculateConditionalProbaility(processCls, activityCls); + Double pr = this.calculateConditionalProbaility(activityCls, processCls); + if (bestPr == null || pr >= bestPr) { + Activity a = new Activity(activityCls, g, contextId); + a.strength = pr; + bestActivity = a; + bestPr = pr; + } + } + return bestActivity; + } + + + + /** + * + * Pr( F | P ) = Pr(F,P) / Pr(P) + * + */ + + public Double calculateConditionalProbaility(OWLClass wholeCls, OWLClass partCls) { + Set wgs = getGenes(wholeCls); + Set cgs = getGenes(partCls); + cgs.retainAll(wgs); + double n = getNumberOfGenes(); + Double pr = (cgs.size() / n) / ( wgs.size() / n); + return pr; + } + + + /** + * Get all activity types a gene enables (i.e. direct MF annotations) + * @param g + * @return { t : t ∈ TA, g x t ∈ Enables } + */ + public Set getActivityTypes(String g) { + HashSet cset = new HashSet(clsByGeneMap.get(g)); + cset.retainAll(activityClassSet); + return cset; + } + + + /** + * @param g + * @return { t : t ∈ getActivityTypes(g), ¬ ∃ t' : t' ∈ getActivityTypes(g), t' ProperInferredßSubClassOf t } + */ + public Set getMostSpecificActivityTypes(String g) { + Set cset = getActivityTypes(g); + removeRedundant(cset, null); + return cset; + } + + public Set getProcessTypes(String g) { + HashSet cset = new HashSet(clsByGeneMap.get(g)); + cset.retainAll(processClassSet); + return cset; + } + + + + private void removeRedundant(Set cset, Set props) { + Set allAncs = new HashSet(); + for (OWLClass c : cset) { + Set ancClsSet = ogw.getAncestors(c, props); + for (OWLObject obj : ancClsSet) { + if (obj instanceof OWLClass) { + // named ancestors only + allAncs.add((OWLClass) obj); + } + + } + } + cset.removeAll(allAncs); + } + + /** + * Gets all genes that enable a given activity type (i.e. inverred annotations to MF term) + * @param t + * @return { g : g x t ∈ InferredInvolvedIn } + */ + public Set getGenes(OWLClass wholeCls) { + if (!geneByInferredClsMap.containsKey(wholeCls)) { + LOG.info("Nothing known about "+wholeCls); + return new HashSet(); + } + return new HashSet(geneByInferredClsMap.get(wholeCls)); + } + + /** + * @return |G| + */ + public int getNumberOfGenes() { + return populationGeneSet.size(); + } + + public void initialize(GafDocument gafdoc, OWLGraphWrapper g) { + ogw = g; + geneByInferredClsMap = new HashMap>(); + populationGeneSet = new HashSet(); + clsByGeneMap = new HashMap>(); + labelMap = new HashMap(); + proteinInteractionMap = new HashMap>(); + // TODO - set context from GAF Doc + + for (GeneAnnotation ann : gafdoc.getGeneAnnotations()) { + String c = ann.getCls(); + OWLClass cls = ogw.getOWLClassByIdentifier(c); + String gene = ann.getBioentity(); + + // special case : protein binding + if (c.equals("GO:0005515")) { + for (String b : ann.getWithInfos()) { + addPPI(gene, b); + } + continue; + } + + for (List eel : ann.getExtensionExpressions()) { + for (ExtensionExpression ee : eel) { + // temporary measure - treat all ext expressions as PPIs + addPPI(gene, ee.getCls()); + } + } + + populationGeneSet.add(gene); + String sym = ann.getBioentityObject().getSymbol(); + if (sym != null && !sym.equals("")) + labelMap.put(gene, sym); + + + if (!clsByGeneMap.containsKey(gene)) + clsByGeneMap.put(gene, new HashSet()); + clsByGeneMap.get(gene).add(cls); + + for (OWLObject ancCls : g.getNamedAncestorsReflexive(cls)) { + if (!(ancCls instanceof OWLClass)) { + LOG.error(ancCls + " is ancestor of "+cls+" and not a class...?"); + } + OWLClass anc = (OWLClass) ancCls; + //LOG.info(" "+gene + " => "+c+" => "+anc + " // "+ancCls); + if (!geneByInferredClsMap.containsKey(anc)) + geneByInferredClsMap.put(anc, new HashSet()); + geneByInferredClsMap.get(anc).add(gene); + } + } + + activityClassSet = new HashSet(); + processClassSet = new HashSet(); + for (OWLClass cls : g.getAllOWLClasses()) { + String ns = g.getNamespace(cls); + if (ns == null) ns = ""; + if (ns.equals("molecular_function")) { + activityClassSet.add(cls); + } + else if (ns.equals("biological_process")) { + processClassSet.add(cls); + } + else if (!ns.equals("cellular_component")) { + LOG.info("Adding "+cls+" to process subset - I assume anything not a CC or MF is a process"); + // todo - make configurable. The default assumption is that phenotypes etc are treated as pathological process + processClassSet.add(cls); + } + String label = g.getLabel(cls); + if (label != "" && label != null) + labelMap.put(cls, label); + } + + } + + // adds an (external) protein-protein interaction + private void addPPI(String a, String b) { + if (!proteinInteractionMap.containsKey(a)) + proteinInteractionMap.put(a, new HashSet()); + proteinInteractionMap.get(a).add(b); + + } + + /** + * @param id + * @return label for any class or entity in the graph + */ + public String getLabel(Object k) { + if (k == null) + return "Null"; + if (labelMap.containsKey(k)) + return this.labelMap.get(k); + return k.toString(); + } + + public Map getGraphStatistics() { + Map sm = new HashMap(); + sm.put("activity_node_count", activityNetwork.activitySet.size()); + sm.put("activity_edge_count", activityNetwork.activityEdgeSet.size()); + sm.put("process_count", processSet.size()); + return sm; + } + + /** + * Translates ontological activation network into OWL (aka lego model) + *
      + *
    • a = g x t ∈ A → a ∈ OWLNamedIndividual, a.iri = genIRI(g, t), a rdf:type t, a rdf:type (enabled_by some g) + *
    • g ∈ G → g ∈ OWLClass, g SubClassOf Protein + *
    • t ∈ T → t ∈ OWLClass + *
    • e = a1 x a2 x t ∈ E → e ∈ OWLObjectPropertyAssertion, e.subject = a1, e.object = a2, e.property = t + *
    • p ∈ P → p ∈ OWLNamedIndividual + *
    • m = p1 x p2 & ∈ M → m ∈ OWLObjectPropertyAssertion, m.subject = p1, m.object = p2, m.property = part_of + *
    • + *
    + * Notes: we treat all members of G as proteins, but these may be other kinds of gene product. Note also the source ID may be a gene ID. + * In this case we can substitute "enabled_by some g" with "enabled_by some (product_of some g)" + * + * In some cases the edge type is not known - here we can use a generic owlTopProperty - or we can assume an activates relation, and leave the user to prune/modify + * + * Warning: may possibly be refactored into a separate writer class. + * + * @return + * @throws OWLOntologyCreationException + */ + @Deprecated + public OWLOntology translateNetworkToOWL() throws OWLOntologyCreationException { + //if (exportOntology == null) { + //IRI ontIRI = this.getIRI("TEMP:" + contextId); + //LOG.info("ONT IRI = "+ontIRI); + //exportOntology = getOWLOntologyManager().createOntology(ontIRI); + //} + // a = g x t ∈ A → a ∈ OWLNamedIndividual, a.iri = genIRI(g, t), a rdf:type t, a rdf:type (enabled_by some g) + Map activityToIdMap = new HashMap(); + for (Activity a : activityNetwork.activitySet) { + OWLClassExpression activityClass = a.typeOf; + String gene = a.gene; + if (activityClass == null) + activityClass = ogw.getOWLClassByIdentifier("GO:0003674"); // TODO - use vocab + if (gene == null) + gene = "PR:00000001"; + //activityToIdMap.put(a, id); + //addOwlInstanceRelationType(a.owlObject, "enabled_by", gene); + //addOwlInstanceType(id, activityClass); + String label = getLabel(a.owlObject) + " enabled by "+getLabel(gene); + addOwlLabel(a.owlObject, label); + } + for (Edge e : partonomy.edgeSet) { + LOG.info("PTNMY="+e.subject + " --> "+e.object); + // TODO - this is really contorted, all because we are overloading String in the partonomy + /* + Set aset = activityNetwork.lookupByActivityType(e.subject); + if (aset.size() > 0) { + Activity a = aset.iterator().next(); + addOwlFact(activityToIdMap.get(a), e.type, e.object); + } + else { + addOwlFact(e.subject, e.type, e.object); + } + */ + //addOwlLabel(e.subject, getLabel(e.subject)); + addOwlLabel(e.object.owlObject, getLabel(e.object)); // TODO <-- do this earlier + //this.addOwlInstanceType(e.object, e.object); // PUNNING!!! + } + for (Edge e : activityNetwork.activityEdgeSet) { + + addOwlFact(e.subject.owlObject, + e.type, + e.object.owlObject + ); + } + + return exportOntology; + } + + public OWLOntology translateNetworkToOWL(OWLOntology ont) throws OWLOntologyCreationException { + exportOntology = ont; + return translateNetworkToOWL(); + } + + + private OWLOntologyManager getOWLOntologyManager() { + if (owlOntologyManager == null) + owlOntologyManager = OWLManager.createOWLOntologyManager(); + return owlOntologyManager; + } + + + private OWLDataFactory getOWLDataFactory() { + return exportOntology.getOWLOntologyManager().getOWLDataFactory(); + } + + private void addAxiom(OWLAxiom ax) { + exportOntology.getOWLOntologyManager().addAxiom(exportOntology, ax); + } + + private IRI getIRI(String id) { + return ogw.getIRIByIdentifier(id); + } + + private OWLNamedIndividual getIndividual(String id) { + return getOWLDataFactory().getOWLNamedIndividual(getIRI(id)); + } + private OWLClass getOWLClass(String id) { + return getOWLDataFactory().getOWLClass(getIRI(id)); + } + + // TODO - use a vocabulary/enum + private OWLObjectPropertyExpression getObjectProperty(String rel) { + IRI iri; + if (rel.equals("part_of")) + rel = "BFO:0000050"; + if (rel.equals("occurs_in")) + rel = "BFO:0000066"; + if (rel.contains(":")) { + iri = getIRI(rel); + } + else { + iri = getIRI("http://purl.obolibrary.org/obo/"+rel); // TODO + } + return getOWLDataFactory().getOWLObjectProperty(iri); + } + + @Deprecated + private void addOwlFact(OWLIndividual subj, OWLObjectPropertyExpression type, OWLIndividual obj) { + //LOG.info("Adding " + subj + " "+rel + " "+obj); + addAxiom(getOWLDataFactory().getOWLObjectPropertyAssertionAxiom(type, subj, obj)); + } + + private void addOwlData(OWLObject subj, OWLAnnotationProperty p, String val) { + OWLLiteral lit = getOWLDataFactory().getOWLLiteral(val); + addAxiom(getOWLDataFactory().getOWLAnnotationAssertionAxiom( + p, + ((OWLNamedObject) subj).getIRI(), + lit)); + } + + private void addOwlLabel(OWLObject owlObject, String val) { + addOwlData(owlObject, + getOWLDataFactory().getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()), + val); + } + + + @Deprecated + private void addOwlInstanceType(String i, String t) { + //LOG.info("Adding " + i + " instance of "+t); + addAxiom(getOWLDataFactory().getOWLClassAssertionAxiom( + getOWLClass(t), + getIndividual(i))); + } + + @Deprecated + private void addOwlInstanceRelationType(String i, String r, String t) { + //LOG.info("Adding " + i + " instance of "+r+" some "+t); + OWLClassExpression x = getOWLDataFactory().getOWLObjectSomeValuesFrom( + getObjectProperty(r), + getOWLClass(t)); + addAxiom(getOWLDataFactory().getOWLClassAssertionAxiom( + x, + getIndividual(i))); + } + + + +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/json/JsonTools.java b/minerva-core/src/main/java/org/geneontology/minerva/json/JsonTools.java new file mode 100644 index 00000000..1971b7df --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/json/JsonTools.java @@ -0,0 +1,150 @@ +package org.geneontology.minerva.json; + +import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.util.IdStringManager; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAnnotationValue; +import org.semanticweb.owlapi.model.OWLAnnotationValueVisitorEx; +import org.semanticweb.owlapi.model.OWLAnonymousIndividual; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLDataProperty; +import org.semanticweb.owlapi.model.OWLDatatype; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.vocab.OWL2Datatype; + +public class JsonTools { + + private static final String VALUE_TYPE_IRI = "IRI"; + + public static JsonAnnotation create(OWLAnnotationProperty p, OWLAnnotationValue value) { + AnnotationShorthand annotationShorthand = AnnotationShorthand.getShorthand(p.getIRI()); + if (annotationShorthand != null) { + // try to shorten IRIs for shorthand annotations + return create(annotationShorthand.name(), value, true); + } + // use full IRI strings for non-shorthand annotations + return create(p.getIRI().toString(), value, false); + } + + public static JsonAnnotation create(OWLDataProperty p, OWLLiteral value) { + String type = getType(value); + return JsonAnnotation.create(p.getIRI().toString(), value.getLiteral(), type); + } + + private static String getType(OWLLiteral literal) { + OWLDatatype datatype = literal.getDatatype(); + String type = null; + if (datatype.isString() || datatype.isRDFPlainLiteral()) { + // do nothing + } + else if (datatype.isBuiltIn()) { + type = datatype.getBuiltInDatatype().getPrefixedName(); + } + return type; + } + + public static Pair createSimplePair(OWLAnnotation an) { + Pair result = null; + // only render shorthand annotations in simple pairs + AnnotationShorthand shorthand = AnnotationShorthand.getShorthand(an.getProperty().getIRI()); + if (shorthand != null) { + String value = an.getValue().accept(new OWLAnnotationValueVisitorEx() { + + @Override + public String visit(IRI iri) { + return IdStringManager.getId(iri); + } + + @Override + public String visit(OWLAnonymousIndividual individual) { + return null; + } + + @Override + public String visit(OWLLiteral literal) { + return literal.getLiteral(); + } + }); + if (value != null) { + result = Pair.of(shorthand.name(), value); + } + } + return result; + } + + private static JsonAnnotation create(final String key, OWLAnnotationValue value, final boolean useShortId) { + return value.accept(new OWLAnnotationValueVisitorEx() { + + @Override + public JsonAnnotation visit(IRI iri) { + String iriString; + if (useShortId) { + iriString = IdStringManager.getId(iri); + } + else { + iriString = iri.toString(); + } + return JsonAnnotation.create(key, iriString, VALUE_TYPE_IRI); + } + + @Override + public JsonAnnotation visit(OWLAnonymousIndividual individual) { + return null; // do nothing + } + + @Override + public JsonAnnotation visit(OWLLiteral literal) { + return JsonAnnotation.create(key, literal.getLiteral(), getType(literal)); + } + }); + } + + public static JsonAnnotation create(AnnotationShorthand key, String value) { + return JsonAnnotation.create(key.name(), value, null); + } + + private static boolean isIRIValue(JsonAnnotation ann) { + return VALUE_TYPE_IRI.equalsIgnoreCase(ann.valueType); + } + + public static OWLAnnotationValue createAnnotationValue(JsonAnnotation ann, OWLDataFactory f) { + OWLAnnotationValue annotationValue; + if (isIRIValue(ann)) { + annotationValue = IRI.create(ann.value); + } + else { + annotationValue = createLiteralInternal(ann, f); + } + return annotationValue; + } + + public static OWLLiteral createLiteral(JsonAnnotation ann, OWLDataFactory f) { + OWLLiteral literal = null; + if (isIRIValue(ann) == false) { + literal = createLiteralInternal(ann, f); + } + return literal; + } + + private static OWLLiteral createLiteralInternal(JsonAnnotation ann, OWLDataFactory f) { + OWLLiteral literal; + OWL2Datatype datatype = null; + for(OWL2Datatype current : OWL2Datatype.values()) { + if (current.getPrefixedName().equalsIgnoreCase(ann.valueType) + || current.getShortForm().equalsIgnoreCase(ann.valueType)) { + datatype = current; + break; + } + } + if (datatype != null) { + literal = f.getOWLLiteral(ann.value, datatype); + } + else { + literal = f.getOWLLiteral(ann.value); + } + return literal; + } +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/json/MolecularModelJsonRenderer.java b/minerva-core/src/main/java/org/geneontology/minerva/json/MolecularModelJsonRenderer.java new file mode 100644 index 00000000..7f41836d --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/json/MolecularModelJsonRenderer.java @@ -0,0 +1,534 @@ +package org.geneontology.minerva.json; + +import java.io.IOException; +import java.lang.reflect.Type; +import java.text.DateFormat; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.apache.commons.lang3.tuple.Pair; +import org.apache.log4j.Logger; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.MolecularModelManager; +import org.geneontology.minerva.util.IdStringManager; +import org.semanticweb.owlapi.model.AxiomType; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataProperty; +import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLException; +import org.semanticweb.owlapi.model.OWLIndividual; +import org.semanticweb.owlapi.model.OWLIndividualAxiom; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLNamedObject; +import org.semanticweb.owlapi.model.OWLObjectIntersectionOf; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLObjectUnionOf; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyDocumentAlreadyExistsException; +import org.semanticweb.owlapi.model.OWLOntologyID; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.reasoner.OWLReasoner; + +import owltools.gaf.eco.EcoMapper; +import owltools.gaf.eco.EcoMapperFactory; +import owltools.gaf.eco.EcoMapperFactory.OntologyMapperPair; +import owltools.graph.OWLGraphWrapper; + +import com.google.gson.Gson; +import com.google.gson.GsonBuilder; + +/** + * A Renderer that takes a MolecularModel (an OWL ABox) and generates Map objects + * that can be translated to JSON using Gson. + * + * TODO - make this inherit from a generic renderer - use OWLAPI visitor? + * TODO - abstract some of this into a generic OWL to JSON-LD converter + * + * @author cjm + * + */ +public class MolecularModelJsonRenderer { + + private static Logger LOG = Logger.getLogger(MolecularModelJsonRenderer.class); + + private final OWLOntology ont; + private final OWLGraphWrapper graph; + +// private boolean includeObjectPropertyValues = true; + + public static final ThreadLocal AnnotationTypeDateFormat = new ThreadLocal(){ + + @Override + protected DateFormat initialValue() { + return new SimpleDateFormat("yyyy-MM-dd"); + } + + }; + + /** + * @param model + */ + public MolecularModelJsonRenderer(ModelContainer model) { + this(model.getAboxOntology(), new OWLGraphWrapper(model.getAboxOntology())); + } + + /** + * @param ontology + */ + public MolecularModelJsonRenderer(OWLOntology ontology) { + this(ontology, new OWLGraphWrapper(ontology)); + } + + /** + * @param graph + */ + public MolecularModelJsonRenderer(OWLGraphWrapper graph) { + this(graph.getSourceOntology(), graph); + } + + private MolecularModelJsonRenderer(OWLOntology ont, OWLGraphWrapper graph) { + super(); + this.ont = ont; + this.graph = graph; + } + + /** + * @return Map to be passed to Gson + */ + public JsonModel renderModel() { + JsonModel json = new JsonModel(); + + // per-Individual + List iObjs = new ArrayList(); + for (OWLNamedIndividual i : ont.getIndividualsInSignature()) { + iObjs.add(renderObject(i)); + } + json.individuals = iObjs.toArray(new JsonOwlIndividual[iObjs.size()]); + + // per-Assertion + Set usedProps = new HashSet(); + + List aObjs = new ArrayList(); + for (OWLObjectPropertyAssertionAxiom opa : ont.getAxioms(AxiomType.OBJECT_PROPERTY_ASSERTION)) { + JsonOwlFact fact = renderObject(opa); + if (fact != null) { + aObjs.add(fact); + usedProps.addAll(opa.getObjectPropertiesInSignature()); + } + } + json.facts = aObjs.toArray(new JsonOwlFact[aObjs.size()]); + + // per-Property + List pObjs = new ArrayList(); + for (OWLObjectProperty p : usedProps) { + pObjs.add(renderObject(p)); + } + json.properties = pObjs.toArray(new JsonOwlObject[pObjs.size()]); + + JsonAnnotation[] anObjs = renderAnnotations(ont.getAnnotations()); + if (anObjs != null && anObjs.length > 0) { + json.annotations = anObjs; + } + + return json; + + } + + /** + * Add the available inferences to the given JSON map. + * + * @param reasoner + * @return inferences or null + */ + public JsonOwlIndividual[] renderModelInferences(OWLReasoner reasoner) { + JsonOwlIndividual[] inferences = null; + if (reasoner.isConsistent()) { + Set individuals = ont.getIndividualsInSignature(); + inferences = renderInferences(individuals, reasoner); + } + return inferences; + } + + public static JsonAnnotation[] renderModelAnnotations(OWLOntology ont) { + JsonAnnotation[] anObjs = renderAnnotations(ont.getAnnotations()); + return anObjs; + } + + private static JsonAnnotation[] renderAnnotations(Set annotations) { + List anObjs = new ArrayList(); + for (OWLAnnotation annotation : annotations) { + JsonAnnotation json = JsonTools.create(annotation.getProperty(), annotation.getValue()); + if (json != null) { + anObjs.add(json); + } + } + return anObjs.toArray(new JsonAnnotation[anObjs.size()]); + } + + public Pair renderIndividuals(Collection individuals) { + OWLOntology ont = graph.getSourceOntology(); + List iObjs = new ArrayList(); + List individualIds = new ArrayList(); + Set opAxioms = new HashSet(); + for (OWLIndividual i : individuals) { + if (i instanceof OWLNamedIndividual) { + OWLNamedIndividual named = (OWLNamedIndividual)i; + iObjs.add(renderObject(named)); + individualIds.add(named); + + Set iAxioms = ont.getAxioms(i); + for (OWLIndividualAxiom owlIndividualAxiom : iAxioms) { + if (owlIndividualAxiom instanceof OWLObjectPropertyAssertionAxiom) { + opAxioms.add((OWLObjectPropertyAssertionAxiom) owlIndividualAxiom); + } + } + } + } + List aObjs = new ArrayList(); + for (OWLObjectPropertyAssertionAxiom opa : opAxioms) { + JsonOwlFact fact = renderObject(opa); + if (fact != null) { + aObjs.add(fact); + } + } + + return Pair.of(iObjs.toArray(new JsonOwlIndividual[iObjs.size()]), + aObjs.toArray(new JsonOwlFact[aObjs.size()])); + } + + /** + * Retrieve the inferences for the given individuals. + * + * @param individuals + * @param reasoner + * @return individual inferences or null + */ + public JsonOwlIndividual[] renderInferences(Collection individuals, OWLReasoner reasoner) { + if (individuals != null && reasoner.isConsistent()) { + List iObjs = new ArrayList(individuals.size()); + for (OWLNamedIndividual i : individuals) { + JsonOwlIndividual json = new JsonOwlIndividual(); + json.id = IdStringManager.getId(i, graph); + Set types = reasoner.getTypes(i, true).getFlattened(); + List typeObjs = new ArrayList(types.size()); + for (OWLClass x : types) { + if (x.isBuiltIn()) { + continue; + } + typeObjs.add(renderObject(x)); + } + json.type = typeObjs.toArray(new JsonOwlObject[typeObjs.size()]); + iObjs.add(json); + } + return iObjs.toArray(new JsonOwlIndividual[iObjs.size()]); + } + return null; + } + + /** + * @param i + * @return Map to be passed to Gson + */ + public JsonOwlIndividual renderObject(OWLNamedIndividual i) { + JsonOwlIndividual json = new JsonOwlIndividual(); + json.id = IdStringManager.getId(i, graph); + json.label = getLabel(i, json.id); + + List typeObjs = new ArrayList(); + for (OWLClassExpression x : i.getTypes(ont)) { + typeObjs.add(renderObject(x)); + } +// if (includeObjectPropertyValues) { +// Map> pvs = i.getObjectPropertyValues(ont); +// for (OWLObjectPropertyExpression p : pvs.keySet()) { +// List valObjs = new ArrayList(); +// for (OWLIndividual v : pvs.get(p)) { +// if (v.isNamed()) { +// valObjs.add(renderObject(v.asOWLNamedIndividual())); +// } +// } +// iObj.put(getId((OWLNamedObject) p, graph), valObjs); +// } +// } + json.type = typeObjs.toArray(new JsonOwlObject[typeObjs.size()]); + final List anObjs = new ArrayList(); + Set annotationAxioms = ont.getAnnotationAssertionAxioms(i.getIRI()); + for (OWLAnnotationAssertionAxiom ax : annotationAxioms) { + JsonAnnotation jsonAnn = JsonTools.create(ax.getProperty(), ax.getValue()); + if (jsonAnn != null) { + anObjs.add(jsonAnn); + } + } + Set dataPropertyAxioms = ont.getDataPropertyAssertionAxioms(i); + for (OWLDataPropertyAssertionAxiom ax : dataPropertyAxioms) { + OWLDataProperty property = ax.getProperty().asOWLDataProperty(); + JsonAnnotation jsonAnn = JsonTools.create(property, ax.getObject()); + if (jsonAnn != null) { + anObjs.add(jsonAnn); + } + } + + if (anObjs.isEmpty() == false) { + json.annotations = anObjs.toArray(new JsonAnnotation[anObjs.size()]); + } + return json; + } + + /** + * @param opa + * @return Map to be passed to Gson + */ + public JsonOwlFact renderObject(OWLObjectPropertyAssertionAxiom opa) { + OWLNamedIndividual subject; + OWLObjectProperty property; + OWLNamedIndividual object; + + JsonOwlFact fact = null; + if (opa.getSubject().isNamed() && opa.getObject().isNamed() && opa.getProperty().isAnonymous() == false) { + subject = (OWLNamedIndividual) opa.getSubject(); + property = (OWLObjectProperty) opa.getProperty(); + object = (OWLNamedIndividual) opa.getObject(); + + fact = new JsonOwlFact(); + fact.subject = IdStringManager.getId(subject, graph); + fact.property = IdStringManager.getId(property, graph); + fact.object = IdStringManager.getId(object, graph); + + JsonAnnotation[] anObjs = renderAnnotations(opa.getAnnotations()); + if (anObjs != null && anObjs.length > 0) { + fact.annotations = anObjs; + } + } + return fact; + } + + public JsonOwlObject renderObject(OWLObjectProperty p) { + String id = IdStringManager.getId(p, graph); + String label = getLabel(p, id); + JsonOwlObject json = JsonOwlObject.createProperty(id, label); + return json; + } + + private JsonOwlObject renderObject(OWLObjectPropertyExpression p) { + if (p.isAnonymous()) { + return null; + } + return renderObject(p.asOWLObjectProperty()); + } + /** + * @param x + * @return Object to be passed to Gson + */ + private JsonOwlObject renderObject(OWLClassExpression x) { + if (x.isAnonymous()) { + JsonOwlObject json = null; + if (x instanceof OWLObjectIntersectionOf) { + List expressions = new ArrayList(); + for (OWLClassExpression y : ((OWLObjectIntersectionOf)x).getOperands()) { + expressions.add(renderObject(y)); + } + json = JsonOwlObject.createIntersection(expressions); + } + else if (x instanceof OWLObjectUnionOf) { + List expressions = new ArrayList(); + for (OWLClassExpression y : ((OWLObjectUnionOf)x).getOperands()) { + expressions.add(renderObject(y)); + } + json = JsonOwlObject.createUnion(expressions); + } + else if (x instanceof OWLObjectSomeValuesFrom) { + OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom)x; + JsonOwlObject prop = renderObject(svf.getProperty()); + JsonOwlObject filler = renderObject(svf.getFiller()); + if (prop != null && filler != null) { + json = JsonOwlObject.createSvf(prop, filler); + } + } + else { + // TODO + } + return json; + } + else { + return renderObject(x.asOWLClass()); + } + } + + private JsonOwlObject renderObject(OWLClass cls) { + String id = IdStringManager.getId(cls, graph); + JsonOwlObject json = JsonOwlObject.createCls(id, getLabel(cls, id)); + return json; + } + + protected String getLabel(OWLNamedObject i, String id) { + return graph.getLabel(i); + } + + + public static Pair,List> renderProperties(MolecularModelManager mmm, Set importantRelations) throws OWLOntologyCreationException { + /* [{ + * id: {String} + * label: {String} + * relevant: {boolean} // flag to indicate if this is a relation to be used in the model + * ?color: {String} // TODO in the future + * ?glyph: {String} // TODO in the future + * }] + */ + // retrieve (or load) all ontologies + // put in a new wrapper + OWLGraphWrapper wrapper = new OWLGraphWrapper(mmm.getOntology()); + Collection imports = mmm.getImports(); + OWLOntologyManager manager = wrapper.getManager(); + for (IRI iri : imports) { + OWLOntology ontology = manager.getOntology(iri); + if (ontology == null) { + // only try to load it, if it isn't already loaded + try { + ontology = manager.loadOntology(iri); + } catch (OWLOntologyDocumentAlreadyExistsException e) { + IRI existing = e.getOntologyDocumentIRI(); + ontology = manager.getOntology(existing); + } catch (OWLOntologyAlreadyExistsException e) { + OWLOntologyID id = e.getOntologyID(); + ontology = manager.getOntology(id); + } + } + if (ontology == null) { + LOG.warn("Could not find an ontology for IRI: "+iri); + } + else { + wrapper.addSupportOntology(ontology); + } + } + + // get all properties from all loaded ontologies + Set properties = new HashSet(); + Set dataProperties = new HashSet(); + Set allOntologies = wrapper.getAllOntologies(); + for(OWLOntology o : allOntologies) { + properties.addAll(o.getObjectPropertiesInSignature()); + dataProperties.addAll(o.getDataPropertiesInSignature()); + } + + // sort properties + List propertyList = new ArrayList(properties); + List dataPropertyList = new ArrayList(dataProperties); + Collections.sort(propertyList); + Collections.sort(dataPropertyList); + + // retrieve id and label for all properties + List relList = new ArrayList(); + for (OWLObjectProperty p : propertyList) { + if (p.isBuiltIn()) { + // skip owl:topObjectProperty + continue; + } + JsonRelationInfo json = new JsonRelationInfo(); + json.id = IdStringManager.getId(p, wrapper); + json.label = wrapper.getLabel(p); + if (importantRelations != null && (importantRelations.contains(p))) { + json.relevant = true; + } + else { + json.relevant = false; + } + relList.add(json); + } + + // retrieve id and label for all data properties + List dataList = new ArrayList(); + for(OWLDataProperty p : dataPropertyList) { + if(p.isBuiltIn()) { + continue; + } + JsonRelationInfo json = new JsonRelationInfo(); + json.id = p.getIRI().toString(); + json.label = wrapper.getLabelOrDisplayId(p); + dataList.add(json); + } + + return Pair.of(relList, dataList); + } + + public static List renderEvidences(MolecularModelManager mmm) throws OWLException, IOException { + return renderEvidences(mmm.getGraph().getManager()); + } + + public static List renderEvidences(OWLOntologyManager manager) throws OWLException, IOException { + // TODO remove the hard coded ECO dependencies + OntologyMapperPair pair = EcoMapperFactory.createEcoMapper(manager); + final OWLGraphWrapper graph = pair.getGraph(); + final EcoMapper mapper = pair.getMapper(); + Set ecoClasses = graph.getAllOWLClasses(); + Map codesForEcoClasses = mapper.getCodesForEcoClasses(); + List relList = new ArrayList(); + for (OWLClass ecoClass : ecoClasses) { + if (ecoClass.isBuiltIn()) { + continue; + } + JsonEvidenceInfo json = new JsonEvidenceInfo(); + json.id = IdStringManager.getId(ecoClass, graph); + json.label = graph.getLabel(ecoClass); + String code = codesForEcoClasses.get(ecoClass); + if (code != null) { + json.code = code; + } + relList.add(json); + } + return relList; + } + + public static String renderToJson(OWLOntology ont) { + return renderToJson(ont, false); + } + + public static String renderToJson(OWLOntology ont, boolean allIndividuals) { + return renderToJson(ont, allIndividuals, false); + } + + public static String renderToJson(OWLOntology ont, boolean allIndividuals, boolean prettyPrint) { + MolecularModelJsonRenderer r = new MolecularModelJsonRenderer(ont); +// if (allIndividuals) { +// r.includeObjectPropertyValues = false; +// } + JsonModel model = r.renderModel(); + return renderToJson(model, prettyPrint); + } + + public static String renderToJson(Object model, boolean prettyPrint) { + GsonBuilder builder = new GsonBuilder(); + if (prettyPrint) { + builder = builder.setPrettyPrinting(); + } + Gson gson = builder.create(); + String json = gson.toJson(model); + return json; + } + + public static T parseFromJson(String json, Class type) { + Gson gson = new GsonBuilder().create(); + T result = gson.fromJson(json, type); + return result; + } + + public static T[] parseFromJson(String requestString, Type requestType) { + Gson gson = new GsonBuilder().create(); + return gson.fromJson(requestString, requestType); + } + +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/util/IdStringManager.java b/minerva-core/src/main/java/org/geneontology/minerva/util/IdStringManager.java new file mode 100644 index 00000000..73c39236 --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/util/IdStringManager.java @@ -0,0 +1,141 @@ +package org.geneontology.minerva.util; + +import org.apache.commons.lang3.StringUtils; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLNamedObject; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.vocab.OWLRDFVocabulary; + +import com.google.gson.annotations.SerializedName; + +import owltools.graph.OWLGraphWrapper; +import owltools.vocab.OBOUpperVocabulary; + +/** + * Handle IRI to id string conversions. + */ +public class IdStringManager { + + /** + * @param i + * @param graph + * @return id + * + * @see IdStringManager#getIRI + */ + public static String getId(OWLNamedObject i, OWLGraphWrapper graph) { + if (i instanceof OWLObjectProperty) { + String relId = graph.getIdentifier(i); + return relId; + } + IRI iri = i.getIRI(); + return getId(iri); + } + + /** + * @param iri + * @return id + */ + public static String getId(IRI iri) { + String iriString = iri.toString(); + // remove obo prefix from IRI + String full = StringUtils.removeStart(iriString, OBOUpperVocabulary.OBO); + String replaced; + if (full.startsWith("#")) { + replaced = StringUtils.removeStart(full, "#"); + } + else { + // replace first '_' char with ':' char + replaced = StringUtils.replaceOnce(full, "_", ":"); + } + return replaced; + } + + /** + * Inverse method to {@link #getId} + * + * @param id + * @param graph + * @return IRI + * + * @see IdStringManager#getId + */ + public static IRI getIRI(String id, OWLGraphWrapper graph) { + if (id.indexOf(':') < 0) { + return graph.getIRIByIdentifier(id); + } + if(id.startsWith(OBOUpperVocabulary.OBO) ){ + return IRI.create(id); + } + String fullIRI = OBOUpperVocabulary.OBO + StringUtils.replaceOnce(id, ":", "_"); + return IRI.create(fullIRI); + } + + /** + * Inverse method to {@link #getId} for IRIs only! + * + * @param id + * @return IRI + * + * @see IdStringManager#getId + */ + public static IRI getIRI(String id) { + if(id.startsWith(OBOUpperVocabulary.OBO) ){ + return IRI.create(id); + } + String fullIRI = OBOUpperVocabulary.OBO + StringUtils.replaceOnce(id, ":", "_"); + return IRI.create(fullIRI); + } + + public IdStringManager() { + super(); + } + + public enum AnnotationShorthand { + + @SerializedName("layout-hint-x") + x(IRI.create("http://geneontology.org/lego/layout/hint/x")), + + @SerializedName("layout-hint-y") + y(IRI.create("http://geneontology.org/lego/layout/hint/y")), + comment(OWLRDFVocabulary.RDFS_COMMENT.getIRI()), // arbitrary String + evidence(IRI.create("http://geneontology.org/lego/evidence")), // eco class iri + date(IRI.create("http://purl.org/dc/elements/1.1/date")), // arbitrary string at the moment, define date format? + // DC recommends http://www.w3.org/TR/NOTE-datetime, one example format is YYYY-MM-DD + source(IRI.create("http://purl.org/dc/elements/1.1/source")), // arbitrary string, such as PMID:000000 + contributor(IRI.create("http://purl.org/dc/elements/1.1/contributor")), // who contributed to the annotation + title(IRI.create("http://purl.org/dc/elements/1.1/title")), // title (of the model) + deprecated(OWLRDFVocabulary.OWL_DEPRECATED.getIRI()); // model annotation to indicate deprecated models + + + private final IRI annotationProperty; + + AnnotationShorthand(IRI annotationProperty) { + this.annotationProperty = annotationProperty; + } + + public IRI getAnnotationProperty() { + return annotationProperty; + } + + + public static AnnotationShorthand getShorthand(IRI iri) { + for (AnnotationShorthand type : AnnotationShorthand.values()) { + if (type.annotationProperty.equals(iri)) { + return type; + } + } + return null; + } + + public static AnnotationShorthand getShorthand(String name) { + for (AnnotationShorthand type : AnnotationShorthand.values()) { + if (type.name().equals(name)) { + return type; + } + } + return null; + } + } + +} \ No newline at end of file diff --git a/minerva-core/src/main/java/org/geneontology/minerva/util/ManchesterSyntaxTool.java b/minerva-core/src/main/java/org/geneontology/minerva/util/ManchesterSyntaxTool.java new file mode 100644 index 00000000..a6b67a67 --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/util/ManchesterSyntaxTool.java @@ -0,0 +1,197 @@ +package org.geneontology.minerva.util; + +import java.util.Collections; +import java.util.HashMap; +import java.util.Map; + +import org.apache.commons.lang3.StringUtils; +import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser; +import org.semanticweb.owlapi.expression.OWLEntityChecker; +import org.semanticweb.owlapi.expression.ParserException; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLDataProperty; +import org.semanticweb.owlapi.model.OWLDatatype; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObject; +import org.semanticweb.owlapi.model.OWLObjectProperty; + +import owltools.graph.OWLGraphWrapper; + + +/** + * Wrapper for parsing OWL Manchester Syntax using a {@link OWLGraphWrapper}. + * This is a simplified re-implementation. + */ +public class ManchesterSyntaxTool { + + private final OWLDataFactory dataFactory; + private final OWLEntityChecker entityChecker; + private final Map createdClassesMap; + + /** + * Create new instance. + * + * @param graph + * @param createClasses if set to true, classes are generated even if they are not declared. + */ + public ManchesterSyntaxTool(OWLGraphWrapper graph, boolean createClasses) { + super(); + this.dataFactory = graph.getDataFactory(); + createdClassesMap = new HashMap(); + entityChecker = new AdvancedEntityChecker(graph, createClasses, createdClassesMap); + } + + /** + * @return the createdClasses + */ + public Map getCreatedClasses() { + return Collections.unmodifiableMap(createdClassesMap); + } + + /** + * Parse a class expression in Manchester syntax. + * + * @param expression + * @return {@link OWLClassExpression} + * @throws ParserException + */ + public OWLClassExpression parseManchesterExpression(String expression) throws ParserException { + ManchesterOWLSyntaxEditorParser parser = createParser(expression); + OWLClassExpression ce = parser.parseClassExpression(); + return ce; + } + + + private ManchesterOWLSyntaxEditorParser createParser(String expression) { + ManchesterOWLSyntaxEditorParser parser = + new ManchesterOWLSyntaxEditorParser(dataFactory, expression); + + parser.setOWLEntityChecker(entityChecker); + + return parser; + } + + static class AdvancedEntityChecker implements OWLEntityChecker { + + private final OWLGraphWrapper graph; + private final boolean createClasses; + private final Map createdClassesMap; + + AdvancedEntityChecker(OWLGraphWrapper graph, boolean createClasses, + Map createdClassesMap) { + super(); + this.graph = graph; + this.createClasses = createClasses; + this.createdClassesMap = createdClassesMap; + } + + public OWLClass getOWLClass(String name) { + if (name.length() < 2) { + return null; + } + OWLObject owlObject; + if (name.charAt(0) == '\'') { + name = trimQuotes(name); + owlObject = graph.getOWLObjectByLabel(name); + } + else { + owlObject = graph.getOWLObjectByIdentifier(name); + if (owlObject == null) { + owlObject = graph.getOWLObjectByLabel(name); + } + } + if (owlObject != null) { + if (owlObject instanceof OWLClass) { + return (OWLClass) owlObject; + } + return null; + } + if (name.startsWith("http:")) { + IRI iri = IRI.create(name); + owlObject = graph.getOWLObject(iri); + if (owlObject != null) { + if (owlObject instanceof OWLClass) { + return (OWLClass) owlObject; + } + return null; + } + OWLClass c = null; + if (createClasses) { + String id = graph.getIdentifier(iri); + c = createdClassesMap.get(id); + if (c == null) { + c = graph.getDataFactory().getOWLClass(iri); + createdClassesMap.put(name, c); + } + } + return c; + } + else { + if (createClasses && !StringUtils.contains(name, ' ')) { + OWLClass c = createdClassesMap.get(name); + if (c == null) { + IRI iri = graph.getIRIByIdentifier(name); + c = graph.getDataFactory().getOWLClass(iri); + createdClassesMap.put(name, c); + } + return c; + } + } + return null; + } + + public OWLObjectProperty getOWLObjectProperty(String name) { + if (name.length() < 2) { + return null; + } + name = trimQuotes(name); + OWLObjectProperty p = null; + if (StringUtils.contains(name, ' ') == false) { + p = graph.getOWLObjectPropertyByIdentifier(name); + if (p == null) { + p = graph.getOWLObjectProperty(name); + } + } + if (p == null) { + graph.getIRIByLabel(name); + OWLObject owlObject = graph.getOWLObjectByLabel(name); + if (owlObject != null && owlObject instanceof OWLObjectProperty) { + p = (OWLObjectProperty) owlObject; + } + } + return p; + } + + private String trimQuotes(String s) { + if (s.startsWith("'") && s.endsWith("'")) { + s = s.substring(1, s.length() - 1); + } + return s; + } + + public OWLDataProperty getOWLDataProperty(String name) { + return null; + } + + public OWLNamedIndividual getOWLIndividual(String name) { + OWLNamedIndividual i = graph.getOWLIndividualByIdentifier(name); + if (i == null) { + i = graph.getOWLIndividual(name); + } + return i; + } + + public OWLDatatype getOWLDatatype(String name) { + return null; + } + + public OWLAnnotationProperty getOWLAnnotationProperty(String name) { + return null; + } + + } +} diff --git a/minerva-core/src/main/java/org/geneontology/minerva/util/MinimalModelGenerator.java b/minerva-core/src/main/java/org/geneontology/minerva/util/MinimalModelGenerator.java new file mode 100644 index 00000000..10801a2e --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/util/MinimalModelGenerator.java @@ -0,0 +1,1171 @@ +package org.geneontology.minerva.util; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.Stack; +import java.util.UUID; + +import org.apache.log4j.Level; +import org.apache.log4j.Logger; +import org.geneontology.minerva.ModelContainer; +import org.semanticweb.owlapi.model.AxiomType; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLEntity; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; +import org.semanticweb.owlapi.model.OWLIndividual; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectIntersectionOf; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyChange; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.RemoveImport; +import org.semanticweb.owlapi.util.OWLEntityRenamer; + +import uk.ac.manchester.cs.owlapi.modularity.ModuleType; +import uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor; + +/** + * Given a class C, materialize a minimal ABox M from the existential graph of C. + * + * The graph will have a root instance i, where type(i,C) and i is connected to every node in the graph directly, + * or indirectly via instances of other classes entailed to exist. + * + * + * @author cjm + * + */ +public class MinimalModelGenerator { + + private static Logger LOG = Logger.getLogger(MinimalModelGenerator.class); + static { + Logger.getLogger("org.semanticweb.elk").setLevel(Level.ERROR); + } + protected final ModelContainer model; + + private String contextualizingSuffix = null; + boolean isPrecomputePropertyClassCombinations = true; + boolean isAssertInverses = true; + boolean isRemoveAmbiguousIndividuals = true; + Set inclusionSet = null; + Set exclusionSet = null; + Set directExclusionSet = null; + public boolean isStrict; + + protected Map prototypeIndividualMap = + new HashMap(); + + public MinimalModelGenerator(ModelContainer model) throws OWLOntologyCreationException { + this.model = model; + init(); + } + + public ModelContainer getModel() { + return model; + } + + /** + * {@link #setAssertInverses(boolean)} + * + * @return true is inverses are to be asserted + */ + public boolean isAssertInverses() { + return isAssertInverses; + } + /** + * If set, every asserted OPE(P X Y) will also generate OPE(P' Y X) where P' InverseOf P + * @param isAssertInverses + */ + public void setAssertInverses(boolean isAssertInverses) { + this.isAssertInverses = isAssertInverses; + } + + + public boolean isRemoveAmbiguousIndividuals() { + return isRemoveAmbiguousIndividuals; + } + + /** + * @param isRemoveAmbiguousIndividuals + */ + public void setRemoveAmbiguousIndividuals(boolean isRemoveAmbiguousIndividuals) { + this.isRemoveAmbiguousIndividuals = isRemoveAmbiguousIndividuals; + } + + + + public Set getInclusionSet() { + return inclusionSet; + } + public void setInclusionSet(Set inclusionSet) { + this.inclusionSet = inclusionSet; + } + public Set getExclusionSet() { + return exclusionSet; + } + public void setExclusionSet(Set exclusionSet) { + this.exclusionSet = exclusionSet; + } + public Set getDirectExclusionSet() { + return directExclusionSet; + } + public void setDirectExclusionSet(Set directExclusionSet) { + this.directExclusionSet = directExclusionSet; + } + /** + * Initialization consists of: + * + *
      + *
    • Setting aboxOntology, if not set - defaults to a new ontology using tbox.IRI as base. + * Adds import to tbox. + *
    • Setting queryOntology, if not set. Adds abox imports queryOntology declaration + *
    • Creates a reasoner using reasonerFactory + *
    + * + * @throws OWLOntologyCreationException + */ + private void init() throws OWLOntologyCreationException { + if (contextualizingSuffix == null) { + contextualizingSuffix = "-proto"; + } + } + +// private OWLReasoner createReasoner() { +// // reasoner -> query -> abox -> tbox +// if (reasoner == null) { +// LOG.debug("Creating reasoner on "+queryOntology+" ImportsClosure="+ +// queryOntology.getImportsClosure()); +// reasoner = reasonerFactory.createReasoner(queryOntology); +// } +// else { +// LOG.debug("reusing reasoner: "+reasoner); +// LOG.warn("check reasoning is pointing to query ontology"); +// } +// return reasoner; +// } + + private String getContextualizingSuffix() { + return contextualizingSuffix; + } + /** + * @param contextualizingSuffix TODO + */ + public void setContextualizingSuffix(String contextualizingSuffix) { + this.contextualizingSuffix = contextualizingSuffix; + } + + /** + * @return true if configured to precompute PxC query classes + */ + public boolean isPrecomputePropertyClassCombinations() { + return isPrecomputePropertyClassCombinations; + } + + + + /** + * If set, all combinations of PxC will be generated for query purposes + * + * This is not necessary for minimal model generation, as the set of + * existential expressions used in the tbox is sufficient to calculate + * the existential graph, but this precompute may be useful for other + * purposes - e.g. finding all ancestors over any relations + * + * @param isPrecomputePropertyClassCombinations + */ + public void setPrecomputePropertyClassCombinations( + boolean isPrecomputePropertyClassCombinations) { + this.isPrecomputePropertyClassCombinations = isPrecomputePropertyClassCombinations; + } + + /** + * @return all individuals that have been generated by this MMG so far + */ + public Collection getGeneratedIndividuals() { + return prototypeIndividualMap.values(); + } + + /** + * Note that the reasoner may be able to provide a more specific class + * @param i + * @return class that was used to generate i + */ + protected OWLClass getPrototypeClass(OWLNamedIndividual i) { + if (prototypeIndividualMap.containsValue(i)) { + for (OWLClass c : prototypeIndividualMap.keySet()) { + if (prototypeIndividualMap.get(c).equals(i)) { + return c; + } + } + } + return null; + } + + // Generate an individual and a triple + // [ incomingSource, incomingProperty, generatedIndividual ] + // where generatedIndividual is of type. + // will also generate additional triples, where existence is entailed + private OWLNamedIndividual generateNecessaryIndividualsImpl(OWLClassExpression c, + OWLNamedIndividual incomingSource, OWLObjectPropertyExpression incomingProperty) { + if (LOG.isDebugEnabled()) { + LOG.debug("GNI type:"+c+" // src="+incomingSource+" via "+incomingProperty); + } + OWLNamedIndividual generatedIndividual; + if (prototypeIndividualMap.containsKey(c)) { + // we assume a single prototype per class; + // this also prevents cycles + + generatedIndividual = prototypeIndividualMap.get(c); + if (incomingProperty != null) { + addTriple(incomingSource, incomingProperty, generatedIndividual); + } + return generatedIndividual; + } + Set rels = new HashSet(); + OWLClassExpression baseClass = null; + if (c instanceof OWLClass) { + // all is good + baseClass = c; + } + else if (c instanceof OWLObjectIntersectionOf) { + // decompose expression + for (OWLClassExpression x : ((OWLObjectIntersectionOf)c).getOperands()) { + if (x instanceof OWLObjectSomeValuesFrom) { + rels.add((OWLObjectSomeValuesFrom) x); + } + else if (x instanceof OWLClass) { + if (c instanceof OWLClass) { + LOG.warn("Cannot handle expressions with >1 genus"); + } + c = x; + baseClass = x; + } + else { + LOG.warn("Ignoring: "+x+" in "+c); + } + } + } + else if (c instanceof OWLObjectSomeValuesFrom) { + rels.add((OWLObjectSomeValuesFrom) c); + c = model.getOWLDataFactory().getOWLThing(); + baseClass = model.getOWLDataFactory().getOWLThing(); + } + else { + LOG.warn("Using unhandled class expression: "+c); + baseClass = c; + } + + generatedIndividual = generateBaseIndividual(c); + LOG.debug(" I:"+generatedIndividual); + + if (incomingProperty != null) { + addTriple(incomingSource, incomingProperty, generatedIndividual); + } + + + rels.addAll(getExistentialRelationships(generatedIndividual)); + // The sorting makes the traversal of the graph deterministic + // Handles the different sort order of sets in Java 8 + List sortedRels = new ArrayList(rels); + Collections.sort(sortedRels); + for (OWLObjectSomeValuesFrom rel : sortedRels) { + + OWLClassExpression jType = deepen(rel.getFiller(), rel.getProperty(), c); + + boolean isExcluded = false; + if (directExclusionSet != null) { + if (directExclusionSet.contains(jType)) { + isExcluded = true; + } + } + if (isExcluded) { + continue; + } + if (exclusionSet != null) { + for (OWLClass testC : exclusionSet) { + if (model.getReasoner().getSuperClasses(jType, false).getFlattened().contains(testC)) { + isExcluded = true; + break; + } + } + } + if (isExcluded) { + continue; + } + if (inclusionSet != null) { + isExcluded = true; + for (OWLClass testC : inclusionSet) { + if (model.getReasoner().getSuperClasses(jType, false).getFlattened().contains(testC)) { + isExcluded = false; + break; + } + + + } + } + if (isExcluded) { + continue; + } + OWLNamedIndividual targetIndividual = + generateNecessaryIndividualsImpl(jType, generatedIndividual, rel.getProperty()); + } + return generatedIndividual; + } + + /** + * Generates a graph of ABox axioms rooted at proto(c), where proto(c) is + * the prototype individual of class c. + * + * For example, if c SubClassOf finger, SubClassOf part_of some some hand, then + * generate a finger individual, a hand individual, connect them via part_of + * + * + * @param c + * @return prototype individual of type c + */ + public OWLNamedIndividual generateNecessaryIndividuals(OWLClassExpression c) { + return generateNecessaryIndividuals(c, true, true); + } + + + /** + * Calls {@link #generateNecessaryIndividuals(OWLClassExpression)}, and if isCollapse is set, + * will call {@link #collapseIndividuals()} + * + * @param c + * @param isCollapse + * @return individual + */ + public OWLNamedIndividual generateNecessaryIndividuals(OWLClassExpression c, boolean isCollapse) { + return generateNecessaryIndividuals(c, isCollapse, true); + } + + /** + * Calls {@link #generateNecessaryIndividuals(OWLClassExpression)} + * + *
  • if isCollapse is set, will call {@link #collapseIndividuals()} + *
  • if isTransitivelyReduce is set, will call {@link #performTransitiveReduction()} + * @param c + * @param isCollapse + * @param isTransitivelyReduce + * @return individual + */ + public OWLNamedIndividual generateNecessaryIndividuals(OWLClassExpression c, boolean isCollapse, + boolean isTransitivelyReduce) { + OWLNamedIndividual ind = generateNecessaryIndividualsImpl(c, null, null); + if (isCollapse) { + collapseIndividuals(); + } + if (isTransitivelyReduce) { + performTransitiveReduction(); + } + return ind; + } + + + /** + * Adds a prototypical individual to the abox. + * + * fills in prototypeIndividualMap, unless c satisfies {@link #isNeverMerge} + * + * @param c + * @return individual + */ + private OWLNamedIndividual generateBaseIndividual(OWLClassExpression c) { + IRI iri; + boolean isUniq = true; + if (c instanceof OWLClass && !this.isNeverMerge((OWLClass)c)) { + iri = IRI.create(((OWLClass) c).getIRI().toString()+getContextualizingSuffix()); + } + else { + iri = IRI.create(model.getAboxOntology().getOntologyID().getOntologyIRI()+"-"+UUID.randomUUID()); + isUniq = false; + } + OWLNamedIndividual ind = model.getOWLDataFactory().getOWLNamedIndividual(iri); + model.addAxiom(model.getOWLDataFactory().getOWLClassAssertionAxiom(c, ind)); + if (isUniq) { + prototypeIndividualMap.put((OWLClass) c, ind); + } + + return ind; + } + + public void generateAllNecessaryIndividuals() { + generateAllNecessaryIndividuals(false, false); + } + public void generateAllNecessaryIndividuals(boolean isCollapse, boolean isReduce) { + OWLEntityRenamer renamer = new OWLEntityRenamer(model.getOWLOntologyManager(), + Collections.singleton(model.getAboxOntology())); + List chgs = new ArrayList(); + for (OWLNamedIndividual ind : model.getTboxOntology().getIndividualsInSignature(true)) { + for (OWLClassExpression cx : ind.getTypes(model.getTboxOntology())) { + OWLNamedIndividual j = + generateNecessaryIndividuals(cx, isCollapse, isReduce); + chgs.addAll(renamer.changeIRI(j.getIRI(), ind.getIRI())); + //m.addAxiom(m.getOWLDataFactory().getOWLO, axiom) + } + } + LOG.debug("Changes = "+chgs.size()); + model.getOWLOntologyManager().applyChanges(chgs); + } + + /** + * attempt to deepen a class expression based on properties the individual holds. + * + * E.g. if i=hand and j=digit, and p=has_part, then + * we can reason that (digit and inverseOf(has_part) some hand) is a subclass + * of or equivalent to 'finger' + * + * This may typically require hermit + * + * @param jType + * @param invProperty + * @param incoming + * @return expression + */ + private OWLClassExpression deepen(OWLClassExpression jType, + OWLObjectPropertyExpression invProperty, OWLClassExpression incoming) { + OWLObjectPropertyExpression ipe = model.getOWLDataFactory().getOWLObjectInverseOf(invProperty); + Set invProps = getInverseObjectProperties(invProperty); + if (invProps.size() > 0) { + // it should not matter which one is selected, unless + // ontology has equiv properties and reasoner does not handle equiv props + // (Elk is fine - http://code.google.com/p/elk-reasoner/wiki/OwlFeatures) + ipe = invProps.iterator().next(); + } + OWLObjectIntersectionOf jExpr = model.getOWLDataFactory().getOWLObjectIntersectionOf( + jType, + model.getOWLDataFactory().getOWLObjectSomeValuesFrom( + ipe, + incoming) + ); + Set deeperClasses = model.getReasoner().getSuperClasses( + jExpr, + true).getFlattened(); + deeperClasses.addAll(model.getReasoner().getEquivalentClasses(jExpr).getEntities()); + for (OWLClass dc: deeperClasses) { + // don't include artificial + if (model.isQueryClass(dc)) + continue; + //LOG.debug(fo(" Deepen_candidate="+dc); + if (model.getReasoner().getSuperClasses(dc, false).getFlattened().contains(jType)) { + LOG.debug(" DEEPENED_TO="+dc); + // must be more specific that original choice + jType = dc; // TODO - check for >1 + } + } + return jType; + } + + + /** + * generation of prototypes often generate multiple individuals where there + * should in fact be one. E.g. + * + * 
    +	 * hand SubClassOf: autopod, part_of some forelimb
+	 * autopod SubClassOf: part_of some limb
+	 *
    + * + * here the generated instance graph is + * + * 
    +	 * hand-1 part_of forelimb-1
+	 *        part_of some limb-1
+	 *
    + * + * There is nothing in the OWL to state that these are the same individual, but + * we make that assumption here. + * + */ + public void collapseIndividuals() { + LOG.debug("Collapsing..."); + + // map between generic prototypes and specific + // prototypes - at the end, if this 1:1, + // the generic will be mapped into the specific. + // e.g. limb(limb-proto) -> forelimb(limb-proto) + Map mergeMap = + new HashMap(); + + // set of prototypes that are possibly ambiguous; + // e.g. limb -> {forelimb, hindlimb} + Set hasMultipleCandidates = new HashSet(); + + // iterate through all classes that have prototypes + Collection individuals = this.getGeneratedIndividuals(); + for (OWLNamedIndividual targetSpecificPrototype : individuals) { + // e.g. forelimb (target) + //LOG.debug(" testing SPECIFIC target prototype (to be merged into): "+targetSpecificPrototype); + + // e.g. limb (candidate merge: limb -> forelimb) + Set mergeClassCandidates = + model.getReasoner().getTypes(targetSpecificPrototype, false).getFlattened(); + + // all types for target prototype + Set targetInferredTypes = model.getReasoner().getTypes(targetSpecificPrototype, false). + getFlattened(); + + for (OWLClass sourceGenericClass : mergeClassCandidates) { + + // only classes that correspond to a prototype + if (!prototypeIndividualMap.containsKey(sourceGenericClass)) + continue; + + OWLNamedIndividual sourceGenericPrototype = + prototypeIndividualMap.get(sourceGenericClass); + + if (sourceGenericPrototype.equals(targetSpecificPrototype)) + continue; + + // never merge owl:Thing, etc + if (isNeverMerge(sourceGenericClass)) + continue; + + // avoid splits: check if a merge has already been proposed for the source + if (mergeMap.containsKey(sourceGenericPrototype)) { + + //LOG.debug(" considering pushing down: "+sourceGenericPrototype); + + // Test if generic class already slated for merging; + // e.g. src = limb, tgt = forelimb, existing = hindlimb + OWLNamedIndividual existingTargetPrototype = + mergeMap.get(sourceGenericPrototype); + //LOG.debug(" existingTgt = "+existingTargetPrototype); + + Set existingInferredTypes = + model.getReasoner().getTypes(existingTargetPrototype, false).getFlattened(); + + // overwrite existing entity if more specific. + // src=forelimb, existing=limb, tgt=left_forelimb + // TODO? this: src = limb, tgt = left_forelimb, existing=forelimb + if (targetInferredTypes.containsAll(existingInferredTypes)) { + // overwrite with target, as target is more specific + mergeMap.put(sourceGenericPrototype, targetSpecificPrototype); + LOG.debug(" overwriting existing target "+existingTargetPrototype+" ==> "+targetSpecificPrototype); + } + else if (existingInferredTypes.containsAll(targetInferredTypes)) { + // keep existing, as existing is more specific + LOG.debug(" keeping existing target "+existingTargetPrototype+", which is more specific than "+targetSpecificPrototype); + } + else { + // this blocks the merge of s + Set uniqueToTarget = new HashSet(targetInferredTypes); + uniqueToTarget.removeAll(existingInferredTypes); + LOG.debug(" DUAL TARGETS "+sourceGenericPrototype+ " ==> { "+existingTargetPrototype+" ==OR== "+targetSpecificPrototype+" }"); + hasMultipleCandidates.add(sourceGenericPrototype); + } + } + else { + mergeMap.put(sourceGenericPrototype, targetSpecificPrototype); + } + } + } + + // perform merge + Set staleClasses = new HashSet(); + + // TODO - a more elegant way to do this is to first to start without assumptions of individual + // distinctness or identity, incrementally added sameAs axioms (based on heuristics and user params) + // testing for inconsistency with each step. + // as a final step all sameAs axioms could be merged using the OER + OWLEntityRenamer renamer = new OWLEntityRenamer(model.getAboxOntology().getOWLOntologyManager(), + Collections.singleton(model.getAboxOntology())); + for (OWLNamedIndividual sourceIndividual : mergeMap.keySet()) { + OWLNamedIndividual targetIndividual = mergeMap.get(sourceIndividual); + + LOG.debug(" ?collapsing "+sourceIndividual+ " -> "+targetIndividual); + if (hasMultipleCandidates.contains(sourceIndividual)) { + LOG.debug(" **multi-candidate; skipping"); + continue; + } + LOG.debug(" ACTUALLY collapsing "+sourceIndividual+ " -> "+targetIndividual); + for (OWLClass c: prototypeIndividualMap.keySet()) { + if (prototypeIndividualMap.get(c).equals(sourceIndividual)) { + staleClasses.add(c); + } + } + model.applyChanges(renamer.changeIRI(sourceIndividual.getIRI(), + targetIndividual.getIRI())); + } + + if (this.isRemoveAmbiguousIndividuals) { + for (OWLNamedIndividual i : hasMultipleCandidates) { + for (OWLClass c: prototypeIndividualMap.keySet()) { + if (prototypeIndividualMap.get(c).equals(i)) { + staleClasses.add(c); + } + } + } + Set rmAxioms = new HashSet(); + for (OWLAxiom ax : model.getAboxOntology().getAxioms()) { + Set inds = ax.getIndividualsInSignature(); + inds.retainAll(hasMultipleCandidates); + if (inds.size() > 0) { + LOG.debug("REMOVING AMBIGUOUS INDIVIDUAL:"+ax); + rmAxioms.add(ax); + } + } + model.getAboxOntology().getOWLOntologyManager().removeAxioms(model.getAboxOntology(), rmAxioms); + } + + for (OWLClass c : staleClasses) + prototypeIndividualMap.remove(c); + + } + + /** + * Moves all axioms about src to tgt + * + * @param src + * @param tgt + * @return true if success (currently always true) + */ + protected boolean mergeInto(OWLNamedIndividual src, OWLNamedIndividual tgt) { + if (src.equals(tgt)) + return true; + LOG.debug("Merging "+src+" into "+tgt); + OWLEntityRenamer renamer = new OWLEntityRenamer(model.getAboxOntology().getOWLOntologyManager(), + Collections.singleton(model.getAboxOntology())); + model.applyChanges(renamer.changeIRI(src.getIRI(), + tgt.getIRI())); + return true; + } + + private boolean isNeverMerge(OWLClass c) { + if (c.equals(model.getOWLDataFactory().getOWLNothing())) + return true; + // TODO - customize + if (isStrict) + return true; + return false; + } + + /** + * calls {@link #anonymizeIndividual(OWLNamedIndividual)} + * + * @param c + */ + public void anonymizeIndividualsNotIn(OWLClass c) { + anonymizeIndividualsNotIn(Collections.singleton(c)); + } + + /** + * calls {@link #anonymizeIndividual(OWLNamedIndividual)} on any individual not in one of c1, ..., cn + * + * @param cs + */ + public void anonymizeIndividualsNotIn(Set cs) { + Set inds = new HashSet(); + for (OWLNamedIndividual ind : model.getAboxOntology().getIndividualsInSignature(true)) { + Set sups = model.getReasoner().getTypes(ind, false).getFlattened(); + sups.retainAll(cs); + if (sups.size() == 0) { + LOG.debug("SCHEDULING: "+ind); + inds.add(ind); + } + } + anonymizeIndividuals(inds); + } + + + /** + * calls {@link #anonymizeIndividual(OWLNamedIndividual)} on each member of the set + * @param inds + */ + public void anonymizeIndividuals(Set inds) { + for (OWLNamedIndividual ind : inds) { + anonymizeIndividual(ind); + } + } + + /** + * Remove all mention of ind, but retain equivalence in the ontology by replacing all OPEs that + * reference ind with an existential axiom. + * + * E.g. if: p1 occurs_in c1, c1 Type C and we anonymize c1, then we add an axiom p1 Type occurs_in some C + * + * @param ind + */ + private void anonymizeIndividual(OWLNamedIndividual ind) { + Set types = model.getReasoner().getTypes(ind, true).getFlattened(); + LOG.debug("ANONYMIZING:"+ind); + // replace incoming with class expressions + Set refAxioms = ind.getReferencingAxioms(model.getAboxOntology(), false); + for (OWLAxiom ax : refAxioms) { + if (ax instanceof OWLObjectPropertyAssertionAxiom) { + OWLObjectPropertyAssertionAxiom pa = (OWLObjectPropertyAssertionAxiom)ax; + for (OWLClass type : types) { + if (type.equals(model.getOWLDataFactory().getOWLNothing())) + continue; + OWLClassExpression classExpression = + model.getOWLDataFactory().getOWLObjectSomeValuesFrom(pa.getProperty(), type); + OWLClassAssertionAxiom newAx = + model.getOWLDataFactory().getOWLClassAssertionAxiom(classExpression, pa.getSubject()); + model.addAxiom(newAx); + } + } + } + // remove incoming + model.getOWLOntologyManager().removeAxioms(model.getAboxOntology(), refAxioms); + + // remove outgoing + model.getOWLOntologyManager().removeAxioms(model.getAboxOntology(), model.getAboxOntology().getAxioms(ind)); + + // remove delcarations + model.getOWLOntologyManager().removeAxiom(model.getAboxOntology(), model.getOWLDataFactory().getOWLDeclarationAxiom(ind)); + } + + /** + * Generate a class expression CE such that i instantiates CE, and there + * is no other CE' such that CE' is more specific that CE, and i instantiates CE', + * and CE' is guaranteed to subsume i even if additional facts are added to the ABox + * or TBox + * + * This is equivalent to (TODO: proof) the class expression formed by walking + * the ABox graph starting from i, creating an existential restriction for each edge + * and intersecting it with the type of each node. + * + * For more sophisticated algorithms, see the DL-learner package, which will + * abduce over multiple instances. + * + * Alternatively we should start with the maximal path spanning all nodes - TODO + * http://en.wikipedia.org/wiki/Widest_path_problem + * (here it is actually the maximal widest path for all possible sink nodes) + * + * @param i + * @return expression + */ + public OWLClassExpression getMostSpecificClassExpression(OWLNamedIndividual i) { + return getMostSpecificClassExpression(i, new HashSet(), null); + } + public OWLClassExpression getMostSpecificClassExpression( + OWLNamedIndividual i, List propertySet) { + return getMostSpecificClassExpression(i, new HashSet(), propertySet); + } + public OWLClassExpression getMostSpecificClassExpression(OWLNamedIndividual i, + Set visited, + List propertySet) { + visited.add(i); + LOG.debug("i="+i); + Set elements = new HashSet(); + model.getReasoner().flush(); + for (OWLClass typeClass : model.getReasoner().getTypes(i, true).getFlattened()) { + LOG.debug(" t="+typeClass); + if (model.isQueryClass(typeClass)) + continue; + elements.add(typeClass); + } + // supplement this with asserted class expression types + for (OWLClassExpression x : i.getTypes(model.getAboxOntology().getImportsClosure())) { + if (x.isAnonymous()) { + Set xDescs = model.getReasoner().getSubClasses(x, false).getFlattened(); + xDescs.retainAll(elements); + if (xDescs.size() == 0) { + elements.add(x); + } + } + } + if (propertySet == null || propertySet.size() == 0) { + propertySet = new ArrayList(); + for (OWLObjectProperty p : model.getAboxOntology().getObjectPropertiesInSignature(true)) { + propertySet.add(p); + } + } + + for (OWLObjectProperty p : propertySet) { + LOG.debug(" p="+p); + + // TODO - use core method + Set invProps = getInverseObjectProperties(p); + + + for (OWLOntology ont : model.getAboxOntology().getImportsClosure()) { + Set js = new HashSet(i.getObjectPropertyValues(p, ont)); + // todo - make this more efficient + if (invProps.size() > 0) { + for (OWLObjectPropertyExpression invProp : invProps) { + LOG.debug(" invP="+invProp); + for (OWLIndividual j : model.getAboxOntology().getIndividualsInSignature(true)) { + if (j.getObjectPropertyValues((OWLObjectPropertyExpression) invProp, ont).contains(i)) { + js.add(j); + } + } + } + } + for (OWLIndividual j : js) { + LOG.debug(" j="+j); + + // note that as this method is recursive, it is possible to end up with + // multiple paths. this could be resolved by rewriting to perform BF-search, + // or by making the visitor set object-wide (should be synchronized) + if (visited.contains(j)) { + // TODO - provide an option to include back the original class + // for example, if we have a cycle of carbon atoms. + // only do this for non-trivial cycles + continue; + } + if (j instanceof OWLNamedIndividual) { + OWLClassExpression jce = getMostSpecificClassExpression((OWLNamedIndividual) j, visited, propertySet); + LOG.debug(" jce="+jce); + elements.add( + model.getOWLDataFactory().getOWLObjectSomeValuesFrom(p, jce) + ); + } + else { + LOG.warn("I wasn't expecting anonymous individuals in the abox: "+j); + } + } + } + } + return model.getOWLDataFactory().getOWLObjectIntersectionOf(elements); + } + + // UTIL + + protected Map getQueryClassMap() { + return model.getQueryClassMap(isPrecomputePropertyClassCombinations); + } + + private Set getInverseObjectProperties( + OWLObjectPropertyExpression property) { + Set invProps = new HashSet(); + for (OWLOntology ont : model.getAboxOntology().getImportsClosure()) { + invProps.addAll(property.getInverses(ont)); + } + return invProps; + } + /** + * Given an individual i, return a set of existential restrictions , + * where i instantiates P some C. + * + * The implementation for this method depends on the pre-materialization of a + * Query Ontology containing

    combinations. + * + * Redundant expressions are filtered out + * + * @param ind + * @return set of existential restrictions + */ + protected Set getExistentialRelationships(OWLNamedIndividual ind) { + //LOG.debug("Querying: "+c); + Map queryClassMap = getQueryClassMap(); + Set results = new HashSet(); + + model.getReasoner().flush(); + + // all supers (direct and indirect) + Set supers = model.getReasoner().getTypes(ind, false).getFlattened(); + LOG.debug("Supers for "+ind+" is "+supers.size()); + + // we only case about expressions in the query ontology, which should have + // all expressions required + supers.retainAll(queryClassMap.keySet()); + LOG.debug("Supers in QMAP for "+ind+" is "+supers.size()); + + // use only classes that are non-redundant (within QSet) + Set nrSet = new HashSet(supers); + for (OWLClass s : supers) { + nrSet.removeAll(model.getReasoner().getSuperClasses(s, false).getFlattened()); + } + + // map from materialized class to original expression + for (OWLClass s : nrSet) { + //LOG.debug(" SUP:"+s); + OWLClassExpression x = queryClassMap.get(s); + if (x instanceof OWLObjectSomeValuesFrom) { + //LOG.debug(" Result:"+x); + results.add((OWLObjectSomeValuesFrom)x); + } + else { + LOG.warn("Skipping: "+x+" (future versions may handle this)"); + } + } + return results; + } + + protected Set getExistentialRelationships(OWLClassExpression c) { + return getExistentialRelationships(c, true); + } + protected Set getExistentialRelationships(OWLClassExpression c, boolean isDirect) { + //LOG.debug("Querying: "+c); + Map queryClassMap = getQueryClassMap(); + Set results = new HashSet(); + + model.getReasoner().flush(); + + // all supers (direct and indirect) + Set supers = model.getReasoner().getSuperClasses(c, false).getFlattened(); + supers.addAll(model.getReasoner().getEquivalentClasses(c).getEntities()); + + // we only case about expressions in the query ontology, which should have + // all expressions required + supers.retainAll(queryClassMap.keySet()); + + // use only classes that are non-redundant (within QSet) + Set nrSet = new HashSet(supers); + if (isDirect) { + for (OWLClass s : supers) { + nrSet.removeAll(model.getReasoner().getSuperClasses(s, false).getFlattened()); + } + } + + // map from materialized class to original expression + for (OWLClass s : nrSet) { + //LOG.debug(" SUP:"+s); + OWLClassExpression x = queryClassMap.get(s); + if (x instanceof OWLObjectSomeValuesFrom) { + //LOG.debug(" Result:"+x); + results.add((OWLObjectSomeValuesFrom)x); + } + else { + LOG.warn("Skipping: "+x+" (future versions may handle this)"); + } + } + return results; + } + + public Set getSuperClassExpressions(OWLClassExpression x, boolean isDirect) { + Set results = new HashSet(getExistentialRelationships(x, isDirect)); + Set supers = new HashSet(model.getReasoner().getSuperClasses(x, false).getFlattened()); + supers.removeAll(model.getQueryClasses()); + Set nrSet = new HashSet(supers); + if (isDirect) { + for (OWLClass s : supers) { + nrSet.removeAll(model.getReasoner().getSuperClasses(s, false).getFlattened()); + } + } + results.addAll(nrSet); + return results; + } + + // ABOX ONTOLOGY MANAGEMENT + + + protected void addTriple(OWLNamedIndividual sourceIndividual, + OWLObjectPropertyExpression property, + OWLNamedIndividual targetIndividual) { + Set axioms = + getFactAxioms(sourceIndividual, property, targetIndividual, isAssertInverses()); + model.addAxioms(axioms); + } + + private Set getFactAxioms(OWLNamedIndividual sourceIndividual, + OWLObjectPropertyExpression property, + OWLNamedIndividual targetIndividual, + boolean isIncludeInverses) { + Set axioms = + new HashSet(); + axioms.add(model.getOWLDataFactory().getOWLObjectPropertyAssertionAxiom(property, + sourceIndividual, targetIndividual)); + if (isIncludeInverses) { + for (OWLObjectPropertyExpression ip : this.getInverseObjectProperties(property)) { + //LOG.debug("Including inverse: "+ip+" "+targetIndividual+" "+sourceIndividual); + axioms.add(model.getOWLDataFactory().getOWLObjectPropertyAssertionAxiom(ip, + targetIndividual, + sourceIndividual + )); + + } + } + return axioms; + } + + + /** + * Extract a module from tboxOntology using aboxOntology as seed. + * As a side-effect, will remove abox imports tbox axiom, and add extracted axioms + * to abox. + * + * + * @see SyntacticLocalityModuleExtractor + */ + public void extractModule() { + SyntacticLocalityModuleExtractor sme = new SyntacticLocalityModuleExtractor(model.getOWLOntologyManager(), + model.getAboxOntology(), + ModuleType.BOT); + + Set objs = new HashSet(); + objs.addAll( model.getAboxOntology().getObjectPropertiesInSignature() ); + objs.addAll( model.getAboxOntology().getClassesInSignature() ); + + + Set modAxioms = sme.extract(objs); + for (OWLImportsDeclaration oid : model.getAboxOntology().getImportsDeclarations()) { + model.getOWLOntologyManager().applyChange(new RemoveImport(model.getAboxOntology(), oid)); + } + model.getOWLOntologyManager().addAxioms(model.getAboxOntology(), modAxioms); + } + + /** + * Motivation: + * + * After generation, we may be left with axioms: + * 

    +	 * OPE(P X Y)
+	 * OPE(P' Y X)
+	 * InverseProperties(P P')
+	 *
    + * + * This is useful for reasoning with inverse-unaware reasoners, + * but is otherwise redundant and can clutter displays. + * + * An alternate scenario is where we have a mixture of P and P' + * non-redundant assertions, and wish to choose one direction + * as the standard. + * + * Calling normalizeDirections(P) will remove OPE(P' Y X) in the above + * if OPE(P X Y) is not present, this will be added. + * + * @param p + */ + public void normalizeDirections(OWLObjectPropertyExpression p) { + LOG.debug("Normalizing: "+p); + Set invProps = + p.getInverses(model.getAboxOntology().getImportsClosure()); + LOG.debug("Inverse props: "+invProps); + Set rmAxioms = new HashSet(); + Set newAxioms = new HashSet(); + for (OWLObjectPropertyAssertionAxiom opa : + model.getAboxOntology().getAxioms(AxiomType.OBJECT_PROPERTY_ASSERTION)) { + if (invProps.contains(opa.getProperty())) { + LOG.debug(" FLIPPING:"+opa); + rmAxioms.add(opa); + newAxioms.add(model.getOWLDataFactory().getOWLObjectPropertyAssertionAxiom(p, + opa.getObject(), opa.getSubject())); + + } + } + model.getAboxOntology().getOWLOntologyManager().addAxioms(model.getAboxOntology(), newAxioms); + model.getAboxOntology().getOWLOntologyManager().removeAxioms(model.getAboxOntology(), rmAxioms); + } + + public void performTransitiveReduction() { + for (OWLObjectProperty p : model.getAboxOntology().getObjectPropertiesInSignature(true)) { + if (p.isTransitive(model.getAboxOntology().getImportsClosure())) { + performTransitiveReduction(p); + } + } + } + + /** + * TODO - use reasoner if DL reasoner available + * (currently Elk 0.4.x will not perform OPE inferences) + * + * Limitations: + * does not use + * - subPropertyOf + * - equivalentProperties + * - subPropertyChain + * @param p + */ + public void performTransitiveReduction(OWLObjectPropertyExpression p) { + Set rmAxioms = new HashSet(); + for (OWLNamedIndividual i : model.getAboxOntology().getIndividualsInSignature()) { + if (hasCycle(i, p)) { + if (LOG.isDebugEnabled()) { + LOG.debug("Property "+p+" has cyles from "+i+" -- no transitive reductions"); + } + continue; + } + + Set redundant = new HashSet(); + Set js = getIndividualsInProperPath(i, p); + //LOG.debug("PATH("+i+") ==> "+js); + for (OWLIndividual j : js) { + redundant.addAll(getIndividualsInProperPath(j, p)); + } + for (OWLIndividual j : redundant) { + // TODO - check for cycles (can happen in pathological scenarios) + if (j instanceof OWLNamedIndividual) { + //LOG.debug("redundant: OPE("+p+" "+i+" "+j+"); PATH(i) = "+js); + rmAxioms.addAll(this.getFactAxioms(i, p, (OWLNamedIndividual) j, true)); + } + else { + LOG.warn("Ignoring redundant link to anon individual: "+i+" -> "+j+" over "+p); + } + } + } + if (LOG.isDebugEnabled()) { + LOG.debug("removing redundant axioms, #="+rmAxioms.size()); + } + model.getAboxOntology().getOWLOntologyManager().removeAxioms(model.getAboxOntology(), rmAxioms); + } + + public boolean hasCycle(OWLIndividual i, OWLObjectPropertyExpression p) { + return hasCycle(i, p, new HashSet()); + } + public boolean hasCycle(OWLIndividual i, OWLObjectPropertyExpression p, + Set visited) { + if (visited.contains(i)) { + return true; + } + // make a copy + Set v2 = new HashSet(visited); + v2.add(i); + Set nextSet = + getDirectOutgoingIndividuals(i, Collections.singleton(p)); + + for (OWLIndividual j : nextSet) { + if (hasCycle(j, p, v2)) { + return true; + } + } + return false; + } + + public Set getIndividualsInProperPath(OWLIndividual i, OWLObjectPropertyExpression p) { + return getIndividualsInProperPath(i, Collections.singleton(p)); + } + + public Set getIndividualsInProperPath(OWLIndividual i, Set ps) { + // TODO - use reasoner if not hermit + Set results = new HashSet(); + Set visited = new HashSet(); + Stack stack = new Stack(); + stack.add(i); + while (!stack.isEmpty()) { + OWLIndividual x = stack.pop(); + Set nextSet = getDirectOutgoingIndividuals(x, ps); + nextSet.removeAll(visited); + stack.addAll(nextSet); + results.addAll(nextSet); + visited.addAll(nextSet); + } + return results; + } + + private Set getDirectOutgoingIndividuals(OWLIndividual i, + Set ps) { + // TODO - subproperties + Set results = new HashSet(); + + for (OWLObjectPropertyExpression p : ps) { + results.addAll(i.getObjectPropertyValues(p, model.getAboxOntology())); + for (OWLObjectPropertyExpression invProp : getInverseObjectProperties(p)) { + // todo - make this more efficient + //LOG.debug(" invP="+invProp); + for (OWLIndividual j : model.getAboxOntology().getIndividualsInSignature(true)) { + if (j.getObjectPropertyValues((OWLObjectPropertyExpression) invProp, model.getAboxOntology()).contains(i)) { + results.add(j); + } + } + } + } + return results; + } + +} \ No newline at end of file diff --git a/minerva-core/src/main/java/org/geneontology/minerva/util/ReverseChangeGenerator.java b/minerva-core/src/main/java/org/geneontology/minerva/util/ReverseChangeGenerator.java new file mode 100644 index 00000000..0f0a3f03 --- /dev/null +++ b/minerva-core/src/main/java/org/geneontology/minerva/util/ReverseChangeGenerator.java @@ -0,0 +1,72 @@ +package org.geneontology.minerva.util; + +import java.util.LinkedList; +import java.util.List; + +import org.semanticweb.owlapi.model.AddAxiom; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.AddOntologyAnnotation; +import org.semanticweb.owlapi.model.OWLOntologyChange; +import org.semanticweb.owlapi.model.OWLOntologyChangeVisitorEx; +import org.semanticweb.owlapi.model.RemoveAxiom; +import org.semanticweb.owlapi.model.RemoveImport; +import org.semanticweb.owlapi.model.RemoveOntologyAnnotation; +import org.semanticweb.owlapi.model.SetOntologyID; + +/** + * Create the reverse of an {@link OWLOntologyChange}. + */ +public class ReverseChangeGenerator implements OWLOntologyChangeVisitorEx { + + public static final ReverseChangeGenerator INSTANCE = new ReverseChangeGenerator(); + + private ReverseChangeGenerator() { + // only one instance + } + + public OWLOntologyChange visit(AddAxiom change) { + return new RemoveAxiom(change.getOntology(), change.getAxiom()); + } + + + public OWLOntologyChange visit(RemoveAxiom change) { + return new AddAxiom(change.getOntology(), change.getAxiom()); + } + + + public OWLOntologyChange visit(SetOntologyID change) { + return new SetOntologyID(change.getOntology(), change.getOriginalOntologyID()); + } + + + public OWLOntologyChange visit(AddImport addImport) { + return new RemoveImport(addImport.getOntology(), addImport.getImportDeclaration()); + } + + + public OWLOntologyChange visit(RemoveImport removeImport) { + return new AddImport(removeImport.getOntology(), removeImport.getImportDeclaration()); + } + + + public OWLOntologyChange visit(AddOntologyAnnotation addOntologyAnnotation) { + return new RemoveOntologyAnnotation(addOntologyAnnotation.getOntology(), addOntologyAnnotation.getAnnotation()); + } + + + public OWLOntologyChange visit(RemoveOntologyAnnotation removeOntologyAnnotation) { + return new AddOntologyAnnotation(removeOntologyAnnotation.getOntology(), removeOntologyAnnotation.getAnnotation()); + } + + public static List invertChanges(List originalChanges) { + final LinkedList invertedChanges = new LinkedList(); + for (OWLOntologyChange originalChange : originalChanges) { + OWLOntologyChange invertedChange = originalChange.accept(ReverseChangeGenerator.INSTANCE); + invertedChanges.push(invertedChange); + } + if (invertedChanges.isEmpty()) { + return null; + } + return invertedChanges; + } +} diff --git a/minerva-core/src/test/java/org/geneontology/minerva/CoreMolecularModelManagerTest.java b/minerva-core/src/test/java/org/geneontology/minerva/CoreMolecularModelManagerTest.java new file mode 100644 index 00000000..e037c93e --- /dev/null +++ b/minerva-core/src/test/java/org/geneontology/minerva/CoreMolecularModelManagerTest.java @@ -0,0 +1,76 @@ +package org.geneontology.minerva; + +import static org.junit.Assert.*; + +import java.util.HashSet; +import java.util.Set; + +import org.geneontology.minerva.CoreMolecularModelManager; +import org.junit.Test; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyManager; + +public class CoreMolecularModelManagerTest { + + @Test + public void testUpdateImports() throws Exception { + final OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + final OWLDataFactory f = m.getOWLDataFactory(); + + // setup other import + final IRI other = IRI.generateDocumentIRI(); + m.createOntology(other); + + // setup obsolete + final IRI obs1 = IRI.generateDocumentIRI(); + final IRI obs2 = IRI.generateDocumentIRI(); + final IRI obs3 = IRI.generateDocumentIRI(); + final Set obsoletes = new HashSet(); + obsoletes.add(obs1); m.createOntology(obs1); + obsoletes.add(obs2); m.createOntology(obs2); + obsoletes.add(obs3); m.createOntology(obs3); + + // setup additional + final IRI add1 = IRI.generateDocumentIRI(); + m.createOntology(add1); + final IRI add2 = IRI.generateDocumentIRI(); + m.createOntology(add2); + final Set additional = new HashSet(); + additional.add(add1); + additional.add(add2); + + // setup tbox + final IRI tboxIRI = IRI.generateDocumentIRI(); + m.createOntology(tboxIRI); + + // setup abox + final OWLOntology abox = m.createOntology(IRI.generateDocumentIRI()); + // add initial imports to abox + m.applyChange(new AddImport(abox, f.getOWLImportsDeclaration(other))); + m.applyChange(new AddImport(abox, f.getOWLImportsDeclaration(obs1))); + m.applyChange(new AddImport(abox, f.getOWLImportsDeclaration(obs2))); + m.applyChange(new AddImport(abox, f.getOWLImportsDeclaration(obs3))); + + // update imports + CoreMolecularModelManager.updateImports(abox, tboxIRI, additional, obsoletes); + + // check the resulting imports + Set declarations = abox.getImportsDeclarations(); + assertEquals(4, declarations.size()); + Set declaredImports = new HashSet(); + for (OWLImportsDeclaration importsDeclaration : declarations) { + declaredImports.add(importsDeclaration.getIRI()); + } + assertEquals(4, declaredImports.size()); + assertTrue(declaredImports.contains(tboxIRI)); + assertTrue(declaredImports.contains(add1)); + assertTrue(declaredImports.contains(add1)); + assertTrue(declaredImports.contains(other)); + } + +} diff --git a/minerva-core/src/test/java/org/geneontology/minerva/MolecularModelManagerTest.java b/minerva-core/src/test/java/org/geneontology/minerva/MolecularModelManagerTest.java new file mode 100644 index 00000000..16071c6f --- /dev/null +++ b/minerva-core/src/test/java/org/geneontology/minerva/MolecularModelManagerTest.java @@ -0,0 +1,201 @@ +package org.geneontology.minerva; + +import static org.junit.Assert.*; + +import java.io.File; +import java.util.Collection; +import java.util.Set; + +import org.apache.commons.lang3.tuple.Pair; +import org.apache.log4j.Level; +import org.apache.log4j.Logger; +import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.junit.Rule; +import org.junit.Test; +import org.junit.rules.TemporaryFolder; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLNamedIndividual; + +import owltools.OWLToolsTestBasics; +import owltools.graph.OWLGraphWrapper; +import owltools.io.ParserWrapper; + +public class MolecularModelManagerTest extends OWLToolsTestBasics { + + // JUnit way of creating a temporary test folder + // will be deleted after the test has run, by JUnit. + @Rule + public TemporaryFolder folder = new TemporaryFolder(); + + MolecularModelManager mmm; + + static{ + Logger.getLogger("org.semanticweb.elk").setLevel(Level.ERROR); + } + + + private String renderJSON(String modelId) throws UnknownIdentifierException { + + ModelContainer model = mmm.getModel(modelId); + String js = MolecularModelJsonRenderer.renderToJson(model.getAboxOntology(), true, true); + return js; + } + + @Test + public void testDeleteIndividual() throws Exception { + ParserWrapper pw = new ParserWrapper(); + OWLGraphWrapper g = pw.parseToOWLGraph(getResourceIRIString("go-mgi-signaling-test.obo")); + + // GO:0038024 ! cargo receptor activity + // GO:0042803 ! protein homodimerization activity + + mmm = new MolecularModelManager(g); + + String modelId = mmm.generateBlankModel(null, null); + String i1 = mmm.createIndividual(modelId, "GO:0038024", null, null).getKey(); + + String i2 = mmm.createIndividual(modelId, "GO:0042803", null, null).getKey(); + + mmm.addPartOf(modelId, i1, i2, null); + + // String js = renderJSON(modelId); + // System.out.println("-------------"); + // System.out.println("INDS:" + js); + // + // System.out.println("-------------"); + + mmm.deleteIndividual(modelId, i2, null); + + // js = renderJSON(modelId); + // System.out.println("INDS:" + js); + // System.out.println("-------------"); + + Set individuals = mmm.getIndividuals(modelId); + assertEquals(1, individuals.size()); + } + + @Test + public void testExportImport() throws Exception { + ParserWrapper pw = new ParserWrapper(); + OWLGraphWrapper g = pw.parseToOWLGraph(getResourceIRIString("go-mgi-signaling-test.obo")); + + // GO:0038024 ! cargo receptor activity + // GO:0042803 ! protein homodimerization activity + // GO:0008233 ! peptidase activity + + mmm = new MolecularModelManager(g); + + final String modelId = mmm.generateBlankModel(null, null); + final Pair i1 = mmm.createIndividual(modelId, "GO:0038024", null, null); + + final Pair i2 = mmm.createIndividual(modelId, "GO:0042803", null, null); + + mmm.addPartOf(modelId, i1.getKey(), i2.getKey(), null); + + // export + final String modelContent = mmm.exportModel(modelId); + System.out.println("-------------------"); + System.out.println(modelContent); + System.out.println("-------------------"); + + // add an additional individual to model after export + final Pair i3 = mmm.createIndividual(modelId, "GO:0008233", null, null); + assertEquals(3, mmm.getIndividuals(modelId).size()); + + + // import + final String modelId2 = mmm.importModel(modelContent); + + assertEquals(modelId, modelId2); + Set loaded = mmm.getIndividuals(modelId2); + assertEquals(2, loaded.size()); + for (OWLNamedIndividual i : loaded) { + IRI iri = i.getIRI(); + // check that the model only contains the individuals created before the export + assertTrue(iri.equals(i1.getRight().getIRI()) || iri.equals(i2.getRight().getIRI())); + assertFalse(iri.equals(i3.getRight().getIRI())); + } + } + + @Test + public void testSaveModel() throws Exception { + final File saveFolder = folder.newFolder(); + final ParserWrapper pw1 = new ParserWrapper(); + OWLGraphWrapper g = pw1.parseToOWLGraph(getResourceIRIString("go-mgi-signaling-test.obo")); + + mmm = new MolecularModelManager(g); + mmm.setPathToOWLFiles(saveFolder.getCanonicalPath()); + + // GO:0038024 ! cargo receptor activity + // GO:0042803 ! protein homodimerization activity + // GO:0008233 ! peptidase activity + + final String modelId = mmm.generateBlankModel(null, null); + final Pair i1 = mmm.createIndividual(modelId, "GO:0038024", null, null); + + final Pair i2 = mmm.createIndividual(modelId, "GO:0042803", null, null); + + mmm.addPartOf(modelId, i1.getKey(), i2.getKey(), null); + + // save + mmm.saveModel(modelId, null, null); + + // add an additional individual to model after export + final Pair i3 = mmm.createIndividual(modelId, "GO:0008233", null, null); + assertEquals(3, mmm.getIndividuals(modelId).size()); + + // discard mmm + mmm.dispose(); + mmm = null; + + final ParserWrapper pw2 = new ParserWrapper(); + g = pw2.parseToOWLGraph(getResourceIRIString("go-mgi-signaling-test.obo")); + + + mmm = new MolecularModelManager(g); + mmm.setPathToOWLFiles(saveFolder.getCanonicalPath()); + + Set availableModelIds = mmm.getAvailableModelIds(); + assertTrue(availableModelIds.contains(modelId)); + + final ModelContainer model = mmm.getModel(modelId); + assertNotNull(model); + + Collection loaded = mmm.getIndividuals(modelId); + assertEquals(2, loaded.size()); + for (OWLNamedIndividual i : loaded) { + IRI iri = i.getIRI(); + // check that the model only contains the individuals created before the save + assertTrue(iri.equals(i1.getRight().getIRI()) || iri.equals(i2.getRight().getIRI())); + assertFalse(iri.equals(i3.getRight().getIRI())); + } + } + + @Test + public void testInferredType() throws Exception { + ParserWrapper pw = new ParserWrapper(); + OWLGraphWrapper g = pw.parseToOWLGraph(getResourceIRIString("go-mgi-signaling-test.obo")); + + // GO:0038024 ! cargo receptor activity + // GO:0042803 ! protein homodimerization activity + + mmm = new MolecularModelManager(g); + + String modelId = mmm.generateBlankModel(null, null); + String cc = mmm.createIndividual(modelId, "GO:0004872", null, null).getKey(); // receptor activity + + + String mit = mmm.createIndividual(modelId, "GO:0007166", null, null).getKey(); // cell surface receptor signaling pathway + + mmm.addPartOf(modelId, mit, cc, null); + + // we expect inference to be to: GO:0038023 signaling receptor activity + // See discussion here: https://github.com/kltm/go-mme/issues/3 + + System.out.println(renderJSON(modelId)); + //List> gson = mmm.getIndividualObjects(modelId); + //assertEquals(1, individuals.size()); + } + +} diff --git a/minerva-core/src/test/java/org/geneontology/minerva/UndoAwareMolecularModelManagerTest.java b/minerva-core/src/test/java/org/geneontology/minerva/UndoAwareMolecularModelManagerTest.java new file mode 100644 index 00000000..c7884195 --- /dev/null +++ b/minerva-core/src/test/java/org/geneontology/minerva/UndoAwareMolecularModelManagerTest.java @@ -0,0 +1,93 @@ +package org.geneontology.minerva; + +import static org.junit.Assert.*; + +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.UndoAwareMolecularModelManager; +import org.geneontology.minerva.UndoAwareMolecularModelManager.ChangeEvent; +import org.geneontology.minerva.UndoAwareMolecularModelManager.UndoMetadata; +import org.geneontology.minerva.json.JsonOwlIndividual; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.junit.AfterClass; +import org.junit.BeforeClass; +import org.junit.Test; +import org.semanticweb.owlapi.model.OWLNamedIndividual; + +import owltools.OWLToolsTestBasics; +import owltools.graph.OWLGraphWrapper; +import owltools.io.ParserWrapper; + +public class UndoAwareMolecularModelManagerTest extends OWLToolsTestBasics { + + static OWLGraphWrapper g = null; + static UndoAwareMolecularModelManager m3 = null; + + @BeforeClass + public static void beforeClass() throws Exception { + ParserWrapper pw = new ParserWrapper(); + g = pw.parseToOWLGraph(getResourceIRIString("go-mgi-signaling-test.obo")); + m3 = new UndoAwareMolecularModelManager(g); + } + + @AfterClass + public static void afterClass() throws Exception { + if (m3 != null) { + m3.dispose(); + } + } + + @Test + public void testUndoRedo() throws Exception { + String userId = "test-user-id"; + String modelId = m3.generateBlankModel(null, null); + // GO:0001158 ! enhancer sequence-specific DNA binding + Pair bindingId = m3.createIndividual(modelId, "GO:0001158", null, new UndoMetadata(userId)); + // BFO:0000066 GO:0005654 ! occurs_in nucleoplasm + m3.addType(modelId, bindingId.getKey(), "BFO:0000066", "GO:0005654", new UndoMetadata(userId)); + + ModelContainer model = m3.getModel(modelId); + MolecularModelJsonRenderer renderer = new MolecularModelJsonRenderer(model); + JsonOwlIndividual render1 = renderer.renderObject(bindingId.getRight()); + assertEquals(2, render1.type.length); + + // check event count + Pair,List> undoRedoEvents = m3.getUndoRedoEvents(modelId); + List undoEvents = undoRedoEvents.getLeft(); + List redoEvents = undoRedoEvents.getRight(); + assertEquals(0, redoEvents.size()); + assertEquals(2, undoEvents.size()); + + // undo + assertTrue(m3.undo(modelId, userId)); + + JsonOwlIndividual render2 = renderer.renderObject(bindingId.getRight()); + assertEquals(1, render2.type.length); + + // redo + assertTrue(m3.redo(modelId, userId)); + JsonOwlIndividual render3 = renderer.renderObject(bindingId.getRight()); + assertEquals(2, render3.type.length); + + // undo again + assertTrue(m3.undo(modelId, userId)); + JsonOwlIndividual render4 = renderer.renderObject(bindingId.getRight()); + assertEquals(1, render4.type.length); + + // add new type + // GO:0001664 ! G-protein coupled receptor binding + m3.addType(modelId, bindingId.getKey(), "GO:0001664", new UndoMetadata(userId)); + + // redo again, should fail + assertFalse(m3.redo(modelId, userId)); + } + + static void printToJson(Object obj) { + String json = MolecularModelJsonRenderer.renderToJson(obj, true); + System.out.println("---------"); + System.out.println(json); + System.out.println("---------"); + } + +} diff --git a/minerva-core/src/test/java/org/geneontology/minerva/json/MolecularModelJsonRendererTest.java b/minerva-core/src/test/java/org/geneontology/minerva/json/MolecularModelJsonRendererTest.java new file mode 100644 index 00000000..5be155be --- /dev/null +++ b/minerva-core/src/test/java/org/geneontology/minerva/json/MolecularModelJsonRendererTest.java @@ -0,0 +1,242 @@ +package org.geneontology.minerva.json; + +import static org.junit.Assert.*; + +import java.io.File; +import java.util.HashSet; +import java.util.Set; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; +import org.geneontology.minerva.json.JsonOwlIndividual; +import org.geneontology.minerva.json.JsonOwlObject; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.geneontology.minerva.json.JsonOwlObject.JsonOwlObjectType; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; +import org.junit.AfterClass; +import org.junit.BeforeClass; +import org.junit.Test; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyManager; + +import owltools.graph.OWLGraphWrapper; +import owltools.io.ParserWrapper; + +public class MolecularModelJsonRendererTest { + + private static OWLGraphWrapper g = null; + private static OWLOntologyManager m = null; + private static OWLDataFactory f = null; + + @BeforeClass + public static void setUpBeforeClass() throws Exception { + ParserWrapper pw = new ParserWrapper(); + File file = new File("src/test/resources/mgi-go.obo").getCanonicalFile(); + OWLOntology ont = pw.parseOWL(IRI.create(file)); + g = new OWLGraphWrapper(ont); + f = g.getDataFactory(); + m = g.getManager(); + } + + @AfterClass + public static void tearDownAfterClass() throws Exception { + IOUtils.closeQuietly(g); + } + + @Test + public void testSimpleClass() throws Exception { + testSimpleClassExpression(g.getOWLClassByIdentifier("GO:0000003"), "class"); + } + + @Test + public void testSimpleSVF() throws Exception { + OWLObjectSomeValuesFrom svf = f.getOWLObjectSomeValuesFrom(g.getOWLObjectPropertyByIdentifier("BFO:0000050"), g.getOWLClassByIdentifier("GO:0000003")); + testSimpleClassExpression(svf, "svf"); + } + + @Test + public void testSimpleUnion() throws Exception { + OWLObjectSomeValuesFrom svf = f.getOWLObjectSomeValuesFrom(g.getOWLObjectPropertyByIdentifier("BFO:0000050"), g.getOWLClassByIdentifier("GO:0000003")); + OWLClass cls = g.getOWLClassByIdentifier("GO:0000122"); + testSimpleClassExpression(f.getOWLObjectUnionOf(cls, svf), "union"); + } + + @Test + public void testSimpleIntersection() throws Exception { + OWLObjectSomeValuesFrom svf = f.getOWLObjectSomeValuesFrom(g.getOWLObjectPropertyByIdentifier("BFO:0000050"), g.getOWLClassByIdentifier("GO:0000003")); + OWLClass cls = g.getOWLClassByIdentifier("GO:0000122"); + testSimpleClassExpression(f.getOWLObjectIntersectionOf(cls, svf), "intersection"); + } + + @Test + public void testAnnotations() throws Exception { + // setup test model/ontology + OWLOntology o = m.createOntology(); + OWLImportsDeclaration importDeclaration = f.getOWLImportsDeclaration(g.getSourceOntology().getOntologyID().getOntologyIRI()); + m.applyChange(new AddImport(o, importDeclaration)); + + final IRI i1IRI = IRI.generateDocumentIRI(); + final OWLNamedIndividual ni1 = f.getOWLNamedIndividual(i1IRI); + // declare individual + m.addAxiom(o, f.getOWLDeclarationAxiom(ni1)); + // add annotations + m.addAxiom(o, f.getOWLAnnotationAssertionAxiom(i1IRI, + f.getOWLAnnotation(f.getOWLAnnotationProperty( + AnnotationShorthand.comment.getAnnotationProperty()), + f.getOWLLiteral("Comment 1")))); + m.addAxiom(o, f.getOWLAnnotationAssertionAxiom(i1IRI, + f.getOWLAnnotation(f.getOWLAnnotationProperty( + AnnotationShorthand.comment.getAnnotationProperty()), + f.getOWLLiteral("Comment 2")))); + // declare type + m.addAxiom(o, f.getOWLClassAssertionAxiom(g.getOWLClassByIdentifier("GO:0000003"), ni1)); + + MolecularModelJsonRenderer r = new MolecularModelJsonRenderer(o); + + JsonOwlIndividual jsonOwlIndividualOriginal = r.renderObject(ni1); + assertEquals(2, jsonOwlIndividualOriginal.annotations.length); + + String json = MolecularModelJsonRenderer.renderToJson(jsonOwlIndividualOriginal, true); + + JsonOwlIndividual jsonOwlIndividualParse = MolecularModelJsonRenderer.parseFromJson(json, JsonOwlIndividual.class); + + assertNotNull(jsonOwlIndividualParse); + assertEquals(jsonOwlIndividualOriginal, jsonOwlIndividualParse); + } + + private void testSimpleClassExpression(OWLClassExpression ce, String expectedJsonType) throws Exception { + // setup test model/ontology + OWLOntology o = m.createOntology(); + OWLImportsDeclaration importDeclaration = f.getOWLImportsDeclaration(g.getSourceOntology().getOntologyID().getOntologyIRI()); + m.applyChange(new AddImport(o, importDeclaration)); + + // create indivdual with a ce type + final IRI i1IRI = IRI.generateDocumentIRI(); + final OWLNamedIndividual ni1 = f.getOWLNamedIndividual(i1IRI); + // declare individual + m.addAxiom(o, f.getOWLDeclarationAxiom(ni1)); + // declare type + m.addAxiom(o, f.getOWLClassAssertionAxiom(ce, ni1)); + + + MolecularModelJsonRenderer r = new MolecularModelJsonRenderer(o); + + JsonOwlIndividual jsonOwlIndividualOriginal = r.renderObject(ni1); + + String json = MolecularModelJsonRenderer.renderToJson(jsonOwlIndividualOriginal, true); + assertTrue(json, json.contains("\"type\": \""+expectedJsonType+"\"")); + + JsonOwlIndividual jsonOwlIndividualParse = MolecularModelJsonRenderer.parseFromJson(json, JsonOwlIndividual.class); + + assertNotNull(jsonOwlIndividualParse); + assertEquals(jsonOwlIndividualOriginal, jsonOwlIndividualParse); + + Set ces = TestJsonOwlObjectParser.parse(new OWLGraphWrapper(o), jsonOwlIndividualParse.type); + assertEquals(1, ces.size()); + assertEquals(ce, ces.iterator().next()); + } + + + static class TestJsonOwlObjectParser { + static OWLClassExpression parse(OWLGraphWrapper g, JsonOwlObject expression) + throws Exception { + if (expression == null) { + throw new Exception("Missing expression: null is not a valid expression."); + } + if (expression.type == null) { + throw new Exception("An expression type is required."); + } + if (JsonOwlObjectType.Class == expression.type) { + if (expression.id == null) { + throw new Exception("Missing literal for expression of type 'class'"); + } + if (StringUtils.containsWhitespace(expression.id)) { + throw new Exception("Identifiers may not contain whitespaces: '"+expression.id+"'"); + } + OWLClass cls = g.getOWLClassByIdentifier(expression.id); + if (cls == null) { + throw new Exception("Could not retrieve a class for id: "+expression.id); + } + return cls; + } + else if (JsonOwlObjectType.SomeValueFrom == expression.type) { + if (expression.property == null) { + throw new Exception("Missing property for expression of type 'svf'"); + } + if (expression.property.type != JsonOwlObjectType.ObjectProperty) { + throw new Exception("Unexpected type for Property in 'svf': "+expression.property.type); + } + if (expression.property.id == null) { + throw new Exception("Missing property id for expression of type 'svf'"); + } + OWLObjectProperty p = g.getOWLObjectPropertyByIdentifier(expression.property.id); + if (p == null) { + throw new UnknownIdentifierException("Could not find a property for: "+expression.property); + } + if (expression.filler != null) { + OWLClassExpression ce = parse(g, expression.filler); + return g.getDataFactory().getOWLObjectSomeValuesFrom(p, ce); + } + else { + throw new Exception("Missing literal or expression for expression of type 'svf'."); + } + } + else if (JsonOwlObjectType.IntersectionOf == expression.type) { + return parse(g, expression.expressions, JsonOwlObjectType.IntersectionOf); + } + else if (JsonOwlObjectType.UnionOf == expression.type) { + return parse(g, expression.expressions, JsonOwlObjectType.UnionOf); + } + else { + throw new UnknownIdentifierException("Unknown expression type: "+expression.type); + } + } + + static OWLClassExpression parse(OWLGraphWrapper g, JsonOwlObject[] expressions, JsonOwlObjectType type) + throws Exception { + if (expressions.length == 0) { + throw new Exception("Missing expressions: empty expression list is not allowed."); + } + if (expressions.length == 1) { + return parse(g, expressions[0]); + } + Set clsExpressions = new HashSet(); + for (JsonOwlObject m3Expression : expressions) { + OWLClassExpression ce = parse(g, m3Expression); + clsExpressions.add(ce); + } + if (type == JsonOwlObjectType.UnionOf) { + return g.getDataFactory().getOWLObjectUnionOf(clsExpressions); + } + else if (type == JsonOwlObjectType.IntersectionOf) { + return g.getDataFactory().getOWLObjectIntersectionOf(clsExpressions); + } + else { + throw new UnknownIdentifierException("Unsupported expression type: "+type); + } + } + + static Set parse(OWLGraphWrapper g, JsonOwlObject[] expressions) + throws Exception { + if (expressions.length == 0) { + throw new Exception("Missing expressions: empty expression list is not allowed."); + } + Set clsExpressions = new HashSet(); + for (JsonOwlObject m3Expression : expressions) { + OWLClassExpression ce = parse(g, m3Expression); + clsExpressions.add(ce); + } + return clsExpressions; + } + } +} diff --git a/minerva-core/src/test/java/org/geneontology/minerva/util/AbstractMinimalModelGeneratorTest.java b/minerva-core/src/test/java/org/geneontology/minerva/util/AbstractMinimalModelGeneratorTest.java new file mode 100644 index 00000000..12632f15 --- /dev/null +++ b/minerva-core/src/test/java/org/geneontology/minerva/util/AbstractMinimalModelGeneratorTest.java @@ -0,0 +1,91 @@ +package org.geneontology.minerva.util; + +import static org.junit.Assert.*; + +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.util.Set; + +import org.apache.log4j.Logger; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.util.MinimalModelGenerator; +import org.semanticweb.owlapi.model.AxiomType; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLIndividual; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; + +import owltools.OWLToolsTestBasics; +import owltools.vocab.OBOUpperVocabulary; + +public class AbstractMinimalModelGeneratorTest extends OWLToolsTestBasics { + private static Logger LOG = Logger.getLogger(AbstractMinimalModelGeneratorTest.class); + + protected ModelContainer mc; + protected MinimalModelGenerator mmg; + + protected void expectedOPAs(String msg, Integer size) { + Set opas = + mc.getAboxOntology().getAxioms(AxiomType.OBJECT_PROPERTY_ASSERTION); + for (OWLObjectPropertyAssertionAxiom opa : opas) { + LOG.info(msg+" : "+opa); + } + if (size != null) + assertEquals(size.intValue(), opas.size()); + } + + protected void expectFact(OWLIndividual subj, OWLObjectProperty prop, OWLIndividual obj) { + OWLAxiom ax = mc.getOWLDataFactory().getOWLObjectPropertyAssertionAxiom( + prop, + subj, + obj); + assertTrue(mc.getAboxOntology().containsAxiom(ax, false)); + } + + protected void expectedIndividiuals(OWLClass c, Integer size) { + Set inds = + mc.getReasoner().getInstances(c, false).getFlattened(); + LOG.info("|" + c+"| = "+inds.size()); + if (size != null) + assertEquals(size.intValue(), inds.size()); + } + + @Deprecated + protected IRI oboIRI(String frag) { + return IRI.create("http://purl.obolibrary.org/obo/"+frag); + } + protected OWLObjectProperty getObjectProperty(IRI iri) { + return mc.getTboxOntology().getOWLOntologyManager().getOWLDataFactory().getOWLObjectProperty(iri); + } + + protected OWLClass getClass(IRI iri) { + return mc.getTboxOntology().getOWLOntologyManager().getOWLDataFactory().getOWLClass(iri); + } + protected OWLClass getClass(OBOUpperVocabulary v) { + return mc.getTboxOntology().getOWLOntologyManager().getOWLDataFactory().getOWLClass(v.getIRI()); + } + protected OWLNamedIndividual getIndividual(IRI iri) { + return mc.getTboxOntology().getOWLOntologyManager().getOWLDataFactory().getOWLNamedIndividual(iri); + } + + @Deprecated + protected OWLClass getOboClass(String id) { + return mc.getTboxOntology().getOWLOntologyManager().getOWLDataFactory().getOWLClass(oboIRI(id)); + } + + protected void save(String fn) throws OWLOntologyStorageException, IOException { + save(fn, mc.getAboxOntology()); + } + + protected void save(String fn, OWLOntology mont) throws OWLOntologyStorageException, IOException { + FileOutputStream os = new FileOutputStream(new File("target/"+fn+".owl")); + mc.getOWLOntologyManager().saveOntology(mont, os); + os.close(); + } +} diff --git a/minerva-core/src/test/java/org/geneontology/minerva/util/MinimalModelGeneratorTest.java b/minerva-core/src/test/java/org/geneontology/minerva/util/MinimalModelGeneratorTest.java new file mode 100644 index 00000000..a9bb544d --- /dev/null +++ b/minerva-core/src/test/java/org/geneontology/minerva/util/MinimalModelGeneratorTest.java @@ -0,0 +1,700 @@ +package org.geneontology.minerva.util; + +import static org.junit.Assert.*; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.Set; + +import org.apache.log4j.Logger; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.util.MinimalModelGenerator; +import org.junit.Test; +import org.semanticweb.elk.owlapi.ElkReasonerFactory; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; + +import owltools.io.CatalogXmlIRIMapper; +import owltools.vocab.OBOUpperVocabulary; + +/** + * + * + * + */ +public class MinimalModelGeneratorTest extends AbstractMinimalModelGeneratorTest { + private static Logger LOG = Logger.getLogger(MinimalModelGeneratorTest.class); + + OWLOntologyManager m; + + /** + * Basic test of minimal model generation. Takes an existential model of + * limb anatomy, creates prototype individuals. + * + * Addresses following challenges + * - autoclassification of digits into 'finger' or 'toe' (requires inverses) + * - heuristic collapse of 'limb' into forelimb and generation of a single 'organism' + * + * This test is done using a DL reasoner, which is inverse-aware + * + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + @Test + public void testGenerateAnatomyDL() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + m.addIRIMapper(new CatalogXmlIRIMapper(getResource("mmg/catalog-v001.xml"))); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/basic-tbox-importer.omn")); + mc = new ModelContainer(tbox, new org.semanticweb.HermiT.Reasoner.ReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + mmg.setAssertInverses(false); // NOT NECESSARY FOR A DL REASONER + int aboxImportsSize = mc.getAboxOntology().getImportsClosure().size(); + int qboxImportsSize = mc.getQueryOntology().getImportsClosure().size(); + + LOG.info("Abox ontology imports: "+aboxImportsSize); + LOG.info("Q ontology imports: "+qboxImportsSize); + assertEquals(3, aboxImportsSize); + assertEquals(4, qboxImportsSize); + OWLClass c = getClass("hand"); + mmg.generateNecessaryIndividuals(c); + + // test that there is only one limb in the model + // (collapsing step reduces the limb that must exist if an autopod exists + // into the already existing forelimb) + LOG.info("#inds (after adding hand):"+mmg.getGeneratedIndividuals().size()); + assertEquals(4, mmg.getGeneratedIndividuals().size()); + + // we have added hand, which generates at least one digit, which + // is inferred to be of type finger (via inverse axioms) + this.expectedIndividiuals("digit", 1); + // test deepening + this.expectedIndividiuals("finger", 1); + + expectedOPAs("post-hand, un-normalized", 6); + mmg.normalizeDirections(partOf()); + expectedOPAs("post-hand, normalized", 3); + + // for debugging + save("basic-abox"); + + mmg.generateNecessaryIndividuals(getClass("foot"), true); + LOG.info("#inds (after adding foot):"+mmg.getGeneratedIndividuals().size()); + assertEquals(7, mmg.getGeneratedIndividuals().size()); + + this.expectedIndividiuals("digit", 2); + + // test deepening + this.expectedIndividiuals("toe", 1); + this.expectedIndividiuals("finger", 1); + + expectedOPAs("post-foot", 8); + + // for debugging + save("basic-abox2"); + } + + /** + * As DL test @see #testGenerateAnatomyDL(), + * but using Elk, with additional inverse assertion being provided by + * MM + * + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + @Test + public void testGenerateAnatomyUsingElk() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/basic-tbox.omn")); + mc = new ModelContainer(tbox, new org.semanticweb.HermiT.Reasoner.ReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + mmg.setAssertInverses(true); // NECESSARY FOR ELK + int aboxImportsSize = mc.getAboxOntology().getImportsClosure().size(); + int qboxImportsSize = mc.getQueryOntology().getImportsClosure().size(); + + LOG.info("Abox ontology imports: "+aboxImportsSize); + LOG.info("Q ontology imports: "+qboxImportsSize); + assertEquals(2, aboxImportsSize); + assertEquals(3, qboxImportsSize); + + + OWLClass c = getClass("hand"); + + // for this test we leave the transitive reduction stee until later + mmg.generateNecessaryIndividuals(c, true, false); + + // test that there is only one limb in the model + // (collapsing step reduces the limb that must exist if an autopod exists + // into the already existing forelimb) + LOG.info("#inds (after adding hand):"+mmg.getGeneratedIndividuals().size()); + assertEquals(4, mmg.getGeneratedIndividuals().size()); + + // we have added hand, which generates at least one digit, which + // is inferred to be of type finger (via inverse axioms) + expectedIndividiuals("digit", 1); + // test deepening + expectedIndividiuals("finger", 1); + + expectFact("finger-proto", "part_of", "hand-proto"); + expectFact("hand-proto", "part_of", "forelimb-proto"); + expectFact("forelimb-proto", "part_of", "organism-proto"); + + expectedOPAs("post-hand, un-normalized, no reduction", 8); + + mmg.performTransitiveReduction(partOf()); + expectedOPAs("post-hand, reduced", 6); + + //mmg.normalizeDirections(partOf()); + //expectedOPAs("post-hand, reduced, normalized", 3); + + + // for debugging + save("basic-abox-elk"); + + mmg.generateNecessaryIndividuals(getClass("foot"), true); + LOG.info("#inds (after adding foot):"+mmg.getGeneratedIndividuals().size()); + assertEquals(7, mmg.getGeneratedIndividuals().size()); + + expectedIndividiuals("digit", 2); + // test deepening + expectedIndividiuals("finger", 1); + expectedIndividiuals("toe", 1); + + expectedOPAs("post-foot, unprocessed", 12); + + + mmg.normalizeDirections(partOf()); + expectedOPAs("post-foot, normalized", 6); + + expectFact("finger-proto", "part_of", "hand-proto"); + expectFact("hand-proto", "part_of", "forelimb-proto"); + expectFact("forelimb-proto", "part_of", "organism-proto"); + expectFact("toe-proto", "part_of", "foot-proto"); + expectFact("foot-proto", "part_of", "hindlimb-proto"); + expectFact("hindlimb-proto", "part_of", "organism-proto"); + + + mmg.extractModule(); + // for debugging + save("basic-abox2-elk"); + } + + @Test + public void testGenerateAnatomyNoCollapse() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/basic-tbox.omn")); + mc = new ModelContainer(tbox, new ElkReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + mmg.setAssertInverses(true); // NECESSARY FOR ELK + int aboxImportsSize = mc.getAboxOntology().getImportsClosure().size(); + int qboxImportsSize = mc.getQueryOntology().getImportsClosure().size(); + + LOG.info("Abox ontology imports: "+aboxImportsSize); + LOG.info("Q ontology imports: "+qboxImportsSize); + assertEquals(2, aboxImportsSize); + assertEquals(3, qboxImportsSize); + + + OWLClass c = getClass("hand"); + + // for this test we do NOT collapse. + // The model should be valid, but may be incomplete w.r.t + // sameAs assertions + mmg.generateNecessaryIndividuals(c, false, true); + + // test that there is only one limb in the model + // (collapsing step reduces the limb that must exist if an autopod exists + // into the already existing forelimb) + LOG.info("#inds (after adding hand):"+mmg.getGeneratedIndividuals().size()); + assertEquals(4, mmg.getGeneratedIndividuals().size()); + + // we have added hand, which generates at least one digit, which + // is inferred to be of type finger (via inverse axioms) + expectedIndividiuals("digit", 1); + // test deepening + expectedIndividiuals("finger", 1); + + + mmg.generateNecessaryIndividuals(getClass("foot"), false, true); + LOG.info("#inds (after adding foot):"+mmg.getGeneratedIndividuals().size()); + //assertEquals(7, mmg.getGeneratedIndividuals().size()); + + expectedIndividiuals("digit", 2); + // test deepening + expectedIndividiuals("finger", 1); + expectedIndividiuals("toe", 1); + + expectedOPAs("post-foot, unprocessed", 12); + + + mmg.normalizeDirections(partOf()); + + + mmg.extractModule(); + // for debugging + save("basic-abox-uncollapsed"); + } + + @Test + public void testGeneratePrototypicalHuman() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/basic-tbox.omn")); + mc = new ModelContainer(tbox, new ElkReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + mmg.setAssertInverses(true); + int aboxImportsSize = mc.getAboxOntology().getImportsClosure().size(); + int qboxImportsSize = mc.getQueryOntology().getImportsClosure().size(); + + LOG.info("Abox ontology imports: "+aboxImportsSize); + LOG.info("Q ontology imports: "+qboxImportsSize); + assertEquals(2, aboxImportsSize); + assertEquals(3, qboxImportsSize); + OWLClass c = getClass("human"); + mmg.generateNecessaryIndividuals(c); + + OWLNamedIndividual forelimb = mc.getOWLDataFactory().getOWLNamedIndividual(this.getIRI("forelimb-proto")); + Set rels = mmg.getExistentialRelationships(forelimb); + for (OWLObjectSomeValuesFrom rel : rels) { + LOG.info(" proto-forelimb IREL: "+rel); + } + + // test that there is only one limb in the model + // (collapsing step reduces the limb that must exist if an autopod exists + // into the already existing forelimb) + LOG.info("#inds (after adding human):"+mmg.getGeneratedIndividuals().size()); + assertEquals(7, mmg.getGeneratedIndividuals().size()); + + expectedIndividiuals("digit", 2); + // test deepening + expectedIndividiuals("finger", 1); + expectedIndividiuals("toe", 1); + expectedIndividiuals("limb", 2); + + expectedIndividiuals("forelimb", 1); + expectedIndividiuals("hindlimb", 1); + expectedIndividiuals("human", 1); + + mmg.normalizeDirections(partOf()); + + expectedOPAs("normalized", 6); + + expectFact("finger-proto", "part_of", "hand-proto"); + expectFact("hand-proto", "part_of", "forelimb-proto"); + expectFact("forelimb-proto", "part_of", "human-proto"); + expectFact("toe-proto", "part_of", "foot-proto"); + expectFact("foot-proto", "part_of", "hindlimb-proto"); + expectFact("hindlimb-proto", "part_of", "human-proto"); + + // for debugging + mmg.extractModule(); + save("prototypical-human"); + } + + /** + * as above, but in scenario where we want to add abox assertions + * directly into main ontology + * + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + @Test + public void testGenerateAnatomySameOntology() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/basic-tbox.omn")); + //OWLReasoner reasoner = new org.semanticweb.HermiT.Reasoner.ReasonerFactory().createReasoner(tbox); + mc = new ModelContainer(tbox, tbox, new ElkReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + OWLClass c = getClass("hand"); + mmg.generateNecessaryIndividuals(c); + + // we have added hand, which generates at least one digit, which + // is inferred to be of type finger (via inverse axioms) + expectedIndividiuals("digit", 1); + // test deepening + expectedIndividiuals("finger", 1); + + expectFact("finger-proto", "part_of", "hand-proto"); + expectFact("hand-proto", "part_of", "forelimb-proto"); + expectFact("forelimb-proto", "part_of", "organism-proto"); + + expectedOPAs("post-hand, reduced, but not normalized", 6); + mmg.normalizeDirections(partOf()); + expectedOPAs("post-hand, reduced, normalized", 3); + + // TODO - check + save("basic-abox-v2"); + } + + @Test + public void testGenerateAnatomyWithImport() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology abox = m.createOntology(IRI.create("http://x.org/foo/bar")); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/basic-tbox.omn")); + AddImport ai = new AddImport(abox, + m.getOWLDataFactory().getOWLImportsDeclaration( + tbox.getOntologyID().getOntologyIRI())); + m.applyChange(ai); + mc = new ModelContainer(abox, abox, new ElkReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + OWLClass c = getClass("hand"); + mmg.generateNecessaryIndividuals(c); + + // we have added hand, which generates at least one digit, which + // is inferred to be of type finger (via inverse axioms) + expectedIndividiuals("digit", 1); + // test deepening + expectedIndividiuals("finger", 1); + + expectFact("finger-proto", "part_of", "hand-proto"); + expectFact("hand-proto", "part_of", "forelimb-proto"); + expectFact("forelimb-proto", "part_of", "organism-proto"); + + expectedOPAs("post-hand, reduced, but not normalized", 6); + mmg.normalizeDirections(partOf()); + expectedOPAs("post-hand, reduced, normalized", 3); + + // TODO - check + save("basic-abox-v2"); + } + + + /** + * tests generation of a set of instances for glycolysis based on an axiom + * + * has_part some (a1 and activates some (..(..(..)))) + * + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + @Test + public void testGenerateGlycolysis() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/glycolysis-tbox.omn")); + mc = new ModelContainer(tbox, tbox, new org.semanticweb.HermiT.Reasoner.ReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + OWLClass c = + tbox.getOWLOntologyManager().getOWLDataFactory().getOWLClass(IRI.create("http://purl.obolibrary.org/obo/GO_0006096")); + + mmg.generateNecessaryIndividuals(c); + mmg.normalizeDirections(mc.getOWLDataFactory().getOWLObjectProperty( + OBOUpperVocabulary.BFO_part_of.getIRI())); + + this.expectedOPAs("glyc", 15); + + mmg.extractModule(); + //mmg.generateNecessaryIndividuals(getClass("foot"), true); + save("glycolysis-tbox2abox"); + } + + /** + * DNA replication + * + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + @Test + public void testGenerateDNAReplication() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/dna-replication-tbox.owl")); + mc = new ModelContainer(tbox, tbox, new ElkReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + LOG.info("MMG = "+mmg); + OWLClass c = + tbox.getOWLOntologyManager().getOWLDataFactory().getOWLClass(IRI.create("http://purl.obolibrary.org/obo/GO_0006261")); + + LOG.info("Generating for :"+c); + mmg.generateNecessaryIndividuals(c); + mmg.normalizeDirections(mc.getOWLDataFactory().getOWLObjectProperty( + OBOUpperVocabulary.BFO_part_of.getIRI())); + + //this.expectedOPAs("glyc", 15); + + mmg.extractModule(); + //mmg.generateNecessaryIndividuals(getClass("foot"), true); + save("dna-replication-tbox2abox"); + } + + + /** + * tests {@link MinimalModelGenerator#generateNecessaryIndividuals(OWLClassExpression)} + * + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + @Test + public void testGeneratePathway() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/basic-tbox.omn")); + mc = new ModelContainer(tbox, new org.semanticweb.HermiT.Reasoner.ReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + //mmg.setPrecomputePropertyClassCombinations(false); + OWLClass c = getClass("bar_response_pathway"); + mmg.generateNecessaryIndividuals(c, true); + // TODO - check + save("pathway-abox"); + + mmg.normalizeDirections(partOf()); + mmg.normalizeDirections(getObjectProperty(getIRI("activates"))); + + Set occs = new HashSet(); + occs.add(getClass(OBOUpperVocabulary.GO_molecular_function)); + occs.add(getClass(OBOUpperVocabulary.GO_biological_process)); + mmg.anonymizeIndividualsNotIn(occs); + + this.expectFact("mapkkk_activity-proto", "directly_activates", "mapkk_activity-proto"); + this.expectFact("mapkk_activity-proto", "directly_activates", "mapk_activity-proto"); + this.expectedIndividiuals("cellular_process", 5); + + this.expectedOPAs("all", 18); + + mmg.extractModule(); + // futzing +// m.addAxioms(mmg.getAboxOntology(), tbox.getAxioms()); +// Set onts = new HashSet(); +// onts.add(tbox); +// onts.add(mmg.getAboxOntology()); +// OWLOntology mont = m.createOntology(IRI.create("hhtp://x.org/merged"), onts); + save("pathway-abox-merged"); + } + + /** + * + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + @Test + public void testGeneratePathwayWithInclusionSets() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/basic-tbox.omn")); + mc = new ModelContainer(tbox, new org.semanticweb.HermiT.Reasoner.ReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + + Set occs = new HashSet(); + occs.add(getClass(OBOUpperVocabulary.GO_molecular_function)); + occs.add(getClass(OBOUpperVocabulary.GO_biological_process)); + + mmg.setInclusionSet(occs); + + //mmg.setPrecomputePropertyClassCombinations(false); + OWLClass c = getClass("bar_response_pathway"); + mmg.generateNecessaryIndividuals(c, true); + + mmg.normalizeDirections(partOf()); + mmg.normalizeDirections(getObjectProperty(getIRI("activates"))); + + this.expectFact("mapkkk_activity-proto", "directly_activates", "mapkk_activity-proto"); + this.expectFact("mapkk_activity-proto", "directly_activates", "mapk_activity-proto"); + this.expectedIndividiuals("cellular_process", 5); + + this.expectedOPAs("all", 18); + + mmg.extractModule(); + save("pathway-abox-merged2"); + } + + /** + * Tests {@link MinimalModelGenerator#getMostSpecificClassExpression(OWLNamedIndividual)} + * + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + @Test + public void testMSC() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/pathway-abox.omn")); + mc = new ModelContainer(tbox, new org.semanticweb.HermiT.Reasoner.ReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + OWLNamedIndividual i = getIndividual("pathway1"); + OWLClassExpression x = mmg.getMostSpecificClassExpression(i, null); + LOG.info("MSCE:"+x); // TODO - roundtrip + Set sig = x.getClassesInSignature(); + LOG.info("|Sig|="+sig.size()); + assertEquals(4, sig.size()); + Set psig = x.getObjectPropertiesInSignature(); + LOG.info("|PSig|="+psig.size()); + assertEquals(3, psig.size()); + } + + /** + * Tests {@link MinimalModelGenerator#getMostSpecificClassExpression(OWLNamedIndividual)} + * + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + @Test + public void testMSCGlycolysis() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/glycolysis-abox.omn")); + mc = new ModelContainer(tbox, new org.semanticweb.HermiT.Reasoner.ReasonerFactory()); + mmg = new MinimalModelGenerator(mc); + OWLNamedIndividual i = + tbox.getOWLOntologyManager().getOWLDataFactory().getOWLNamedIndividual(IRI.create("http://purl.obolibrary.org/obo/GLY_TEST_0000001")); + ArrayList propertySet = new ArrayList(); + propertySet.add(getObjectProperty(oboIRI("directly_activates"))); + propertySet.add(getObjectProperty(oboIRI("BFO_0000051"))); + OWLClassExpression x = mmg.getMostSpecificClassExpression(i, propertySet); + LOG.info("MSCE:"+x); // TODO - roundtrip this + Set sig = x.getClassesInSignature(); + LOG.info("|Sig|="+sig.size()); + assertEquals(11, sig.size()); + Set psig = x.getObjectPropertiesInSignature(); + LOG.info("|PSig|="+psig.size()); + assertEquals(2, psig.size()); + } + + @Test + public void testAllIndividuals() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/anonClassAssertions.owl")); + mc = new ModelContainer(tbox); + mmg = new MinimalModelGenerator(mc); + mmg.isStrict = true; + mmg.generateAllNecessaryIndividuals(); +// OWLEntityRenamer renamer = new OWLEntityRenamer(m, +// Collections.singleton(mmg.getAboxOntology())); +// List chgs = new ArrayList(); +// for (OWLNamedIndividual ind : tbox.getIndividualsInSignature(true)) { +// //OWLDeclarationAxiom decl = m.getOWLDataFactory().getOWLDeclarationAxiom(ind); +// //m.addAxiom(mmg.getAboxOntology(), decl); +// for (OWLClassExpression cx : ind.getTypes(tbox)) { +// OWLNamedIndividual j = +// mmg.generateNecessaryIndividuals(cx, false, false); +// chgs.addAll(renamer.changeIRI(j.getIRI(), ind.getIRI())); +// //m.addAxiom(m.getOWLDataFactory().getOWLO, axiom) +// } +// } +// LOG.info("Changes = "+chgs.size()); +// m.applyChanges(chgs); + save("foo"); + } + + + @Test + public void testTransitiveCycle2() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + m = OWLManager.createOWLOntologyManager(); + OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/cycle.omn")); + mc = new ModelContainer(tbox); + mmg = new MinimalModelGenerator(mc); + mmg.setAssertInverses(true); // NECESSARY FOR ELK + + + OWLClass c = getClass("cyclic_molecule2"); + + // for this test we leave the transitive reduction stee until later + mmg.generateNecessaryIndividuals(c, true, false); + + // we expect the molecule plus 6 atoms = 7 + LOG.info("#inds (after adding CM):"+mmg.getGeneratedIndividuals().size()); + assertEquals(7, mmg.getGeneratedIndividuals().size()); + + expectedIndividiuals("c", 6); + // test deepening + expectedIndividiuals("molecule", 1); + + expectFact("c1-proto", "part_of", "cyclic_molecule2-proto"); + expectFact("c1-proto", "connected_to", "c2-proto"); + expectFact("c6-proto", "connected_to", "c1-proto"); + + OWLObjectProperty connectedTo = mc.getOWLDataFactory().getOWLObjectProperty(this.getIRI("connected_to")); + expectedOPAs("pre-reduced", 8); + // we expect this to have no-effect; connected_to should not be reduced + // as it contains cycles + mmg.performTransitiveReduction(connectedTo); + expectedOPAs("reduced", 8); + + mmg.normalizeDirections(connectedTo); + //expectedOPAs("post-hand, reduced, normalized", 3); + + + // for debugging + save("cycle-abox-elk"); + } + +// This one can lead to cycles: +// @Test +// public void testTransitiveCycle1() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { +// m = OWLManager.createOWLOntologyManager(); +// OWLOntology tbox = m.loadOntologyFromOntologyDocument(getResource("mmg/scycle.omn")); +// mmg = new MinimalModelGenerator(tbox); +// mmg.setAssertInverses(true); // NECESSARY FOR ELK +// +// +// OWLClass c = getClass("cyclic_molecule"); +// +// // for this test we leave the transitive reduction stee until later +// mmg.generateNecessaryIndividuals(c, true, false); +// +// // we expect the molecule plus 6 atoms = 7 +// LOG.info("#inds (after adding CM):"+mmg.getGeneratedIndividuals().size()); +// assertEquals(7, mmg.getGeneratedIndividuals().size()); +// +// expectedIndividiuals("c", 6); +// // test deepening +// expectedIndividiuals("molecule", 1); +// +// expectFact("c1-proto", "part_of", "cyclic_molecule2-proto"); +// expectFact("c1-proto", "connected_to", "c2-proto"); +// expectFact("c6-proto", "connected_to", "c1-proto"); +// +// OWLObjectProperty connectedTo = mmg.getOWLDataFactory().getOWLObjectProperty(this.getIRI("connected_to")); +// expectedOPAs("pre-reduced", 8); +// // we expect this to have no-effect; connected_to should not be reduced +// // as it contains cycles +// mmg.performTransitiveReduction(connectedTo); +// expectedOPAs("reduced", 8); +// +// mmg.normalizeDirections(connectedTo); +// //expectedOPAs("post-hand, reduced, normalized", 3); +// +// +// // for debugging +// save("cycle-abox-elk"); +// } + // UTIL + + private OWLObjectProperty partOf() { + return mc.getOWLDataFactory().getOWLObjectProperty(this.getIRI("part_of")); + } + + + protected void expectFact(String subj, String prop, String obj) { + expectFact(getIndividual(subj), getObjectProperty(getIRI(prop)), getIndividual(obj)); + } + + protected void expectedIndividiuals(String cn, Integer size) { + expectedIndividiuals(getClass(cn), size); + } + + + protected IRI getIRI(String frag) { + return IRI.create("http://x.org/"+frag); + } + + protected OWLClass getClass(String frag) { + return getClass(getIRI(frag)); + } + protected OWLNamedIndividual getIndividual(String frag) { + return mc.getTboxOntology().getOWLOntologyManager().getOWLDataFactory().getOWLNamedIndividual(getIRI(frag)); + } + + +} diff --git a/minerva-core/src/test/resources/go-mgi-signaling-test.obo b/minerva-core/src/test/resources/go-mgi-signaling-test.obo new file mode 100644 index 00000000..1526e526 --- /dev/null +++ b/minerva-core/src/test/resources/go-mgi-signaling-test.obo @@ -0,0 +1,19230 @@ +format-version: 1.2 +ontology: owlapi:ontology:ont2 + +[Term] +id: GO:0000003 +name: reproduction +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0000122 +name: negative regulation of transcription from RNA polymerase II promoter +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter +relationship: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0000165 +name: MAPK cascade +is_a: GO:0007243 ! intracellular protein kinase cascade + +[Term] +id: GO:0000187 +name: activation of MAPK activity +is_a: GO:0032147 ! activation of protein kinase activity +is_a: GO:0043406 ! positive regulation of MAP kinase activity + +[Term] +id: GO:0000226 +name: microtubule cytoskeleton organization +is_a: GO:0007010 ! cytoskeleton organization +is_a: GO:0007017 ! microtubule-based process + +[Term] +id: GO:0000228 +name: nuclear chromosome +is_a: GO:0005694 ! chromosome +is_a: GO:0044428 ! nuclear part +intersection_of: GO:0005694 ! chromosome +intersection_of: part_of GO:0005634 ! nucleus +relationship: part_of GO:0031981 ! nuclear lumen + +[Term] +id: GO:0000278 +name: mitotic cell cycle +is_a: GO:0007049 ! cell cycle +intersection_of: GO:0007049 ! cell cycle +intersection_of: has_part GO:0007067 ! mitosis + +[Term] +id: GO:0000280 +name: nuclear division +is_a: GO:0048285 ! organelle fission + +[Term] +id: GO:0000429 +name: carbon catabolite regulation of transcription from RNA polymerase II promoter +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0045990 ! carbon catabolite regulation of transcription + +[Term] +id: GO:0000430 +name: regulation of transcription from RNA polymerase II promoter by glucose +is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter +is_a: GO:0046015 ! regulation of transcription by glucose + +[Term] +id: GO:0000432 +name: positive regulation of transcription from RNA polymerase II promoter by glucose +is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose +is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter +is_a: GO:0046016 ! positive regulation of transcription by glucose + +[Term] +id: GO:0000433 +name: negative regulation of transcription from RNA polymerase II promoter by glucose +is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose +is_a: GO:0000437 ! carbon catabolite repression of transcription from RNA polymerase II promoter +is_a: GO:0045014 ! negative regulation of transcription by glucose + +[Term] +id: GO:0000436 +name: carbon catabolite activation of transcription from RNA polymerase II promoter +is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter +is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter +is_a: GO:0045991 ! carbon catabolite activation of transcription + +[Term] +id: GO:0000437 +name: carbon catabolite repression of transcription from RNA polymerase II promoter +is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter +is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter +is_a: GO:0045013 ! carbon catabolite repression of transcription + +[Term] +id: GO:0000578 +name: embryonic axis specification +is_a: GO:0009798 ! axis specification +is_a: GO:0009880 ! embryonic pattern specification + +[Term] +id: GO:0000737 +name: DNA catabolic process, endonucleolytic +is_a: GO:0006308 ! DNA catabolic process +is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis + +[Term] +id: GO:0000768 +name: syncytium formation by plasma membrane fusion +is_a: GO:0006949 ! syncytium formation +relationship: has_part GO:0045026 ! plasma membrane fusion + +[Term] +id: GO:0000785 +name: chromatin +is_a: GO:0044427 ! chromosomal part + +[Term] +id: GO:0000790 +name: nuclear chromatin +is_a: GO:0000785 ! chromatin +is_a: GO:0044454 ! nuclear chromosome part +intersection_of: GO:0000785 ! chromatin +intersection_of: part_of GO:0005634 ! nucleus + +[Term] +id: GO:0000792 +name: heterochromatin +is_a: GO:0000785 ! chromatin + +[Term] +id: GO:0000902 +name: cell morphogenesis +is_a: GO:0032989 ! cellular component morphogenesis + +[Term] +id: GO:0000904 +name: cell morphogenesis involved in differentiation +is_a: GO:0000902 ! cell morphogenesis +intersection_of: GO:0000902 ! cell morphogenesis +intersection_of: part_of GO:0048468 ! cell development +relationship: part_of GO:0048468 ! cell development + +[Term] +id: GO:0000975 +name: regulatory region DNA binding +is_a: GO:0001067 ! regulatory region nucleic acid binding +is_a: GO:0003677 ! DNA binding + +[Term] +id: GO:0000976 +name: transcription regulatory region sequence-specific DNA binding +is_a: GO:0043565 ! sequence-specific DNA binding +is_a: GO:0044212 ! transcription regulatory region DNA binding + +[Term] +id: GO:0000977 +name: RNA polymerase II regulatory region sequence-specific DNA binding +is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding +is_a: GO:0001012 ! RNA polymerase II regulatory region DNA binding + +[Term] +id: GO:0000978 +name: RNA polymerase II core promoter proximal region sequence-specific DNA binding +is_a: GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding +is_a: GO:0000987 ! core promoter proximal region sequence-specific DNA binding + +[Term] +id: GO:0000980 +name: RNA polymerase II distal enhancer sequence-specific DNA binding +is_a: GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding +is_a: GO:0001158 ! enhancer sequence-specific DNA binding + +[Term] +id: GO:0000981 +name: sequence-specific DNA binding RNA polymerase II transcription factor activity +is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity +relationship: has_part GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding +relationship: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter +relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0000982 +name: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: has_part GO:0000978 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding + +[Term] +id: GO:0000987 +name: core promoter proximal region sequence-specific DNA binding +is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding +is_a: GO:0001159 ! core promoter proximal region DNA binding + +[Term] +id: GO:0000988 +name: protein binding transcription factor activity +is_a: GO:0003674 ! molecular_function +relationship: has_part GO:0005515 ! protein binding +relationship: part_of GO:2001141 ! regulation of RNA biosynthetic process + +[Term] +id: GO:0000989 +name: transcription factor binding transcription factor activity +is_a: GO:0000988 ! protein binding transcription factor activity +relationship: has_part GO:0008134 ! transcription factor binding + +[Term] +id: GO:0001012 +name: RNA polymerase II regulatory region DNA binding +is_a: GO:0044212 ! transcription regulatory region DNA binding + +[Term] +id: GO:0001067 +name: regulatory region nucleic acid binding +is_a: GO:0003676 ! nucleic acid binding + +[Term] +id: GO:0001071 +name: nucleic acid binding transcription factor activity +is_a: GO:0003674 ! molecular_function +relationship: has_part GO:0003676 ! nucleic acid binding +relationship: part_of GO:2001141 ! regulation of RNA biosynthetic process + +[Term] +id: GO:0001076 +name: RNA polymerase II transcription factor binding transcription factor activity +is_a: GO:0000989 ! transcription factor binding transcription factor activity +relationship: has_part GO:0001085 ! RNA polymerase II transcription factor binding +relationship: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter +relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0001077 +name: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription +is_a: GO:0000982 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity +is_a: GO:0001228 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription + +[Term] +id: GO:0001085 +name: RNA polymerase II transcription factor binding +is_a: GO:0008134 ! transcription factor binding + +[Term] +id: GO:0001098 +name: basal transcription machinery binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0001099 +name: basal RNA polymerase II transcription machinery binding +is_a: GO:0001098 ! basal transcription machinery binding + +[Term] +id: GO:0001101 +name: response to acid +is_a: GO:0042221 ! response to chemical stimulus + +[Term] +id: GO:0001102 +name: RNA polymerase II activating transcription factor binding +is_a: GO:0001085 ! RNA polymerase II transcription factor binding +is_a: GO:0033613 ! activating transcription factor binding + +[Term] +id: GO:0001104 +name: RNA polymerase II transcription cofactor activity +is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity +is_a: GO:0003712 ! transcription cofactor activity +relationship: has_part GO:0001099 ! basal RNA polymerase II transcription machinery binding + +[Term] +id: GO:0001158 +name: enhancer sequence-specific DNA binding +is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding +is_a: GO:0035326 ! enhancer binding + +[Term] +id: GO:0001159 +name: core promoter proximal region DNA binding +is_a: GO:0044212 ! transcription regulatory region DNA binding + +[Term] +id: GO:0001190 +name: RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription +is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity +relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter + +[Term] +id: GO:0001205 +name: RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription +is_a: GO:0001228 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription +is_a: GO:0003705 ! RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0001227 +name: RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: part_of GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter + +[Term] +id: GO:0001228 +name: RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter + +[Term] +id: GO:0001501 +name: skeletal system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0001502 +name: cartilage condensation +is_a: GO:0016337 ! cell-cell adhesion +relationship: part_of GO:0048705 ! skeletal system morphogenesis +relationship: part_of GO:0051216 ! cartilage development + +[Term] +id: GO:0001503 +name: ossification +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0001505 +name: regulation of neurotransmitter levels +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0007268 ! synaptic transmission + +[Term] +id: GO:0001508 +name: regulation of action potential +is_a: GO:0042391 ! regulation of membrane potential + +[Term] +id: GO:0001525 +name: angiogenesis +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0048514 ! blood vessel morphogenesis + +[Term] +id: GO:0001541 +name: ovarian follicle development +is_a: GO:0022602 ! ovulation cycle process +relationship: part_of GO:0008585 ! female gonad development + +[Term] +id: GO:0001558 +name: regulation of cell growth +is_a: GO:0040008 ! regulation of growth +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016049 ! cell growth +relationship: regulates GO:0016049 ! cell growth + +[Term] +id: GO:0001568 +name: blood vessel development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001944 ! vasculature development + +[Term] +id: GO:0001569 +name: patterning of blood vessels +is_a: GO:0007389 ! pattern specification process +is_a: GO:0048754 ! branching morphogenesis of an epithelial tube +relationship: part_of GO:0001525 ! angiogenesis + +[Term] +id: GO:0001570 +name: vasculogenesis +is_a: GO:0030154 ! cell differentiation +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048514 ! blood vessel morphogenesis + +[Term] +id: GO:0001649 +name: osteoblast differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0001503 ! ossification + +[Term] +id: GO:0001654 +name: eye development +is_a: GO:0007423 ! sensory organ development + +[Term] +id: GO:0001655 +name: urogenital system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0001656 +name: metanephros development +is_a: GO:0001822 ! kidney development + +[Term] +id: GO:0001657 +name: ureteric bud development +is_a: GO:0035295 ! tube development +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0001658 +name: branching involved in ureteric bud morphogenesis +is_a: GO:0048754 ! branching morphogenesis of an epithelial tube +intersection_of: GO:0001763 ! morphogenesis of a branching structure +intersection_of: part_of GO:0060675 ! ureteric bud morphogenesis +relationship: part_of GO:0060675 ! ureteric bud morphogenesis + +[Term] +id: GO:0001664 +name: G-protein coupled receptor binding +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0001667 +name: ameboidal cell migration +is_a: GO:0016477 ! cell migration + +[Term] +id: GO:0001678 +name: cellular glucose homeostasis +is_a: GO:0042593 ! glucose homeostasis +is_a: GO:0055082 ! cellular chemical homeostasis + +[Term] +id: GO:0001701 +name: in utero embryonic development +is_a: GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0001702 +name: gastrulation with mouth forming second +is_a: GO:0007369 ! gastrulation + +[Term] +id: GO:0001704 +name: formation of primary germ layer +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0007369 ! gastrulation + +[Term] +id: GO:0001705 +name: ectoderm formation +is_a: GO:0001704 ! formation of primary germ layer +relationship: part_of GO:0007398 ! ectoderm development + +[Term] +id: GO:0001706 +name: endoderm formation +is_a: GO:0001704 ! formation of primary germ layer +relationship: part_of GO:0007492 ! endoderm development + +[Term] +id: GO:0001707 +name: mesoderm formation +is_a: GO:0001704 ! formation of primary germ layer +relationship: part_of GO:0048332 ! mesoderm morphogenesis + +[Term] +id: GO:0001708 +name: cell fate specification +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0045165 ! cell fate commitment + +[Term] +id: GO:0001709 +name: cell fate determination +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0045165 ! cell fate commitment + +[Term] +id: GO:0001710 +name: mesodermal cell fate commitment +is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer +relationship: part_of GO:0048333 ! mesodermal cell differentiation + +[Term] +id: GO:0001711 +name: endodermal cell fate commitment +is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer +relationship: part_of GO:0035987 ! endodermal cell differentiation + +[Term] +id: GO:0001736 +name: establishment of planar polarity +is_a: GO:0007164 ! establishment of tissue polarity +relationship: part_of GO:0001738 ! morphogenesis of a polarized epithelium + +[Term] +id: GO:0001738 +name: morphogenesis of a polarized epithelium +is_a: GO:0002009 ! morphogenesis of an epithelium + +[Term] +id: GO:0001755 +name: neural crest cell migration +is_a: GO:0001667 ! ameboidal cell migration +relationship: part_of GO:0014032 ! neural crest cell development + +[Term] +id: GO:0001756 +name: somitogenesis +is_a: GO:0009952 ! anterior/posterior pattern specification +is_a: GO:0035282 ! segmentation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0043009 ! chordate embryonic development +relationship: part_of GO:0061053 ! somite development + +[Term] +id: GO:0001759 +name: organ induction +is_a: GO:0003156 ! regulation of organ formation +is_a: GO:0031128 ! developmental induction +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +relationship: positively_regulates GO:0010092 ! specification of organ identity + +[Term] +id: GO:0001763 +name: morphogenesis of a branching structure +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0001764 +name: neuron migration +is_a: GO:0016477 ! cell migration +relationship: part_of GO:0048699 ! generation of neurons + +[Term] +id: GO:0001775 +name: cell activation +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0001816 +name: cytokine production +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0001817 +name: regulation of cytokine production +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001816 ! cytokine production +relationship: regulates GO:0001816 ! cytokine production + +[Term] +id: GO:0001819 +name: positive regulation of cytokine production +is_a: GO:0001817 ! regulation of cytokine production +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001816 ! cytokine production +relationship: positively_regulates GO:0001816 ! cytokine production + +[Term] +id: GO:0001822 +name: kidney development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0001823 +name: mesonephros development +is_a: GO:0001822 ! kidney development + +[Term] +id: GO:0001824 +name: blastocyst development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001701 ! in utero embryonic development + +[Term] +id: GO:0001825 +name: blastocyst formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0001824 ! blastocyst development + +[Term] +id: GO:0001829 +name: trophectodermal cell differentiation +is_a: GO:0030154 ! cell differentiation +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001825 ! blastocyst formation + +[Term] +id: GO:0001837 +name: epithelial to mesenchymal transition +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +relationship: part_of GO:0014031 ! mesenchymal cell development + +[Term] +id: GO:0001838 +name: embryonic epithelial tube formation +is_a: GO:0072175 ! epithelial tube formation +relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium + +[Term] +id: GO:0001840 +name: neural plate development +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0001841 +name: neural tube formation +is_a: GO:0001838 ! embryonic epithelial tube formation +relationship: part_of GO:0021915 ! neural tube development + +[Term] +id: GO:0001843 +name: neural tube closure +is_a: GO:0060606 ! tube closure +relationship: part_of GO:0014020 ! primary neural tube formation + +[Term] +id: GO:0001885 +name: endothelial cell development +is_a: GO:0002064 ! epithelial cell development +relationship: part_of GO:0045446 ! endothelial cell differentiation + +[Term] +id: GO:0001889 +name: liver development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0061008 ! hepaticobiliary system development + +[Term] +id: GO:0001890 +name: placenta development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0001892 +name: embryonic placenta development +is_a: GO:0048568 ! embryonic organ development +relationship: part_of GO:0001701 ! in utero embryonic development +relationship: part_of GO:0001890 ! placenta development + +[Term] +id: GO:0001894 +name: tissue homeostasis +is_a: GO:0060249 ! anatomical structure homeostasis +relationship: part_of GO:0048871 ! multicellular organismal homeostasis + +[Term] +id: GO:0001932 +name: regulation of protein phosphorylation +is_a: GO:0031399 ! regulation of protein modification process +is_a: GO:0042325 ! regulation of phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006468 ! protein phosphorylation +relationship: regulates GO:0006468 ! protein phosphorylation + +[Term] +id: GO:0001933 +name: negative regulation of protein phosphorylation +is_a: GO:0001932 ! regulation of protein phosphorylation +is_a: GO:0031400 ! negative regulation of protein modification process +is_a: GO:0042326 ! negative regulation of phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006468 ! protein phosphorylation +relationship: negatively_regulates GO:0006468 ! protein phosphorylation + +[Term] +id: GO:0001934 +name: positive regulation of protein phosphorylation +is_a: GO:0001932 ! regulation of protein phosphorylation +is_a: GO:0031401 ! positive regulation of protein modification process +is_a: GO:0042327 ! positive regulation of phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006468 ! protein phosphorylation +relationship: positively_regulates GO:0006468 ! protein phosphorylation + +[Term] +id: GO:0001935 +name: endothelial cell proliferation +is_a: GO:0050673 ! epithelial cell proliferation + +[Term] +id: GO:0001936 +name: regulation of endothelial cell proliferation +is_a: GO:0050678 ! regulation of epithelial cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001935 ! endothelial cell proliferation +relationship: regulates GO:0001935 ! endothelial cell proliferation + +[Term] +id: GO:0001938 +name: positive regulation of endothelial cell proliferation +is_a: GO:0001936 ! regulation of endothelial cell proliferation +is_a: GO:0050679 ! positive regulation of epithelial cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001935 ! endothelial cell proliferation +relationship: positively_regulates GO:0001935 ! endothelial cell proliferation + +[Term] +id: GO:0001942 +name: hair follicle development +is_a: GO:0008544 ! epidermis development +is_a: GO:0022405 ! hair cycle process + +[Term] +id: GO:0001944 +name: vasculature development +is_a: GO:0048731 ! system development +relationship: part_of GO:0072358 ! cardiovascular system development + +[Term] +id: GO:0001945 +name: lymph vessel development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001944 ! vasculature development + +[Term] +id: GO:0001946 +name: lymphangiogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0036303 ! lymph vessel morphogenesis + +[Term] +id: GO:0001947 +name: heart looping +is_a: GO:0003143 ! embryonic heart tube morphogenesis +relationship: part_of GO:0061371 ! determination of heart left/right asymmetry + +[Term] +id: GO:0001948 +name: glycoprotein binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0001952 +name: regulation of cell-matrix adhesion +is_a: GO:0010810 ! regulation of cell-substrate adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007160 ! cell-matrix adhesion +relationship: regulates GO:0007160 ! cell-matrix adhesion + +[Term] +id: GO:0001954 +name: positive regulation of cell-matrix adhesion +is_a: GO:0001952 ! regulation of cell-matrix adhesion +is_a: GO:0010811 ! positive regulation of cell-substrate adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007160 ! cell-matrix adhesion +relationship: positively_regulates GO:0007160 ! cell-matrix adhesion + +[Term] +id: GO:0001959 +name: regulation of cytokine-mediated signaling pathway +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0060759 ! regulation of response to cytokine stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0019221 ! cytokine-mediated signaling pathway +relationship: regulates GO:0019221 ! cytokine-mediated signaling pathway + +[Term] +id: GO:0001961 +name: positive regulation of cytokine-mediated signaling pathway +is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0060760 ! positive regulation of response to cytokine stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0019221 ! cytokine-mediated signaling pathway +relationship: positively_regulates GO:0019221 ! cytokine-mediated signaling pathway + +[Term] +id: GO:0001974 +name: blood vessel remodeling +is_a: GO:0048771 ! tissue remodeling + +[Term] +id: GO:0002009 +name: morphogenesis of an epithelium +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0060429 ! epithelium development + +[Term] +id: GO:0002011 +name: morphogenesis of an epithelial sheet +is_a: GO:0002009 ! morphogenesis of an epithelium + +[Term] +id: GO:0002040 +name: sprouting angiogenesis +is_a: GO:0001525 ! angiogenesis + +[Term] +id: GO:0002042 +name: cell migration involved in sprouting angiogenesis +is_a: GO:0043534 ! blood vessel endothelial cell migration +intersection_of: GO:0016477 ! cell migration +intersection_of: part_of GO:0002040 ! sprouting angiogenesis +relationship: part_of GO:0002040 ! sprouting angiogenesis + +[Term] +id: GO:0002052 +name: positive regulation of neuroblast proliferation +is_a: GO:0050769 ! positive regulation of neurogenesis +is_a: GO:2000179 ! positive regulation of neural precursor cell proliferation +is_a: GO:2000648 ! positive regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007405 ! neuroblast proliferation +relationship: positively_regulates GO:0007405 ! neuroblast proliferation + +[Term] +id: GO:0002053 +name: positive regulation of mesenchymal cell proliferation +is_a: GO:0010464 ! regulation of mesenchymal cell proliferation +is_a: GO:2000648 ! positive regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010463 ! mesenchymal cell proliferation +relationship: positively_regulates GO:0010463 ! mesenchymal cell proliferation + +[Term] +id: GO:0002062 +name: chondrocyte differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0051216 ! cartilage development + +[Term] +id: GO:0002063 +name: chondrocyte development +is_a: GO:0048468 ! cell development +relationship: part_of GO:0002062 ! chondrocyte differentiation + +[Term] +id: GO:0002064 +name: epithelial cell development +is_a: GO:0048468 ! cell development +relationship: part_of GO:0030855 ! epithelial cell differentiation + +[Term] +id: GO:0002065 +name: columnar/cuboidal epithelial cell differentiation +is_a: GO:0030855 ! epithelial cell differentiation + +[Term] +id: GO:0002066 +name: columnar/cuboidal epithelial cell development +is_a: GO:0002064 ! epithelial cell development +relationship: part_of GO:0002065 ! columnar/cuboidal epithelial cell differentiation + +[Term] +id: GO:0002067 +name: glandular epithelial cell differentiation +is_a: GO:0002065 ! columnar/cuboidal epithelial cell differentiation + +[Term] +id: GO:0002068 +name: glandular epithelial cell development +is_a: GO:0002066 ! columnar/cuboidal epithelial cell development +relationship: part_of GO:0002067 ! glandular epithelial cell differentiation + +[Term] +id: GO:0002076 +name: osteoblast development +is_a: GO:0048468 ! cell development +relationship: part_of GO:0001649 ! osteoblast differentiation + +[Term] +id: GO:0002088 +name: lens development in camera-type eye +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0043010 ! camera-type eye development + +[Term] +id: GO:0002089 +name: lens morphogenesis in camera-type eye +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0002088 ! lens development in camera-type eye +relationship: part_of GO:0048593 ! camera-type eye morphogenesis + +[Term] +id: GO:0002090 +name: regulation of receptor internalization +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0048259 ! regulation of receptor-mediated endocytosis +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031623 ! receptor internalization +relationship: regulates GO:0031623 ! receptor internalization + +[Term] +id: GO:0002092 +name: positive regulation of receptor internalization +is_a: GO:0002090 ! regulation of receptor internalization +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0048260 ! positive regulation of receptor-mediated endocytosis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031623 ! receptor internalization +relationship: positively_regulates GO:0031623 ! receptor internalization + +[Term] +id: GO:0002237 +name: response to molecule of bacterial origin +is_a: GO:0009607 ! response to biotic stimulus +is_a: GO:0010033 ! response to organic substance +relationship: part_of GO:0009617 ! response to bacterium + +[Term] +id: GO:0002244 +name: hematopoietic progenitor cell differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030097 ! hemopoiesis + +[Term] +id: GO:0002250 +name: adaptive immune response +is_a: GO:0006955 ! immune response + +[Term] +id: GO:0002252 +name: immune effector process +is_a: GO:0002376 ! immune system process + +[Term] +id: GO:0002274 +name: myeloid leukocyte activation +is_a: GO:0045321 ! leukocyte activation + +[Term] +id: GO:0002367 +name: cytokine production involved in immune response +is_a: GO:0001816 ! cytokine production +is_a: GO:0002440 ! production of molecular mediator of immune response +intersection_of: GO:0001816 ! cytokine production +intersection_of: part_of GO:0006955 ! immune response +relationship: part_of GO:0006955 ! immune response + +[Term] +id: GO:0002374 +name: cytokine secretion involved in immune response +is_a: GO:0050663 ! cytokine secretion +intersection_of: GO:0050663 ! cytokine secretion +intersection_of: part_of GO:0006955 ! immune response +relationship: part_of GO:0002367 ! cytokine production involved in immune response + +[Term] +id: GO:0002376 +name: immune system process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0002440 +name: production of molecular mediator of immune response +is_a: GO:0002376 ! immune system process + +[Term] +id: GO:0002443 +name: leukocyte mediated immunity +is_a: GO:0002252 ! immune effector process + +[Term] +id: GO:0002449 +name: lymphocyte mediated immunity +is_a: GO:0002443 ! leukocyte mediated immunity + +[Term] +id: GO:0002455 +name: humoral immune response mediated by circulating immunoglobulin +is_a: GO:0006959 ! humoral immune response +is_a: GO:0016064 ! immunoglobulin mediated immune response + +[Term] +id: GO:0002460 +name: adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +is_a: GO:0002250 ! adaptive immune response + +[Term] +id: GO:0002467 +name: germinal center formation +is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + +[Term] +id: GO:0002507 +name: tolerance induction +is_a: GO:0002376 ! immune system process +relationship: part_of GO:0002520 ! immune system development + +[Term] +id: GO:0002508 +name: central tolerance induction +is_a: GO:0002507 ! tolerance induction + +[Term] +id: GO:0002510 +name: central B cell tolerance induction +is_a: GO:0002508 ! central tolerance induction +is_a: GO:0002514 ! B cell tolerance induction + +[Term] +id: GO:0002514 +name: B cell tolerance induction +is_a: GO:0002507 ! tolerance induction + +[Term] +id: GO:0002520 +name: immune system development +is_a: GO:0002376 ! immune system process +is_a: GO:0048731 ! system development + +[Term] +id: GO:0002521 +name: leukocyte differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030097 ! hemopoiesis + +[Term] +id: GO:0002526 +name: acute inflammatory response +is_a: GO:0006954 ! inflammatory response + +[Term] +id: GO:0002528 +name: regulation of vascular permeability involved in acute inflammatory response +is_a: GO:0043114 ! regulation of vascular permeability +intersection_of: GO:0043114 ! regulation of vascular permeability +intersection_of: part_of GO:0002526 ! acute inflammatory response +relationship: part_of GO:0002526 ! acute inflammatory response + +[Term] +id: GO:0002573 +name: myeloid leukocyte differentiation +is_a: GO:0002521 ! leukocyte differentiation +is_a: GO:0030099 ! myeloid cell differentiation + +[Term] +id: GO:0002634 +name: regulation of germinal center formation +is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002467 ! germinal center formation +relationship: regulates GO:0002467 ! germinal center formation + +[Term] +id: GO:0002635 +name: negative regulation of germinal center formation +is_a: GO:0002634 ! regulation of germinal center formation +is_a: GO:0002823 ! negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002467 ! germinal center formation +relationship: negatively_regulates GO:0002467 ! germinal center formation + +[Term] +id: GO:0002643 +name: regulation of tolerance induction +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002507 ! tolerance induction +relationship: regulates GO:0002507 ! tolerance induction + +[Term] +id: GO:0002645 +name: positive regulation of tolerance induction +is_a: GO:0002643 ! regulation of tolerance induction +is_a: GO:0002684 ! positive regulation of immune system process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002507 ! tolerance induction +relationship: positively_regulates GO:0002507 ! tolerance induction + +[Term] +id: GO:0002646 +name: regulation of central tolerance induction +is_a: GO:0002643 ! regulation of tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002508 ! central tolerance induction +relationship: regulates GO:0002508 ! central tolerance induction + +[Term] +id: GO:0002648 +name: positive regulation of central tolerance induction +is_a: GO:0002645 ! positive regulation of tolerance induction +is_a: GO:0002646 ! regulation of central tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002508 ! central tolerance induction +relationship: positively_regulates GO:0002508 ! central tolerance induction + +[Term] +id: GO:0002661 +name: regulation of B cell tolerance induction +is_a: GO:0002643 ! regulation of tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002514 ! B cell tolerance induction +relationship: regulates GO:0002514 ! B cell tolerance induction + +[Term] +id: GO:0002663 +name: positive regulation of B cell tolerance induction +is_a: GO:0002645 ! positive regulation of tolerance induction +is_a: GO:0002661 ! regulation of B cell tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002514 ! B cell tolerance induction +relationship: positively_regulates GO:0002514 ! B cell tolerance induction + +[Term] +id: GO:0002682 +name: regulation of immune system process +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002376 ! immune system process +relationship: regulates GO:0002376 ! immune system process + +[Term] +id: GO:0002683 +name: negative regulation of immune system process +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002376 ! immune system process +relationship: negatively_regulates GO:0002376 ! immune system process + +[Term] +id: GO:0002684 +name: positive regulation of immune system process +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002376 ! immune system process +relationship: positively_regulates GO:0002376 ! immune system process + +[Term] +id: GO:0002685 +name: regulation of leukocyte migration +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0030334 ! regulation of cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050900 ! leukocyte migration +relationship: regulates GO:0050900 ! leukocyte migration + +[Term] +id: GO:0002687 +name: positive regulation of leukocyte migration +is_a: GO:0002684 ! positive regulation of immune system process +is_a: GO:0002685 ! regulation of leukocyte migration +is_a: GO:0030335 ! positive regulation of cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050900 ! leukocyte migration +relationship: positively_regulates GO:0050900 ! leukocyte migration + +[Term] +id: GO:0002688 +name: regulation of leukocyte chemotaxis +is_a: GO:0002685 ! regulation of leukocyte migration +is_a: GO:0050920 ! regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030595 ! leukocyte chemotaxis +relationship: regulates GO:0030595 ! leukocyte chemotaxis + +[Term] +id: GO:0002690 +name: positive regulation of leukocyte chemotaxis +is_a: GO:0002687 ! positive regulation of leukocyte migration +is_a: GO:0002688 ! regulation of leukocyte chemotaxis +is_a: GO:0050921 ! positive regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030595 ! leukocyte chemotaxis +relationship: positively_regulates GO:0030595 ! leukocyte chemotaxis + +[Term] +id: GO:0002694 +name: regulation of leukocyte activation +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0050865 ! regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045321 ! leukocyte activation +relationship: regulates GO:0045321 ! leukocyte activation + +[Term] +id: GO:0002695 +name: negative regulation of leukocyte activation +is_a: GO:0002683 ! negative regulation of immune system process +is_a: GO:0002694 ! regulation of leukocyte activation +is_a: GO:0050866 ! negative regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0045321 ! leukocyte activation +relationship: negatively_regulates GO:0045321 ! leukocyte activation + +[Term] +id: GO:0002696 +name: positive regulation of leukocyte activation +is_a: GO:0002684 ! positive regulation of immune system process +is_a: GO:0002694 ! regulation of leukocyte activation +is_a: GO:0050867 ! positive regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0045321 ! leukocyte activation +relationship: positively_regulates GO:0045321 ! leukocyte activation + +[Term] +id: GO:0002697 +name: regulation of immune effector process +is_a: GO:0002682 ! regulation of immune system process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002252 ! immune effector process +relationship: regulates GO:0002252 ! immune effector process + +[Term] +id: GO:0002698 +name: negative regulation of immune effector process +is_a: GO:0002683 ! negative regulation of immune system process +is_a: GO:0002697 ! regulation of immune effector process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002252 ! immune effector process +relationship: negatively_regulates GO:0002252 ! immune effector process + +[Term] +id: GO:0002699 +name: positive regulation of immune effector process +is_a: GO:0002684 ! positive regulation of immune system process +is_a: GO:0002697 ! regulation of immune effector process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002252 ! immune effector process +relationship: positively_regulates GO:0002252 ! immune effector process + +[Term] +id: GO:0002700 +name: regulation of production of molecular mediator of immune response +is_a: GO:0002697 ! regulation of immune effector process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002440 ! production of molecular mediator of immune response +relationship: regulates GO:0002440 ! production of molecular mediator of immune response + +[Term] +id: GO:0002702 +name: positive regulation of production of molecular mediator of immune response +is_a: GO:0002699 ! positive regulation of immune effector process +is_a: GO:0002700 ! regulation of production of molecular mediator of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002440 ! production of molecular mediator of immune response +relationship: positively_regulates GO:0002440 ! production of molecular mediator of immune response + +[Term] +id: GO:0002703 +name: regulation of leukocyte mediated immunity +is_a: GO:0002697 ! regulation of immune effector process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002443 ! leukocyte mediated immunity +relationship: regulates GO:0002443 ! leukocyte mediated immunity + +[Term] +id: GO:0002704 +name: negative regulation of leukocyte mediated immunity +is_a: GO:0002698 ! negative regulation of immune effector process +is_a: GO:0002703 ! regulation of leukocyte mediated immunity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002443 ! leukocyte mediated immunity +relationship: negatively_regulates GO:0002443 ! leukocyte mediated immunity + +[Term] +id: GO:0002706 +name: regulation of lymphocyte mediated immunity +is_a: GO:0002703 ! regulation of leukocyte mediated immunity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002449 ! lymphocyte mediated immunity +relationship: regulates GO:0002449 ! lymphocyte mediated immunity + +[Term] +id: GO:0002707 +name: negative regulation of lymphocyte mediated immunity +is_a: GO:0002704 ! negative regulation of leukocyte mediated immunity +is_a: GO:0002706 ! regulation of lymphocyte mediated immunity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002449 ! lymphocyte mediated immunity +relationship: negatively_regulates GO:0002449 ! lymphocyte mediated immunity + +[Term] +id: GO:0002712 +name: regulation of B cell mediated immunity +is_a: GO:0002706 ! regulation of lymphocyte mediated immunity +is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0019724 ! B cell mediated immunity +relationship: regulates GO:0019724 ! B cell mediated immunity + +[Term] +id: GO:0002713 +name: negative regulation of B cell mediated immunity +is_a: GO:0002707 ! negative regulation of lymphocyte mediated immunity +is_a: GO:0002712 ! regulation of B cell mediated immunity +is_a: GO:0002823 ! negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0019724 ! B cell mediated immunity +relationship: negatively_regulates GO:0019724 ! B cell mediated immunity + +[Term] +id: GO:0002718 +name: regulation of cytokine production involved in immune response +is_a: GO:0001817 ! regulation of cytokine production +is_a: GO:0002700 ! regulation of production of molecular mediator of immune response +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002367 ! cytokine production involved in immune response +relationship: regulates GO:0002367 ! cytokine production involved in immune response + +[Term] +id: GO:0002720 +name: positive regulation of cytokine production involved in immune response +is_a: GO:0001819 ! positive regulation of cytokine production +is_a: GO:0002702 ! positive regulation of production of molecular mediator of immune response +is_a: GO:0002718 ! regulation of cytokine production involved in immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002367 ! cytokine production involved in immune response +relationship: positively_regulates GO:0002367 ! cytokine production involved in immune response + +[Term] +id: GO:0002739 +name: regulation of cytokine secretion involved in immune response +is_a: GO:0002718 ! regulation of cytokine production involved in immune response +is_a: GO:0050707 ! regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002374 ! cytokine secretion involved in immune response +relationship: regulates GO:0002374 ! cytokine secretion involved in immune response + +[Term] +id: GO:0002741 +name: positive regulation of cytokine secretion involved in immune response +is_a: GO:0002739 ! regulation of cytokine secretion involved in immune response +is_a: GO:0050715 ! positive regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002374 ! cytokine secretion involved in immune response +relationship: positively_regulates GO:0002374 ! cytokine secretion involved in immune response + +[Term] +id: GO:0002761 +name: regulation of myeloid leukocyte differentiation +is_a: GO:0045637 ! regulation of myeloid cell differentiation +is_a: GO:1902105 ! regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002573 ! myeloid leukocyte differentiation +relationship: regulates GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0002762 +name: negative regulation of myeloid leukocyte differentiation +is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation +is_a: GO:0045638 ! negative regulation of myeloid cell differentiation +is_a: GO:1902106 ! negative regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002573 ! myeloid leukocyte differentiation +relationship: negatively_regulates GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0002763 +name: positive regulation of myeloid leukocyte differentiation +is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation +is_a: GO:0045639 ! positive regulation of myeloid cell differentiation +is_a: GO:1902107 ! positive regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002573 ! myeloid leukocyte differentiation +relationship: positively_regulates GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0002790 +name: peptide secretion +is_a: GO:0015833 ! peptide transport +is_a: GO:0046903 ! secretion + +[Term] +id: GO:0002791 +name: regulation of peptide secretion +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0090087 ! regulation of peptide transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002790 ! peptide secretion +relationship: regulates GO:0002790 ! peptide secretion + +[Term] +id: GO:0002792 +name: negative regulation of peptide secretion +is_a: GO:0002791 ! regulation of peptide secretion +is_a: GO:0051048 ! negative regulation of secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002790 ! peptide secretion +relationship: negatively_regulates GO:0002790 ! peptide secretion + +[Term] +id: GO:0002819 +name: regulation of adaptive immune response +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002250 ! adaptive immune response +relationship: regulates GO:0002250 ! adaptive immune response + +[Term] +id: GO:0002820 +name: negative regulation of adaptive immune response +is_a: GO:0002819 ! regulation of adaptive immune response +is_a: GO:0050777 ! negative regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002250 ! adaptive immune response +relationship: negatively_regulates GO:0002250 ! adaptive immune response + +[Term] +id: GO:0002822 +name: regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +is_a: GO:0002819 ! regulation of adaptive immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +relationship: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + +[Term] +id: GO:0002823 +name: negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +is_a: GO:0002820 ! negative regulation of adaptive immune response +is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +relationship: negatively_regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + +[Term] +id: GO:0002889 +name: regulation of immunoglobulin mediated immune response +is_a: GO:0002712 ! regulation of B cell mediated immunity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016064 ! immunoglobulin mediated immune response +relationship: regulates GO:0016064 ! immunoglobulin mediated immune response + +[Term] +id: GO:0002890 +name: negative regulation of immunoglobulin mediated immune response +is_a: GO:0002713 ! negative regulation of B cell mediated immunity +is_a: GO:0002889 ! regulation of immunoglobulin mediated immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016064 ! immunoglobulin mediated immune response +relationship: negatively_regulates GO:0016064 ! immunoglobulin mediated immune response + +[Term] +id: GO:0002895 +name: regulation of central B cell tolerance induction +is_a: GO:0002646 ! regulation of central tolerance induction +is_a: GO:0002661 ! regulation of B cell tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002510 ! central B cell tolerance induction +relationship: regulates GO:0002510 ! central B cell tolerance induction + +[Term] +id: GO:0002897 +name: positive regulation of central B cell tolerance induction +is_a: GO:0002648 ! positive regulation of central tolerance induction +is_a: GO:0002663 ! positive regulation of B cell tolerance induction +is_a: GO:0002895 ! regulation of central B cell tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002510 ! central B cell tolerance induction +relationship: positively_regulates GO:0002510 ! central B cell tolerance induction + +[Term] +id: GO:0002920 +name: regulation of humoral immune response +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006959 ! humoral immune response +relationship: regulates GO:0006959 ! humoral immune response + +[Term] +id: GO:0002921 +name: negative regulation of humoral immune response +is_a: GO:0002920 ! regulation of humoral immune response +is_a: GO:0050777 ! negative regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006959 ! humoral immune response +relationship: negatively_regulates GO:0006959 ! humoral immune response + +[Term] +id: GO:0002923 +name: regulation of humoral immune response mediated by circulating immunoglobulin +is_a: GO:0002889 ! regulation of immunoglobulin mediated immune response +is_a: GO:0002920 ! regulation of humoral immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002455 ! humoral immune response mediated by circulating immunoglobulin +relationship: regulates GO:0002455 ! humoral immune response mediated by circulating immunoglobulin + +[Term] +id: GO:0002924 +name: negative regulation of humoral immune response mediated by circulating immunoglobulin +is_a: GO:0002890 ! negative regulation of immunoglobulin mediated immune response +is_a: GO:0002921 ! negative regulation of humoral immune response +is_a: GO:0002923 ! regulation of humoral immune response mediated by circulating immunoglobulin +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002455 ! humoral immune response mediated by circulating immunoglobulin +relationship: negatively_regulates GO:0002455 ! humoral immune response mediated by circulating immunoglobulin + +[Term] +id: GO:0003001 +name: generation of a signal involved in cell-cell signaling +is_a: GO:0044763 ! single-organism cellular process +relationship: part_of GO:0007267 ! cell-cell signaling + +[Term] +id: GO:0003002 +name: regionalization +is_a: GO:0007389 ! pattern specification process + +[Term] +id: GO:0003006 +name: developmental process involved in reproduction +is_a: GO:0022414 ! reproductive process +is_a: GO:0032502 ! developmental process +intersection_of: GO:0032502 ! developmental process +intersection_of: part_of GO:0000003 ! reproduction + +[Term] +id: GO:0003007 +name: heart morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0003008 +name: system process +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0003013 +name: circulatory system process +is_a: GO:0003008 ! system process + +[Term] +id: GO:0003015 +name: heart process +is_a: GO:0003013 ! circulatory system process + +[Term] +id: GO:0003018 +name: vascular process in circulatory system +is_a: GO:0003013 ! circulatory system process + +[Term] +id: GO:0003128 +name: heart field specification +is_a: GO:0010092 ! specification of organ identity +relationship: part_of GO:0060914 ! heart formation + +[Term] +id: GO:0003129 +name: heart induction +is_a: GO:0001759 ! organ induction +is_a: GO:2000826 ! regulation of heart morphogenesis +relationship: positively_regulates GO:0003128 ! heart field specification + +[Term] +id: GO:0003136 +name: negative regulation of heart induction by canonical Wnt receptor signaling pathway +is_a: GO:0009997 ! negative regulation of cardioblast cell fate specification +is_a: GO:0061316 ! canonical Wnt receptor signaling pathway involved in heart development +is_a: GO:1901320 ! negative regulation of heart induction +relationship: negatively_regulates GO:0003129 ! heart induction + +[Term] +id: GO:0003139 +name: secondary heart field specification +is_a: GO:0003128 ! heart field specification + +[Term] +id: GO:0003143 +name: embryonic heart tube morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +is_a: GO:0060562 ! epithelial tube morphogenesis +relationship: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0035050 ! embryonic heart tube development +relationship: part_of GO:0048562 ! embryonic organ morphogenesis + +[Term] +id: GO:0003151 +name: outflow tract morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0003007 ! heart morphogenesis + +[Term] +id: GO:0003156 +name: regulation of organ formation +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048645 ! organ formation +relationship: regulates GO:0048645 ! organ formation + +[Term] +id: GO:0003158 +name: endothelium development +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0003159 +name: morphogenesis of an endothelium +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0003158 ! endothelium development + +[Term] +id: GO:0003205 +name: cardiac chamber development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0003206 +name: cardiac chamber morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0003205 ! cardiac chamber development + +[Term] +id: GO:0003208 +name: cardiac ventricle morphogenesis +is_a: GO:0003206 ! cardiac chamber morphogenesis +relationship: part_of GO:0003231 ! cardiac ventricle development + +[Term] +id: GO:0003209 +name: cardiac atrium morphogenesis +is_a: GO:0003206 ! cardiac chamber morphogenesis +relationship: part_of GO:0003230 ! cardiac atrium development + +[Term] +id: GO:0003213 +name: cardiac right atrium morphogenesis +is_a: GO:0003209 ! cardiac atrium morphogenesis + +[Term] +id: GO:0003214 +name: cardiac left ventricle morphogenesis +is_a: GO:0003208 ! cardiac ventricle morphogenesis + +[Term] +id: GO:0003215 +name: cardiac right ventricle morphogenesis +is_a: GO:0003208 ! cardiac ventricle morphogenesis + +[Term] +id: GO:0003222 +name: ventricular trabecula myocardium morphogenesis +is_a: GO:0055010 ! ventricular cardiac muscle tissue morphogenesis +is_a: GO:0061384 ! heart trabecula morphogenesis + +[Term] +id: GO:0003223 +name: ventricular compact myocardium morphogenesis +is_a: GO:0055010 ! ventricular cardiac muscle tissue morphogenesis + +[Term] +id: GO:0003229 +name: ventricular cardiac muscle tissue development +is_a: GO:0048738 ! cardiac muscle tissue development + +[Term] +id: GO:0003230 +name: cardiac atrium development +is_a: GO:0003205 ! cardiac chamber development + +[Term] +id: GO:0003231 +name: cardiac ventricle development +is_a: GO:0003205 ! cardiac chamber development + +[Term] +id: GO:0003263 +name: cardioblast proliferation +is_a: GO:0061323 ! cell proliferation involved in heart morphogenesis +relationship: part_of GO:0060914 ! heart formation + +[Term] +id: GO:0003264 +name: regulation of cardioblast proliferation +is_a: GO:0003156 ! regulation of organ formation +is_a: GO:2000136 ! regulation of cell proliferation involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003263 ! cardioblast proliferation +relationship: regulates GO:0003263 ! cardioblast proliferation + +[Term] +id: GO:0003266 +name: regulation of secondary heart field cardioblast proliferation +is_a: GO:0003264 ! regulation of cardioblast proliferation + +[Term] +id: GO:0003275 +name: apoptotic process involved in outflow tract morphogenesis +is_a: GO:0003278 ! apoptotic process involved in heart morphogenesis +intersection_of: GO:0006915 ! apoptotic process +intersection_of: part_of GO:0003151 ! outflow tract morphogenesis +relationship: part_of GO:0003151 ! outflow tract morphogenesis + +[Term] +id: GO:0003278 +name: apoptotic process involved in heart morphogenesis +is_a: GO:0060561 ! apoptotic process involved in morphogenesis +intersection_of: GO:0006915 ! apoptotic process +intersection_of: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0003007 ! heart morphogenesis + +[Term] +id: GO:0003279 +name: cardiac septum development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0003205 ! cardiac chamber development + +[Term] +id: GO:0003281 +name: ventricular septum development +is_a: GO:0003279 ! cardiac septum development +relationship: part_of GO:0003231 ! cardiac ventricle development + +[Term] +id: GO:0003306 +name: Wnt receptor signaling pathway involved in heart development +is_a: GO:0016055 ! Wnt receptor signaling pathway +is_a: GO:0061311 ! cell surface receptor signaling pathway involved in heart development +intersection_of: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: part_of GO:0007507 ! heart development + +[Term] +id: GO:0003307 +name: regulation of Wnt receptor signaling pathway involved in heart development +is_a: GO:0030111 ! regulation of Wnt receptor signaling pathway +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003306 ! Wnt receptor signaling pathway involved in heart development +relationship: regulates GO:0003306 ! Wnt receptor signaling pathway involved in heart development + +[Term] +id: GO:0003308 +name: negative regulation of Wnt receptor signaling pathway involved in heart development +is_a: GO:0003307 ! regulation of Wnt receptor signaling pathway involved in heart development +is_a: GO:0030178 ! negative regulation of Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003306 ! Wnt receptor signaling pathway involved in heart development +relationship: negatively_regulates GO:0003306 ! Wnt receptor signaling pathway involved in heart development + +[Term] +id: GO:0003309 +name: type B pancreatic cell differentiation +is_a: GO:0035883 ! enteroendocrine cell differentiation +relationship: part_of GO:0031018 ! endocrine pancreas development + +[Term] +id: GO:0003323 +name: type B pancreatic cell development +is_a: GO:0002068 ! glandular epithelial cell development +relationship: part_of GO:0003309 ! type B pancreatic cell differentiation + +[Term] +id: GO:0003337 +name: mesenchymal to epithelial transition involved in metanephros morphogenesis +is_a: GO:0060231 ! mesenchymal to epithelial transition +intersection_of: GO:0060231 ! mesenchymal to epithelial transition +intersection_of: part_of GO:0003338 ! metanephros morphogenesis +relationship: part_of GO:0072283 ! metanephric renal vesicle morphogenesis + +[Term] +id: GO:0003338 +name: metanephros morphogenesis +is_a: GO:0060993 ! kidney morphogenesis +relationship: part_of GO:0001656 ! metanephros development + +[Term] +id: GO:0003344 +name: pericardium morphogenesis +is_a: GO:0002011 ! morphogenesis of an epithelial sheet +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0060039 ! pericardium development + +[Term] +id: GO:0003382 +name: epithelial cell morphogenesis +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +relationship: part_of GO:0002064 ! epithelial cell development + +[Term] +id: GO:0003401 +name: axis elongation +is_a: GO:0060560 ! developmental growth involved in morphogenesis + +[Term] +id: GO:0003402 +name: planar cell polarity pathway involved in axis elongation +is_a: GO:0060071 ! Wnt receptor signaling pathway, planar cell polarity pathway +intersection_of: GO:0060071 ! Wnt receptor signaling pathway, planar cell polarity pathway +intersection_of: part_of GO:0003401 ! axis elongation +relationship: part_of GO:0003401 ! axis elongation + +[Term] +id: GO:0003674 +name: molecular_function + +[Term] +id: GO:0003676 +name: nucleic acid binding +is_a: GO:0097159 ! organic cyclic compound binding +is_a: GO:1901363 ! heterocyclic compound binding + +[Term] +id: GO:0003677 +name: DNA binding +is_a: GO:0003676 ! nucleic acid binding + +[Term] +id: GO:0003682 +name: chromatin binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:0003690 +name: double-stranded DNA binding +is_a: GO:0043566 ! structure-specific DNA binding + +[Term] +id: GO:0003700 +name: sequence-specific DNA binding transcription factor activity +is_a: GO:0001071 ! nucleic acid binding transcription factor activity +relationship: has_part GO:0000976 ! transcription regulatory region sequence-specific DNA binding +relationship: part_of GO:0006355 ! regulation of transcription, DNA-dependent + +[Term] +id: GO:0003705 +name: RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: has_part GO:0000980 ! RNA polymerase II distal enhancer sequence-specific DNA binding + +[Term] +id: GO:0003707 +name: steroid hormone receptor activity +is_a: GO:0038023 ! signaling receptor activity +relationship: part_of GO:0043401 ! steroid hormone mediated signaling pathway + +[Term] +id: GO:0003712 +name: transcription cofactor activity +is_a: GO:0000989 ! transcription factor binding transcription factor activity +relationship: has_part GO:0001098 ! basal transcription machinery binding + +[Term] +id: GO:0003713 +name: transcription coactivator activity +is_a: GO:0003712 ! transcription cofactor activity +relationship: has_part GO:0033613 ! activating transcription factor binding + +[Term] +id: GO:0003714 +name: transcription corepressor activity +is_a: GO:0003712 ! transcription cofactor activity +relationship: has_part GO:0070491 ! repressing transcription factor binding + +[Term] +id: GO:0003824 +name: catalytic activity +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0008152 ! metabolic process + +[Term] +id: GO:0003924 +name: GTPase activity +is_a: GO:0017111 ! nucleoside-triphosphatase activity +relationship: part_of GO:0006184 ! GTP catabolic process + +[Term] +id: GO:0004175 +name: endopeptidase activity +is_a: GO:0070011 ! peptidase activity, acting on L-amino acid peptides + +[Term] +id: GO:0004197 +name: cysteine-type endopeptidase activity +is_a: GO:0004175 ! endopeptidase activity +is_a: GO:0008234 ! cysteine-type peptidase activity + +[Term] +id: GO:0004340 +name: glucokinase activity +is_a: GO:0004396 ! hexokinase activity +relationship: part_of GO:0051156 ! glucose 6-phosphate metabolic process + +[Term] +id: GO:0004396 +name: hexokinase activity +is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor +is_a: GO:0019200 ! carbohydrate kinase activity + +[Term] +id: GO:0004672 +name: protein kinase activity +is_a: GO:0016301 ! kinase activity +is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor +relationship: part_of GO:0006468 ! protein phosphorylation + +[Term] +id: GO:0004674 +name: protein serine/threonine kinase activity +is_a: GO:0004672 ! protein kinase activity + +[Term] +id: GO:0004702 +name: receptor signaling protein serine/threonine kinase activity +is_a: GO:0004674 ! protein serine/threonine kinase activity +is_a: GO:0005057 ! receptor signaling protein activity +relationship: part_of GO:0023014 ! signal transduction by phosphorylation + +[Term] +id: GO:0004705 +name: JUN kinase activity +is_a: GO:0016909 ! SAP kinase activity +relationship: part_of GO:0007258 ! JUN phosphorylation + +[Term] +id: GO:0004707 +name: MAP kinase activity +is_a: GO:0004702 ! receptor signaling protein serine/threonine kinase activity +relationship: part_of GO:0000165 ! MAPK cascade + +[Term] +id: GO:0004713 +name: protein tyrosine kinase activity +is_a: GO:0004672 ! protein kinase activity + +[Term] +id: GO:0004857 +name: enzyme inhibitor activity +is_a: GO:0030234 ! enzyme regulator activity +relationship: part_of GO:0043086 ! negative regulation of catalytic activity + +[Term] +id: GO:0004871 +name: signal transducer activity +is_a: GO:0060089 ! molecular transducer activity +relationship: part_of GO:0007165 ! signal transduction + +[Term] +id: GO:0004872 +name: receptor activity +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0004879 +name: ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +is_a: GO:0038023 ! signaling receptor activity +relationship: part_of GO:0030522 ! intracellular receptor signaling pathway + +[Term] +id: GO:0004882 +name: androgen receptor activity +is_a: GO:0003707 ! steroid hormone receptor activity +is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: has_part GO:0005497 ! androgen binding +relationship: part_of GO:0030521 ! androgen receptor signaling pathway + +[Term] +id: GO:0004888 +name: transmembrane signaling receptor activity +is_a: GO:0038023 ! signaling receptor activity + +[Term] +id: GO:0005041 +name: low-density lipoprotein receptor activity +is_a: GO:0030228 ! lipoprotein particle receptor activity +relationship: has_part GO:0030169 ! low-density lipoprotein particle binding + +[Term] +id: GO:0005057 +name: receptor signaling protein activity +is_a: GO:0004871 ! signal transducer activity + +[Term] +id: GO:0005102 +name: receptor binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0005109 +name: frizzled binding +is_a: GO:0001664 ! G-protein coupled receptor binding + +[Term] +id: GO:0005110 +name: frizzled-2 binding +is_a: GO:0005109 ! frizzled binding + +[Term] +id: GO:0005115 +name: receptor tyrosine kinase-like orphan receptor binding +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0005125 +name: cytokine activity +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0005198 +name: structural molecule activity +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0005215 +name: transporter activity +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0006810 ! transport + +[Term] +id: GO:0005488 +name: binding +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0005496 +name: steroid binding +is_a: GO:0008289 ! lipid binding +is_a: GO:0097159 ! organic cyclic compound binding + +[Term] +id: GO:0005497 +name: androgen binding +is_a: GO:0005496 ! steroid binding +is_a: GO:0042562 ! hormone binding + +[Term] +id: GO:0005509 +name: calcium ion binding +is_a: GO:0046872 ! metal ion binding + +[Term] +id: GO:0005515 +name: protein binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:0005539 +name: glycosaminoglycan binding +is_a: GO:0097367 ! carbohydrate derivative binding + +[Term] +id: GO:0005575 +name: cellular_component + +[Term] +id: GO:0005576 +name: extracellular region +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0005578 +name: proteinaceous extracellular matrix +is_a: GO:0031012 ! extracellular matrix +is_a: GO:0044421 ! extracellular region part + +[Term] +id: GO:0005615 +name: extracellular space +is_a: GO:0044421 ! extracellular region part + +[Term] +id: GO:0005622 +name: intracellular +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0005623 +name: cell +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0005634 +name: nucleus +is_a: GO:0043231 ! intracellular membrane-bounded organelle + +[Term] +id: GO:0005654 +name: nucleoplasm +is_a: GO:0044428 ! nuclear part +relationship: part_of GO:0031981 ! nuclear lumen + +[Term] +id: GO:0005667 +name: transcription factor complex +is_a: GO:0043234 ! protein complex +is_a: GO:0044451 ! nucleoplasm part + +[Term] +id: GO:0005694 +name: chromosome +is_a: GO:0043232 ! intracellular non-membrane-bounded organelle + +[Term] +id: GO:0005720 +name: nuclear heterochromatin +is_a: GO:0000790 ! nuclear chromatin +is_a: GO:0000792 ! heterochromatin +intersection_of: GO:0000792 ! heterochromatin +intersection_of: part_of GO:0000228 ! nuclear chromosome + +[Term] +id: GO:0005737 +name: cytoplasm +is_a: GO:0044424 ! intracellular part + +[Term] +id: GO:0005739 +name: mitochondrion +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0005768 +name: endosome +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0005769 +name: early endosome +is_a: GO:0005768 ! endosome + +[Term] +id: GO:0005783 +name: endoplasmic reticulum +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0005788 +name: endoplasmic reticulum lumen +is_a: GO:0044432 ! endoplasmic reticulum part +is_a: GO:0070013 ! intracellular organelle lumen + +[Term] +id: GO:0005791 +name: rough endoplasmic reticulum +is_a: GO:0005783 ! endoplasmic reticulum + +[Term] +id: GO:0005794 +name: Golgi apparatus +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0005813 +name: centrosome +is_a: GO:0005815 ! microtubule organizing center +is_a: GO:0043232 ! intracellular non-membrane-bounded organelle + +[Term] +id: GO:0005815 +name: microtubule organizing center +is_a: GO:0044430 ! cytoskeletal part +relationship: part_of GO:0015630 ! microtubule cytoskeleton + +[Term] +id: GO:0005829 +name: cytosol +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0005856 +name: cytoskeleton +is_a: GO:0043232 ! intracellular non-membrane-bounded organelle + +[Term] +id: GO:0005875 +name: microtubule associated complex +is_a: GO:0043234 ! protein complex +is_a: GO:0044430 ! cytoskeletal part +relationship: part_of GO:0015630 ! microtubule cytoskeleton + +[Term] +id: GO:0005886 +name: plasma membrane +is_a: GO:0016020 ! membrane +is_a: GO:0044464 ! cell part +relationship: part_of GO:0071944 ! cell periphery + +[Term] +id: GO:0005901 +name: caveola +is_a: GO:0044459 ! plasma membrane part +is_a: GO:0045121 ! membrane raft + +[Term] +id: GO:0005902 +name: microvillus +is_a: GO:0042995 ! cell projection + +[Term] +id: GO:0005903 +name: brush border +is_a: GO:0042995 ! cell projection + +[Term] +id: GO:0005905 +name: coated pit +is_a: GO:0044425 ! membrane part +is_a: GO:0044464 ! cell part +relationship: part_of GO:0012505 ! endomembrane system + +[Term] +id: GO:0005911 +name: cell-cell junction +is_a: GO:0030054 ! cell junction + +[Term] +id: GO:0005912 +name: adherens junction +is_a: GO:0070161 ! anchoring junction + +[Term] +id: GO:0005913 +name: cell-cell adherens junction +is_a: GO:0005911 ! cell-cell junction +is_a: GO:0005912 ! adherens junction + +[Term] +id: GO:0005915 +name: zonula adherens +is_a: GO:0005913 ! cell-cell adherens junction +relationship: part_of GO:0043296 ! apical junction complex + +[Term] +id: GO:0005916 +name: fascia adherens +is_a: GO:0005913 ! cell-cell adherens junction +relationship: part_of GO:0014704 ! intercalated disc + +[Term] +id: GO:0005924 +name: cell-substrate adherens junction +is_a: GO:0005912 ! adherens junction +is_a: GO:0030055 ! cell-substrate junction + +[Term] +id: GO:0005938 +name: cell cortex +is_a: GO:0044444 ! cytoplasmic part +relationship: part_of GO:0071944 ! cell periphery + +[Term] +id: GO:0005975 +name: carbohydrate metabolic process +is_a: GO:0044238 ! primary metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0005996 +name: monosaccharide metabolic process +is_a: GO:0044723 ! single-organism carbohydrate metabolic process + +[Term] +id: GO:0006006 +name: glucose metabolic process +is_a: GO:0019318 ! hexose metabolic process + +[Term] +id: GO:0006007 +name: glucose catabolic process +is_a: GO:0006006 ! glucose metabolic process +is_a: GO:0019320 ! hexose catabolic process + +[Term] +id: GO:0006022 +name: aminoglycan metabolic process +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process + +[Term] +id: GO:0006029 +name: proteoglycan metabolic process +is_a: GO:0009100 ! glycoprotein metabolic process + +[Term] +id: GO:0006066 +name: alcohol metabolic process +is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:1901615 ! organic hydroxy compound metabolic process + +[Term] +id: GO:0006082 +name: organic acid metabolic process +is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0006109 +name: regulation of carbohydrate metabolic process +is_a: GO:0080090 ! regulation of primary metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0005975 ! carbohydrate metabolic process +relationship: regulates GO:0005975 ! carbohydrate metabolic process + +[Term] +id: GO:0006139 +name: nucleobase-containing compound metabolic process +is_a: GO:0006725 ! cellular aromatic compound metabolic process +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +is_a: GO:0044238 ! primary metabolic process +is_a: GO:0046483 ! heterocycle metabolic process +is_a: GO:1901360 ! organic cyclic compound metabolic process + +[Term] +id: GO:0006140 +name: regulation of nucleotide metabolic process +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +is_a: GO:0019220 ! regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009117 ! nucleotide metabolic process +relationship: regulates GO:0009117 ! nucleotide metabolic process + +[Term] +id: GO:0006152 +name: purine nucleoside catabolic process +is_a: GO:0009164 ! nucleoside catabolic process +is_a: GO:0042278 ! purine nucleoside metabolic process +is_a: GO:0072523 ! purine-containing compound catabolic process + +[Term] +id: GO:0006163 +name: purine nucleotide metabolic process +is_a: GO:0009117 ! nucleotide metabolic process +is_a: GO:0072521 ! purine-containing compound metabolic process + +[Term] +id: GO:0006184 +name: GTP catabolic process +is_a: GO:0009154 ! purine ribonucleotide catabolic process +is_a: GO:0009207 ! purine ribonucleoside triphosphate catabolic process +is_a: GO:0046039 ! GTP metabolic process +is_a: GO:1901069 ! guanosine-containing compound catabolic process + +[Term] +id: GO:0006195 +name: purine nucleotide catabolic process +is_a: GO:0006163 ! purine nucleotide metabolic process +is_a: GO:0009166 ! nucleotide catabolic process +is_a: GO:0072523 ! purine-containing compound catabolic process + +[Term] +id: GO:0006259 +name: DNA metabolic process +is_a: GO:0044260 ! cellular macromolecule metabolic process +is_a: GO:0090304 ! nucleic acid metabolic process + +[Term] +id: GO:0006308 +name: DNA catabolic process +is_a: GO:0006259 ! DNA metabolic process +is_a: GO:0034655 ! nucleobase-containing compound catabolic process +is_a: GO:0044265 ! cellular macromolecule catabolic process + +[Term] +id: GO:0006309 +name: apoptotic DNA fragmentation +is_a: GO:0000737 ! DNA catabolic process, endonucleolytic +intersection_of: GO:0000737 ! DNA catabolic process, endonucleolytic +intersection_of: part_of GO:0030262 ! apoptotic nuclear changes +relationship: part_of GO:0030262 ! apoptotic nuclear changes + +[Term] +id: GO:0006325 +name: chromatin organization +is_a: GO:0051276 ! chromosome organization + +[Term] +id: GO:0006351 +name: transcription, DNA-dependent +is_a: GO:0032774 ! RNA biosynthetic process +is_a: GO:0034645 ! cellular macromolecule biosynthetic process +relationship: part_of GO:0010467 ! gene expression + +[Term] +id: GO:0006352 +name: DNA-dependent transcription, initiation +is_a: GO:0032774 ! RNA biosynthetic process +relationship: part_of GO:0006351 ! transcription, DNA-dependent + +[Term] +id: GO:0006355 +name: regulation of transcription, DNA-dependent +is_a: GO:0010468 ! regulation of gene expression +is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process +is_a: GO:2001141 ! regulation of RNA biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006351 ! transcription, DNA-dependent +relationship: regulates GO:0006351 ! transcription, DNA-dependent + +[Term] +id: GO:0006357 +name: regulation of transcription from RNA polymerase II promoter +is_a: GO:0006355 ! regulation of transcription, DNA-dependent +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter +relationship: regulates GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0006359 +name: regulation of transcription from RNA polymerase III promoter +is_a: GO:0006355 ! regulation of transcription, DNA-dependent +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006383 ! transcription from RNA polymerase III promoter +relationship: regulates GO:0006383 ! transcription from RNA polymerase III promoter + +[Term] +id: GO:0006366 +name: transcription from RNA polymerase II promoter +is_a: GO:0006351 ! transcription, DNA-dependent + +[Term] +id: GO:0006367 +name: transcription initiation from RNA polymerase II promoter +is_a: GO:0006352 ! DNA-dependent transcription, initiation +relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0006383 +name: transcription from RNA polymerase III promoter +is_a: GO:0006351 ! transcription, DNA-dependent + +[Term] +id: GO:0006461 +name: protein complex assembly +is_a: GO:0065003 ! macromolecular complex assembly +is_a: GO:0071822 ! protein complex subunit organization +relationship: part_of GO:0070271 ! protein complex biogenesis + +[Term] +id: GO:0006464 +name: cellular protein modification process +is_a: GO:0036211 ! protein modification process +is_a: GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0006468 +name: protein phosphorylation +is_a: GO:0006464 ! cellular protein modification process +is_a: GO:0016310 ! phosphorylation + +[Term] +id: GO:0006469 +name: negative regulation of protein kinase activity +is_a: GO:0001933 ! negative regulation of protein phosphorylation +is_a: GO:0033673 ! negative regulation of kinase activity +is_a: GO:0045859 ! regulation of protein kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004672 ! protein kinase activity +relationship: negatively_regulates GO:0004672 ! protein kinase activity + +[Term] +id: GO:0006497 +name: protein lipidation +is_a: GO:0006464 ! cellular protein modification process +relationship: part_of GO:0042158 ! lipoprotein biosynthetic process + +[Term] +id: GO:0006508 +name: proteolysis +is_a: GO:0019538 ! protein metabolic process + +[Term] +id: GO:0006511 +name: ubiquitin-dependent protein catabolic process +is_a: GO:0019941 ! modification-dependent protein catabolic process + +[Term] +id: GO:0006605 +name: protein targeting +is_a: GO:0006886 ! intracellular protein transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0006606 +name: protein import into nucleus +is_a: GO:0006886 ! intracellular protein transport +is_a: GO:0017038 ! protein import +is_a: GO:0051170 ! nuclear import +relationship: part_of GO:0034504 ! protein localization to nucleus +relationship: part_of GO:0044744 ! protein targeting to nucleus + +[Term] +id: GO:0006629 +name: lipid metabolic process +is_a: GO:0044238 ! primary metabolic process +is_a: GO:0044710 ! single-organism metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0006694 +name: steroid biosynthetic process +is_a: GO:0008202 ! steroid metabolic process +is_a: GO:0008610 ! lipid biosynthetic process +is_a: GO:1901362 ! organic cyclic compound biosynthetic process + +[Term] +id: GO:0006700 +name: C21-steroid hormone biosynthetic process +is_a: GO:0006694 ! steroid biosynthetic process +is_a: GO:0008207 ! C21-steroid hormone metabolic process +is_a: GO:0042446 ! hormone biosynthetic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0006702 +name: androgen biosynthetic process +is_a: GO:0006694 ! steroid biosynthetic process +is_a: GO:0008209 ! androgen metabolic process +is_a: GO:0042446 ! hormone biosynthetic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0006704 +name: glucocorticoid biosynthetic process +is_a: GO:0006694 ! steroid biosynthetic process +is_a: GO:0008211 ! glucocorticoid metabolic process + +[Term] +id: GO:0006705 +name: mineralocorticoid biosynthetic process +is_a: GO:0006694 ! steroid biosynthetic process +is_a: GO:0008212 ! mineralocorticoid metabolic process +is_a: GO:0042446 ! hormone biosynthetic process + +[Term] +id: GO:0006725 +name: cellular aromatic compound metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0006753 +name: nucleoside phosphate metabolic process +is_a: GO:0006796 ! phosphate-containing compound metabolic process +is_a: GO:0019637 ! organophosphate metabolic process +is_a: GO:0055086 ! nucleobase-containing small molecule metabolic process + +[Term] +id: GO:0006766 +name: vitamin metabolic process +is_a: GO:0044281 ! small molecule metabolic process + +[Term] +id: GO:0006790 +name: sulfur compound metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0006793 +name: phosphorus metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0006796 +name: phosphate-containing compound metabolic process +is_a: GO:0006793 ! phosphorus metabolic process + +[Term] +id: GO:0006807 +name: nitrogen compound metabolic process +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0006810 +name: transport +is_a: GO:0051234 ! establishment of localization + +[Term] +id: GO:0006811 +name: ion transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0006812 +name: cation transport +is_a: GO:0006811 ! ion transport + +[Term] +id: GO:0006816 +name: calcium ion transport +is_a: GO:0070838 ! divalent metal ion transport + +[Term] +id: GO:0006836 +name: neurotransmitter transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0006869 +name: lipid transport +is_a: GO:0044765 ! single-organism transport +is_a: GO:0071702 ! organic substance transport +relationship: part_of GO:0010876 ! lipid localization + +[Term] +id: GO:0006873 +name: cellular ion homeostasis +is_a: GO:0050801 ! ion homeostasis +is_a: GO:0055082 ! cellular chemical homeostasis + +[Term] +id: GO:0006874 +name: cellular calcium ion homeostasis +is_a: GO:0006875 ! cellular metal ion homeostasis +is_a: GO:0055074 ! calcium ion homeostasis +is_a: GO:0072503 ! cellular divalent inorganic cation homeostasis + +[Term] +id: GO:0006875 +name: cellular metal ion homeostasis +is_a: GO:0030003 ! cellular cation homeostasis +is_a: GO:0055065 ! metal ion homeostasis + +[Term] +id: GO:0006886 +name: intracellular protein transport +is_a: GO:0015031 ! protein transport +is_a: GO:0046907 ! intracellular transport +intersection_of: GO:0015031 ! protein transport +intersection_of: occurs_in GO:0005622 ! intracellular +relationship: part_of GO:0034613 ! cellular protein localization + +[Term] +id: GO:0006897 +name: endocytosis +is_a: GO:0016192 ! vesicle-mediated transport +relationship: has_part GO:0010324 ! membrane invagination + +[Term] +id: GO:0006898 +name: receptor-mediated endocytosis +is_a: GO:0006897 ! endocytosis + +[Term] +id: GO:0006913 +name: nucleocytoplasmic transport +is_a: GO:0051169 ! nuclear transport + +[Term] +id: GO:0006915 +name: apoptotic process +is_a: GO:0012501 ! programmed cell death + +[Term] +id: GO:0006921 +name: cellular component disassembly involved in execution phase of apoptosis +is_a: GO:0022411 ! cellular component disassembly +intersection_of: GO:0022411 ! cellular component disassembly +intersection_of: part_of GO:0097194 ! execution phase of apoptosis +relationship: part_of GO:0097194 ! execution phase of apoptosis + +[Term] +id: GO:0006928 +name: cellular component movement +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0006935 +name: chemotaxis +is_a: GO:0042221 ! response to chemical stimulus +is_a: GO:0042330 ! taxis + +[Term] +id: GO:0006944 +name: cellular membrane fusion +is_a: GO:0016044 ! cellular membrane organization +is_a: GO:0061025 ! membrane fusion + +[Term] +id: GO:0006949 +name: syncytium formation +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis + +[Term] +id: GO:0006950 +name: response to stress +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0006952 +name: defense response +is_a: GO:0006950 ! response to stress + +[Term] +id: GO:0006954 +name: inflammatory response +is_a: GO:0006952 ! defense response +is_a: GO:0009611 ! response to wounding + +[Term] +id: GO:0006955 +name: immune response +is_a: GO:0002376 ! immune system process +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0006959 +name: humoral immune response +is_a: GO:0006955 ! immune response + +[Term] +id: GO:0006974 +name: response to DNA damage stimulus +is_a: GO:0033554 ! cellular response to stress + +[Term] +id: GO:0006996 +name: organelle organization +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007009 +name: plasma membrane organization +is_a: GO:0016044 ! cellular membrane organization + +[Term] +id: GO:0007010 +name: cytoskeleton organization +is_a: GO:0006996 ! organelle organization + +[Term] +id: GO:0007015 +name: actin filament organization +is_a: GO:0071822 ! protein complex subunit organization +relationship: part_of GO:0030036 ! actin cytoskeleton organization + +[Term] +id: GO:0007016 +name: cytoskeletal anchoring at plasma membrane +is_a: GO:0007010 ! cytoskeleton organization +is_a: GO:0032507 ! maintenance of protein location in cell + +[Term] +id: GO:0007017 +name: microtubule-based process +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007044 +name: cell-substrate junction assembly +is_a: GO:0034329 ! cell junction assembly + +[Term] +id: GO:0007045 +name: cell-substrate adherens junction assembly +is_a: GO:0007044 ! cell-substrate junction assembly +is_a: GO:0034333 ! adherens junction assembly + +[Term] +id: GO:0007049 +name: cell cycle +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007059 +name: chromosome segregation +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007062 +name: sister chromatid cohesion +is_a: GO:0022402 ! cell cycle process +is_a: GO:0051276 ! chromosome organization +relationship: part_of GO:0007059 ! chromosome segregation + +[Term] +id: GO:0007063 +name: regulation of sister chromatid cohesion +is_a: GO:0010564 ! regulation of cell cycle process +is_a: GO:0033044 ! regulation of chromosome organization +is_a: GO:0051983 ! regulation of chromosome segregation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007062 ! sister chromatid cohesion +relationship: regulates GO:0007062 ! sister chromatid cohesion + +[Term] +id: GO:0007067 +name: mitosis +is_a: GO:0000280 ! nuclear division +is_a: GO:0022402 ! cell cycle process +relationship: part_of GO:0000278 ! mitotic cell cycle + +[Term] +id: GO:0007088 +name: regulation of mitosis +is_a: GO:0007346 ! regulation of mitotic cell cycle +is_a: GO:0010564 ! regulation of cell cycle process +is_a: GO:0051783 ! regulation of nuclear division +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007067 ! mitosis +relationship: regulates GO:0007067 ! mitosis + +[Term] +id: GO:0007098 +name: centrosome cycle +is_a: GO:0022402 ! cell cycle process +is_a: GO:0051297 ! centrosome organization + +[Term] +id: GO:0007126 +name: meiosis +is_a: GO:0022402 ! cell cycle process +is_a: GO:0048610 ! cellular process involved in reproduction +relationship: part_of GO:0051321 ! meiotic cell cycle + +[Term] +id: GO:0007154 +name: cell communication +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007155 +name: cell adhesion +is_a: GO:0022610 ! biological adhesion +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007160 +name: cell-matrix adhesion +is_a: GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0007162 +name: negative regulation of cell adhesion +is_a: GO:0030155 ! regulation of cell adhesion +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007155 ! cell adhesion +relationship: negatively_regulates GO:0007155 ! cell adhesion + +[Term] +id: GO:0007163 +name: establishment or maintenance of cell polarity +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007164 +name: establishment of tissue polarity +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0007165 +name: signal transduction +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051716 ! cellular response to stimulus +relationship: part_of GO:0007154 ! cell communication +relationship: part_of GO:0044700 ! single organism signaling + +[Term] +id: GO:0007166 +name: cell surface receptor signaling pathway +is_a: GO:0007165 ! signal transduction + +[Term] +id: GO:0007167 +name: enzyme linked receptor protein signaling pathway +is_a: GO:0007166 ! cell surface receptor signaling pathway + +[Term] +id: GO:0007169 +name: transmembrane receptor protein tyrosine kinase signaling pathway +is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway + +[Term] +id: GO:0007178 +name: transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway + +[Term] +id: GO:0007179 +name: transforming growth factor beta receptor signaling pathway +is_a: GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0071560 ! cellular response to transforming growth factor beta stimulus + +[Term] +id: GO:0007204 +name: elevation of cytosolic calcium ion concentration +is_a: GO:0051480 ! cytosolic calcium ion homeostasis + +[Term] +id: GO:0007219 +name: Notch signaling pathway +is_a: GO:0007166 ! cell surface receptor signaling pathway + +[Term] +id: GO:0007223 +name: Wnt receptor signaling pathway, calcium modulating pathway +is_a: GO:0035567 ! non-canonical Wnt receptor signaling pathway + +[Term] +id: GO:0007224 +name: smoothened signaling pathway +is_a: GO:0007166 ! cell surface receptor signaling pathway + +[Term] +id: GO:0007243 +name: intracellular protein kinase cascade +is_a: GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0007249 +name: I-kappaB kinase/NF-kappaB cascade +is_a: GO:0007243 ! intracellular protein kinase cascade +relationship: has_part GO:0051092 ! positive regulation of NF-kappaB transcription factor activity + +[Term] +id: GO:0007254 +name: JNK cascade +is_a: GO:0051403 ! stress-activated MAPK cascade + +[Term] +id: GO:0007257 +name: activation of JUN kinase activity +is_a: GO:0000187 ! activation of MAPK activity +is_a: GO:0043507 ! positive regulation of JUN kinase activity +relationship: part_of GO:0007254 ! JNK cascade + +[Term] +id: GO:0007258 +name: JUN phosphorylation +is_a: GO:0006468 ! protein phosphorylation +relationship: part_of GO:0007254 ! JNK cascade + +[Term] +id: GO:0007264 +name: small GTPase mediated signal transduction +is_a: GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0007265 +name: Ras protein signal transduction +is_a: GO:0007264 ! small GTPase mediated signal transduction + +[Term] +id: GO:0007266 +name: Rho protein signal transduction +is_a: GO:0007265 ! Ras protein signal transduction + +[Term] +id: GO:0007267 +name: cell-cell signaling +is_a: GO:0007154 ! cell communication +is_a: GO:0044700 ! single organism signaling + +[Term] +id: GO:0007268 +name: synaptic transmission +is_a: GO:0007267 ! cell-cell signaling +relationship: part_of GO:0019226 ! transmission of nerve impulse + +[Term] +id: GO:0007269 +name: neurotransmitter secretion +is_a: GO:0001505 ! regulation of neurotransmitter levels +is_a: GO:0006836 ! neurotransmitter transport +is_a: GO:0023061 ! signal release + +[Term] +id: GO:0007272 +name: ensheathment of neurons +is_a: GO:0044763 ! single-organism cellular process +relationship: part_of GO:0007399 ! nervous system development +relationship: part_of GO:0019228 ! regulation of action potential in neuron + +[Term] +id: GO:0007275 +name: multicellular organismal development +is_a: GO:0032502 ! developmental process +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0007276 +name: gamete generation +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048609 ! multicellular organismal reproductive process +relationship: part_of GO:0019953 ! sexual reproduction + +[Term] +id: GO:0007281 +name: germ cell development +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism +is_a: GO:0048468 ! cell development +relationship: part_of GO:0007276 ! gamete generation + +[Term] +id: GO:0007292 +name: female gamete generation +is_a: GO:0007276 ! gamete generation + +[Term] +id: GO:0007346 +name: regulation of mitotic cell cycle +is_a: GO:0051726 ! regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000278 ! mitotic cell cycle +relationship: regulates GO:0000278 ! mitotic cell cycle + +[Term] +id: GO:0007350 +name: blastoderm segmentation +is_a: GO:0009880 ! embryonic pattern specification +is_a: GO:0035282 ! segmentation + +[Term] +id: GO:0007351 +name: tripartite regional subdivision +is_a: GO:0003002 ! regionalization +relationship: part_of GO:0007350 ! blastoderm segmentation + +[Term] +id: GO:0007368 +name: determination of left/right symmetry +is_a: GO:0009855 ! determination of bilateral symmetry + +[Term] +id: GO:0007369 +name: gastrulation +is_a: GO:0048598 ! embryonic morphogenesis + +[Term] +id: GO:0007389 +name: pattern specification process +is_a: GO:0032502 ! developmental process +is_a: GO:0044707 ! single-multicellular organism process +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0007398 +name: ectoderm development +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0007399 +name: nervous system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0007403 +name: glial cell fate determination +is_a: GO:0001709 ! cell fate determination +relationship: part_of GO:0021781 ! glial cell fate commitment + +[Term] +id: GO:0007405 +name: neuroblast proliferation +is_a: GO:0061351 ! neural precursor cell proliferation +is_a: GO:0072089 ! stem cell proliferation +relationship: part_of GO:0048699 ! generation of neurons + +[Term] +id: GO:0007409 +name: axonogenesis +is_a: GO:0048812 ! neuron projection morphogenesis +relationship: part_of GO:0048667 ! cell morphogenesis involved in neuron differentiation +relationship: part_of GO:0061564 ! axon development + +[Term] +id: GO:0007411 +name: axon guidance +is_a: GO:0097485 ! neuron projection guidance +relationship: part_of GO:0007409 ! axonogenesis + +[Term] +id: GO:0007412 +name: axon target recognition +is_a: GO:0007154 ! cell communication +relationship: part_of GO:0007409 ! axonogenesis + +[Term] +id: GO:0007416 +name: synapse assembly +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0050808 ! synapse organization +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0007417 +name: central nervous system development +is_a: GO:0048731 ! system development +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0007418 +name: ventral midline development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0007420 +name: brain development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0007422 +name: peripheral nervous system development +is_a: GO:0048731 ! system development +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0007423 +name: sensory organ development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0007440 +name: foregut morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048546 ! digestive tract morphogenesis + +[Term] +id: GO:0007442 +name: hindgut morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048546 ! digestive tract morphogenesis +relationship: part_of GO:0061525 ! hindgut development + +[Term] +id: GO:0007492 +name: endoderm development +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0007494 +name: midgut development +is_a: GO:0048565 ! digestive tract development + +[Term] +id: GO:0007498 +name: mesoderm development +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0007501 +name: mesodermal cell fate specification +is_a: GO:0001708 ! cell fate specification +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001710 ! mesodermal cell fate commitment + +[Term] +id: GO:0007507 +name: heart development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0072358 ! cardiovascular system development + +[Term] +id: GO:0007517 +name: muscle organ development +is_a: GO:0048513 ! organ development +is_a: GO:0061061 ! muscle structure development + +[Term] +id: GO:0007519 +name: skeletal muscle tissue development +is_a: GO:0014706 ! striated muscle tissue development +relationship: part_of GO:0060538 ! skeletal muscle organ development + +[Term] +id: GO:0007520 +name: myoblast fusion +is_a: GO:0000768 ! syncytium formation by plasma membrane fusion +relationship: part_of GO:0014902 ! myotube differentiation + +[Term] +id: GO:0007528 +name: neuromuscular junction development +is_a: GO:0050808 ! synapse organization +relationship: part_of GO:0048741 ! skeletal muscle fiber development + +[Term] +id: GO:0007530 +name: sex determination +is_a: GO:0003006 ! developmental process involved in reproduction + +[Term] +id: GO:0007548 +name: sex differentiation +is_a: GO:0003006 ! developmental process involved in reproduction + +[Term] +id: GO:0007565 +name: female pregnancy +is_a: GO:0044703 ! multi-organism reproductive process +is_a: GO:0044706 ! multi-multicellular organism process + +[Term] +id: GO:0007568 +name: aging +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0007569 +name: cell aging +is_a: GO:0007568 ! aging +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007584 +name: response to nutrient +is_a: GO:0031667 ! response to nutrient levels +is_a: GO:0042221 ! response to chemical stimulus + +[Term] +id: GO:0007589 +name: body fluid secretion +is_a: GO:0046903 ! secretion +is_a: GO:0050878 ! regulation of body fluid levels + +[Term] +id: GO:0007595 +name: lactation +is_a: GO:0007589 ! body fluid secretion +is_a: GO:0032941 ! secretion by tissue +is_a: GO:0048609 ! multicellular organismal reproductive process +relationship: part_of GO:0030879 ! mammary gland development + +[Term] +id: GO:0007596 +name: blood coagulation +is_a: GO:0007599 ! hemostasis +is_a: GO:0050817 ! coagulation +relationship: part_of GO:0042060 ! wound healing + +[Term] +id: GO:0007599 +name: hemostasis +is_a: GO:0050878 ! regulation of body fluid levels + +[Term] +id: GO:0007610 +name: behavior +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0007611 +name: learning or memory +is_a: GO:0044708 ! single-organism behavior +is_a: GO:0050890 ! cognition + +[Term] +id: GO:0007612 +name: learning +is_a: GO:0007611 ! learning or memory + +[Term] +id: GO:0007626 +name: locomotory behavior +is_a: GO:0044708 ! single-organism behavior + +[Term] +id: GO:0007632 +name: visual behavior +is_a: GO:0009416 ! response to light stimulus +is_a: GO:0044704 ! single-organism reproductive behavior +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0007638 +name: mechanosensory behavior +is_a: GO:0009612 ! response to mechanical stimulus +is_a: GO:0044708 ! single-organism behavior + +[Term] +id: GO:0008013 +name: beta-catenin binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0008015 +name: blood circulation +is_a: GO:0003013 ! circulatory system process + +[Term] +id: GO:0008016 +name: regulation of heart contraction +is_a: GO:0044057 ! regulation of system process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060047 ! heart contraction +relationship: regulates GO:0060047 ! heart contraction + +[Term] +id: GO:0008022 +name: protein C-terminus binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0008035 +name: high-density lipoprotein particle binding +is_a: GO:0071813 ! lipoprotein particle binding + +[Term] +id: GO:0008037 +name: cell recognition +is_a: GO:0044763 ! single-organism cellular process +relationship: part_of GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0008038 +name: neuron recognition +is_a: GO:0008037 ! cell recognition +relationship: part_of GO:0048666 ! neuron development + +[Term] +id: GO:0008047 +name: enzyme activator activity +is_a: GO:0030234 ! enzyme regulator activity +relationship: part_of GO:0043085 ! positive regulation of catalytic activity + +[Term] +id: GO:0008092 +name: cytoskeletal protein binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0008104 +name: protein localization +is_a: GO:0033036 ! macromolecule localization + +[Term] +id: GO:0008105 +name: asymmetric protein localization +is_a: GO:0008104 ! protein localization + +[Term] +id: GO:0008134 +name: transcription factor binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0008144 +name: drug binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:0008150 +name: biological_process + +[Term] +id: GO:0008152 +name: metabolic process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0008201 +name: heparin binding +is_a: GO:0005539 ! glycosaminoglycan binding +is_a: GO:0043168 ! anion binding +is_a: GO:1901681 ! sulfur compound binding + +[Term] +id: GO:0008202 +name: steroid metabolic process +is_a: GO:0006629 ! lipid metabolic process +is_a: GO:1901360 ! organic cyclic compound metabolic process + +[Term] +id: GO:0008203 +name: cholesterol metabolic process +is_a: GO:0016125 ! sterol metabolic process + +[Term] +id: GO:0008207 +name: C21-steroid hormone metabolic process +is_a: GO:0008202 ! steroid metabolic process +is_a: GO:0034754 ! cellular hormone metabolic process + +[Term] +id: GO:0008209 +name: androgen metabolic process +is_a: GO:0008202 ! steroid metabolic process +is_a: GO:0034754 ! cellular hormone metabolic process + +[Term] +id: GO:0008211 +name: glucocorticoid metabolic process +is_a: GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0008212 +name: mineralocorticoid metabolic process +is_a: GO:0008202 ! steroid metabolic process +is_a: GO:0034754 ! cellular hormone metabolic process + +[Term] +id: GO:0008217 +name: regulation of blood pressure +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0008015 ! blood circulation + +[Term] +id: GO:0008219 +name: cell death +is_a: GO:0016265 ! death +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0008233 +name: peptidase activity +is_a: GO:0016787 ! hydrolase activity + +[Term] +id: GO:0008234 +name: cysteine-type peptidase activity +is_a: GO:0070011 ! peptidase activity, acting on L-amino acid peptides + +[Term] +id: GO:0008283 +name: cell proliferation +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0008284 +name: positive regulation of cell proliferation +is_a: GO:0042127 ! regulation of cell proliferation +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008283 ! cell proliferation +relationship: positively_regulates GO:0008283 ! cell proliferation + +[Term] +id: GO:0008285 +name: negative regulation of cell proliferation +is_a: GO:0042127 ! regulation of cell proliferation +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008283 ! cell proliferation +relationship: negatively_regulates GO:0008283 ! cell proliferation + +[Term] +id: GO:0008286 +name: insulin receptor signaling pathway +is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway +is_a: GO:0032869 ! cellular response to insulin stimulus + +[Term] +id: GO:0008289 +name: lipid binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:0008301 +name: DNA binding, bending +is_a: GO:0003677 ! DNA binding + +[Term] +id: GO:0008306 +name: associative learning +is_a: GO:0007612 ! learning + +[Term] +id: GO:0008344 +name: adult locomotory behavior +is_a: GO:0007626 ! locomotory behavior +is_a: GO:0030534 ! adult behavior + +[Term] +id: GO:0008354 +name: germ cell migration +is_a: GO:0016477 ! cell migration +is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism +relationship: part_of GO:0007276 ! gamete generation + +[Term] +id: GO:0008361 +name: regulation of cell size +is_a: GO:0032535 ! regulation of cellular component size + +[Term] +id: GO:0008366 +name: axon ensheathment +is_a: GO:0007272 ! ensheathment of neurons + +[Term] +id: GO:0008406 +name: gonad development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +is_a: GO:0048608 ! reproductive structure development +relationship: part_of GO:0045137 ! development of primary sexual characteristics + +[Term] +id: GO:0008542 +name: visual learning +is_a: GO:0007632 ! visual behavior +is_a: GO:0008306 ! associative learning + +[Term] +id: GO:0008543 +name: fibroblast growth factor receptor signaling pathway +is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway +is_a: GO:0044344 ! cellular response to fibroblast growth factor stimulus + +[Term] +id: GO:0008544 +name: epidermis development +is_a: GO:0009888 ! tissue development +relationship: part_of GO:0043588 ! skin development + +[Term] +id: GO:0008565 +name: protein transporter activity +is_a: GO:0022892 ! substrate-specific transporter activity +relationship: part_of GO:0015031 ! protein transport + +[Term] +id: GO:0008584 +name: male gonad development +is_a: GO:0008406 ! gonad development +relationship: part_of GO:0046546 ! development of primary male sexual characteristics + +[Term] +id: GO:0008585 +name: female gonad development +is_a: GO:0008406 ! gonad development +relationship: part_of GO:0046545 ! development of primary female sexual characteristics + +[Term] +id: GO:0008589 +name: regulation of smoothened signaling pathway +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007224 ! smoothened signaling pathway +relationship: regulates GO:0007224 ! smoothened signaling pathway + +[Term] +id: GO:0008593 +name: regulation of Notch signaling pathway +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007219 ! Notch signaling pathway +relationship: regulates GO:0007219 ! Notch signaling pathway + +[Term] +id: GO:0008595 +name: anterior/posterior axis specification, embryo +is_a: GO:0000578 ! embryonic axis specification +is_a: GO:0009948 ! anterior/posterior axis specification +relationship: part_of GO:0007351 ! tripartite regional subdivision + +[Term] +id: GO:0008610 +name: lipid biosynthetic process +is_a: GO:0006629 ! lipid metabolic process +is_a: GO:1901576 ! organic substance biosynthetic process + +[Term] +id: GO:0008625 +name: extrinsic apoptotic signaling pathway via death domain receptors +is_a: GO:0097191 ! extrinsic apoptotic signaling pathway + +[Term] +id: GO:0009056 +name: catabolic process +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0009057 +name: macromolecule catabolic process +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:1901575 ! organic substance catabolic process + +[Term] +id: GO:0009058 +name: biosynthetic process +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0009059 +name: macromolecule biosynthetic process +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:1901576 ! organic substance biosynthetic process + +[Term] +id: GO:0009100 +name: glycoprotein metabolic process +is_a: GO:0019538 ! protein metabolic process +is_a: GO:0044260 ! cellular macromolecule metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process + +[Term] +id: GO:0009101 +name: glycoprotein biosynthetic process +is_a: GO:0009100 ! glycoprotein metabolic process +is_a: GO:0034645 ! cellular macromolecule biosynthetic process +is_a: GO:1901137 ! carbohydrate derivative biosynthetic process + +[Term] +id: GO:0009116 +name: nucleoside metabolic process +is_a: GO:0055086 ! nucleobase-containing small molecule metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process +is_a: GO:1901657 ! glycosyl compound metabolic process + +[Term] +id: GO:0009117 +name: nucleotide metabolic process +is_a: GO:0006753 ! nucleoside phosphate metabolic process + +[Term] +id: GO:0009118 +name: regulation of nucleoside metabolic process +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009116 ! nucleoside metabolic process +relationship: regulates GO:0009116 ! nucleoside metabolic process + +[Term] +id: GO:0009119 +name: ribonucleoside metabolic process +is_a: GO:0009116 ! nucleoside metabolic process + +[Term] +id: GO:0009141 +name: nucleoside triphosphate metabolic process +is_a: GO:0006753 ! nucleoside phosphate metabolic process + +[Term] +id: GO:0009143 +name: nucleoside triphosphate catabolic process +is_a: GO:0009141 ! nucleoside triphosphate metabolic process +is_a: GO:1901292 ! nucleoside phosphate catabolic process + +[Term] +id: GO:0009144 +name: purine nucleoside triphosphate metabolic process +is_a: GO:0009141 ! nucleoside triphosphate metabolic process + +[Term] +id: GO:0009146 +name: purine nucleoside triphosphate catabolic process +is_a: GO:0009143 ! nucleoside triphosphate catabolic process +is_a: GO:0009144 ! purine nucleoside triphosphate metabolic process + +[Term] +id: GO:0009150 +name: purine ribonucleotide metabolic process +is_a: GO:0006163 ! purine nucleotide metabolic process +is_a: GO:0009259 ! ribonucleotide metabolic process + +[Term] +id: GO:0009154 +name: purine ribonucleotide catabolic process +is_a: GO:0006195 ! purine nucleotide catabolic process +is_a: GO:0009150 ! purine ribonucleotide metabolic process +is_a: GO:0009261 ! ribonucleotide catabolic process + +[Term] +id: GO:0009164 +name: nucleoside catabolic process +is_a: GO:0009116 ! nucleoside metabolic process +is_a: GO:0034655 ! nucleobase-containing compound catabolic process +is_a: GO:1901136 ! carbohydrate derivative catabolic process +is_a: GO:1901565 ! organonitrogen compound catabolic process +is_a: GO:1901658 ! glycosyl compound catabolic process + +[Term] +id: GO:0009166 +name: nucleotide catabolic process +is_a: GO:0009117 ! nucleotide metabolic process +is_a: GO:1901292 ! nucleoside phosphate catabolic process + +[Term] +id: GO:0009187 +name: cyclic nucleotide metabolic process +is_a: GO:0009117 ! nucleotide metabolic process + +[Term] +id: GO:0009199 +name: ribonucleoside triphosphate metabolic process +is_a: GO:0009141 ! nucleoside triphosphate metabolic process + +[Term] +id: GO:0009203 +name: ribonucleoside triphosphate catabolic process +is_a: GO:0009143 ! nucleoside triphosphate catabolic process +is_a: GO:0009199 ! ribonucleoside triphosphate metabolic process + +[Term] +id: GO:0009205 +name: purine ribonucleoside triphosphate metabolic process +is_a: GO:0009144 ! purine nucleoside triphosphate metabolic process +is_a: GO:0009199 ! ribonucleoside triphosphate metabolic process + +[Term] +id: GO:0009207 +name: purine ribonucleoside triphosphate catabolic process +is_a: GO:0009146 ! purine nucleoside triphosphate catabolic process +is_a: GO:0009203 ! ribonucleoside triphosphate catabolic process +is_a: GO:0009205 ! purine ribonucleoside triphosphate metabolic process + +[Term] +id: GO:0009259 +name: ribonucleotide metabolic process +is_a: GO:0009117 ! nucleotide metabolic process +is_a: GO:0019693 ! ribose phosphate metabolic process + +[Term] +id: GO:0009261 +name: ribonucleotide catabolic process +is_a: GO:0009166 ! nucleotide catabolic process +is_a: GO:0009259 ! ribonucleotide metabolic process +is_a: GO:1901136 ! carbohydrate derivative catabolic process + +[Term] +id: GO:0009306 +name: protein secretion +is_a: GO:0015031 ! protein transport +is_a: GO:0032940 ! secretion by cell + +[Term] +id: GO:0009314 +name: response to radiation +is_a: GO:0009628 ! response to abiotic stimulus + +[Term] +id: GO:0009416 +name: response to light stimulus +is_a: GO:0009314 ! response to radiation + +[Term] +id: GO:0009593 +name: detection of chemical stimulus +is_a: GO:0042221 ! response to chemical stimulus +is_a: GO:0051606 ! detection of stimulus + +[Term] +id: GO:0009605 +name: response to external stimulus +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0009607 +name: response to biotic stimulus +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0009611 +name: response to wounding +is_a: GO:0006950 ! response to stress + +[Term] +id: GO:0009612 +name: response to mechanical stimulus +is_a: GO:0009605 ! response to external stimulus +is_a: GO:0009628 ! response to abiotic stimulus + +[Term] +id: GO:0009617 +name: response to bacterium +is_a: GO:0051707 ! response to other organism + +[Term] +id: GO:0009628 +name: response to abiotic stimulus +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0009653 +name: anatomical structure morphogenesis +is_a: GO:0032502 ! developmental process +relationship: part_of GO:0048856 ! anatomical structure development + +[Term] +id: GO:0009719 +name: response to endogenous stimulus +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0009725 +name: response to hormone stimulus +is_a: GO:0009719 ! response to endogenous stimulus +is_a: GO:0010033 ! response to organic substance + +[Term] +id: GO:0009730 +name: detection of carbohydrate stimulus +is_a: GO:0009593 ! detection of chemical stimulus +is_a: GO:0009743 ! response to carbohydrate stimulus + +[Term] +id: GO:0009732 +name: detection of hexose stimulus +is_a: GO:0009746 ! response to hexose stimulus +is_a: GO:0034287 ! detection of monosaccharide stimulus + +[Term] +id: GO:0009743 +name: response to carbohydrate stimulus +is_a: GO:0010033 ! response to organic substance +is_a: GO:1901700 ! response to oxygen-containing compound + +[Term] +id: GO:0009746 +name: response to hexose stimulus +is_a: GO:0034284 ! response to monosaccharide stimulus + +[Term] +id: GO:0009749 +name: response to glucose stimulus +is_a: GO:0009746 ! response to hexose stimulus + +[Term] +id: GO:0009755 +name: hormone-mediated signaling pathway +is_a: GO:0007165 ! signal transduction +is_a: GO:0032870 ! cellular response to hormone stimulus + +[Term] +id: GO:0009790 +name: embryo development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0009791 +name: post-embryonic development +is_a: GO:0032502 ! developmental process +is_a: GO:0044707 ! single-multicellular organism process +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0009792 +name: embryo development ending in birth or egg hatching +is_a: GO:0009790 ! embryo development + +[Term] +id: GO:0009798 +name: axis specification +is_a: GO:0007389 ! pattern specification process + +[Term] +id: GO:0009799 +name: specification of symmetry +is_a: GO:0007389 ! pattern specification process + +[Term] +id: GO:0009855 +name: determination of bilateral symmetry +is_a: GO:0009799 ! specification of symmetry + +[Term] +id: GO:0009880 +name: embryonic pattern specification +is_a: GO:0007389 ! pattern specification process +relationship: part_of GO:0009790 ! embryo development + +[Term] +id: GO:0009887 +name: organ morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048513 ! organ development + +[Term] +id: GO:0009888 +name: tissue development +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0009889 +name: regulation of biosynthetic process +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009058 ! biosynthetic process +relationship: regulates GO:0009058 ! biosynthetic process + +[Term] +id: GO:0009890 +name: negative regulation of biosynthetic process +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0009892 ! negative regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009058 ! biosynthetic process +relationship: negatively_regulates GO:0009058 ! biosynthetic process + +[Term] +id: GO:0009891 +name: positive regulation of biosynthetic process +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0009893 ! positive regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009058 ! biosynthetic process +relationship: positively_regulates GO:0009058 ! biosynthetic process + +[Term] +id: GO:0009892 +name: negative regulation of metabolic process +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008152 ! metabolic process +relationship: negatively_regulates GO:0008152 ! metabolic process + +[Term] +id: GO:0009893 +name: positive regulation of metabolic process +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008152 ! metabolic process +relationship: positively_regulates GO:0008152 ! metabolic process + +[Term] +id: GO:0009894 +name: regulation of catabolic process +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009056 ! catabolic process +relationship: regulates GO:0009056 ! catabolic process + +[Term] +id: GO:0009896 +name: positive regulation of catabolic process +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0009894 ! regulation of catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009056 ! catabolic process +relationship: positively_regulates GO:0009056 ! catabolic process + +[Term] +id: GO:0009898 +name: internal side of plasma membrane +is_a: GO:0044459 ! plasma membrane part + +[Term] +id: GO:0009913 +name: epidermal cell differentiation +is_a: GO:0030855 ! epithelial cell differentiation +relationship: part_of GO:0008544 ! epidermis development + +[Term] +id: GO:0009914 +name: hormone transport +is_a: GO:0010817 ! regulation of hormone levels +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0009948 +name: anterior/posterior axis specification +is_a: GO:0009798 ! axis specification +relationship: part_of GO:0009952 ! anterior/posterior pattern specification + +[Term] +id: GO:0009950 +name: dorsal/ventral axis specification +is_a: GO:0009798 ! axis specification +relationship: part_of GO:0009953 ! dorsal/ventral pattern formation + +[Term] +id: GO:0009952 +name: anterior/posterior pattern specification +is_a: GO:0003002 ! regionalization + +[Term] +id: GO:0009953 +name: dorsal/ventral pattern formation +is_a: GO:0003002 ! regionalization + +[Term] +id: GO:0009954 +name: proximal/distal pattern formation +is_a: GO:0003002 ! regionalization + +[Term] +id: GO:0009957 +name: epidermal cell fate specification +is_a: GO:0001708 ! cell fate specification +relationship: part_of GO:0009913 ! epidermal cell differentiation + +[Term] +id: GO:0009966 +name: regulation of signal transduction +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0023051 ! regulation of signaling +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007165 ! signal transduction +relationship: regulates GO:0007165 ! signal transduction + +[Term] +id: GO:0009967 +name: positive regulation of signal transduction +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0010647 ! positive regulation of cell communication +is_a: GO:0023056 ! positive regulation of signaling +is_a: GO:0048584 ! positive regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007165 ! signal transduction +relationship: positively_regulates GO:0007165 ! signal transduction + +[Term] +id: GO:0009968 +name: negative regulation of signal transduction +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0010648 ! negative regulation of cell communication +is_a: GO:0023057 ! negative regulation of signaling +is_a: GO:0048585 ! negative regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007165 ! signal transduction +relationship: negatively_regulates GO:0007165 ! signal transduction + +[Term] +id: GO:0009986 +name: cell surface +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0009987 +name: cellular process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0009991 +name: response to extracellular stimulus +is_a: GO:0009605 ! response to external stimulus + +[Term] +id: GO:0009994 +name: oocyte differentiation +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0048477 ! oogenesis + +[Term] +id: GO:0009996 +name: negative regulation of cell fate specification +is_a: GO:0010454 ! negative regulation of cell fate commitment +is_a: GO:0042659 ! regulation of cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001708 ! cell fate specification +relationship: negatively_regulates GO:0001708 ! cell fate specification + +[Term] +id: GO:0009997 +name: negative regulation of cardioblast cell fate specification +is_a: GO:0042686 ! regulation of cardioblast cell fate specification +is_a: GO:2000044 ! negative regulation of cardiac cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042685 ! cardioblast cell fate specification +relationship: negatively_regulates GO:0042685 ! cardioblast cell fate specification + +[Term] +id: GO:0010001 +name: glial cell differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0042063 ! gliogenesis + +[Term] +id: GO:0010002 +name: cardioblast differentiation +is_a: GO:0035051 ! cardiocyte differentiation +is_a: GO:0048863 ! stem cell differentiation + +[Term] +id: GO:0010033 +name: response to organic substance +is_a: GO:0042221 ! response to chemical stimulus + +[Term] +id: GO:0010092 +name: specification of organ identity +is_a: GO:0003002 ! regionalization +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048645 ! organ formation + +[Term] +id: GO:0010159 +name: specification of organ position +is_a: GO:0003002 ! regionalization +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0009887 ! organ morphogenesis + +[Term] +id: GO:0010165 +name: response to X-ray +is_a: GO:0010212 ! response to ionizing radiation + +[Term] +id: GO:0010171 +name: body morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0010212 +name: response to ionizing radiation +is_a: GO:0009314 ! response to radiation + +[Term] +id: GO:0010243 +name: response to organonitrogen compound +is_a: GO:0009719 ! response to endogenous stimulus +is_a: GO:0010033 ! response to organic substance +is_a: GO:1901698 ! response to nitrogen compound + +[Term] +id: GO:0010324 +name: membrane invagination +is_a: GO:0016044 ! cellular membrane organization + +[Term] +id: GO:0010387 +name: COP9 signalosome assembly +is_a: GO:0043623 ! cellular protein complex assembly + +[Term] +id: GO:0010453 +name: regulation of cell fate commitment +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045165 ! cell fate commitment +relationship: regulates GO:0045165 ! cell fate commitment + +[Term] +id: GO:0010454 +name: negative regulation of cell fate commitment +is_a: GO:0010453 ! regulation of cell fate commitment +is_a: GO:0045596 ! negative regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0045165 ! cell fate commitment +relationship: negatively_regulates GO:0045165 ! cell fate commitment + +[Term] +id: GO:0010457 +name: centriole-centriole cohesion +is_a: GO:0051297 ! centrosome organization + +[Term] +id: GO:0010463 +name: mesenchymal cell proliferation +is_a: GO:0072089 ! stem cell proliferation + +[Term] +id: GO:0010464 +name: regulation of mesenchymal cell proliferation +is_a: GO:0072091 ! regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010463 ! mesenchymal cell proliferation +relationship: regulates GO:0010463 ! mesenchymal cell proliferation + +[Term] +id: GO:0010466 +name: negative regulation of peptidase activity +is_a: GO:0051346 ! negative regulation of hydrolase activity +is_a: GO:0052547 ! regulation of peptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008233 ! peptidase activity +relationship: negatively_regulates GO:0008233 ! peptidase activity + +[Term] +id: GO:0010467 +name: gene expression +is_a: GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0010468 +name: regulation of gene expression +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010467 ! gene expression +relationship: regulates GO:0010467 ! gene expression + +[Term] +id: GO:0010469 +name: regulation of receptor activity +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004872 ! receptor activity +relationship: regulates GO:0004872 ! receptor activity + +[Term] +id: GO:0010470 +name: regulation of gastrulation +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0045995 ! regulation of embryonic development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007369 ! gastrulation +relationship: regulates GO:0007369 ! gastrulation + +[Term] +id: GO:0010556 +name: regulation of macromolecule biosynthetic process +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009059 ! macromolecule biosynthetic process +relationship: regulates GO:0009059 ! macromolecule biosynthetic process + +[Term] +id: GO:0010557 +name: positive regulation of macromolecule biosynthetic process +is_a: GO:0009891 ! positive regulation of biosynthetic process +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009059 ! macromolecule biosynthetic process +relationship: positively_regulates GO:0009059 ! macromolecule biosynthetic process + +[Term] +id: GO:0010558 +name: negative regulation of macromolecule biosynthetic process +is_a: GO:0009890 ! negative regulation of biosynthetic process +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009059 ! macromolecule biosynthetic process +relationship: negatively_regulates GO:0009059 ! macromolecule biosynthetic process + +[Term] +id: GO:0010559 +name: regulation of glycoprotein biosynthetic process +is_a: GO:0051246 ! regulation of protein metabolic process +is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009101 ! glycoprotein biosynthetic process +relationship: regulates GO:0009101 ! glycoprotein biosynthetic process + +[Term] +id: GO:0010560 +name: positive regulation of glycoprotein biosynthetic process +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process +is_a: GO:0010559 ! regulation of glycoprotein biosynthetic process +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0051247 ! positive regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009101 ! glycoprotein biosynthetic process +relationship: positively_regulates GO:0009101 ! glycoprotein biosynthetic process + +[Term] +id: GO:0010562 +name: positive regulation of phosphorus metabolic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0051174 ! regulation of phosphorus metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006793 ! phosphorus metabolic process +relationship: positively_regulates GO:0006793 ! phosphorus metabolic process + +[Term] +id: GO:0010563 +name: negative regulation of phosphorus metabolic process +is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0051174 ! regulation of phosphorus metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006793 ! phosphorus metabolic process +relationship: negatively_regulates GO:0006793 ! phosphorus metabolic process + +[Term] +id: GO:0010564 +name: regulation of cell cycle process +is_a: GO:0051726 ! regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0022402 ! cell cycle process +relationship: regulates GO:0022402 ! cell cycle process + +[Term] +id: GO:0010565 +name: regulation of cellular ketone metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042180 ! cellular ketone metabolic process +relationship: regulates GO:0042180 ! cellular ketone metabolic process + +[Term] +id: GO:0010566 +name: regulation of ketone biosynthetic process +is_a: GO:0010565 ! regulation of cellular ketone metabolic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042181 ! ketone biosynthetic process +relationship: regulates GO:0042181 ! ketone biosynthetic process + +[Term] +id: GO:0010576 +name: metalloenzyme regulator activity +is_a: GO:0030234 ! enzyme regulator activity + +[Term] +id: GO:0010577 +name: metalloenzyme activator activity +is_a: GO:0008047 ! enzyme activator activity +is_a: GO:0010576 ! metalloenzyme regulator activity + +[Term] +id: GO:0010591 +name: regulation of lamellipodium assembly +is_a: GO:0060491 ! regulation of cell projection assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030032 ! lamellipodium assembly +relationship: regulates GO:0030032 ! lamellipodium assembly + +[Term] +id: GO:0010592 +name: positive regulation of lamellipodium assembly +is_a: GO:0010591 ! regulation of lamellipodium assembly +is_a: GO:0031346 ! positive regulation of cell projection organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030032 ! lamellipodium assembly +relationship: positively_regulates GO:0030032 ! lamellipodium assembly + +[Term] +id: GO:0010594 +name: regulation of endothelial cell migration +is_a: GO:0010632 ! regulation of epithelial cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043542 ! endothelial cell migration +relationship: regulates GO:0043542 ! endothelial cell migration + +[Term] +id: GO:0010595 +name: positive regulation of endothelial cell migration +is_a: GO:0010594 ! regulation of endothelial cell migration +is_a: GO:0010634 ! positive regulation of epithelial cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0043542 ! endothelial cell migration +relationship: positively_regulates GO:0043542 ! endothelial cell migration + +[Term] +id: GO:0010604 +name: positive regulation of macromolecule metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0043170 ! macromolecule metabolic process +relationship: positively_regulates GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0010605 +name: negative regulation of macromolecule metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0043170 ! macromolecule metabolic process +relationship: negatively_regulates GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0010623 +name: developmental programmed cell death +is_a: GO:0012501 ! programmed cell death +is_a: GO:0048869 ! cellular developmental process +intersection_of: GO:0012501 ! programmed cell death +intersection_of: part_of GO:0048468 ! cell development +relationship: part_of GO:0048468 ! cell development + +[Term] +id: GO:0010627 +name: regulation of intracellular protein kinase cascade +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007243 ! intracellular protein kinase cascade +relationship: regulates GO:0007243 ! intracellular protein kinase cascade + +[Term] +id: GO:0010628 +name: positive regulation of gene expression +is_a: GO:0010468 ! regulation of gene expression +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010467 ! gene expression +relationship: positively_regulates GO:0010467 ! gene expression + +[Term] +id: GO:0010629 +name: negative regulation of gene expression +is_a: GO:0010468 ! regulation of gene expression +is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010467 ! gene expression +relationship: negatively_regulates GO:0010467 ! gene expression + +[Term] +id: GO:0010631 +name: epithelial cell migration +is_a: GO:0001667 ! ameboidal cell migration +relationship: part_of GO:0090132 ! epithelium migration + +[Term] +id: GO:0010632 +name: regulation of epithelial cell migration +is_a: GO:0030334 ! regulation of cell migration +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010631 ! epithelial cell migration +relationship: regulates GO:0010631 ! epithelial cell migration + +[Term] +id: GO:0010634 +name: positive regulation of epithelial cell migration +is_a: GO:0010632 ! regulation of epithelial cell migration +is_a: GO:0030335 ! positive regulation of cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010631 ! epithelial cell migration +relationship: positively_regulates GO:0010631 ! epithelial cell migration + +[Term] +id: GO:0010638 +name: positive regulation of organelle organization +is_a: GO:0033043 ! regulation of organelle organization +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006996 ! organelle organization +relationship: positively_regulates GO:0006996 ! organelle organization + +[Term] +id: GO:0010646 +name: regulation of cell communication +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007154 ! cell communication +relationship: regulates GO:0007154 ! cell communication + +[Term] +id: GO:0010647 +name: positive regulation of cell communication +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007154 ! cell communication +relationship: positively_regulates GO:0007154 ! cell communication + +[Term] +id: GO:0010648 +name: negative regulation of cell communication +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007154 ! cell communication +relationship: negatively_regulates GO:0007154 ! cell communication + +[Term] +id: GO:0010656 +name: negative regulation of muscle cell apoptotic process +is_a: GO:0010660 ! regulation of muscle cell apoptotic process +is_a: GO:0043066 ! negative regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010657 ! muscle cell apoptotic process +relationship: negatively_regulates GO:0010657 ! muscle cell apoptotic process + +[Term] +id: GO:0010657 +name: muscle cell apoptotic process +is_a: GO:0097285 ! cell-type specific apoptotic process + +[Term] +id: GO:0010658 +name: striated muscle cell apoptotic process +is_a: GO:0010657 ! muscle cell apoptotic process + +[Term] +id: GO:0010659 +name: cardiac muscle cell apoptotic process +is_a: GO:0010658 ! striated muscle cell apoptotic process + +[Term] +id: GO:0010660 +name: regulation of muscle cell apoptotic process +is_a: GO:0042981 ! regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010657 ! muscle cell apoptotic process +relationship: regulates GO:0010657 ! muscle cell apoptotic process + +[Term] +id: GO:0010662 +name: regulation of striated muscle cell apoptotic process +is_a: GO:0010660 ! regulation of muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010658 ! striated muscle cell apoptotic process +relationship: regulates GO:0010658 ! striated muscle cell apoptotic process + +[Term] +id: GO:0010664 +name: negative regulation of striated muscle cell apoptotic process +is_a: GO:0010656 ! negative regulation of muscle cell apoptotic process +is_a: GO:0010662 ! regulation of striated muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010658 ! striated muscle cell apoptotic process +relationship: negatively_regulates GO:0010658 ! striated muscle cell apoptotic process + +[Term] +id: GO:0010665 +name: regulation of cardiac muscle cell apoptotic process +is_a: GO:0010662 ! regulation of striated muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010659 ! cardiac muscle cell apoptotic process +relationship: regulates GO:0010659 ! cardiac muscle cell apoptotic process + +[Term] +id: GO:0010667 +name: negative regulation of cardiac muscle cell apoptotic process +is_a: GO:0010664 ! negative regulation of striated muscle cell apoptotic process +is_a: GO:0010665 ! regulation of cardiac muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010659 ! cardiac muscle cell apoptotic process +relationship: negatively_regulates GO:0010659 ! cardiac muscle cell apoptotic process + +[Term] +id: GO:0010675 +name: regulation of cellular carbohydrate metabolic process +is_a: GO:0006109 ! regulation of carbohydrate metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044262 ! cellular carbohydrate metabolic process +relationship: regulates GO:0044262 ! cellular carbohydrate metabolic process + +[Term] +id: GO:0010712 +name: regulation of collagen metabolic process +is_a: GO:0044246 ! regulation of multicellular organismal metabolic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032963 ! collagen metabolic process +relationship: regulates GO:0032963 ! collagen metabolic process + +[Term] +id: GO:0010714 +name: positive regulation of collagen metabolic process +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0010712 ! regulation of collagen metabolic process +is_a: GO:0044253 ! positive regulation of multicellular organismal metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032963 ! collagen metabolic process +relationship: positively_regulates GO:0032963 ! collagen metabolic process + +[Term] +id: GO:0010717 +name: regulation of epithelial to mesenchymal transition +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:2000736 ! regulation of stem cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001837 ! epithelial to mesenchymal transition +relationship: regulates GO:0001837 ! epithelial to mesenchymal transition + +[Term] +id: GO:0010718 +name: positive regulation of epithelial to mesenchymal transition +is_a: GO:0010717 ! regulation of epithelial to mesenchymal transition +is_a: GO:0010770 ! positive regulation of cell morphogenesis involved in differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001837 ! epithelial to mesenchymal transition +relationship: positively_regulates GO:0001837 ! epithelial to mesenchymal transition + +[Term] +id: GO:0010719 +name: negative regulation of epithelial to mesenchymal transition +is_a: GO:0010717 ! regulation of epithelial to mesenchymal transition +is_a: GO:0010771 ! negative regulation of cell morphogenesis involved in differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001837 ! epithelial to mesenchymal transition +relationship: negatively_regulates GO:0001837 ! epithelial to mesenchymal transition + +[Term] +id: GO:0010720 +name: positive regulation of cell development +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048468 ! cell development +relationship: positively_regulates GO:0048468 ! cell development + +[Term] +id: GO:0010721 +name: negative regulation of cell development +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048468 ! cell development +relationship: negatively_regulates GO:0048468 ! cell development + +[Term] +id: GO:0010740 +name: positive regulation of intracellular protein kinase cascade +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0010627 ! regulation of intracellular protein kinase cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007243 ! intracellular protein kinase cascade +relationship: positively_regulates GO:0007243 ! intracellular protein kinase cascade + +[Term] +id: GO:0010741 +name: negative regulation of intracellular protein kinase cascade +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:0010627 ! regulation of intracellular protein kinase cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007243 ! intracellular protein kinase cascade +relationship: negatively_regulates GO:0007243 ! intracellular protein kinase cascade + +[Term] +id: GO:0010769 +name: regulation of cell morphogenesis involved in differentiation +is_a: GO:0022604 ! regulation of cell morphogenesis +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000904 ! cell morphogenesis involved in differentiation +relationship: regulates GO:0000904 ! cell morphogenesis involved in differentiation + +[Term] +id: GO:0010770 +name: positive regulation of cell morphogenesis involved in differentiation +is_a: GO:0010720 ! positive regulation of cell development +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0000904 ! cell morphogenesis involved in differentiation +relationship: positively_regulates GO:0000904 ! cell morphogenesis involved in differentiation + +[Term] +id: GO:0010771 +name: negative regulation of cell morphogenesis involved in differentiation +is_a: GO:0010721 ! negative regulation of cell development +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:0051129 ! negative regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0000904 ! cell morphogenesis involved in differentiation +relationship: negatively_regulates GO:0000904 ! cell morphogenesis involved in differentiation + +[Term] +id: GO:0010799 +name: regulation of peptidyl-threonine phosphorylation +is_a: GO:0001932 ! regulation of protein phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0018107 ! peptidyl-threonine phosphorylation +relationship: regulates GO:0018107 ! peptidyl-threonine phosphorylation + +[Term] +id: GO:0010800 +name: positive regulation of peptidyl-threonine phosphorylation +is_a: GO:0001934 ! positive regulation of protein phosphorylation +is_a: GO:0010799 ! regulation of peptidyl-threonine phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0018107 ! peptidyl-threonine phosphorylation +relationship: positively_regulates GO:0018107 ! peptidyl-threonine phosphorylation + +[Term] +id: GO:0010810 +name: regulation of cell-substrate adhesion +is_a: GO:0030155 ! regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031589 ! cell-substrate adhesion +relationship: regulates GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0010811 +name: positive regulation of cell-substrate adhesion +is_a: GO:0010810 ! regulation of cell-substrate adhesion +is_a: GO:0045785 ! positive regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031589 ! cell-substrate adhesion +relationship: positively_regulates GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0010812 +name: negative regulation of cell-substrate adhesion +is_a: GO:0007162 ! negative regulation of cell adhesion +is_a: GO:0010810 ! regulation of cell-substrate adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0031589 ! cell-substrate adhesion +relationship: negatively_regulates GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0010817 +name: regulation of hormone levels +is_a: GO:0065008 ! regulation of biological quality + +[Term] +id: GO:0010818 +name: T cell chemotaxis +is_a: GO:0048247 ! lymphocyte chemotaxis +is_a: GO:0072678 ! T cell migration + +[Term] +id: GO:0010819 +name: regulation of T cell chemotaxis +is_a: GO:1901623 ! regulation of lymphocyte chemotaxis +is_a: GO:2000404 ! regulation of T cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010818 ! T cell chemotaxis +relationship: regulates GO:0010818 ! T cell chemotaxis + +[Term] +id: GO:0010820 +name: positive regulation of T cell chemotaxis +is_a: GO:0002690 ! positive regulation of leukocyte chemotaxis +is_a: GO:0010819 ! regulation of T cell chemotaxis +is_a: GO:2000406 ! positive regulation of T cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010818 ! T cell chemotaxis +relationship: positively_regulates GO:0010818 ! T cell chemotaxis + +[Term] +id: GO:0010876 +name: lipid localization +is_a: GO:0033036 ! macromolecule localization + +[Term] +id: GO:0010893 +name: positive regulation of steroid biosynthetic process +is_a: GO:0045940 ! positive regulation of steroid metabolic process +is_a: GO:0046889 ! positive regulation of lipid biosynthetic process +is_a: GO:0050810 ! regulation of steroid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006694 ! steroid biosynthetic process +relationship: positively_regulates GO:0006694 ! steroid biosynthetic process + +[Term] +id: GO:0010894 +name: negative regulation of steroid biosynthetic process +is_a: GO:0045939 ! negative regulation of steroid metabolic process +is_a: GO:0050810 ! regulation of steroid biosynthetic process +is_a: GO:0051055 ! negative regulation of lipid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006694 ! steroid biosynthetic process +relationship: negatively_regulates GO:0006694 ! steroid biosynthetic process + +[Term] +id: GO:0010906 +name: regulation of glucose metabolic process +is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006006 ! glucose metabolic process +relationship: regulates GO:0006006 ! glucose metabolic process + +[Term] +id: GO:0010908 +name: regulation of heparan sulfate proteoglycan biosynthetic process +is_a: GO:0010559 ! regulation of glycoprotein biosynthetic process +is_a: GO:0042762 ! regulation of sulfur metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process +relationship: regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process + +[Term] +id: GO:0010909 +name: positive regulation of heparan sulfate proteoglycan biosynthetic process +is_a: GO:0010560 ! positive regulation of glycoprotein biosynthetic process +is_a: GO:0010908 ! regulation of heparan sulfate proteoglycan biosynthetic process +is_a: GO:0051176 ! positive regulation of sulfur metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process +relationship: positively_regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process + +[Term] +id: GO:0010915 +name: regulation of very-low-density lipoprotein particle clearance +is_a: GO:0010984 ! regulation of lipoprotein particle clearance +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034447 ! very-low-density lipoprotein particle clearance +relationship: regulates GO:0034447 ! very-low-density lipoprotein particle clearance + +[Term] +id: GO:0010916 +name: negative regulation of very-low-density lipoprotein particle clearance +is_a: GO:0010915 ! regulation of very-low-density lipoprotein particle clearance +is_a: GO:0010985 ! negative regulation of lipoprotein particle clearance +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0034447 ! very-low-density lipoprotein particle clearance +relationship: negatively_regulates GO:0034447 ! very-low-density lipoprotein particle clearance + +[Term] +id: GO:0010927 +name: cellular component assembly involved in morphogenesis +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis +relationship: part_of GO:0032989 ! cellular component morphogenesis + +[Term] +id: GO:0010934 +name: macrophage cytokine production +is_a: GO:0061082 ! myeloid leukocyte cytokine production + +[Term] +id: GO:0010935 +name: regulation of macrophage cytokine production +is_a: GO:0002718 ! regulation of cytokine production involved in immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010934 ! macrophage cytokine production +relationship: regulates GO:0010934 ! macrophage cytokine production + +[Term] +id: GO:0010941 +name: regulation of cell death +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008219 ! cell death +relationship: regulates GO:0008219 ! cell death + +[Term] +id: GO:0010942 +name: positive regulation of cell death +is_a: GO:0010941 ! regulation of cell death +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008219 ! cell death +relationship: positively_regulates GO:0008219 ! cell death + +[Term] +id: GO:0010950 +name: positive regulation of endopeptidase activity +is_a: GO:0010952 ! positive regulation of peptidase activity +is_a: GO:0052548 ! regulation of endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004175 ! endopeptidase activity +relationship: positively_regulates GO:0004175 ! endopeptidase activity + +[Term] +id: GO:0010951 +name: negative regulation of endopeptidase activity +is_a: GO:0010466 ! negative regulation of peptidase activity +is_a: GO:0052548 ! regulation of endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004175 ! endopeptidase activity +relationship: negatively_regulates GO:0004175 ! endopeptidase activity + +[Term] +id: GO:0010952 +name: positive regulation of peptidase activity +is_a: GO:0051345 ! positive regulation of hydrolase activity +is_a: GO:0052547 ! regulation of peptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008233 ! peptidase activity +relationship: positively_regulates GO:0008233 ! peptidase activity + +[Term] +id: GO:0010959 +name: regulation of metal ion transport +is_a: GO:0043269 ! regulation of ion transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030001 ! metal ion transport +relationship: regulates GO:0030001 ! metal ion transport + +[Term] +id: GO:0010975 +name: regulation of neuron projection development +is_a: GO:0031344 ! regulation of cell projection organization +is_a: GO:0045664 ! regulation of neuron differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031175 ! neuron projection development +relationship: regulates GO:0031175 ! neuron projection development + +[Term] +id: GO:0010976 +name: positive regulation of neuron projection development +is_a: GO:0010975 ! regulation of neuron projection development +is_a: GO:0031346 ! positive regulation of cell projection organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031175 ! neuron projection development +relationship: positively_regulates GO:0031175 ! neuron projection development + +[Term] +id: GO:0010977 +name: negative regulation of neuron projection development +is_a: GO:0010975 ! regulation of neuron projection development +is_a: GO:0031345 ! negative regulation of cell projection organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0031175 ! neuron projection development +relationship: negatively_regulates GO:0031175 ! neuron projection development + +[Term] +id: GO:0010984 +name: regulation of lipoprotein particle clearance +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034381 ! plasma lipoprotein particle clearance +relationship: regulates GO:0034381 ! plasma lipoprotein particle clearance + +[Term] +id: GO:0010985 +name: negative regulation of lipoprotein particle clearance +is_a: GO:0010984 ! regulation of lipoprotein particle clearance +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0034381 ! plasma lipoprotein particle clearance +relationship: negatively_regulates GO:0034381 ! plasma lipoprotein particle clearance + +[Term] +id: GO:0010996 +name: response to auditory stimulus +is_a: GO:0009612 ! response to mechanical stimulus + +[Term] +id: GO:0012501 +name: programmed cell death +is_a: GO:0008219 ! cell death + +[Term] +id: GO:0012505 +name: endomembrane system +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0014003 +name: oligodendrocyte development +is_a: GO:0021782 ! glial cell development +relationship: part_of GO:0048709 ! oligodendrocyte differentiation + +[Term] +id: GO:0014009 +name: glial cell proliferation +is_a: GO:0008283 ! cell proliferation +relationship: part_of GO:0042063 ! gliogenesis + +[Term] +id: GO:0014010 +name: Schwann cell proliferation +is_a: GO:0014009 ! glial cell proliferation + +[Term] +id: GO:0014013 +name: regulation of gliogenesis +is_a: GO:0050767 ! regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042063 ! gliogenesis +relationship: regulates GO:0042063 ! gliogenesis + +[Term] +id: GO:0014014 +name: negative regulation of gliogenesis +is_a: GO:0014013 ! regulation of gliogenesis +is_a: GO:0050768 ! negative regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042063 ! gliogenesis +relationship: negatively_regulates GO:0042063 ! gliogenesis + +[Term] +id: GO:0014020 +name: primary neural tube formation +is_a: GO:0001838 ! embryonic epithelial tube formation +relationship: part_of GO:0001841 ! neural tube formation + +[Term] +id: GO:0014029 +name: neural crest formation +is_a: GO:0001837 ! epithelial to mesenchymal transition +relationship: part_of GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0014031 +name: mesenchymal cell development +is_a: GO:0048864 ! stem cell development +relationship: part_of GO:0048762 ! mesenchymal cell differentiation + +[Term] +id: GO:0014032 +name: neural crest cell development +is_a: GO:0014031 ! mesenchymal cell development +relationship: part_of GO:0014033 ! neural crest cell differentiation + +[Term] +id: GO:0014033 +name: neural crest cell differentiation +is_a: GO:0048762 ! mesenchymal cell differentiation + +[Term] +id: GO:0014034 +name: neural crest cell fate commitment +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0014029 ! neural crest formation +relationship: part_of GO:0014033 ! neural crest cell differentiation + +[Term] +id: GO:0014045 +name: establishment of endothelial blood-brain barrier +is_a: GO:0060856 ! establishment of blood-brain barrier +is_a: GO:0061028 ! establishment of endothelial barrier +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0014069 +name: postsynaptic density +is_a: GO:0044430 ! cytoskeletal part +is_a: GO:0044456 ! synapse part +is_a: GO:0044463 ! cell projection part + +[Term] +id: GO:0014070 +name: response to organic cyclic compound +is_a: GO:0010033 ! response to organic substance + +[Term] +id: GO:0014704 +name: intercalated disc +is_a: GO:0044291 ! cell-cell contact zone + +[Term] +id: GO:0014706 +name: striated muscle tissue development +is_a: GO:0060537 ! muscle tissue development + +[Term] +id: GO:0014719 +name: satellite cell activation +is_a: GO:0001775 ! cell activation + +[Term] +id: GO:0014834 +name: satellite cell maintenance involved in skeletal muscle regeneration +is_a: GO:0035019 ! somatic stem cell maintenance +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0043403 ! skeletal muscle tissue regeneration + +[Term] +id: GO:0014855 +name: striated muscle cell proliferation +is_a: GO:0033002 ! muscle cell proliferation + +[Term] +id: GO:0014902 +name: myotube differentiation +is_a: GO:0035914 ! skeletal muscle cell differentiation + +[Term] +id: GO:0015012 +name: heparan sulfate proteoglycan biosynthetic process +is_a: GO:0030166 ! proteoglycan biosynthetic process +is_a: GO:0030201 ! heparan sulfate proteoglycan metabolic process +is_a: GO:0044272 ! sulfur compound biosynthetic process + +[Term] +id: GO:0015026 +name: coreceptor activity +is_a: GO:0038023 ! signaling receptor activity + +[Term] +id: GO:0015031 +name: protein transport +is_a: GO:0045184 ! establishment of protein localization +is_a: GO:0071702 ! organic substance transport + +[Term] +id: GO:0015630 +name: microtubule cytoskeleton +is_a: GO:0005856 ! cytoskeleton + +[Term] +id: GO:0015833 +name: peptide transport +is_a: GO:0042886 ! amide transport +is_a: GO:0071702 ! organic substance transport + +[Term] +id: GO:0015850 +name: organic hydroxy compound transport +is_a: GO:0044765 ! single-organism transport +is_a: GO:0071702 ! organic substance transport + +[Term] +id: GO:0015918 +name: sterol transport +is_a: GO:0006869 ! lipid transport +is_a: GO:0015850 ! organic hydroxy compound transport + +[Term] +id: GO:0016020 +name: membrane +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0016021 +name: integral to membrane +is_a: GO:0031224 ! intrinsic to membrane + +[Term] +id: GO:0016023 +name: cytoplasmic membrane-bounded vesicle +is_a: GO:0031410 ! cytoplasmic vesicle +is_a: GO:0031988 ! membrane-bounded vesicle +is_a: GO:0043231 ! intracellular membrane-bounded organelle +intersection_of: GO:0031988 ! membrane-bounded vesicle +intersection_of: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0016043 +name: cellular component organization +is_a: GO:0071840 ! cellular component organization or biogenesis + +[Term] +id: GO:0016044 +name: cellular membrane organization +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0061024 ! membrane organization + +[Term] +id: GO:0016049 +name: cell growth +is_a: GO:0040007 ! growth +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0016052 +name: carbohydrate catabolic process +is_a: GO:0005975 ! carbohydrate metabolic process +is_a: GO:1901575 ! organic substance catabolic process + +[Term] +id: GO:0016055 +name: Wnt receptor signaling pathway +is_a: GO:0007166 ! cell surface receptor signaling pathway + +[Term] +id: GO:0016064 +name: immunoglobulin mediated immune response +is_a: GO:0019724 ! B cell mediated immunity + +[Term] +id: GO:0016070 +name: RNA metabolic process +is_a: GO:0044260 ! cellular macromolecule metabolic process +is_a: GO:0090304 ! nucleic acid metabolic process + +[Term] +id: GO:0016125 +name: sterol metabolic process +is_a: GO:0006066 ! alcohol metabolic process +is_a: GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0016192 +name: vesicle-mediated transport +is_a: GO:0006810 ! transport + +[Term] +id: GO:0016197 +name: endosomal transport +is_a: GO:0044765 ! single-organism transport +is_a: GO:0046907 ! intracellular transport + +[Term] +id: GO:0016198 +name: axon choice point recognition +is_a: GO:0008038 ! neuron recognition +relationship: part_of GO:0007411 ! axon guidance + +[Term] +id: GO:0016199 +name: axon midline choice point recognition +is_a: GO:0016198 ! axon choice point recognition + +[Term] +id: GO:0016202 +name: regulation of striated muscle tissue development +is_a: GO:0048634 ! regulation of muscle organ development +is_a: GO:1901861 ! regulation of muscle tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0014706 ! striated muscle tissue development +relationship: regulates GO:0014706 ! striated muscle tissue development + +[Term] +id: GO:0016265 +name: death +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0016301 +name: kinase activity +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups +relationship: part_of GO:0016310 ! phosphorylation + +[Term] +id: GO:0016310 +name: phosphorylation +is_a: GO:0006796 ! phosphate-containing compound metabolic process + +[Term] +id: GO:0016323 +name: basolateral plasma membrane +is_a: GO:0044459 ! plasma membrane part + +[Term] +id: GO:0016324 +name: apical plasma membrane +is_a: GO:0044459 ! plasma membrane part +relationship: part_of GO:0045177 ! apical part of cell + +[Term] +id: GO:0016328 +name: lateral plasma membrane +is_a: GO:0044459 ! plasma membrane part + +[Term] +id: GO:0016331 +name: morphogenesis of embryonic epithelium +is_a: GO:0002009 ! morphogenesis of an epithelium +is_a: GO:0048598 ! embryonic morphogenesis + +[Term] +id: GO:0016332 +name: establishment or maintenance of polarity of embryonic epithelium +is_a: GO:0007163 ! establishment or maintenance of cell polarity +relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium + +[Term] +id: GO:0016337 +name: cell-cell adhesion +is_a: GO:0007155 ! cell adhesion + +[Term] +id: GO:0016342 +name: catenin complex +is_a: GO:0019897 ! extrinsic to plasma membrane +is_a: GO:0043234 ! protein complex + +[Term] +id: GO:0016358 +name: dendrite development +is_a: GO:0031175 ! neuron projection development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0016462 +name: pyrophosphatase activity +is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides + +[Term] +id: GO:0016477 +name: cell migration +is_a: GO:0048870 ! cell motility + +[Term] +id: GO:0016482 +name: cytoplasmic transport +is_a: GO:0046907 ! intracellular transport + +[Term] +id: GO:0016504 +name: peptidase activator activity +is_a: GO:0008047 ! enzyme activator activity +is_a: GO:0061134 ! peptidase regulator activity +relationship: part_of GO:0010952 ! positive regulation of peptidase activity +relationship: positively_regulates GO:0008233 ! peptidase activity + +[Term] +id: GO:0016567 +name: protein ubiquitination +is_a: GO:0032446 ! protein modification by small protein conjugation + +[Term] +id: GO:0016568 +name: chromatin modification +is_a: GO:0006325 ! chromatin organization + +[Term] +id: GO:0016740 +name: transferase activity +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +is_a: GO:0016740 ! transferase activity + +[Term] +id: GO:0016773 +name: phosphotransferase activity, alcohol group as acceptor +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups + +[Term] +id: GO:0016787 +name: hydrolase activity +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0016817 +name: hydrolase activity, acting on acid anhydrides +is_a: GO:0016787 ! hydrolase activity + +[Term] +id: GO:0016818 +name: hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides +is_a: GO:0016817 ! hydrolase activity, acting on acid anhydrides + +[Term] +id: GO:0016909 +name: SAP kinase activity +is_a: GO:0004707 ! MAP kinase activity + +[Term] +id: GO:0016925 +name: protein sumoylation +is_a: GO:0032446 ! protein modification by small protein conjugation + +[Term] +id: GO:0017015 +name: regulation of transforming growth factor beta receptor signaling pathway +is_a: GO:0090092 ! regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0090287 ! regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007179 ! transforming growth factor beta receptor signaling pathway +relationship: regulates GO:0007179 ! transforming growth factor beta receptor signaling pathway + +[Term] +id: GO:0017038 +name: protein import +is_a: GO:0015031 ! protein transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0017111 +name: nucleoside-triphosphatase activity +is_a: GO:0016462 ! pyrophosphatase activity + +[Term] +id: GO:0017124 +name: SH3 domain binding +is_a: GO:0019904 ! protein domain specific binding + +[Term] +id: GO:0017145 +name: stem cell division +is_a: GO:0051301 ! cell division + +[Term] +id: GO:0017147 +name: Wnt-protein binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0018105 +name: peptidyl-serine phosphorylation +is_a: GO:0006468 ! protein phosphorylation +is_a: GO:0018209 ! peptidyl-serine modification + +[Term] +id: GO:0018107 +name: peptidyl-threonine phosphorylation +is_a: GO:0006468 ! protein phosphorylation +is_a: GO:0018210 ! peptidyl-threonine modification + +[Term] +id: GO:0018108 +name: peptidyl-tyrosine phosphorylation +is_a: GO:0006468 ! protein phosphorylation +is_a: GO:0018212 ! peptidyl-tyrosine modification + +[Term] +id: GO:0018130 +name: heterocycle biosynthetic process +is_a: GO:0044249 ! cellular biosynthetic process +is_a: GO:0046483 ! heterocycle metabolic process + +[Term] +id: GO:0018193 +name: peptidyl-amino acid modification +is_a: GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0018209 +name: peptidyl-serine modification +is_a: GO:0018193 ! peptidyl-amino acid modification + +[Term] +id: GO:0018210 +name: peptidyl-threonine modification +is_a: GO:0018193 ! peptidyl-amino acid modification + +[Term] +id: GO:0018212 +name: peptidyl-tyrosine modification +is_a: GO:0018193 ! peptidyl-amino acid modification + +[Term] +id: GO:0018345 +name: protein palmitoylation +is_a: GO:0006497 ! protein lipidation +is_a: GO:0043543 ! protein acylation + +[Term] +id: GO:0019098 +name: reproductive behavior +is_a: GO:0007610 ! behavior +is_a: GO:0022414 ! reproductive process + +[Term] +id: GO:0019200 +name: carbohydrate kinase activity +is_a: GO:0016301 ! kinase activity +relationship: part_of GO:0046835 ! carbohydrate phosphorylation + +[Term] +id: GO:0019207 +name: kinase regulator activity +is_a: GO:0030234 ! enzyme regulator activity +relationship: part_of GO:0042325 ! regulation of phosphorylation +relationship: regulates GO:0016301 ! kinase activity + +[Term] +id: GO:0019210 +name: kinase inhibitor activity +is_a: GO:0004857 ! enzyme inhibitor activity +is_a: GO:0019207 ! kinase regulator activity +relationship: negatively_regulates GO:0016301 ! kinase activity +relationship: part_of GO:0042326 ! negative regulation of phosphorylation + +[Term] +id: GO:0019216 +name: regulation of lipid metabolic process +is_a: GO:0080090 ! regulation of primary metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006629 ! lipid metabolic process +relationship: regulates GO:0006629 ! lipid metabolic process + +[Term] +id: GO:0019218 +name: regulation of steroid metabolic process +is_a: GO:0019216 ! regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008202 ! steroid metabolic process +relationship: regulates GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0019219 +name: regulation of nucleobase-containing compound metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0051171 ! regulation of nitrogen compound metabolic process +is_a: GO:0080090 ! regulation of primary metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006139 ! nucleobase-containing compound metabolic process +relationship: regulates GO:0006139 ! nucleobase-containing compound metabolic process + +[Term] +id: GO:0019220 +name: regulation of phosphate metabolic process +is_a: GO:0051174 ! regulation of phosphorus metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006796 ! phosphate-containing compound metabolic process +relationship: regulates GO:0006796 ! phosphate-containing compound metabolic process + +[Term] +id: GO:0019221 +name: cytokine-mediated signaling pathway +is_a: GO:0007166 ! cell surface receptor signaling pathway +is_a: GO:0071345 ! cellular response to cytokine stimulus + +[Term] +id: GO:0019222 +name: regulation of metabolic process +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008152 ! metabolic process +relationship: regulates GO:0008152 ! metabolic process + +[Term] +id: GO:0019226 +name: transmission of nerve impulse +is_a: GO:0035637 ! multicellular organismal signaling +is_a: GO:0050877 ! neurological system process +relationship: part_of GO:0007154 ! cell communication + +[Term] +id: GO:0019228 +name: regulation of action potential in neuron +is_a: GO:0001508 ! regulation of action potential +relationship: part_of GO:0019226 ! transmission of nerve impulse + +[Term] +id: GO:0019318 +name: hexose metabolic process +is_a: GO:0005996 ! monosaccharide metabolic process + +[Term] +id: GO:0019320 +name: hexose catabolic process +is_a: GO:0019318 ! hexose metabolic process +is_a: GO:0046365 ! monosaccharide catabolic process + +[Term] +id: GO:0019438 +name: aromatic compound biosynthetic process +is_a: GO:0006725 ! cellular aromatic compound metabolic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0019439 +name: aromatic compound catabolic process +is_a: GO:0006725 ! cellular aromatic compound metabolic process +is_a: GO:0044248 ! cellular catabolic process + +[Term] +id: GO:0019534 +name: toxin transporter activity +is_a: GO:0005215 ! transporter activity +relationship: part_of GO:1901998 ! toxin transport + +[Term] +id: GO:0019538 +name: protein metabolic process +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0044238 ! primary metabolic process + +[Term] +id: GO:0019637 +name: organophosphate metabolic process +is_a: GO:0006793 ! phosphorus metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0019693 +name: ribose phosphate metabolic process +is_a: GO:0006796 ! phosphate-containing compound metabolic process +is_a: GO:0019637 ! organophosphate metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process + +[Term] +id: GO:0019724 +name: B cell mediated immunity +is_a: GO:0002449 ! lymphocyte mediated immunity +is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + +[Term] +id: GO:0019725 +name: cellular homeostasis +is_a: GO:0042592 ! homeostatic process +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0019827 +name: stem cell maintenance +is_a: GO:0032502 ! developmental process +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0045596 ! negative regulation of cell differentiation +relationship: part_of GO:0048864 ! stem cell development + +[Term] +id: GO:0019894 +name: kinesin binding +is_a: GO:0008092 ! cytoskeletal protein binding + +[Term] +id: GO:0019897 +name: extrinsic to plasma membrane +is_a: GO:0019898 ! extrinsic to membrane +is_a: GO:0044459 ! plasma membrane part + +[Term] +id: GO:0019898 +name: extrinsic to membrane +is_a: GO:0044425 ! membrane part + +[Term] +id: GO:0019899 +name: enzyme binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0019900 +name: kinase binding +is_a: GO:0019899 ! enzyme binding + +[Term] +id: GO:0019901 +name: protein kinase binding +is_a: GO:0019900 ! kinase binding + +[Term] +id: GO:0019902 +name: phosphatase binding +is_a: GO:0019899 ! enzyme binding + +[Term] +id: GO:0019903 +name: protein phosphatase binding +is_a: GO:0019902 ! phosphatase binding + +[Term] +id: GO:0019904 +name: protein domain specific binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0019941 +name: modification-dependent protein catabolic process +is_a: GO:0043632 ! modification-dependent macromolecule catabolic process +is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process + +[Term] +id: GO:0019953 +name: sexual reproduction +is_a: GO:0000003 ! reproduction + +[Term] +id: GO:0020028 +name: hemoglobin import +is_a: GO:0017038 ! protein import + +[Term] +id: GO:0021508 +name: floor plate formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0007418 ! ventral midline development +relationship: part_of GO:0033505 ! floor plate morphogenesis + +[Term] +id: GO:0021510 +name: spinal cord development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0021515 +name: cell differentiation in spinal cord +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0021510 ! spinal cord development + +[Term] +id: GO:0021516 +name: dorsal spinal cord development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021510 ! spinal cord development + +[Term] +id: GO:0021527 +name: spinal cord association neuron differentiation +is_a: GO:0021515 ! cell differentiation in spinal cord +is_a: GO:0021953 ! central nervous system neuron differentiation +relationship: part_of GO:0021516 ! dorsal spinal cord development + +[Term] +id: GO:0021532 +name: neural tube patterning +is_a: GO:0003002 ! regionalization +relationship: part_of GO:0021915 ! neural tube development + +[Term] +id: GO:0021533 +name: cell differentiation in hindbrain +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030902 ! hindbrain development + +[Term] +id: GO:0021535 +name: cell migration in hindbrain +is_a: GO:0016477 ! cell migration +relationship: part_of GO:0030902 ! hindbrain development + +[Term] +id: GO:0021536 +name: diencephalon development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021537 +name: telencephalon development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021541 +name: ammon gyrus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021766 ! hippocampus development + +[Term] +id: GO:0021543 +name: pallium development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021537 ! telencephalon development + +[Term] +id: GO:0021544 +name: subpallium development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021537 ! telencephalon development + +[Term] +id: GO:0021545 +name: cranial nerve development +is_a: GO:0021675 ! nerve development + +[Term] +id: GO:0021549 +name: cerebellum development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0022037 ! metencephalon development + +[Term] +id: GO:0021551 +name: central nervous system morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0021575 +name: hindbrain morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0030902 ! hindbrain development + +[Term] +id: GO:0021576 +name: hindbrain formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021575 ! hindbrain morphogenesis + +[Term] +id: GO:0021587 +name: cerebellum morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021549 ! cerebellum development +relationship: part_of GO:0021575 ! hindbrain morphogenesis + +[Term] +id: GO:0021588 +name: cerebellum formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021576 ! hindbrain formation +relationship: part_of GO:0021587 ! cerebellum morphogenesis + +[Term] +id: GO:0021675 +name: nerve development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0021681 +name: cerebellar granular layer development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021695 ! cerebellar cortex development + +[Term] +id: GO:0021683 +name: cerebellar granular layer morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021681 ! cerebellar granular layer development +relationship: part_of GO:0021696 ! cerebellar cortex morphogenesis + +[Term] +id: GO:0021684 +name: cerebellar granular layer formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021683 ! cerebellar granular layer morphogenesis +relationship: part_of GO:0021697 ! cerebellar cortex formation + +[Term] +id: GO:0021695 +name: cerebellar cortex development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021549 ! cerebellum development + +[Term] +id: GO:0021696 +name: cerebellar cortex morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021587 ! cerebellum morphogenesis +relationship: part_of GO:0021695 ! cerebellar cortex development + +[Term] +id: GO:0021697 +name: cerebellar cortex formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021696 ! cerebellar cortex morphogenesis + +[Term] +id: GO:0021700 +name: developmental maturation +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0021707 +name: cerebellar granule cell differentiation +is_a: GO:0021533 ! cell differentiation in hindbrain +is_a: GO:0021953 ! central nervous system neuron differentiation +relationship: part_of GO:0021684 ! cerebellar granular layer formation + +[Term] +id: GO:0021732 +name: midbrain-hindbrain boundary maturation +is_a: GO:0071695 ! anatomical structure maturation +relationship: part_of GO:0030917 ! midbrain-hindbrain boundary development + +[Term] +id: GO:0021756 +name: striatum development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021544 ! subpallium development + +[Term] +id: GO:0021757 +name: caudate nucleus development +is_a: GO:0048857 ! neural nucleus development +relationship: part_of GO:0021756 ! striatum development + +[Term] +id: GO:0021758 +name: putamen development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021756 ! striatum development + +[Term] +id: GO:0021761 +name: limbic system development +is_a: GO:0048731 ! system development +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021766 +name: hippocampus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021543 ! pallium development +relationship: part_of GO:0021761 ! limbic system development + +[Term] +id: GO:0021767 +name: mammillary body development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021536 ! diencephalon development +relationship: part_of GO:0021761 ! limbic system development + +[Term] +id: GO:0021772 +name: olfactory bulb development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021988 ! olfactory lobe development + +[Term] +id: GO:0021779 +name: oligodendrocyte cell fate commitment +is_a: GO:0021781 ! glial cell fate commitment +is_a: GO:0048709 ! oligodendrocyte differentiation + +[Term] +id: GO:0021781 +name: glial cell fate commitment +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0021782 +name: glial cell development +is_a: GO:0048468 ! cell development +relationship: part_of GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0021794 +name: thalamus development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021536 ! diencephalon development + +[Term] +id: GO:0021795 +name: cerebral cortex cell migration +is_a: GO:0022029 ! telencephalon cell migration +relationship: part_of GO:0021987 ! cerebral cortex development + +[Term] +id: GO:0021797 +name: forebrain anterior/posterior pattern specification +is_a: GO:0009952 ! anterior/posterior pattern specification +relationship: part_of GO:0021871 ! forebrain regionalization + +[Term] +id: GO:0021799 +name: cerebral cortex radially oriented cell migration +is_a: GO:0021795 ! cerebral cortex cell migration + +[Term] +id: GO:0021801 +name: cerebral cortex radial glia guided migration +is_a: GO:0021799 ! cerebral cortex radially oriented cell migration + +[Term] +id: GO:0021819 +name: layer formation in cerebral cortex +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021801 ! cerebral cortex radial glia guided migration + +[Term] +id: GO:0021846 +name: cell proliferation in forebrain +is_a: GO:0061351 ! neural precursor cell proliferation +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021852 +name: pyramidal neuron migration +is_a: GO:0001764 ! neuron migration +is_a: GO:0021801 ! cerebral cortex radial glia guided migration +relationship: part_of GO:0021860 ! pyramidal neuron development + +[Term] +id: GO:0021854 +name: hypothalamus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021536 ! diencephalon development +relationship: part_of GO:0021761 ! limbic system development + +[Term] +id: GO:0021855 +name: hypothalamus cell migration +is_a: GO:0016477 ! cell migration +relationship: part_of GO:0021854 ! hypothalamus development + +[Term] +id: GO:0021859 +name: pyramidal neuron differentiation +is_a: GO:0030182 ! neuron differentiation + +[Term] +id: GO:0021860 +name: pyramidal neuron development +is_a: GO:0021884 ! forebrain neuron development +relationship: part_of GO:0021859 ! pyramidal neuron differentiation + +[Term] +id: GO:0021861 +name: forebrain radial glial cell differentiation +is_a: GO:0060019 ! radial glial cell differentiation +relationship: part_of GO:0021872 ! forebrain generation of neurons + +[Term] +id: GO:0021871 +name: forebrain regionalization +is_a: GO:0003002 ! regionalization +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021872 +name: forebrain generation of neurons +is_a: GO:0048699 ! generation of neurons +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021873 +name: forebrain neuroblast division +is_a: GO:0055057 ! neuroblast division +relationship: part_of GO:0021872 ! forebrain generation of neurons + +[Term] +id: GO:0021874 +name: Wnt receptor signaling pathway involved in forebrain neuroblast division +is_a: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: part_of GO:0021873 ! forebrain neuroblast division +relationship: part_of GO:0021873 ! forebrain neuroblast division + +[Term] +id: GO:0021879 +name: forebrain neuron differentiation +is_a: GO:0021953 ! central nervous system neuron differentiation +relationship: part_of GO:0021872 ! forebrain generation of neurons + +[Term] +id: GO:0021884 +name: forebrain neuron development +is_a: GO:0021954 ! central nervous system neuron development +relationship: part_of GO:0021879 ! forebrain neuron differentiation + +[Term] +id: GO:0021885 +name: forebrain cell migration +is_a: GO:0016477 ! cell migration +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021889 +name: olfactory bulb interneuron differentiation +is_a: GO:0021879 ! forebrain neuron differentiation +relationship: part_of GO:0021772 ! olfactory bulb development + +[Term] +id: GO:0021891 +name: olfactory bulb interneuron development +is_a: GO:0048666 ! neuron development +relationship: part_of GO:0021889 ! olfactory bulb interneuron differentiation + +[Term] +id: GO:0021903 +name: rostrocaudal neural tube patterning +is_a: GO:0009952 ! anterior/posterior pattern specification +relationship: part_of GO:0021532 ! neural tube patterning + +[Term] +id: GO:0021904 +name: dorsal/ventral neural tube patterning +is_a: GO:0009953 ! dorsal/ventral pattern formation +relationship: part_of GO:0021532 ! neural tube patterning + +[Term] +id: GO:0021915 +name: neural tube development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007399 ! nervous system development +relationship: part_of GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0021932 +name: hindbrain radial glia guided cell migration +is_a: GO:0021535 ! cell migration in hindbrain + +[Term] +id: GO:0021943 +name: formation of radial glial scaffolds +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +relationship: part_of GO:0021932 ! hindbrain radial glia guided cell migration + +[Term] +id: GO:0021953 +name: central nervous system neuron differentiation +is_a: GO:0030182 ! neuron differentiation +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0021954 +name: central nervous system neuron development +is_a: GO:0048666 ! neuron development +relationship: part_of GO:0021953 ! central nervous system neuron differentiation + +[Term] +id: GO:0021983 +name: pituitary gland development +is_a: GO:0048732 ! gland development +relationship: part_of GO:0021536 ! diencephalon development +relationship: part_of GO:0035270 ! endocrine system development + +[Term] +id: GO:0021984 +name: adenohypophysis development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021983 ! pituitary gland development + +[Term] +id: GO:0021987 +name: cerebral cortex development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021543 ! pallium development + +[Term] +id: GO:0021988 +name: olfactory lobe development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021537 ! telencephalon development + +[Term] +id: GO:0022004 +name: midbrain-hindbrain boundary maturation during brain development +is_a: GO:0032502 ! developmental process +is_a: GO:0044707 ! single-multicellular organism process +relationship: part_of GO:0021732 ! midbrain-hindbrain boundary maturation + +[Term] +id: GO:0022008 +name: neurogenesis +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0022009 +name: central nervous system vasculogenesis +is_a: GO:0001570 ! vasculogenesis +relationship: part_of GO:0014045 ! establishment of endothelial blood-brain barrier + +[Term] +id: GO:0022010 +name: central nervous system myelination +is_a: GO:0032291 ! axon ensheathment in central nervous system +is_a: GO:0042552 ! myelination +relationship: part_of GO:0014003 ! oligodendrocyte development + +[Term] +id: GO:0022029 +name: telencephalon cell migration +is_a: GO:0021885 ! forebrain cell migration +relationship: part_of GO:0021537 ! telencephalon development + +[Term] +id: GO:0022037 +name: metencephalon development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030902 ! hindbrain development + +[Term] +id: GO:0022402 +name: cell cycle process +is_a: GO:0044763 ! single-organism cellular process +intersection_of: GO:0044763 ! single-organism cellular process +intersection_of: part_of GO:0007049 ! cell cycle +relationship: part_of GO:0007049 ! cell cycle + +[Term] +id: GO:0022404 +name: molting cycle process +is_a: GO:0044707 ! single-multicellular organism process +relationship: part_of GO:0042303 ! molting cycle + +[Term] +id: GO:0022405 +name: hair cycle process +is_a: GO:0022404 ! molting cycle process +relationship: part_of GO:0042633 ! hair cycle + +[Term] +id: GO:0022407 +name: regulation of cell-cell adhesion +is_a: GO:0030155 ! regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016337 ! cell-cell adhesion +relationship: regulates GO:0016337 ! cell-cell adhesion + +[Term] +id: GO:0022408 +name: negative regulation of cell-cell adhesion +is_a: GO:0007162 ! negative regulation of cell adhesion +is_a: GO:0022407 ! regulation of cell-cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016337 ! cell-cell adhesion +relationship: negatively_regulates GO:0016337 ! cell-cell adhesion + +[Term] +id: GO:0022409 +name: positive regulation of cell-cell adhesion +is_a: GO:0022407 ! regulation of cell-cell adhesion +is_a: GO:0045785 ! positive regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016337 ! cell-cell adhesion +relationship: positively_regulates GO:0016337 ! cell-cell adhesion + +[Term] +id: GO:0022411 +name: cellular component disassembly +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0022412 +name: cellular process involved in reproduction in multicellular organism +is_a: GO:0048610 ! cellular process involved in reproduction +intersection_of: GO:0044763 ! single-organism cellular process +intersection_of: part_of GO:0032504 ! multicellular organism reproduction +relationship: part_of GO:0032504 ! multicellular organism reproduction + +[Term] +id: GO:0022414 +name: reproductive process +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0000003 ! reproduction + +[Term] +id: GO:0022602 +name: ovulation cycle process +is_a: GO:0044699 ! single-organism process +is_a: GO:0048511 ! rhythmic process +relationship: part_of GO:0042698 ! ovulation cycle + +[Term] +id: GO:0022603 +name: regulation of anatomical structure morphogenesis +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009653 ! anatomical structure morphogenesis +relationship: regulates GO:0009653 ! anatomical structure morphogenesis + +[Term] +id: GO:0022604 +name: regulation of cell morphogenesis +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000902 ! cell morphogenesis +relationship: regulates GO:0000902 ! cell morphogenesis + +[Term] +id: GO:0022607 +name: cellular component assembly +is_a: GO:0016043 ! cellular component organization +relationship: part_of GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0022610 +name: biological adhesion +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0022612 +name: gland morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048732 ! gland development + +[Term] +id: GO:0022892 +name: substrate-specific transporter activity +is_a: GO:0005215 ! transporter activity + +[Term] +id: GO:0023014 +name: signal transduction by phosphorylation +is_a: GO:0007165 ! signal transduction +is_a: GO:0016310 ! phosphorylation + +[Term] +id: GO:0023019 +name: signal transduction involved in regulation of gene expression +is_a: GO:0007165 ! signal transduction +intersection_of: GO:0007165 ! signal transduction +intersection_of: part_of GO:0010468 ! regulation of gene expression +relationship: part_of GO:0010468 ! regulation of gene expression + +[Term] +id: GO:0023051 +name: regulation of signaling +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0023052 ! signaling +relationship: regulates GO:0044700 ! single organism signaling + +[Term] +id: GO:0023052 +name: signaling +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0023056 +name: positive regulation of signaling +is_a: GO:0023051 ! regulation of signaling +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0023052 ! signaling +relationship: positively_regulates GO:0044700 ! single organism signaling + +[Term] +id: GO:0023057 +name: negative regulation of signaling +is_a: GO:0023051 ! regulation of signaling +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0023052 ! signaling +relationship: negatively_regulates GO:0044700 ! single organism signaling + +[Term] +id: GO:0023061 +name: signal release +is_a: GO:0032940 ! secretion by cell +relationship: part_of GO:0003001 ! generation of a signal involved in cell-cell signaling + +[Term] +id: GO:0030001 +name: metal ion transport +is_a: GO:0006812 ! cation transport + +[Term] +id: GO:0030003 +name: cellular cation homeostasis +is_a: GO:0006873 ! cellular ion homeostasis +is_a: GO:0055080 ! cation homeostasis + +[Term] +id: GO:0030010 +name: establishment of cell polarity +is_a: GO:0007163 ! establishment or maintenance of cell polarity + +[Term] +id: GO:0030016 +name: myofibril +is_a: GO:0043292 ! contractile fiber + +[Term] +id: GO:0030017 +name: sarcomere +is_a: GO:0044449 ! contractile fiber part +relationship: part_of GO:0030016 ! myofibril + +[Term] +id: GO:0030018 +name: Z disc +is_a: GO:0044449 ! contractile fiber part +relationship: part_of GO:0031674 ! I band + +[Term] +id: GO:0030027 +name: lamellipodium +is_a: GO:0042995 ! cell projection +relationship: part_of GO:0031252 ! cell leading edge + +[Term] +id: GO:0030029 +name: actin filament-based process +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0030030 +name: cell projection organization +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0030031 +name: cell projection assembly +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0030030 ! cell projection organization + +[Term] +id: GO:0030032 +name: lamellipodium assembly +is_a: GO:0030031 ! cell projection assembly + +[Term] +id: GO:0030036 +name: actin cytoskeleton organization +is_a: GO:0007010 ! cytoskeleton organization +is_a: GO:0030029 ! actin filament-based process + +[Term] +id: GO:0030054 +name: cell junction +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0030055 +name: cell-substrate junction +is_a: GO:0030054 ! cell junction + +[Term] +id: GO:0030057 +name: desmosome +is_a: GO:0005911 ! cell-cell junction +is_a: GO:0070161 ! anchoring junction + +[Term] +id: GO:0030072 +name: peptide hormone secretion +is_a: GO:0002790 ! peptide secretion +is_a: GO:0046879 ! hormone secretion + +[Term] +id: GO:0030073 +name: insulin secretion +is_a: GO:0030072 ! peptide hormone secretion + +[Term] +id: GO:0030097 +name: hemopoiesis +is_a: GO:0048534 ! hematopoietic or lymphoid organ development + +[Term] +id: GO:0030098 +name: lymphocyte differentiation +is_a: GO:0002521 ! leukocyte differentiation +is_a: GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0030099 +name: myeloid cell differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030097 ! hemopoiesis + +[Term] +id: GO:0030100 +name: regulation of endocytosis +is_a: GO:0051128 ! regulation of cellular component organization +is_a: GO:0060627 ! regulation of vesicle-mediated transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006897 ! endocytosis +relationship: regulates GO:0006897 ! endocytosis + +[Term] +id: GO:0030111 +name: regulation of Wnt receptor signaling pathway +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016055 ! Wnt receptor signaling pathway +relationship: regulates GO:0016055 ! Wnt receptor signaling pathway + +[Term] +id: GO:0030139 +name: endocytic vesicle +is_a: GO:0016023 ! cytoplasmic membrane-bounded vesicle + +[Term] +id: GO:0030154 +name: cell differentiation +is_a: GO:0048869 ! cellular developmental process + +[Term] +id: GO:0030155 +name: regulation of cell adhesion +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007155 ! cell adhesion +relationship: regulates GO:0007155 ! cell adhesion + +[Term] +id: GO:0030162 +name: regulation of proteolysis +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006508 ! proteolysis +relationship: regulates GO:0006508 ! proteolysis + +[Term] +id: GO:0030163 +name: protein catabolic process +is_a: GO:0009057 ! macromolecule catabolic process +is_a: GO:0019538 ! protein metabolic process + +[Term] +id: GO:0030165 +name: PDZ domain binding +is_a: GO:0019904 ! protein domain specific binding + +[Term] +id: GO:0030166 +name: proteoglycan biosynthetic process +is_a: GO:0006029 ! proteoglycan metabolic process +is_a: GO:0009101 ! glycoprotein biosynthetic process + +[Term] +id: GO:0030168 +name: platelet activation +is_a: GO:0001775 ! cell activation +relationship: part_of GO:0007596 ! blood coagulation + +[Term] +id: GO:0030169 +name: low-density lipoprotein particle binding +is_a: GO:0071813 ! lipoprotein particle binding + +[Term] +id: GO:0030177 +name: positive regulation of Wnt receptor signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0030111 ! regulation of Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016055 ! Wnt receptor signaling pathway +relationship: positively_regulates GO:0016055 ! Wnt receptor signaling pathway + +[Term] +id: GO:0030178 +name: negative regulation of Wnt receptor signaling pathway +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:0030111 ! regulation of Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016055 ! Wnt receptor signaling pathway +relationship: negatively_regulates GO:0016055 ! Wnt receptor signaling pathway + +[Term] +id: GO:0030182 +name: neuron differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0048699 ! generation of neurons + +[Term] +id: GO:0030183 +name: B cell differentiation +is_a: GO:0030098 ! lymphocyte differentiation +is_a: GO:0042113 ! B cell activation + +[Term] +id: GO:0030193 +name: regulation of blood coagulation +is_a: GO:0032101 ! regulation of response to external stimulus +is_a: GO:0050818 ! regulation of coagulation +is_a: GO:0061041 ! regulation of wound healing +is_a: GO:1900046 ! regulation of hemostasis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007596 ! blood coagulation +relationship: regulates GO:0007596 ! blood coagulation + +[Term] +id: GO:0030198 +name: extracellular matrix organization +is_a: GO:0043062 ! extracellular structure organization + +[Term] +id: GO:0030199 +name: collagen fibril organization +is_a: GO:0030198 ! extracellular matrix organization + +[Term] +id: GO:0030201 +name: heparan sulfate proteoglycan metabolic process +is_a: GO:0006029 ! proteoglycan metabolic process +is_a: GO:0006790 ! sulfur compound metabolic process +is_a: GO:0043436 ! oxoacid metabolic process + +[Term] +id: GO:0030203 +name: glycosaminoglycan metabolic process +is_a: GO:0006022 ! aminoglycan metabolic process + +[Term] +id: GO:0030217 +name: T cell differentiation +is_a: GO:0030098 ! lymphocyte differentiation +is_a: GO:0042110 ! T cell activation + +[Term] +id: GO:0030224 +name: monocyte differentiation +is_a: GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0030228 +name: lipoprotein particle receptor activity +is_a: GO:0038024 ! cargo receptor activity +relationship: has_part GO:0071813 ! lipoprotein particle binding + +[Term] +id: GO:0030229 +name: very-low-density lipoprotein particle receptor activity +is_a: GO:0030228 ! lipoprotein particle receptor activity +relationship: has_part GO:0034189 ! very-low-density lipoprotein particle binding + +[Term] +id: GO:0030234 +name: enzyme regulator activity +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0050790 ! regulation of catalytic activity +relationship: regulates GO:0003824 ! catalytic activity + +[Term] +id: GO:0030237 +name: female sex determination +is_a: GO:0007530 ! sex determination +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0030262 +name: apoptotic nuclear changes +is_a: GO:0006921 ! cellular component disassembly involved in execution phase of apoptosis + +[Term] +id: GO:0030278 +name: regulation of ossification +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001503 ! ossification +relationship: regulates GO:0001503 ! ossification + +[Term] +id: GO:0030279 +name: negative regulation of ossification +is_a: GO:0030278 ! regulation of ossification +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001503 ! ossification +relationship: negatively_regulates GO:0001503 ! ossification + +[Term] +id: GO:0030282 +name: bone mineralization +is_a: GO:0031214 ! biomineral tissue development +relationship: part_of GO:0001503 ! ossification + +[Term] +id: GO:0030301 +name: cholesterol transport +is_a: GO:0015918 ! sterol transport + +[Term] +id: GO:0030307 +name: positive regulation of cell growth +is_a: GO:0001558 ! regulation of cell growth +is_a: GO:0045927 ! positive regulation of growth +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016049 ! cell growth +relationship: positively_regulates GO:0016049 ! cell growth + +[Term] +id: GO:0030308 +name: negative regulation of cell growth +is_a: GO:0001558 ! regulation of cell growth +is_a: GO:0045926 ! negative regulation of growth +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016049 ! cell growth +relationship: negatively_regulates GO:0016049 ! cell growth + +[Term] +id: GO:0030316 +name: osteoclast differentiation +is_a: GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0030318 +name: melanocyte differentiation +is_a: GO:0050931 ! pigment cell differentiation +is_a: GO:0060563 ! neuroepithelial cell differentiation + +[Term] +id: GO:0030323 +name: respiratory tube development +is_a: GO:0035295 ! tube development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0030324 +name: lung development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0030323 ! respiratory tube development +relationship: part_of GO:0060541 ! respiratory system development + +[Term] +id: GO:0030326 +name: embryonic limb morphogenesis +is_a: GO:0035108 ! limb morphogenesis +is_a: GO:0035113 ! embryonic appendage morphogenesis + +[Term] +id: GO:0030331 +name: estrogen receptor binding +is_a: GO:0035258 ! steroid hormone receptor binding + +[Term] +id: GO:0030334 +name: regulation of cell migration +is_a: GO:2000145 ! regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016477 ! cell migration +relationship: regulates GO:0016477 ! cell migration + +[Term] +id: GO:0030335 +name: positive regulation of cell migration +is_a: GO:0030334 ! regulation of cell migration +is_a: GO:2000147 ! positive regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016477 ! cell migration +relationship: positively_regulates GO:0016477 ! cell migration + +[Term] +id: GO:0030336 +name: negative regulation of cell migration +is_a: GO:0030334 ! regulation of cell migration +is_a: GO:2000146 ! negative regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016477 ! cell migration +relationship: negatively_regulates GO:0016477 ! cell migration + +[Term] +id: GO:0030424 +name: axon +is_a: GO:0043005 ! neuron projection + +[Term] +id: GO:0030425 +name: dendrite +is_a: GO:0043005 ! neuron projection + +[Term] +id: GO:0030492 +name: hemoglobin binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0030500 +name: regulation of bone mineralization +is_a: GO:0030278 ! regulation of ossification +is_a: GO:0070167 ! regulation of biomineral tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030282 ! bone mineralization +relationship: regulates GO:0030282 ! bone mineralization + +[Term] +id: GO:0030501 +name: positive regulation of bone mineralization +is_a: GO:0030500 ! regulation of bone mineralization +is_a: GO:0045778 ! positive regulation of ossification +is_a: GO:0070169 ! positive regulation of biomineral tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030282 ! bone mineralization +relationship: positively_regulates GO:0030282 ! bone mineralization + +[Term] +id: GO:0030509 +name: BMP signaling pathway +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway + +[Term] +id: GO:0030510 +name: regulation of BMP signaling pathway +is_a: GO:0090092 ! regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030509 ! BMP signaling pathway +relationship: regulates GO:0030509 ! BMP signaling pathway + +[Term] +id: GO:0030512 +name: negative regulation of transforming growth factor beta receptor signaling pathway +is_a: GO:0017015 ! regulation of transforming growth factor beta receptor signaling pathway +is_a: GO:0090101 ! negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0090288 ! negative regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007179 ! transforming growth factor beta receptor signaling pathway +relationship: negatively_regulates GO:0007179 ! transforming growth factor beta receptor signaling pathway + +[Term] +id: GO:0030513 +name: positive regulation of BMP signaling pathway +is_a: GO:0030510 ! regulation of BMP signaling pathway +is_a: GO:0090100 ! positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030509 ! BMP signaling pathway +relationship: positively_regulates GO:0030509 ! BMP signaling pathway + +[Term] +id: GO:0030514 +name: negative regulation of BMP signaling pathway +is_a: GO:0030510 ! regulation of BMP signaling pathway +is_a: GO:0090101 ! negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030509 ! BMP signaling pathway +relationship: negatively_regulates GO:0030509 ! BMP signaling pathway + +[Term] +id: GO:0030516 +name: regulation of axon extension +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:0050770 ! regulation of axonogenesis +is_a: GO:0061387 ! regulation of extent of cell growth +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048675 ! axon extension +relationship: regulates GO:0048675 ! axon extension + +[Term] +id: GO:0030517 +name: negative regulation of axon extension +is_a: GO:0030308 ! negative regulation of cell growth +is_a: GO:0030516 ! regulation of axon extension +is_a: GO:0048640 ! negative regulation of developmental growth +is_a: GO:0050771 ! negative regulation of axonogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048675 ! axon extension +relationship: negatively_regulates GO:0048675 ! axon extension + +[Term] +id: GO:0030518 +name: intracellular steroid hormone receptor signaling pathway +is_a: GO:0030522 ! intracellular receptor signaling pathway + +[Term] +id: GO:0030520 +name: intracellular estrogen receptor signaling pathway +is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway + +[Term] +id: GO:0030521 +name: androgen receptor signaling pathway +is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway + +[Term] +id: GO:0030522 +name: intracellular receptor signaling pathway +is_a: GO:0007165 ! signal transduction + +[Term] +id: GO:0030534 +name: adult behavior +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044708 ! single-organism behavior + +[Term] +id: GO:0030539 +name: male genitalia development +is_a: GO:0048806 ! genitalia development +relationship: part_of GO:0046546 ! development of primary male sexual characteristics + +[Term] +id: GO:0030540 +name: female genitalia development +is_a: GO:0048806 ! genitalia development +relationship: part_of GO:0046545 ! development of primary female sexual characteristics + +[Term] +id: GO:0030545 +name: receptor regulator activity +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0010469 ! regulation of receptor activity +relationship: regulates GO:0004872 ! receptor activity + +[Term] +id: GO:0030546 +name: receptor activator activity +is_a: GO:0030545 ! receptor regulator activity +relationship: part_of GO:2000273 ! positive regulation of receptor activity +relationship: positively_regulates GO:0004872 ! receptor activity + +[Term] +id: GO:0030547 +name: receptor inhibitor activity +is_a: GO:0030545 ! receptor regulator activity +relationship: negatively_regulates GO:0004872 ! receptor activity +relationship: part_of GO:2000272 ! negative regulation of receptor activity + +[Term] +id: GO:0030579 +name: ubiquitin-dependent SMAD protein catabolic process +is_a: GO:0006511 ! ubiquitin-dependent protein catabolic process +relationship: part_of GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway + +[Term] +id: GO:0030595 +name: leukocyte chemotaxis +is_a: GO:0050900 ! leukocyte migration +is_a: GO:0060326 ! cell chemotaxis + +[Term] +id: GO:0030799 +name: regulation of cyclic nucleotide metabolic process +is_a: GO:0006140 ! regulation of nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009187 ! cyclic nucleotide metabolic process +relationship: regulates GO:0009187 ! cyclic nucleotide metabolic process + +[Term] +id: GO:0030801 +name: positive regulation of cyclic nucleotide metabolic process +is_a: GO:0030799 ! regulation of cyclic nucleotide metabolic process +is_a: GO:0045981 ! positive regulation of nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009187 ! cyclic nucleotide metabolic process +relationship: positively_regulates GO:0009187 ! cyclic nucleotide metabolic process + +[Term] +id: GO:0030811 +name: regulation of nucleotide catabolic process +is_a: GO:0006140 ! regulation of nucleotide metabolic process +is_a: GO:0031329 ! regulation of cellular catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009166 ! nucleotide catabolic process +relationship: regulates GO:0009166 ! nucleotide catabolic process + +[Term] +id: GO:0030823 +name: regulation of cGMP metabolic process +is_a: GO:0030799 ! regulation of cyclic nucleotide metabolic process +is_a: GO:1900542 ! regulation of purine nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046068 ! cGMP metabolic process +relationship: regulates GO:0046068 ! cGMP metabolic process + +[Term] +id: GO:0030825 +name: positive regulation of cGMP metabolic process +is_a: GO:0030801 ! positive regulation of cyclic nucleotide metabolic process +is_a: GO:0030823 ! regulation of cGMP metabolic process +is_a: GO:1900544 ! positive regulation of purine nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046068 ! cGMP metabolic process +relationship: positively_regulates GO:0046068 ! cGMP metabolic process + +[Term] +id: GO:0030850 +name: prostate gland development +is_a: GO:0048608 ! reproductive structure development +is_a: GO:0048732 ! gland development +relationship: part_of GO:0001655 ! urogenital system development + +[Term] +id: GO:0030855 +name: epithelial cell differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0060429 ! epithelium development + +[Term] +id: GO:0030856 +name: regulation of epithelial cell differentiation +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030855 ! epithelial cell differentiation +relationship: regulates GO:0030855 ! epithelial cell differentiation + +[Term] +id: GO:0030858 +name: positive regulation of epithelial cell differentiation +is_a: GO:0030856 ! regulation of epithelial cell differentiation +is_a: GO:0045597 ! positive regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030855 ! epithelial cell differentiation +relationship: positively_regulates GO:0030855 ! epithelial cell differentiation + +[Term] +id: GO:0030877 +name: beta-catenin destruction complex +is_a: GO:0043234 ! protein complex +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0030879 +name: mammary gland development +is_a: GO:0048732 ! gland development + +[Term] +id: GO:0030888 +name: regulation of B cell proliferation +is_a: GO:0050670 ! regulation of lymphocyte proliferation +is_a: GO:0050864 ! regulation of B cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042100 ! B cell proliferation +relationship: regulates GO:0042100 ! B cell proliferation + +[Term] +id: GO:0030890 +name: positive regulation of B cell proliferation +is_a: GO:0030888 ! regulation of B cell proliferation +is_a: GO:0050671 ! positive regulation of lymphocyte proliferation +is_a: GO:0050871 ! positive regulation of B cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042100 ! B cell proliferation +relationship: positively_regulates GO:0042100 ! B cell proliferation + +[Term] +id: GO:0030900 +name: forebrain development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007420 ! brain development + +[Term] +id: GO:0030901 +name: midbrain development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007420 ! brain development + +[Term] +id: GO:0030902 +name: hindbrain development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007420 ! brain development + +[Term] +id: GO:0030916 +name: otic vesicle formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0071600 ! otic vesicle morphogenesis + +[Term] +id: GO:0030917 +name: midbrain-hindbrain boundary development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007420 ! brain development +relationship: part_of GO:0021903 ! rostrocaudal neural tube patterning + +[Term] +id: GO:0030971 +name: receptor tyrosine kinase binding +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0030997 +name: regulation of centriole-centriole cohesion +is_a: GO:0070507 ! regulation of microtubule cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010457 ! centriole-centriole cohesion +relationship: part_of GO:0007098 ! centrosome cycle +relationship: regulates GO:0010457 ! centriole-centriole cohesion + +[Term] +id: GO:0031012 +name: extracellular matrix +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0031016 +name: pancreas development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0031018 +name: endocrine pancreas development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0031016 ! pancreas development +relationship: part_of GO:0035270 ! endocrine system development + +[Term] +id: GO:0031023 +name: microtubule organizing center organization +is_a: GO:0006996 ! organelle organization +relationship: part_of GO:0000226 ! microtubule cytoskeleton organization + +[Term] +id: GO:0031069 +name: hair follicle morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0022405 ! hair cycle process +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001942 ! hair follicle development +relationship: part_of GO:0048730 ! epidermis morphogenesis + +[Term] +id: GO:0031076 +name: embryonic camera-type eye development +is_a: GO:0043010 ! camera-type eye development +is_a: GO:0048568 ! embryonic organ development + +[Term] +id: GO:0031098 +name: stress-activated protein kinase signaling cascade +is_a: GO:0007243 ! intracellular protein kinase cascade +is_a: GO:0033554 ! cellular response to stress + +[Term] +id: GO:0031099 +name: regeneration +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0031100 +name: organ regeneration +is_a: GO:0031099 ! regeneration +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0031128 +name: developmental induction +is_a: GO:0045168 ! cell-cell signaling involved in cell fate commitment + +[Term] +id: GO:0031133 +name: regulation of axon diameter +is_a: GO:0032536 ! regulation of cell projection size +is_a: GO:0050770 ! regulation of axonogenesis + +[Term] +id: GO:0031175 +name: neuron projection development +is_a: GO:0030030 ! cell projection organization +relationship: part_of GO:0048666 ! neuron development + +[Term] +id: GO:0031214 +name: biomineral tissue development +is_a: GO:0009888 ! tissue development +relationship: part_of GO:0048513 ! organ development + +[Term] +id: GO:0031223 +name: auditory behavior +is_a: GO:0007638 ! mechanosensory behavior +is_a: GO:0010996 ! response to auditory stimulus + +[Term] +id: GO:0031224 +name: intrinsic to membrane +is_a: GO:0044425 ! membrane part + +[Term] +id: GO:0031252 +name: cell leading edge +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0031253 +name: cell projection membrane +is_a: GO:0044459 ! plasma membrane part +is_a: GO:0044463 ! cell projection part + +[Term] +id: GO:0031323 +name: regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044237 ! cellular metabolic process +relationship: regulates GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0031324 +name: negative regulation of cellular metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044237 ! cellular metabolic process +relationship: negatively_regulates GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0031325 +name: positive regulation of cellular metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044237 ! cellular metabolic process +relationship: positively_regulates GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0031326 +name: regulation of cellular biosynthetic process +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044249 ! cellular biosynthetic process +relationship: regulates GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0031327 +name: negative regulation of cellular biosynthetic process +is_a: GO:0009890 ! negative regulation of biosynthetic process +is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044249 ! cellular biosynthetic process +relationship: negatively_regulates GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0031328 +name: positive regulation of cellular biosynthetic process +is_a: GO:0009891 ! positive regulation of biosynthetic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044249 ! cellular biosynthetic process +relationship: positively_regulates GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0031329 +name: regulation of cellular catabolic process +is_a: GO:0009894 ! regulation of catabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044248 ! cellular catabolic process +relationship: regulates GO:0044248 ! cellular catabolic process + +[Term] +id: GO:0031333 +name: negative regulation of protein complex assembly +is_a: GO:0043254 ! regulation of protein complex assembly +is_a: GO:0051129 ! negative regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006461 ! protein complex assembly +relationship: negatively_regulates GO:0006461 ! protein complex assembly + +[Term] +id: GO:0031334 +name: positive regulation of protein complex assembly +is_a: GO:0043254 ! regulation of protein complex assembly +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006461 ! protein complex assembly +relationship: positively_regulates GO:0006461 ! protein complex assembly + +[Term] +id: GO:0031344 +name: regulation of cell projection organization +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030030 ! cell projection organization +relationship: regulates GO:0030030 ! cell projection organization + +[Term] +id: GO:0031345 +name: negative regulation of cell projection organization +is_a: GO:0031344 ! regulation of cell projection organization +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051129 ! negative regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030030 ! cell projection organization +relationship: negatively_regulates GO:0030030 ! cell projection organization + +[Term] +id: GO:0031346 +name: positive regulation of cell projection organization +is_a: GO:0031344 ! regulation of cell projection organization +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030030 ! cell projection organization +relationship: positively_regulates GO:0030030 ! cell projection organization + +[Term] +id: GO:0031347 +name: regulation of defense response +is_a: GO:0080134 ! regulation of response to stress +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006952 ! defense response +relationship: regulates GO:0006952 ! defense response + +[Term] +id: GO:0031349 +name: positive regulation of defense response +is_a: GO:0031347 ! regulation of defense response +is_a: GO:0048584 ! positive regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006952 ! defense response +relationship: positively_regulates GO:0006952 ! defense response + +[Term] +id: GO:0031396 +name: regulation of protein ubiquitination +is_a: GO:0031399 ! regulation of protein modification process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016567 ! protein ubiquitination +relationship: regulates GO:0016567 ! protein ubiquitination + +[Term] +id: GO:0031397 +name: negative regulation of protein ubiquitination +is_a: GO:0031396 ! regulation of protein ubiquitination +is_a: GO:0031400 ! negative regulation of protein modification process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016567 ! protein ubiquitination +relationship: negatively_regulates GO:0016567 ! protein ubiquitination + +[Term] +id: GO:0031399 +name: regulation of protein modification process +is_a: GO:0032268 ! regulation of cellular protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006464 ! cellular protein modification process +relationship: regulates GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0031400 +name: negative regulation of protein modification process +is_a: GO:0031399 ! regulation of protein modification process +is_a: GO:0032269 ! negative regulation of cellular protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006464 ! cellular protein modification process +relationship: negatively_regulates GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0031401 +name: positive regulation of protein modification process +is_a: GO:0031399 ! regulation of protein modification process +is_a: GO:0032270 ! positive regulation of cellular protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006464 ! cellular protein modification process +relationship: positively_regulates GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0031410 +name: cytoplasmic vesicle +is_a: GO:0031982 ! vesicle +is_a: GO:0043229 ! intracellular organelle +is_a: GO:0044444 ! cytoplasmic part +intersection_of: GO:0031982 ! vesicle +intersection_of: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0031490 +name: chromatin DNA binding +is_a: GO:0003682 ! chromatin binding +is_a: GO:0043566 ! structure-specific DNA binding + +[Term] +id: GO:0031526 +name: brush border membrane +is_a: GO:0031253 ! cell projection membrane +relationship: part_of GO:0005903 ! brush border + +[Term] +id: GO:0031528 +name: microvillus membrane +is_a: GO:0031253 ! cell projection membrane +relationship: part_of GO:0005902 ! microvillus + +[Term] +id: GO:0031589 +name: cell-substrate adhesion +is_a: GO:0007155 ! cell adhesion + +[Term] +id: GO:0031623 +name: receptor internalization +is_a: GO:0006898 ! receptor-mediated endocytosis +is_a: GO:0043112 ! receptor metabolic process +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0031624 +name: ubiquitin conjugating enzyme binding +is_a: GO:0044390 ! small protein conjugating enzyme binding + +[Term] +id: GO:0031641 +name: regulation of myelination +is_a: GO:0051960 ! regulation of nervous system development +is_a: GO:0051969 ! regulation of transmission of nerve impulse +is_a: GO:2000021 ! regulation of ion homeostasis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042552 ! myelination +relationship: regulates GO:0042552 ! myelination + +[Term] +id: GO:0031644 +name: regulation of neurological system process +is_a: GO:0044057 ! regulation of system process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050877 ! neurological system process +relationship: regulates GO:0050877 ! neurological system process + +[Term] +id: GO:0031667 +name: response to nutrient levels +is_a: GO:0009991 ! response to extracellular stimulus + +[Term] +id: GO:0031668 +name: cellular response to extracellular stimulus +is_a: GO:0007154 ! cell communication +is_a: GO:0009991 ! response to extracellular stimulus +is_a: GO:0051716 ! cellular response to stimulus +is_a: GO:0071496 ! cellular response to external stimulus + +[Term] +id: GO:0031669 +name: cellular response to nutrient levels +is_a: GO:0031667 ! response to nutrient levels +is_a: GO:0031668 ! cellular response to extracellular stimulus + +[Term] +id: GO:0031670 +name: cellular response to nutrient +is_a: GO:0007584 ! response to nutrient +is_a: GO:0031669 ! cellular response to nutrient levels +is_a: GO:0070887 ! cellular response to chemical stimulus + +[Term] +id: GO:0031674 +name: I band +is_a: GO:0044449 ! contractile fiber part +relationship: part_of GO:0030017 ! sarcomere + +[Term] +id: GO:0031943 +name: regulation of glucocorticoid metabolic process +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008211 ! glucocorticoid metabolic process +relationship: regulates GO:0008211 ! glucocorticoid metabolic process + +[Term] +id: GO:0031945 +name: positive regulation of glucocorticoid metabolic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0031943 ! regulation of glucocorticoid metabolic process +is_a: GO:0032352 ! positive regulation of hormone metabolic process +is_a: GO:0045940 ! positive regulation of steroid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008211 ! glucocorticoid metabolic process +relationship: positively_regulates GO:0008211 ! glucocorticoid metabolic process + +[Term] +id: GO:0031946 +name: regulation of glucocorticoid biosynthetic process +is_a: GO:0031943 ! regulation of glucocorticoid metabolic process +is_a: GO:0090030 ! regulation of steroid hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006704 ! glucocorticoid biosynthetic process +relationship: regulates GO:0006704 ! glucocorticoid biosynthetic process + +[Term] +id: GO:0031948 +name: positive regulation of glucocorticoid biosynthetic process +is_a: GO:0031945 ! positive regulation of glucocorticoid metabolic process +is_a: GO:0031946 ! regulation of glucocorticoid biosynthetic process +is_a: GO:0090031 ! positive regulation of steroid hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006704 ! glucocorticoid biosynthetic process +relationship: positively_regulates GO:0006704 ! glucocorticoid biosynthetic process + +[Term] +id: GO:0031974 +name: membrane-enclosed lumen +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0031981 +name: nuclear lumen +is_a: GO:0044428 ! nuclear part +is_a: GO:0070013 ! intracellular organelle lumen + +[Term] +id: GO:0031982 +name: vesicle +is_a: GO:0043226 ! organelle + +[Term] +id: GO:0031988 +name: membrane-bounded vesicle +is_a: GO:0031982 ! vesicle + +[Term] +id: GO:0032088 +name: negative regulation of NF-kappaB transcription factor activity +is_a: GO:0043433 ! negative regulation of sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0032091 +name: negative regulation of protein binding +is_a: GO:0043393 ! regulation of protein binding +is_a: GO:0051100 ! negative regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0005515 ! protein binding +relationship: negatively_regulates GO:0005515 ! protein binding + +[Term] +id: GO:0032092 +name: positive regulation of protein binding +is_a: GO:0043393 ! regulation of protein binding +is_a: GO:0051099 ! positive regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0005515 ! protein binding +relationship: positively_regulates GO:0005515 ! protein binding + +[Term] +id: GO:0032101 +name: regulation of response to external stimulus +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009605 ! response to external stimulus +relationship: regulates GO:0009605 ! response to external stimulus + +[Term] +id: GO:0032102 +name: negative regulation of response to external stimulus +is_a: GO:0032101 ! regulation of response to external stimulus +is_a: GO:0048585 ! negative regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009605 ! response to external stimulus +relationship: negatively_regulates GO:0009605 ! response to external stimulus + +[Term] +id: GO:0032103 +name: positive regulation of response to external stimulus +is_a: GO:0032101 ! regulation of response to external stimulus +is_a: GO:0048584 ! positive regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009605 ! response to external stimulus +relationship: positively_regulates GO:0009605 ! response to external stimulus + +[Term] +id: GO:0032147 +name: activation of protein kinase activity +is_a: GO:0045860 ! positive regulation of protein kinase activity + +[Term] +id: GO:0032148 +name: activation of protein kinase B activity +is_a: GO:0032147 ! activation of protein kinase activity + +[Term] +id: GO:0032231 +name: regulation of actin filament bundle assembly +is_a: GO:0032956 ! regulation of actin cytoskeleton organization +is_a: GO:0044087 ! regulation of cellular component biogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051017 ! actin filament bundle assembly +relationship: regulates GO:0051017 ! actin filament bundle assembly + +[Term] +id: GO:0032233 +name: positive regulation of actin filament bundle assembly +is_a: GO:0032231 ! regulation of actin filament bundle assembly +is_a: GO:0051495 ! positive regulation of cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0051017 ! actin filament bundle assembly +relationship: positively_regulates GO:0051017 ! actin filament bundle assembly + +[Term] +id: GO:0032268 +name: regulation of cellular protein metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044267 ! cellular protein metabolic process +relationship: regulates GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0032269 +name: negative regulation of cellular protein metabolic process +is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0032268 ! regulation of cellular protein metabolic process +is_a: GO:0051248 ! negative regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044267 ! cellular protein metabolic process +relationship: negatively_regulates GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0032270 +name: positive regulation of cellular protein metabolic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0032268 ! regulation of cellular protein metabolic process +is_a: GO:0051247 ! positive regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044267 ! cellular protein metabolic process +relationship: positively_regulates GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0032288 +name: myelin assembly +is_a: GO:0010927 ! cellular component assembly involved in morphogenesis +relationship: part_of GO:0042552 ! myelination + +[Term] +id: GO:0032289 +name: central nervous system myelin formation +is_a: GO:0032288 ! myelin assembly +relationship: part_of GO:0022010 ! central nervous system myelination + +[Term] +id: GO:0032291 +name: axon ensheathment in central nervous system +is_a: GO:0008366 ! axon ensheathment + +[Term] +id: GO:0032318 +name: regulation of Ras GTPase activity +is_a: GO:0043087 ! regulation of GTPase activity +relationship: part_of GO:0046578 ! regulation of Ras protein signal transduction + +[Term] +id: GO:0032319 +name: regulation of Rho GTPase activity +is_a: GO:0032318 ! regulation of Ras GTPase activity +relationship: part_of GO:0035023 ! regulation of Rho protein signal transduction + +[Term] +id: GO:0032320 +name: positive regulation of Ras GTPase activity +is_a: GO:0032318 ! regulation of Ras GTPase activity +is_a: GO:0043547 ! positive regulation of GTPase activity + +[Term] +id: GO:0032321 +name: positive regulation of Rho GTPase activity +is_a: GO:0032319 ! regulation of Rho GTPase activity +is_a: GO:0032320 ! positive regulation of Ras GTPase activity + +[Term] +id: GO:0032330 +name: regulation of chondrocyte differentiation +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0061035 ! regulation of cartilage development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002062 ! chondrocyte differentiation +relationship: regulates GO:0002062 ! chondrocyte differentiation + +[Term] +id: GO:0032331 +name: negative regulation of chondrocyte differentiation +is_a: GO:0032330 ! regulation of chondrocyte differentiation +is_a: GO:0045596 ! negative regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002062 ! chondrocyte differentiation +relationship: negatively_regulates GO:0002062 ! chondrocyte differentiation + +[Term] +id: GO:0032341 +name: aldosterone metabolic process +is_a: GO:0006066 ! alcohol metabolic process +is_a: GO:0008207 ! C21-steroid hormone metabolic process +is_a: GO:0008212 ! mineralocorticoid metabolic process +is_a: GO:0042180 ! cellular ketone metabolic process + +[Term] +id: GO:0032342 +name: aldosterone biosynthetic process +is_a: GO:0006700 ! C21-steroid hormone biosynthetic process +is_a: GO:0006705 ! mineralocorticoid biosynthetic process +is_a: GO:0032341 ! aldosterone metabolic process +is_a: GO:0042181 ! ketone biosynthetic process +is_a: GO:0046165 ! alcohol biosynthetic process + +[Term] +id: GO:0032344 +name: regulation of aldosterone metabolic process +is_a: GO:0010565 ! regulation of cellular ketone metabolic process +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032341 ! aldosterone metabolic process +relationship: regulates GO:0032341 ! aldosterone metabolic process + +[Term] +id: GO:0032346 +name: positive regulation of aldosterone metabolic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0032344 ! regulation of aldosterone metabolic process +is_a: GO:0032352 ! positive regulation of hormone metabolic process +is_a: GO:0045940 ! positive regulation of steroid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032341 ! aldosterone metabolic process +relationship: positively_regulates GO:0032341 ! aldosterone metabolic process + +[Term] +id: GO:0032347 +name: regulation of aldosterone biosynthetic process +is_a: GO:0010566 ! regulation of ketone biosynthetic process +is_a: GO:0032344 ! regulation of aldosterone metabolic process +is_a: GO:0090030 ! regulation of steroid hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032342 ! aldosterone biosynthetic process +relationship: regulates GO:0032342 ! aldosterone biosynthetic process + +[Term] +id: GO:0032349 +name: positive regulation of aldosterone biosynthetic process +is_a: GO:0032346 ! positive regulation of aldosterone metabolic process +is_a: GO:0032347 ! regulation of aldosterone biosynthetic process +is_a: GO:0090031 ! positive regulation of steroid hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032342 ! aldosterone biosynthetic process +relationship: positively_regulates GO:0032342 ! aldosterone biosynthetic process + +[Term] +id: GO:0032350 +name: regulation of hormone metabolic process +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042445 ! hormone metabolic process +relationship: regulates GO:0042445 ! hormone metabolic process + +[Term] +id: GO:0032351 +name: negative regulation of hormone metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042445 ! hormone metabolic process +relationship: negatively_regulates GO:0042445 ! hormone metabolic process + +[Term] +id: GO:0032352 +name: positive regulation of hormone metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042445 ! hormone metabolic process +relationship: positively_regulates GO:0042445 ! hormone metabolic process + +[Term] +id: GO:0032353 +name: negative regulation of hormone biosynthetic process +is_a: GO:0031327 ! negative regulation of cellular biosynthetic process +is_a: GO:0032351 ! negative regulation of hormone metabolic process +is_a: GO:0046885 ! regulation of hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042446 ! hormone biosynthetic process +relationship: negatively_regulates GO:0042446 ! hormone biosynthetic process + +[Term] +id: GO:0032355 +name: response to estradiol stimulus +is_a: GO:0043627 ! response to estrogen stimulus +is_a: GO:0097305 ! response to alcohol + +[Term] +id: GO:0032364 +name: oxygen homeostasis +is_a: GO:0033483 ! gas homeostasis + +[Term] +id: GO:0032365 +name: intracellular lipid transport +is_a: GO:0006869 ! lipid transport +is_a: GO:0046907 ! intracellular transport +intersection_of: GO:0006869 ! lipid transport +intersection_of: occurs_in GO:0005622 ! intracellular + +[Term] +id: GO:0032366 +name: intracellular sterol transport +is_a: GO:0015918 ! sterol transport +is_a: GO:0032365 ! intracellular lipid transport +intersection_of: GO:0015918 ! sterol transport +intersection_of: occurs_in GO:0005622 ! intracellular + +[Term] +id: GO:0032367 +name: intracellular cholesterol transport +is_a: GO:0030301 ! cholesterol transport +is_a: GO:0032366 ! intracellular sterol transport +intersection_of: GO:0030301 ! cholesterol transport +intersection_of: occurs_in GO:0005622 ! intracellular + +[Term] +id: GO:0032386 +name: regulation of intracellular transport +is_a: GO:0051049 ! regulation of transport +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046907 ! intracellular transport +relationship: regulates GO:0046907 ! intracellular transport + +[Term] +id: GO:0032387 +name: negative regulation of intracellular transport +is_a: GO:0032386 ! regulation of intracellular transport +is_a: GO:0051051 ! negative regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046907 ! intracellular transport +relationship: negatively_regulates GO:0046907 ! intracellular transport + +[Term] +id: GO:0032388 +name: positive regulation of intracellular transport +is_a: GO:0032386 ! regulation of intracellular transport +is_a: GO:0051050 ! positive regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046907 ! intracellular transport +relationship: positively_regulates GO:0046907 ! intracellular transport + +[Term] +id: GO:0032403 +name: protein complex binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0032444 +name: activin responsive factor complex +is_a: GO:0005667 ! transcription factor complex + +[Term] +id: GO:0032446 +name: protein modification by small protein conjugation +is_a: GO:0070647 ! protein modification by small protein conjugation or removal + +[Term] +id: GO:0032501 +name: multicellular organismal process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0032502 +name: developmental process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0032504 +name: multicellular organism reproduction +is_a: GO:0000003 ! reproduction +is_a: GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0032507 +name: maintenance of protein location in cell +is_a: GO:0045185 ! maintenance of protein location +is_a: GO:0051651 ! maintenance of location in cell +intersection_of: GO:0045185 ! maintenance of protein location +intersection_of: occurs_in GO:0005623 ! cell +relationship: part_of GO:0034613 ! cellular protein localization + +[Term] +id: GO:0032525 +name: somite rostral/caudal axis specification +is_a: GO:0000578 ! embryonic axis specification +is_a: GO:0009948 ! anterior/posterior axis specification +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001756 ! somitogenesis + +[Term] +id: GO:0032535 +name: regulation of cellular component size +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0090066 ! regulation of anatomical structure size + +[Term] +id: GO:0032536 +name: regulation of cell projection size +is_a: GO:0032535 ! regulation of cellular component size + +[Term] +id: GO:0032602 +name: chemokine production +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032609 +name: interferon-gamma production +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032611 +name: interleukin-1 beta production +is_a: GO:0032612 ! interleukin-1 production + +[Term] +id: GO:0032612 +name: interleukin-1 production +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032635 +name: interleukin-6 production +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032637 +name: interleukin-8 production +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032642 +name: regulation of chemokine production +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032602 ! chemokine production +relationship: regulates GO:0032602 ! chemokine production + +[Term] +id: GO:0032649 +name: regulation of interferon-gamma production +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032609 ! interferon-gamma production +relationship: regulates GO:0032609 ! interferon-gamma production + +[Term] +id: GO:0032651 +name: regulation of interleukin-1 beta production +is_a: GO:0032652 ! regulation of interleukin-1 production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032611 ! interleukin-1 beta production +relationship: regulates GO:0032611 ! interleukin-1 beta production + +[Term] +id: GO:0032652 +name: regulation of interleukin-1 production +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032612 ! interleukin-1 production +relationship: regulates GO:0032612 ! interleukin-1 production + +[Term] +id: GO:0032675 +name: regulation of interleukin-6 production +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032635 ! interleukin-6 production +relationship: regulates GO:0032635 ! interleukin-6 production + +[Term] +id: GO:0032677 +name: regulation of interleukin-8 production +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032637 ! interleukin-8 production +relationship: regulates GO:0032637 ! interleukin-8 production + +[Term] +id: GO:0032729 +name: positive regulation of interferon-gamma production +is_a: GO:0001819 ! positive regulation of cytokine production +is_a: GO:0032649 ! regulation of interferon-gamma production +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032609 ! interferon-gamma production +relationship: positively_regulates GO:0032609 ! interferon-gamma production + +[Term] +id: GO:0032731 +name: positive regulation of interleukin-1 beta production +is_a: GO:0032651 ! regulation of interleukin-1 beta production +is_a: GO:0032732 ! positive regulation of interleukin-1 production +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032611 ! interleukin-1 beta production +relationship: positively_regulates GO:0032611 ! interleukin-1 beta production + +[Term] +id: GO:0032732 +name: positive regulation of interleukin-1 production +is_a: GO:0001819 ! positive regulation of cytokine production +is_a: GO:0032652 ! regulation of interleukin-1 production +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032612 ! interleukin-1 production +relationship: positively_regulates GO:0032612 ! interleukin-1 production + +[Term] +id: GO:0032755 +name: positive regulation of interleukin-6 production +is_a: GO:0001819 ! positive regulation of cytokine production +is_a: GO:0032675 ! regulation of interleukin-6 production +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032635 ! interleukin-6 production +relationship: positively_regulates GO:0032635 ! interleukin-6 production + +[Term] +id: GO:0032774 +name: RNA biosynthetic process +is_a: GO:0009059 ! macromolecule biosynthetic process +is_a: GO:0016070 ! RNA metabolic process +is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process + +[Term] +id: GO:0032793 +name: positive regulation of CREB transcription factor activity +is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0032808 +name: lacrimal gland development +is_a: GO:0048732 ! gland development +relationship: part_of GO:0035272 ! exocrine system development + +[Term] +id: GO:0032835 +name: glomerulus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0072006 ! nephron development + +[Term] +id: GO:0032844 +name: regulation of homeostatic process +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042592 ! homeostatic process +relationship: regulates GO:0042592 ! homeostatic process + +[Term] +id: GO:0032846 +name: positive regulation of homeostatic process +is_a: GO:0032844 ! regulation of homeostatic process +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042592 ! homeostatic process +relationship: positively_regulates GO:0042592 ! homeostatic process + +[Term] +id: GO:0032856 +name: activation of Ras GTPase activity +is_a: GO:0032320 ! positive regulation of Ras GTPase activity + +[Term] +id: GO:0032862 +name: activation of Rho GTPase activity +is_a: GO:0032321 ! positive regulation of Rho GTPase activity +is_a: GO:0032856 ! activation of Ras GTPase activity + +[Term] +id: GO:0032868 +name: response to insulin stimulus +is_a: GO:0043434 ! response to peptide hormone stimulus + +[Term] +id: GO:0032869 +name: cellular response to insulin stimulus +is_a: GO:0032868 ! response to insulin stimulus +is_a: GO:0071375 ! cellular response to peptide hormone stimulus + +[Term] +id: GO:0032870 +name: cellular response to hormone stimulus +is_a: GO:0009725 ! response to hormone stimulus +is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:0071495 ! cellular response to endogenous stimulus + +[Term] +id: GO:0032872 +name: regulation of stress-activated MAPK cascade +is_a: GO:0043408 ! regulation of MAPK cascade +is_a: GO:0070302 ! regulation of stress-activated protein kinase signaling cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051403 ! stress-activated MAPK cascade +relationship: regulates GO:0051403 ! stress-activated MAPK cascade + +[Term] +id: GO:0032874 +name: positive regulation of stress-activated MAPK cascade +is_a: GO:0032872 ! regulation of stress-activated MAPK cascade +is_a: GO:0043410 ! positive regulation of MAPK cascade +is_a: GO:0070304 ! positive regulation of stress-activated protein kinase signaling cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0051403 ! stress-activated MAPK cascade +relationship: positively_regulates GO:0051403 ! stress-activated MAPK cascade + +[Term] +id: GO:0032879 +name: regulation of localization +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051179 ! localization +relationship: regulates GO:0051179 ! localization + +[Term] +id: GO:0032880 +name: regulation of protein localization +is_a: GO:0032879 ! regulation of localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008104 ! protein localization +relationship: regulates GO:0008104 ! protein localization + +[Term] +id: GO:0032886 +name: regulation of microtubule-based process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007017 ! microtubule-based process +relationship: regulates GO:0007017 ! microtubule-based process + +[Term] +id: GO:0032940 +name: secretion by cell +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0046903 ! secretion +is_a: GO:0051649 ! establishment of localization in cell + +[Term] +id: GO:0032941 +name: secretion by tissue +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0046903 ! secretion + +[Term] +id: GO:0032943 +name: mononuclear cell proliferation +is_a: GO:0070661 ! leukocyte proliferation + +[Term] +id: GO:0032944 +name: regulation of mononuclear cell proliferation +is_a: GO:0070663 ! regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032943 ! mononuclear cell proliferation +relationship: regulates GO:0032943 ! mononuclear cell proliferation + +[Term] +id: GO:0032945 +name: negative regulation of mononuclear cell proliferation +is_a: GO:0032944 ! regulation of mononuclear cell proliferation +is_a: GO:0070664 ! negative regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032943 ! mononuclear cell proliferation +relationship: negatively_regulates GO:0032943 ! mononuclear cell proliferation + +[Term] +id: GO:0032946 +name: positive regulation of mononuclear cell proliferation +is_a: GO:0032944 ! regulation of mononuclear cell proliferation +is_a: GO:0070665 ! positive regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032943 ! mononuclear cell proliferation +relationship: positively_regulates GO:0032943 ! mononuclear cell proliferation + +[Term] +id: GO:0032956 +name: regulation of actin cytoskeleton organization +is_a: GO:0032970 ! regulation of actin filament-based process +is_a: GO:0051493 ! regulation of cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030036 ! actin cytoskeleton organization +relationship: regulates GO:0030036 ! actin cytoskeleton organization + +[Term] +id: GO:0032963 +name: collagen metabolic process +is_a: GO:0044259 ! multicellular organismal macromolecule metabolic process + +[Term] +id: GO:0032964 +name: collagen biosynthetic process +is_a: GO:0009059 ! macromolecule biosynthetic process +is_a: GO:0032963 ! collagen metabolic process + +[Term] +id: GO:0032965 +name: regulation of collagen biosynthetic process +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0010712 ! regulation of collagen metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032964 ! collagen biosynthetic process +relationship: regulates GO:0032964 ! collagen biosynthetic process + +[Term] +id: GO:0032967 +name: positive regulation of collagen biosynthetic process +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process +is_a: GO:0010714 ! positive regulation of collagen metabolic process +is_a: GO:0032965 ! regulation of collagen biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032964 ! collagen biosynthetic process +relationship: positively_regulates GO:0032964 ! collagen biosynthetic process + +[Term] +id: GO:0032970 +name: regulation of actin filament-based process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030029 ! actin filament-based process +relationship: regulates GO:0030029 ! actin filament-based process + +[Term] +id: GO:0032984 +name: macromolecular complex disassembly +is_a: GO:0022411 ! cellular component disassembly +is_a: GO:0043933 ! macromolecular complex subunit organization + +[Term] +id: GO:0032987 +name: protein-lipid complex disassembly +is_a: GO:0032984 ! macromolecular complex disassembly +is_a: GO:0071825 ! protein-lipid complex subunit organization + +[Term] +id: GO:0032989 +name: cellular component morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048869 ! cellular developmental process + +[Term] +id: GO:0032990 +name: cell part morphogenesis +is_a: GO:0032989 ! cellular component morphogenesis + +[Term] +id: GO:0032991 +name: macromolecular complex +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0032993 +name: protein-DNA complex +is_a: GO:0032991 ! macromolecular complex + +[Term] +id: GO:0033002 +name: muscle cell proliferation +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0033036 +name: macromolecule localization +is_a: GO:0051179 ! localization + +[Term] +id: GO:0033043 +name: regulation of organelle organization +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006996 ! organelle organization +relationship: regulates GO:0006996 ! organelle organization + +[Term] +id: GO:0033044 +name: regulation of chromosome organization +is_a: GO:0033043 ! regulation of organelle organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051276 ! chromosome organization +relationship: regulates GO:0051276 ! chromosome organization + +[Term] +id: GO:0033077 +name: T cell differentiation in thymus +is_a: GO:0030217 ! T cell differentiation + +[Term] +id: GO:0033079 +name: immature T cell proliferation +is_a: GO:0042098 ! T cell proliferation + +[Term] +id: GO:0033080 +name: immature T cell proliferation in thymus +is_a: GO:0033079 ! immature T cell proliferation +relationship: part_of GO:0033077 ! T cell differentiation in thymus + +[Term] +id: GO:0033081 +name: regulation of T cell differentiation in thymus +is_a: GO:0045580 ! regulation of T cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033077 ! T cell differentiation in thymus +relationship: regulates GO:0033077 ! T cell differentiation in thymus + +[Term] +id: GO:0033085 +name: negative regulation of T cell differentiation in thymus +is_a: GO:0033081 ! regulation of T cell differentiation in thymus +is_a: GO:0045581 ! negative regulation of T cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0033077 ! T cell differentiation in thymus +relationship: negatively_regulates GO:0033077 ! T cell differentiation in thymus + +[Term] +id: GO:0033121 +name: regulation of purine nucleotide catabolic process +is_a: GO:0030811 ! regulation of nucleotide catabolic process +is_a: GO:1900542 ! regulation of purine nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006195 ! purine nucleotide catabolic process +relationship: regulates GO:0006195 ! purine nucleotide catabolic process + +[Term] +id: GO:0033124 +name: regulation of GTP catabolic process +is_a: GO:0009118 ! regulation of nucleoside metabolic process +is_a: GO:0033121 ! regulation of purine nucleotide catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006184 ! GTP catabolic process +relationship: regulates GO:0006184 ! GTP catabolic process + +[Term] +id: GO:0033131 +name: regulation of glucokinase activity +is_a: GO:0010906 ! regulation of glucose metabolic process +is_a: GO:0043549 ! regulation of kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004340 ! glucokinase activity +relationship: regulates GO:0004340 ! glucokinase activity + +[Term] +id: GO:0033132 +name: negative regulation of glucokinase activity +is_a: GO:0033131 ! regulation of glucokinase activity +is_a: GO:0033673 ! negative regulation of kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004340 ! glucokinase activity +relationship: negatively_regulates GO:0004340 ! glucokinase activity + +[Term] +id: GO:0033135 +name: regulation of peptidyl-serine phosphorylation +is_a: GO:0001932 ! regulation of protein phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0018105 ! peptidyl-serine phosphorylation +relationship: regulates GO:0018105 ! peptidyl-serine phosphorylation + +[Term] +id: GO:0033138 +name: positive regulation of peptidyl-serine phosphorylation +is_a: GO:0001934 ! positive regulation of protein phosphorylation +is_a: GO:0033135 ! regulation of peptidyl-serine phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0018105 ! peptidyl-serine phosphorylation +relationship: positively_regulates GO:0018105 ! peptidyl-serine phosphorylation + +[Term] +id: GO:0033143 +name: regulation of intracellular steroid hormone receptor signaling pathway +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway +relationship: regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway + +[Term] +id: GO:0033144 +name: negative regulation of intracellular steroid hormone receptor signaling pathway +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway +relationship: negatively_regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway + +[Term] +id: GO:0033146 +name: regulation of intracellular estrogen receptor signaling pathway +is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030520 ! intracellular estrogen receptor signaling pathway +relationship: regulates GO:0030520 ! intracellular estrogen receptor signaling pathway + +[Term] +id: GO:0033147 +name: negative regulation of intracellular estrogen receptor signaling pathway +is_a: GO:0033144 ! negative regulation of intracellular steroid hormone receptor signaling pathway +is_a: GO:0033146 ! regulation of intracellular estrogen receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030520 ! intracellular estrogen receptor signaling pathway +relationship: negatively_regulates GO:0030520 ! intracellular estrogen receptor signaling pathway + +[Term] +id: GO:0033157 +name: regulation of intracellular protein transport +is_a: GO:0032386 ! regulation of intracellular transport +is_a: GO:0051223 ! regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006886 ! intracellular protein transport +relationship: regulates GO:0006886 ! intracellular protein transport + +[Term] +id: GO:0033233 +name: regulation of protein sumoylation +is_a: GO:0031399 ! regulation of protein modification process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016925 ! protein sumoylation +relationship: regulates GO:0016925 ! protein sumoylation + +[Term] +id: GO:0033234 +name: negative regulation of protein sumoylation +is_a: GO:0031400 ! negative regulation of protein modification process +is_a: GO:0033233 ! regulation of protein sumoylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016925 ! protein sumoylation +relationship: negatively_regulates GO:0016925 ! protein sumoylation + +[Term] +id: GO:0033267 +name: axon part +is_a: GO:0044463 ! cell projection part +is_a: GO:0097458 ! neuron part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0030424 ! axon +relationship: part_of GO:0030424 ! axon + +[Term] +id: GO:0033273 +name: response to vitamin +is_a: GO:0007584 ! response to nutrient + +[Term] +id: GO:0033365 +name: protein localization to organelle +is_a: GO:0034613 ! cellular protein localization + +[Term] +id: GO:0033483 +name: gas homeostasis +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0033500 +name: carbohydrate homeostasis +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0033504 +name: floor plate development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021915 ! neural tube development + +[Term] +id: GO:0033505 +name: floor plate morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0033504 ! floor plate development + +[Term] +id: GO:0033554 +name: cellular response to stress +is_a: GO:0006950 ! response to stress +is_a: GO:0051716 ! cellular response to stimulus + +[Term] +id: GO:0033598 +name: mammary gland epithelial cell proliferation +is_a: GO:0050673 ! epithelial cell proliferation +relationship: part_of GO:0061180 ! mammary gland epithelium development + +[Term] +id: GO:0033613 +name: activating transcription factor binding +is_a: GO:0008134 ! transcription factor binding + +[Term] +id: GO:0033622 +name: integrin activation +is_a: GO:0006461 ! protein complex assembly + +[Term] +id: GO:0033623 +name: regulation of integrin activation +is_a: GO:0043254 ! regulation of protein complex assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033622 ! integrin activation +relationship: regulates GO:0033622 ! integrin activation + +[Term] +id: GO:0033625 +name: positive regulation of integrin activation +is_a: GO:0031334 ! positive regulation of protein complex assembly +is_a: GO:0033623 ! regulation of integrin activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0033622 ! integrin activation +relationship: positively_regulates GO:0033622 ! integrin activation + +[Term] +id: GO:0033627 +name: cell adhesion mediated by integrin +is_a: GO:0007155 ! cell adhesion + +[Term] +id: GO:0033628 +name: regulation of cell adhesion mediated by integrin +is_a: GO:0030155 ! regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033627 ! cell adhesion mediated by integrin +relationship: regulates GO:0033627 ! cell adhesion mediated by integrin + +[Term] +id: GO:0033630 +name: positive regulation of cell adhesion mediated by integrin +is_a: GO:0033628 ! regulation of cell adhesion mediated by integrin +is_a: GO:0045785 ! positive regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0033627 ! cell adhesion mediated by integrin +relationship: positively_regulates GO:0033627 ! cell adhesion mediated by integrin + +[Term] +id: GO:0033631 +name: cell-cell adhesion mediated by integrin +is_a: GO:0016337 ! cell-cell adhesion +is_a: GO:0033627 ! cell adhesion mediated by integrin + +[Term] +id: GO:0033632 +name: regulation of cell-cell adhesion mediated by integrin +is_a: GO:0022407 ! regulation of cell-cell adhesion +is_a: GO:0033628 ! regulation of cell adhesion mediated by integrin +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033631 ! cell-cell adhesion mediated by integrin +relationship: regulates GO:0033631 ! cell-cell adhesion mediated by integrin + +[Term] +id: GO:0033634 +name: positive regulation of cell-cell adhesion mediated by integrin +is_a: GO:0022409 ! positive regulation of cell-cell adhesion +is_a: GO:0033630 ! positive regulation of cell adhesion mediated by integrin +is_a: GO:0033632 ! regulation of cell-cell adhesion mediated by integrin +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0033631 ! cell-cell adhesion mediated by integrin +relationship: positively_regulates GO:0033631 ! cell-cell adhesion mediated by integrin + +[Term] +id: GO:0033673 +name: negative regulation of kinase activity +is_a: GO:0043549 ! regulation of kinase activity +is_a: GO:0051348 ! negative regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016301 ! kinase activity +relationship: negatively_regulates GO:0016301 ! kinase activity + +[Term] +id: GO:0033674 +name: positive regulation of kinase activity +is_a: GO:0043549 ! regulation of kinase activity +is_a: GO:0051347 ! positive regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016301 ! kinase activity +relationship: positively_regulates GO:0016301 ! kinase activity + +[Term] +id: GO:0033687 +name: osteoblast proliferation +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0033688 +name: regulation of osteoblast proliferation +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033687 ! osteoblast proliferation +relationship: regulates GO:0033687 ! osteoblast proliferation + +[Term] +id: GO:0033689 +name: negative regulation of osteoblast proliferation +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0033688 ! regulation of osteoblast proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0033687 ! osteoblast proliferation +relationship: negatively_regulates GO:0033687 ! osteoblast proliferation + +[Term] +id: GO:0033690 +name: positive regulation of osteoblast proliferation +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0033688 ! regulation of osteoblast proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0033687 ! osteoblast proliferation +relationship: positively_regulates GO:0033687 ! osteoblast proliferation + +[Term] +id: GO:0033993 +name: response to lipid +is_a: GO:0010033 ! response to organic substance + +[Term] +id: GO:0034097 +name: response to cytokine stimulus +is_a: GO:0010033 ! response to organic substance + +[Term] +id: GO:0034103 +name: regulation of tissue remodeling +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048771 ! tissue remodeling +relationship: regulates GO:0048771 ! tissue remodeling + +[Term] +id: GO:0034104 +name: negative regulation of tissue remodeling +is_a: GO:0034103 ! regulation of tissue remodeling +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048771 ! tissue remodeling +relationship: negatively_regulates GO:0048771 ! tissue remodeling + +[Term] +id: GO:0034105 +name: positive regulation of tissue remodeling +is_a: GO:0034103 ! regulation of tissue remodeling +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048771 ! tissue remodeling +relationship: positively_regulates GO:0048771 ! tissue remodeling + +[Term] +id: GO:0034109 +name: homotypic cell-cell adhesion +is_a: GO:0016337 ! cell-cell adhesion + +[Term] +id: GO:0034185 +name: apolipoprotein binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0034189 +name: very-low-density lipoprotein particle binding +is_a: GO:0071813 ! lipoprotein particle binding + +[Term] +id: GO:0034220 +name: ion transmembrane transport +is_a: GO:0006811 ! ion transport +is_a: GO:0055085 ! transmembrane transport + +[Term] +id: GO:0034284 +name: response to monosaccharide stimulus +is_a: GO:0009743 ! response to carbohydrate stimulus + +[Term] +id: GO:0034287 +name: detection of monosaccharide stimulus +is_a: GO:0009730 ! detection of carbohydrate stimulus +is_a: GO:0034284 ! response to monosaccharide stimulus + +[Term] +id: GO:0034329 +name: cell junction assembly +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0034330 ! cell junction organization + +[Term] +id: GO:0034330 +name: cell junction organization +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0034332 +name: adherens junction organization +is_a: GO:0045216 ! cell-cell junction organization + +[Term] +id: GO:0034333 +name: adherens junction assembly +is_a: GO:0034329 ! cell junction assembly +is_a: GO:0034332 ! adherens junction organization + +[Term] +id: GO:0034340 +name: response to type I interferon +is_a: GO:0034097 ! response to cytokine stimulus +relationship: part_of GO:0045087 ! innate immune response + +[Term] +id: GO:0034381 +name: plasma lipoprotein particle clearance +is_a: GO:0044707 ! single-multicellular organism process +relationship: has_part GO:0006898 ! receptor-mediated endocytosis +relationship: has_part GO:0071829 ! plasma lipoprotein particle disassembly +relationship: part_of GO:0097006 ! regulation of plasma lipoprotein particle levels + +[Term] +id: GO:0034383 +name: low-density lipoprotein particle clearance +is_a: GO:0034381 ! plasma lipoprotein particle clearance +relationship: has_part GO:0090495 ! low-density lipoprotein particle disassembly + +[Term] +id: GO:0034390 +name: smooth muscle cell apoptotic process +is_a: GO:0010657 ! muscle cell apoptotic process + +[Term] +id: GO:0034391 +name: regulation of smooth muscle cell apoptotic process +is_a: GO:0010660 ! regulation of muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034390 ! smooth muscle cell apoptotic process +relationship: regulates GO:0034390 ! smooth muscle cell apoptotic process + +[Term] +id: GO:0034392 +name: negative regulation of smooth muscle cell apoptotic process +is_a: GO:0010656 ! negative regulation of muscle cell apoptotic process +is_a: GO:0034391 ! regulation of smooth muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0034390 ! smooth muscle cell apoptotic process +relationship: negatively_regulates GO:0034390 ! smooth muscle cell apoptotic process + +[Term] +id: GO:0034394 +name: protein localization to cell surface +is_a: GO:0034613 ! cellular protein localization + +[Term] +id: GO:0034446 +name: substrate adhesion-dependent cell spreading +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +is_a: GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0034447 +name: very-low-density lipoprotein particle clearance +is_a: GO:0034381 ! plasma lipoprotein particle clearance + +[Term] +id: GO:0034504 +name: protein localization to nucleus +is_a: GO:0033365 ! protein localization to organelle + +[Term] +id: GO:0034612 +name: response to tumor necrosis factor +is_a: GO:0034097 ! response to cytokine stimulus + +[Term] +id: GO:0034613 +name: cellular protein localization +is_a: GO:0008104 ! protein localization +is_a: GO:0070727 ! cellular macromolecule localization + +[Term] +id: GO:0034622 +name: cellular macromolecular complex assembly +is_a: GO:0065003 ! macromolecular complex assembly + +[Term] +id: GO:0034641 +name: cellular nitrogen compound metabolic process +is_a: GO:0006807 ! nitrogen compound metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0034645 +name: cellular macromolecule biosynthetic process +is_a: GO:0009059 ! macromolecule biosynthetic process +is_a: GO:0044249 ! cellular biosynthetic process +is_a: GO:0044260 ! cellular macromolecule metabolic process + +[Term] +id: GO:0034650 +name: cortisol metabolic process +is_a: GO:0006066 ! alcohol metabolic process +is_a: GO:0008211 ! glucocorticoid metabolic process +is_a: GO:0042180 ! cellular ketone metabolic process + +[Term] +id: GO:0034651 +name: cortisol biosynthetic process +is_a: GO:0006704 ! glucocorticoid biosynthetic process +is_a: GO:0034650 ! cortisol metabolic process +is_a: GO:0042181 ! ketone biosynthetic process +is_a: GO:0046165 ! alcohol biosynthetic process + +[Term] +id: GO:0034654 +name: nucleobase-containing compound biosynthetic process +is_a: GO:0006139 ! nucleobase-containing compound metabolic process +is_a: GO:0018130 ! heterocycle biosynthetic process +is_a: GO:0019438 ! aromatic compound biosynthetic process +is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process +is_a: GO:1901362 ! organic cyclic compound biosynthetic process + +[Term] +id: GO:0034655 +name: nucleobase-containing compound catabolic process +is_a: GO:0006139 ! nucleobase-containing compound metabolic process +is_a: GO:0019439 ! aromatic compound catabolic process +is_a: GO:0044270 ! cellular nitrogen compound catabolic process +is_a: GO:0046700 ! heterocycle catabolic process +is_a: GO:1901361 ! organic cyclic compound catabolic process + +[Term] +id: GO:0034750 +name: Scrib-APC-beta-catenin complex +is_a: GO:0043234 ! protein complex +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0034754 +name: cellular hormone metabolic process +is_a: GO:0042445 ! hormone metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0034762 +name: regulation of transmembrane transport +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0055085 ! transmembrane transport +relationship: regulates GO:0055085 ! transmembrane transport + +[Term] +id: GO:0034765 +name: regulation of ion transmembrane transport +is_a: GO:0034762 ! regulation of transmembrane transport +is_a: GO:0043269 ! regulation of ion transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034220 ! ion transmembrane transport +relationship: regulates GO:0034220 ! ion transmembrane transport + +[Term] +id: GO:0035019 +name: somatic stem cell maintenance +is_a: GO:0019827 ! stem cell maintenance + +[Term] +id: GO:0035023 +name: regulation of Rho protein signal transduction +is_a: GO:0046578 ! regulation of Ras protein signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007266 ! Rho protein signal transduction +relationship: regulates GO:0007266 ! Rho protein signal transduction + +[Term] +id: GO:0035050 +name: embryonic heart tube development +is_a: GO:0035295 ! tube development +relationship: part_of GO:0007507 ! heart development +relationship: part_of GO:0009790 ! embryo development +relationship: part_of GO:0048568 ! embryonic organ development + +[Term] +id: GO:0035051 +name: cardiocyte differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0035054 +name: embryonic heart tube anterior/posterior pattern specification +is_a: GO:0009952 ! anterior/posterior pattern specification +relationship: part_of GO:0035050 ! embryonic heart tube development + +[Term] +id: GO:0035058 +name: nonmotile primary cilium assembly +is_a: GO:0042384 ! cilium assembly + +[Term] +id: GO:0035088 +name: establishment or maintenance of apical/basal cell polarity +is_a: GO:0061245 ! establishment or maintenance of bipolar cell polarity + +[Term] +id: GO:0035089 +name: establishment of apical/basal cell polarity +is_a: GO:0035088 ! establishment or maintenance of apical/basal cell polarity +is_a: GO:0061162 ! establishment of monopolar cell polarity + +[Term] +id: GO:0035107 +name: appendage morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048736 ! appendage development + +[Term] +id: GO:0035108 +name: limb morphogenesis +is_a: GO:0035107 ! appendage morphogenesis +relationship: part_of GO:0060173 ! limb development + +[Term] +id: GO:0035112 +name: genitalia morphogenesis +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0048806 ! genitalia development + +[Term] +id: GO:0035113 +name: embryonic appendage morphogenesis +is_a: GO:0035107 ! appendage morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis + +[Term] +id: GO:0035115 +name: embryonic forelimb morphogenesis +is_a: GO:0030326 ! embryonic limb morphogenesis +is_a: GO:0035136 ! forelimb morphogenesis + +[Term] +id: GO:0035116 +name: embryonic hindlimb morphogenesis +is_a: GO:0030326 ! embryonic limb morphogenesis +is_a: GO:0035137 ! hindlimb morphogenesis + +[Term] +id: GO:0035136 +name: forelimb morphogenesis +is_a: GO:0035108 ! limb morphogenesis + +[Term] +id: GO:0035137 +name: hindlimb morphogenesis +is_a: GO:0035108 ! limb morphogenesis + +[Term] +id: GO:0035148 +name: tube formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0035239 ! tube morphogenesis + +[Term] +id: GO:0035150 +name: regulation of tube size +is_a: GO:0090066 ! regulation of anatomical structure size + +[Term] +id: GO:0035239 +name: tube morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0035295 ! tube development + +[Term] +id: GO:0035254 +name: glutamate receptor binding +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0035255 +name: ionotropic glutamate receptor binding +is_a: GO:0035254 ! glutamate receptor binding + +[Term] +id: GO:0035257 +name: nuclear hormone receptor binding +is_a: GO:0051427 ! hormone receptor binding + +[Term] +id: GO:0035258 +name: steroid hormone receptor binding +is_a: GO:0035257 ! nuclear hormone receptor binding + +[Term] +id: GO:0035261 +name: external genitalia morphogenesis +is_a: GO:0035112 ! genitalia morphogenesis + +[Term] +id: GO:0035265 +name: organ growth +is_a: GO:0040007 ! growth +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0035270 +name: endocrine system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0035272 +name: exocrine system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0035282 +name: segmentation +is_a: GO:0003002 ! regionalization + +[Term] +id: GO:0035295 +name: tube development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0035313 +name: wound healing, spreading of epidermal cells +is_a: GO:0044319 ! wound healing, spreading of cells + +[Term] +id: GO:0035326 +name: enhancer binding +is_a: GO:0044212 ! transcription regulatory region DNA binding + +[Term] +id: GO:0035411 +name: catenin import into nucleus +is_a: GO:0006606 ! protein import into nucleus + +[Term] +id: GO:0035412 +name: regulation of catenin import into nucleus +is_a: GO:0042306 ! regulation of protein import into nucleus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035411 ! catenin import into nucleus +relationship: regulates GO:0035411 ! catenin import into nucleus + +[Term] +id: GO:0035413 +name: positive regulation of catenin import into nucleus +is_a: GO:0035412 ! regulation of catenin import into nucleus +is_a: GO:0042307 ! positive regulation of protein import into nucleus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0035411 ! catenin import into nucleus +relationship: positively_regulates GO:0035411 ! catenin import into nucleus + +[Term] +id: GO:0035414 +name: negative regulation of catenin import into nucleus +is_a: GO:0035412 ! regulation of catenin import into nucleus +is_a: GO:0042308 ! negative regulation of protein import into nucleus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0035411 ! catenin import into nucleus +relationship: negatively_regulates GO:0035411 ! catenin import into nucleus + +[Term] +id: GO:0035426 +name: extracellular matrix-cell signaling +is_a: GO:0007154 ! cell communication +is_a: GO:0044700 ! single organism signaling + +[Term] +id: GO:0035470 +name: positive regulation of vascular wound healing +is_a: GO:0045766 ! positive regulation of angiogenesis +is_a: GO:0061043 ! regulation of vascular wound healing +is_a: GO:0090303 ! positive regulation of wound healing +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061042 ! vascular wound healing +relationship: positively_regulates GO:0061042 ! vascular wound healing + +[Term] +id: GO:0035473 +name: lipase binding +is_a: GO:0019899 ! enzyme binding + +[Term] +id: GO:0035556 +name: intracellular signal transduction +is_a: GO:0007165 ! signal transduction +intersection_of: GO:0007165 ! signal transduction +intersection_of: occurs_in GO:0005622 ! intracellular + +[Term] +id: GO:0035567 +name: non-canonical Wnt receptor signaling pathway +is_a: GO:0016055 ! Wnt receptor signaling pathway + +[Term] +id: GO:0035637 +name: multicellular organismal signaling +is_a: GO:0044700 ! single organism signaling +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0035659 +name: Wnt receptor signaling pathway involved in wound healing, spreading of epidermal cells +is_a: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: part_of GO:0035313 ! wound healing, spreading of epidermal cells +relationship: part_of GO:0035313 ! wound healing, spreading of epidermal cells + +[Term] +id: GO:0035773 +name: insulin secretion involved in cellular response to glucose stimulus +is_a: GO:0030073 ! insulin secretion +intersection_of: GO:0030073 ! insulin secretion +intersection_of: part_of GO:0071333 ! cellular response to glucose stimulus +relationship: part_of GO:0071333 ! cellular response to glucose stimulus + +[Term] +id: GO:0035850 +name: epithelial cell differentiation involved in kidney development +is_a: GO:0030855 ! epithelial cell differentiation +is_a: GO:0061005 ! cell differentiation involved in kidney development +intersection_of: GO:0030855 ! epithelial cell differentiation +intersection_of: part_of GO:0001822 ! kidney development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0035883 +name: enteroendocrine cell differentiation +is_a: GO:0002067 ! glandular epithelial cell differentiation + +[Term] +id: GO:0035886 +name: vascular smooth muscle cell differentiation +is_a: GO:0051145 ! smooth muscle cell differentiation +relationship: part_of GO:0001944 ! vasculature development + +[Term] +id: GO:0035904 +name: aorta development +is_a: GO:0060840 ! artery development + +[Term] +id: GO:0035909 +name: aorta morphogenesis +is_a: GO:0048844 ! artery morphogenesis +relationship: part_of GO:0035904 ! aorta development + +[Term] +id: GO:0035914 +name: skeletal muscle cell differentiation +is_a: GO:0051146 ! striated muscle cell differentiation +relationship: part_of GO:0007519 ! skeletal muscle tissue development + +[Term] +id: GO:0035987 +name: endodermal cell differentiation +is_a: GO:0030154 ! cell differentiation +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001706 ! endoderm formation + +[Term] +id: GO:0036022 +name: limb joint morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0035108 ! limb morphogenesis + +[Term] +id: GO:0036023 +name: embryonic skeletal limb joint morphogenesis +is_a: GO:0036022 ! limb joint morphogenesis +is_a: GO:0060272 ! embryonic skeletal joint morphogenesis +relationship: part_of GO:0030326 ! embryonic limb morphogenesis + +[Term] +id: GO:0036211 +name: protein modification process +is_a: GO:0019538 ! protein metabolic process +is_a: GO:0043412 ! macromolecule modification + +[Term] +id: GO:0036303 +name: lymph vessel morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001945 ! lymph vessel development + +[Term] +id: GO:0036314 +name: response to sterol +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0033993 ! response to lipid +is_a: GO:0097305 ! response to alcohol + +[Term] +id: GO:0036315 +name: cellular response to sterol +is_a: GO:0036314 ! response to sterol +is_a: GO:0071396 ! cellular response to lipid +is_a: GO:0071407 ! cellular response to organic cyclic compound +is_a: GO:0097306 ! cellular response to alcohol + +[Term] +id: GO:0036342 +name: post-anal tail morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0038023 +name: signaling receptor activity +is_a: GO:0004871 ! signal transducer activity +is_a: GO:0004872 ! receptor activity +intersection_of: GO:0004872 ! receptor activity +intersection_of: part_of GO:0007165 ! signal transduction + +[Term] +id: GO:0038024 +name: cargo receptor activity +is_a: GO:0004872 ! receptor activity +intersection_of: GO:0004872 ! receptor activity +intersection_of: part_of GO:0006898 ! receptor-mediated endocytosis +relationship: part_of GO:0006898 ! receptor-mediated endocytosis + +[Term] +id: GO:0038025 +name: reelin receptor activity +is_a: GO:0004888 ! transmembrane signaling receptor activity +relationship: part_of GO:0038026 ! reelin-mediated signaling pathway + +[Term] +id: GO:0038026 +name: reelin-mediated signaling pathway +is_a: GO:0007166 ! cell surface receptor signaling pathway + +[Term] +id: GO:0038030 +name: non-canonical Wnt receptor signaling pathway via MAPK cascade +is_a: GO:0035567 ! non-canonical Wnt receptor signaling pathway +relationship: has_part GO:0000165 ! MAPK cascade + +[Term] +id: GO:0038031 +name: non-canonical Wnt receptor signaling pathway via JNK cascade +is_a: GO:0038030 ! non-canonical Wnt receptor signaling pathway via MAPK cascade +relationship: has_part GO:0007254 ! JNK cascade + +[Term] +id: GO:0040007 +name: growth +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0040008 +name: regulation of growth +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0040007 ! growth +relationship: regulates GO:0040007 ! growth + +[Term] +id: GO:0040011 +name: locomotion +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0040012 +name: regulation of locomotion +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0040011 ! locomotion +relationship: regulates GO:0040011 ! locomotion + +[Term] +id: GO:0040013 +name: negative regulation of locomotion +is_a: GO:0040012 ! regulation of locomotion +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0040011 ! locomotion +relationship: negatively_regulates GO:0040011 ! locomotion + +[Term] +id: GO:0040017 +name: positive regulation of locomotion +is_a: GO:0040012 ! regulation of locomotion +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0040011 ! locomotion +relationship: positively_regulates GO:0040011 ! locomotion + +[Term] +id: GO:0040019 +name: positive regulation of embryonic development +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009790 ! embryo development +relationship: positively_regulates GO:0009790 ! embryo development + +[Term] +id: GO:0040020 +name: regulation of meiosis +is_a: GO:0010564 ! regulation of cell cycle process +is_a: GO:0051445 ! regulation of meiotic cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007126 ! meiosis +relationship: regulates GO:0007126 ! meiosis + +[Term] +id: GO:0040036 +name: regulation of fibroblast growth factor receptor signaling pathway +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0090287 ! regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway +relationship: regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway + +[Term] +id: GO:0040037 +name: negative regulation of fibroblast growth factor receptor signaling pathway +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:0040036 ! regulation of fibroblast growth factor receptor signaling pathway +is_a: GO:0090288 ! negative regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway +relationship: negatively_regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway + +[Term] +id: GO:0042033 +name: chemokine biosynthetic process +is_a: GO:0042089 ! cytokine biosynthetic process +is_a: GO:0050755 ! chemokine metabolic process +relationship: part_of GO:0032602 ! chemokine production + +[Term] +id: GO:0042035 +name: regulation of cytokine biosynthetic process +is_a: GO:0001817 ! regulation of cytokine production +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042089 ! cytokine biosynthetic process +relationship: regulates GO:0042089 ! cytokine biosynthetic process + +[Term] +id: GO:0042036 +name: negative regulation of cytokine biosynthetic process +is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process +is_a: GO:0031327 ! negative regulation of cellular biosynthetic process +is_a: GO:0042035 ! regulation of cytokine biosynthetic process +is_a: GO:0051248 ! negative regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042089 ! cytokine biosynthetic process +relationship: negatively_regulates GO:0042089 ! cytokine biosynthetic process + +[Term] +id: GO:0042060 +name: wound healing +is_a: GO:0009611 ! response to wounding + +[Term] +id: GO:0042063 +name: gliogenesis +is_a: GO:0022008 ! neurogenesis + +[Term] +id: GO:0042074 +name: cell migration involved in gastrulation +is_a: GO:0001667 ! ameboidal cell migration +intersection_of: GO:0016477 ! cell migration +intersection_of: part_of GO:0007369 ! gastrulation +relationship: part_of GO:0007369 ! gastrulation + +[Term] +id: GO:0042089 +name: cytokine biosynthetic process +is_a: GO:0042107 ! cytokine metabolic process +relationship: part_of GO:0001816 ! cytokine production + +[Term] +id: GO:0042098 +name: T cell proliferation +is_a: GO:0042110 ! T cell activation +is_a: GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0042100 +name: B cell proliferation +is_a: GO:0042113 ! B cell activation +is_a: GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0042107 +name: cytokine metabolic process +is_a: GO:0019538 ! protein metabolic process + +[Term] +id: GO:0042108 +name: positive regulation of cytokine biosynthetic process +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0042035 ! regulation of cytokine biosynthetic process +is_a: GO:0051247 ! positive regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042089 ! cytokine biosynthetic process +relationship: positively_regulates GO:0042089 ! cytokine biosynthetic process + +[Term] +id: GO:0042110 +name: T cell activation +is_a: GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0042113 +name: B cell activation +is_a: GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0042116 +name: macrophage activation +is_a: GO:0002274 ! myeloid leukocyte activation + +[Term] +id: GO:0042127 +name: regulation of cell proliferation +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008283 ! cell proliferation +relationship: regulates GO:0008283 ! cell proliferation + +[Term] +id: GO:0042129 +name: regulation of T cell proliferation +is_a: GO:0050670 ! regulation of lymphocyte proliferation +is_a: GO:0050863 ! regulation of T cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042098 ! T cell proliferation +relationship: regulates GO:0042098 ! T cell proliferation + +[Term] +id: GO:0042130 +name: negative regulation of T cell proliferation +is_a: GO:0042129 ! regulation of T cell proliferation +is_a: GO:0050672 ! negative regulation of lymphocyte proliferation +is_a: GO:0050868 ! negative regulation of T cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042098 ! T cell proliferation +relationship: negatively_regulates GO:0042098 ! T cell proliferation + +[Term] +id: GO:0042157 +name: lipoprotein metabolic process +is_a: GO:0019538 ! protein metabolic process + +[Term] +id: GO:0042158 +name: lipoprotein biosynthetic process +is_a: GO:0034645 ! cellular macromolecule biosynthetic process +is_a: GO:0042157 ! lipoprotein metabolic process + +[Term] +id: GO:0042176 +name: regulation of protein catabolic process +is_a: GO:0009894 ! regulation of catabolic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030163 ! protein catabolic process +relationship: regulates GO:0030163 ! protein catabolic process + +[Term] +id: GO:0042180 +name: cellular ketone metabolic process +is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0042181 +name: ketone biosynthetic process +is_a: GO:0042180 ! cellular ketone metabolic process +is_a: GO:0044249 ! cellular biosynthetic process +is_a: GO:0044283 ! small molecule biosynthetic process +is_a: GO:1901576 ! organic substance biosynthetic process + +[Term] +id: GO:0042221 +name: response to chemical stimulus +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0042226 +name: interleukin-6 biosynthetic process +is_a: GO:0042089 ! cytokine biosynthetic process +relationship: part_of GO:0032635 ! interleukin-6 production + +[Term] +id: GO:0042246 +name: tissue regeneration +is_a: GO:0009888 ! tissue development +is_a: GO:0031099 ! regeneration +is_a: GO:0048589 ! developmental growth +relationship: part_of GO:0042060 ! wound healing + +[Term] +id: GO:0042249 +name: establishment of planar polarity of embryonic epithelium +is_a: GO:0001736 ! establishment of planar polarity + +[Term] +id: GO:0042278 +name: purine nucleoside metabolic process +is_a: GO:0009116 ! nucleoside metabolic process +is_a: GO:0072521 ! purine-containing compound metabolic process + +[Term] +id: GO:0042297 +name: vocal learning +is_a: GO:0007612 ! learning +is_a: GO:0031223 ! auditory behavior + +[Term] +id: GO:0042303 +name: molting cycle +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0042306 +name: regulation of protein import into nucleus +is_a: GO:0033157 ! regulation of intracellular protein transport +is_a: GO:0046822 ! regulation of nucleocytoplasmic transport +is_a: GO:1900180 ! regulation of protein localization to nucleus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006606 ! protein import into nucleus +relationship: regulates GO:0006606 ! protein import into nucleus + +[Term] +id: GO:0042307 +name: positive regulation of protein import into nucleus +is_a: GO:0042306 ! regulation of protein import into nucleus +is_a: GO:0046824 ! positive regulation of nucleocytoplasmic transport +is_a: GO:0090316 ! positive regulation of intracellular protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006606 ! protein import into nucleus +relationship: positively_regulates GO:0006606 ! protein import into nucleus + +[Term] +id: GO:0042308 +name: negative regulation of protein import into nucleus +is_a: GO:0042306 ! regulation of protein import into nucleus +is_a: GO:0046823 ! negative regulation of nucleocytoplasmic transport +is_a: GO:0090317 ! negative regulation of intracellular protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006606 ! protein import into nucleus +relationship: negatively_regulates GO:0006606 ! protein import into nucleus + +[Term] +id: GO:0042325 +name: regulation of phosphorylation +is_a: GO:0019220 ! regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016310 ! phosphorylation +relationship: regulates GO:0016310 ! phosphorylation + +[Term] +id: GO:0042326 +name: negative regulation of phosphorylation +is_a: GO:0042325 ! regulation of phosphorylation +is_a: GO:0045936 ! negative regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016310 ! phosphorylation +relationship: negatively_regulates GO:0016310 ! phosphorylation + +[Term] +id: GO:0042327 +name: positive regulation of phosphorylation +is_a: GO:0042325 ! regulation of phosphorylation +is_a: GO:0045937 ! positive regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016310 ! phosphorylation +relationship: positively_regulates GO:0016310 ! phosphorylation + +[Term] +id: GO:0042330 +name: taxis +is_a: GO:0009605 ! response to external stimulus +is_a: GO:0040011 ! locomotion + +[Term] +id: GO:0042384 +name: cilium assembly +is_a: GO:0010927 ! cellular component assembly involved in morphogenesis +is_a: GO:0030031 ! cell projection assembly +is_a: GO:0044782 ! cilium organization +is_a: GO:0070925 ! organelle assembly +relationship: part_of GO:0060271 ! cilium morphogenesis + +[Term] +id: GO:0042391 +name: regulation of membrane potential +is_a: GO:0065008 ! regulation of biological quality + +[Term] +id: GO:0042445 +name: hormone metabolic process +is_a: GO:0008152 ! metabolic process +is_a: GO:0010817 ! regulation of hormone levels + +[Term] +id: GO:0042446 +name: hormone biosynthetic process +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0042445 ! hormone metabolic process + +[Term] +id: GO:0042454 +name: ribonucleoside catabolic process +is_a: GO:0009119 ! ribonucleoside metabolic process +is_a: GO:0009164 ! nucleoside catabolic process + +[Term] +id: GO:0042471 +name: ear morphogenesis +is_a: GO:0048562 ! embryonic organ morphogenesis +relationship: part_of GO:0043583 ! ear development + +[Term] +id: GO:0042472 +name: inner ear morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0042471 ! ear morphogenesis +relationship: part_of GO:0048839 ! inner ear development + +[Term] +id: GO:0042475 +name: odontogenesis of dentin-containing tooth +is_a: GO:0042476 ! odontogenesis + +[Term] +id: GO:0042476 +name: odontogenesis +is_a: GO:0009887 ! organ morphogenesis + +[Term] +id: GO:0042493 +name: response to drug +is_a: GO:0042221 ! response to chemical stimulus + +[Term] +id: GO:0042552 +name: myelination +is_a: GO:0008366 ! axon ensheathment + +[Term] +id: GO:0042562 +name: hormone binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:0042592 +name: homeostatic process +is_a: GO:0065008 ! regulation of biological quality + +[Term] +id: GO:0042593 +name: glucose homeostasis +is_a: GO:0033500 ! carbohydrate homeostasis + +[Term] +id: GO:0042632 +name: cholesterol homeostasis +is_a: GO:0055092 ! sterol homeostasis + +[Term] +id: GO:0042633 +name: hair cycle +is_a: GO:0042303 ! molting cycle + +[Term] +id: GO:0042659 +name: regulation of cell fate specification +is_a: GO:0010453 ! regulation of cell fate commitment +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001708 ! cell fate specification +relationship: regulates GO:0001708 ! cell fate specification + +[Term] +id: GO:0042660 +name: positive regulation of cell fate specification +is_a: GO:0042659 ! regulation of cell fate specification +is_a: GO:0045597 ! positive regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001708 ! cell fate specification +relationship: positively_regulates GO:0001708 ! cell fate specification + +[Term] +id: GO:0042661 +name: regulation of mesodermal cell fate specification +is_a: GO:0010470 ! regulation of gastrulation +is_a: GO:0042659 ! regulation of cell fate specification +is_a: GO:2000027 ! regulation of organ morphogenesis +is_a: GO:2000380 ! regulation of mesoderm development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007501 ! mesodermal cell fate specification +relationship: regulates GO:0007501 ! mesodermal cell fate specification + +[Term] +id: GO:0042662 +name: negative regulation of mesodermal cell fate specification +is_a: GO:0009996 ! negative regulation of cell fate specification +is_a: GO:0042661 ! regulation of mesodermal cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007501 ! mesodermal cell fate specification +relationship: negatively_regulates GO:0007501 ! mesodermal cell fate specification + +[Term] +id: GO:0042684 +name: cardioblast cell fate commitment +is_a: GO:0060911 ! cardiac cell fate commitment +relationship: part_of GO:0010002 ! cardioblast differentiation + +[Term] +id: GO:0042685 +name: cardioblast cell fate specification +is_a: GO:0060912 ! cardiac cell fate specification +relationship: part_of GO:0042684 ! cardioblast cell fate commitment + +[Term] +id: GO:0042686 +name: regulation of cardioblast cell fate specification +is_a: GO:0051890 ! regulation of cardioblast differentiation +is_a: GO:2000043 ! regulation of cardiac cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042685 ! cardioblast cell fate specification +relationship: regulates GO:0042685 ! cardioblast cell fate specification + +[Term] +id: GO:0042692 +name: muscle cell differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0061061 ! muscle structure development + +[Term] +id: GO:0042693 +name: muscle cell fate commitment +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0042695 +name: thelarche +is_a: GO:0046543 ! development of secondary female sexual characteristics +relationship: part_of GO:0030879 ! mammary gland development + +[Term] +id: GO:0042698 +name: ovulation cycle +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048511 ! rhythmic process +is_a: GO:0048609 ! multicellular organismal reproductive process + +[Term] +id: GO:0042733 +name: embryonic digit morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0030326 ! embryonic limb morphogenesis + +[Term] +id: GO:0042762 +name: regulation of sulfur metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006790 ! sulfur compound metabolic process +relationship: regulates GO:0006790 ! sulfur compound metabolic process + +[Term] +id: GO:0042770 +name: signal transduction in response to DNA damage +is_a: GO:0006974 ! response to DNA damage stimulus +is_a: GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0042787 +name: protein ubiquitination involved in ubiquitin-dependent protein catabolic process +is_a: GO:0016567 ! protein ubiquitination +intersection_of: GO:0016567 ! protein ubiquitination +intersection_of: part_of GO:0006511 ! ubiquitin-dependent protein catabolic process +relationship: part_of GO:0006511 ! ubiquitin-dependent protein catabolic process + +[Term] +id: GO:0042802 +name: identical protein binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0042803 +name: protein homodimerization activity +is_a: GO:0042802 ! identical protein binding +is_a: GO:0046983 ! protein dimerization activity + +[Term] +id: GO:0042813 +name: Wnt-activated receptor activity +is_a: GO:0004888 ! transmembrane signaling receptor activity +relationship: has_part GO:0017147 ! Wnt-protein binding + +[Term] +id: GO:0042886 +name: amide transport +is_a: GO:0044765 ! single-organism transport +is_a: GO:0071705 ! nitrogen compound transport + +[Term] +id: GO:0042953 +name: lipoprotein transport +is_a: GO:0015031 ! protein transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0042954 +name: lipoprotein transporter activity +is_a: GO:0008565 ! protein transporter activity +relationship: part_of GO:0042953 ! lipoprotein transport + +[Term] +id: GO:0042981 +name: regulation of apoptotic process +is_a: GO:0043067 ! regulation of programmed cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006915 ! apoptotic process +relationship: regulates GO:0006915 ! apoptotic process + +[Term] +id: GO:0042995 +name: cell projection +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0043005 +name: neuron projection +is_a: GO:0042995 ! cell projection +is_a: GO:0097458 ! neuron part + +[Term] +id: GO:0043009 +name: chordate embryonic development +is_a: GO:0009792 ! embryo development ending in birth or egg hatching + +[Term] +id: GO:0043010 +name: camera-type eye development +is_a: GO:0001654 ! eye development + +[Term] +id: GO:0043025 +name: neuronal cell body +is_a: GO:0044297 ! cell body +is_a: GO:0097458 ! neuron part + +[Term] +id: GO:0043028 +name: cysteine-type endopeptidase regulator activity involved in apoptotic process +is_a: GO:0030234 ! enzyme regulator activity +relationship: part_of GO:0043281 ! regulation of cysteine-type endopeptidase activity involved in apoptotic process + +[Term] +id: GO:0043030 +name: regulation of macrophage activation +is_a: GO:0002694 ! regulation of leukocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042116 ! macrophage activation +relationship: regulates GO:0042116 ! macrophage activation + +[Term] +id: GO:0043032 +name: positive regulation of macrophage activation +is_a: GO:0002696 ! positive regulation of leukocyte activation +is_a: GO:0043030 ! regulation of macrophage activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042116 ! macrophage activation +relationship: positively_regulates GO:0042116 ! macrophage activation + +[Term] +id: GO:0043049 +name: otic placode formation +is_a: GO:0060788 ! ectodermal placode formation +relationship: part_of GO:0030916 ! otic vesicle formation + +[Term] +id: GO:0043062 +name: extracellular structure organization +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0043065 +name: positive regulation of apoptotic process +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:0043068 ! positive regulation of programmed cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006915 ! apoptotic process +relationship: positively_regulates GO:0006915 ! apoptotic process + +[Term] +id: GO:0043066 +name: negative regulation of apoptotic process +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:0043069 ! negative regulation of programmed cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006915 ! apoptotic process +relationship: negatively_regulates GO:0006915 ! apoptotic process + +[Term] +id: GO:0043067 +name: regulation of programmed cell death +is_a: GO:0010941 ! regulation of cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0012501 ! programmed cell death +relationship: regulates GO:0012501 ! programmed cell death + +[Term] +id: GO:0043068 +name: positive regulation of programmed cell death +is_a: GO:0010942 ! positive regulation of cell death +is_a: GO:0043067 ! regulation of programmed cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0012501 ! programmed cell death +relationship: positively_regulates GO:0012501 ! programmed cell death + +[Term] +id: GO:0043069 +name: negative regulation of programmed cell death +is_a: GO:0043067 ! regulation of programmed cell death +is_a: GO:0060548 ! negative regulation of cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0012501 ! programmed cell death +relationship: negatively_regulates GO:0012501 ! programmed cell death + +[Term] +id: GO:0043085 +name: positive regulation of catalytic activity +is_a: GO:0044093 ! positive regulation of molecular function +is_a: GO:0050790 ! regulation of catalytic activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0003824 ! catalytic activity +relationship: positively_regulates GO:0003824 ! catalytic activity + +[Term] +id: GO:0043086 +name: negative regulation of catalytic activity +is_a: GO:0044092 ! negative regulation of molecular function +is_a: GO:0050790 ! regulation of catalytic activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003824 ! catalytic activity +relationship: negatively_regulates GO:0003824 ! catalytic activity + +[Term] +id: GO:0043087 +name: regulation of GTPase activity +is_a: GO:0033124 ! regulation of GTP catabolic process +is_a: GO:0051336 ! regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003924 ! GTPase activity +relationship: regulates GO:0003924 ! GTPase activity + +[Term] +id: GO:0043112 +name: receptor metabolic process +is_a: GO:0044260 ! cellular macromolecule metabolic process + +[Term] +id: GO:0043113 +name: receptor clustering +is_a: GO:0072657 ! protein localization to membrane + +[Term] +id: GO:0043114 +name: regulation of vascular permeability +is_a: GO:0003018 ! vascular process in circulatory system +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0008015 ! blood circulation + +[Term] +id: GO:0043122 +name: regulation of I-kappaB kinase/NF-kappaB cascade +is_a: GO:0010627 ! regulation of intracellular protein kinase cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade +relationship: regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade + +[Term] +id: GO:0043123 +name: positive regulation of I-kappaB kinase/NF-kappaB cascade +is_a: GO:0010740 ! positive regulation of intracellular protein kinase cascade +is_a: GO:0043122 ! regulation of I-kappaB kinase/NF-kappaB cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade +relationship: positively_regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade + +[Term] +id: GO:0043149 +name: stress fiber assembly +is_a: GO:0051017 ! actin filament bundle assembly + +[Term] +id: GO:0043154 +name: negative regulation of cysteine-type endopeptidase activity involved in apoptotic process +is_a: GO:0043281 ! regulation of cysteine-type endopeptidase activity involved in apoptotic process +is_a: GO:2000117 ! negative regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097153 ! cysteine-type endopeptidase activity involved in apoptotic process +relationship: part_of GO:0006915 ! apoptotic process + +[Term] +id: GO:0043167 +name: ion binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:0043168 +name: anion binding +is_a: GO:0043167 ! ion binding + +[Term] +id: GO:0043169 +name: cation binding +is_a: GO:0043167 ! ion binding + +[Term] +id: GO:0043170 +name: macromolecule metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0043198 +name: dendritic shaft +is_a: GO:0044463 ! cell projection part +is_a: GO:0097458 ! neuron part +relationship: part_of GO:0030425 ! dendrite + +[Term] +id: GO:0043200 +name: response to amino acid stimulus +is_a: GO:0001101 ! response to acid +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:1901700 ! response to oxygen-containing compound + +[Term] +id: GO:0043226 +name: organelle +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0043227 +name: membrane-bounded organelle +is_a: GO:0043226 ! organelle + +[Term] +id: GO:0043228 +name: non-membrane-bounded organelle +is_a: GO:0043226 ! organelle + +[Term] +id: GO:0043229 +name: intracellular organelle +is_a: GO:0043226 ! organelle +is_a: GO:0044424 ! intracellular part + +[Term] +id: GO:0043231 +name: intracellular membrane-bounded organelle +is_a: GO:0043227 ! membrane-bounded organelle +is_a: GO:0043229 ! intracellular organelle + +[Term] +id: GO:0043232 +name: intracellular non-membrane-bounded organelle +is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043229 ! intracellular organelle + +[Term] +id: GO:0043233 +name: organelle lumen +is_a: GO:0031974 ! membrane-enclosed lumen +is_a: GO:0044422 ! organelle part + +[Term] +id: GO:0043234 +name: protein complex +is_a: GO:0032991 ! macromolecular complex + +[Term] +id: GO:0043235 +name: receptor complex +is_a: GO:0043234 ! protein complex + +[Term] +id: GO:0043254 +name: regulation of protein complex assembly +is_a: GO:0044087 ! regulation of cellular component biogenesis +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006461 ! protein complex assembly +relationship: regulates GO:0006461 ! protein complex assembly + +[Term] +id: GO:0043269 +name: regulation of ion transport +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006811 ! ion transport +relationship: regulates GO:0006811 ! ion transport + +[Term] +id: GO:0043280 +name: positive regulation of cysteine-type endopeptidase activity involved in apoptotic process +is_a: GO:0043281 ! regulation of cysteine-type endopeptidase activity involved in apoptotic process +is_a: GO:2001056 ! positive regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0097153 ! cysteine-type endopeptidase activity involved in apoptotic process +relationship: part_of GO:0006915 ! apoptotic process + +[Term] +id: GO:0043281 +name: regulation of cysteine-type endopeptidase activity involved in apoptotic process +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:2000116 ! regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097153 ! cysteine-type endopeptidase activity involved in apoptotic process +relationship: part_of GO:0006915 ! apoptotic process + +[Term] +id: GO:0043292 +name: contractile fiber +is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0043296 +name: apical junction complex +is_a: GO:0005911 ! cell-cell junction + +[Term] +id: GO:0043392 +name: negative regulation of DNA binding +is_a: GO:0051100 ! negative regulation of binding +is_a: GO:0051101 ! regulation of DNA binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003677 ! DNA binding +relationship: negatively_regulates GO:0003677 ! DNA binding + +[Term] +id: GO:0043393 +name: regulation of protein binding +is_a: GO:0051098 ! regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0005515 ! protein binding +relationship: regulates GO:0005515 ! protein binding + +[Term] +id: GO:0043401 +name: steroid hormone mediated signaling pathway +is_a: GO:0009755 ! hormone-mediated signaling pathway +is_a: GO:0071383 ! cellular response to steroid hormone stimulus + +[Term] +id: GO:0043403 +name: skeletal muscle tissue regeneration +is_a: GO:0042246 ! tissue regeneration + +[Term] +id: GO:0043405 +name: regulation of MAP kinase activity +is_a: GO:0043408 ! regulation of MAPK cascade +is_a: GO:0071900 ! regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004707 ! MAP kinase activity +relationship: regulates GO:0004707 ! MAP kinase activity + +[Term] +id: GO:0043406 +name: positive regulation of MAP kinase activity +is_a: GO:0043405 ! regulation of MAP kinase activity +is_a: GO:0043410 ! positive regulation of MAPK cascade +is_a: GO:0071902 ! positive regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004707 ! MAP kinase activity +relationship: positively_regulates GO:0004707 ! MAP kinase activity + +[Term] +id: GO:0043407 +name: negative regulation of MAP kinase activity +is_a: GO:0043405 ! regulation of MAP kinase activity +is_a: GO:0043409 ! negative regulation of MAPK cascade +is_a: GO:0071901 ! negative regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004707 ! MAP kinase activity +relationship: negatively_regulates GO:0004707 ! MAP kinase activity + +[Term] +id: GO:0043408 +name: regulation of MAPK cascade +is_a: GO:0010627 ! regulation of intracellular protein kinase cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000165 ! MAPK cascade +relationship: regulates GO:0000165 ! MAPK cascade + +[Term] +id: GO:0043409 +name: negative regulation of MAPK cascade +is_a: GO:0010741 ! negative regulation of intracellular protein kinase cascade +is_a: GO:0043408 ! regulation of MAPK cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0000165 ! MAPK cascade +relationship: negatively_regulates GO:0000165 ! MAPK cascade + +[Term] +id: GO:0043410 +name: positive regulation of MAPK cascade +is_a: GO:0010740 ! positive regulation of intracellular protein kinase cascade +is_a: GO:0043408 ! regulation of MAPK cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0000165 ! MAPK cascade +relationship: positively_regulates GO:0000165 ! MAPK cascade + +[Term] +id: GO:0043412 +name: macromolecule modification +is_a: GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0043433 +name: negative regulation of sequence-specific DNA binding transcription factor activity +is_a: GO:0044092 ! negative regulation of molecular function +is_a: GO:0051090 ! regulation of sequence-specific DNA binding transcription factor activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity +relationship: negatively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0043434 +name: response to peptide hormone stimulus +is_a: GO:0009725 ! response to hormone stimulus +is_a: GO:1901652 ! response to peptide + +[Term] +id: GO:0043436 +name: oxoacid metabolic process +is_a: GO:0006082 ! organic acid metabolic process + +[Term] +id: GO:0043473 +name: pigmentation +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0043491 +name: protein kinase B signaling cascade +is_a: GO:0007243 ! intracellular protein kinase cascade + +[Term] +id: GO:0043506 +name: regulation of JUN kinase activity +is_a: GO:0043405 ! regulation of MAP kinase activity +is_a: GO:0046328 ! regulation of JNK cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004705 ! JUN kinase activity +relationship: regulates GO:0004705 ! JUN kinase activity + +[Term] +id: GO:0043507 +name: positive regulation of JUN kinase activity +is_a: GO:0043406 ! positive regulation of MAP kinase activity +is_a: GO:0043506 ! regulation of JUN kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004705 ! JUN kinase activity +relationship: positively_regulates GO:0004705 ! JUN kinase activity + +[Term] +id: GO:0043508 +name: negative regulation of JUN kinase activity +is_a: GO:0043407 ! negative regulation of MAP kinase activity +is_a: GO:0043506 ! regulation of JUN kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004705 ! JUN kinase activity +relationship: negatively_regulates GO:0004705 ! JUN kinase activity + +[Term] +id: GO:0043523 +name: regulation of neuron apoptotic process +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:1901214 ! regulation of neuron death +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051402 ! neuron apoptotic process +relationship: regulates GO:0051402 ! neuron apoptotic process + +[Term] +id: GO:0043524 +name: negative regulation of neuron apoptotic process +is_a: GO:0043066 ! negative regulation of apoptotic process +is_a: GO:0043523 ! regulation of neuron apoptotic process +is_a: GO:1901215 ! negative regulation of neuron death +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0051402 ! neuron apoptotic process +relationship: negatively_regulates GO:0051402 ! neuron apoptotic process + +[Term] +id: GO:0043534 +name: blood vessel endothelial cell migration +is_a: GO:0043542 ! endothelial cell migration + +[Term] +id: GO:0043535 +name: regulation of blood vessel endothelial cell migration +is_a: GO:0010594 ! regulation of endothelial cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043534 ! blood vessel endothelial cell migration +relationship: regulates GO:0043534 ! blood vessel endothelial cell migration + +[Term] +id: GO:0043536 +name: positive regulation of blood vessel endothelial cell migration +is_a: GO:0010595 ! positive regulation of endothelial cell migration +is_a: GO:0043535 ! regulation of blood vessel endothelial cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0043534 ! blood vessel endothelial cell migration +relationship: positively_regulates GO:0043534 ! blood vessel endothelial cell migration + +[Term] +id: GO:0043542 +name: endothelial cell migration +is_a: GO:0010631 ! epithelial cell migration + +[Term] +id: GO:0043543 +name: protein acylation +is_a: GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0043547 +name: positive regulation of GTPase activity +is_a: GO:0043087 ! regulation of GTPase activity +is_a: GO:0051345 ! positive regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0003924 ! GTPase activity +relationship: positively_regulates GO:0003924 ! GTPase activity + +[Term] +id: GO:0043549 +name: regulation of kinase activity +is_a: GO:0042325 ! regulation of phosphorylation +is_a: GO:0051338 ! regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016301 ! kinase activity +relationship: regulates GO:0016301 ! kinase activity + +[Term] +id: GO:0043565 +name: sequence-specific DNA binding +is_a: GO:0003677 ! DNA binding + +[Term] +id: GO:0043566 +name: structure-specific DNA binding +is_a: GO:0003677 ! DNA binding + +[Term] +id: GO:0043567 +name: regulation of insulin-like growth factor receptor signaling pathway +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048009 ! insulin-like growth factor receptor signaling pathway +relationship: regulates GO:0048009 ! insulin-like growth factor receptor signaling pathway + +[Term] +id: GO:0043568 +name: positive regulation of insulin-like growth factor receptor signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0043567 ! regulation of insulin-like growth factor receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048009 ! insulin-like growth factor receptor signaling pathway +relationship: positively_regulates GO:0048009 ! insulin-like growth factor receptor signaling pathway + +[Term] +id: GO:0043583 +name: ear development +is_a: GO:0007423 ! sensory organ development + +[Term] +id: GO:0043584 +name: nose development +is_a: GO:0007423 ! sensory organ development +relationship: part_of GO:0060541 ! respiratory system development + +[Term] +id: GO:0043586 +name: tongue development +is_a: GO:0007423 ! sensory organ development + +[Term] +id: GO:0043587 +name: tongue morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0043586 ! tongue development + +[Term] +id: GO:0043588 +name: skin development +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0043589 +name: skin morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0043588 ! skin development + +[Term] +id: GO:0043623 +name: cellular protein complex assembly +is_a: GO:0006461 ! protein complex assembly +is_a: GO:0034622 ! cellular macromolecular complex assembly + +[Term] +id: GO:0043627 +name: response to estrogen stimulus +is_a: GO:0048545 ! response to steroid hormone stimulus + +[Term] +id: GO:0043632 +name: modification-dependent macromolecule catabolic process +is_a: GO:0044265 ! cellular macromolecule catabolic process + +[Term] +id: GO:0043933 +name: macromolecular complex subunit organization +is_a: GO:0016043 ! cellular component organization + +[Term] +id: GO:0044057 +name: regulation of system process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003008 ! system process +relationship: regulates GO:0003008 ! system process + +[Term] +id: GO:0044085 +name: cellular component biogenesis +is_a: GO:0071840 ! cellular component organization or biogenesis + +[Term] +id: GO:0044087 +name: regulation of cellular component biogenesis +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044085 ! cellular component biogenesis +relationship: regulates GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0044089 +name: positive regulation of cellular component biogenesis +is_a: GO:0044087 ! regulation of cellular component biogenesis +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044085 ! cellular component biogenesis +relationship: positively_regulates GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0044092 +name: negative regulation of molecular function +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003674 ! molecular_function +relationship: negatively_regulates GO:0003674 ! molecular_function + +[Term] +id: GO:0044093 +name: positive regulation of molecular function +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0003674 ! molecular_function +relationship: positively_regulates GO:0003674 ! molecular_function + +[Term] +id: GO:0044212 +name: transcription regulatory region DNA binding +is_a: GO:0000975 ! regulatory region DNA binding + +[Term] +id: GO:0044236 +name: multicellular organismal metabolic process +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044710 ! single-organism metabolic process + +[Term] +id: GO:0044237 +name: cellular metabolic process +is_a: GO:0008152 ! metabolic process +is_a: GO:0009987 ! cellular process + +[Term] +id: GO:0044238 +name: primary metabolic process +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0044246 +name: regulation of multicellular organismal metabolic process +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044236 ! multicellular organismal metabolic process +relationship: regulates GO:0044236 ! multicellular organismal metabolic process + +[Term] +id: GO:0044248 +name: cellular catabolic process +is_a: GO:0009056 ! catabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0044249 +name: cellular biosynthetic process +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0044253 +name: positive regulation of multicellular organismal metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0044246 ! regulation of multicellular organismal metabolic process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044236 ! multicellular organismal metabolic process +relationship: positively_regulates GO:0044236 ! multicellular organismal metabolic process + +[Term] +id: GO:0044257 +name: cellular protein catabolic process +is_a: GO:0030163 ! protein catabolic process +is_a: GO:0044265 ! cellular macromolecule catabolic process +is_a: GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0044259 +name: multicellular organismal macromolecule metabolic process +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0044236 ! multicellular organismal metabolic process + +[Term] +id: GO:0044260 +name: cellular macromolecule metabolic process +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0044262 +name: cellular carbohydrate metabolic process +is_a: GO:0005975 ! carbohydrate metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0044265 +name: cellular macromolecule catabolic process +is_a: GO:0009057 ! macromolecule catabolic process +is_a: GO:0044248 ! cellular catabolic process +is_a: GO:0044260 ! cellular macromolecule metabolic process + +[Term] +id: GO:0044267 +name: cellular protein metabolic process +is_a: GO:0019538 ! protein metabolic process +is_a: GO:0044260 ! cellular macromolecule metabolic process + +[Term] +id: GO:0044270 +name: cellular nitrogen compound catabolic process +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +is_a: GO:0044248 ! cellular catabolic process + +[Term] +id: GO:0044271 +name: cellular nitrogen compound biosynthetic process +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0044272 +name: sulfur compound biosynthetic process +is_a: GO:0006790 ! sulfur compound metabolic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0044281 +name: small molecule metabolic process +is_a: GO:0044710 ! single-organism metabolic process + +[Term] +id: GO:0044283 +name: small molecule biosynthetic process +is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:0044711 ! single-organism biosynthetic process + +[Term] +id: GO:0044291 +name: cell-cell contact zone +is_a: GO:0005911 ! cell-cell junction + +[Term] +id: GO:0044297 +name: cell body +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0044319 +name: wound healing, spreading of cells +is_a: GO:0016477 ! cell migration +intersection_of: GO:0016477 ! cell migration +intersection_of: part_of GO:0090505 ! epiboly involved in wound healing +relationship: part_of GO:0090505 ! epiboly involved in wound healing + +[Term] +id: GO:0044325 +name: ion channel binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0044331 +name: cell-cell adhesion mediated by cadherin +is_a: GO:0033631 ! cell-cell adhesion mediated by integrin + +[Term] +id: GO:0044332 +name: Wnt receptor signaling pathway involved in dorsal/ventral axis specification +is_a: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: part_of GO:0009950 ! dorsal/ventral axis specification +relationship: part_of GO:0009950 ! dorsal/ventral axis specification + +[Term] +id: GO:0044333 +name: Wnt receptor signaling pathway involved in digestive tract morphogenesis +is_a: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: part_of GO:0048546 ! digestive tract morphogenesis +relationship: part_of GO:0048546 ! digestive tract morphogenesis + +[Term] +id: GO:0044334 +name: canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition +is_a: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: part_of GO:0010718 ! positive regulation of epithelial to mesenchymal transition +relationship: part_of GO:0010718 ! positive regulation of epithelial to mesenchymal transition + +[Term] +id: GO:0044335 +name: canonical Wnt receptor signaling pathway involved in neural crest cell differentiation +is_a: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: part_of GO:0014033 ! neural crest cell differentiation +relationship: part_of GO:0014033 ! neural crest cell differentiation + +[Term] +id: GO:0044336 +name: canonical Wnt receptor signaling pathway involved in negative regulation of apoptotic process +is_a: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: part_of GO:0043066 ! negative regulation of apoptotic process +relationship: part_of GO:0043066 ! negative regulation of apoptotic process + +[Term] +id: GO:0044340 +name: canonical Wnt receptor signaling pathway involved in regulation of cell proliferation +is_a: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: part_of GO:0008283 ! cell proliferation +relationship: part_of GO:0042127 ! regulation of cell proliferation + +[Term] +id: GO:0044342 +name: type B pancreatic cell proliferation +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0044343 +name: canonical Wnt receptor signaling pathway involved in regulation of type B pancreatic cell proliferation +is_a: GO:0044340 ! canonical Wnt receptor signaling pathway involved in regulation of cell proliferation +intersection_of: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: part_of GO:0061469 ! regulation of type B pancreatic cell proliferation +relationship: part_of GO:0061469 ! regulation of type B pancreatic cell proliferation + +[Term] +id: GO:0044344 +name: cellular response to fibroblast growth factor stimulus +is_a: GO:0071363 ! cellular response to growth factor stimulus +is_a: GO:0071495 ! cellular response to endogenous stimulus +is_a: GO:0071774 ! response to fibroblast growth factor stimulus + +[Term] +id: GO:0044346 +name: fibroblast apoptotic process +is_a: GO:0097285 ! cell-type specific apoptotic process + +[Term] +id: GO:0044390 +name: small protein conjugating enzyme binding +is_a: GO:0019899 ! enzyme binding + +[Term] +id: GO:0044421 +name: extracellular region part +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005576 ! extracellular region +relationship: part_of GO:0005576 ! extracellular region + +[Term] +id: GO:0044422 +name: organelle part +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0043226 ! organelle +relationship: part_of GO:0043226 ! organelle + +[Term] +id: GO:0044424 +name: intracellular part +is_a: GO:0044464 ! cell part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005622 ! intracellular +relationship: part_of GO:0005622 ! intracellular + +[Term] +id: GO:0044425 +name: membrane part +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0016020 ! membrane +relationship: part_of GO:0016020 ! membrane + +[Term] +id: GO:0044427 +name: chromosomal part +is_a: GO:0044446 ! intracellular organelle part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005694 ! chromosome +relationship: part_of GO:0005694 ! chromosome + +[Term] +id: GO:0044428 +name: nuclear part +is_a: GO:0044446 ! intracellular organelle part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005634 ! nucleus +relationship: part_of GO:0005634 ! nucleus + +[Term] +id: GO:0044430 +name: cytoskeletal part +is_a: GO:0044446 ! intracellular organelle part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005856 ! cytoskeleton +relationship: part_of GO:0005856 ! cytoskeleton + +[Term] +id: GO:0044432 +name: endoplasmic reticulum part +is_a: GO:0044444 ! cytoplasmic part +is_a: GO:0044446 ! intracellular organelle part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005783 ! endoplasmic reticulum +relationship: part_of GO:0005783 ! endoplasmic reticulum + +[Term] +id: GO:0044444 +name: cytoplasmic part +is_a: GO:0044424 ! intracellular part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005737 ! cytoplasm +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0044446 +name: intracellular organelle part +is_a: GO:0044422 ! organelle part +is_a: GO:0044424 ! intracellular part +relationship: part_of GO:0043229 ! intracellular organelle + +[Term] +id: GO:0044449 +name: contractile fiber part +is_a: GO:0044422 ! organelle part +is_a: GO:0044444 ! cytoplasmic part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0043292 ! contractile fiber +relationship: part_of GO:0043292 ! contractile fiber + +[Term] +id: GO:0044451 +name: nucleoplasm part +is_a: GO:0044428 ! nuclear part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005654 ! nucleoplasm +relationship: part_of GO:0005654 ! nucleoplasm + +[Term] +id: GO:0044454 +name: nuclear chromosome part +is_a: GO:0044427 ! chromosomal part +is_a: GO:0044428 ! nuclear part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0000228 ! nuclear chromosome +relationship: part_of GO:0000228 ! nuclear chromosome + +[Term] +id: GO:0044456 +name: synapse part +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0045202 ! synapse +relationship: part_of GO:0045202 ! synapse + +[Term] +id: GO:0044459 +name: plasma membrane part +is_a: GO:0044425 ! membrane part +is_a: GO:0044464 ! cell part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005886 ! plasma membrane +relationship: part_of GO:0005886 ! plasma membrane + +[Term] +id: GO:0044463 +name: cell projection part +is_a: GO:0044464 ! cell part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0042995 ! cell projection +relationship: part_of GO:0042995 ! cell projection + +[Term] +id: GO:0044464 +name: cell part +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005623 ! cell +relationship: part_of GO:0005623 ! cell + +[Term] +id: GO:0044699 +name: single-organism process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0044700 +name: single organism signaling +is_a: GO:0023052 ! signaling +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0044702 +name: single organism reproductive process +is_a: GO:0022414 ! reproductive process +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0044703 +name: multi-organism reproductive process +is_a: GO:0022414 ! reproductive process + +[Term] +id: GO:0044704 +name: single-organism reproductive behavior +is_a: GO:0019098 ! reproductive behavior +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0044708 ! single-organism behavior + +[Term] +id: GO:0044706 +name: multi-multicellular organism process +is_a: GO:0032501 ! multicellular organismal process +is_a: GO:0051704 ! multi-organism process + +[Term] +id: GO:0044707 +name: single-multicellular organism process +is_a: GO:0032501 ! multicellular organismal process +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0044708 +name: single-organism behavior +is_a: GO:0007610 ! behavior + +[Term] +id: GO:0044710 +name: single-organism metabolic process +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0044711 +name: single-organism biosynthetic process +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0044710 ! single-organism metabolic process + +[Term] +id: GO:0044723 +name: single-organism carbohydrate metabolic process +is_a: GO:0005975 ! carbohydrate metabolic process + +[Term] +id: GO:0044724 +name: single-organism carbohydrate catabolic process +is_a: GO:0016052 ! carbohydrate catabolic process +is_a: GO:0044723 ! single-organism carbohydrate metabolic process + +[Term] +id: GO:0044744 +name: protein targeting to nucleus +is_a: GO:0006605 ! protein targeting + +[Term] +id: GO:0044763 +name: single-organism cellular process +is_a: GO:0009987 ! cellular process +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0044765 +name: single-organism transport +is_a: GO:0006810 ! transport +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0044767 +name: single-organism developmental process +is_a: GO:0032502 ! developmental process +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0044782 +name: cilium organization +is_a: GO:0030030 ! cell projection organization + +[Term] +id: GO:0045013 +name: carbon catabolite repression of transcription +is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent +is_a: GO:0045990 ! carbon catabolite regulation of transcription + +[Term] +id: GO:0045014 +name: negative regulation of transcription by glucose +is_a: GO:0045013 ! carbon catabolite repression of transcription +is_a: GO:0046015 ! regulation of transcription by glucose + +[Term] +id: GO:0045026 +name: plasma membrane fusion +is_a: GO:0006944 ! cellular membrane fusion + +[Term] +id: GO:0045056 +name: transcytosis +is_a: GO:0016192 ! vesicle-mediated transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0045073 +name: regulation of chemokine biosynthetic process +is_a: GO:0032642 ! regulation of chemokine production +is_a: GO:0042035 ! regulation of cytokine biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042033 ! chemokine biosynthetic process +relationship: regulates GO:0042033 ! chemokine biosynthetic process + +[Term] +id: GO:0045080 +name: positive regulation of chemokine biosynthetic process +is_a: GO:0042108 ! positive regulation of cytokine biosynthetic process +is_a: GO:0045073 ! regulation of chemokine biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042033 ! chemokine biosynthetic process +relationship: positively_regulates GO:0042033 ! chemokine biosynthetic process + +[Term] +id: GO:0045087 +name: innate immune response +is_a: GO:0006952 ! defense response +is_a: GO:0006955 ! immune response + +[Term] +id: GO:0045088 +name: regulation of innate immune response +is_a: GO:0031347 ! regulation of defense response +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045087 ! innate immune response +relationship: regulates GO:0045087 ! innate immune response + +[Term] +id: GO:0045121 +name: membrane raft +is_a: GO:0044425 ! membrane part + +[Term] +id: GO:0045124 +name: regulation of bone resorption +is_a: GO:0032844 ! regulation of homeostatic process +is_a: GO:0046850 ! regulation of bone remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045453 ! bone resorption +relationship: regulates GO:0045453 ! bone resorption + +[Term] +id: GO:0045136 +name: development of secondary sexual characteristics +is_a: GO:0003006 ! developmental process involved in reproduction +relationship: part_of GO:0007275 ! multicellular organismal development +relationship: part_of GO:0007548 ! sex differentiation + +[Term] +id: GO:0045137 +name: development of primary sexual characteristics +is_a: GO:0003006 ! developmental process involved in reproduction +relationship: part_of GO:0007275 ! multicellular organismal development +relationship: part_of GO:0007548 ! sex differentiation + +[Term] +id: GO:0045165 +name: cell fate commitment +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0030154 ! cell differentiation + +[Term] +id: GO:0045168 +name: cell-cell signaling involved in cell fate commitment +is_a: GO:0007267 ! cell-cell signaling +intersection_of: GO:0007267 ! cell-cell signaling +intersection_of: part_of GO:0045165 ! cell fate commitment +relationship: part_of GO:0045165 ! cell fate commitment + +[Term] +id: GO:0045177 +name: apical part of cell +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0045184 +name: establishment of protein localization +is_a: GO:0051234 ! establishment of localization +relationship: part_of GO:0008104 ! protein localization + +[Term] +id: GO:0045185 +name: maintenance of protein location +is_a: GO:0051235 ! maintenance of location +relationship: part_of GO:0008104 ! protein localization + +[Term] +id: GO:0045202 +name: synapse +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0045216 +name: cell-cell junction organization +is_a: GO:0034330 ! cell junction organization + +[Term] +id: GO:0045294 +name: alpha-catenin binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0045296 +name: cadherin binding +is_a: GO:0050839 ! cell adhesion molecule binding + +[Term] +id: GO:0045321 +name: leukocyte activation +is_a: GO:0001775 ! cell activation +is_a: GO:0002376 ! immune system process + +[Term] +id: GO:0045408 +name: regulation of interleukin-6 biosynthetic process +is_a: GO:0032675 ! regulation of interleukin-6 production +is_a: GO:0042035 ! regulation of cytokine biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042226 ! interleukin-6 biosynthetic process +relationship: regulates GO:0042226 ! interleukin-6 biosynthetic process + +[Term] +id: GO:0045409 +name: negative regulation of interleukin-6 biosynthetic process +is_a: GO:0042036 ! negative regulation of cytokine biosynthetic process +is_a: GO:0045408 ! regulation of interleukin-6 biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042226 ! interleukin-6 biosynthetic process +relationship: negatively_regulates GO:0042226 ! interleukin-6 biosynthetic process + +[Term] +id: GO:0045444 +name: fat cell differentiation +is_a: GO:0030154 ! cell differentiation + +[Term] +id: GO:0045446 +name: endothelial cell differentiation +is_a: GO:0030855 ! epithelial cell differentiation +relationship: part_of GO:0003158 ! endothelium development + +[Term] +id: GO:0045453 +name: bone resorption +is_a: GO:0001894 ! tissue homeostasis +relationship: part_of GO:0046849 ! bone remodeling + +[Term] +id: GO:0045577 +name: regulation of B cell differentiation +is_a: GO:0045619 ! regulation of lymphocyte differentiation +is_a: GO:0050864 ! regulation of B cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030183 ! B cell differentiation +relationship: regulates GO:0030183 ! B cell differentiation + +[Term] +id: GO:0045578 +name: negative regulation of B cell differentiation +is_a: GO:0045577 ! regulation of B cell differentiation +is_a: GO:0045620 ! negative regulation of lymphocyte differentiation +is_a: GO:0050869 ! negative regulation of B cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030183 ! B cell differentiation +relationship: negatively_regulates GO:0030183 ! B cell differentiation + +[Term] +id: GO:0045580 +name: regulation of T cell differentiation +is_a: GO:0045619 ! regulation of lymphocyte differentiation +is_a: GO:0050863 ! regulation of T cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030217 ! T cell differentiation +relationship: regulates GO:0030217 ! T cell differentiation + +[Term] +id: GO:0045581 +name: negative regulation of T cell differentiation +is_a: GO:0045580 ! regulation of T cell differentiation +is_a: GO:0045620 ! negative regulation of lymphocyte differentiation +is_a: GO:0050868 ! negative regulation of T cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030217 ! T cell differentiation +relationship: negatively_regulates GO:0030217 ! T cell differentiation + +[Term] +id: GO:0045595 +name: regulation of cell differentiation +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030154 ! cell differentiation +relationship: regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045596 +name: negative regulation of cell differentiation +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051093 ! negative regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030154 ! cell differentiation +relationship: negatively_regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045597 +name: positive regulation of cell differentiation +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030154 ! cell differentiation +relationship: positively_regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045598 +name: regulation of fat cell differentiation +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045444 ! fat cell differentiation +relationship: regulates GO:0045444 ! fat cell differentiation + +[Term] +id: GO:0045599 +name: negative regulation of fat cell differentiation +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0045598 ! regulation of fat cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0045444 ! fat cell differentiation +relationship: negatively_regulates GO:0045444 ! fat cell differentiation + +[Term] +id: GO:0045600 +name: positive regulation of fat cell differentiation +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0045598 ! regulation of fat cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0045444 ! fat cell differentiation +relationship: positively_regulates GO:0045444 ! fat cell differentiation + +[Term] +id: GO:0045601 +name: regulation of endothelial cell differentiation +is_a: GO:0030856 ! regulation of epithelial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045446 ! endothelial cell differentiation +relationship: regulates GO:0045446 ! endothelial cell differentiation + +[Term] +id: GO:0045603 +name: positive regulation of endothelial cell differentiation +is_a: GO:0030858 ! positive regulation of epithelial cell differentiation +is_a: GO:0045601 ! regulation of endothelial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0045446 ! endothelial cell differentiation +relationship: positively_regulates GO:0045446 ! endothelial cell differentiation + +[Term] +id: GO:0045619 +name: regulation of lymphocyte differentiation +is_a: GO:0051249 ! regulation of lymphocyte activation +is_a: GO:1902105 ! regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030098 ! lymphocyte differentiation +relationship: regulates GO:0030098 ! lymphocyte differentiation + +[Term] +id: GO:0045620 +name: negative regulation of lymphocyte differentiation +is_a: GO:0045619 ! regulation of lymphocyte differentiation +is_a: GO:0051250 ! negative regulation of lymphocyte activation +is_a: GO:1902106 ! negative regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030098 ! lymphocyte differentiation +relationship: negatively_regulates GO:0030098 ! lymphocyte differentiation + +[Term] +id: GO:0045637 +name: regulation of myeloid cell differentiation +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030099 ! myeloid cell differentiation +relationship: regulates GO:0030099 ! myeloid cell differentiation + +[Term] +id: GO:0045638 +name: negative regulation of myeloid cell differentiation +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0045637 ! regulation of myeloid cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030099 ! myeloid cell differentiation +relationship: negatively_regulates GO:0030099 ! myeloid cell differentiation + +[Term] +id: GO:0045639 +name: positive regulation of myeloid cell differentiation +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0045637 ! regulation of myeloid cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030099 ! myeloid cell differentiation +relationship: positively_regulates GO:0030099 ! myeloid cell differentiation + +[Term] +id: GO:0045655 +name: regulation of monocyte differentiation +is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030224 ! monocyte differentiation +relationship: regulates GO:0030224 ! monocyte differentiation + +[Term] +id: GO:0045657 +name: positive regulation of monocyte differentiation +is_a: GO:0002763 ! positive regulation of myeloid leukocyte differentiation +is_a: GO:0045655 ! regulation of monocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030224 ! monocyte differentiation +relationship: positively_regulates GO:0030224 ! monocyte differentiation + +[Term] +id: GO:0045664 +name: regulation of neuron differentiation +is_a: GO:0050767 ! regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030182 ! neuron differentiation +relationship: regulates GO:0030182 ! neuron differentiation + +[Term] +id: GO:0045665 +name: negative regulation of neuron differentiation +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0045664 ! regulation of neuron differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030182 ! neuron differentiation +relationship: negatively_regulates GO:0030182 ! neuron differentiation + +[Term] +id: GO:0045666 +name: positive regulation of neuron differentiation +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0045664 ! regulation of neuron differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030182 ! neuron differentiation +relationship: positively_regulates GO:0030182 ! neuron differentiation + +[Term] +id: GO:0045667 +name: regulation of osteoblast differentiation +is_a: GO:0030278 ! regulation of ossification +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001649 ! osteoblast differentiation +relationship: regulates GO:0001649 ! osteoblast differentiation + +[Term] +id: GO:0045668 +name: negative regulation of osteoblast differentiation +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0045667 ! regulation of osteoblast differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001649 ! osteoblast differentiation +relationship: negatively_regulates GO:0001649 ! osteoblast differentiation + +[Term] +id: GO:0045669 +name: positive regulation of osteoblast differentiation +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0045667 ! regulation of osteoblast differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001649 ! osteoblast differentiation +relationship: positively_regulates GO:0001649 ! osteoblast differentiation + +[Term] +id: GO:0045670 +name: regulation of osteoclast differentiation +is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030316 ! osteoclast differentiation +relationship: regulates GO:0030316 ! osteoclast differentiation + +[Term] +id: GO:0045671 +name: negative regulation of osteoclast differentiation +is_a: GO:0002762 ! negative regulation of myeloid leukocyte differentiation +is_a: GO:0045670 ! regulation of osteoclast differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030316 ! osteoclast differentiation +relationship: negatively_regulates GO:0030316 ! osteoclast differentiation + +[Term] +id: GO:0045685 +name: regulation of glial cell differentiation +is_a: GO:0014013 ! regulation of gliogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010001 ! glial cell differentiation +relationship: regulates GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0045686 +name: negative regulation of glial cell differentiation +is_a: GO:0014014 ! negative regulation of gliogenesis +is_a: GO:0045685 ! regulation of glial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010001 ! glial cell differentiation +relationship: negatively_regulates GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0045732 +name: positive regulation of protein catabolic process +is_a: GO:0009896 ! positive regulation of catabolic process +is_a: GO:0042176 ! regulation of protein catabolic process +is_a: GO:0051247 ! positive regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030163 ! protein catabolic process +relationship: positively_regulates GO:0030163 ! protein catabolic process + +[Term] +id: GO:0045743 +name: positive regulation of fibroblast growth factor receptor signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0040036 ! regulation of fibroblast growth factor receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway +relationship: positively_regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway + +[Term] +id: GO:0045747 +name: positive regulation of Notch signaling pathway +is_a: GO:0008593 ! regulation of Notch signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007219 ! Notch signaling pathway +relationship: positively_regulates GO:0007219 ! Notch signaling pathway + +[Term] +id: GO:0045765 +name: regulation of angiogenesis +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:1901342 ! regulation of vasculature development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001525 ! angiogenesis +relationship: regulates GO:0001525 ! angiogenesis + +[Term] +id: GO:0045766 +name: positive regulation of angiogenesis +is_a: GO:0045765 ! regulation of angiogenesis +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001525 ! angiogenesis +relationship: positively_regulates GO:0001525 ! angiogenesis + +[Term] +id: GO:0045778 +name: positive regulation of ossification +is_a: GO:0030278 ! regulation of ossification +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001503 ! ossification +relationship: positively_regulates GO:0001503 ! ossification + +[Term] +id: GO:0045780 +name: positive regulation of bone resorption +is_a: GO:0032846 ! positive regulation of homeostatic process +is_a: GO:0045124 ! regulation of bone resorption +is_a: GO:0046852 ! positive regulation of bone remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0045453 ! bone resorption +relationship: positively_regulates GO:0045453 ! bone resorption + +[Term] +id: GO:0045785 +name: positive regulation of cell adhesion +is_a: GO:0030155 ! regulation of cell adhesion +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007155 ! cell adhesion +relationship: positively_regulates GO:0007155 ! cell adhesion + +[Term] +id: GO:0045786 +name: negative regulation of cell cycle +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051726 ! regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007049 ! cell cycle +relationship: negatively_regulates GO:0007049 ! cell cycle + +[Term] +id: GO:0045787 +name: positive regulation of cell cycle +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051726 ! regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007049 ! cell cycle +relationship: positively_regulates GO:0007049 ! cell cycle + +[Term] +id: GO:0045807 +name: positive regulation of endocytosis +is_a: GO:0030100 ! regulation of endocytosis +is_a: GO:0051050 ! positive regulation of transport +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006897 ! endocytosis +relationship: positively_regulates GO:0006897 ! endocytosis + +[Term] +id: GO:0045833 +name: negative regulation of lipid metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0019216 ! regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006629 ! lipid metabolic process +relationship: negatively_regulates GO:0006629 ! lipid metabolic process + +[Term] +id: GO:0045834 +name: positive regulation of lipid metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0019216 ! regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006629 ! lipid metabolic process +relationship: positively_regulates GO:0006629 ! lipid metabolic process + +[Term] +id: GO:0045836 +name: positive regulation of meiosis +is_a: GO:0040020 ! regulation of meiosis +is_a: GO:0090068 ! positive regulation of cell cycle process +is_a: GO:2000243 ! positive regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007126 ! meiosis +relationship: positively_regulates GO:0007126 ! meiosis + +[Term] +id: GO:0045840 +name: positive regulation of mitosis +is_a: GO:0007088 ! regulation of mitosis +is_a: GO:0045787 ! positive regulation of cell cycle +is_a: GO:0051785 ! positive regulation of nuclear division +is_a: GO:0090068 ! positive regulation of cell cycle process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007067 ! mitosis +relationship: positively_regulates GO:0007067 ! mitosis + +[Term] +id: GO:0045859 +name: regulation of protein kinase activity +is_a: GO:0001932 ! regulation of protein phosphorylation +is_a: GO:0043549 ! regulation of kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004672 ! protein kinase activity +relationship: regulates GO:0004672 ! protein kinase activity + +[Term] +id: GO:0045860 +name: positive regulation of protein kinase activity +is_a: GO:0001934 ! positive regulation of protein phosphorylation +is_a: GO:0033674 ! positive regulation of kinase activity +is_a: GO:0045859 ! regulation of protein kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004672 ! protein kinase activity +relationship: positively_regulates GO:0004672 ! protein kinase activity + +[Term] +id: GO:0045879 +name: negative regulation of smoothened signaling pathway +is_a: GO:0008589 ! regulation of smoothened signaling pathway +is_a: GO:0009968 ! negative regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007224 ! smoothened signaling pathway +relationship: negatively_regulates GO:0007224 ! smoothened signaling pathway + +[Term] +id: GO:0045880 +name: positive regulation of smoothened signaling pathway +is_a: GO:0008589 ! regulation of smoothened signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007224 ! smoothened signaling pathway +relationship: positively_regulates GO:0007224 ! smoothened signaling pathway + +[Term] +id: GO:0045892 +name: negative regulation of transcription, DNA-dependent +is_a: GO:0006355 ! regulation of transcription, DNA-dependent +is_a: GO:0010629 ! negative regulation of gene expression +is_a: GO:0051253 ! negative regulation of RNA metabolic process +is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006351 ! transcription, DNA-dependent +relationship: negatively_regulates GO:0006351 ! transcription, DNA-dependent + +[Term] +id: GO:0045893 +name: positive regulation of transcription, DNA-dependent +is_a: GO:0006355 ! regulation of transcription, DNA-dependent +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process +is_a: GO:0010628 ! positive regulation of gene expression +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0051254 ! positive regulation of RNA metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006351 ! transcription, DNA-dependent +relationship: positively_regulates GO:0006351 ! transcription, DNA-dependent + +[Term] +id: GO:0045926 +name: negative regulation of growth +is_a: GO:0040008 ! regulation of growth +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0040007 ! growth +relationship: negatively_regulates GO:0040007 ! growth + +[Term] +id: GO:0045927 +name: positive regulation of growth +is_a: GO:0040008 ! regulation of growth +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0040007 ! growth +relationship: positively_regulates GO:0040007 ! growth + +[Term] +id: GO:0045930 +name: negative regulation of mitotic cell cycle +is_a: GO:0007346 ! regulation of mitotic cell cycle +is_a: GO:0045786 ! negative regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0000278 ! mitotic cell cycle +relationship: negatively_regulates GO:0000278 ! mitotic cell cycle + +[Term] +id: GO:0045934 +name: negative regulation of nucleobase-containing compound metabolic process +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process +relationship: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process + +[Term] +id: GO:0045935 +name: positive regulation of nucleobase-containing compound metabolic process +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006139 ! nucleobase-containing compound metabolic process +relationship: positively_regulates GO:0006139 ! nucleobase-containing compound metabolic process + +[Term] +id: GO:0045936 +name: negative regulation of phosphate metabolic process +is_a: GO:0010563 ! negative regulation of phosphorus metabolic process +is_a: GO:0019220 ! regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006796 ! phosphate-containing compound metabolic process +relationship: negatively_regulates GO:0006796 ! phosphate-containing compound metabolic process + +[Term] +id: GO:0045937 +name: positive regulation of phosphate metabolic process +is_a: GO:0010562 ! positive regulation of phosphorus metabolic process +is_a: GO:0019220 ! regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006796 ! phosphate-containing compound metabolic process +relationship: positively_regulates GO:0006796 ! phosphate-containing compound metabolic process + +[Term] +id: GO:0045939 +name: negative regulation of steroid metabolic process +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0045833 ! negative regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008202 ! steroid metabolic process +relationship: negatively_regulates GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0045940 +name: positive regulation of steroid metabolic process +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0045834 ! positive regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008202 ! steroid metabolic process +relationship: positively_regulates GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0045944 +name: positive regulation of transcription from RNA polymerase II promoter +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter +relationship: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0045945 +name: positive regulation of transcription from RNA polymerase III promoter +is_a: GO:0006359 ! regulation of transcription from RNA polymerase III promoter +is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006383 ! transcription from RNA polymerase III promoter +relationship: positively_regulates GO:0006383 ! transcription from RNA polymerase III promoter + +[Term] +id: GO:0045981 +name: positive regulation of nucleotide metabolic process +is_a: GO:0006140 ! regulation of nucleotide metabolic process +is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process +is_a: GO:0045937 ! positive regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009117 ! nucleotide metabolic process +relationship: positively_regulates GO:0009117 ! nucleotide metabolic process + +[Term] +id: GO:0045990 +name: carbon catabolite regulation of transcription +is_a: GO:0006355 ! regulation of transcription, DNA-dependent +is_a: GO:0031670 ! cellular response to nutrient + +[Term] +id: GO:0045991 +name: carbon catabolite activation of transcription +is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent +is_a: GO:0045990 ! carbon catabolite regulation of transcription + +[Term] +id: GO:0045992 +name: negative regulation of embryonic development +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051093 ! negative regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009790 ! embryo development +relationship: negatively_regulates GO:0009790 ! embryo development + +[Term] +id: GO:0045995 +name: regulation of embryonic development +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009790 ! embryo development +relationship: regulates GO:0009790 ! embryo development + +[Term] +id: GO:0046015 +name: regulation of transcription by glucose +is_a: GO:0045990 ! carbon catabolite regulation of transcription + +[Term] +id: GO:0046016 +name: positive regulation of transcription by glucose +is_a: GO:0045991 ! carbon catabolite activation of transcription +is_a: GO:0046015 ! regulation of transcription by glucose + +[Term] +id: GO:0046039 +name: GTP metabolic process +is_a: GO:0009150 ! purine ribonucleotide metabolic process +is_a: GO:0009205 ! purine ribonucleoside triphosphate metabolic process +is_a: GO:1901068 ! guanosine-containing compound metabolic process + +[Term] +id: GO:0046068 +name: cGMP metabolic process +is_a: GO:0009150 ! purine ribonucleotide metabolic process +is_a: GO:0009187 ! cyclic nucleotide metabolic process + +[Term] +id: GO:0046128 +name: purine ribonucleoside metabolic process +is_a: GO:0009119 ! ribonucleoside metabolic process +is_a: GO:0042278 ! purine nucleoside metabolic process + +[Term] +id: GO:0046130 +name: purine ribonucleoside catabolic process +is_a: GO:0006152 ! purine nucleoside catabolic process +is_a: GO:0042454 ! ribonucleoside catabolic process +is_a: GO:0046128 ! purine ribonucleoside metabolic process + +[Term] +id: GO:0046165 +name: alcohol biosynthetic process +is_a: GO:0006066 ! alcohol metabolic process +is_a: GO:0044283 ! small molecule biosynthetic process +is_a: GO:1901617 ! organic hydroxy compound biosynthetic process + +[Term] +id: GO:0046328 +name: regulation of JNK cascade +is_a: GO:0032872 ! regulation of stress-activated MAPK cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007254 ! JNK cascade +relationship: regulates GO:0007254 ! JNK cascade + +[Term] +id: GO:0046330 +name: positive regulation of JNK cascade +is_a: GO:0032874 ! positive regulation of stress-activated MAPK cascade +is_a: GO:0046328 ! regulation of JNK cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007254 ! JNK cascade +relationship: positively_regulates GO:0007254 ! JNK cascade + +[Term] +id: GO:0046332 +name: SMAD binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0046365 +name: monosaccharide catabolic process +is_a: GO:0005996 ! monosaccharide metabolic process +is_a: GO:0044724 ! single-organism carbohydrate catabolic process + +[Term] +id: GO:0046434 +name: organophosphate catabolic process +is_a: GO:0019637 ! organophosphate metabolic process +is_a: GO:1901575 ! organic substance catabolic process + +[Term] +id: GO:0046483 +name: heterocycle metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0046543 +name: development of secondary female sexual characteristics +is_a: GO:0045136 ! development of secondary sexual characteristics +relationship: part_of GO:0046660 ! female sex differentiation + +[Term] +id: GO:0046545 +name: development of primary female sexual characteristics +is_a: GO:0045137 ! development of primary sexual characteristics +relationship: part_of GO:0046660 ! female sex differentiation + +[Term] +id: GO:0046546 +name: development of primary male sexual characteristics +is_a: GO:0045137 ! development of primary sexual characteristics +relationship: part_of GO:0046661 ! male sex differentiation + +[Term] +id: GO:0046578 +name: regulation of Ras protein signal transduction +is_a: GO:0051056 ! regulation of small GTPase mediated signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007265 ! Ras protein signal transduction +relationship: regulates GO:0007265 ! Ras protein signal transduction + +[Term] +id: GO:0046620 +name: regulation of organ growth +is_a: GO:0040008 ! regulation of growth +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035265 ! organ growth +relationship: regulates GO:0035265 ! organ growth + +[Term] +id: GO:0046649 +name: lymphocyte activation +is_a: GO:0045321 ! leukocyte activation + +[Term] +id: GO:0046651 +name: lymphocyte proliferation +is_a: GO:0032943 ! mononuclear cell proliferation +is_a: GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0046660 +name: female sex differentiation +is_a: GO:0007548 ! sex differentiation +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0046661 +name: male sex differentiation +is_a: GO:0007548 ! sex differentiation +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0046676 +name: negative regulation of insulin secretion +is_a: GO:0050796 ! regulation of insulin secretion +is_a: GO:0090278 ! negative regulation of peptide hormone secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030073 ! insulin secretion +relationship: negatively_regulates GO:0030073 ! insulin secretion + +[Term] +id: GO:0046700 +name: heterocycle catabolic process +is_a: GO:0044248 ! cellular catabolic process +is_a: GO:0046483 ! heterocycle metabolic process + +[Term] +id: GO:0046822 +name: regulation of nucleocytoplasmic transport +is_a: GO:0032386 ! regulation of intracellular transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006913 ! nucleocytoplasmic transport +relationship: regulates GO:0006913 ! nucleocytoplasmic transport + +[Term] +id: GO:0046823 +name: negative regulation of nucleocytoplasmic transport +is_a: GO:0032387 ! negative regulation of intracellular transport +is_a: GO:0046822 ! regulation of nucleocytoplasmic transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006913 ! nucleocytoplasmic transport +relationship: negatively_regulates GO:0006913 ! nucleocytoplasmic transport + +[Term] +id: GO:0046824 +name: positive regulation of nucleocytoplasmic transport +is_a: GO:0032388 ! positive regulation of intracellular transport +is_a: GO:0046822 ! regulation of nucleocytoplasmic transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006913 ! nucleocytoplasmic transport +relationship: positively_regulates GO:0006913 ! nucleocytoplasmic transport + +[Term] +id: GO:0046835 +name: carbohydrate phosphorylation +is_a: GO:0016310 ! phosphorylation +is_a: GO:0044262 ! cellular carbohydrate metabolic process + +[Term] +id: GO:0046849 +name: bone remodeling +is_a: GO:0048771 ! tissue remodeling + +[Term] +id: GO:0046850 +name: regulation of bone remodeling +is_a: GO:0034103 ! regulation of tissue remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046849 ! bone remodeling +relationship: regulates GO:0046849 ! bone remodeling + +[Term] +id: GO:0046851 +name: negative regulation of bone remodeling +is_a: GO:0034104 ! negative regulation of tissue remodeling +is_a: GO:0046850 ! regulation of bone remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046849 ! bone remodeling +relationship: negatively_regulates GO:0046849 ! bone remodeling + +[Term] +id: GO:0046852 +name: positive regulation of bone remodeling +is_a: GO:0034105 ! positive regulation of tissue remodeling +is_a: GO:0046850 ! regulation of bone remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046849 ! bone remodeling +relationship: positively_regulates GO:0046849 ! bone remodeling + +[Term] +id: GO:0046872 +name: metal ion binding +is_a: GO:0043169 ! cation binding + +[Term] +id: GO:0046879 +name: hormone secretion +is_a: GO:0009914 ! hormone transport +is_a: GO:0023061 ! signal release + +[Term] +id: GO:0046883 +name: regulation of hormone secretion +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0023051 ! regulation of signaling +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046879 ! hormone secretion +relationship: regulates GO:0046879 ! hormone secretion + +[Term] +id: GO:0046885 +name: regulation of hormone biosynthetic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042446 ! hormone biosynthetic process +relationship: regulates GO:0042446 ! hormone biosynthetic process + +[Term] +id: GO:0046886 +name: positive regulation of hormone biosynthetic process +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0032352 ! positive regulation of hormone metabolic process +is_a: GO:0046885 ! regulation of hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042446 ! hormone biosynthetic process +relationship: positively_regulates GO:0042446 ! hormone biosynthetic process + +[Term] +id: GO:0046888 +name: negative regulation of hormone secretion +is_a: GO:0046883 ! regulation of hormone secretion +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051048 ! negative regulation of secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046879 ! hormone secretion +relationship: negatively_regulates GO:0046879 ! hormone secretion + +[Term] +id: GO:0046889 +name: positive regulation of lipid biosynthetic process +is_a: GO:0009891 ! positive regulation of biosynthetic process +is_a: GO:0045834 ! positive regulation of lipid metabolic process +is_a: GO:0046890 ! regulation of lipid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008610 ! lipid biosynthetic process +relationship: positively_regulates GO:0008610 ! lipid biosynthetic process + +[Term] +id: GO:0046890 +name: regulation of lipid biosynthetic process +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0019216 ! regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008610 ! lipid biosynthetic process +relationship: regulates GO:0008610 ! lipid biosynthetic process + +[Term] +id: GO:0046903 +name: secretion +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0046907 +name: intracellular transport +is_a: GO:0006810 ! transport +is_a: GO:0051649 ! establishment of localization in cell +intersection_of: GO:0006810 ! transport +intersection_of: occurs_in GO:0005622 ! intracellular + +[Term] +id: GO:0046982 +name: protein heterodimerization activity +is_a: GO:0046983 ! protein dimerization activity + +[Term] +id: GO:0046983 +name: protein dimerization activity +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0048009 +name: insulin-like growth factor receptor signaling pathway +is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway + +[Term] +id: GO:0048010 +name: vascular endothelial growth factor receptor signaling pathway +is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway + +[Term] +id: GO:0048018 +name: receptor agonist activity +is_a: GO:0005102 ! receptor binding +is_a: GO:0030546 ! receptor activator activity +relationship: part_of GO:0007165 ! signal transduction + +[Term] +id: GO:0048019 +name: receptor antagonist activity +is_a: GO:0005102 ! receptor binding +is_a: GO:0030547 ! receptor inhibitor activity +relationship: part_of GO:1900116 ! extracellular negative regulation of signal transduction + +[Term] +id: GO:0048041 +name: focal adhesion assembly +is_a: GO:0007045 ! cell-substrate adherens junction assembly +relationship: part_of GO:0007160 ! cell-matrix adhesion + +[Term] +id: GO:0048048 +name: embryonic eye morphogenesis +is_a: GO:0048562 ! embryonic organ morphogenesis +is_a: GO:0048592 ! eye morphogenesis + +[Term] +id: GO:0048066 +name: developmental pigmentation +is_a: GO:0032502 ! developmental process +is_a: GO:0043473 ! pigmentation + +[Term] +id: GO:0048103 +name: somatic stem cell division +is_a: GO:0017145 ! stem cell division + +[Term] +id: GO:0048144 +name: fibroblast proliferation +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0048145 +name: regulation of fibroblast proliferation +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048144 ! fibroblast proliferation +relationship: regulates GO:0048144 ! fibroblast proliferation + +[Term] +id: GO:0048146 +name: positive regulation of fibroblast proliferation +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0048145 ! regulation of fibroblast proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048144 ! fibroblast proliferation +relationship: positively_regulates GO:0048144 ! fibroblast proliferation + +[Term] +id: GO:0048147 +name: negative regulation of fibroblast proliferation +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0048145 ! regulation of fibroblast proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048144 ! fibroblast proliferation +relationship: negatively_regulates GO:0048144 ! fibroblast proliferation + +[Term] +id: GO:0048237 +name: rough endoplasmic reticulum lumen +is_a: GO:0005788 ! endoplasmic reticulum lumen +relationship: part_of GO:0005791 ! rough endoplasmic reticulum + +[Term] +id: GO:0048247 +name: lymphocyte chemotaxis +is_a: GO:0030595 ! leukocyte chemotaxis +is_a: GO:0072676 ! lymphocyte migration + +[Term] +id: GO:0048259 +name: regulation of receptor-mediated endocytosis +is_a: GO:0030100 ! regulation of endocytosis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006898 ! receptor-mediated endocytosis +relationship: regulates GO:0006898 ! receptor-mediated endocytosis + +[Term] +id: GO:0048260 +name: positive regulation of receptor-mediated endocytosis +is_a: GO:0045807 ! positive regulation of endocytosis +is_a: GO:0048259 ! regulation of receptor-mediated endocytosis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006898 ! receptor-mediated endocytosis +relationship: positively_regulates GO:0006898 ! receptor-mediated endocytosis + +[Term] +id: GO:0048262 +name: determination of dorsal/ventral asymmetry +is_a: GO:0009855 ! determination of bilateral symmetry +relationship: part_of GO:0009953 ! dorsal/ventral pattern formation + +[Term] +id: GO:0048263 +name: determination of dorsal identity +is_a: GO:0009953 ! dorsal/ventral pattern formation +relationship: part_of GO:0048262 ! determination of dorsal/ventral asymmetry + +[Term] +id: GO:0048285 +name: organelle fission +is_a: GO:0006996 ! organelle organization + +[Term] +id: GO:0048286 +name: lung alveolus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0048306 +name: calcium-dependent protein binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0048318 +name: axial mesoderm development +is_a: GO:0007498 ! mesoderm development + +[Term] +id: GO:0048332 +name: mesoderm morphogenesis +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0007498 ! mesoderm development + +[Term] +id: GO:0048333 +name: mesodermal cell differentiation +is_a: GO:0030154 ! cell differentiation +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001707 ! mesoderm formation + +[Term] +id: GO:0048337 +name: positive regulation of mesodermal cell fate specification +is_a: GO:0042660 ! positive regulation of cell fate specification +is_a: GO:0042661 ! regulation of mesodermal cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007501 ! mesodermal cell fate specification +relationship: positively_regulates GO:0007501 ! mesodermal cell fate specification + +[Term] +id: GO:0048339 +name: paraxial mesoderm development +is_a: GO:0007498 ! mesoderm development + +[Term] +id: GO:0048340 +name: paraxial mesoderm morphogenesis +is_a: GO:0048332 ! mesoderm morphogenesis +relationship: part_of GO:0048339 ! paraxial mesoderm development + +[Term] +id: GO:0048341 +name: paraxial mesoderm formation +is_a: GO:0001707 ! mesoderm formation +relationship: part_of GO:0048340 ! paraxial mesoderm morphogenesis + +[Term] +id: GO:0048342 +name: paraxial mesodermal cell differentiation +is_a: GO:0048333 ! mesodermal cell differentiation +relationship: part_of GO:0048341 ! paraxial mesoderm formation + +[Term] +id: GO:0048343 +name: paraxial mesodermal cell fate commitment +is_a: GO:0001710 ! mesodermal cell fate commitment +relationship: part_of GO:0048342 ! paraxial mesodermal cell differentiation + +[Term] +id: GO:0048468 +name: cell development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0030154 ! cell differentiation + +[Term] +id: GO:0048469 +name: cell maturation +is_a: GO:0021700 ! developmental maturation +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0048468 ! cell development + +[Term] +id: GO:0048471 +name: perinuclear region of cytoplasm +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0048477 +name: oogenesis +is_a: GO:0007292 ! female gamete generation + +[Term] +id: GO:0048483 +name: autonomic nervous system development +is_a: GO:0048731 ! system development +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0048484 +name: enteric nervous system development +is_a: GO:0048731 ! system development +relationship: part_of GO:0048483 ! autonomic nervous system development + +[Term] +id: GO:0048485 +name: sympathetic nervous system development +is_a: GO:0048731 ! system development +relationship: part_of GO:0048483 ! autonomic nervous system development + +[Term] +id: GO:0048489 +name: synaptic vesicle transport +is_a: GO:0016192 ! vesicle-mediated transport +is_a: GO:0044765 ! single-organism transport +is_a: GO:0097480 ! establishment of synaptic vesicle localization +relationship: part_of GO:0007268 ! synaptic transmission + +[Term] +id: GO:0048511 +name: rhythmic process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0048513 +name: organ development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0048731 ! system development + +[Term] +id: GO:0048514 +name: blood vessel morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001568 ! blood vessel development + +[Term] +id: GO:0048518 +name: positive regulation of biological process +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008150 ! biological_process +relationship: positively_regulates GO:0008150 ! biological_process + +[Term] +id: GO:0048519 +name: negative regulation of biological process +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008150 ! biological_process +relationship: negatively_regulates GO:0008150 ! biological_process + +[Term] +id: GO:0048520 +name: positive regulation of behavior +is_a: GO:0048584 ! positive regulation of response to stimulus +is_a: GO:0050795 ! regulation of behavior +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007610 ! behavior +relationship: positively_regulates GO:0007610 ! behavior + +[Term] +id: GO:0048521 +name: negative regulation of behavior +is_a: GO:0048585 ! negative regulation of response to stimulus +is_a: GO:0050795 ! regulation of behavior +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007610 ! behavior +relationship: negatively_regulates GO:0007610 ! behavior + +[Term] +id: GO:0048522 +name: positive regulation of cellular process +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009987 ! cellular process +relationship: positively_regulates GO:0009987 ! cellular process + +[Term] +id: GO:0048523 +name: negative regulation of cellular process +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009987 ! cellular process +relationship: negatively_regulates GO:0009987 ! cellular process + +[Term] +id: GO:0048534 +name: hematopoietic or lymphoid organ development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0002520 ! immune system development + +[Term] +id: GO:0048538 +name: thymus development +is_a: GO:0048534 ! hematopoietic or lymphoid organ development + +[Term] +id: GO:0048539 +name: bone marrow development +is_a: GO:0048534 ! hematopoietic or lymphoid organ development +relationship: part_of GO:0060348 ! bone development + +[Term] +id: GO:0048545 +name: response to steroid hormone stimulus +is_a: GO:0009725 ! response to hormone stimulus +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0033993 ! response to lipid + +[Term] +id: GO:0048546 +name: digestive tract morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048565 ! digestive tract development + +[Term] +id: GO:0048562 +name: embryonic organ morphogenesis +is_a: GO:0009887 ! organ morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0048568 ! embryonic organ development + +[Term] +id: GO:0048565 +name: digestive tract development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0055123 ! digestive system development + +[Term] +id: GO:0048568 +name: embryonic organ development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0009790 ! embryo development + +[Term] +id: GO:0048583 +name: regulation of response to stimulus +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050896 ! response to stimulus +relationship: regulates GO:0050896 ! response to stimulus + +[Term] +id: GO:0048584 +name: positive regulation of response to stimulus +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050896 ! response to stimulus +relationship: positively_regulates GO:0050896 ! response to stimulus + +[Term] +id: GO:0048585 +name: negative regulation of response to stimulus +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0050896 ! response to stimulus +relationship: negatively_regulates GO:0050896 ! response to stimulus + +[Term] +id: GO:0048588 +name: developmental cell growth +is_a: GO:0016049 ! cell growth +is_a: GO:0048589 ! developmental growth +relationship: part_of GO:0048468 ! cell development + +[Term] +id: GO:0048589 +name: developmental growth +is_a: GO:0040007 ! growth +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0048592 +name: eye morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0001654 ! eye development + +[Term] +id: GO:0048593 +name: camera-type eye morphogenesis +is_a: GO:0048592 ! eye morphogenesis +relationship: part_of GO:0043010 ! camera-type eye development + +[Term] +id: GO:0048596 +name: embryonic camera-type eye morphogenesis +is_a: GO:0048048 ! embryonic eye morphogenesis +relationship: part_of GO:0031076 ! embryonic camera-type eye development +relationship: part_of GO:0048593 ! camera-type eye morphogenesis + +[Term] +id: GO:0048598 +name: embryonic morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0009790 ! embryo development + +[Term] +id: GO:0048599 +name: oocyte development +is_a: GO:0007281 ! germ cell development +relationship: part_of GO:0009994 ! oocyte differentiation + +[Term] +id: GO:0048608 +name: reproductive structure development +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061458 ! reproductive system development + +[Term] +id: GO:0048609 +name: multicellular organismal reproductive process +is_a: GO:0022414 ! reproductive process +relationship: part_of GO:0032504 ! multicellular organism reproduction + +[Term] +id: GO:0048610 +name: cellular process involved in reproduction +is_a: GO:0009987 ! cellular process +intersection_of: GO:0009987 ! cellular process +intersection_of: part_of GO:0000003 ! reproduction +relationship: part_of GO:0000003 ! reproduction + +[Term] +id: GO:0048617 +name: embryonic foregut morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0007440 ! foregut morphogenesis + +[Term] +id: GO:0048634 +name: regulation of muscle organ development +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007517 ! muscle organ development +relationship: regulates GO:0007517 ! muscle organ development + +[Term] +id: GO:0048638 +name: regulation of developmental growth +is_a: GO:0040008 ! regulation of growth +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048589 ! developmental growth +relationship: regulates GO:0048589 ! developmental growth + +[Term] +id: GO:0048639 +name: positive regulation of developmental growth +is_a: GO:0045927 ! positive regulation of growth +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048589 ! developmental growth +relationship: positively_regulates GO:0048589 ! developmental growth + +[Term] +id: GO:0048640 +name: negative regulation of developmental growth +is_a: GO:0045926 ! negative regulation of growth +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:0051093 ! negative regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048589 ! developmental growth +relationship: negatively_regulates GO:0048589 ! developmental growth + +[Term] +id: GO:0048644 +name: muscle organ morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0007517 ! muscle organ development + +[Term] +id: GO:0048645 +name: organ formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0009887 ! organ morphogenesis + +[Term] +id: GO:0048646 +name: anatomical structure formation involved in morphogenesis +is_a: GO:0032502 ! developmental process +relationship: part_of GO:0009653 ! anatomical structure morphogenesis + +[Term] +id: GO:0048659 +name: smooth muscle cell proliferation +is_a: GO:0033002 ! muscle cell proliferation + +[Term] +id: GO:0048660 +name: regulation of smooth muscle cell proliferation +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048659 ! smooth muscle cell proliferation +relationship: regulates GO:0048659 ! smooth muscle cell proliferation + +[Term] +id: GO:0048662 +name: negative regulation of smooth muscle cell proliferation +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0048660 ! regulation of smooth muscle cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048659 ! smooth muscle cell proliferation +relationship: negatively_regulates GO:0048659 ! smooth muscle cell proliferation + +[Term] +id: GO:0048663 +name: neuron fate commitment +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0030182 ! neuron differentiation + +[Term] +id: GO:0048664 +name: neuron fate determination +is_a: GO:0001709 ! cell fate determination +relationship: part_of GO:0048663 ! neuron fate commitment + +[Term] +id: GO:0048665 +name: neuron fate specification +is_a: GO:0001708 ! cell fate specification +relationship: part_of GO:0048663 ! neuron fate commitment + +[Term] +id: GO:0048666 +name: neuron development +is_a: GO:0048468 ! cell development +relationship: part_of GO:0030182 ! neuron differentiation + +[Term] +id: GO:0048667 +name: cell morphogenesis involved in neuron differentiation +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +intersection_of: GO:0000902 ! cell morphogenesis +intersection_of: part_of GO:0030182 ! neuron differentiation +relationship: part_of GO:0048666 ! neuron development + +[Term] +id: GO:0048668 +name: collateral sprouting +is_a: GO:0048588 ! developmental cell growth +is_a: GO:0060560 ! developmental growth involved in morphogenesis +relationship: part_of GO:0007409 ! axonogenesis + +[Term] +id: GO:0048669 +name: collateral sprouting in absence of injury +is_a: GO:0048668 ! collateral sprouting + +[Term] +id: GO:0048670 +name: regulation of collateral sprouting +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:0050770 ! regulation of axonogenesis +is_a: GO:0061387 ! regulation of extent of cell growth +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048668 ! collateral sprouting +relationship: regulates GO:0048668 ! collateral sprouting + +[Term] +id: GO:0048672 +name: positive regulation of collateral sprouting +is_a: GO:0030307 ! positive regulation of cell growth +is_a: GO:0048639 ! positive regulation of developmental growth +is_a: GO:0048670 ! regulation of collateral sprouting +is_a: GO:0050772 ! positive regulation of axonogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048668 ! collateral sprouting +relationship: positively_regulates GO:0048668 ! collateral sprouting + +[Term] +id: GO:0048675 +name: axon extension +is_a: GO:1990138 ! neuron projection extension +relationship: part_of GO:0007409 ! axonogenesis + +[Term] +id: GO:0048696 +name: regulation of collateral sprouting in absence of injury +is_a: GO:0048670 ! regulation of collateral sprouting +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048669 ! collateral sprouting in absence of injury +relationship: regulates GO:0048669 ! collateral sprouting in absence of injury + +[Term] +id: GO:0048697 +name: positive regulation of collateral sprouting in absence of injury +is_a: GO:0048672 ! positive regulation of collateral sprouting +is_a: GO:0048696 ! regulation of collateral sprouting in absence of injury +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048669 ! collateral sprouting in absence of injury +relationship: positively_regulates GO:0048669 ! collateral sprouting in absence of injury + +[Term] +id: GO:0048699 +name: generation of neurons +is_a: GO:0022008 ! neurogenesis + +[Term] +id: GO:0048701 +name: embryonic cranial skeleton morphogenesis +is_a: GO:0048704 ! embryonic skeletal system morphogenesis + +[Term] +id: GO:0048703 +name: embryonic viscerocranium morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0048701 ! embryonic cranial skeleton morphogenesis + +[Term] +id: GO:0048704 +name: embryonic skeletal system morphogenesis +is_a: GO:0048562 ! embryonic organ morphogenesis +is_a: GO:0048705 ! skeletal system morphogenesis +relationship: part_of GO:0048706 ! embryonic skeletal system development + +[Term] +id: GO:0048705 +name: skeletal system morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0001501 ! skeletal system development + +[Term] +id: GO:0048706 +name: embryonic skeletal system development +is_a: GO:0001501 ! skeletal system development +relationship: part_of GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0048709 +name: oligodendrocyte differentiation +is_a: GO:0010001 ! glial cell differentiation +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0048713 +name: regulation of oligodendrocyte differentiation +is_a: GO:0045685 ! regulation of glial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048709 ! oligodendrocyte differentiation +relationship: regulates GO:0048709 ! oligodendrocyte differentiation + +[Term] +id: GO:0048715 +name: negative regulation of oligodendrocyte differentiation +is_a: GO:0045686 ! negative regulation of glial cell differentiation +is_a: GO:0048713 ! regulation of oligodendrocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048709 ! oligodendrocyte differentiation +relationship: negatively_regulates GO:0048709 ! oligodendrocyte differentiation + +[Term] +id: GO:0048729 +name: tissue morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0009888 ! tissue development + +[Term] +id: GO:0048730 +name: epidermis morphogenesis +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0008544 ! epidermis development +relationship: part_of GO:0043589 ! skin morphogenesis + +[Term] +id: GO:0048731 +name: system development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0048732 +name: gland development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0048736 +name: appendage development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0048738 +name: cardiac muscle tissue development +is_a: GO:0014706 ! striated muscle tissue development +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0048741 +name: skeletal muscle fiber development +is_a: GO:0048747 ! muscle fiber development +relationship: part_of GO:0007519 ! skeletal muscle tissue development + +[Term] +id: GO:0048745 +name: smooth muscle tissue development +is_a: GO:0060537 ! muscle tissue development + +[Term] +id: GO:0048747 +name: muscle fiber development +is_a: GO:0055002 ! striated muscle cell development + +[Term] +id: GO:0048754 +name: branching morphogenesis of an epithelial tube +is_a: GO:0061138 ! morphogenesis of a branching epithelium +relationship: part_of GO:0060562 ! epithelial tube morphogenesis + +[Term] +id: GO:0048762 +name: mesenchymal cell differentiation +is_a: GO:0048863 ! stem cell differentiation +relationship: part_of GO:0060485 ! mesenchyme development + +[Term] +id: GO:0048771 +name: tissue remodeling +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0048806 +name: genitalia development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +is_a: GO:0048608 ! reproductive structure development +relationship: part_of GO:0007548 ! sex differentiation + +[Term] +id: GO:0048812 +name: neuron projection morphogenesis +is_a: GO:0048858 ! cell projection morphogenesis +relationship: part_of GO:0031175 ! neuron projection development + +[Term] +id: GO:0048813 +name: dendrite morphogenesis +is_a: GO:0048812 ! neuron projection morphogenesis +relationship: part_of GO:0016358 ! dendrite development +relationship: part_of GO:0048667 ! cell morphogenesis involved in neuron differentiation + +[Term] +id: GO:0048814 +name: regulation of dendrite morphogenesis +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:0050773 ! regulation of dendrite development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048813 ! dendrite morphogenesis +relationship: regulates GO:0048813 ! dendrite morphogenesis + +[Term] +id: GO:0048839 +name: inner ear development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0043583 ! ear development + +[Term] +id: GO:0048841 +name: regulation of axon extension involved in axon guidance +is_a: GO:0030516 ! regulation of axon extension +is_a: GO:0050920 ! regulation of chemotaxis +is_a: GO:0051270 ! regulation of cellular component movement +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048846 ! axon extension involved in axon guidance +relationship: regulates GO:0048846 ! axon extension involved in axon guidance + +[Term] +id: GO:0048843 +name: negative regulation of axon extension involved in axon guidance +is_a: GO:0030517 ! negative regulation of axon extension +is_a: GO:0048841 ! regulation of axon extension involved in axon guidance +is_a: GO:0050922 ! negative regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048846 ! axon extension involved in axon guidance +relationship: negatively_regulates GO:0048846 ! axon extension involved in axon guidance + +[Term] +id: GO:0048844 +name: artery morphogenesis +is_a: GO:0048514 ! blood vessel morphogenesis +relationship: part_of GO:0060840 ! artery development + +[Term] +id: GO:0048846 +name: axon extension involved in axon guidance +is_a: GO:0048675 ! axon extension +is_a: GO:1902284 ! neuron projection extension involved in neuron projection guidance +intersection_of: GO:0048675 ! axon extension +intersection_of: part_of GO:0007411 ! axon guidance +relationship: part_of GO:0007411 ! axon guidance + +[Term] +id: GO:0048850 +name: hypophysis morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021983 ! pituitary gland development +relationship: part_of GO:0022612 ! gland morphogenesis +relationship: part_of GO:0048852 ! diencephalon morphogenesis + +[Term] +id: GO:0048852 +name: diencephalon morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021536 ! diencephalon development +relationship: part_of GO:0048853 ! forebrain morphogenesis + +[Term] +id: GO:0048853 +name: forebrain morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0030900 ! forebrain development +relationship: part_of GO:0048854 ! brain morphogenesis + +[Term] +id: GO:0048854 +name: brain morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0007420 ! brain development + +[Term] +id: GO:0048856 +name: anatomical structure development +is_a: GO:0032502 ! developmental process + +[Term] +id: GO:0048857 +name: neural nucleus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0048858 +name: cell projection morphogenesis +is_a: GO:0030030 ! cell projection organization +is_a: GO:0032990 ! cell part morphogenesis +relationship: part_of GO:0000902 ! cell morphogenesis + +[Term] +id: GO:0048863 +name: stem cell differentiation +is_a: GO:0030154 ! cell differentiation + +[Term] +id: GO:0048864 +name: stem cell development +is_a: GO:0048468 ! cell development +relationship: part_of GO:0048863 ! stem cell differentiation + +[Term] +id: GO:0048869 +name: cellular developmental process +is_a: GO:0032502 ! developmental process +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0048870 +name: cell motility +is_a: GO:0006928 ! cellular component movement +is_a: GO:0040011 ! locomotion +relationship: part_of GO:0051674 ! localization of cell + +[Term] +id: GO:0048871 +name: multicellular organismal homeostasis +is_a: GO:0042592 ! homeostatic process +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0048878 +name: chemical homeostasis +is_a: GO:0042592 ! homeostatic process + +[Term] +id: GO:0048880 +name: sensory system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0048892 +name: lateral line nerve development +is_a: GO:0021545 ! cranial nerve development +relationship: part_of GO:0048925 ! lateral line system development + +[Term] +id: GO:0048895 +name: lateral line nerve glial cell differentiation +is_a: GO:0010001 ! glial cell differentiation +relationship: part_of GO:0048892 ! lateral line nerve development + +[Term] +id: GO:0048925 +name: lateral line system development +is_a: GO:0048880 ! sensory system development + +[Term] +id: GO:0048937 +name: lateral line nerve glial cell development +is_a: GO:0021782 ! glial cell development +relationship: part_of GO:0048895 ! lateral line nerve glial cell differentiation + +[Term] +id: GO:0050663 +name: cytokine secretion +is_a: GO:0009306 ! protein secretion +relationship: part_of GO:0001816 ! cytokine production + +[Term] +id: GO:0050670 +name: regulation of lymphocyte proliferation +is_a: GO:0032944 ! regulation of mononuclear cell proliferation +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046651 ! lymphocyte proliferation +relationship: regulates GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0050671 +name: positive regulation of lymphocyte proliferation +is_a: GO:0032946 ! positive regulation of mononuclear cell proliferation +is_a: GO:0050670 ! regulation of lymphocyte proliferation +is_a: GO:0051251 ! positive regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046651 ! lymphocyte proliferation +relationship: positively_regulates GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0050672 +name: negative regulation of lymphocyte proliferation +is_a: GO:0032945 ! negative regulation of mononuclear cell proliferation +is_a: GO:0050670 ! regulation of lymphocyte proliferation +is_a: GO:0051250 ! negative regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046651 ! lymphocyte proliferation +relationship: negatively_regulates GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0050673 +name: epithelial cell proliferation +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0050678 +name: regulation of epithelial cell proliferation +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050673 ! epithelial cell proliferation +relationship: regulates GO:0050673 ! epithelial cell proliferation + +[Term] +id: GO:0050679 +name: positive regulation of epithelial cell proliferation +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0050678 ! regulation of epithelial cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050673 ! epithelial cell proliferation +relationship: positively_regulates GO:0050673 ! epithelial cell proliferation + +[Term] +id: GO:0050680 +name: negative regulation of epithelial cell proliferation +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0050678 ! regulation of epithelial cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0050673 ! epithelial cell proliferation +relationship: negatively_regulates GO:0050673 ! epithelial cell proliferation + +[Term] +id: GO:0050681 +name: androgen receptor binding +is_a: GO:0035258 ! steroid hormone receptor binding + +[Term] +id: GO:0050701 +name: interleukin-1 secretion +is_a: GO:0050663 ! cytokine secretion +relationship: part_of GO:0032612 ! interleukin-1 production + +[Term] +id: GO:0050702 +name: interleukin-1 beta secretion +is_a: GO:0050701 ! interleukin-1 secretion +relationship: part_of GO:0032611 ! interleukin-1 beta production + +[Term] +id: GO:0050704 +name: regulation of interleukin-1 secretion +is_a: GO:0032652 ! regulation of interleukin-1 production +is_a: GO:0050707 ! regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050701 ! interleukin-1 secretion +relationship: regulates GO:0050701 ! interleukin-1 secretion + +[Term] +id: GO:0050706 +name: regulation of interleukin-1 beta secretion +is_a: GO:0032651 ! regulation of interleukin-1 beta production +is_a: GO:0050704 ! regulation of interleukin-1 secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050702 ! interleukin-1 beta secretion +relationship: regulates GO:0050702 ! interleukin-1 beta secretion + +[Term] +id: GO:0050707 +name: regulation of cytokine secretion +is_a: GO:0001817 ! regulation of cytokine production +is_a: GO:0050708 ! regulation of protein secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050663 ! cytokine secretion +relationship: regulates GO:0050663 ! cytokine secretion + +[Term] +id: GO:0050708 +name: regulation of protein secretion +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0051223 ! regulation of protein transport +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009306 ! protein secretion +relationship: regulates GO:0009306 ! protein secretion + +[Term] +id: GO:0050714 +name: positive regulation of protein secretion +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0050708 ! regulation of protein secretion +is_a: GO:0051047 ! positive regulation of secretion +is_a: GO:0051222 ! positive regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009306 ! protein secretion +relationship: positively_regulates GO:0009306 ! protein secretion + +[Term] +id: GO:0050715 +name: positive regulation of cytokine secretion +is_a: GO:0050707 ! regulation of cytokine secretion +is_a: GO:0050714 ! positive regulation of protein secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050663 ! cytokine secretion +relationship: positively_regulates GO:0050663 ! cytokine secretion + +[Term] +id: GO:0050716 +name: positive regulation of interleukin-1 secretion +is_a: GO:0032732 ! positive regulation of interleukin-1 production +is_a: GO:0050704 ! regulation of interleukin-1 secretion +is_a: GO:0050715 ! positive regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050701 ! interleukin-1 secretion +relationship: positively_regulates GO:0050701 ! interleukin-1 secretion + +[Term] +id: GO:0050718 +name: positive regulation of interleukin-1 beta secretion +is_a: GO:0032731 ! positive regulation of interleukin-1 beta production +is_a: GO:0050706 ! regulation of interleukin-1 beta secretion +is_a: GO:0050716 ! positive regulation of interleukin-1 secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050702 ! interleukin-1 beta secretion +relationship: positively_regulates GO:0050702 ! interleukin-1 beta secretion + +[Term] +id: GO:0050727 +name: regulation of inflammatory response +is_a: GO:0031347 ! regulation of defense response +is_a: GO:0032101 ! regulation of response to external stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006954 ! inflammatory response +relationship: regulates GO:0006954 ! inflammatory response + +[Term] +id: GO:0050729 +name: positive regulation of inflammatory response +is_a: GO:0031349 ! positive regulation of defense response +is_a: GO:0032103 ! positive regulation of response to external stimulus +is_a: GO:0050727 ! regulation of inflammatory response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006954 ! inflammatory response +relationship: positively_regulates GO:0006954 ! inflammatory response + +[Term] +id: GO:0050730 +name: regulation of peptidyl-tyrosine phosphorylation +is_a: GO:0001932 ! regulation of protein phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0018108 ! peptidyl-tyrosine phosphorylation +relationship: regulates GO:0018108 ! peptidyl-tyrosine phosphorylation + +[Term] +id: GO:0050731 +name: positive regulation of peptidyl-tyrosine phosphorylation +is_a: GO:0001934 ! positive regulation of protein phosphorylation +is_a: GO:0050730 ! regulation of peptidyl-tyrosine phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation +relationship: positively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation + +[Term] +id: GO:0050732 +name: negative regulation of peptidyl-tyrosine phosphorylation +is_a: GO:0001933 ! negative regulation of protein phosphorylation +is_a: GO:0050730 ! regulation of peptidyl-tyrosine phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation +relationship: negatively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation + +[Term] +id: GO:0050750 +name: low-density lipoprotein particle receptor binding +is_a: GO:0070325 ! lipoprotein particle receptor binding + +[Term] +id: GO:0050755 +name: chemokine metabolic process +is_a: GO:0042107 ! cytokine metabolic process + +[Term] +id: GO:0050767 +name: regulation of neurogenesis +is_a: GO:0051960 ! regulation of nervous system development +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0022008 ! neurogenesis +relationship: part_of GO:0048699 ! generation of neurons +relationship: regulates GO:0022008 ! neurogenesis + +[Term] +id: GO:0050768 +name: negative regulation of neurogenesis +is_a: GO:0010721 ! negative regulation of cell development +is_a: GO:0050767 ! regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0022008 ! neurogenesis +relationship: negatively_regulates GO:0022008 ! neurogenesis + +[Term] +id: GO:0050769 +name: positive regulation of neurogenesis +is_a: GO:0010720 ! positive regulation of cell development +is_a: GO:0050767 ! regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0022008 ! neurogenesis +relationship: positively_regulates GO:0022008 ! neurogenesis + +[Term] +id: GO:0050770 +name: regulation of axonogenesis +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:0010975 ! regulation of neuron projection development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007409 ! axonogenesis +relationship: regulates GO:0007409 ! axonogenesis + +[Term] +id: GO:0050771 +name: negative regulation of axonogenesis +is_a: GO:0031345 ! negative regulation of cell projection organization +is_a: GO:0050768 ! negative regulation of neurogenesis +is_a: GO:0050770 ! regulation of axonogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007409 ! axonogenesis +relationship: negatively_regulates GO:0007409 ! axonogenesis + +[Term] +id: GO:0050772 +name: positive regulation of axonogenesis +is_a: GO:0031346 ! positive regulation of cell projection organization +is_a: GO:0050769 ! positive regulation of neurogenesis +is_a: GO:0050770 ! regulation of axonogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007409 ! axonogenesis +relationship: positively_regulates GO:0007409 ! axonogenesis + +[Term] +id: GO:0050773 +name: regulation of dendrite development +is_a: GO:0010975 ! regulation of neuron projection development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016358 ! dendrite development +relationship: regulates GO:0016358 ! dendrite development + +[Term] +id: GO:0050776 +name: regulation of immune response +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006955 ! immune response +relationship: regulates GO:0006955 ! immune response + +[Term] +id: GO:0050777 +name: negative regulation of immune response +is_a: GO:0002683 ! negative regulation of immune system process +is_a: GO:0048585 ! negative regulation of response to stimulus +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006955 ! immune response +relationship: negatively_regulates GO:0006955 ! immune response + +[Term] +id: GO:0050789 +name: regulation of biological process +is_a: GO:0065007 ! biological regulation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008150 ! biological_process +relationship: regulates GO:0008150 ! biological_process + +[Term] +id: GO:0050790 +name: regulation of catalytic activity +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003824 ! catalytic activity +relationship: regulates GO:0003824 ! catalytic activity + +[Term] +id: GO:0050793 +name: regulation of developmental process +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032502 ! developmental process +relationship: regulates GO:0032502 ! developmental process + +[Term] +id: GO:0050794 +name: regulation of cellular process +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009987 ! cellular process +relationship: regulates GO:0009987 ! cellular process + +[Term] +id: GO:0050795 +name: regulation of behavior +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007610 ! behavior +relationship: regulates GO:0007610 ! behavior + +[Term] +id: GO:0050796 +name: regulation of insulin secretion +is_a: GO:0090276 ! regulation of peptide hormone secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030073 ! insulin secretion +relationship: regulates GO:0030073 ! insulin secretion + +[Term] +id: GO:0050801 +name: ion homeostasis +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0050803 +name: regulation of synapse structure and activity +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0007268 ! synaptic transmission + +[Term] +id: GO:0050804 +name: regulation of synaptic transmission +is_a: GO:0051969 ! regulation of transmission of nerve impulse +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007268 ! synaptic transmission +relationship: regulates GO:0007268 ! synaptic transmission + +[Term] +id: GO:0050807 +name: regulation of synapse organization +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050808 ! synapse organization +relationship: part_of GO:0050803 ! regulation of synapse structure and activity +relationship: regulates GO:0050808 ! synapse organization + +[Term] +id: GO:0050808 +name: synapse organization +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0050810 +name: regulation of steroid biosynthetic process +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0046890 ! regulation of lipid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006694 ! steroid biosynthetic process +relationship: regulates GO:0006694 ! steroid biosynthetic process + +[Term] +id: GO:0050817 +name: coagulation +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0050818 +name: regulation of coagulation +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050817 ! coagulation +relationship: regulates GO:0050817 ! coagulation + +[Term] +id: GO:0050839 +name: cell adhesion molecule binding +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0050863 +name: regulation of T cell activation +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042110 ! T cell activation +relationship: regulates GO:0042110 ! T cell activation + +[Term] +id: GO:0050864 +name: regulation of B cell activation +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042113 ! B cell activation +relationship: regulates GO:0042113 ! B cell activation + +[Term] +id: GO:0050865 +name: regulation of cell activation +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001775 ! cell activation +relationship: regulates GO:0001775 ! cell activation + +[Term] +id: GO:0050866 +name: negative regulation of cell activation +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0050865 ! regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001775 ! cell activation +relationship: negatively_regulates GO:0001775 ! cell activation + +[Term] +id: GO:0050867 +name: positive regulation of cell activation +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0050865 ! regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001775 ! cell activation +relationship: positively_regulates GO:0001775 ! cell activation + +[Term] +id: GO:0050868 +name: negative regulation of T cell activation +is_a: GO:0050863 ! regulation of T cell activation +is_a: GO:0051250 ! negative regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042110 ! T cell activation +relationship: negatively_regulates GO:0042110 ! T cell activation + +[Term] +id: GO:0050869 +name: negative regulation of B cell activation +is_a: GO:0050864 ! regulation of B cell activation +is_a: GO:0051250 ! negative regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042113 ! B cell activation +relationship: negatively_regulates GO:0042113 ! B cell activation + +[Term] +id: GO:0050871 +name: positive regulation of B cell activation +is_a: GO:0050864 ! regulation of B cell activation +is_a: GO:0051251 ! positive regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042113 ! B cell activation +relationship: positively_regulates GO:0042113 ! B cell activation + +[Term] +id: GO:0050877 +name: neurological system process +is_a: GO:0003008 ! system process + +[Term] +id: GO:0050878 +name: regulation of body fluid levels +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0065008 ! regulation of biological quality + +[Term] +id: GO:0050880 +name: regulation of blood vessel size +is_a: GO:0003018 ! vascular process in circulatory system +is_a: GO:0035150 ! regulation of tube size +relationship: part_of GO:0008015 ! blood circulation + +[Term] +id: GO:0050890 +name: cognition +is_a: GO:0050877 ! neurological system process + +[Term] +id: GO:0050896 +name: response to stimulus +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0050900 +name: leukocyte migration +is_a: GO:0002376 ! immune system process +is_a: GO:0016477 ! cell migration + +[Term] +id: GO:0050919 +name: negative chemotaxis +is_a: GO:0006935 ! chemotaxis + +[Term] +id: GO:0050920 +name: regulation of chemotaxis +is_a: GO:0032101 ! regulation of response to external stimulus +is_a: GO:0040012 ! regulation of locomotion +is_a: GO:0050795 ! regulation of behavior +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006935 ! chemotaxis +relationship: regulates GO:0006935 ! chemotaxis + +[Term] +id: GO:0050921 +name: positive regulation of chemotaxis +is_a: GO:0032103 ! positive regulation of response to external stimulus +is_a: GO:0040017 ! positive regulation of locomotion +is_a: GO:0048520 ! positive regulation of behavior +is_a: GO:0050920 ! regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006935 ! chemotaxis +relationship: positively_regulates GO:0006935 ! chemotaxis + +[Term] +id: GO:0050922 +name: negative regulation of chemotaxis +is_a: GO:0032102 ! negative regulation of response to external stimulus +is_a: GO:0040013 ! negative regulation of locomotion +is_a: GO:0048521 ! negative regulation of behavior +is_a: GO:0050920 ! regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006935 ! chemotaxis +relationship: negatively_regulates GO:0006935 ! chemotaxis + +[Term] +id: GO:0050931 +name: pigment cell differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0048066 ! developmental pigmentation + +[Term] +id: GO:0050935 +name: iridophore differentiation +is_a: GO:0050931 ! pigment cell differentiation + +[Term] +id: GO:0051017 +name: actin filament bundle assembly +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0061572 ! actin filament bundle organization + +[Term] +id: GO:0051046 +name: regulation of secretion +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046903 ! secretion +relationship: regulates GO:0046903 ! secretion + +[Term] +id: GO:0051047 +name: positive regulation of secretion +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0051050 ! positive regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046903 ! secretion +relationship: positively_regulates GO:0046903 ! secretion + +[Term] +id: GO:0051048 +name: negative regulation of secretion +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0051051 ! negative regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046903 ! secretion +relationship: negatively_regulates GO:0046903 ! secretion + +[Term] +id: GO:0051049 +name: regulation of transport +is_a: GO:0032879 ! regulation of localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006810 ! transport +relationship: regulates GO:0006810 ! transport + +[Term] +id: GO:0051050 +name: positive regulation of transport +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006810 ! transport +relationship: positively_regulates GO:0006810 ! transport + +[Term] +id: GO:0051051 +name: negative regulation of transport +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006810 ! transport +relationship: negatively_regulates GO:0006810 ! transport + +[Term] +id: GO:0051055 +name: negative regulation of lipid biosynthetic process +is_a: GO:0009890 ! negative regulation of biosynthetic process +is_a: GO:0045833 ! negative regulation of lipid metabolic process +is_a: GO:0046890 ! regulation of lipid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008610 ! lipid biosynthetic process +relationship: negatively_regulates GO:0008610 ! lipid biosynthetic process + +[Term] +id: GO:0051056 +name: regulation of small GTPase mediated signal transduction +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007264 ! small GTPase mediated signal transduction +relationship: regulates GO:0007264 ! small GTPase mediated signal transduction + +[Term] +id: GO:0051090 +name: regulation of sequence-specific DNA binding transcription factor activity +is_a: GO:0006355 ! regulation of transcription, DNA-dependent +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity +relationship: regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0051091 +name: positive regulation of sequence-specific DNA binding transcription factor activity +is_a: GO:0044093 ! positive regulation of molecular function +is_a: GO:0051090 ! regulation of sequence-specific DNA binding transcription factor activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity +relationship: positively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0051092 +name: positive regulation of NF-kappaB transcription factor activity +is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0051093 +name: negative regulation of developmental process +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032502 ! developmental process +relationship: negatively_regulates GO:0032502 ! developmental process + +[Term] +id: GO:0051094 +name: positive regulation of developmental process +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032502 ! developmental process +relationship: positively_regulates GO:0032502 ! developmental process + +[Term] +id: GO:0051098 +name: regulation of binding +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0005488 ! binding +relationship: regulates GO:0005488 ! binding + +[Term] +id: GO:0051099 +name: positive regulation of binding +is_a: GO:0044093 ! positive regulation of molecular function +is_a: GO:0051098 ! regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0005488 ! binding +relationship: positively_regulates GO:0005488 ! binding + +[Term] +id: GO:0051100 +name: negative regulation of binding +is_a: GO:0044092 ! negative regulation of molecular function +is_a: GO:0051098 ! regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0005488 ! binding +relationship: negatively_regulates GO:0005488 ! binding + +[Term] +id: GO:0051101 +name: regulation of DNA binding +is_a: GO:0051098 ! regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003677 ! DNA binding +relationship: regulates GO:0003677 ! DNA binding + +[Term] +id: GO:0051124 +name: synaptic growth at neuromuscular junction +is_a: GO:0007416 ! synapse assembly +is_a: GO:0007528 ! neuromuscular junction development +is_a: GO:0048589 ! developmental growth + +[Term] +id: GO:0051128 +name: regulation of cellular component organization +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016043 ! cellular component organization +relationship: regulates GO:0016043 ! cellular component organization + +[Term] +id: GO:0051129 +name: negative regulation of cellular component organization +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016043 ! cellular component organization +relationship: negatively_regulates GO:0016043 ! cellular component organization + +[Term] +id: GO:0051130 +name: positive regulation of cellular component organization +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016043 ! cellular component organization +relationship: positively_regulates GO:0016043 ! cellular component organization + +[Term] +id: GO:0051145 +name: smooth muscle cell differentiation +is_a: GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0051146 +name: striated muscle cell differentiation +is_a: GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0051147 +name: regulation of muscle cell differentiation +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042692 ! muscle cell differentiation +relationship: regulates GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0051149 +name: positive regulation of muscle cell differentiation +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0051147 ! regulation of muscle cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042692 ! muscle cell differentiation +relationship: positively_regulates GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0051153 +name: regulation of striated muscle cell differentiation +is_a: GO:0051147 ! regulation of muscle cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051146 ! striated muscle cell differentiation +relationship: regulates GO:0051146 ! striated muscle cell differentiation + +[Term] +id: GO:0051155 +name: positive regulation of striated muscle cell differentiation +is_a: GO:0051149 ! positive regulation of muscle cell differentiation +is_a: GO:0051153 ! regulation of striated muscle cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0051146 ! striated muscle cell differentiation +relationship: positively_regulates GO:0051146 ! striated muscle cell differentiation + +[Term] +id: GO:0051156 +name: glucose 6-phosphate metabolic process +is_a: GO:0006796 ! phosphate-containing compound metabolic process +is_a: GO:0019637 ! organophosphate metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process + +[Term] +id: GO:0051169 +name: nuclear transport +is_a: GO:0046907 ! intracellular transport + +[Term] +id: GO:0051170 +name: nuclear import +is_a: GO:0006913 ! nucleocytoplasmic transport +is_a: GO:0016482 ! cytoplasmic transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0051171 +name: regulation of nitrogen compound metabolic process +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006807 ! nitrogen compound metabolic process +relationship: regulates GO:0006807 ! nitrogen compound metabolic process + +[Term] +id: GO:0051172 +name: negative regulation of nitrogen compound metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0051171 ! regulation of nitrogen compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006807 ! nitrogen compound metabolic process +relationship: negatively_regulates GO:0006807 ! nitrogen compound metabolic process + +[Term] +id: GO:0051173 +name: positive regulation of nitrogen compound metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0051171 ! regulation of nitrogen compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006807 ! nitrogen compound metabolic process +relationship: positively_regulates GO:0006807 ! nitrogen compound metabolic process + +[Term] +id: GO:0051174 +name: regulation of phosphorus metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006793 ! phosphorus metabolic process +relationship: regulates GO:0006793 ! phosphorus metabolic process + +[Term] +id: GO:0051176 +name: positive regulation of sulfur metabolic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0042762 ! regulation of sulfur metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006790 ! sulfur compound metabolic process +relationship: positively_regulates GO:0006790 ! sulfur compound metabolic process + +[Term] +id: GO:0051179 +name: localization +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0051216 +name: cartilage development +is_a: GO:0061448 ! connective tissue development +relationship: part_of GO:0001501 ! skeletal system development +relationship: part_of GO:0048513 ! organ development + +[Term] +id: GO:0051222 +name: positive regulation of protein transport +is_a: GO:0051050 ! positive regulation of transport +is_a: GO:0051223 ! regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0015031 ! protein transport +relationship: positively_regulates GO:0015031 ! protein transport + +[Term] +id: GO:0051223 +name: regulation of protein transport +is_a: GO:0051049 ! regulation of transport +is_a: GO:0070201 ! regulation of establishment of protein localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0015031 ! protein transport +relationship: regulates GO:0015031 ! protein transport + +[Term] +id: GO:0051224 +name: negative regulation of protein transport +is_a: GO:0051051 ! negative regulation of transport +is_a: GO:0051223 ! regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0015031 ! protein transport +relationship: negatively_regulates GO:0015031 ! protein transport + +[Term] +id: GO:0051234 +name: establishment of localization +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0051179 ! localization + +[Term] +id: GO:0051235 +name: maintenance of location +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0051179 ! localization + +[Term] +id: GO:0051239 +name: regulation of multicellular organismal process +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0051240 +name: positive regulation of multicellular organismal process +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032501 ! multicellular organismal process +relationship: positively_regulates GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0051241 +name: negative regulation of multicellular organismal process +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032501 ! multicellular organismal process +relationship: negatively_regulates GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0051246 +name: regulation of protein metabolic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +is_a: GO:0080090 ! regulation of primary metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0019538 ! protein metabolic process +relationship: regulates GO:0019538 ! protein metabolic process + +[Term] +id: GO:0051247 +name: positive regulation of protein metabolic process +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0019538 ! protein metabolic process +relationship: positively_regulates GO:0019538 ! protein metabolic process + +[Term] +id: GO:0051248 +name: negative regulation of protein metabolic process +is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0019538 ! protein metabolic process +relationship: negatively_regulates GO:0019538 ! protein metabolic process + +[Term] +id: GO:0051249 +name: regulation of lymphocyte activation +is_a: GO:0002694 ! regulation of leukocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046649 ! lymphocyte activation +relationship: regulates GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0051250 +name: negative regulation of lymphocyte activation +is_a: GO:0002695 ! negative regulation of leukocyte activation +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046649 ! lymphocyte activation +relationship: negatively_regulates GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0051251 +name: positive regulation of lymphocyte activation +is_a: GO:0002696 ! positive regulation of leukocyte activation +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046649 ! lymphocyte activation +relationship: positively_regulates GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0051252 +name: regulation of RNA metabolic process +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016070 ! RNA metabolic process +relationship: regulates GO:0016070 ! RNA metabolic process + +[Term] +id: GO:0051253 +name: negative regulation of RNA metabolic process +is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process +is_a: GO:0051252 ! regulation of RNA metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016070 ! RNA metabolic process +relationship: negatively_regulates GO:0016070 ! RNA metabolic process + +[Term] +id: GO:0051254 +name: positive regulation of RNA metabolic process +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process +is_a: GO:0051252 ! regulation of RNA metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016070 ! RNA metabolic process +relationship: positively_regulates GO:0016070 ! RNA metabolic process + +[Term] +id: GO:0051259 +name: protein oligomerization +is_a: GO:0006461 ! protein complex assembly + +[Term] +id: GO:0051270 +name: regulation of cellular component movement +is_a: GO:0032879 ! regulation of localization +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006928 ! cellular component movement +relationship: regulates GO:0006928 ! cellular component movement + +[Term] +id: GO:0051271 +name: negative regulation of cellular component movement +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051270 ! regulation of cellular component movement +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006928 ! cellular component movement +relationship: negatively_regulates GO:0006928 ! cellular component movement + +[Term] +id: GO:0051272 +name: positive regulation of cellular component movement +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051270 ! regulation of cellular component movement +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006928 ! cellular component movement +relationship: positively_regulates GO:0006928 ! cellular component movement + +[Term] +id: GO:0051276 +name: chromosome organization +is_a: GO:0006996 ! organelle organization + +[Term] +id: GO:0051291 +name: protein heterooligomerization +is_a: GO:0051259 ! protein oligomerization + +[Term] +id: GO:0051297 +name: centrosome organization +is_a: GO:0031023 ! microtubule organizing center organization + +[Term] +id: GO:0051301 +name: cell division +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0051302 +name: regulation of cell division +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051301 ! cell division +relationship: regulates GO:0051301 ! cell division + +[Term] +id: GO:0051321 +name: meiotic cell cycle +is_a: GO:0007049 ! cell cycle +is_a: GO:0048610 ! cellular process involved in reproduction +intersection_of: GO:0007049 ! cell cycle +intersection_of: has_part GO:0007126 ! meiosis + +[Term] +id: GO:0051336 +name: regulation of hydrolase activity +is_a: GO:0050790 ! regulation of catalytic activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016787 ! hydrolase activity +relationship: regulates GO:0016787 ! hydrolase activity + +[Term] +id: GO:0051338 +name: regulation of transferase activity +is_a: GO:0050790 ! regulation of catalytic activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016740 ! transferase activity +relationship: regulates GO:0016740 ! transferase activity + +[Term] +id: GO:0051345 +name: positive regulation of hydrolase activity +is_a: GO:0043085 ! positive regulation of catalytic activity +is_a: GO:0051336 ! regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016787 ! hydrolase activity +relationship: positively_regulates GO:0016787 ! hydrolase activity + +[Term] +id: GO:0051346 +name: negative regulation of hydrolase activity +is_a: GO:0043086 ! negative regulation of catalytic activity +is_a: GO:0051336 ! regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016787 ! hydrolase activity +relationship: negatively_regulates GO:0016787 ! hydrolase activity + +[Term] +id: GO:0051347 +name: positive regulation of transferase activity +is_a: GO:0043085 ! positive regulation of catalytic activity +is_a: GO:0051338 ! regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016740 ! transferase activity +relationship: positively_regulates GO:0016740 ! transferase activity + +[Term] +id: GO:0051348 +name: negative regulation of transferase activity +is_a: GO:0043086 ! negative regulation of catalytic activity +is_a: GO:0051338 ! regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016740 ! transferase activity +relationship: negatively_regulates GO:0016740 ! transferase activity + +[Term] +id: GO:0051402 +name: neuron apoptotic process +is_a: GO:0070997 ! neuron death +is_a: GO:0097285 ! cell-type specific apoptotic process + +[Term] +id: GO:0051403 +name: stress-activated MAPK cascade +is_a: GO:0000165 ! MAPK cascade +is_a: GO:0031098 ! stress-activated protein kinase signaling cascade + +[Term] +id: GO:0051427 +name: hormone receptor binding +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0051445 +name: regulation of meiotic cell cycle +is_a: GO:0051726 ! regulation of cell cycle +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051321 ! meiotic cell cycle +relationship: regulates GO:0051321 ! meiotic cell cycle + +[Term] +id: GO:0051480 +name: cytosolic calcium ion homeostasis +is_a: GO:0006874 ! cellular calcium ion homeostasis + +[Term] +id: GO:0051492 +name: regulation of stress fiber assembly +is_a: GO:0032231 ! regulation of actin filament bundle assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043149 ! stress fiber assembly +relationship: regulates GO:0043149 ! stress fiber assembly + +[Term] +id: GO:0051493 +name: regulation of cytoskeleton organization +is_a: GO:0033043 ! regulation of organelle organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007010 ! cytoskeleton organization +relationship: regulates GO:0007010 ! cytoskeleton organization + +[Term] +id: GO:0051495 +name: positive regulation of cytoskeleton organization +is_a: GO:0010638 ! positive regulation of organelle organization +is_a: GO:0051493 ! regulation of cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007010 ! cytoskeleton organization +relationship: positively_regulates GO:0007010 ! cytoskeleton organization + +[Term] +id: GO:0051496 +name: positive regulation of stress fiber assembly +is_a: GO:0032233 ! positive regulation of actin filament bundle assembly +is_a: GO:0051492 ! regulation of stress fiber assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0043149 ! stress fiber assembly +relationship: positively_regulates GO:0043149 ! stress fiber assembly + +[Term] +id: GO:0051593 +name: response to folic acid +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0033273 ! response to vitamin +is_a: GO:0043200 ! response to amino acid stimulus + +[Term] +id: GO:0051594 +name: detection of glucose +is_a: GO:0009732 ! detection of hexose stimulus +is_a: GO:0009749 ! response to glucose stimulus + +[Term] +id: GO:0051603 +name: proteolysis involved in cellular protein catabolic process +is_a: GO:0006508 ! proteolysis +intersection_of: GO:0006508 ! proteolysis +intersection_of: part_of GO:0044257 ! cellular protein catabolic process +relationship: part_of GO:0044257 ! cellular protein catabolic process + +[Term] +id: GO:0051606 +name: detection of stimulus +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0051640 +name: organelle localization +is_a: GO:0051641 ! cellular localization + +[Term] +id: GO:0051641 +name: cellular localization +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0051179 ! localization + +[Term] +id: GO:0051648 +name: vesicle localization +is_a: GO:0051640 ! organelle localization + +[Term] +id: GO:0051649 +name: establishment of localization in cell +is_a: GO:0051234 ! establishment of localization +intersection_of: GO:0051234 ! establishment of localization +intersection_of: occurs_in GO:0005623 ! cell +relationship: part_of GO:0051641 ! cellular localization + +[Term] +id: GO:0051650 +name: establishment of vesicle localization +is_a: GO:0051649 ! establishment of localization in cell +is_a: GO:0051656 ! establishment of organelle localization +relationship: part_of GO:0051648 ! vesicle localization + +[Term] +id: GO:0051651 +name: maintenance of location in cell +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0051235 ! maintenance of location +relationship: part_of GO:0051641 ! cellular localization + +[Term] +id: GO:0051656 +name: establishment of organelle localization +is_a: GO:0051234 ! establishment of localization +relationship: part_of GO:0051640 ! organelle localization + +[Term] +id: GO:0051674 +name: localization of cell +is_a: GO:0051179 ! localization + +[Term] +id: GO:0051704 +name: multi-organism process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0051707 +name: response to other organism +is_a: GO:0009607 ! response to biotic stimulus +is_a: GO:0051704 ! multi-organism process + +[Term] +id: GO:0051716 +name: cellular response to stimulus +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0051726 +name: regulation of cell cycle +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007049 ! cell cycle +relationship: regulates GO:0007049 ! cell cycle + +[Term] +id: GO:0051783 +name: regulation of nuclear division +is_a: GO:0033043 ! regulation of organelle organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000280 ! nuclear division +relationship: regulates GO:0000280 ! nuclear division + +[Term] +id: GO:0051785 +name: positive regulation of nuclear division +is_a: GO:0010638 ! positive regulation of organelle organization +is_a: GO:0051783 ! regulation of nuclear division +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0000280 ! nuclear division +relationship: positively_regulates GO:0000280 ! nuclear division + +[Term] +id: GO:0051890 +name: regulation of cardioblast differentiation +is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:2000736 ! regulation of stem cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010002 ! cardioblast differentiation +relationship: regulates GO:0010002 ! cardioblast differentiation + +[Term] +id: GO:0051893 +name: regulation of focal adhesion assembly +is_a: GO:0001952 ! regulation of cell-matrix adhesion +is_a: GO:0090109 ! regulation of cell-substrate junction assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048041 ! focal adhesion assembly +relationship: regulates GO:0048041 ! focal adhesion assembly + +[Term] +id: GO:0051894 +name: positive regulation of focal adhesion assembly +is_a: GO:0001954 ! positive regulation of cell-matrix adhesion +is_a: GO:0051893 ! regulation of focal adhesion assembly +is_a: GO:1901890 ! positive regulation of cell junction assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048041 ! focal adhesion assembly +relationship: positively_regulates GO:0048041 ! focal adhesion assembly + +[Term] +id: GO:0051896 +name: regulation of protein kinase B signaling cascade +is_a: GO:0010627 ! regulation of intracellular protein kinase cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043491 ! protein kinase B signaling cascade +relationship: regulates GO:0043491 ! protein kinase B signaling cascade + +[Term] +id: GO:0051898 +name: negative regulation of protein kinase B signaling cascade +is_a: GO:0010741 ! negative regulation of intracellular protein kinase cascade +is_a: GO:0051896 ! regulation of protein kinase B signaling cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0043491 ! protein kinase B signaling cascade +relationship: negatively_regulates GO:0043491 ! protein kinase B signaling cascade + +[Term] +id: GO:0051924 +name: regulation of calcium ion transport +is_a: GO:0010959 ! regulation of metal ion transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006816 ! calcium ion transport +relationship: regulates GO:0006816 ! calcium ion transport + +[Term] +id: GO:0051960 +name: regulation of nervous system development +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007399 ! nervous system development +relationship: regulates GO:0007399 ! nervous system development + +[Term] +id: GO:0051961 +name: negative regulation of nervous system development +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0051960 ! regulation of nervous system development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007399 ! nervous system development +relationship: negatively_regulates GO:0007399 ! nervous system development + +[Term] +id: GO:0051962 +name: positive regulation of nervous system development +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051960 ! regulation of nervous system development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007399 ! nervous system development +relationship: positively_regulates GO:0007399 ! nervous system development + +[Term] +id: GO:0051963 +name: regulation of synapse assembly +is_a: GO:0044087 ! regulation of cellular component biogenesis +is_a: GO:0050807 ! regulation of synapse organization +is_a: GO:0051960 ! regulation of nervous system development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007416 ! synapse assembly +relationship: regulates GO:0007416 ! synapse assembly + +[Term] +id: GO:0051964 +name: negative regulation of synapse assembly +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051129 ! negative regulation of cellular component organization +is_a: GO:0051961 ! negative regulation of nervous system development +is_a: GO:0051963 ! regulation of synapse assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007416 ! synapse assembly +relationship: negatively_regulates GO:0007416 ! synapse assembly + +[Term] +id: GO:0051965 +name: positive regulation of synapse assembly +is_a: GO:0044089 ! positive regulation of cellular component biogenesis +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051130 ! positive regulation of cellular component organization +is_a: GO:0051962 ! positive regulation of nervous system development +is_a: GO:0051963 ! regulation of synapse assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007416 ! synapse assembly +relationship: positively_regulates GO:0007416 ! synapse assembly + +[Term] +id: GO:0051969 +name: regulation of transmission of nerve impulse +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0023051 ! regulation of signaling +is_a: GO:0031644 ! regulation of neurological system process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0019226 ! transmission of nerve impulse +relationship: regulates GO:0019226 ! transmission of nerve impulse + +[Term] +id: GO:0051983 +name: regulation of chromosome segregation +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007059 ! chromosome segregation +relationship: regulates GO:0007059 ! chromosome segregation + +[Term] +id: GO:0052547 +name: regulation of peptidase activity +is_a: GO:0051336 ! regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008233 ! peptidase activity +relationship: regulates GO:0008233 ! peptidase activity + +[Term] +id: GO:0052548 +name: regulation of endopeptidase activity +is_a: GO:0052547 ! regulation of peptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004175 ! endopeptidase activity +relationship: regulates GO:0004175 ! endopeptidase activity + +[Term] +id: GO:0055001 +name: muscle cell development +is_a: GO:0048468 ! cell development +relationship: part_of GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0055002 +name: striated muscle cell development +is_a: GO:0055001 ! muscle cell development +relationship: part_of GO:0051146 ! striated muscle cell differentiation + +[Term] +id: GO:0055007 +name: cardiac muscle cell differentiation +is_a: GO:0035051 ! cardiocyte differentiation +is_a: GO:0051146 ! striated muscle cell differentiation +relationship: part_of GO:0048738 ! cardiac muscle tissue development + +[Term] +id: GO:0055008 +name: cardiac muscle tissue morphogenesis +is_a: GO:0060415 ! muscle tissue morphogenesis +relationship: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0048738 ! cardiac muscle tissue development + +[Term] +id: GO:0055010 +name: ventricular cardiac muscle tissue morphogenesis +is_a: GO:0055008 ! cardiac muscle tissue morphogenesis +relationship: part_of GO:0003208 ! cardiac ventricle morphogenesis +relationship: part_of GO:0003229 ! ventricular cardiac muscle tissue development + +[Term] +id: GO:0055017 +name: cardiac muscle tissue growth +is_a: GO:0040007 ! growth +relationship: part_of GO:0048738 ! cardiac muscle tissue development +relationship: part_of GO:0060419 ! heart growth + +[Term] +id: GO:0055024 +name: regulation of cardiac muscle tissue development +is_a: GO:0016202 ! regulation of striated muscle tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048738 ! cardiac muscle tissue development +relationship: regulates GO:0048738 ! cardiac muscle tissue development + +[Term] +id: GO:0055057 +name: neuroblast division +is_a: GO:0048103 ! somatic stem cell division +relationship: part_of GO:0007405 ! neuroblast proliferation + +[Term] +id: GO:0055065 +name: metal ion homeostasis +is_a: GO:0055080 ! cation homeostasis + +[Term] +id: GO:0055074 +name: calcium ion homeostasis +is_a: GO:0055065 ! metal ion homeostasis +is_a: GO:0072507 ! divalent inorganic cation homeostasis + +[Term] +id: GO:0055080 +name: cation homeostasis +is_a: GO:0050801 ! ion homeostasis + +[Term] +id: GO:0055082 +name: cellular chemical homeostasis +is_a: GO:0019725 ! cellular homeostasis +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0055085 +name: transmembrane transport +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0055086 +name: nucleobase-containing small molecule metabolic process +is_a: GO:0006139 ! nucleobase-containing compound metabolic process +is_a: GO:0044281 ! small molecule metabolic process + +[Term] +id: GO:0055088 +name: lipid homeostasis +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0055092 +name: sterol homeostasis +is_a: GO:0055088 ! lipid homeostasis + +[Term] +id: GO:0055123 +name: digestive system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0060004 +name: reflex +is_a: GO:0009605 ! response to external stimulus + +[Term] +id: GO:0060013 +name: righting reflex +is_a: GO:0060004 ! reflex + +[Term] +id: GO:0060019 +name: radial glial cell differentiation +is_a: GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0060021 +name: palate development +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0060026 +name: convergent extension +is_a: GO:0002009 ! morphogenesis of an epithelium + +[Term] +id: GO:0060028 +name: convergent extension involved in axis elongation +is_a: GO:0060026 ! convergent extension +intersection_of: GO:0060026 ! convergent extension +intersection_of: part_of GO:0003401 ! axis elongation +relationship: part_of GO:0003401 ! axis elongation + +[Term] +id: GO:0060029 +name: convergent extension involved in organogenesis +is_a: GO:0060026 ! convergent extension +intersection_of: GO:0060026 ! convergent extension +intersection_of: part_of GO:0048513 ! organ development + +[Term] +id: GO:0060033 +name: anatomical structure regression +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0009653 ! anatomical structure morphogenesis + +[Term] +id: GO:0060038 +name: cardiac muscle cell proliferation +is_a: GO:0014855 ! striated muscle cell proliferation +relationship: part_of GO:0055017 ! cardiac muscle tissue growth + +[Term] +id: GO:0060039 +name: pericardium development +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0060041 +name: retina development in camera-type eye +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0043010 ! camera-type eye development + +[Term] +id: GO:0060042 +name: retina morphogenesis in camera-type eye +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048593 ! camera-type eye morphogenesis +relationship: part_of GO:0060041 ! retina development in camera-type eye + +[Term] +id: GO:0060047 +name: heart contraction +is_a: GO:0003015 ! heart process +relationship: part_of GO:0008015 ! blood circulation + +[Term] +id: GO:0060054 +name: positive regulation of epithelial cell proliferation involved in wound healing +is_a: GO:0050679 ! positive regulation of epithelial cell proliferation +intersection_of: GO:0050679 ! positive regulation of epithelial cell proliferation +intersection_of: part_of GO:0042060 ! wound healing +relationship: part_of GO:0042060 ! wound healing + +[Term] +id: GO:0060055 +name: angiogenesis involved in wound healing +is_a: GO:0001525 ! angiogenesis +intersection_of: GO:0001525 ! angiogenesis +intersection_of: part_of GO:0042060 ! wound healing +relationship: part_of GO:0042060 ! wound healing + +[Term] +id: GO:0060059 +name: embryonic retina morphogenesis in camera-type eye +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0060042 ! retina morphogenesis in camera-type eye + +[Term] +id: GO:0060061 +name: Spemann organizer formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0031128 ! developmental induction + +[Term] +id: GO:0060065 +name: uterus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +is_a: GO:0048608 ! reproductive structure development + +[Term] +id: GO:0060066 +name: oviduct development +is_a: GO:0035295 ! tube development +is_a: GO:0048608 ! reproductive structure development + +[Term] +id: GO:0060067 +name: cervix development +is_a: GO:0048608 ! reproductive structure development + +[Term] +id: GO:0060068 +name: vagina development +is_a: GO:0030540 ! female genitalia development + +[Term] +id: GO:0060070 +name: canonical Wnt receptor signaling pathway +is_a: GO:0016055 ! Wnt receptor signaling pathway + +[Term] +id: GO:0060071 +name: Wnt receptor signaling pathway, planar cell polarity pathway +is_a: GO:0035567 ! non-canonical Wnt receptor signaling pathway +is_a: GO:0090175 ! regulation of establishment of planar polarity + +[Term] +id: GO:0060089 +name: molecular transducer activity +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0060126 +name: somatotropin secreting cell differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0021984 ! adenohypophysis development + +[Term] +id: GO:0060129 +name: thyroid-stimulating hormone-secreting cell differentiation +is_a: GO:0002067 ! glandular epithelial cell differentiation +is_a: GO:0061101 ! neuroendocrine cell differentiation +relationship: part_of GO:0021984 ! adenohypophysis development + +[Term] +id: GO:0060135 +name: maternal process involved in female pregnancy +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048609 ! multicellular organismal reproductive process +relationship: part_of GO:0007565 ! female pregnancy + +[Term] +id: GO:0060157 +name: urinary bladder development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0060173 +name: limb development +is_a: GO:0048736 ! appendage development + +[Term] +id: GO:0060218 +name: hematopoietic stem cell differentiation +is_a: GO:0048863 ! stem cell differentiation +relationship: part_of GO:0030097 ! hemopoiesis + +[Term] +id: GO:0060231 +name: mesenchymal to epithelial transition +is_a: GO:0003382 ! epithelial cell morphogenesis + +[Term] +id: GO:0060249 +name: anatomical structure homeostasis +is_a: GO:0042592 ! homeostatic process + +[Term] +id: GO:0060255 +name: regulation of macromolecule metabolic process +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043170 ! macromolecule metabolic process +relationship: regulates GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0060260 +name: regulation of transcription initiation from RNA polymerase II promoter +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:2000142 ! regulation of DNA-dependent transcription, initiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter +relationship: regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter + +[Term] +id: GO:0060271 +name: cilium morphogenesis +is_a: GO:0048858 ! cell projection morphogenesis + +[Term] +id: GO:0060272 +name: embryonic skeletal joint morphogenesis +is_a: GO:0048704 ! embryonic skeletal system morphogenesis +relationship: part_of GO:0072498 ! embryonic skeletal joint development + +[Term] +id: GO:0060284 +name: regulation of cell development +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048468 ! cell development +relationship: regulates GO:0048468 ! cell development + +[Term] +id: GO:0060322 +name: head development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0060323 +name: head morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0010171 ! body morphogenesis +relationship: part_of GO:0060322 ! head development + +[Term] +id: GO:0060324 +name: face development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0060322 ! head development + +[Term] +id: GO:0060325 +name: face morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0060323 ! head morphogenesis +relationship: part_of GO:0060324 ! face development + +[Term] +id: GO:0060326 +name: cell chemotaxis +is_a: GO:0006935 ! chemotaxis +is_a: GO:0016477 ! cell migration +is_a: GO:0070887 ! cellular response to chemical stimulus + +[Term] +id: GO:0060337 +name: type I interferon-mediated signaling pathway +is_a: GO:0019221 ! cytokine-mediated signaling pathway +is_a: GO:0071357 ! cellular response to type I interferon + +[Term] +id: GO:0060338 +name: regulation of type I interferon-mediated signaling pathway +is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway +is_a: GO:0045088 ! regulation of innate immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060337 ! type I interferon-mediated signaling pathway +relationship: regulates GO:0060337 ! type I interferon-mediated signaling pathway + +[Term] +id: GO:0060340 +name: positive regulation of type I interferon-mediated signaling pathway +is_a: GO:0001961 ! positive regulation of cytokine-mediated signaling pathway +is_a: GO:0060338 ! regulation of type I interferon-mediated signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060337 ! type I interferon-mediated signaling pathway +relationship: positively_regulates GO:0060337 ! type I interferon-mediated signaling pathway + +[Term] +id: GO:0060341 +name: regulation of cellular localization +is_a: GO:0032879 ! regulation of localization +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051641 ! cellular localization +relationship: regulates GO:0051641 ! cellular localization + +[Term] +id: GO:0060343 +name: trabecula formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0009887 ! organ morphogenesis +relationship: part_of GO:0061383 ! trabecula morphogenesis + +[Term] +id: GO:0060346 +name: bone trabecula formation +is_a: GO:0060343 ! trabecula formation +relationship: part_of GO:0048705 ! skeletal system morphogenesis +relationship: part_of GO:0061430 ! bone trabecula morphogenesis + +[Term] +id: GO:0060348 +name: bone development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001501 ! skeletal system development + +[Term] +id: GO:0060349 +name: bone morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048705 ! skeletal system morphogenesis +relationship: part_of GO:0060348 ! bone development + +[Term] +id: GO:0060411 +name: cardiac septum morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0003206 ! cardiac chamber morphogenesis +relationship: part_of GO:0003279 ! cardiac septum development + +[Term] +id: GO:0060412 +name: ventricular septum morphogenesis +is_a: GO:0060411 ! cardiac septum morphogenesis +relationship: part_of GO:0003281 ! ventricular septum development + +[Term] +id: GO:0060415 +name: muscle tissue morphogenesis +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0048644 ! muscle organ morphogenesis + +[Term] +id: GO:0060419 +name: heart growth +is_a: GO:0035265 ! organ growth +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0060423 +name: foregut regionalization +is_a: GO:0009952 ! anterior/posterior pattern specification + +[Term] +id: GO:0060424 +name: lung field specification +is_a: GO:0010092 ! specification of organ identity +is_a: GO:0060423 ! foregut regionalization +relationship: part_of GO:0060431 ! primary lung bud formation + +[Term] +id: GO:0060425 +name: lung morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0060428 +name: lung epithelium development +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0060429 +name: epithelium development +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0060431 +name: primary lung bud formation +is_a: GO:0016331 ! morphogenesis of embryonic epithelium +is_a: GO:0048645 ! organ formation +is_a: GO:0060441 ! epithelial tube branching involved in lung morphogenesis +is_a: GO:0060572 ! morphogenesis of an epithelial bud + +[Term] +id: GO:0060433 +name: bronchus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0060541 ! respiratory system development + +[Term] +id: GO:0060438 +name: trachea development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0060541 ! respiratory system development + +[Term] +id: GO:0060439 +name: trachea morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0060438 ! trachea development + +[Term] +id: GO:0060440 +name: trachea formation +is_a: GO:0048645 ! organ formation +relationship: part_of GO:0060439 ! trachea morphogenesis + +[Term] +id: GO:0060441 +name: epithelial tube branching involved in lung morphogenesis +is_a: GO:0048754 ! branching morphogenesis of an epithelial tube +intersection_of: GO:0048754 ! branching morphogenesis of an epithelial tube +intersection_of: part_of GO:0060425 ! lung morphogenesis +relationship: part_of GO:0060425 ! lung morphogenesis + +[Term] +id: GO:0060442 +name: branching involved in prostate gland morphogenesis +is_a: GO:0060740 ! prostate gland epithelium morphogenesis +is_a: GO:0061138 ! morphogenesis of a branching epithelium +intersection_of: GO:0061138 ! morphogenesis of a branching epithelium +intersection_of: part_of GO:0060512 ! prostate gland morphogenesis + +[Term] +id: GO:0060443 +name: mammary gland morphogenesis +is_a: GO:0022612 ! gland morphogenesis +relationship: part_of GO:0030879 ! mammary gland development + +[Term] +id: GO:0060444 +name: branching involved in mammary gland duct morphogenesis +is_a: GO:0048754 ! branching morphogenesis of an epithelial tube +intersection_of: GO:0061138 ! morphogenesis of a branching epithelium +intersection_of: part_of GO:0060603 ! mammary gland duct morphogenesis +relationship: part_of GO:0060603 ! mammary gland duct morphogenesis + +[Term] +id: GO:0060479 +name: lung cell differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0060482 +name: lobar bronchus development +is_a: GO:0060433 ! bronchus development + +[Term] +id: GO:0060484 +name: lung-associated mesenchyme development +is_a: GO:0060485 ! mesenchyme development +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0060485 +name: mesenchyme development +is_a: GO:0009888 ! tissue development +relationship: part_of GO:0048513 ! organ development + +[Term] +id: GO:0060487 +name: lung epithelial cell differentiation +is_a: GO:0030855 ! epithelial cell differentiation +is_a: GO:0060479 ! lung cell differentiation +relationship: part_of GO:0060428 ! lung epithelium development + +[Term] +id: GO:0060491 +name: regulation of cell projection assembly +is_a: GO:0031344 ! regulation of cell projection organization +is_a: GO:0044087 ! regulation of cellular component biogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030031 ! cell projection assembly +relationship: regulates GO:0030031 ! cell projection assembly + +[Term] +id: GO:0060492 +name: lung induction +is_a: GO:0001759 ! organ induction +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0061046 ! regulation of branching involved in lung morphogenesis +relationship: positively_regulates GO:0060424 ! lung field specification + +[Term] +id: GO:0060501 +name: positive regulation of epithelial cell proliferation involved in lung morphogenesis +is_a: GO:0050679 ! positive regulation of epithelial cell proliferation +is_a: GO:2000794 ! regulation of epithelial cell proliferation involved in lung morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis +relationship: positively_regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis + +[Term] +id: GO:0060502 +name: epithelial cell proliferation involved in lung morphogenesis +is_a: GO:0050673 ! epithelial cell proliferation +intersection_of: GO:0050673 ! epithelial cell proliferation +intersection_of: part_of GO:0060425 ! lung morphogenesis +relationship: part_of GO:0060425 ! lung morphogenesis +relationship: part_of GO:0060428 ! lung epithelium development + +[Term] +id: GO:0060512 +name: prostate gland morphogenesis +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0009887 ! organ morphogenesis +is_a: GO:0022612 ! gland morphogenesis +relationship: part_of GO:0030850 ! prostate gland development + +[Term] +id: GO:0060513 +name: prostatic bud formation +is_a: GO:0016331 ! morphogenesis of embryonic epithelium +is_a: GO:0048645 ! organ formation +is_a: GO:0060572 ! morphogenesis of an epithelial bud +is_a: GO:0060601 ! lateral sprouting from an epithelium +is_a: GO:0060740 ! prostate gland epithelium morphogenesis + +[Term] +id: GO:0060525 +name: prostate glandular acinus development +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030850 ! prostate gland development + +[Term] +id: GO:0060526 +name: prostate glandular acinus morphogenesis +is_a: GO:0060740 ! prostate gland epithelium morphogenesis +relationship: part_of GO:0060525 ! prostate glandular acinus development + +[Term] +id: GO:0060527 +name: prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis +is_a: GO:0060442 ! branching involved in prostate gland morphogenesis +relationship: part_of GO:0060526 ! prostate glandular acinus morphogenesis + +[Term] +id: GO:0060534 +name: trachea cartilage development +is_a: GO:0051216 ! cartilage development +relationship: part_of GO:0060438 ! trachea development + +[Term] +id: GO:0060535 +name: trachea cartilage morphogenesis +is_a: GO:0060536 ! cartilage morphogenesis +relationship: part_of GO:0060439 ! trachea morphogenesis +relationship: part_of GO:0060534 ! trachea cartilage development + +[Term] +id: GO:0060536 +name: cartilage morphogenesis +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0009887 ! organ morphogenesis +relationship: part_of GO:0051216 ! cartilage development + +[Term] +id: GO:0060537 +name: muscle tissue development +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0060538 +name: skeletal muscle organ development +is_a: GO:0007517 ! muscle organ development + +[Term] +id: GO:0060541 +name: respiratory system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0060548 +name: negative regulation of cell death +is_a: GO:0010941 ! regulation of cell death +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008219 ! cell death +relationship: negatively_regulates GO:0008219 ! cell death + +[Term] +id: GO:0060560 +name: developmental growth involved in morphogenesis +is_a: GO:0048589 ! developmental growth +intersection_of: GO:0048589 ! developmental growth +intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis +relationship: part_of GO:0009653 ! anatomical structure morphogenesis + +[Term] +id: GO:0060561 +name: apoptotic process involved in morphogenesis +is_a: GO:0006915 ! apoptotic process +is_a: GO:0010623 ! developmental programmed cell death +is_a: GO:0044767 ! single-organism developmental process +intersection_of: GO:0006915 ! apoptotic process +intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis +relationship: part_of GO:0009653 ! anatomical structure morphogenesis + +[Term] +id: GO:0060562 +name: epithelial tube morphogenesis +is_a: GO:0002009 ! morphogenesis of an epithelium +is_a: GO:0035239 ! tube morphogenesis + +[Term] +id: GO:0060563 +name: neuroepithelial cell differentiation +is_a: GO:0002065 ! columnar/cuboidal epithelial cell differentiation + +[Term] +id: GO:0060571 +name: morphogenesis of an epithelial fold +is_a: GO:0002009 ! morphogenesis of an epithelium + +[Term] +id: GO:0060572 +name: morphogenesis of an epithelial bud +is_a: GO:0060571 ! morphogenesis of an epithelial fold + +[Term] +id: GO:0060592 +name: mammary gland formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0060443 ! mammary gland morphogenesis + +[Term] +id: GO:0060596 +name: mammary placode formation +is_a: GO:0060788 ! ectodermal placode formation +relationship: part_of GO:0060592 ! mammary gland formation + +[Term] +id: GO:0060599 +name: lateral sprouting involved in mammary gland duct morphogenesis +is_a: GO:0060601 ! lateral sprouting from an epithelium +intersection_of: GO:0060601 ! lateral sprouting from an epithelium +intersection_of: part_of GO:0060444 ! branching involved in mammary gland duct morphogenesis +relationship: part_of GO:0060444 ! branching involved in mammary gland duct morphogenesis + +[Term] +id: GO:0060600 +name: dichotomous subdivision of an epithelial terminal unit +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0061138 ! morphogenesis of a branching epithelium + +[Term] +id: GO:0060601 +name: lateral sprouting from an epithelium +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0061138 ! morphogenesis of a branching epithelium + +[Term] +id: GO:0060602 +name: branch elongation of an epithelium +is_a: GO:0003401 ! axis elongation +relationship: part_of GO:0061138 ! morphogenesis of a branching epithelium + +[Term] +id: GO:0060603 +name: mammary gland duct morphogenesis +is_a: GO:0060562 ! epithelial tube morphogenesis +relationship: part_of GO:0060443 ! mammary gland morphogenesis +relationship: part_of GO:0061180 ! mammary gland epithelium development + +[Term] +id: GO:0060606 +name: tube closure +is_a: GO:0035148 ! tube formation + +[Term] +id: GO:0060612 +name: adipose tissue development +is_a: GO:0061448 ! connective tissue development +relationship: part_of GO:0048513 ! organ development + +[Term] +id: GO:0060627 +name: regulation of vesicle-mediated transport +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016192 ! vesicle-mediated transport +relationship: regulates GO:0016192 ! vesicle-mediated transport + +[Term] +id: GO:0060633 +name: negative regulation of transcription initiation from RNA polymerase II promoter +is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter +is_a: GO:2000143 ! negative regulation of DNA-dependent transcription, initiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter +relationship: negatively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter + +[Term] +id: GO:0060638 +name: mesenchymal-epithelial cell signaling +is_a: GO:0007267 ! cell-cell signaling + +[Term] +id: GO:0060644 +name: mammary gland epithelial cell differentiation +is_a: GO:0030855 ! epithelial cell differentiation +relationship: part_of GO:0061180 ! mammary gland epithelium development + +[Term] +id: GO:0060669 +name: embryonic placenta morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0001892 ! embryonic placenta development + +[Term] +id: GO:0060675 +name: ureteric bud morphogenesis +is_a: GO:0060562 ! epithelial tube morphogenesis +relationship: part_of GO:0001657 ! ureteric bud development + +[Term] +id: GO:0060678 +name: dichotomous subdivision of terminal units involved in ureteric bud branching +is_a: GO:0060600 ! dichotomous subdivision of an epithelial terminal unit +intersection_of: GO:0060600 ! dichotomous subdivision of an epithelial terminal unit +intersection_of: part_of GO:0001658 ! branching involved in ureteric bud morphogenesis +relationship: part_of GO:0001658 ! branching involved in ureteric bud morphogenesis + +[Term] +id: GO:0060685 +name: regulation of prostatic bud formation +is_a: GO:0003156 ! regulation of organ formation +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0060688 ! regulation of morphogenesis of a branching structure +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060513 ! prostatic bud formation +relationship: regulates GO:0060513 ! prostatic bud formation + +[Term] +id: GO:0060686 +name: negative regulation of prostatic bud formation +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0060685 ! regulation of prostatic bud formation +is_a: GO:2000242 ! negative regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0060513 ! prostatic bud formation +relationship: negatively_regulates GO:0060513 ! prostatic bud formation + +[Term] +id: GO:0060687 +name: regulation of branching involved in prostate gland morphogenesis +is_a: GO:0060688 ! regulation of morphogenesis of a branching structure +is_a: GO:2000027 ! regulation of organ morphogenesis +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060442 ! branching involved in prostate gland morphogenesis +relationship: regulates GO:0060442 ! branching involved in prostate gland morphogenesis + +[Term] +id: GO:0060688 +name: regulation of morphogenesis of a branching structure +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001763 ! morphogenesis of a branching structure +relationship: regulates GO:0001763 ! morphogenesis of a branching structure + +[Term] +id: GO:0060710 +name: chorio-allantoic fusion +is_a: GO:0016337 ! cell-cell adhesion +relationship: part_of GO:0060713 ! labyrinthine layer morphogenesis + +[Term] +id: GO:0060711 +name: labyrinthine layer development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001892 ! embryonic placenta development + +[Term] +id: GO:0060713 +name: labyrinthine layer morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0060669 ! embryonic placenta morphogenesis +relationship: part_of GO:0060711 ! labyrinthine layer development + +[Term] +id: GO:0060740 +name: prostate gland epithelium morphogenesis +is_a: GO:0002009 ! morphogenesis of an epithelium +is_a: GO:0003006 ! developmental process involved in reproduction +relationship: part_of GO:0060512 ! prostate gland morphogenesis + +[Term] +id: GO:0060742 +name: epithelial cell differentiation involved in prostate gland development +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0030855 ! epithelial cell differentiation +is_a: GO:0048610 ! cellular process involved in reproduction +intersection_of: GO:0030855 ! epithelial cell differentiation +intersection_of: part_of GO:0030850 ! prostate gland development +relationship: part_of GO:0030850 ! prostate gland development + +[Term] +id: GO:0060744 +name: mammary gland branching involved in thelarche +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0060444 ! branching involved in mammary gland duct morphogenesis +intersection_of: GO:0060444 ! branching involved in mammary gland duct morphogenesis +intersection_of: part_of GO:0042695 ! thelarche +relationship: part_of GO:0042695 ! thelarche + +[Term] +id: GO:0060745 +name: mammary gland branching involved in pregnancy +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0060135 ! maternal process involved in female pregnancy +is_a: GO:0060444 ! branching involved in mammary gland duct morphogenesis + +[Term] +id: GO:0060748 +name: tertiary branching involved in mammary gland duct morphogenesis +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0060444 ! branching involved in mammary gland duct morphogenesis +relationship: part_of GO:0060745 ! mammary gland branching involved in pregnancy + +[Term] +id: GO:0060749 +name: mammary gland alveolus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061377 ! mammary gland lobule development + +[Term] +id: GO:0060750 +name: epithelial cell proliferation involved in mammary gland duct elongation +is_a: GO:0033598 ! mammary gland epithelial cell proliferation +intersection_of: GO:0033598 ! mammary gland epithelial cell proliferation +intersection_of: part_of GO:0060751 ! branch elongation involved in mammary gland duct branching +relationship: part_of GO:0060751 ! branch elongation involved in mammary gland duct branching + +[Term] +id: GO:0060751 +name: branch elongation involved in mammary gland duct branching +is_a: GO:0060602 ! branch elongation of an epithelium +intersection_of: GO:0060602 ! branch elongation of an epithelium +intersection_of: part_of GO:0060603 ! mammary gland duct morphogenesis +relationship: part_of GO:0060444 ! branching involved in mammary gland duct morphogenesis + +[Term] +id: GO:0060759 +name: regulation of response to cytokine stimulus +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034097 ! response to cytokine stimulus +relationship: regulates GO:0034097 ! response to cytokine stimulus + +[Term] +id: GO:0060760 +name: positive regulation of response to cytokine stimulus +is_a: GO:0048584 ! positive regulation of response to stimulus +is_a: GO:0060759 ! regulation of response to cytokine stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0034097 ! response to cytokine stimulus +relationship: positively_regulates GO:0034097 ! response to cytokine stimulus + +[Term] +id: GO:0060762 +name: regulation of branching involved in mammary gland duct morphogenesis +is_a: GO:0060688 ! regulation of morphogenesis of a branching structure +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060444 ! branching involved in mammary gland duct morphogenesis +relationship: regulates GO:0060444 ! branching involved in mammary gland duct morphogenesis + +[Term] +id: GO:0060764 +name: cell-cell signaling involved in mammary gland development +is_a: GO:0007267 ! cell-cell signaling +intersection_of: GO:0007267 ! cell-cell signaling +intersection_of: part_of GO:0030879 ! mammary gland development +relationship: part_of GO:0030879 ! mammary gland development + +[Term] +id: GO:0060765 +name: regulation of androgen receptor signaling pathway +is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030521 ! androgen receptor signaling pathway +relationship: regulates GO:0030521 ! androgen receptor signaling pathway + +[Term] +id: GO:0060766 +name: negative regulation of androgen receptor signaling pathway +is_a: GO:0033144 ! negative regulation of intracellular steroid hormone receptor signaling pathway +is_a: GO:0060765 ! regulation of androgen receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030521 ! androgen receptor signaling pathway +relationship: negatively_regulates GO:0030521 ! androgen receptor signaling pathway + +[Term] +id: GO:0060767 +name: epithelial cell proliferation involved in prostate gland development +is_a: GO:0048610 ! cellular process involved in reproduction +is_a: GO:0050673 ! epithelial cell proliferation +intersection_of: GO:0050673 ! epithelial cell proliferation +intersection_of: part_of GO:0030850 ! prostate gland development +relationship: part_of GO:0030850 ! prostate gland development + +[Term] +id: GO:0060768 +name: regulation of epithelial cell proliferation involved in prostate gland development +is_a: GO:0050678 ! regulation of epithelial cell proliferation +is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development +relationship: regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development + +[Term] +id: GO:0060769 +name: positive regulation of epithelial cell proliferation involved in prostate gland development +is_a: GO:0050679 ! positive regulation of epithelial cell proliferation +is_a: GO:0060768 ! regulation of epithelial cell proliferation involved in prostate gland development +is_a: GO:2000243 ! positive regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development +relationship: positively_regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development + +[Term] +id: GO:0060788 +name: ectodermal placode formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0071697 ! ectodermal placode morphogenesis + +[Term] +id: GO:0060789 +name: hair follicle placode formation +is_a: GO:0060788 ! ectodermal placode formation +relationship: part_of GO:0001942 ! hair follicle development + +[Term] +id: GO:0060795 +name: cell fate commitment involved in formation of primary germ layer +is_a: GO:0045165 ! cell fate commitment +intersection_of: GO:0045165 ! cell fate commitment +intersection_of: part_of GO:0001704 ! formation of primary germ layer +relationship: part_of GO:0001704 ! formation of primary germ layer + +[Term] +id: GO:0060828 +name: regulation of canonical Wnt receptor signaling pathway +is_a: GO:0030111 ! regulation of Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060070 ! canonical Wnt receptor signaling pathway +relationship: regulates GO:0060070 ! canonical Wnt receptor signaling pathway + +[Term] +id: GO:0060840 +name: artery development +is_a: GO:0001568 ! blood vessel development + +[Term] +id: GO:0060856 +name: establishment of blood-brain barrier +is_a: GO:0048468 ! cell development + +[Term] +id: GO:0060907 +name: positive regulation of macrophage cytokine production +is_a: GO:0010935 ! regulation of macrophage cytokine production +is_a: GO:0061081 ! positive regulation of myeloid leukocyte cytokine production involved in immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010934 ! macrophage cytokine production +relationship: positively_regulates GO:0010934 ! macrophage cytokine production + +[Term] +id: GO:0060911 +name: cardiac cell fate commitment +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0035051 ! cardiocyte differentiation + +[Term] +id: GO:0060912 +name: cardiac cell fate specification +is_a: GO:0001708 ! cell fate specification +relationship: part_of GO:0060911 ! cardiac cell fate commitment + +[Term] +id: GO:0060914 +name: heart formation +is_a: GO:0048645 ! organ formation +relationship: part_of GO:0003007 ! heart morphogenesis + +[Term] +id: GO:0060916 +name: mesenchymal cell proliferation involved in lung development +is_a: GO:0010463 ! mesenchymal cell proliferation +intersection_of: GO:0010463 ! mesenchymal cell proliferation +intersection_of: part_of GO:0030324 ! lung development +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0060923 +name: cardiac muscle cell fate commitment +is_a: GO:0042693 ! muscle cell fate commitment +is_a: GO:0060911 ! cardiac cell fate commitment +relationship: part_of GO:0055007 ! cardiac muscle cell differentiation + +[Term] +id: GO:0060947 +name: cardiac vascular smooth muscle cell differentiation +is_a: GO:0035051 ! cardiocyte differentiation +is_a: GO:0035886 ! vascular smooth muscle cell differentiation +relationship: part_of GO:0060976 ! coronary vasculature development + +[Term] +id: GO:0060972 +name: left/right pattern formation +is_a: GO:0003002 ! regionalization + +[Term] +id: GO:0060976 +name: coronary vasculature development +is_a: GO:0001568 ! blood vessel development +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0060977 +name: coronary vasculature morphogenesis +is_a: GO:0048514 ! blood vessel morphogenesis +relationship: part_of GO:0060976 ! coronary vasculature development + +[Term] +id: GO:0060982 +name: coronary artery morphogenesis +is_a: GO:0048844 ! artery morphogenesis +is_a: GO:0060977 ! coronary vasculature morphogenesis + +[Term] +id: GO:0060983 +name: epicardium-derived cardiac vascular smooth muscle cell differentiation +is_a: GO:0060947 ! cardiac vascular smooth muscle cell differentiation + +[Term] +id: GO:0060993 +name: kidney morphogenesis +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0060996 +name: dendritic spine development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0016358 ! dendrite development + +[Term] +id: GO:0060997 +name: dendritic spine morphogenesis +is_a: GO:0048812 ! neuron projection morphogenesis +is_a: GO:0097061 ! dendritic spine organization +relationship: part_of GO:0048813 ! dendrite morphogenesis +relationship: part_of GO:0060996 ! dendritic spine development + +[Term] +id: GO:0060998 +name: regulation of dendritic spine development +is_a: GO:0050773 ! regulation of dendrite development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060996 ! dendritic spine development +relationship: regulates GO:0060996 ! dendritic spine development + +[Term] +id: GO:0060999 +name: positive regulation of dendritic spine development +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0060998 ! regulation of dendritic spine development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060996 ! dendritic spine development +relationship: positively_regulates GO:0060996 ! dendritic spine development + +[Term] +id: GO:0061001 +name: regulation of dendritic spine morphogenesis +is_a: GO:0048814 ! regulation of dendrite morphogenesis +is_a: GO:0060998 ! regulation of dendritic spine development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060997 ! dendritic spine morphogenesis +relationship: regulates GO:0060997 ! dendritic spine morphogenesis + +[Term] +id: GO:0061003 +name: positive regulation of dendritic spine morphogenesis +is_a: GO:0031346 ! positive regulation of cell projection organization +is_a: GO:0060999 ! positive regulation of dendritic spine development +is_a: GO:0061001 ! regulation of dendritic spine morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060997 ! dendritic spine morphogenesis +relationship: positively_regulates GO:0060997 ! dendritic spine morphogenesis + +[Term] +id: GO:0061004 +name: pattern specification involved in kidney development +is_a: GO:0007389 ! pattern specification process +intersection_of: GO:0007389 ! pattern specification process +intersection_of: part_of GO:0001822 ! kidney development +relationship: part_of GO:0001822 ! kidney development +relationship: part_of GO:0072048 ! renal system pattern specification + +[Term] +id: GO:0061005 +name: cell differentiation involved in kidney development +is_a: GO:0030154 ! cell differentiation +intersection_of: GO:0030154 ! cell differentiation +intersection_of: part_of GO:0001822 ! kidney development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0061008 +name: hepaticobiliary system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0061024 +name: membrane organization +is_a: GO:0016043 ! cellular component organization + +[Term] +id: GO:0061025 +name: membrane fusion +is_a: GO:0061024 ! membrane organization + +[Term] +id: GO:0061028 +name: establishment of endothelial barrier +is_a: GO:0001885 ! endothelial cell development + +[Term] +id: GO:0061030 +name: epithelial cell differentiation involved in mammary gland alveolus development +is_a: GO:0060644 ! mammary gland epithelial cell differentiation +intersection_of: GO:0030855 ! epithelial cell differentiation +intersection_of: part_of GO:0060749 ! mammary gland alveolus development +relationship: part_of GO:0060749 ! mammary gland alveolus development + +[Term] +id: GO:0061035 +name: regulation of cartilage development +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051216 ! cartilage development +relationship: regulates GO:0051216 ! cartilage development + +[Term] +id: GO:0061036 +name: positive regulation of cartilage development +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0061035 ! regulation of cartilage development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0051216 ! cartilage development +relationship: positively_regulates GO:0051216 ! cartilage development + +[Term] +id: GO:0061038 +name: uterus morphogenesis +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0060065 ! uterus development + +[Term] +id: GO:0061041 +name: regulation of wound healing +is_a: GO:0080134 ! regulation of response to stress +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042060 ! wound healing +relationship: regulates GO:0042060 ! wound healing + +[Term] +id: GO:0061042 +name: vascular wound healing +is_a: GO:0060055 ! angiogenesis involved in wound healing + +[Term] +id: GO:0061043 +name: regulation of vascular wound healing +is_a: GO:0045765 ! regulation of angiogenesis +is_a: GO:0061041 ! regulation of wound healing +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061042 ! vascular wound healing +relationship: regulates GO:0061042 ! vascular wound healing + +[Term] +id: GO:0061045 +name: negative regulation of wound healing +is_a: GO:0032102 ! negative regulation of response to external stimulus +is_a: GO:0061041 ! regulation of wound healing +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042060 ! wound healing +relationship: negatively_regulates GO:0042060 ! wound healing + +[Term] +id: GO:0061046 +name: regulation of branching involved in lung morphogenesis +is_a: GO:0060688 ! regulation of morphogenesis of a branching structure +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis +relationship: regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis + +[Term] +id: GO:0061047 +name: positive regulation of branching involved in lung morphogenesis +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +is_a: GO:0061046 ! regulation of branching involved in lung morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis +relationship: positively_regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis + +[Term] +id: GO:0061053 +name: somite development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0009790 ! embryo development + +[Term] +id: GO:0061054 +name: dermatome development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061053 ! somite development + +[Term] +id: GO:0061061 +name: muscle structure development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0061081 +name: positive regulation of myeloid leukocyte cytokine production involved in immune response +is_a: GO:0002720 ! positive regulation of cytokine production involved in immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061082 ! myeloid leukocyte cytokine production +relationship: positively_regulates GO:0061082 ! myeloid leukocyte cytokine production + +[Term] +id: GO:0061082 +name: myeloid leukocyte cytokine production +is_a: GO:0002367 ! cytokine production involved in immune response + +[Term] +id: GO:0061097 +name: regulation of protein tyrosine kinase activity +is_a: GO:0045859 ! regulation of protein kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004713 ! protein tyrosine kinase activity +relationship: regulates GO:0004713 ! protein tyrosine kinase activity + +[Term] +id: GO:0061098 +name: positive regulation of protein tyrosine kinase activity +is_a: GO:0045860 ! positive regulation of protein kinase activity +is_a: GO:0050731 ! positive regulation of peptidyl-tyrosine phosphorylation +is_a: GO:0061097 ! regulation of protein tyrosine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004713 ! protein tyrosine kinase activity +relationship: positively_regulates GO:0004713 ! protein tyrosine kinase activity + +[Term] +id: GO:0061101 +name: neuroendocrine cell differentiation +is_a: GO:0060563 ! neuroepithelial cell differentiation + +[Term] +id: GO:0061133 +name: endopeptidase activator activity +is_a: GO:0016504 ! peptidase activator activity +is_a: GO:0061135 ! endopeptidase regulator activity +relationship: part_of GO:0010950 ! positive regulation of endopeptidase activity +relationship: positively_regulates GO:0004175 ! endopeptidase activity + +[Term] +id: GO:0061134 +name: peptidase regulator activity +is_a: GO:0030234 ! enzyme regulator activity +relationship: part_of GO:0052547 ! regulation of peptidase activity +relationship: regulates GO:0008233 ! peptidase activity + +[Term] +id: GO:0061135 +name: endopeptidase regulator activity +is_a: GO:0061134 ! peptidase regulator activity +relationship: part_of GO:0052548 ! regulation of endopeptidase activity +relationship: regulates GO:0004175 ! endopeptidase activity + +[Term] +id: GO:0061138 +name: morphogenesis of a branching epithelium +is_a: GO:0001763 ! morphogenesis of a branching structure +is_a: GO:0002009 ! morphogenesis of an epithelium + +[Term] +id: GO:0061141 +name: lung ciliated cell differentiation +is_a: GO:0060487 ! lung epithelial cell differentiation + +[Term] +id: GO:0061154 +name: endothelial tube morphogenesis +is_a: GO:0003159 ! morphogenesis of an endothelium +is_a: GO:0060562 ! epithelial tube morphogenesis + +[Term] +id: GO:0061162 +name: establishment of monopolar cell polarity +is_a: GO:0030010 ! establishment of cell polarity +is_a: GO:0061339 ! establishment or maintenance of monopolar cell polarity + +[Term] +id: GO:0061178 +name: regulation of insulin secretion involved in cellular response to glucose stimulus +is_a: GO:0032844 ! regulation of homeostatic process +is_a: GO:0048583 ! regulation of response to stimulus +is_a: GO:0050796 ! regulation of insulin secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus +relationship: regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus + +[Term] +id: GO:0061180 +name: mammary gland epithelium development +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0030879 ! mammary gland development + +[Term] +id: GO:0061183 +name: regulation of dermatome development +is_a: GO:0045995 ! regulation of embryonic development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061054 ! dermatome development +relationship: regulates GO:0061054 ! dermatome development + +[Term] +id: GO:0061184 +name: positive regulation of dermatome development +is_a: GO:0040019 ! positive regulation of embryonic development +is_a: GO:0061183 ! regulation of dermatome development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061054 ! dermatome development +relationship: positively_regulates GO:0061054 ! dermatome development + +[Term] +id: GO:0061185 +name: negative regulation of dermatome development +is_a: GO:0045992 ! negative regulation of embryonic development +is_a: GO:0061183 ! regulation of dermatome development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061054 ! dermatome development +relationship: negatively_regulates GO:0061054 ! dermatome development + +[Term] +id: GO:0061196 +name: fungiform papilla development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0043586 ! tongue development + +[Term] +id: GO:0061197 +name: fungiform papilla morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0043587 ! tongue morphogenesis +relationship: part_of GO:0061196 ! fungiform papilla development + +[Term] +id: GO:0061198 +name: fungiform papilla formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0061197 ! fungiform papilla morphogenesis + +[Term] +id: GO:0061205 +name: paramesonephric duct development +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0061245 +name: establishment or maintenance of bipolar cell polarity +is_a: GO:0007163 ! establishment or maintenance of cell polarity + +[Term] +id: GO:0061298 +name: retina vasculature development in camera-type eye +is_a: GO:0001944 ! vasculature development +relationship: part_of GO:0060041 ! retina development in camera-type eye + +[Term] +id: GO:0061299 +name: retina vasculature morphogenesis in camera-type eye +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0061298 ! retina vasculature development in camera-type eye + +[Term] +id: GO:0061304 +name: retinal blood vessel morphogenesis +is_a: GO:0048514 ! blood vessel morphogenesis +is_a: GO:0061299 ! retina vasculature morphogenesis in camera-type eye + +[Term] +id: GO:0061307 +name: cardiac neural crest cell differentiation involved in heart development +is_a: GO:0014033 ! neural crest cell differentiation +is_a: GO:0035051 ! cardiocyte differentiation +intersection_of: GO:0014033 ! neural crest cell differentiation +intersection_of: part_of GO:0007507 ! heart development + +[Term] +id: GO:0061310 +name: canonical Wnt receptor signaling pathway involved in cardiac neural crest cell differentiation involved in heart development +is_a: GO:0044335 ! canonical Wnt receptor signaling pathway involved in neural crest cell differentiation +is_a: GO:0061316 ! canonical Wnt receptor signaling pathway involved in heart development +intersection_of: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: part_of GO:0061307 ! cardiac neural crest cell differentiation involved in heart development +relationship: part_of GO:0061307 ! cardiac neural crest cell differentiation involved in heart development + +[Term] +id: GO:0061311 +name: cell surface receptor signaling pathway involved in heart development +is_a: GO:0007166 ! cell surface receptor signaling pathway +intersection_of: GO:0007166 ! cell surface receptor signaling pathway +intersection_of: part_of GO:0007507 ! heart development +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0061316 +name: canonical Wnt receptor signaling pathway involved in heart development +is_a: GO:0003306 ! Wnt receptor signaling pathway involved in heart development +is_a: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: part_of GO:0007507 ! heart development + +[Term] +id: GO:0061317 +name: canonical Wnt receptor signaling pathway involved in cardiac muscle cell fate commitment +is_a: GO:0061316 ! canonical Wnt receptor signaling pathway involved in heart development +intersection_of: GO:0060070 ! canonical Wnt receptor signaling pathway +intersection_of: part_of GO:0060923 ! cardiac muscle cell fate commitment +relationship: part_of GO:0060923 ! cardiac muscle cell fate commitment + +[Term] +id: GO:0061318 +name: renal filtration cell differentiation +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0061323 +name: cell proliferation involved in heart morphogenesis +is_a: GO:0008283 ! cell proliferation +intersection_of: GO:0008283 ! cell proliferation +intersection_of: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0003007 ! heart morphogenesis + +[Term] +id: GO:0061324 +name: canonical Wnt receptor signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation +is_a: GO:0044340 ! canonical Wnt receptor signaling pathway involved in regulation of cell proliferation +is_a: GO:0061316 ! canonical Wnt receptor signaling pathway involved in heart development +is_a: GO:1901963 ! regulation of cell proliferation involved in outflow tract morphogenesis +relationship: regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis + +[Term] +id: GO:0061325 +name: cell proliferation involved in outflow tract morphogenesis +is_a: GO:0061323 ! cell proliferation involved in heart morphogenesis +intersection_of: GO:0008283 ! cell proliferation +intersection_of: part_of GO:0003151 ! outflow tract morphogenesis +relationship: part_of GO:0003151 ! outflow tract morphogenesis + +[Term] +id: GO:0061326 +name: renal tubule development +is_a: GO:0035295 ! tube development +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0061333 +name: renal tubule morphogenesis +is_a: GO:0060562 ! epithelial tube morphogenesis +relationship: part_of GO:0061326 ! renal tubule development + +[Term] +id: GO:0061339 +name: establishment or maintenance of monopolar cell polarity +is_a: GO:0007163 ! establishment or maintenance of cell polarity + +[Term] +id: GO:0061341 +name: non-canonical Wnt receptor signaling pathway involved in heart development +is_a: GO:0003306 ! Wnt receptor signaling pathway involved in heart development +is_a: GO:0035567 ! non-canonical Wnt receptor signaling pathway +intersection_of: GO:0035567 ! non-canonical Wnt receptor signaling pathway +intersection_of: part_of GO:0007507 ! heart development + +[Term] +id: GO:0061346 +name: planar cell polarity pathway involved in heart morphogenesis +is_a: GO:0060071 ! Wnt receptor signaling pathway, planar cell polarity pathway +is_a: GO:0061341 ! non-canonical Wnt receptor signaling pathway involved in heart development +relationship: part_of GO:0003007 ! heart morphogenesis + +[Term] +id: GO:0061347 +name: planar cell polarity pathway involved in outflow tract morphogenesis +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0060071 ! Wnt receptor signaling pathway, planar cell polarity pathway +intersection_of: part_of GO:0003151 ! outflow tract morphogenesis +relationship: part_of GO:0003151 ! outflow tract morphogenesis + +[Term] +id: GO:0061348 +name: planar cell polarity pathway involved in ventricular septum morphogenesis +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: part_of GO:0060412 ! ventricular septum morphogenesis + +[Term] +id: GO:0061349 +name: planar cell polarity pathway involved in cardiac right atrium morphogenesis +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: part_of GO:0003213 ! cardiac right atrium morphogenesis + +[Term] +id: GO:0061350 +name: planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: part_of GO:0055008 ! cardiac muscle tissue morphogenesis + +[Term] +id: GO:0061351 +name: neural precursor cell proliferation +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0061354 +name: planar cell polarity pathway involved in pericardium morphogenesis +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: part_of GO:0003344 ! pericardium morphogenesis + +[Term] +id: GO:0061369 +name: negative regulation of testicular blood vessel morphogenesis +is_a: GO:2000181 ! negative regulation of blood vessel morphogenesis + +[Term] +id: GO:0061370 +name: testosterone biosynthetic process +is_a: GO:0006702 ! androgen biosynthetic process +is_a: GO:0042181 ! ketone biosynthetic process +is_a: GO:0046165 ! alcohol biosynthetic process + +[Term] +id: GO:0061371 +name: determination of heart left/right asymmetry +is_a: GO:0007368 ! determination of left/right symmetry +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0061373 +name: mammillary axonal complex development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021767 ! mammillary body development + +[Term] +id: GO:0061374 +name: mammillothalamic axonal tract development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061373 ! mammillary axonal complex development + +[Term] +id: GO:0061377 +name: mammary gland lobule development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030879 ! mammary gland development + +[Term] +id: GO:0061378 +name: corpora quadrigemina development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030901 ! midbrain development + +[Term] +id: GO:0061379 +name: inferior colliculus development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061378 ! corpora quadrigemina development + +[Term] +id: GO:0061381 +name: cell migration in diencephalon +is_a: GO:0021885 ! forebrain cell migration +relationship: part_of GO:0021536 ! diencephalon development + +[Term] +id: GO:0061383 +name: trabecula morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0061384 +name: heart trabecula morphogenesis +is_a: GO:0061383 ! trabecula morphogenesis + +[Term] +id: GO:0061387 +name: regulation of extent of cell growth +is_a: GO:0001558 ! regulation of cell growth +relationship: part_of GO:0008361 ! regulation of cell size + +[Term] +id: GO:0061430 +name: bone trabecula morphogenesis +is_a: GO:0061383 ! trabecula morphogenesis + +[Term] +id: GO:0061437 +name: renal system vasculature development +is_a: GO:0001944 ! vasculature development +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0061440 +name: kidney vasculature development +is_a: GO:0061437 ! renal system vasculature development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0061448 +name: connective tissue development +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0061458 +name: reproductive system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0061469 +name: regulation of type B pancreatic cell proliferation +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044342 ! type B pancreatic cell proliferation +relationship: regulates GO:0044342 ! type B pancreatic cell proliferation + +[Term] +id: GO:0061525 +name: hindgut development +is_a: GO:0048565 ! digestive tract development + +[Term] +id: GO:0061564 +name: axon development +is_a: GO:0031175 ! neuron projection development + +[Term] +id: GO:0061572 +name: actin filament bundle organization +is_a: GO:0007015 ! actin filament organization + +[Term] +id: GO:0065003 +name: macromolecular complex assembly +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0043933 ! macromolecular complex subunit organization + +[Term] +id: GO:0065007 +name: biological regulation +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0065008 +name: regulation of biological quality +is_a: GO:0065007 ! biological regulation + +[Term] +id: GO:0065009 +name: regulation of molecular function +is_a: GO:0065007 ! biological regulation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003674 ! molecular_function +relationship: regulates GO:0003674 ! molecular_function + +[Term] +id: GO:0070011 +name: peptidase activity, acting on L-amino acid peptides +is_a: GO:0008233 ! peptidase activity + +[Term] +id: GO:0070013 +name: intracellular organelle lumen +is_a: GO:0043233 ! organelle lumen +is_a: GO:0044446 ! intracellular organelle part + +[Term] +id: GO:0070016 +name: armadillo repeat domain binding +is_a: GO:0019904 ! protein domain specific binding + +[Term] +id: GO:0070161 +name: anchoring junction +is_a: GO:0030054 ! cell junction + +[Term] +id: GO:0070167 +name: regulation of biomineral tissue development +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031214 ! biomineral tissue development +relationship: regulates GO:0031214 ! biomineral tissue development + +[Term] +id: GO:0070169 +name: positive regulation of biomineral tissue development +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +is_a: GO:0070167 ! regulation of biomineral tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031214 ! biomineral tissue development +relationship: positively_regulates GO:0031214 ! biomineral tissue development + +[Term] +id: GO:0070201 +name: regulation of establishment of protein localization +is_a: GO:0032880 ! regulation of protein localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045184 ! establishment of protein localization +relationship: regulates GO:0045184 ! establishment of protein localization + +[Term] +id: GO:0070227 +name: lymphocyte apoptotic process +is_a: GO:0071887 ! leukocyte apoptotic process + +[Term] +id: GO:0070228 +name: regulation of lymphocyte apoptotic process +is_a: GO:2000106 ! regulation of leukocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070227 ! lymphocyte apoptotic process +relationship: regulates GO:0070227 ! lymphocyte apoptotic process + +[Term] +id: GO:0070230 +name: positive regulation of lymphocyte apoptotic process +is_a: GO:0070228 ! regulation of lymphocyte apoptotic process +is_a: GO:2000108 ! positive regulation of leukocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070227 ! lymphocyte apoptotic process +relationship: positively_regulates GO:0070227 ! lymphocyte apoptotic process + +[Term] +id: GO:0070231 +name: T cell apoptotic process +is_a: GO:0070227 ! lymphocyte apoptotic process + +[Term] +id: GO:0070232 +name: regulation of T cell apoptotic process +is_a: GO:0070228 ! regulation of lymphocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070231 ! T cell apoptotic process +relationship: regulates GO:0070231 ! T cell apoptotic process + +[Term] +id: GO:0070234 +name: positive regulation of T cell apoptotic process +is_a: GO:0070230 ! positive regulation of lymphocyte apoptotic process +is_a: GO:0070232 ! regulation of T cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070231 ! T cell apoptotic process +relationship: positively_regulates GO:0070231 ! T cell apoptotic process + +[Term] +id: GO:0070242 +name: thymocyte apoptotic process +is_a: GO:0070231 ! T cell apoptotic process + +[Term] +id: GO:0070243 +name: regulation of thymocyte apoptotic process +is_a: GO:0070232 ! regulation of T cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070242 ! thymocyte apoptotic process +relationship: regulates GO:0070242 ! thymocyte apoptotic process + +[Term] +id: GO:0070245 +name: positive regulation of thymocyte apoptotic process +is_a: GO:0070234 ! positive regulation of T cell apoptotic process +is_a: GO:0070243 ! regulation of thymocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070242 ! thymocyte apoptotic process +relationship: positively_regulates GO:0070242 ! thymocyte apoptotic process + +[Term] +id: GO:0070271 +name: protein complex biogenesis +is_a: GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0070302 +name: regulation of stress-activated protein kinase signaling cascade +is_a: GO:0010627 ! regulation of intracellular protein kinase cascade +is_a: GO:0080135 ! regulation of cellular response to stress +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031098 ! stress-activated protein kinase signaling cascade +relationship: regulates GO:0031098 ! stress-activated protein kinase signaling cascade + +[Term] +id: GO:0070304 +name: positive regulation of stress-activated protein kinase signaling cascade +is_a: GO:0010740 ! positive regulation of intracellular protein kinase cascade +is_a: GO:0070302 ! regulation of stress-activated protein kinase signaling cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031098 ! stress-activated protein kinase signaling cascade +relationship: positively_regulates GO:0031098 ! stress-activated protein kinase signaling cascade + +[Term] +id: GO:0070325 +name: lipoprotein particle receptor binding +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0070326 +name: very-low-density lipoprotein particle receptor binding +is_a: GO:0070325 ! lipoprotein particle receptor binding + +[Term] +id: GO:0070365 +name: hepatocyte differentiation +is_a: GO:0030855 ! epithelial cell differentiation +relationship: part_of GO:0001889 ! liver development + +[Term] +id: GO:0070369 +name: beta-catenin-TCF7L2 complex +is_a: GO:0071664 ! catenin-TCF7L2 complex + +[Term] +id: GO:0070410 +name: co-SMAD binding +is_a: GO:0046332 ! SMAD binding + +[Term] +id: GO:0070411 +name: I-SMAD binding +is_a: GO:0046332 ! SMAD binding + +[Term] +id: GO:0070412 +name: R-SMAD binding +is_a: GO:0046332 ! SMAD binding + +[Term] +id: GO:0070491 +name: repressing transcription factor binding +is_a: GO:0008134 ! transcription factor binding + +[Term] +id: GO:0070507 +name: regulation of microtubule cytoskeleton organization +is_a: GO:0032886 ! regulation of microtubule-based process +is_a: GO:0051493 ! regulation of cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000226 ! microtubule cytoskeleton organization +relationship: regulates GO:0000226 ! microtubule cytoskeleton organization + +[Term] +id: GO:0070509 +name: calcium ion import +is_a: GO:0070588 ! calcium ion transmembrane transport + +[Term] +id: GO:0070527 +name: platelet aggregation +is_a: GO:0034109 ! homotypic cell-cell adhesion +relationship: part_of GO:0030168 ! platelet activation + +[Term] +id: GO:0070528 +name: protein kinase C signaling cascade +is_a: GO:0007243 ! intracellular protein kinase cascade + +[Term] +id: GO:0070588 +name: calcium ion transmembrane transport +is_a: GO:0006816 ! calcium ion transport +is_a: GO:0034220 ! ion transmembrane transport + +[Term] +id: GO:0070601 +name: centromeric sister chromatid cohesion +is_a: GO:0007062 ! sister chromatid cohesion + +[Term] +id: GO:0070602 +name: regulation of centromeric sister chromatid cohesion +is_a: GO:0007063 ! regulation of sister chromatid cohesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070601 ! centromeric sister chromatid cohesion +relationship: regulates GO:0070601 ! centromeric sister chromatid cohesion + +[Term] +id: GO:0070647 +name: protein modification by small protein conjugation or removal +is_a: GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0070661 +name: leukocyte proliferation +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0070663 +name: regulation of leukocyte proliferation +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070661 ! leukocyte proliferation +relationship: regulates GO:0070661 ! leukocyte proliferation + +[Term] +id: GO:0070664 +name: negative regulation of leukocyte proliferation +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0070663 ! regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0070661 ! leukocyte proliferation +relationship: negatively_regulates GO:0070661 ! leukocyte proliferation + +[Term] +id: GO:0070665 +name: positive regulation of leukocyte proliferation +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0070663 ! regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070661 ! leukocyte proliferation +relationship: positively_regulates GO:0070661 ! leukocyte proliferation + +[Term] +id: GO:0070723 +name: response to cholesterol +is_a: GO:0036314 ! response to sterol + +[Term] +id: GO:0070727 +name: cellular macromolecule localization +is_a: GO:0033036 ! macromolecule localization +is_a: GO:0051641 ! cellular localization + +[Term] +id: GO:0070741 +name: response to interleukin-6 +is_a: GO:0034097 ! response to cytokine stimulus + +[Term] +id: GO:0070838 +name: divalent metal ion transport +is_a: GO:0030001 ! metal ion transport +is_a: GO:0072511 ! divalent inorganic cation transport + +[Term] +id: GO:0070848 +name: response to growth factor stimulus +is_a: GO:0010033 ! response to organic substance + +[Term] +id: GO:0070887 +name: cellular response to chemical stimulus +is_a: GO:0042221 ! response to chemical stimulus +is_a: GO:0051716 ! cellular response to stimulus + +[Term] +id: GO:0070925 +name: organelle assembly +is_a: GO:0022607 ! cellular component assembly +relationship: part_of GO:0006996 ! organelle organization + +[Term] +id: GO:0070997 +name: neuron death +is_a: GO:0008219 ! cell death + +[Term] +id: GO:0071214 +name: cellular response to abiotic stimulus +is_a: GO:0009628 ! response to abiotic stimulus +is_a: GO:0051716 ! cellular response to stimulus + +[Term] +id: GO:0071216 +name: cellular response to biotic stimulus +is_a: GO:0009607 ! response to biotic stimulus +is_a: GO:0051716 ! cellular response to stimulus + +[Term] +id: GO:0071219 +name: cellular response to molecule of bacterial origin +is_a: GO:0002237 ! response to molecule of bacterial origin +is_a: GO:0071216 ! cellular response to biotic stimulus + +[Term] +id: GO:0071260 +name: cellular response to mechanical stimulus +is_a: GO:0009612 ! response to mechanical stimulus +is_a: GO:0071214 ! cellular response to abiotic stimulus +is_a: GO:0071496 ! cellular response to external stimulus + +[Term] +id: GO:0071310 +name: cellular response to organic substance +is_a: GO:0010033 ! response to organic substance +is_a: GO:0070887 ! cellular response to chemical stimulus + +[Term] +id: GO:0071322 +name: cellular response to carbohydrate stimulus +is_a: GO:0009743 ! response to carbohydrate stimulus +is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:1901701 ! cellular response to oxygen-containing compound + +[Term] +id: GO:0071326 +name: cellular response to monosaccharide stimulus +is_a: GO:0034284 ! response to monosaccharide stimulus +is_a: GO:0071322 ! cellular response to carbohydrate stimulus + +[Term] +id: GO:0071331 +name: cellular response to hexose stimulus +is_a: GO:0009746 ! response to hexose stimulus +is_a: GO:0071326 ! cellular response to monosaccharide stimulus + +[Term] +id: GO:0071333 +name: cellular response to glucose stimulus +is_a: GO:0001678 ! cellular glucose homeostasis +is_a: GO:0009749 ! response to glucose stimulus +is_a: GO:0071331 ! cellular response to hexose stimulus + +[Term] +id: GO:0071345 +name: cellular response to cytokine stimulus +is_a: GO:0034097 ! response to cytokine stimulus +is_a: GO:0071310 ! cellular response to organic substance + +[Term] +id: GO:0071356 +name: cellular response to tumor necrosis factor +is_a: GO:0034612 ! response to tumor necrosis factor +is_a: GO:0071345 ! cellular response to cytokine stimulus + +[Term] +id: GO:0071357 +name: cellular response to type I interferon +is_a: GO:0034340 ! response to type I interferon +is_a: GO:0071345 ! cellular response to cytokine stimulus + +[Term] +id: GO:0071363 +name: cellular response to growth factor stimulus +is_a: GO:0070848 ! response to growth factor stimulus +is_a: GO:0071310 ! cellular response to organic substance + +[Term] +id: GO:0071375 +name: cellular response to peptide hormone stimulus +is_a: GO:0032870 ! cellular response to hormone stimulus +is_a: GO:0043434 ! response to peptide hormone stimulus +is_a: GO:1901653 ! cellular response to peptide + +[Term] +id: GO:0071383 +name: cellular response to steroid hormone stimulus +is_a: GO:0032870 ! cellular response to hormone stimulus +is_a: GO:0048545 ! response to steroid hormone stimulus +is_a: GO:0071396 ! cellular response to lipid +is_a: GO:0071407 ! cellular response to organic cyclic compound + +[Term] +id: GO:0071391 +name: cellular response to estrogen stimulus +is_a: GO:0043627 ! response to estrogen stimulus +is_a: GO:0071383 ! cellular response to steroid hormone stimulus + +[Term] +id: GO:0071396 +name: cellular response to lipid +is_a: GO:0033993 ! response to lipid +is_a: GO:0071310 ! cellular response to organic substance + +[Term] +id: GO:0071397 +name: cellular response to cholesterol +is_a: GO:0036315 ! cellular response to sterol +is_a: GO:0070723 ! response to cholesterol + +[Term] +id: GO:0071407 +name: cellular response to organic cyclic compound +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0071310 ! cellular response to organic substance + +[Term] +id: GO:0071417 +name: cellular response to organonitrogen compound +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:0071495 ! cellular response to endogenous stimulus +is_a: GO:1901699 ! cellular response to nitrogen compound + +[Term] +id: GO:0071425 +name: hematopoietic stem cell proliferation +is_a: GO:0072089 ! stem cell proliferation +relationship: part_of GO:0030097 ! hemopoiesis + +[Term] +id: GO:0071478 +name: cellular response to radiation +is_a: GO:0009314 ! response to radiation +is_a: GO:0071214 ! cellular response to abiotic stimulus + +[Term] +id: GO:0071479 +name: cellular response to ionizing radiation +is_a: GO:0010212 ! response to ionizing radiation +is_a: GO:0071478 ! cellular response to radiation + +[Term] +id: GO:0071481 +name: cellular response to X-ray +is_a: GO:0010165 ! response to X-ray +is_a: GO:0071479 ! cellular response to ionizing radiation + +[Term] +id: GO:0071495 +name: cellular response to endogenous stimulus +is_a: GO:0009719 ! response to endogenous stimulus + +[Term] +id: GO:0071496 +name: cellular response to external stimulus +is_a: GO:0009605 ! response to external stimulus + +[Term] +id: GO:0071503 +name: response to heparin +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:1901700 ! response to oxygen-containing compound + +[Term] +id: GO:0071504 +name: cellular response to heparin +is_a: GO:0071417 ! cellular response to organonitrogen compound +is_a: GO:0071503 ! response to heparin +is_a: GO:1901701 ! cellular response to oxygen-containing compound + +[Term] +id: GO:0071542 +name: dopaminergic neuron differentiation +is_a: GO:0030182 ! neuron differentiation + +[Term] +id: GO:0071559 +name: response to transforming growth factor beta stimulus +is_a: GO:0009719 ! response to endogenous stimulus +is_a: GO:0070848 ! response to growth factor stimulus + +[Term] +id: GO:0071560 +name: cellular response to transforming growth factor beta stimulus +is_a: GO:0071363 ! cellular response to growth factor stimulus +is_a: GO:0071495 ! cellular response to endogenous stimulus +is_a: GO:0071559 ! response to transforming growth factor beta stimulus + +[Term] +id: GO:0071599 +name: otic vesicle development +is_a: GO:0007423 ! sensory organ development +is_a: GO:0048839 ! inner ear development + +[Term] +id: GO:0071600 +name: otic vesicle morphogenesis +is_a: GO:0042472 ! inner ear morphogenesis +is_a: GO:0048562 ! embryonic organ morphogenesis +relationship: part_of GO:0071599 ! otic vesicle development + +[Term] +id: GO:0071664 +name: catenin-TCF7L2 complex +is_a: GO:0043234 ! protein complex +is_a: GO:0044428 ! nuclear part + +[Term] +id: GO:0071680 +name: response to indole-3-methanol +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0097305 ! response to alcohol + +[Term] +id: GO:0071681 +name: cellular response to indole-3-methanol +is_a: GO:0071407 ! cellular response to organic cyclic compound +is_a: GO:0071417 ! cellular response to organonitrogen compound +is_a: GO:0071680 ! response to indole-3-methanol +is_a: GO:0097306 ! cellular response to alcohol + +[Term] +id: GO:0071695 +name: anatomical structure maturation +is_a: GO:0021700 ! developmental maturation +relationship: part_of GO:0048856 ! anatomical structure development + +[Term] +id: GO:0071696 +name: ectodermal placode development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0071697 +name: ectodermal placode morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0071696 ! ectodermal placode development + +[Term] +id: GO:0071702 +name: organic substance transport +is_a: GO:0006810 ! transport + +[Term] +id: GO:0071704 +name: organic substance metabolic process +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0071705 +name: nitrogen compound transport +is_a: GO:0006810 ! transport + +[Term] +id: GO:0071774 +name: response to fibroblast growth factor stimulus +is_a: GO:0009719 ! response to endogenous stimulus +is_a: GO:0070848 ! response to growth factor stimulus + +[Term] +id: GO:0071813 +name: lipoprotein particle binding +is_a: GO:0071814 ! protein-lipid complex binding + +[Term] +id: GO:0071814 +name: protein-lipid complex binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:0071822 +name: protein complex subunit organization +is_a: GO:0043933 ! macromolecular complex subunit organization + +[Term] +id: GO:0071825 +name: protein-lipid complex subunit organization +is_a: GO:0043933 ! macromolecular complex subunit organization + +[Term] +id: GO:0071827 +name: plasma lipoprotein particle organization +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0071825 ! protein-lipid complex subunit organization + +[Term] +id: GO:0071829 +name: plasma lipoprotein particle disassembly +is_a: GO:0032987 ! protein-lipid complex disassembly +is_a: GO:0071827 ! plasma lipoprotein particle organization +relationship: part_of GO:0097006 ! regulation of plasma lipoprotein particle levels + +[Term] +id: GO:0071840 +name: cellular component organization or biogenesis +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0071887 +name: leukocyte apoptotic process +is_a: GO:0097285 ! cell-type specific apoptotic process + +[Term] +id: GO:0071900 +name: regulation of protein serine/threonine kinase activity +is_a: GO:0045859 ! regulation of protein kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004674 ! protein serine/threonine kinase activity +relationship: regulates GO:0004674 ! protein serine/threonine kinase activity + +[Term] +id: GO:0071901 +name: negative regulation of protein serine/threonine kinase activity +is_a: GO:0006469 ! negative regulation of protein kinase activity +is_a: GO:0071900 ! regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004674 ! protein serine/threonine kinase activity +relationship: negatively_regulates GO:0004674 ! protein serine/threonine kinase activity + +[Term] +id: GO:0071902 +name: positive regulation of protein serine/threonine kinase activity +is_a: GO:0045860 ! positive regulation of protein kinase activity +is_a: GO:0071900 ! regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004674 ! protein serine/threonine kinase activity +relationship: positively_regulates GO:0004674 ! protein serine/threonine kinase activity + +[Term] +id: GO:0071936 +name: coreceptor activity involved in Wnt receptor signaling pathway +is_a: GO:0015026 ! coreceptor activity +intersection_of: GO:0015026 ! coreceptor activity +intersection_of: part_of GO:0016055 ! Wnt receptor signaling pathway +relationship: part_of GO:0016055 ! Wnt receptor signaling pathway + +[Term] +id: GO:0071944 +name: cell periphery +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0072001 +name: renal system development +is_a: GO:0048731 ! system development +relationship: part_of GO:0001655 ! urogenital system development + +[Term] +id: GO:0072006 +name: nephron development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0072007 +name: mesangial cell differentiation +is_a: GO:0061005 ! cell differentiation involved in kidney development + +[Term] +id: GO:0072008 +name: glomerular mesangial cell differentiation +is_a: GO:0035850 ! epithelial cell differentiation involved in kidney development +is_a: GO:0072007 ! mesangial cell differentiation +is_a: GO:0072071 ! renal interstitial cell differentiation +relationship: part_of GO:0072109 ! glomerular mesangium development + +[Term] +id: GO:0072009 +name: nephron epithelium development +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0072006 ! nephron development + +[Term] +id: GO:0072010 +name: glomerular epithelium development +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0032835 ! glomerulus development + +[Term] +id: GO:0072011 +name: glomerular endothelium development +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0072012 ! glomerulus vasculature development + +[Term] +id: GO:0072012 +name: glomerulus vasculature development +is_a: GO:0001568 ! blood vessel development +relationship: part_of GO:0032835 ! glomerulus development +relationship: part_of GO:0061440 ! kidney vasculature development + +[Term] +id: GO:0072028 +name: nephron morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0060993 ! kidney morphogenesis +relationship: part_of GO:0072006 ! nephron development + +[Term] +id: GO:0072033 +name: renal vesicle formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0072077 ! renal vesicle morphogenesis + +[Term] +id: GO:0072034 +name: renal vesicle induction +is_a: GO:0031128 ! developmental induction +is_a: GO:0090184 ! positive regulation of kidney development +is_a: GO:2000027 ! regulation of organ morphogenesis +relationship: positively_regulates GO:0072033 ! renal vesicle formation + +[Term] +id: GO:0072044 +name: collecting duct development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0072048 +name: renal system pattern specification +is_a: GO:0007389 ! pattern specification process +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0072053 +name: renal inner medulla development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0072054 +name: renal outer medulla development +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0072060 +name: outer medullary collecting duct development +is_a: GO:0072044 ! collecting duct development + +[Term] +id: GO:0072061 +name: inner medullary collecting duct development +is_a: GO:0072044 ! collecting duct development + +[Term] +id: GO:0072070 +name: loop of Henle development +is_a: GO:0072080 ! nephron tubule development + +[Term] +id: GO:0072071 +name: renal interstitial cell differentiation +is_a: GO:0061005 ! cell differentiation involved in kidney development + +[Term] +id: GO:0072073 +name: kidney epithelium development +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0072074 +name: kidney mesenchyme development +is_a: GO:0060485 ! mesenchyme development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0072075 +name: metanephric mesenchyme development +is_a: GO:0072074 ! kidney mesenchyme development +relationship: part_of GO:0001656 ! metanephros development + +[Term] +id: GO:0072076 +name: nephrogenic mesenchyme development +is_a: GO:0072074 ! kidney mesenchyme development +relationship: part_of GO:0072006 ! nephron development + +[Term] +id: GO:0072077 +name: renal vesicle morphogenesis +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0072028 ! nephron morphogenesis +relationship: part_of GO:0072087 ! renal vesicle development +relationship: part_of GO:0072088 ! nephron epithelium morphogenesis + +[Term] +id: GO:0072078 +name: nephron tubule morphogenesis +is_a: GO:0061333 ! renal tubule morphogenesis +is_a: GO:0072088 ! nephron epithelium morphogenesis +relationship: part_of GO:0072080 ! nephron tubule development + +[Term] +id: GO:0072079 +name: nephron tubule formation +is_a: GO:0001838 ! embryonic epithelial tube formation +relationship: part_of GO:0072078 ! nephron tubule morphogenesis + +[Term] +id: GO:0072080 +name: nephron tubule development +is_a: GO:0061326 ! renal tubule development +is_a: GO:0072009 ! nephron epithelium development + +[Term] +id: GO:0072087 +name: renal vesicle development +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0072009 ! nephron epithelium development + +[Term] +id: GO:0072088 +name: nephron epithelium morphogenesis +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0072009 ! nephron epithelium development +relationship: part_of GO:0072028 ! nephron morphogenesis + +[Term] +id: GO:0072089 +name: stem cell proliferation +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0072091 +name: regulation of stem cell proliferation +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072089 ! stem cell proliferation +relationship: regulates GO:0072089 ! stem cell proliferation + +[Term] +id: GO:0072109 +name: glomerular mesangium development +is_a: GO:0061448 ! connective tissue development +relationship: part_of GO:0072012 ! glomerulus vasculature development + +[Term] +id: GO:0072112 +name: glomerular visceral epithelial cell differentiation +is_a: GO:0061318 ! renal filtration cell differentiation +is_a: GO:0072311 ! glomerular epithelial cell differentiation + +[Term] +id: GO:0072127 +name: renal capsule development +is_a: GO:0061448 ! connective tissue development +relationship: part_of GO:0001822 ! kidney development + +[Term] +id: GO:0072128 +name: renal capsule morphogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0072127 ! renal capsule development + +[Term] +id: GO:0072129 +name: renal capsule formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0072128 ! renal capsule morphogenesis + +[Term] +id: GO:0072130 +name: renal capsule specification +is_a: GO:0003002 ! regionalization +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0061004 ! pattern specification involved in kidney development +relationship: part_of GO:0072129 ! renal capsule formation + +[Term] +id: GO:0072132 +name: mesenchyme morphogenesis +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0009887 ! organ morphogenesis +relationship: part_of GO:0060485 ! mesenchyme development + +[Term] +id: GO:0072141 +name: renal interstitial cell development +is_a: GO:0048468 ! cell development +relationship: part_of GO:0072071 ! renal interstitial cell differentiation + +[Term] +id: GO:0072143 +name: mesangial cell development +is_a: GO:0048468 ! cell development +relationship: part_of GO:0072007 ! mesangial cell differentiation + +[Term] +id: GO:0072144 +name: glomerular mesangial cell development +is_a: GO:0002064 ! epithelial cell development +is_a: GO:0072141 ! renal interstitial cell development +is_a: GO:0072143 ! mesangial cell development +relationship: part_of GO:0072008 ! glomerular mesangial cell differentiation + +[Term] +id: GO:0072160 +name: nephron tubule epithelial cell differentiation +is_a: GO:0035850 ! epithelial cell differentiation involved in kidney development +relationship: part_of GO:0072080 ! nephron tubule development + +[Term] +id: GO:0072161 +name: mesenchymal cell differentiation involved in kidney development +is_a: GO:0061005 ! cell differentiation involved in kidney development +is_a: GO:2001012 ! mesenchymal cell differentiation involved in renal system development +intersection_of: GO:0048762 ! mesenchymal cell differentiation +intersection_of: part_of GO:0001822 ! kidney development +relationship: part_of GO:0072074 ! kidney mesenchyme development + +[Term] +id: GO:0072162 +name: metanephric mesenchymal cell differentiation +is_a: GO:0072161 ! mesenchymal cell differentiation involved in kidney development +is_a: GO:0072202 ! cell differentiation involved in metanephros development +relationship: part_of GO:0072075 ! metanephric mesenchyme development + +[Term] +id: GO:0072163 +name: mesonephric epithelium development +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0001823 ! mesonephros development + +[Term] +id: GO:0072164 +name: mesonephric tubule development +is_a: GO:0035295 ! tube development +is_a: GO:0072163 ! mesonephric epithelium development + +[Term] +id: GO:0072170 +name: metanephric tubule development +is_a: GO:0035295 ! tube development +relationship: part_of GO:0001656 ! metanephros development + +[Term] +id: GO:0072175 +name: epithelial tube formation +is_a: GO:0035148 ! tube formation +relationship: part_of GO:0060562 ! epithelial tube morphogenesis + +[Term] +id: GO:0072182 +name: regulation of nephron tubule epithelial cell differentiation +is_a: GO:2000696 ! regulation of epithelial cell differentiation involved in kidney development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072160 ! nephron tubule epithelial cell differentiation +relationship: regulates GO:0072160 ! nephron tubule epithelial cell differentiation + +[Term] +id: GO:0072201 +name: negative regulation of mesenchymal cell proliferation +is_a: GO:0010464 ! regulation of mesenchymal cell proliferation +is_a: GO:2000647 ! negative regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010463 ! mesenchymal cell proliferation +relationship: negatively_regulates GO:0010463 ! mesenchymal cell proliferation + +[Term] +id: GO:0072202 +name: cell differentiation involved in metanephros development +is_a: GO:0061005 ! cell differentiation involved in kidney development +intersection_of: GO:0030154 ! cell differentiation +intersection_of: part_of GO:0001656 ! metanephros development +relationship: part_of GO:0001656 ! metanephros development + +[Term] +id: GO:0072205 +name: metanephric collecting duct development +is_a: GO:0072044 ! collecting duct development +relationship: part_of GO:0001656 ! metanephros development + +[Term] +id: GO:0072207 +name: metanephric epithelium development +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0001656 ! metanephros development + +[Term] +id: GO:0072210 +name: metanephric nephron development +is_a: GO:0072006 ! nephron development +relationship: part_of GO:0001656 ! metanephros development + +[Term] +id: GO:0072213 +name: metanephric capsule development +is_a: GO:0072127 ! renal capsule development +relationship: part_of GO:0001656 ! metanephros development + +[Term] +id: GO:0072234 +name: metanephric nephron tubule development +is_a: GO:0072080 ! nephron tubule development +is_a: GO:0072170 ! metanephric tubule development +is_a: GO:0072243 ! metanephric nephron epithelium development + +[Term] +id: GO:0072236 +name: metanephric loop of Henle development +is_a: GO:0072070 ! loop of Henle development +relationship: part_of GO:0072234 ! metanephric nephron tubule development + +[Term] +id: GO:0072243 +name: metanephric nephron epithelium development +is_a: GO:0072009 ! nephron epithelium development +is_a: GO:0072207 ! metanephric epithelium development + +[Term] +id: GO:0072265 +name: metanephric capsule morphogenesis +is_a: GO:0072128 ! renal capsule morphogenesis +relationship: part_of GO:0072213 ! metanephric capsule development + +[Term] +id: GO:0072266 +name: metanephric capsule formation +is_a: GO:0072129 ! renal capsule formation +relationship: part_of GO:0072265 ! metanephric capsule morphogenesis + +[Term] +id: GO:0072267 +name: metanephric capsule specification +is_a: GO:0072130 ! renal capsule specification +is_a: GO:0072268 ! pattern specification involved in metanephros development +relationship: part_of GO:0072266 ! metanephric capsule formation + +[Term] +id: GO:0072268 +name: pattern specification involved in metanephros development +is_a: GO:0061004 ! pattern specification involved in kidney development +intersection_of: GO:0007389 ! pattern specification process +intersection_of: part_of GO:0001656 ! metanephros development +relationship: part_of GO:0001656 ! metanephros development + +[Term] +id: GO:0072273 +name: metanephric nephron morphogenesis +is_a: GO:0072028 ! nephron morphogenesis +relationship: part_of GO:0003338 ! metanephros morphogenesis +relationship: part_of GO:0072210 ! metanephric nephron development + +[Term] +id: GO:0072283 +name: metanephric renal vesicle morphogenesis +is_a: GO:0072077 ! renal vesicle morphogenesis +relationship: part_of GO:0072273 ! metanephric nephron morphogenesis + +[Term] +id: GO:0072311 +name: glomerular epithelial cell differentiation +is_a: GO:0035850 ! epithelial cell differentiation involved in kidney development +relationship: part_of GO:0072010 ! glomerular epithelium development + +[Term] +id: GO:0072358 +name: cardiovascular system development +is_a: GO:0048731 ! system development +relationship: part_of GO:0072359 ! circulatory system development + +[Term] +id: GO:0072359 +name: circulatory system development +is_a: GO:0048731 ! system development + +[Term] +id: GO:0072498 +name: embryonic skeletal joint development +is_a: GO:0048706 ! embryonic skeletal system development + +[Term] +id: GO:0072503 +name: cellular divalent inorganic cation homeostasis +is_a: GO:0030003 ! cellular cation homeostasis +is_a: GO:0072507 ! divalent inorganic cation homeostasis + +[Term] +id: GO:0072507 +name: divalent inorganic cation homeostasis +is_a: GO:0055080 ! cation homeostasis + +[Term] +id: GO:0072511 +name: divalent inorganic cation transport +is_a: GO:0006812 ! cation transport + +[Term] +id: GO:0072521 +name: purine-containing compound metabolic process +is_a: GO:0006725 ! cellular aromatic compound metabolic process +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +is_a: GO:0046483 ! heterocycle metabolic process +is_a: GO:1901360 ! organic cyclic compound metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process + +[Term] +id: GO:0072523 +name: purine-containing compound catabolic process +is_a: GO:0019439 ! aromatic compound catabolic process +is_a: GO:0044270 ! cellular nitrogen compound catabolic process +is_a: GO:0046700 ! heterocycle catabolic process +is_a: GO:0072521 ! purine-containing compound metabolic process +is_a: GO:1901361 ! organic cyclic compound catabolic process +is_a: GO:1901565 ! organonitrogen compound catabolic process + +[Term] +id: GO:0072606 +name: interleukin-8 secretion +is_a: GO:0050663 ! cytokine secretion +relationship: part_of GO:0032637 ! interleukin-8 production + +[Term] +id: GO:0072657 +name: protein localization to membrane +is_a: GO:0016044 ! cellular membrane organization +is_a: GO:0034613 ! cellular protein localization + +[Term] +id: GO:0072659 +name: protein localization to plasma membrane +is_a: GO:0007009 ! plasma membrane organization +is_a: GO:0072657 ! protein localization to membrane + +[Term] +id: GO:0072676 +name: lymphocyte migration +is_a: GO:0050900 ! leukocyte migration + +[Term] +id: GO:0072678 +name: T cell migration +is_a: GO:0072676 ! lymphocyte migration + +[Term] +id: GO:0080090 +name: regulation of primary metabolic process +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044238 ! primary metabolic process +relationship: regulates GO:0044238 ! primary metabolic process + +[Term] +id: GO:0080134 +name: regulation of response to stress +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006950 ! response to stress +relationship: regulates GO:0006950 ! response to stress + +[Term] +id: GO:0080135 +name: regulation of cellular response to stress +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0080134 ! regulation of response to stress +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033554 ! cellular response to stress +relationship: regulates GO:0033554 ! cellular response to stress + +[Term] +id: GO:0090002 +name: establishment of protein localization to plasma membrane +is_a: GO:0090150 ! establishment of protein localization to membrane +relationship: part_of GO:0072659 ! protein localization to plasma membrane + +[Term] +id: GO:0090009 +name: primitive streak formation +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0001702 ! gastrulation with mouth forming second +relationship: part_of GO:0009948 ! anterior/posterior axis specification + +[Term] +id: GO:0090030 +name: regulation of steroid hormone biosynthetic process +is_a: GO:0046885 ! regulation of hormone biosynthetic process +is_a: GO:0050810 ! regulation of steroid biosynthetic process + +[Term] +id: GO:0090031 +name: positive regulation of steroid hormone biosynthetic process +is_a: GO:0010893 ! positive regulation of steroid biosynthetic process +is_a: GO:0046886 ! positive regulation of hormone biosynthetic process +is_a: GO:0090030 ! regulation of steroid hormone biosynthetic process + +[Term] +id: GO:0090036 +name: regulation of protein kinase C signaling cascade +is_a: GO:0010627 ! regulation of intracellular protein kinase cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070528 ! protein kinase C signaling cascade +relationship: regulates GO:0070528 ! protein kinase C signaling cascade + +[Term] +id: GO:0090037 +name: positive regulation of protein kinase C signaling cascade +is_a: GO:0010740 ! positive regulation of intracellular protein kinase cascade +is_a: GO:0090036 ! regulation of protein kinase C signaling cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070528 ! protein kinase C signaling cascade +relationship: positively_regulates GO:0070528 ! protein kinase C signaling cascade + +[Term] +id: GO:0090049 +name: regulation of cell migration involved in sprouting angiogenesis +is_a: GO:0043535 ! regulation of blood vessel endothelial cell migration +is_a: GO:0045765 ! regulation of angiogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002042 ! cell migration involved in sprouting angiogenesis +relationship: regulates GO:0002042 ! cell migration involved in sprouting angiogenesis + +[Term] +id: GO:0090050 +name: positive regulation of cell migration involved in sprouting angiogenesis +is_a: GO:0043536 ! positive regulation of blood vessel endothelial cell migration +is_a: GO:0045766 ! positive regulation of angiogenesis +is_a: GO:0090049 ! regulation of cell migration involved in sprouting angiogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002042 ! cell migration involved in sprouting angiogenesis +relationship: positively_regulates GO:0002042 ! cell migration involved in sprouting angiogenesis + +[Term] +id: GO:0090066 +name: regulation of anatomical structure size +is_a: GO:0065008 ! regulation of biological quality + +[Term] +id: GO:0090068 +name: positive regulation of cell cycle process +is_a: GO:0010564 ! regulation of cell cycle process +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0022402 ! cell cycle process +relationship: positively_regulates GO:0022402 ! cell cycle process + +[Term] +id: GO:0090087 +name: regulation of peptide transport +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0015833 ! peptide transport +relationship: regulates GO:0015833 ! peptide transport + +[Term] +id: GO:0090090 +name: negative regulation of canonical Wnt receptor signaling pathway +is_a: GO:0030178 ! negative regulation of Wnt receptor signaling pathway +is_a: GO:0060828 ! regulation of canonical Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0060070 ! canonical Wnt receptor signaling pathway +relationship: negatively_regulates GO:0060070 ! canonical Wnt receptor signaling pathway + +[Term] +id: GO:0090092 +name: regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +relationship: regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway + +[Term] +id: GO:0090100 +name: positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0090092 ! regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +relationship: positively_regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway + +[Term] +id: GO:0090101 +name: negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:0090092 ! regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +relationship: negatively_regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway + +[Term] +id: GO:0090102 +name: cochlea development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0048839 ! inner ear development + +[Term] +id: GO:0090103 +name: cochlea morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0042472 ! inner ear morphogenesis +relationship: part_of GO:0090102 ! cochlea development + +[Term] +id: GO:0090109 +name: regulation of cell-substrate junction assembly +is_a: GO:1901888 ! regulation of cell junction assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007044 ! cell-substrate junction assembly +relationship: regulates GO:0007044 ! cell-substrate junction assembly + +[Term] +id: GO:0090118 +name: receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport +is_a: GO:0006898 ! receptor-mediated endocytosis +is_a: GO:0044765 ! single-organism transport +relationship: part_of GO:0032367 ! intracellular cholesterol transport +relationship: part_of GO:0034383 ! low-density lipoprotein particle clearance + +[Term] +id: GO:0090130 +name: tissue migration +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0090132 +name: epithelium migration +is_a: GO:0090130 ! tissue migration + +[Term] +id: GO:0090150 +name: establishment of protein localization to membrane +is_a: GO:0045184 ! establishment of protein localization +relationship: part_of GO:0072657 ! protein localization to membrane + +[Term] +id: GO:0090175 +name: regulation of establishment of planar polarity +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001736 ! establishment of planar polarity +relationship: regulates GO:0001736 ! establishment of planar polarity + +[Term] +id: GO:0090177 +name: establishment of planar polarity involved in neural tube closure +is_a: GO:0042249 ! establishment of planar polarity of embryonic epithelium +is_a: GO:0048598 ! embryonic morphogenesis +intersection_of: GO:0001736 ! establishment of planar polarity +intersection_of: part_of GO:0001843 ! neural tube closure +relationship: part_of GO:0001843 ! neural tube closure + +[Term] +id: GO:0090178 +name: regulation of establishment of planar polarity involved in neural tube closure +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051960 ! regulation of nervous system development +is_a: GO:0090175 ! regulation of establishment of planar polarity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0090177 ! establishment of planar polarity involved in neural tube closure +relationship: regulates GO:0090177 ! establishment of planar polarity involved in neural tube closure + +[Term] +id: GO:0090179 +name: planar cell polarity pathway involved in neural tube closure +is_a: GO:0060071 ! Wnt receptor signaling pathway, planar cell polarity pathway +is_a: GO:0090178 ! regulation of establishment of planar polarity involved in neural tube closure + +[Term] +id: GO:0090183 +name: regulation of kidney development +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001822 ! kidney development +relationship: regulates GO:0001822 ! kidney development + +[Term] +id: GO:0090184 +name: positive regulation of kidney development +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +is_a: GO:0090183 ! regulation of kidney development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001822 ! kidney development +relationship: positively_regulates GO:0001822 ! kidney development + +[Term] +id: GO:0090244 +name: Wnt receptor signaling pathway involved in somitogenesis +is_a: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: GO:0016055 ! Wnt receptor signaling pathway +intersection_of: part_of GO:0001756 ! somitogenesis +relationship: part_of GO:0001756 ! somitogenesis + +[Term] +id: GO:0090245 +name: axis elongation involved in somitogenesis +is_a: GO:0003401 ! axis elongation +intersection_of: GO:0003401 ! axis elongation +intersection_of: part_of GO:0001756 ! somitogenesis +relationship: part_of GO:0001756 ! somitogenesis + +[Term] +id: GO:0090246 +name: convergent extension involved in somitogenesis +is_a: GO:0048598 ! embryonic morphogenesis +is_a: GO:0060028 ! convergent extension involved in axis elongation +intersection_of: GO:0060026 ! convergent extension +intersection_of: part_of GO:0001756 ! somitogenesis +relationship: part_of GO:0090245 ! axis elongation involved in somitogenesis + +[Term] +id: GO:0090263 +name: positive regulation of canonical Wnt receptor signaling pathway +is_a: GO:0030177 ! positive regulation of Wnt receptor signaling pathway +is_a: GO:0060828 ! regulation of canonical Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060070 ! canonical Wnt receptor signaling pathway +relationship: positively_regulates GO:0060070 ! canonical Wnt receptor signaling pathway + +[Term] +id: GO:0090276 +name: regulation of peptide hormone secretion +is_a: GO:0002791 ! regulation of peptide secretion +is_a: GO:0046883 ! regulation of hormone secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030072 ! peptide hormone secretion +relationship: regulates GO:0030072 ! peptide hormone secretion + +[Term] +id: GO:0090278 +name: negative regulation of peptide hormone secretion +is_a: GO:0002792 ! negative regulation of peptide secretion +is_a: GO:0046888 ! negative regulation of hormone secretion +is_a: GO:0090276 ! regulation of peptide hormone secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030072 ! peptide hormone secretion +relationship: negatively_regulates GO:0030072 ! peptide hormone secretion + +[Term] +id: GO:0090279 +name: regulation of calcium ion import +is_a: GO:0034765 ! regulation of ion transmembrane transport +is_a: GO:0051924 ! regulation of calcium ion transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070509 ! calcium ion import +relationship: regulates GO:0070509 ! calcium ion import + +[Term] +id: GO:0090287 +name: regulation of cellular response to growth factor stimulus +is_a: GO:0048583 ! regulation of response to stimulus +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0071363 ! cellular response to growth factor stimulus +relationship: regulates GO:0071363 ! cellular response to growth factor stimulus + +[Term] +id: GO:0090288 +name: negative regulation of cellular response to growth factor stimulus +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0048585 ! negative regulation of response to stimulus +is_a: GO:0090287 ! regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0071363 ! cellular response to growth factor stimulus +relationship: negatively_regulates GO:0071363 ! cellular response to growth factor stimulus + +[Term] +id: GO:0090303 +name: positive regulation of wound healing +is_a: GO:0048584 ! positive regulation of response to stimulus +is_a: GO:0061041 ! regulation of wound healing +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042060 ! wound healing +relationship: positively_regulates GO:0042060 ! wound healing + +[Term] +id: GO:0090304 +name: nucleic acid metabolic process +is_a: GO:0006139 ! nucleobase-containing compound metabolic process +is_a: GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0090305 +name: nucleic acid phosphodiester bond hydrolysis +is_a: GO:0090304 ! nucleic acid metabolic process + +[Term] +id: GO:0090316 +name: positive regulation of intracellular protein transport +is_a: GO:0032388 ! positive regulation of intracellular transport +is_a: GO:0033157 ! regulation of intracellular protein transport +is_a: GO:0051222 ! positive regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006886 ! intracellular protein transport +relationship: positively_regulates GO:0006886 ! intracellular protein transport + +[Term] +id: GO:0090317 +name: negative regulation of intracellular protein transport +is_a: GO:0032387 ! negative regulation of intracellular transport +is_a: GO:0033157 ! regulation of intracellular protein transport +is_a: GO:0051224 ! negative regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006886 ! intracellular protein transport +relationship: negatively_regulates GO:0006886 ! intracellular protein transport + +[Term] +id: GO:0090342 +name: regulation of cell aging +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007569 ! cell aging +relationship: regulates GO:0007569 ! cell aging + +[Term] +id: GO:0090344 +name: negative regulation of cell aging +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0090342 ! regulation of cell aging +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007569 ! cell aging +relationship: negatively_regulates GO:0007569 ! cell aging + +[Term] +id: GO:0090381 +name: regulation of heart induction +is_a: GO:0010453 ! regulation of cell fate commitment +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0023051 ! regulation of signaling +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003129 ! heart induction +relationship: regulates GO:0003129 ! heart induction + +[Term] +id: GO:0090495 +name: low-density lipoprotein particle disassembly +is_a: GO:0071829 ! plasma lipoprotein particle disassembly + +[Term] +id: GO:0090504 +name: epiboly +is_a: GO:0002011 ! morphogenesis of an epithelial sheet + +[Term] +id: GO:0090505 +name: epiboly involved in wound healing +is_a: GO:0090504 ! epiboly +intersection_of: GO:0090504 ! epiboly +intersection_of: part_of GO:0042060 ! wound healing +relationship: part_of GO:0042060 ! wound healing + +[Term] +id: GO:0097006 +name: regulation of plasma lipoprotein particle levels +is_a: GO:0050789 ! regulation of biological process + +[Term] +id: GO:0097061 +name: dendritic spine organization +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0097153 +name: cysteine-type endopeptidase activity involved in apoptotic process +is_a: GO:0004197 ! cysteine-type endopeptidase activity +intersection_of: GO:0004197 ! cysteine-type endopeptidase activity +intersection_of: part_of GO:0006915 ! apoptotic process +relationship: part_of GO:0006915 ! apoptotic process + +[Term] +id: GO:0097159 +name: organic cyclic compound binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:0097190 +name: apoptotic signaling pathway +is_a: GO:0007165 ! signal transduction +relationship: part_of GO:0006915 ! apoptotic process + +[Term] +id: GO:0097191 +name: extrinsic apoptotic signaling pathway +is_a: GO:0007166 ! cell surface receptor signaling pathway +is_a: GO:0097190 ! apoptotic signaling pathway + +[Term] +id: GO:0097194 +name: execution phase of apoptosis +is_a: GO:0044763 ! single-organism cellular process +relationship: part_of GO:0006915 ! apoptotic process + +[Term] +id: GO:0097242 +name: beta-amyloid clearance +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0097285 +name: cell-type specific apoptotic process +is_a: GO:0006915 ! apoptotic process + +[Term] +id: GO:0097305 +name: response to alcohol +is_a: GO:0010033 ! response to organic substance +is_a: GO:1901700 ! response to oxygen-containing compound + +[Term] +id: GO:0097306 +name: cellular response to alcohol +is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:0097305 ! response to alcohol +is_a: GO:1901701 ! cellular response to oxygen-containing compound + +[Term] +id: GO:0097367 +name: carbohydrate derivative binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:0097458 +name: neuron part +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0097479 +name: synaptic vesicle localization +is_a: GO:0051648 ! vesicle localization + +[Term] +id: GO:0097480 +name: establishment of synaptic vesicle localization +is_a: GO:0051650 ! establishment of vesicle localization +relationship: part_of GO:0097479 ! synaptic vesicle localization + +[Term] +id: GO:0097485 +name: neuron projection guidance +is_a: GO:0006928 ! cellular component movement +relationship: part_of GO:0006935 ! chemotaxis +relationship: part_of GO:0048812 ! neuron projection morphogenesis + +[Term] +id: GO:1900006 +name: positive regulation of dendrite development +is_a: GO:0010976 ! positive regulation of neuron projection development +is_a: GO:0050773 ! regulation of dendrite development +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016358 ! dendrite development +relationship: positively_regulates GO:0016358 ! dendrite development + +[Term] +id: GO:1900046 +name: regulation of hemostasis +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007599 ! hemostasis +relationship: regulates GO:0007599 ! hemostasis + +[Term] +id: GO:1900115 +name: extracellular regulation of signal transduction +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0009966 ! regulation of signal transduction +intersection_of: occurs_in GO:0005576 ! extracellular region +relationship: occurs_in GO:0005576 ! extracellular region + +[Term] +id: GO:1900116 +name: extracellular negative regulation of signal transduction +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:1900115 ! extracellular regulation of signal transduction +intersection_of: GO:0009968 ! negative regulation of signal transduction +intersection_of: occurs_in GO:0005576 ! extracellular region +relationship: occurs_in GO:0005576 ! extracellular region + +[Term] +id: GO:1900180 +name: regulation of protein localization to nucleus +is_a: GO:0032880 ! regulation of protein localization +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034504 ! protein localization to nucleus +relationship: regulates GO:0034504 ! protein localization to nucleus + +[Term] +id: GO:1900221 +name: regulation of beta-amyloid clearance +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097242 ! beta-amyloid clearance +relationship: regulates GO:0097242 ! beta-amyloid clearance + +[Term] +id: GO:1900222 +name: negative regulation of beta-amyloid clearance +is_a: GO:0051241 ! negative regulation of multicellular organismal process +is_a: GO:1900221 ! regulation of beta-amyloid clearance +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097242 ! beta-amyloid clearance +relationship: negatively_regulates GO:0097242 ! beta-amyloid clearance + +[Term] +id: GO:1900542 +name: regulation of purine nucleotide metabolic process +is_a: GO:0006140 ! regulation of nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006163 ! purine nucleotide metabolic process +relationship: regulates GO:0006163 ! purine nucleotide metabolic process + +[Term] +id: GO:1900544 +name: positive regulation of purine nucleotide metabolic process +is_a: GO:0045981 ! positive regulation of nucleotide metabolic process +is_a: GO:1900542 ! regulation of purine nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006163 ! purine nucleotide metabolic process +relationship: positively_regulates GO:0006163 ! purine nucleotide metabolic process + +[Term] +id: GO:1901068 +name: guanosine-containing compound metabolic process +is_a: GO:0046128 ! purine ribonucleoside metabolic process + +[Term] +id: GO:1901069 +name: guanosine-containing compound catabolic process +is_a: GO:0046130 ! purine ribonucleoside catabolic process +is_a: GO:1901068 ! guanosine-containing compound metabolic process + +[Term] +id: GO:1901135 +name: carbohydrate derivative metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:1901136 +name: carbohydrate derivative catabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process +is_a: GO:1901575 ! organic substance catabolic process + +[Term] +id: GO:1901137 +name: carbohydrate derivative biosynthetic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process +is_a: GO:1901576 ! organic substance biosynthetic process + +[Term] +id: GO:1901214 +name: regulation of neuron death +is_a: GO:0010941 ! regulation of cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070997 ! neuron death +relationship: regulates GO:0070997 ! neuron death + +[Term] +id: GO:1901215 +name: negative regulation of neuron death +is_a: GO:0060548 ! negative regulation of cell death +is_a: GO:1901214 ! regulation of neuron death +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0070997 ! neuron death +relationship: negatively_regulates GO:0070997 ! neuron death + +[Term] +id: GO:1901219 +name: regulation of cardiac chamber morphogenesis +is_a: GO:2000826 ! regulation of heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003206 ! cardiac chamber morphogenesis +relationship: regulates GO:0003206 ! cardiac chamber morphogenesis + +[Term] +id: GO:1901246 +name: regulation of lung ciliated cell differentiation +is_a: GO:0030856 ! regulation of epithelial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061141 ! lung ciliated cell differentiation +relationship: regulates GO:0061141 ! lung ciliated cell differentiation + +[Term] +id: GO:1901248 +name: positive regulation of lung ciliated cell differentiation +is_a: GO:0030858 ! positive regulation of epithelial cell differentiation +is_a: GO:1901246 ! regulation of lung ciliated cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061141 ! lung ciliated cell differentiation +relationship: positively_regulates GO:0061141 ! lung ciliated cell differentiation + +[Term] +id: GO:1901292 +name: nucleoside phosphate catabolic process +is_a: GO:0006753 ! nucleoside phosphate metabolic process +is_a: GO:0034655 ! nucleobase-containing compound catabolic process +is_a: GO:0046434 ! organophosphate catabolic process + +[Term] +id: GO:1901320 +name: negative regulation of heart induction +is_a: GO:0010648 ! negative regulation of cell communication +is_a: GO:0023057 ! negative regulation of signaling +is_a: GO:0090381 ! regulation of heart induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003129 ! heart induction +relationship: negatively_regulates GO:0003129 ! heart induction + +[Term] +id: GO:1901342 +name: regulation of vasculature development +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001944 ! vasculature development +relationship: regulates GO:0001944 ! vasculature development + +[Term] +id: GO:1901360 +name: organic cyclic compound metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:1901361 +name: organic cyclic compound catabolic process +is_a: GO:1901360 ! organic cyclic compound metabolic process +is_a: GO:1901575 ! organic substance catabolic process + +[Term] +id: GO:1901362 +name: organic cyclic compound biosynthetic process +is_a: GO:1901360 ! organic cyclic compound metabolic process +is_a: GO:1901576 ! organic substance biosynthetic process + +[Term] +id: GO:1901363 +name: heterocyclic compound binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:1901564 +name: organonitrogen compound metabolic process +is_a: GO:0006807 ! nitrogen compound metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:1901565 +name: organonitrogen compound catabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process +is_a: GO:1901575 ! organic substance catabolic process + +[Term] +id: GO:1901575 +name: organic substance catabolic process +is_a: GO:0009056 ! catabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:1901576 +name: organic substance biosynthetic process +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:1901615 +name: organic hydroxy compound metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:1901617 +name: organic hydroxy compound biosynthetic process +is_a: GO:1901576 ! organic substance biosynthetic process +is_a: GO:1901615 ! organic hydroxy compound metabolic process + +[Term] +id: GO:1901623 +name: regulation of lymphocyte chemotaxis +is_a: GO:0002688 ! regulation of leukocyte chemotaxis +is_a: GO:2000401 ! regulation of lymphocyte migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048247 ! lymphocyte chemotaxis +relationship: regulates GO:0048247 ! lymphocyte chemotaxis + +[Term] +id: GO:1901652 +name: response to peptide +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:1901700 ! response to oxygen-containing compound + +[Term] +id: GO:1901653 +name: cellular response to peptide +is_a: GO:0071417 ! cellular response to organonitrogen compound +is_a: GO:1901652 ! response to peptide +is_a: GO:1901701 ! cellular response to oxygen-containing compound + +[Term] +id: GO:1901657 +name: glycosyl compound metabolic process +is_a: GO:0044710 ! single-organism metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:1901658 +name: glycosyl compound catabolic process +is_a: GO:1901575 ! organic substance catabolic process +is_a: GO:1901657 ! glycosyl compound metabolic process + +[Term] +id: GO:1901681 +name: sulfur compound binding +is_a: GO:0005488 ! binding + +[Term] +id: GO:1901698 +name: response to nitrogen compound +is_a: GO:0042221 ! response to chemical stimulus + +[Term] +id: GO:1901699 +name: cellular response to nitrogen compound +is_a: GO:0070887 ! cellular response to chemical stimulus +is_a: GO:1901698 ! response to nitrogen compound + +[Term] +id: GO:1901700 +name: response to oxygen-containing compound +is_a: GO:0042221 ! response to chemical stimulus + +[Term] +id: GO:1901701 +name: cellular response to oxygen-containing compound +is_a: GO:0070887 ! cellular response to chemical stimulus +is_a: GO:1901700 ! response to oxygen-containing compound + +[Term] +id: GO:1901861 +name: regulation of muscle tissue development +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060537 ! muscle tissue development +relationship: regulates GO:0060537 ! muscle tissue development + +[Term] +id: GO:1901888 +name: regulation of cell junction assembly +is_a: GO:0044087 ! regulation of cellular component biogenesis +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034329 ! cell junction assembly +relationship: regulates GO:0034329 ! cell junction assembly + +[Term] +id: GO:1901890 +name: positive regulation of cell junction assembly +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051130 ! positive regulation of cellular component organization +is_a: GO:1901888 ! regulation of cell junction assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0034329 ! cell junction assembly +relationship: positively_regulates GO:0034329 ! cell junction assembly + +[Term] +id: GO:1901963 +name: regulation of cell proliferation involved in outflow tract morphogenesis +is_a: GO:2000136 ! regulation of cell proliferation involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis +relationship: regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis + +[Term] +id: GO:1901998 +name: toxin transport +is_a: GO:0006810 ! transport + +[Term] +id: GO:1902041 +name: regulation of extrinsic apoptotic signaling pathway via death domain receptors +is_a: GO:2001236 ! regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors +relationship: regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors + +[Term] +id: GO:1902042 +name: negative regulation of extrinsic apoptotic signaling pathway via death domain receptors +is_a: GO:1902041 ! regulation of extrinsic apoptotic signaling pathway via death domain receptors +is_a: GO:2001237 ! negative regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors +relationship: negatively_regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors + +[Term] +id: GO:1902043 +name: positive regulation of extrinsic apoptotic signaling pathway via death domain receptors +is_a: GO:1902041 ! regulation of extrinsic apoptotic signaling pathway via death domain receptors +is_a: GO:2001238 ! positive regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors +relationship: positively_regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors + +[Term] +id: GO:1902105 +name: regulation of leukocyte differentiation +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002521 ! leukocyte differentiation +relationship: regulates GO:0002521 ! leukocyte differentiation + +[Term] +id: GO:1902106 +name: negative regulation of leukocyte differentiation +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:1902105 ! regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002521 ! leukocyte differentiation +relationship: negatively_regulates GO:0002521 ! leukocyte differentiation + +[Term] +id: GO:1902107 +name: positive regulation of leukocyte differentiation +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:1902105 ! regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002521 ! leukocyte differentiation +relationship: positively_regulates GO:0002521 ! leukocyte differentiation + +[Term] +id: GO:1902256 +name: regulation of apoptotic process involved in outflow tract morphogenesis +is_a: GO:1902337 ! regulation of apoptotic process involved in morphogenesis +is_a: GO:2000826 ! regulation of heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis +relationship: regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis + +[Term] +id: GO:1902257 +name: negative regulation of apoptotic process involved in outflow tract morphogenesis +is_a: GO:1902256 ! regulation of apoptotic process involved in outflow tract morphogenesis +is_a: GO:1902338 ! negative regulation of apoptotic process involved in morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis +relationship: negatively_regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis + +[Term] +id: GO:1902262 +name: apoptotic process involved in patterning of blood vessels +is_a: GO:0060561 ! apoptotic process involved in morphogenesis +intersection_of: GO:0006915 ! apoptotic process +intersection_of: part_of GO:0001569 ! patterning of blood vessels +relationship: part_of GO:0001569 ! patterning of blood vessels + +[Term] +id: GO:1902284 +name: neuron projection extension involved in neuron projection guidance +is_a: GO:1990138 ! neuron projection extension +intersection_of: GO:1990138 ! neuron projection extension +intersection_of: part_of GO:0097485 ! neuron projection guidance +relationship: part_of GO:0097485 ! neuron projection guidance + +[Term] +id: GO:1902337 +name: regulation of apoptotic process involved in morphogenesis +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060561 ! apoptotic process involved in morphogenesis +relationship: regulates GO:0060561 ! apoptotic process involved in morphogenesis + +[Term] +id: GO:1902338 +name: negative regulation of apoptotic process involved in morphogenesis +is_a: GO:0043066 ! negative regulation of apoptotic process +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:1902337 ! regulation of apoptotic process involved in morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0060561 ! apoptotic process involved in morphogenesis +relationship: negatively_regulates GO:0060561 ! apoptotic process involved in morphogenesis + +[Term] +id: GO:1990138 +name: neuron projection extension +is_a: GO:0048588 ! developmental cell growth +is_a: GO:0060560 ! developmental growth involved in morphogenesis +relationship: part_of GO:0048812 ! neuron projection morphogenesis + +[Term] +id: GO:2000008 +name: regulation of protein localization to cell surface +is_a: GO:0032880 ! regulation of protein localization +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034394 ! protein localization to cell surface +relationship: regulates GO:0034394 ! protein localization to cell surface + +[Term] +id: GO:2000015 +name: regulation of determination of dorsal identity +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048263 ! determination of dorsal identity +relationship: regulates GO:0048263 ! determination of dorsal identity + +[Term] +id: GO:2000017 +name: positive regulation of determination of dorsal identity +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +is_a: GO:2000015 ! regulation of determination of dorsal identity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048263 ! determination of dorsal identity +relationship: positively_regulates GO:0048263 ! determination of dorsal identity + +[Term] +id: GO:2000018 +name: regulation of male gonad development +is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008584 ! male gonad development +relationship: regulates GO:0008584 ! male gonad development + +[Term] +id: GO:2000019 +name: negative regulation of male gonad development +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:2000018 ! regulation of male gonad development +is_a: GO:2000242 ! negative regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008584 ! male gonad development +relationship: negatively_regulates GO:0008584 ! male gonad development + +[Term] +id: GO:2000021 +name: regulation of ion homeostasis +is_a: GO:0032844 ! regulation of homeostatic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050801 ! ion homeostasis +relationship: regulates GO:0050801 ! ion homeostasis + +[Term] +id: GO:2000026 +name: regulation of multicellular organismal development +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007275 ! multicellular organismal development +relationship: regulates GO:0007275 ! multicellular organismal development + +[Term] +id: GO:2000027 +name: regulation of organ morphogenesis +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009887 ! organ morphogenesis +relationship: regulates GO:0009887 ! organ morphogenesis + +[Term] +id: GO:2000035 +name: regulation of stem cell division +is_a: GO:0051302 ! regulation of cell division +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0017145 ! stem cell division +relationship: regulates GO:0017145 ! stem cell division + +[Term] +id: GO:2000040 +name: regulation of planar cell polarity pathway involved in axis elongation +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:2000095 ! regulation of Wnt receptor signaling pathway, planar cell polarity pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003402 ! planar cell polarity pathway involved in axis elongation +relationship: regulates GO:0003402 ! planar cell polarity pathway involved in axis elongation + +[Term] +id: GO:2000041 +name: negative regulation of planar cell polarity pathway involved in axis elongation +is_a: GO:2000040 ! regulation of planar cell polarity pathway involved in axis elongation +is_a: GO:2000051 ! negative regulation of non-canonical Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003402 ! planar cell polarity pathway involved in axis elongation +relationship: negatively_regulates GO:0003402 ! planar cell polarity pathway involved in axis elongation + +[Term] +id: GO:2000043 +name: regulation of cardiac cell fate specification +is_a: GO:0042659 ! regulation of cell fate specification +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060912 ! cardiac cell fate specification +relationship: regulates GO:0060912 ! cardiac cell fate specification + +[Term] +id: GO:2000044 +name: negative regulation of cardiac cell fate specification +is_a: GO:0009996 ! negative regulation of cell fate specification +is_a: GO:2000043 ! regulation of cardiac cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0060912 ! cardiac cell fate specification +relationship: negatively_regulates GO:0060912 ! cardiac cell fate specification + +[Term] +id: GO:2000047 +name: regulation of cell-cell adhesion mediated by cadherin +is_a: GO:0033632 ! regulation of cell-cell adhesion mediated by integrin +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044331 ! cell-cell adhesion mediated by cadherin +relationship: regulates GO:0044331 ! cell-cell adhesion mediated by cadherin + +[Term] +id: GO:2000049 +name: positive regulation of cell-cell adhesion mediated by cadherin +is_a: GO:0033634 ! positive regulation of cell-cell adhesion mediated by integrin +is_a: GO:2000047 ! regulation of cell-cell adhesion mediated by cadherin +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044331 ! cell-cell adhesion mediated by cadherin +relationship: positively_regulates GO:0044331 ! cell-cell adhesion mediated by cadherin + +[Term] +id: GO:2000050 +name: regulation of non-canonical Wnt receptor signaling pathway +is_a: GO:0030111 ! regulation of Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035567 ! non-canonical Wnt receptor signaling pathway +relationship: regulates GO:0035567 ! non-canonical Wnt receptor signaling pathway + +[Term] +id: GO:2000051 +name: negative regulation of non-canonical Wnt receptor signaling pathway +is_a: GO:0030178 ! negative regulation of Wnt receptor signaling pathway +is_a: GO:2000050 ! regulation of non-canonical Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0035567 ! non-canonical Wnt receptor signaling pathway +relationship: negatively_regulates GO:0035567 ! non-canonical Wnt receptor signaling pathway + +[Term] +id: GO:2000052 +name: positive regulation of non-canonical Wnt receptor signaling pathway +is_a: GO:0030177 ! positive regulation of Wnt receptor signaling pathway +is_a: GO:2000050 ! regulation of non-canonical Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0035567 ! non-canonical Wnt receptor signaling pathway +relationship: positively_regulates GO:0035567 ! non-canonical Wnt receptor signaling pathway + +[Term] +id: GO:2000053 +name: regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification +is_a: GO:0030111 ! regulation of Wnt receptor signaling pathway +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044332 ! Wnt receptor signaling pathway involved in dorsal/ventral axis specification +relationship: regulates GO:0044332 ! Wnt receptor signaling pathway involved in dorsal/ventral axis specification + +[Term] +id: GO:2000054 +name: negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification +is_a: GO:0030178 ! negative regulation of Wnt receptor signaling pathway +is_a: GO:2000053 ! regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044332 ! Wnt receptor signaling pathway involved in dorsal/ventral axis specification +relationship: negatively_regulates GO:0044332 ! Wnt receptor signaling pathway involved in dorsal/ventral axis specification + +[Term] +id: GO:2000055 +name: positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification +is_a: GO:0030177 ! positive regulation of Wnt receptor signaling pathway +is_a: GO:2000053 ! regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044332 ! Wnt receptor signaling pathway involved in dorsal/ventral axis specification +relationship: positively_regulates GO:0044332 ! Wnt receptor signaling pathway involved in dorsal/ventral axis specification + +[Term] +id: GO:2000056 +name: regulation of Wnt receptor signaling pathway involved in digestive tract morphogenesis +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0030111 ! regulation of Wnt receptor signaling pathway +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044333 ! Wnt receptor signaling pathway involved in digestive tract morphogenesis +relationship: regulates GO:0044333 ! Wnt receptor signaling pathway involved in digestive tract morphogenesis + +[Term] +id: GO:2000057 +name: negative regulation of Wnt receptor signaling pathway involved in digestive tract morphogenesis +is_a: GO:0030178 ! negative regulation of Wnt receptor signaling pathway +is_a: GO:2000056 ! regulation of Wnt receptor signaling pathway involved in digestive tract morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044333 ! Wnt receptor signaling pathway involved in digestive tract morphogenesis +relationship: negatively_regulates GO:0044333 ! Wnt receptor signaling pathway involved in digestive tract morphogenesis + +[Term] +id: GO:2000058 +name: regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process +is_a: GO:0030162 ! regulation of proteolysis +is_a: GO:0031329 ! regulation of cellular catabolic process +is_a: GO:0031396 ! regulation of protein ubiquitination +is_a: GO:0042176 ! regulation of protein catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042787 ! protein ubiquitination involved in ubiquitin-dependent protein catabolic process +relationship: regulates GO:0042787 ! protein ubiquitination involved in ubiquitin-dependent protein catabolic process + +[Term] +id: GO:2000059 +name: negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process +is_a: GO:0031397 ! negative regulation of protein ubiquitination +is_a: GO:2000058 ! regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042787 ! protein ubiquitination involved in ubiquitin-dependent protein catabolic process +relationship: negatively_regulates GO:0042787 ! protein ubiquitination involved in ubiquitin-dependent protein catabolic process + +[Term] +id: GO:2000064 +name: regulation of cortisol biosynthetic process +is_a: GO:0010566 ! regulation of ketone biosynthetic process +is_a: GO:0031946 ! regulation of glucocorticoid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034651 ! cortisol biosynthetic process +relationship: regulates GO:0034651 ! cortisol biosynthetic process + +[Term] +id: GO:2000066 +name: positive regulation of cortisol biosynthetic process +is_a: GO:0031948 ! positive regulation of glucocorticoid biosynthetic process +is_a: GO:2000064 ! regulation of cortisol biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0034651 ! cortisol biosynthetic process +relationship: positively_regulates GO:0034651 ! cortisol biosynthetic process + +[Term] +id: GO:2000079 +name: regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation +is_a: GO:0042127 ! regulation of cell proliferation +is_a: GO:0060828 ! regulation of canonical Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044343 ! canonical Wnt receptor signaling pathway involved in regulation of type B pancreatic cell proliferation +relationship: regulates GO:0044343 ! canonical Wnt receptor signaling pathway involved in regulation of type B pancreatic cell proliferation + +[Term] +id: GO:2000080 +name: negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation +is_a: GO:0090090 ! negative regulation of canonical Wnt receptor signaling pathway +is_a: GO:2000079 ! regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044343 ! canonical Wnt receptor signaling pathway involved in regulation of type B pancreatic cell proliferation +relationship: negatively_regulates GO:0044343 ! canonical Wnt receptor signaling pathway involved in regulation of type B pancreatic cell proliferation + +[Term] +id: GO:2000081 +name: positive regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation +is_a: GO:0090263 ! positive regulation of canonical Wnt receptor signaling pathway +is_a: GO:2000079 ! regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044343 ! canonical Wnt receptor signaling pathway involved in regulation of type B pancreatic cell proliferation +relationship: positively_regulates GO:0044343 ! canonical Wnt receptor signaling pathway involved in regulation of type B pancreatic cell proliferation + +[Term] +id: GO:2000095 +name: regulation of Wnt receptor signaling pathway, planar cell polarity pathway +is_a: GO:2000050 ! regulation of non-canonical Wnt receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060071 ! Wnt receptor signaling pathway, planar cell polarity pathway +relationship: regulates GO:0060071 ! Wnt receptor signaling pathway, planar cell polarity pathway + +[Term] +id: GO:2000106 +name: regulation of leukocyte apoptotic process +is_a: GO:0042981 ! regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0071887 ! leukocyte apoptotic process +relationship: regulates GO:0071887 ! leukocyte apoptotic process + +[Term] +id: GO:2000108 +name: positive regulation of leukocyte apoptotic process +is_a: GO:0043065 ! positive regulation of apoptotic process +is_a: GO:2000106 ! regulation of leukocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0071887 ! leukocyte apoptotic process +relationship: positively_regulates GO:0071887 ! leukocyte apoptotic process + +[Term] +id: GO:2000112 +name: regulation of cellular macromolecule biosynthetic process +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034645 ! cellular macromolecule biosynthetic process +relationship: regulates GO:0034645 ! cellular macromolecule biosynthetic process + +[Term] +id: GO:2000113 +name: negative regulation of cellular macromolecule biosynthetic process +is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process +is_a: GO:0031327 ! negative regulation of cellular biosynthetic process +is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0034645 ! cellular macromolecule biosynthetic process +relationship: negatively_regulates GO:0034645 ! cellular macromolecule biosynthetic process + +[Term] +id: GO:2000116 +name: regulation of cysteine-type endopeptidase activity +is_a: GO:0052548 ! regulation of endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004197 ! cysteine-type endopeptidase activity +relationship: regulates GO:0004197 ! cysteine-type endopeptidase activity + +[Term] +id: GO:2000117 +name: negative regulation of cysteine-type endopeptidase activity +is_a: GO:0010951 ! negative regulation of endopeptidase activity +is_a: GO:2000116 ! regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004197 ! cysteine-type endopeptidase activity +relationship: negatively_regulates GO:0004197 ! cysteine-type endopeptidase activity + +[Term] +id: GO:2000136 +name: regulation of cell proliferation involved in heart morphogenesis +is_a: GO:0042127 ! regulation of cell proliferation +is_a: GO:2000826 ! regulation of heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061323 ! cell proliferation involved in heart morphogenesis +relationship: regulates GO:0061323 ! cell proliferation involved in heart morphogenesis + +[Term] +id: GO:2000142 +name: regulation of DNA-dependent transcription, initiation +is_a: GO:0006355 ! regulation of transcription, DNA-dependent +is_a: GO:0043254 ! regulation of protein complex assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006352 ! DNA-dependent transcription, initiation +relationship: regulates GO:0006352 ! DNA-dependent transcription, initiation + +[Term] +id: GO:2000143 +name: negative regulation of DNA-dependent transcription, initiation +is_a: GO:0031333 ! negative regulation of protein complex assembly +is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent +is_a: GO:2000142 ! regulation of DNA-dependent transcription, initiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006352 ! DNA-dependent transcription, initiation +relationship: negatively_regulates GO:0006352 ! DNA-dependent transcription, initiation + +[Term] +id: GO:2000145 +name: regulation of cell motility +is_a: GO:0040012 ! regulation of locomotion +is_a: GO:0051270 ! regulation of cellular component movement +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048870 ! cell motility +relationship: regulates GO:0048870 ! cell motility + +[Term] +id: GO:2000146 +name: negative regulation of cell motility +is_a: GO:0040013 ! negative regulation of locomotion +is_a: GO:0051271 ! negative regulation of cellular component movement +is_a: GO:2000145 ! regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048870 ! cell motility +relationship: negatively_regulates GO:0048870 ! cell motility + +[Term] +id: GO:2000147 +name: positive regulation of cell motility +is_a: GO:0040017 ! positive regulation of locomotion +is_a: GO:0051272 ! positive regulation of cellular component movement +is_a: GO:2000145 ! regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048870 ! cell motility +relationship: positively_regulates GO:0048870 ! cell motility + +[Term] +id: GO:2000148 +name: regulation of planar cell polarity pathway involved in ventricular septum morphogenesis +is_a: GO:1901219 ! regulation of cardiac chamber morphogenesis +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061348 ! planar cell polarity pathway involved in ventricular septum morphogenesis +relationship: regulates GO:0061348 ! planar cell polarity pathway involved in ventricular septum morphogenesis + +[Term] +id: GO:2000149 +name: negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis +is_a: GO:2000148 ! regulation of planar cell polarity pathway involved in ventricular septum morphogenesis +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061348 ! planar cell polarity pathway involved in ventricular septum morphogenesis +relationship: negatively_regulates GO:0061348 ! planar cell polarity pathway involved in ventricular septum morphogenesis + +[Term] +id: GO:2000150 +name: regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +is_a: GO:0055024 ! regulation of cardiac muscle tissue development +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061350 ! planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +relationship: regulates GO:0061350 ! planar cell polarity pathway involved in cardiac muscle tissue morphogenesis + +[Term] +id: GO:2000151 +name: negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +is_a: GO:2000150 ! regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061350 ! planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +relationship: negatively_regulates GO:0061350 ! planar cell polarity pathway involved in cardiac muscle tissue morphogenesis + +[Term] +id: GO:2000159 +name: regulation of planar cell polarity pathway involved in heart morphogenesis +is_a: GO:0003307 ! regulation of Wnt receptor signaling pathway involved in heart development +is_a: GO:2000095 ! regulation of Wnt receptor signaling pathway, planar cell polarity pathway +is_a: GO:2000826 ! regulation of heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: regulates GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis + +[Term] +id: GO:2000160 +name: negative regulation of planar cell polarity pathway involved in heart morphogenesis +is_a: GO:0003308 ! negative regulation of Wnt receptor signaling pathway involved in heart development +is_a: GO:2000051 ! negative regulation of non-canonical Wnt receptor signaling pathway +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: negatively_regulates GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis + +[Term] +id: GO:2000161 +name: regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis +is_a: GO:1901219 ! regulation of cardiac chamber morphogenesis +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061349 ! planar cell polarity pathway involved in cardiac right atrium morphogenesis +relationship: regulates GO:0061349 ! planar cell polarity pathway involved in cardiac right atrium morphogenesis + +[Term] +id: GO:2000162 +name: negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +is_a: GO:2000161 ! regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061349 ! planar cell polarity pathway involved in cardiac right atrium morphogenesis +relationship: negatively_regulates GO:0061349 ! planar cell polarity pathway involved in cardiac right atrium morphogenesis + +[Term] +id: GO:2000163 +name: regulation of planar cell polarity pathway involved in outflow tract morphogenesis +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061347 ! planar cell polarity pathway involved in outflow tract morphogenesis +relationship: regulates GO:0061347 ! planar cell polarity pathway involved in outflow tract morphogenesis + +[Term] +id: GO:2000164 +name: negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +is_a: GO:2000163 ! regulation of planar cell polarity pathway involved in outflow tract morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061347 ! planar cell polarity pathway involved in outflow tract morphogenesis +relationship: negatively_regulates GO:0061347 ! planar cell polarity pathway involved in outflow tract morphogenesis + +[Term] +id: GO:2000165 +name: regulation of planar cell polarity pathway involved in pericardium morphogenesis +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061354 ! planar cell polarity pathway involved in pericardium morphogenesis +relationship: regulates GO:0061354 ! planar cell polarity pathway involved in pericardium morphogenesis + +[Term] +id: GO:2000166 +name: negative regulation of planar cell polarity pathway involved in pericardium morphogenesis +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +is_a: GO:2000165 ! regulation of planar cell polarity pathway involved in pericardium morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061354 ! planar cell polarity pathway involved in pericardium morphogenesis +relationship: negatively_regulates GO:0061354 ! planar cell polarity pathway involved in pericardium morphogenesis + +[Term] +id: GO:2000167 +name: regulation of planar cell polarity pathway involved in neural tube closure +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051960 ! regulation of nervous system development +is_a: GO:2000095 ! regulation of Wnt receptor signaling pathway, planar cell polarity pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0090179 ! planar cell polarity pathway involved in neural tube closure +relationship: regulates GO:0090179 ! planar cell polarity pathway involved in neural tube closure + +[Term] +id: GO:2000168 +name: negative regulation of planar cell polarity pathway involved in neural tube closure +is_a: GO:2000051 ! negative regulation of non-canonical Wnt receptor signaling pathway +is_a: GO:2000167 ! regulation of planar cell polarity pathway involved in neural tube closure +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0090179 ! planar cell polarity pathway involved in neural tube closure +relationship: negatively_regulates GO:0090179 ! planar cell polarity pathway involved in neural tube closure + +[Term] +id: GO:2000177 +name: regulation of neural precursor cell proliferation +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061351 ! neural precursor cell proliferation +relationship: regulates GO:0061351 ! neural precursor cell proliferation + +[Term] +id: GO:2000179 +name: positive regulation of neural precursor cell proliferation +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:2000177 ! regulation of neural precursor cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061351 ! neural precursor cell proliferation +relationship: positively_regulates GO:0061351 ! neural precursor cell proliferation + +[Term] +id: GO:2000180 +name: negative regulation of androgen biosynthetic process +is_a: GO:0010894 ! negative regulation of steroid biosynthetic process +is_a: GO:0032353 ! negative regulation of hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006702 ! androgen biosynthetic process +relationship: negatively_regulates GO:0006702 ! androgen biosynthetic process + +[Term] +id: GO:2000181 +name: negative regulation of blood vessel morphogenesis +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:1901342 ! regulation of vasculature development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048514 ! blood vessel morphogenesis +relationship: negatively_regulates GO:0048514 ! blood vessel morphogenesis + +[Term] +id: GO:2000224 +name: regulation of testosterone biosynthetic process +is_a: GO:0010566 ! regulation of ketone biosynthetic process +is_a: GO:0046885 ! regulation of hormone biosynthetic process +is_a: GO:0050810 ! regulation of steroid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061370 ! testosterone biosynthetic process +relationship: regulates GO:0061370 ! testosterone biosynthetic process + +[Term] +id: GO:2000225 +name: negative regulation of testosterone biosynthetic process +is_a: GO:2000180 ! negative regulation of androgen biosynthetic process +is_a: GO:2000224 ! regulation of testosterone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061370 ! testosterone biosynthetic process +relationship: negatively_regulates GO:0061370 ! testosterone biosynthetic process + +[Term] +id: GO:2000241 +name: regulation of reproductive process +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0022414 ! reproductive process +relationship: regulates GO:0022414 ! reproductive process + +[Term] +id: GO:2000242 +name: negative regulation of reproductive process +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0022414 ! reproductive process +relationship: negatively_regulates GO:0022414 ! reproductive process + +[Term] +id: GO:2000243 +name: positive regulation of reproductive process +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0022414 ! reproductive process +relationship: positively_regulates GO:0022414 ! reproductive process + +[Term] +id: GO:2000269 +name: regulation of fibroblast apoptotic process +is_a: GO:0042981 ! regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044346 ! fibroblast apoptotic process +relationship: regulates GO:0044346 ! fibroblast apoptotic process + +[Term] +id: GO:2000270 +name: negative regulation of fibroblast apoptotic process +is_a: GO:0043066 ! negative regulation of apoptotic process +is_a: GO:2000269 ! regulation of fibroblast apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044346 ! fibroblast apoptotic process +relationship: negatively_regulates GO:0044346 ! fibroblast apoptotic process + +[Term] +id: GO:2000271 +name: positive regulation of fibroblast apoptotic process +is_a: GO:0043065 ! positive regulation of apoptotic process +is_a: GO:2000269 ! regulation of fibroblast apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044346 ! fibroblast apoptotic process +relationship: positively_regulates GO:0044346 ! fibroblast apoptotic process + +[Term] +id: GO:2000272 +name: negative regulation of receptor activity +is_a: GO:0010469 ! regulation of receptor activity +is_a: GO:0044092 ! negative regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004872 ! receptor activity +relationship: negatively_regulates GO:0004872 ! receptor activity + +[Term] +id: GO:2000273 +name: positive regulation of receptor activity +is_a: GO:0010469 ! regulation of receptor activity +is_a: GO:0044093 ! positive regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004872 ! receptor activity +relationship: positively_regulates GO:0004872 ! receptor activity + +[Term] +id: GO:2000380 +name: regulation of mesoderm development +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007498 ! mesoderm development +relationship: regulates GO:0007498 ! mesoderm development + +[Term] +id: GO:2000401 +name: regulation of lymphocyte migration +is_a: GO:0002685 ! regulation of leukocyte migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072676 ! lymphocyte migration +relationship: regulates GO:0072676 ! lymphocyte migration + +[Term] +id: GO:2000403 +name: positive regulation of lymphocyte migration +is_a: GO:0002687 ! positive regulation of leukocyte migration +is_a: GO:2000401 ! regulation of lymphocyte migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0072676 ! lymphocyte migration +relationship: positively_regulates GO:0072676 ! lymphocyte migration + +[Term] +id: GO:2000404 +name: regulation of T cell migration +is_a: GO:2000401 ! regulation of lymphocyte migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072678 ! T cell migration +relationship: regulates GO:0072678 ! T cell migration + +[Term] +id: GO:2000406 +name: positive regulation of T cell migration +is_a: GO:2000403 ! positive regulation of lymphocyte migration +is_a: GO:2000404 ! regulation of T cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0072678 ! T cell migration +relationship: positively_regulates GO:0072678 ! T cell migration + +[Term] +id: GO:2000482 +name: regulation of interleukin-8 secretion +is_a: GO:0032677 ! regulation of interleukin-8 production +is_a: GO:0050707 ! regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072606 ! interleukin-8 secretion +relationship: regulates GO:0072606 ! interleukin-8 secretion + +[Term] +id: GO:2000484 +name: positive regulation of interleukin-8 secretion +is_a: GO:0050715 ! positive regulation of cytokine secretion +is_a: GO:2000482 ! regulation of interleukin-8 secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0072606 ! interleukin-8 secretion +relationship: positively_regulates GO:0072606 ! interleukin-8 secretion + +[Term] +id: GO:2000543 +name: positive regulation of gastrulation +is_a: GO:0010470 ! regulation of gastrulation +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007369 ! gastrulation +relationship: positively_regulates GO:0007369 ! gastrulation + +[Term] +id: GO:2000647 +name: negative regulation of stem cell proliferation +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0072091 ! regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0072089 ! stem cell proliferation +relationship: negatively_regulates GO:0072089 ! stem cell proliferation + +[Term] +id: GO:2000648 +name: positive regulation of stem cell proliferation +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0072091 ! regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0072089 ! stem cell proliferation +relationship: positively_regulates GO:0072089 ! stem cell proliferation + +[Term] +id: GO:2000696 +name: regulation of epithelial cell differentiation involved in kidney development +is_a: GO:0030856 ! regulation of epithelial cell differentiation +is_a: GO:0090183 ! regulation of kidney development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035850 ! epithelial cell differentiation involved in kidney development +relationship: regulates GO:0035850 ! epithelial cell differentiation involved in kidney development + +[Term] +id: GO:2000725 +name: regulation of cardiac muscle cell differentiation +is_a: GO:0051153 ! regulation of striated muscle cell differentiation +is_a: GO:0055024 ! regulation of cardiac muscle tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0055007 ! cardiac muscle cell differentiation +relationship: regulates GO:0055007 ! cardiac muscle cell differentiation + +[Term] +id: GO:2000727 +name: positive regulation of cardiac muscle cell differentiation +is_a: GO:0051155 ! positive regulation of striated muscle cell differentiation +is_a: GO:2000725 ! regulation of cardiac muscle cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0055007 ! cardiac muscle cell differentiation +relationship: positively_regulates GO:0055007 ! cardiac muscle cell differentiation + +[Term] +id: GO:2000736 +name: regulation of stem cell differentiation +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048863 ! stem cell differentiation +relationship: regulates GO:0048863 ! stem cell differentiation + +[Term] +id: GO:2000794 +name: regulation of epithelial cell proliferation involved in lung morphogenesis +is_a: GO:0050678 ! regulation of epithelial cell proliferation +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis +relationship: regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis + +[Term] +id: GO:2000823 +name: regulation of androgen receptor activity +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0010469 ! regulation of receptor activity +is_a: GO:0051090 ! regulation of sequence-specific DNA binding transcription factor activity +is_a: GO:0060765 ! regulation of androgen receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004882 ! androgen receptor activity +relationship: regulates GO:0004882 ! androgen receptor activity + +[Term] +id: GO:2000824 +name: negative regulation of androgen receptor activity +is_a: GO:0043433 ! negative regulation of sequence-specific DNA binding transcription factor activity +is_a: GO:2000272 ! negative regulation of receptor activity +is_a: GO:2000823 ! regulation of androgen receptor activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004882 ! androgen receptor activity +relationship: negatively_regulates GO:0004882 ! androgen receptor activity + +[Term] +id: GO:2000826 +name: regulation of heart morphogenesis +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003007 ! heart morphogenesis +relationship: regulates GO:0003007 ! heart morphogenesis + +[Term] +id: GO:2000970 +name: regulation of detection of glucose +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051594 ! detection of glucose +relationship: regulates GO:0051594 ! detection of glucose + +[Term] +id: GO:2000971 +name: negative regulation of detection of glucose +is_a: GO:0048585 ! negative regulation of response to stimulus +is_a: GO:2000970 ! regulation of detection of glucose +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0051594 ! detection of glucose +relationship: negatively_regulates GO:0051594 ! detection of glucose + +[Term] +id: GO:2000976 +name: regulation of transcription from RNA polymerase II promoter involved in detection of glucose +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +intersection_of: part_of GO:0051594 ! detection of glucose +relationship: part_of GO:0051594 ! detection of glucose + +[Term] +id: GO:2001012 +name: mesenchymal cell differentiation involved in renal system development +is_a: GO:0048762 ! mesenchymal cell differentiation +intersection_of: GO:0048762 ! mesenchymal cell differentiation +intersection_of: part_of GO:0072001 ! renal system development +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:2001056 +name: positive regulation of cysteine-type endopeptidase activity +is_a: GO:0010950 ! positive regulation of endopeptidase activity +is_a: GO:2000116 ! regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004197 ! cysteine-type endopeptidase activity +relationship: positively_regulates GO:0004197 ! cysteine-type endopeptidase activity + +[Term] +id: GO:2001141 +name: regulation of RNA biosynthetic process +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0051252 ! regulation of RNA metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032774 ! RNA biosynthetic process +relationship: regulates GO:0032774 ! RNA biosynthetic process + +[Term] +id: GO:2001233 +name: regulation of apoptotic signaling pathway +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0042981 ! regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097190 ! apoptotic signaling pathway +relationship: regulates GO:0097190 ! apoptotic signaling pathway + +[Term] +id: GO:2001234 +name: negative regulation of apoptotic signaling pathway +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:2001233 ! regulation of apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097190 ! apoptotic signaling pathway +relationship: negatively_regulates GO:0097190 ! apoptotic signaling pathway + +[Term] +id: GO:2001235 +name: positive regulation of apoptotic signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:2001233 ! regulation of apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0097190 ! apoptotic signaling pathway +relationship: positively_regulates GO:0097190 ! apoptotic signaling pathway + +[Term] +id: GO:2001236 +name: regulation of extrinsic apoptotic signaling pathway +is_a: GO:2001233 ! regulation of apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: regulates GO:0097191 ! extrinsic apoptotic signaling pathway + +[Term] +id: GO:2001237 +name: negative regulation of extrinsic apoptotic signaling pathway +is_a: GO:2001234 ! negative regulation of apoptotic signaling pathway +is_a: GO:2001236 ! regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: negatively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway + +[Term] +id: GO:2001238 +name: positive regulation of extrinsic apoptotic signaling pathway +is_a: GO:2001235 ! positive regulation of apoptotic signaling pathway +is_a: GO:2001236 ! regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: positively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway + +[Typedef] +id: has_part +name: has_part +xref: BFO:0000051 +xref: OBO_REL:has_part +is_transitive: true +inverse_of: part_of + +[Typedef] +id: negatively_regulates +name: negatively_regulates +xref: RO:0002212 +is_a: regulates ! regulates + +[Typedef] +id: occurs_in +name: occurs in +xref: BFO:0000066 + +[Typedef] +id: part_of +name: part_of +xref: BFO:0000050 +xref: OBO_REL:part_of +is_transitive: true + +[Typedef] +id: positively_regulates +name: positively_regulates +xref: RO:0002213 +is_a: regulates ! regulates + +[Typedef] +id: regulates +name: regulates +xref: RO:0002211 + diff --git a/minerva-core/src/test/resources/mgi-go.obo b/minerva-core/src/test/resources/mgi-go.obo new file mode 100644 index 00000000..7ab19ab2 --- /dev/null +++ b/minerva-core/src/test/resources/mgi-go.obo @@ -0,0 +1,38460 @@ +format-version: 1.2 +subsetdef: Cross_product_review "Involved_in" +subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" +subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" +subsetdef: goslim_aspergillus "Aspergillus GO slim" +subsetdef: goslim_candida "Candida GO slim" +subsetdef: goslim_generic "Generic GO slim" +subsetdef: goslim_metagenomics "Metagenomics GO slim" +subsetdef: goslim_pir "PIR GO slim" +subsetdef: goslim_plant "Plant GO slim" +subsetdef: goslim_pombe "Fission yeast GO slim" +subsetdef: goslim_yeast "Yeast GO slim" +subsetdef: gosubset_prok "Prokaryotic GO subset" +subsetdef: mf_needs_review "Catalytic activity terms in need of attention" +subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors" +subsetdef: virus_checked "Viral overhaul terms" +synonymtypedef: systematic_synonym "Systematic synonym" EXACT +ontology: go-gaf-subset + +[Term] +id: GO:0000003 +name: reproduction +namespace: biological_process +alt_id: GO:0019952 +alt_id: GO:0050876 +def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732] +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "reproductive physiological process" EXACT [] +xref: Wikipedia:Reproduction +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0000122 +name: negative regulation of transcription from RNA polymerase II promoter +namespace: biological_process +alt_id: GO:0010553 +alt_id: GO:0045816 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] +synonym: "down regulation of global transcription from RNA polymerase II promoter" RELATED [] +synonym: "down regulation of transcription from RNA polymerase II promoter" EXACT [] +synonym: "down-regulation of global transcription from RNA polymerase II promoter" RELATED [] +synonym: "down-regulation of transcription from RNA polymerase II promoter" EXACT [] +synonym: "downregulation of global transcription from RNA polymerase II promoter" RELATED [] +synonym: "downregulation of transcription from RNA polymerase II promoter" EXACT [] +synonym: "inhibition of global transcription from RNA polymerase II promoter" RELATED [] +synonym: "inhibition of transcription from RNA polymerase II promoter" EXACT [] +synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] +synonym: "negative regulation of global transcription from Pol II promoter" RELATED [] +synonym: "negative regulation of transcription from Pol II promoter" EXACT [] +synonym: "negative regulation of transcription from RNA polymerase II promoter, global" RELATED [] +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0045892 ! negative regulation of transcription, DNA-templated +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter +relationship: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0000165 +name: MAPK cascade +namespace: biological_process +def: "An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell." [GOC:bf, GOC:mtg_signaling_feb11, PMID:20811974, PMID:9561267] +comment: MAPK cascades lie downstream of many cell surface receptors and cooperate in transmitting various extracellular signals to the nucleus. One way by which the specificity of each cascade is regulated is through the existence of several distinct components in each tier of the different cascades. The cascades are typically named according to the component in the MAPK tier. +synonym: "ERK/MAPK cascade" NARROW [] +synonym: "MAP kinase cascade" EXACT [] +synonym: "MAP kinase kinase kinase cascade" EXACT [] +synonym: "MAPK signal transduction" EXACT [GOC:signaling] +synonym: "MAPK signaling" RELATED [] +synonym: "MAPK signalling" RELATED [] +synonym: "MAPKKK cascade" EXACT [GOC:curators] +synonym: "MAPKKK cascade during sporulation" NARROW [] +synonym: "mitogen-activated protein kinase cascade" EXACT [GOC:bf] +xref: Reactome:REACT_101634 "RAF/MAP kinase cascade, Bos taurus" +xref: Reactome:REACT_107261 "RAF/MAP kinase cascade, Saccharomyces cerevisiae" +xref: Reactome:REACT_107863 "RAF/MAP kinase cascade, Canis familiaris" +xref: Reactome:REACT_108330 "RAF/MAP kinase cascade, Xenopus tropicalis" +xref: Reactome:REACT_112235 "RAF/MAP kinase cascade, Dictyostelium discoideum" +xref: Reactome:REACT_112942 "RAF/MAP kinase cascade, Arabidopsis thaliana" +xref: Reactome:REACT_113285 "RAF/MAP kinase cascade, Oryza sativa" +xref: Reactome:REACT_634 "RAF/MAP kinase cascade, Homo sapiens" +xref: Reactome:REACT_79658 "RAF/MAP kinase cascade, Schizosaccharomyces pombe" +xref: Reactome:REACT_85806 "RAF/MAP kinase cascade, Drosophila melanogaster" +xref: Reactome:REACT_87028 "RAF/MAP kinase cascade, Danio rerio" +xref: Reactome:REACT_87232 "RAF/MAP kinase cascade, Mus musculus" +xref: Reactome:REACT_87855 "RAF/MAP kinase cascade, Rattus norvegicus" +xref: Reactome:REACT_92078 "RAF/MAP kinase cascade, Sus scrofa" +xref: Reactome:REACT_92987 "RAF/MAP kinase cascade, Caenorhabditis elegans" +xref: Reactome:REACT_94585 "RAF/MAP kinase cascade, Taeniopygia guttata" +xref: Reactome:REACT_94805 "RAF/MAP kinase cascade, Gallus gallus" +xref: Wikipedia:MAPK_cascade +xref: Wikipedia:Mitogen-activated_protein_kinase +is_a: GO:0023014 ! signal transduction by phosphorylation +is_a: GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0000187 +name: activation of MAPK activity +namespace: biological_process +def: "The initiation of the activity of the inactive enzyme MAP kinase (MAPK)." [PMID:9561267] +synonym: "activation of MAP kinase" EXACT [] +synonym: "activation of MAPK activity during sporulation" NARROW [] +synonym: "MAPK activation" EXACT [] +xref: Reactome:REACT_100881 "activated TAK1 mediates p38 MAPK activation, Canis familiaris" +xref: Reactome:REACT_101870 "ERK activation, Caenorhabditis elegans" +xref: Reactome:REACT_101978 "ERK activation, Drosophila melanogaster" +xref: Reactome:REACT_102664 "activated TAK1 mediates p38 MAPK activation, Caenorhabditis elegans" +xref: Reactome:REACT_102813 "activated TAK1 mediates p38 MAPK activation, Arabidopsis thaliana" +xref: Reactome:REACT_103235 "ERK activation, Sus scrofa" +xref: Reactome:REACT_103251 "activated TAK1 mediates p38 MAPK activation, Dictyostelium discoideum" +xref: Reactome:REACT_106101 "ERK activation, Bos taurus" +xref: Reactome:REACT_112664 "ERK activation, Oryza sativa" +xref: Reactome:REACT_113767 "ERK activation, Dictyostelium discoideum" +xref: Reactome:REACT_114778 "ERK activation, Arabidopsis thaliana" +xref: Reactome:REACT_1482 "ERK activation, Homo sapiens" +xref: Reactome:REACT_21399 "activated TAK1 mediates p38 MAPK activation, Homo sapiens" +xref: Reactome:REACT_25355 "MAPK activation in TLR cascade, Gallus gallus" +xref: Reactome:REACT_25370 "Activated TAK1 mediates p38 MAP kinase phosphorylation, Gallus gallus" +xref: Reactome:REACT_28684 "ERK activation, Gallus gallus" +xref: Reactome:REACT_29727 "activated TAK1 mediates p38 MAPK activation, Xenopus tropicalis" +xref: Reactome:REACT_30502 "ERK activation, Saccharomyces cerevisiae" +xref: Reactome:REACT_32301 "activated TAK1 mediates p38 MAPK activation, Rattus norvegicus" +xref: Reactome:REACT_34590 "ERK activation, Rattus norvegicus" +xref: Reactome:REACT_77440 "activated TAK1 mediates p38 MAPK activation, Mus musculus" +xref: Reactome:REACT_77987 "ERK activation, Taeniopygia guttata" +xref: Reactome:REACT_78017 "activated TAK1 mediates p38 MAPK activation, Bos taurus" +xref: Reactome:REACT_83894 "activated TAK1 mediates p38 MAPK activation, Sus scrofa" +xref: Reactome:REACT_84937 "ERK activation, Schizosaccharomyces pombe" +xref: Reactome:REACT_86273 "activated TAK1 mediates p38 MAPK activation, Taeniopygia guttata" +xref: Reactome:REACT_86655 "activated TAK1 mediates p38 MAPK activation, Danio rerio" +xref: Reactome:REACT_87442 "activated TAK1 mediates p38 MAPK activation, Drosophila melanogaster" +xref: Reactome:REACT_88492 "ERK activation, Canis familiaris" +xref: Reactome:REACT_88606 "ERK activation, Mus musculus" +xref: Reactome:REACT_91962 "activated TAK1 mediates p38 MAPK activation, Oryza sativa" +xref: Reactome:REACT_93371 "activated TAK1 mediates p38 MAPK activation, Gallus gallus" +xref: Reactome:REACT_98123 "ERK activation, Xenopus tropicalis" +xref: Reactome:REACT_99633 "ERK activation, Danio rerio" +is_a: GO:0032147 ! activation of protein kinase activity +is_a: GO:0043406 ! positive regulation of MAP kinase activity + +[Term] +id: GO:0000226 +name: microtubule cytoskeleton organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GOC:mah] +synonym: "microtubule cytoskeleton organisation" EXACT [GOC:mah] +synonym: "microtubule cytoskeleton organization and biogenesis" RELATED [GOC:mah] +synonym: "microtubule dynamics" EXACT [GOC:dph, GOC:tb] +is_a: GO:0007010 ! cytoskeleton organization +is_a: GO:0007017 ! microtubule-based process +is_a: GO:1902589 ! single-organism organelle organization + +[Term] +id: GO:0000228 +name: nuclear chromosome +namespace: cellular_component +def: "A chromosome found in the nucleus of a eukaryotic cell." [GOC:mah] +subset: goslim_generic +synonym: "nuclear interphase chromosome" NARROW [] +is_a: GO:0005694 ! chromosome +is_a: GO:0044428 ! nuclear part +intersection_of: GO:0005694 ! chromosome +intersection_of: part_of GO:0005634 ! nucleus +relationship: part_of GO:0031981 ! nuclear lumen + +[Term] +id: GO:0000278 +name: mitotic cell cycle +namespace: biological_process +def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] +subset: goslim_yeast +xref: Reactome:REACT_100451 "Cell Cycle, Mitotic, Taeniopygia guttata" +xref: Reactome:REACT_104035 "Cell Cycle, Mitotic, Sus scrofa" +xref: Reactome:REACT_104195 "Cell Cycle, Mitotic, Canis familiaris" +xref: Reactome:REACT_105856 "Cell Cycle, Mitotic, Danio rerio" +xref: Reactome:REACT_108233 "Cell Cycle, Mitotic, Saccharomyces cerevisiae" +xref: Reactome:REACT_152 "Cell Cycle, Mitotic, Homo sapiens" +xref: Reactome:REACT_28464 "Cell Cycle, Mitotic, Xenopus tropicalis" +xref: Reactome:REACT_28953 "Cell Cycle, Mitotic, Bos taurus" +xref: Reactome:REACT_33388 "Cell Cycle, Mitotic, Rattus norvegicus" +xref: Reactome:REACT_53493 "Cell Cycle, Mitotic, Plasmodium falciparum" +xref: Reactome:REACT_79085 "Cell Cycle, Mitotic, Schizosaccharomyces pombe" +xref: Reactome:REACT_84794 "Cell Cycle, Mitotic, Caenorhabditis elegans" +xref: Reactome:REACT_85137 "Cell Cycle, Mitotic, Gallus gallus" +xref: Reactome:REACT_85950 "Cell Cycle, Mitotic, Arabidopsis thaliana" +xref: Reactome:REACT_90332 "Cell Cycle, Mitotic, Mus musculus" +xref: Reactome:REACT_90846 "Cell Cycle, Mitotic, Oryza sativa" +xref: Reactome:REACT_96281 "Cell Cycle, Mitotic, Drosophila melanogaster" +xref: Reactome:REACT_97744 "Cell Cycle, Mitotic, Dictyostelium discoideum" +xref: Reactome:REACT_98208 "Cell Cycle, Mitotic, Mycobacterium tuberculosis" +is_a: GO:0007049 ! cell cycle + +[Term] +id: GO:0000280 +name: nuclear division +namespace: biological_process +def: "The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei." [GOC:mah] +subset: goslim_pir +synonym: "karyokinesis" RELATED [] +is_a: GO:0048285 ! organelle fission +relationship: part_of GO:0051301 ! cell division + +[Term] +id: GO:0000429 +name: carbon catabolite regulation of transcription from RNA polymerase II promoter +namespace: biological_process +def: "A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:krc, GOC:mah] +synonym: "regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah] +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0045990 ! carbon catabolite regulation of transcription + +[Term] +id: GO:0000430 +name: regulation of transcription from RNA polymerase II promoter by glucose +namespace: biological_process +def: "Any process involving glucose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] +is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter +is_a: GO:0046015 ! regulation of transcription by glucose + +[Term] +id: GO:0000432 +name: positive regulation of transcription from RNA polymerase II promoter by glucose +namespace: biological_process +def: "Any process involving glucose that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:krc] +synonym: "activation of transcription from RNA polymerase II promoter by glucose" NARROW [] +synonym: "stimulation of transcription from RNA polymerase II promoter by glucose" NARROW [] +synonym: "up regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] +synonym: "up-regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] +synonym: "upregulation of transcription from RNA polymerase II promoter by glucose" EXACT [] +is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose +is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter +is_a: GO:0046016 ! positive regulation of transcription by glucose + +[Term] +id: GO:0000433 +name: negative regulation of transcription from RNA polymerase II promoter by glucose +namespace: biological_process +def: "Any process involving glucose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:krc] +synonym: "down regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] +synonym: "down-regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] +synonym: "downregulation of transcription from RNA polymerase II promoter by glucose" EXACT [] +synonym: "inhibition of transcription from RNA polymerase II promoter by glucose" NARROW [] +is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose +is_a: GO:0000437 ! carbon catabolite repression of transcription from RNA polymerase II promoter +is_a: GO:0045014 ! negative regulation of transcription by glucose + +[Term] +id: GO:0000436 +name: carbon catabolite activation of transcription from RNA polymerase II promoter +namespace: biological_process +def: "Any process involving carbon catabolites that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] +synonym: "positive regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah] +is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter +is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter +is_a: GO:0045991 ! carbon catabolite activation of transcription + +[Term] +id: GO:0000437 +name: carbon catabolite repression of transcription from RNA polymerase II promoter +namespace: biological_process +def: "A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:krc] +synonym: "negative regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah] +is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter +is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter +is_a: GO:0045013 ! carbon catabolite repression of transcription + +[Term] +id: GO:0000578 +name: embryonic axis specification +namespace: biological_process +def: "The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo." [GOC:dph, GOC:go_curators, GOC:sdb_2009, GOC:tb] +synonym: "embryonic axis determination" RELATED [] +is_a: GO:0009798 ! axis specification +is_a: GO:0009880 ! embryonic pattern specification + +[Term] +id: GO:0000737 +name: DNA catabolic process, endonucleolytic +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." [GOC:elh, GOC:mah] +subset: gosubset_prok +synonym: "DNA breakdown, endonucleolytic" EXACT [] +synonym: "DNA degradation, endonucleolytic" EXACT [] +synonym: "endonucleolytic degradation of DNA" EXACT [] +synonym: "endonucleolytic DNA catabolism" EXACT [] +is_a: GO:0006308 ! DNA catabolic process +is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis + +[Term] +id: GO:0000768 +name: syncytium formation by plasma membrane fusion +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:mtg_muscle, GOC:tb] +synonym: "cell fusion" BROAD [] +synonym: "cell-cell fusion" EXACT [] +is_a: GO:0006949 ! syncytium formation +relationship: has_part GO:0045026 ! plasma membrane fusion + +[Term] +id: GO:0000785 +name: chromatin +namespace: cellular_component +alt_id: GO:0005717 +def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] +synonym: "chromosome scaffold" RELATED [] +xref: NIF_Subcellular:sao1615953555 +is_a: GO:0044427 ! chromosomal part + +[Term] +id: GO:0000790 +name: nuclear chromatin +namespace: cellular_component +def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus." [GOC:elh, PMID:20404130] +is_a: GO:0000785 ! chromatin +is_a: GO:0044454 ! nuclear chromosome part +intersection_of: GO:0000785 ! chromatin +intersection_of: part_of GO:0005634 ! nucleus + +[Term] +id: GO:0000792 +name: heterochromatin +namespace: cellular_component +def: "A compact and highly condensed form of chromatin." [GOC:elh] +xref: NIF_Subcellular:sao581845896 +xref: Wikipedia:Heterochromatin +is_a: GO:0000785 ! chromatin + +[Term] +id: GO:0000902 +name: cell morphogenesis +namespace: biological_process +alt_id: GO:0007148 +alt_id: GO:0045790 +alt_id: GO:0045791 +def: "The developmental process in which the size or shape of a cell is generated and organized." [GOC:clt, GOC:dph, GOC:go_curators, GOC:tb] +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "cellular morphogenesis" EXACT [] +is_a: GO:0032989 ! cellular component morphogenesis + +[Term] +id: GO:0000904 +name: cell morphogenesis involved in differentiation +namespace: biological_process +def: "The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." [GOC:go_curators] +is_a: GO:0000902 ! cell morphogenesis +intersection_of: GO:0000902 ! cell morphogenesis +intersection_of: part_of GO:0048468 ! cell development +relationship: part_of GO:0048468 ! cell development + +[Term] +id: GO:0000975 +name: regulatory region DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH] +is_a: GO:0001067 ! regulatory region nucleic acid binding +is_a: GO:0003677 ! DNA binding +created_by: kchris +creation_date: 2010-08-10T10:56:24Z + +[Term] +id: GO:0000976 +name: transcription regulatory region sequence-specific DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] +comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". +is_a: GO:0043565 ! sequence-specific DNA binding +is_a: GO:0044212 ! transcription regulatory region DNA binding +created_by: kchris +creation_date: 2010-08-10T11:00:02Z + +[Term] +id: GO:0000977 +name: RNA polymerase II regulatory region sequence-specific DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II." [GOC:txnOH] +comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". +is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding +is_a: GO:0001012 ! RNA polymerase II regulatory region DNA binding +created_by: kchris +creation_date: 2010-08-10T11:05:36Z + +[Term] +id: GO:0000978 +name: RNA polymerase II core promoter proximal region sequence-specific DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II." [GOC:txnOH] +comment: Note that the phrase "upstream activating sequence", or UAS is often used in S. cerevisiae literature to refer to regulatory sequences that occur in the region upstream and proximal to the core promoter. In contrast, in bacteria such as E. coli, the phrase "upstream activating sequence", or UAS is a synonym for "enhancer". +synonym: "RNA polymerase II upstream activating sequence (UAS) sequence-specific DNA binding" RELATED [] +is_a: GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding +is_a: GO:0000987 ! core promoter proximal region sequence-specific DNA binding +created_by: kchris +creation_date: 2010-08-10T02:17:19Z + +[Term] +id: GO:0000980 +name: RNA polymerase II distal enhancer sequence-specific DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter." [GOC:txnOH] +comment: Note that distal enhancers of the type found in mammalian cells are not known to occur in either Saccharomyces cerevisiae or Schizosaccharomyces pombe. While some S. cerevisiae literature does refer to sequences distal to the initiation site, these distal sites do not seem to function independently of position or orientation as mammalian distal enhancers do and are not considered to be enhancers. +is_a: GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding +is_a: GO:0001158 ! enhancer sequence-specific DNA binding +created_by: kchris +creation_date: 2010-08-10T02:29:25Z + +[Term] +id: GO:0000981 +name: sequence-specific DNA binding RNA polymerase II transcription factor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] +is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity +relationship: has_part GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding +relationship: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter +relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter +created_by: kchris +creation_date: 2010-08-10T02:37:21Z + +[Term] +id: GO:0000982 +name: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II." [GOC:txnOH] +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: has_part GO:0000978 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding +created_by: kchris +creation_date: 2010-08-10T02:39:46Z + +[Term] +id: GO:0000987 +name: core promoter proximal region sequence-specific DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] +comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". +is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding +is_a: GO:0001159 ! core promoter proximal region DNA binding +created_by: kchris +creation_date: 2010-08-10T03:40:16Z + +[Term] +id: GO:0000988 +name: protein binding transcription factor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. This term does not provide specificity with respect to the type of protein binding, e.g. transcription factor binding or RNA polymerase binding. Please use a child term that provides that specificity or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +synonym: "transcription factor activity" BROAD [] +is_a: GO:0003674 ! molecular_function +relationship: has_part GO:0005515 ! protein binding +relationship: part_of GO:2001141 ! regulation of RNA biosynthetic process +created_by: kchris +creation_date: 2010-08-10T04:03:22Z + +[Term] +id: GO:0000989 +name: transcription factor binding transcription factor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] +is_a: GO:0000988 ! protein binding transcription factor activity +relationship: has_part GO:0008134 ! transcription factor binding +created_by: kchris +creation_date: 2010-08-10T04:57:43Z + +[Term] +id: GO:0001012 +name: RNA polymerase II regulatory region DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw] +is_a: GO:0044212 ! transcription regulatory region DNA binding +created_by: kchris +creation_date: 2010-08-19T09:43:58Z + +[Term] +id: GO:0001067 +name: regulatory region nucleic acid binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH] +is_a: GO:0003676 ! nucleic acid binding +created_by: kchris +creation_date: 2010-10-21T04:08:56Z + +[Term] +id: GO:0001071 +name: nucleic acid binding transcription factor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. This term does not provide specificity with respect to the type of nucleic acid binding, e.g. RNA or DNA. Please use a child term that provides that specificity or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +synonym: "transcription factor activity" BROAD [] +is_a: GO:0003674 ! molecular_function +relationship: has_part GO:0003676 ! nucleic acid binding +relationship: part_of GO:2001141 ! regulation of RNA biosynthetic process +created_by: kchris +creation_date: 2010-10-21T04:37:54Z + +[Term] +id: GO:0001076 +name: RNA polymerase II transcription factor binding transcription factor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] +is_a: GO:0000989 ! transcription factor binding transcription factor activity +relationship: has_part GO:0001085 ! RNA polymerase II transcription factor binding +relationship: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter +relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter +created_by: kchris +creation_date: 2010-10-22T02:49:32Z + +[Term] +id: GO:0001077 +name: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription +namespace: molecular_function +def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH] +is_a: GO:0000982 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity +is_a: GO:0001228 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription +created_by: kchris +creation_date: 2010-10-26T03:40:43Z + +[Term] +id: GO:0001085 +name: RNA polymerase II transcription factor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II." [GOC:txnOH] +is_a: GO:0008134 ! transcription factor binding +created_by: kchris +creation_date: 2010-10-28T02:08:59Z + +[Term] +id: GO:0001098 +name: basal transcription machinery binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with the basal transcription machinery which is composed of the RNA polymerase core enzyme and the basal transcription factor(s), the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH] +comment: Note that the definition of basal, or general, transcription factors has typically been done at a small number of well characterized activator-independent promoters. At an activator-dependent promoter, one or more additional factors are generally required in addition to the basal factors. +is_a: GO:0005515 ! protein binding +created_by: kchris +creation_date: 2010-11-24T12:50:49Z + +[Term] +id: GO:0001099 +name: basal RNA polymerase II transcription machinery binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with the basal transcription machinery for RNA polymerase II which is composed of the RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits, and the basal RNA polymerase II transcription factors, the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH] +comment: Note that the definition of basal, or general, transcription factors has typically been done at a small number of well characterized activator-independent promoters. At an activator-dependent promoter, one or more additional factors are generally required in addition to the basal factors. +is_a: GO:0001098 ! basal transcription machinery binding +created_by: kchris +creation_date: 2010-11-24T12:54:33Z + +[Term] +id: GO:0001101 +name: response to acid +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acid stimulus. The acid may be in gaseous, liquid or solid form." [GOC:rn, http://en.wikipedia.org/wiki/Acid] +is_a: GO:0042221 ! response to chemical + +[Term] +id: GO:0001102 +name: RNA polymerase II activating transcription factor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription." [GOC:txnOH] +is_a: GO:0001085 ! RNA polymerase II transcription factor binding +is_a: GO:0033613 ! activating transcription factor binding +created_by: kchris +creation_date: 2010-11-24T02:17:08Z + +[Term] +id: GO:0001104 +name: RNA polymerase II transcription cofactor activity +namespace: molecular_function +alt_id: GO:0016455 +def: "Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] +subset: gosubset_prok +synonym: "RNA polymerase II transcription mediator activity" RELATED [] +synonym: "RNA polymerase II transcriptional co-regulator" EXACT [] +synonym: "RNA polymerase II transcriptional cofactor activity" EXACT [] +synonym: "thyroid receptor-associated protein" RELATED [] +synonym: "TRAP protein" RELATED [] +is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity +is_a: GO:0003712 ! transcription cofactor activity +relationship: has_part GO:0001099 ! basal RNA polymerase II transcription machinery binding +created_by: kchris +creation_date: 2010-11-24T03:02:15Z + +[Term] +id: GO:0001158 +name: enhancer sequence-specific DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter." [GOC:txnOH] +is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding +is_a: GO:0035326 ! enhancer binding +created_by: kchris +creation_date: 2011-01-28T03:29:40Z + +[Term] +id: GO:0001159 +name: core promoter proximal region DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a region of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] +is_a: GO:0044212 ! transcription regulatory region DNA binding +created_by: kchris +creation_date: 2011-01-28T03:37:52Z + +[Term] +id: GO:0001190 +name: RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription +namespace: molecular_function +def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] +is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity +relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter +created_by: kchris +creation_date: 2011-08-25T02:07:14Z + +[Term] +id: GO:0001205 +name: RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription +namespace: molecular_function +def: "Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH] +synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" EXACT [] +is_a: GO:0001228 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription +is_a: GO:0003705 ! RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity +created_by: kchris +creation_date: 2012-01-26T03:10:20Z + +[Term] +id: GO:0001227 +name: RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription +namespace: molecular_function +def: "Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: part_of GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter +created_by: kchris +creation_date: 2012-04-16T04:41:29Z + +[Term] +id: GO:0001228 +name: RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription +namespace: molecular_function +def: "Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:krc] +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter +created_by: kchris +creation_date: 2012-04-16T04:44:21Z + +[Term] +id: GO:0001501 +name: skeletal system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton)." [GOC:dph, GOC:jid, GOC:tb, http://www.stedmans.com/] +synonym: "skeletal development" EXACT [] +is_a: GO:0048731 ! system development + +[Term] +id: GO:0001502 +name: cartilage condensation +namespace: biological_process +def: "The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes." [ISBN:0878932437] +is_a: GO:0016337 ! cell-cell adhesion +relationship: part_of GO:0048705 ! skeletal system morphogenesis +relationship: part_of GO:0051216 ! cartilage development + +[Term] +id: GO:0001503 +name: ossification +namespace: biological_process +def: "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:mtg_mpo, PMID:17572649] +comment: Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'. +synonym: "bone biosynthesis" EXACT [] +synonym: "bone formation" EXACT [] +synonym: "osteogenesis" EXACT [] +xref: Wikipedia:Ossification +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0001505 +name: regulation of neurotransmitter levels +namespace: biological_process +def: "Any process that modulates levels of neurotransmitter." [GOC:jl] +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0007268 ! synaptic transmission + +[Term] +id: GO:0001508 +name: action potential +namespace: biological_process +def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] +comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. +is_a: GO:0042391 ! regulation of membrane potential + +[Term] +id: GO:0001525 +name: angiogenesis +namespace: biological_process +def: "Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels." [ISBN:0878932453] +synonym: "blood vessel formation from pre-existing blood vessels" EXACT systematic_synonym [] +xref: Wikipedia:Angiogenesis +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0048514 ! blood vessel morphogenesis + +[Term] +id: GO:0001541 +name: ovarian follicle development +namespace: biological_process +def: "The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure." [GOC:go_curators] +synonym: "follicular phase" RELATED [] +is_a: GO:0022602 ! ovulation cycle process +relationship: part_of GO:0008585 ! female gonad development + +[Term] +id: GO:0001558 +name: regulation of cell growth +namespace: biological_process +def: "Any process that modulates the frequency, rate, extent or direction of cell growth." [GOC:go_curators] +subset: gosubset_prok +xref: Reactome:REACT_6201 "DTOR is positively regulated by DRheb-GTP, Drosophila melanogaster" +is_a: GO:0040008 ! regulation of growth +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016049 ! cell growth +relationship: regulates GO:0016049 ! cell growth + +[Term] +id: GO:0001568 +name: blood vessel development +namespace: biological_process +def: "The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood." [GOC:hjd, UBERON:0001981] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001944 ! vasculature development + +[Term] +id: GO:0001569 +name: patterning of blood vessels +namespace: biological_process +def: "The process that regulates the coordinated growth and sprouting of blood vessels giving rise to the organized vascular system." [GOC:dph] +synonym: "branching involved in blood vessel morphogenesis" EXACT [GOC:dph] +is_a: GO:0007389 ! pattern specification process +is_a: GO:0048754 ! branching morphogenesis of an epithelial tube +relationship: part_of GO:0001525 ! angiogenesis + +[Term] +id: GO:0001570 +name: vasculogenesis +namespace: biological_process +def: "The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes." [PMID:8999798] +synonym: "vascular morphogenesis" EXACT [] +xref: Wikipedia:Vasculogenesis +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0048514 ! blood vessel morphogenesis + +[Term] +id: GO:0001649 +name: osteoblast differentiation +namespace: biological_process +def: "The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone." [CL:0000062, GO_REF:0000034, GOC:jid] +synonym: "osteoblast cell differentiation" EXACT [] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0001503 ! ossification + +[Term] +id: GO:0001654 +name: eye development +namespace: biological_process +alt_id: GO:0042460 +def: "The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight." [GOC:jid, GOC:jl] +xref: Wikipedia:Eye_development +is_a: GO:0007423 ! sensory organ development + +[Term] +id: GO:0001655 +name: urogenital system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure." [GOC:go_curators] +is_a: GO:0048731 ! system development + +[Term] +id: GO:0001656 +name: metanephros development +namespace: biological_process +def: "The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine." [GOC:bf, ISBN:0192800752] +is_a: GO:0001822 ! kidney development + +[Term] +id: GO:0001657 +name: ureteric bud development +namespace: biological_process +def: "The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure." [GOC:go_curators] +is_a: GO:0035295 ! tube development +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0001658 +name: branching involved in ureteric bud morphogenesis +namespace: biological_process +def: "The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules." [GOC:dph, PMID:16916378] +synonym: "ureteric bud branching" EXACT [GOC:dph] +is_a: GO:0048754 ! branching morphogenesis of an epithelial tube +intersection_of: GO:0001763 ! morphogenesis of a branching structure +intersection_of: part_of GO:0060675 ! ureteric bud morphogenesis +relationship: part_of GO:0060675 ! ureteric bud morphogenesis + +[Term] +id: GO:0001664 +name: G-protein coupled receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a G-protein coupled receptor." [GOC:ceb, GOC:dph] +synonym: "G protein coupled receptor binding" EXACT [] +synonym: "G protein coupled receptor ligand" NARROW [] +synonym: "G-protein-coupled receptor binding" EXACT [GOC:bf] +synonym: "G-protein-coupled receptor ligand" NARROW [] +xref: Reactome:REACT_21309 "Activation of GRIK3 homomer, Homo sapiens" +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0001667 +name: ameboidal cell migration +namespace: biological_process +def: "Cell migration that is accomplished by extension and retraction of a pseudopodium." [GOC:dph] +synonym: "ameboid cell migration" EXACT [] +synonym: "amoeboid cell migration" EXACT [] +synonym: "amoeboidal cell migration" EXACT [] +is_a: GO:0016477 ! cell migration + +[Term] +id: GO:0001678 +name: cellular glucose homeostasis +namespace: biological_process +def: "A cellular homeostatic process involved in the maintenance of an internal steady state of glucose within a cell or between a cell and its external environment." [GOC:dph, GOC:go_curators, GOC:tb] +subset: gosubset_prok +synonym: "cell glucose homeostasis" EXACT [GOC:dph, GOC:tb] +is_a: GO:0042593 ! glucose homeostasis +is_a: GO:0055082 ! cellular chemical homeostasis + +[Term] +id: GO:0001701 +name: in utero embryonic development +namespace: biological_process +def: "The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus." [GOC:go_curators, GOC:mtg_sensu] +is_a: GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0001702 +name: gastrulation with mouth forming second +namespace: biological_process +alt_id: GO:0010003 +alt_id: GO:0048276 +def: "A gastrulation process in which the initial invagination becomes the anus and the mouth forms second." [GOC:go_curators, GOC:mtg_sensu] +synonym: "deuterostomic gastrulation" EXACT [GOC:dph] +is_a: GO:0007369 ! gastrulation + +[Term] +id: GO:0001704 +name: formation of primary germ layer +namespace: biological_process +def: "The formation of the ectoderm, mesoderm and endoderm during gastrulation." [GOC:go_curators] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0007369 ! gastrulation + +[Term] +id: GO:0001705 +name: ectoderm formation +namespace: biological_process +def: "The formation of ectoderm during gastrulation." [GOC:go_curators] +is_a: GO:0001704 ! formation of primary germ layer +relationship: part_of GO:0007398 ! ectoderm development + +[Term] +id: GO:0001706 +name: endoderm formation +namespace: biological_process +def: "The formation of the endoderm during gastrulation." [GOC:go_curators] +synonym: "endoblast formation" NARROW [GOC:dph, GOC:sdb_2009, GOC:tb] +is_a: GO:0001704 ! formation of primary germ layer +relationship: part_of GO:0007492 ! endoderm development + +[Term] +id: GO:0001707 +name: mesoderm formation +namespace: biological_process +def: "The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts." [GOC:go_curators] +is_a: GO:0001704 ! formation of primary germ layer +relationship: part_of GO:0048332 ! mesoderm morphogenesis + +[Term] +id: GO:0001708 +name: cell fate specification +namespace: biological_process +def: "The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment." [GOC:go_curators] +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0045165 ! cell fate commitment + +[Term] +id: GO:0001709 +name: cell fate determination +namespace: biological_process +def: "A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment." [ISBN:0878932437] +xref: Wikipedia:Cell_fate_determination +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0045165 ! cell fate commitment + +[Term] +id: GO:0001710 +name: mesodermal cell fate commitment +namespace: biological_process +def: "The cell differentiation process that results in commitment of a cell to become part of the mesoderm." [GOC:go_curators, ISBN:0878932437] +synonym: "mesoderm cell fate commitment" EXACT [] +is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer +relationship: part_of GO:0048333 ! mesodermal cell differentiation + +[Term] +id: GO:0001711 +name: endodermal cell fate commitment +namespace: biological_process +def: "The cell differentiation process that results in commitment of a cell to become part of the endoderm." [GOC:go_curators, ISBN:0878932437] +synonym: "endoderm cell fate commitment" EXACT [] +is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer +relationship: part_of GO:0035987 ! endodermal cell differentiation + +[Term] +id: GO:0001736 +name: establishment of planar polarity +namespace: biological_process +def: "Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates." [GOC:dph] +synonym: "establishment of planar cell polarity" NARROW [] +is_a: GO:0007164 ! establishment of tissue polarity +relationship: part_of GO:0001738 ! morphogenesis of a polarized epithelium + +[Term] +id: GO:0001738 +name: morphogenesis of a polarized epithelium +namespace: biological_process +def: "The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis." [GOC:dph] +synonym: "epithelial polarization" EXACT [GOC:dph] +is_a: GO:0002009 ! morphogenesis of an epithelium + +[Term] +id: GO:0001755 +name: neural crest cell migration +namespace: biological_process +def: "The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo." [GOC:ascb_2009, GOC:dph, GOC:tb, ISBN:0878932437] +is_a: GO:0001667 ! ameboidal cell migration +relationship: part_of GO:0014032 ! neural crest cell development + +[Term] +id: GO:0001756 +name: somitogenesis +namespace: biological_process +def: "The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo." [ISBN:0721662544] +synonym: "formation of mesodermal clusters" EXACT systematic_synonym [] +xref: Wikipedia:Somitogenesis +is_a: GO:0009952 ! anterior/posterior pattern specification +is_a: GO:0035282 ! segmentation +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0043009 ! chordate embryonic development +relationship: part_of GO:0061053 ! somite development + +[Term] +id: GO:0001759 +name: organ induction +namespace: biological_process +def: "The interaction of two or more cells or tissues that causes them to change their fates and specify the development of an organ." [ISBN:0878932437] +synonym: "induction of an organ" EXACT [GOC:curators] +is_a: GO:0003156 ! regulation of organ formation +is_a: GO:0031128 ! developmental induction +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +relationship: positively_regulates GO:0010092 ! specification of organ identity + +[Term] +id: GO:0001763 +name: morphogenesis of a branching structure +namespace: biological_process +def: "The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes." [ISBN:0721662544] +synonym: "branching morphogenesis" EXACT [GOC:dph] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0001764 +name: neuron migration +namespace: biological_process +def: "The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature." [CL:0000540, GOC:go_curators] +synonym: "neuron chemotaxis" EXACT [GOC:curators] +synonym: "neuron guidance" RELATED [GOC:curators] +synonym: "neuronal migration" EXACT [] +xref: Wikipedia:Neural_development#Neuron_migration +xref: Wikipedia:Neuron_migration +is_a: GO:0016477 ! cell migration +relationship: part_of GO:0048699 ! generation of neurons + +[Term] +id: GO:0001775 +name: cell activation +namespace: biological_process +def: "A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:mgi_curators] +subset: goslim_pir +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0001816 +name: cytokine production +namespace: biological_process +def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] +comment: Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. +subset: goslim_pir +synonym: "interferon production" NARROW [GOC:add, GOC:mah] +synonym: "interleukin production" NARROW [GOC:add, GOC:mah] +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0001817 +name: regulation of cytokine production +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of production of a cytokine." [GOC:add, ISBN:0781735149] +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001816 ! cytokine production +relationship: regulates GO:0001816 ! cytokine production + +[Term] +id: GO:0001819 +name: positive regulation of cytokine production +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of production of a cytokine." [GOC:add, ISBN:0781735149] +synonym: "activation of cytokine production" NARROW [] +synonym: "stimulation of cytokine production" NARROW [] +synonym: "up regulation of cytokine production" EXACT [] +synonym: "up-regulation of cytokine production" EXACT [] +synonym: "upregulation of cytokine production" EXACT [] +is_a: GO:0001817 ! regulation of cytokine production +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001816 ! cytokine production +relationship: positively_regulates GO:0001816 ! cytokine production + +[Term] +id: GO:0001822 +name: kidney development +namespace: biological_process +def: "The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine." [GOC:dph, GOC:mtg_kidney_jan10, ISBN:0124020607, ISBN:0721662544] +synonym: "nephrogenesis" RELATED [GOC:rph] +xref: Wikipedia:Kidney_development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0001823 +name: mesonephros development +namespace: biological_process +def: "The process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney." [GOC:dph, ISBN:0124020607, ISBN:0721662544, PMID:10535314] +is_a: GO:0001822 ! kidney development + +[Term] +id: GO:0001824 +name: blastocyst development +namespace: biological_process +def: "The process whose specific outcome is the progression of the blastocyst over time, from its formation to the mature structure. The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm." [GOC:dph, ISBN:0124020607, ISBN:0198542771] +comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS5, embryo ; EMAP:23', 'TS5, inner cell mass ; EMAP:24' and 'TS5, trophectoderm; EMAP:28'. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001701 ! in utero embryonic development + +[Term] +id: GO:0001825 +name: blastocyst formation +namespace: biological_process +def: "The initial formation of a blastocyst from a solid ball of cells known as a morula." [GOC:dph, ISBN:0124020607, ISBN:0198542771] +comment: See also the Anatomical Dictionary for Mouse Development ontology term 'TS3, compacted morula ; EMAP:9'. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0001824 ! blastocyst development + +[Term] +id: GO:0001829 +name: trophectodermal cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell." [GOC:dph, ISBN:0124020607, ISBN:0198542771] +comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19'. +synonym: "trophectoderm cell differentiation" EXACT [] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0001825 ! blastocyst formation + +[Term] +id: GO:0001837 +name: epithelial to mesenchymal transition +namespace: biological_process +def: "A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." [GOC:dph, PMID:14701881] +synonym: "EMT" EXACT [] +synonym: "epithelial-mesenchymal transition" EXACT [] +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +relationship: part_of GO:0014031 ! mesenchymal cell development + +[Term] +id: GO:0001838 +name: embryonic epithelial tube formation +namespace: biological_process +def: "The morphogenesis of an embryonic epithelium into a tube-shaped structure." [GOC:dph, ISBN:0824072820] +is_a: GO:0072175 ! epithelial tube formation +relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium + +[Term] +id: GO:0001840 +name: neural plate development +namespace: biological_process +def: "The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system." [GOC:dph, GOC:ef, ISBN:0878932437, ISBN:0878932585] +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0001841 +name: neural tube formation +namespace: biological_process +alt_id: GO:0001679 +def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] +synonym: "neural tube morphogenesis" EXACT [GOC:dph] +synonym: "neurulation" EXACT [] +xref: Wikipedia:Neurulation +is_a: GO:0001838 ! embryonic epithelial tube formation +relationship: part_of GO:0021915 ! neural tube development + +[Term] +id: GO:0001843 +name: neural tube closure +namespace: biological_process +def: "The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline." [GOC:dph, ISBN:0878932437] +is_a: GO:0060606 ! tube closure +relationship: part_of GO:0014020 ! primary neural tube formation + +[Term] +id: GO:0001885 +name: endothelial cell development +namespace: biological_process +def: "The progression of an endothelial cell over time, from its formation to the mature structure." [GOC:dph] +is_a: GO:0002064 ! epithelial cell development +relationship: part_of GO:0045446 ! endothelial cell differentiation + +[Term] +id: GO:0001889 +name: liver development +namespace: biological_process +def: "The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes." [GOC:add, ISBN:068340007X] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0061008 ! hepaticobiliary system development + +[Term] +id: GO:0001890 +name: placenta development +namespace: biological_process +def: "The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." [GOC:add, ISBN:068340007X] +synonym: "placental development" EXACT [] +synonym: "placentation" EXACT [GOC:dph, GOC:tb] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0001892 +name: embryonic placenta development +namespace: biological_process +def: "The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." [GOC:add, ISBN:068340007X] +synonym: "fetal placenta development" EXACT [GOC:dph] +is_a: GO:0048568 ! embryonic organ development +relationship: part_of GO:0001701 ! in utero embryonic development +relationship: part_of GO:0001890 ! placenta development + +[Term] +id: GO:0001894 +name: tissue homeostasis +namespace: biological_process +def: "A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function." [GOC:add, GOC:isa_complete] +synonym: "tissue maintenance" NARROW [GOC:add] +is_a: GO:0060249 ! anatomical structure homeostasis +relationship: part_of GO:0048871 ! multicellular organismal homeostasis + +[Term] +id: GO:0001932 +name: regulation of protein phosphorylation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein." [GOC:hjd] +subset: gosubset_prok +synonym: "regulation of protein amino acid phosphorylation" EXACT [GOC:bf] +is_a: GO:0031399 ! regulation of protein modification process +is_a: GO:0042325 ! regulation of phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006468 ! protein phosphorylation +relationship: regulates GO:0006468 ! protein phosphorylation + +[Term] +id: GO:0001933 +name: negative regulation of protein phosphorylation +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein." [GOC:hjd] +subset: gosubset_prok +synonym: "down regulation of protein amino acid phosphorylation" EXACT [] +synonym: "down-regulation of protein amino acid phosphorylation" EXACT [] +synonym: "downregulation of protein amino acid phosphorylation" EXACT [] +synonym: "inhibition of protein amino acid phosphorylation" NARROW [] +synonym: "negative regulation of protein amino acid phosphorylation" EXACT [GOC:bf] +is_a: GO:0001932 ! regulation of protein phosphorylation +is_a: GO:0031400 ! negative regulation of protein modification process +is_a: GO:0042326 ! negative regulation of phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006468 ! protein phosphorylation +relationship: negatively_regulates GO:0006468 ! protein phosphorylation + +[Term] +id: GO:0001934 +name: positive regulation of protein phosphorylation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein." [GOC:hjd] +subset: gosubset_prok +synonym: "activation of protein amino acid phosphorylation" NARROW [] +synonym: "positive regulation of protein amino acid phosphorylation" EXACT [GOC:bf] +synonym: "stimulation of protein amino acid phosphorylation" NARROW [] +synonym: "up regulation of protein amino acid phosphorylation" EXACT [] +synonym: "up-regulation of protein amino acid phosphorylation" EXACT [] +synonym: "upregulation of protein amino acid phosphorylation" EXACT [] +is_a: GO:0001932 ! regulation of protein phosphorylation +is_a: GO:0031401 ! positive regulation of protein modification process +is_a: GO:0042327 ! positive regulation of phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006468 ! protein phosphorylation +relationship: positively_regulates GO:0006468 ! protein phosphorylation + +[Term] +id: GO:0001935 +name: endothelial cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium." [GOC:add, ISBN:0781735149] +is_a: GO:0050673 ! epithelial cell proliferation + +[Term] +id: GO:0001936 +name: regulation of endothelial cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of endothelial cell proliferation." [GOC:add] +is_a: GO:0050678 ! regulation of epithelial cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001935 ! endothelial cell proliferation +relationship: regulates GO:0001935 ! endothelial cell proliferation + +[Term] +id: GO:0001938 +name: positive regulation of endothelial cell proliferation +namespace: biological_process +def: "Any process that activates or increases the rate or extent of endothelial cell proliferation." [GOC:add] +synonym: "activation of endothelial cell proliferation" NARROW [] +synonym: "stimulation of endothelial cell proliferation" NARROW [] +synonym: "up regulation of endothelial cell proliferation" EXACT [] +synonym: "up-regulation of endothelial cell proliferation" EXACT [] +synonym: "upregulation of endothelial cell proliferation" EXACT [] +is_a: GO:0001936 ! regulation of endothelial cell proliferation +is_a: GO:0050679 ! positive regulation of epithelial cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001935 ! endothelial cell proliferation +relationship: positively_regulates GO:0001935 ! endothelial cell proliferation + +[Term] +id: GO:0001942 +name: hair follicle development +namespace: biological_process +alt_id: GO:0001943 +def: "The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open." [GOC:dph, UBERON:0002073] +is_a: GO:0008544 ! epidermis development +is_a: GO:0022405 ! hair cycle process +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0001944 +name: vasculature development +namespace: biological_process +def: "The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism." [GOC:dph, UBERON:0002409] +synonym: "vascular system development" RELATED [GOC:curators] +is_a: GO:0048731 ! system development +relationship: part_of GO:0072358 ! cardiovascular system development + +[Term] +id: GO:0001945 +name: lymph vessel development +namespace: biological_process +def: "The process whose specific outcome is the progression of a lymph vessel over time, from its formation to the mature structure." [GOC:dph, UBERON:0001473] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001944 ! vasculature development + +[Term] +id: GO:0001946 +name: lymphangiogenesis +namespace: biological_process +def: "Lymph vessel formation when new vessels emerge from the proliferation of pre-existing vessels." [GOC:dph, PMID:11596157] +synonym: "lymph vessel formation" EXACT systematic_synonym [] +xref: Wikipedia:Lymphangiogenesis +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0036303 ! lymph vessel morphogenesis + +[Term] +id: GO:0001947 +name: heart looping +namespace: biological_process +def: "The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation." [GOC:dph, PMID:12094232] +synonym: "cardiac looping" EXACT [] +is_a: GO:0003143 ! embryonic heart tube morphogenesis +relationship: part_of GO:0061371 ! determination of heart left/right asymmetry + +[Term] +id: GO:0001948 +name: glycoprotein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a glycoprotein, a protein that contains covalently bound glycose (monosaccharide) residues. These also include proteoglycans." [GOC:hjd, ISBN:0198506732] +is_a: GO:0005515 ! protein binding +is_a: GO:0097367 ! carbohydrate derivative binding + +[Term] +id: GO:0001952 +name: regulation of cell-matrix adhesion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of attachment of a cell to the extracellular matrix." [GOC:hjd] +is_a: GO:0010810 ! regulation of cell-substrate adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007160 ! cell-matrix adhesion +relationship: regulates GO:0007160 ! cell-matrix adhesion + +[Term] +id: GO:0001954 +name: positive regulation of cell-matrix adhesion +namespace: biological_process +def: "Any process that activates or increases the rate or extent of cell adhesion to an extracellular matrix." [GOC:hjd] +synonym: "activation of cell-matrix adhesion" NARROW [] +synonym: "stimulation of cell-matrix adhesion" NARROW [] +synonym: "up regulation of cell-matrix adhesion" EXACT [] +synonym: "up-regulation of cell-matrix adhesion" EXACT [] +synonym: "upregulation of cell-matrix adhesion" EXACT [] +is_a: GO:0001952 ! regulation of cell-matrix adhesion +is_a: GO:0010811 ! positive regulation of cell-substrate adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007160 ! cell-matrix adhesion +relationship: positively_regulates GO:0007160 ! cell-matrix adhesion + +[Term] +id: GO:0001959 +name: regulation of cytokine-mediated signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the cytokine mediated signaling pathway." [GOC:hjd] +synonym: "regulation of cytokine and chemokine mediated signaling pathway" EXACT [] +synonym: "regulation of cytokine mediated signaling pathway" EXACT [GOC:dph, GOC:tb] +synonym: "regulation of cytokine mediated signalling pathway" EXACT [] +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0060759 ! regulation of response to cytokine stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0019221 ! cytokine-mediated signaling pathway +relationship: regulates GO:0019221 ! cytokine-mediated signaling pathway + +[Term] +id: GO:0001961 +name: positive regulation of cytokine-mediated signaling pathway +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of a cytokine mediated signaling pathway." [GOC:hjd] +synonym: "activation of cytokine mediated signaling pathway" NARROW [] +synonym: "positive regulation of cytokine and chemokine mediated signaling pathway" EXACT [] +synonym: "positive regulation of cytokine mediated signaling pathway" EXACT [GOC:dph, GOC:tb] +synonym: "positive regulation of cytokine mediated signalling pathway" EXACT [] +synonym: "stimulation of cytokine mediated signaling pathway" NARROW [] +synonym: "up regulation of cytokine mediated signaling pathway" EXACT [] +synonym: "up-regulation of cytokine mediated signaling pathway" EXACT [] +synonym: "upregulation of cytokine mediated signaling pathway" EXACT [] +is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0060760 ! positive regulation of response to cytokine stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0019221 ! cytokine-mediated signaling pathway +relationship: positively_regulates GO:0019221 ! cytokine-mediated signaling pathway + +[Term] +id: GO:0001974 +name: blood vessel remodeling +namespace: biological_process +def: "The reorganization or renovation of existing blood vessels." [GOC:hjd] +is_a: GO:0048771 ! tissue remodeling + +[Term] +id: GO:0002009 +name: morphogenesis of an epithelium +namespace: biological_process +def: "The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube." [GOC:dph, GOC:jl, GOC:tb, ISBN:0198506732] +synonym: "epithelium morphogenesis" EXACT [] +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0060429 ! epithelium development + +[Term] +id: GO:0002011 +name: morphogenesis of an epithelial sheet +namespace: biological_process +def: "The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells." [GOC:jl] +is_a: GO:0002009 ! morphogenesis of an epithelium + +[Term] +id: GO:0002020 +name: protease binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any protease or peptidase." [GOC:hjd] +is_a: GO:0019899 ! enzyme binding + +[Term] +id: GO:0002040 +name: sprouting angiogenesis +namespace: biological_process +def: "The extension of new blood vessels from existing capillaries into avascular tissues resulting from the proliferation of blood vessel endothelial cells." [PMID:16391003] +is_a: GO:0001525 ! angiogenesis + +[Term] +id: GO:0002042 +name: cell migration involved in sprouting angiogenesis +namespace: biological_process +def: "The orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels involved in sprouting angiogenesis." [PMID:16391003] +is_a: GO:0043534 ! blood vessel endothelial cell migration +intersection_of: GO:0016477 ! cell migration +intersection_of: part_of GO:0002040 ! sprouting angiogenesis +relationship: part_of GO:0002040 ! sprouting angiogenesis + +[Term] +id: GO:0002052 +name: positive regulation of neuroblast proliferation +namespace: biological_process +def: "Any process that activates or increases the rate of neuroblast proliferation." [GOC:dph] +synonym: "activation of neuroblast proliferation" NARROW [] +synonym: "stimulation of neuroblast proliferation" NARROW [] +synonym: "up regulation of neuroblast proliferation" EXACT [] +synonym: "up-regulation of neuroblast proliferation" EXACT [] +synonym: "upregulation of neuroblast proliferation" EXACT [] +is_a: GO:0050769 ! positive regulation of neurogenesis +is_a: GO:2000179 ! positive regulation of neural precursor cell proliferation +is_a: GO:2000648 ! positive regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007405 ! neuroblast proliferation +relationship: positively_regulates GO:0007405 ! neuroblast proliferation + +[Term] +id: GO:0002053 +name: positive regulation of mesenchymal cell proliferation +namespace: biological_process +def: "The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells." [GOC:dph] +synonym: "activation of mesenchymal cell proliferation" NARROW [] +synonym: "stimulation of mesenchymal cell proliferation" NARROW [] +synonym: "up regulation of mesenchymal cell proliferation" EXACT [] +synonym: "up-regulation of mesenchymal cell proliferation" EXACT [] +synonym: "upregulation of mesenchymal cell proliferation" EXACT [] +is_a: GO:0010464 ! regulation of mesenchymal cell proliferation +is_a: GO:2000648 ! positive regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010463 ! mesenchymal cell proliferation +relationship: positively_regulates GO:0010463 ! mesenchymal cell proliferation + +[Term] +id: GO:0002062 +name: chondrocyte differentiation +namespace: biological_process +def: "The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage." [GOC:dph] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0051216 ! cartilage development + +[Term] +id: GO:0002063 +name: chondrocyte development +namespace: biological_process +def: "The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate." [GOC:dph] +is_a: GO:0048468 ! cell development +relationship: part_of GO:0002062 ! chondrocyte differentiation + +[Term] +id: GO:0002064 +name: epithelial cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface." [GOC:dph] +is_a: GO:0048468 ! cell development +relationship: part_of GO:0030855 ! epithelial cell differentiation + +[Term] +id: GO:0002065 +name: columnar/cuboidal epithelial cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GOC:dph] +is_a: GO:0030855 ! epithelial cell differentiation + +[Term] +id: GO:0002066 +name: columnar/cuboidal epithelial cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell over time, from its formation to the mature structure. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GOC:dph] +is_a: GO:0002064 ! epithelial cell development +relationship: part_of GO:0002065 ! columnar/cuboidal epithelial cell differentiation + +[Term] +id: GO:0002067 +name: glandular epithelial cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a glandular epithelial cell. A glandular epithelial cell is a columnar/cuboidal epithelial cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland." [GOC:dph] +is_a: GO:0002065 ! columnar/cuboidal epithelial cell differentiation + +[Term] +id: GO:0002068 +name: glandular epithelial cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland." [GOC:dph] +is_a: GO:0002066 ! columnar/cuboidal epithelial cell development +relationship: part_of GO:0002067 ! glandular epithelial cell differentiation + +[Term] +id: GO:0002076 +name: osteoblast development +namespace: biological_process +def: "The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone." [GOC:dph] +is_a: GO:0048468 ! cell development +relationship: part_of GO:0001649 ! osteoblast differentiation + +[Term] +id: GO:0002088 +name: lens development in camera-type eye +namespace: biological_process +def: "The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus." [GOC:dph, ISBN:0582064333] +synonym: "lens development" EXACT [] +synonym: "lens development in camera-style eye" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0043010 ! camera-type eye development + +[Term] +id: GO:0002089 +name: lens morphogenesis in camera-type eye +namespace: biological_process +def: "The process in which the anatomical structures of the lens are generated and organized. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus." [GOC:dph, GOC:mtg_sensu] +synonym: "lens morphogenesis" EXACT [] +synonym: "lens morphogenesis in camera-style eye" EXACT [] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0002088 ! lens development in camera-type eye +relationship: part_of GO:0048593 ! camera-type eye morphogenesis + +[Term] +id: GO:0002090 +name: regulation of receptor internalization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of receptor internalization." [GOC:hjd] +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0048259 ! regulation of receptor-mediated endocytosis +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031623 ! receptor internalization +relationship: regulates GO:0031623 ! receptor internalization + +[Term] +id: GO:0002092 +name: positive regulation of receptor internalization +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of receptor internalization." [GOC:hjd] +synonym: "activation of receptor internalization" NARROW [] +synonym: "stimulation of receptor internalization" NARROW [] +synonym: "up regulation of receptor internalization" EXACT [] +synonym: "up-regulation of receptor internalization" EXACT [] +synonym: "upregulation of receptor internalization" EXACT [] +is_a: GO:0002090 ! regulation of receptor internalization +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0048260 ! positive regulation of receptor-mediated endocytosis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031623 ! receptor internalization +relationship: positively_regulates GO:0031623 ! receptor internalization + +[Term] +id: GO:0002237 +name: response to molecule of bacterial origin +namespace: biological_process +def: "Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin." [GOC:rl, GOC:sm] +synonym: "response to bacteria associated molecule" EXACT [] +synonym: "response to bacterial associated molecule" EXACT [] +synonym: "response to bacterium associated molecule" EXACT [] +is_a: GO:0010033 ! response to organic substance +is_a: GO:0043207 ! response to external biotic stimulus +relationship: part_of GO:0009617 ! response to bacterium + +[Term] +id: GO:0002244 +name: hematopoietic progenitor cell differentiation +namespace: biological_process +def: "The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells." [GOC:add, GOC:rl, ISBN:0781735149, PMID:16551251] +synonym: "haematopoietic progenitor cell differentiation" EXACT [] +synonym: "haemopoietic progenitor cell differentiation" EXACT [] +synonym: "hemopoietic progenitor cell differentiation" EXACT [] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030097 ! hemopoiesis + +[Term] +id: GO:0002250 +name: adaptive immune response +namespace: biological_process +def: "An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory)." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. +synonym: "acquired immune response" EXACT [ISBN:068340007X] +xref: Wikipedia:Adaptive_immune_system +is_a: GO:0006955 ! immune response + +[Term] +id: GO:0002252 +name: immune effector process +namespace: biological_process +def: "Any process of the immune system that can potentially contribute to an immune response." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. +is_a: GO:0002376 ! immune system process + +[Term] +id: GO:0002274 +name: myeloid leukocyte activation +namespace: biological_process +def: "A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:add, ISBN:0781735149] +synonym: "myeloid leucocyte activation" EXACT [] +is_a: GO:0045321 ! leukocyte activation + +[Term] +id: GO:0002367 +name: cytokine production involved in immune response +namespace: biological_process +def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. +synonym: "cytokine production during immune response" RELATED [GOC:dph] +is_a: GO:0001816 ! cytokine production +is_a: GO:0002440 ! production of molecular mediator of immune response +intersection_of: GO:0001816 ! cytokine production +intersection_of: part_of GO:0006955 ! immune response +relationship: part_of GO:0006955 ! immune response + +[Term] +id: GO:0002374 +name: cytokine secretion involved in immune response +namespace: biological_process +def: "The regulated release of cytokines from a cell that contributes to an immune response." [GOC:add, ISBN:0781735149] +synonym: "cytokine secretion during immune response" RELATED [GOC:dph] +is_a: GO:0050663 ! cytokine secretion +intersection_of: GO:0050663 ! cytokine secretion +intersection_of: part_of GO:0006955 ! immune response +relationship: part_of GO:0002367 ! cytokine production involved in immune response + +[Term] +id: GO:0002376 +name: immune system process +namespace: biological_process +def: "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05] +comment: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022. +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +xref: Wikipedia:Immune_system +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0002440 +name: production of molecular mediator of immune response +namespace: biological_process +def: "The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. +synonym: "production of cellular mediator of immune response" RELATED [] +is_a: GO:0002376 ! immune system process + +[Term] +id: GO:0002443 +name: leukocyte mediated immunity +namespace: biological_process +alt_id: GO:0019723 +alt_id: GO:0042087 +def: "Any process involved in the carrying out of an immune response by a leukocyte." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. +synonym: "cell-mediated immune response" RELATED [] +synonym: "cellular immune response" RELATED [] +synonym: "immune cell effector process" EXACT [] +synonym: "immune cell mediated immunity" EXACT [] +synonym: "leucocyte immune effector process" EXACT [] +synonym: "leucocyte mediated immunity" EXACT [] +synonym: "leukocyte immune effector process" EXACT [] +is_a: GO:0002252 ! immune effector process + +[Term] +id: GO:0002449 +name: lymphocyte mediated immunity +namespace: biological_process +def: "Any process involved in the carrying out of an immune response by a lymphocyte." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. +synonym: "cell-mediated immunity" BROAD [] +synonym: "cellular immune response" BROAD [] +is_a: GO:0002443 ! leukocyte mediated immunity + +[Term] +id: GO:0002455 +name: humoral immune response mediated by circulating immunoglobulin +namespace: biological_process +def: "An immune response dependent upon secreted immunoglobulin. An example of this process is found in Mus musculus." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. +synonym: "circulating antibody mediated immune response" EXACT [] +synonym: "circulating immunoglobulin mediated immune response" EXACT [] +synonym: "humoral defence mechanism" RELATED [] +synonym: "humoral immune response mediated by circulating antibody" EXACT [] +is_a: GO:0006959 ! humoral immune response +is_a: GO:0016064 ! immunoglobulin mediated immune response + +[Term] +id: GO:0002460 +name: adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +namespace: biological_process +def: "An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus." [GOC:add, GOC:mtg_sensu, ISBN:0781735149] +is_a: GO:0002250 ! adaptive immune response + +[Term] +id: GO:0002467 +name: germinal center formation +namespace: biological_process +def: "The process in which germinal centers form. A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:081533642X] +comment: This term was added by GO_REF:0000022. +is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + +[Term] +id: GO:0002507 +name: tolerance induction +namespace: biological_process +def: "A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. +is_a: GO:0002376 ! immune system process +relationship: part_of GO:0002520 ! immune system development + +[Term] +id: GO:0002508 +name: central tolerance induction +namespace: biological_process +def: "Tolerance induction in the central lymphoid organs: the thymus and bone marrow." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. +is_a: GO:0002507 ! tolerance induction + +[Term] +id: GO:0002510 +name: central B cell tolerance induction +namespace: biological_process +def: "Tolerance induction of B cells in the bone marrow." [GOC:jal, PMID:16460922] +synonym: "central B lymphocyte tolerance induction" EXACT [] +synonym: "central B-cell tolerance induction" EXACT [] +synonym: "central B-lymphocyte tolerance induction" EXACT [] +is_a: GO:0002508 ! central tolerance induction +is_a: GO:0002514 ! B cell tolerance induction + +[Term] +id: GO:0002514 +name: B cell tolerance induction +namespace: biological_process +def: "A process involving any mechanism for tolerance induction in B cells." [GOC:jal, ISBN:0781735149, PMID:16460922] +synonym: "B lymphocyte tolerance induction" EXACT [] +synonym: "B-cell tolerance induction" EXACT [] +synonym: "B-lymphocyte tolerance induction" EXACT [] +is_a: GO:0002507 ! tolerance induction + +[Term] +id: GO:0002520 +name: immune system development +namespace: biological_process +def: "The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." [GOC:add, GOC:dph] +is_a: GO:0002376 ! immune system process +is_a: GO:0048731 ! system development + +[Term] +id: GO:0002521 +name: leukocyte differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [CL:0000738, GOC:add, PMID:16551264] +synonym: "immune cell differentiation" EXACT [] +synonym: "leucocyte differentiation" EXACT [] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030097 ! hemopoiesis + +[Term] +id: GO:0002526 +name: acute inflammatory response +namespace: biological_process +def: "Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was added by GO_REF:0000022. +is_a: GO:0006954 ! inflammatory response + +[Term] +id: GO:0002528 +name: regulation of vascular permeability involved in acute inflammatory response +namespace: biological_process +def: "Any process that modulates the extent to which blood vessels can be pervaded by fluid contributing to an acute inflammatory response." [GOC:jal] +synonym: "regulation of vascular permeability during acute inflammatory response" RELATED [GOC:dph] +is_a: GO:0043114 ! regulation of vascular permeability +intersection_of: GO:0043114 ! regulation of vascular permeability +intersection_of: part_of GO:0002526 ! acute inflammatory response +relationship: part_of GO:0002526 ! acute inflammatory response + +[Term] +id: GO:0002573 +name: myeloid leukocyte differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage." [GOC:add, PMID:16551251] +synonym: "myeloid leucocyte differentiation" EXACT [] +is_a: GO:0002521 ! leukocyte differentiation +is_a: GO:0030099 ! myeloid cell differentiation + +[Term] +id: GO:0002634 +name: regulation of germinal center formation +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of germinal center formation." [GOC:add] +is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002467 ! germinal center formation +relationship: regulates GO:0002467 ! germinal center formation + +[Term] +id: GO:0002635 +name: negative regulation of germinal center formation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of germinal center formation." [GOC:add] +synonym: "down regulation of germinal center formation" EXACT [] +synonym: "down-regulation of germinal center formation" EXACT [] +synonym: "downregulation of germinal center formation" EXACT [] +synonym: "inhibition of germinal center formation" NARROW [] +is_a: GO:0002634 ! regulation of germinal center formation +is_a: GO:0002823 ! negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002467 ! germinal center formation +relationship: negatively_regulates GO:0002467 ! germinal center formation + +[Term] +id: GO:0002643 +name: regulation of tolerance induction +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of tolerance induction." [GOC:add] +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002507 ! tolerance induction +relationship: regulates GO:0002507 ! tolerance induction + +[Term] +id: GO:0002645 +name: positive regulation of tolerance induction +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of tolerance induction." [GOC:add] +synonym: "activation of tolerance induction" NARROW [] +synonym: "stimulation of tolerance induction" NARROW [] +synonym: "up regulation of tolerance induction" EXACT [] +synonym: "up-regulation of tolerance induction" EXACT [] +synonym: "upregulation of tolerance induction" EXACT [] +is_a: GO:0002643 ! regulation of tolerance induction +is_a: GO:0002684 ! positive regulation of immune system process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002507 ! tolerance induction +relationship: positively_regulates GO:0002507 ! tolerance induction + +[Term] +id: GO:0002646 +name: regulation of central tolerance induction +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of central tolerance induction." [GOC:add] +is_a: GO:0002643 ! regulation of tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002508 ! central tolerance induction +relationship: regulates GO:0002508 ! central tolerance induction + +[Term] +id: GO:0002648 +name: positive regulation of central tolerance induction +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of central tolerance induction." [GOC:add] +synonym: "activation of central tolerance induction" NARROW [] +synonym: "stimulation of central tolerance induction" NARROW [] +synonym: "up regulation of central tolerance induction" EXACT [] +synonym: "up-regulation of central tolerance induction" EXACT [] +synonym: "upregulation of central tolerance induction" EXACT [] +is_a: GO:0002645 ! positive regulation of tolerance induction +is_a: GO:0002646 ! regulation of central tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002508 ! central tolerance induction +relationship: positively_regulates GO:0002508 ! central tolerance induction + +[Term] +id: GO:0002661 +name: regulation of B cell tolerance induction +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of B cell tolerance induction." [GOC:add] +synonym: "regulation of B lymphocyte tolerance induction" EXACT [] +synonym: "regulation of B-cell tolerance induction" EXACT [] +synonym: "regulation of B-lymphocyte tolerance induction" EXACT [] +is_a: GO:0002643 ! regulation of tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002514 ! B cell tolerance induction +relationship: regulates GO:0002514 ! B cell tolerance induction + +[Term] +id: GO:0002663 +name: positive regulation of B cell tolerance induction +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of B cell tolerance induction." [GOC:add] +synonym: "activation of B cell tolerance induction" NARROW [] +synonym: "positive regulation of B lymphocyte tolerance induction" EXACT [] +synonym: "positive regulation of B-cell tolerance induction" EXACT [] +synonym: "positive regulation of B-lymphocyte tolerance induction" EXACT [] +synonym: "stimulation of B cell tolerance induction" NARROW [] +synonym: "up regulation of B cell tolerance induction" EXACT [] +synonym: "up-regulation of B cell tolerance induction" EXACT [] +synonym: "upregulation of B cell tolerance induction" EXACT [] +is_a: GO:0002645 ! positive regulation of tolerance induction +is_a: GO:0002661 ! regulation of B cell tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002514 ! B cell tolerance induction +relationship: positively_regulates GO:0002514 ! B cell tolerance induction + +[Term] +id: GO:0002682 +name: regulation of immune system process +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of an immune system process." [GOC:add] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002376 ! immune system process +relationship: regulates GO:0002376 ! immune system process + +[Term] +id: GO:0002683 +name: negative regulation of immune system process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process." [GOC:add] +synonym: "down regulation of immune system process" EXACT [] +synonym: "down-regulation of immune system process" EXACT [] +synonym: "downregulation of immune system process" EXACT [] +synonym: "inhibition of immune system process" NARROW [] +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002376 ! immune system process +relationship: negatively_regulates GO:0002376 ! immune system process + +[Term] +id: GO:0002684 +name: positive regulation of immune system process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of an immune system process." [GOC:add] +synonym: "activation of immune system process" NARROW [] +synonym: "stimulation of immune system process" NARROW [] +synonym: "up regulation of immune system process" EXACT [] +synonym: "up-regulation of immune system process" EXACT [] +synonym: "upregulation of immune system process" EXACT [] +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002376 ! immune system process +relationship: positively_regulates GO:0002376 ! immune system process + +[Term] +id: GO:0002685 +name: regulation of leukocyte migration +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of leukocyte migration." [GOC:add] +synonym: "regulation of immune cell migration" EXACT [] +synonym: "regulation of leucocyte migration" EXACT [] +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0030334 ! regulation of cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050900 ! leukocyte migration +relationship: regulates GO:0050900 ! leukocyte migration + +[Term] +id: GO:0002687 +name: positive regulation of leukocyte migration +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of leukocyte migration." [GOC:add] +synonym: "activation of leukocyte migration" NARROW [] +synonym: "positive regulation of immune cell migration" EXACT [] +synonym: "positive regulation of leucocyte migration" EXACT [] +synonym: "stimulation of leukocyte migration" NARROW [] +synonym: "up regulation of leukocyte migration" EXACT [] +synonym: "up-regulation of leukocyte migration" EXACT [] +synonym: "upregulation of leukocyte migration" EXACT [] +is_a: GO:0002684 ! positive regulation of immune system process +is_a: GO:0002685 ! regulation of leukocyte migration +is_a: GO:0030335 ! positive regulation of cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050900 ! leukocyte migration +relationship: positively_regulates GO:0050900 ! leukocyte migration + +[Term] +id: GO:0002688 +name: regulation of leukocyte chemotaxis +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of leukocyte chemotaxis." [GOC:add] +synonym: "regulation of immune cell chemotaxis" EXACT [] +synonym: "regulation of leucocyte chemotaxis" EXACT [] +is_a: GO:0002685 ! regulation of leukocyte migration +is_a: GO:0050920 ! regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030595 ! leukocyte chemotaxis +relationship: regulates GO:0030595 ! leukocyte chemotaxis + +[Term] +id: GO:0002690 +name: positive regulation of leukocyte chemotaxis +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis." [GOC:add] +synonym: "activation of leukocyte chemotaxis" NARROW [] +synonym: "positive regulation of immune cell chemotaxis" EXACT [] +synonym: "positive regulation of leucocyte chemotaxis" EXACT [] +synonym: "stimulation of leukocyte chemotaxis" NARROW [] +synonym: "up regulation of leukocyte chemotaxis" EXACT [] +synonym: "up-regulation of leukocyte chemotaxis" EXACT [] +synonym: "upregulation of leukocyte chemotaxis" EXACT [] +is_a: GO:0002687 ! positive regulation of leukocyte migration +is_a: GO:0002688 ! regulation of leukocyte chemotaxis +is_a: GO:0050921 ! positive regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030595 ! leukocyte chemotaxis +relationship: positively_regulates GO:0030595 ! leukocyte chemotaxis + +[Term] +id: GO:0002694 +name: regulation of leukocyte activation +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of leukocyte activation." [GOC:add] +synonym: "regulation of immune cell activation" EXACT [] +synonym: "regulation of leucocyte activation" EXACT [] +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0050865 ! regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045321 ! leukocyte activation +relationship: regulates GO:0045321 ! leukocyte activation + +[Term] +id: GO:0002695 +name: negative regulation of leukocyte activation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation." [GOC:add] +synonym: "down regulation of leukocyte activation" EXACT [] +synonym: "down-regulation of leukocyte activation" EXACT [] +synonym: "downregulation of leukocyte activation" EXACT [] +synonym: "inhibition of leukocyte activation" NARROW [] +synonym: "negative regulation of immune cell activation" EXACT [] +synonym: "negative regulation of leucocyte activation" EXACT [] +is_a: GO:0002683 ! negative regulation of immune system process +is_a: GO:0002694 ! regulation of leukocyte activation +is_a: GO:0050866 ! negative regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0045321 ! leukocyte activation +relationship: negatively_regulates GO:0045321 ! leukocyte activation + +[Term] +id: GO:0002696 +name: positive regulation of leukocyte activation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of leukocyte activation." [GOC:add] +synonym: "activation of leukocyte activation" NARROW [] +synonym: "positive regulation of immune cell activation" EXACT [] +synonym: "positive regulation of leucocyte activation" EXACT [] +synonym: "stimulation of leukocyte activation" NARROW [] +synonym: "up regulation of leukocyte activation" EXACT [] +synonym: "up-regulation of leukocyte activation" EXACT [] +synonym: "upregulation of leukocyte activation" EXACT [] +is_a: GO:0002684 ! positive regulation of immune system process +is_a: GO:0002694 ! regulation of leukocyte activation +is_a: GO:0050867 ! positive regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0045321 ! leukocyte activation +relationship: positively_regulates GO:0045321 ! leukocyte activation + +[Term] +id: GO:0002697 +name: regulation of immune effector process +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of an immune effector process." [GOC:add] +is_a: GO:0002682 ! regulation of immune system process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002252 ! immune effector process +relationship: regulates GO:0002252 ! immune effector process + +[Term] +id: GO:0002698 +name: negative regulation of immune effector process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process." [GOC:add] +synonym: "down regulation of immune effector process" EXACT [] +synonym: "down-regulation of immune effector process" EXACT [] +synonym: "downregulation of immune effector process" EXACT [] +synonym: "inhibition of immune effector process" NARROW [] +is_a: GO:0002683 ! negative regulation of immune system process +is_a: GO:0002697 ! regulation of immune effector process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002252 ! immune effector process +relationship: negatively_regulates GO:0002252 ! immune effector process + +[Term] +id: GO:0002699 +name: positive regulation of immune effector process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of an immune effector process." [GOC:add] +synonym: "activation of immune effector process" NARROW [] +synonym: "stimulation of immune effector process" NARROW [] +synonym: "up regulation of immune effector process" EXACT [] +synonym: "up-regulation of immune effector process" EXACT [] +synonym: "upregulation of immune effector process" EXACT [] +is_a: GO:0002684 ! positive regulation of immune system process +is_a: GO:0002697 ! regulation of immune effector process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002252 ! immune effector process +relationship: positively_regulates GO:0002252 ! immune effector process + +[Term] +id: GO:0002700 +name: regulation of production of molecular mediator of immune response +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of the production of molecular mediator of immune response." [GOC:add] +is_a: GO:0002697 ! regulation of immune effector process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002440 ! production of molecular mediator of immune response +relationship: regulates GO:0002440 ! production of molecular mediator of immune response + +[Term] +id: GO:0002702 +name: positive regulation of production of molecular mediator of immune response +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of the production of molecular mediator of immune response." [GOC:add] +synonym: "activation of production of molecular mediator of immune response" NARROW [] +synonym: "stimulation of production of molecular mediator of immune response" NARROW [] +synonym: "up regulation of production of molecular mediator of immune response" EXACT [] +synonym: "up-regulation of production of molecular mediator of immune response" EXACT [] +synonym: "upregulation of production of molecular mediator of immune response" EXACT [] +is_a: GO:0002699 ! positive regulation of immune effector process +is_a: GO:0002700 ! regulation of production of molecular mediator of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002440 ! production of molecular mediator of immune response +relationship: positively_regulates GO:0002440 ! production of molecular mediator of immune response + +[Term] +id: GO:0002703 +name: regulation of leukocyte mediated immunity +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity." [GOC:add] +synonym: "regulation of immune cell mediated immunity" EXACT [] +synonym: "regulation of leucocyte mediated immunity" EXACT [] +is_a: GO:0002697 ! regulation of immune effector process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002443 ! leukocyte mediated immunity +relationship: regulates GO:0002443 ! leukocyte mediated immunity + +[Term] +id: GO:0002704 +name: negative regulation of leukocyte mediated immunity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity." [GOC:add] +synonym: "down regulation of leukocyte mediated immunity" EXACT [] +synonym: "down-regulation of leukocyte mediated immunity" EXACT [] +synonym: "downregulation of leukocyte mediated immunity" EXACT [] +synonym: "inhibition of leukocyte mediated immunity" NARROW [] +synonym: "negative regulation of immune cell mediated immunity" EXACT [] +synonym: "negative regulation of leucocyte mediated immunity" EXACT [] +is_a: GO:0002698 ! negative regulation of immune effector process +is_a: GO:0002703 ! regulation of leukocyte mediated immunity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002443 ! leukocyte mediated immunity +relationship: negatively_regulates GO:0002443 ! leukocyte mediated immunity + +[Term] +id: GO:0002706 +name: regulation of lymphocyte mediated immunity +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of lymphocyte mediated immunity." [GOC:add] +is_a: GO:0002703 ! regulation of leukocyte mediated immunity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002449 ! lymphocyte mediated immunity +relationship: regulates GO:0002449 ! lymphocyte mediated immunity + +[Term] +id: GO:0002707 +name: negative regulation of lymphocyte mediated immunity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of lymphocyte mediated immunity." [GOC:add] +synonym: "down regulation of lymphocyte mediated immunity" EXACT [] +synonym: "down-regulation of lymphocyte mediated immunity" EXACT [] +synonym: "downregulation of lymphocyte mediated immunity" EXACT [] +synonym: "inhibition of lymphocyte mediated immunity" NARROW [] +is_a: GO:0002704 ! negative regulation of leukocyte mediated immunity +is_a: GO:0002706 ! regulation of lymphocyte mediated immunity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002449 ! lymphocyte mediated immunity +relationship: negatively_regulates GO:0002449 ! lymphocyte mediated immunity + +[Term] +id: GO:0002712 +name: regulation of B cell mediated immunity +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of B cell mediated immunity." [GOC:add] +synonym: "regulation of B lymphocyte mediated immunity" EXACT [] +synonym: "regulation of B-cell mediated immunity" EXACT [] +synonym: "regulation of B-lymphocyte mediated immunity" EXACT [] +is_a: GO:0002706 ! regulation of lymphocyte mediated immunity +is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0019724 ! B cell mediated immunity +relationship: regulates GO:0019724 ! B cell mediated immunity + +[Term] +id: GO:0002713 +name: negative regulation of B cell mediated immunity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell mediated immunity." [GOC:add] +synonym: "down regulation of B cell mediated immunity" EXACT [] +synonym: "down-regulation of B cell mediated immunity" EXACT [] +synonym: "downregulation of B cell mediated immunity" EXACT [] +synonym: "inhibition of B cell mediated immunity" NARROW [] +synonym: "negative regulation of B lymphocyte mediated immunity" EXACT [] +synonym: "negative regulation of B-cell mediated immunity" EXACT [] +synonym: "negative regulation of B-lymphocyte mediated immunity" EXACT [] +is_a: GO:0002707 ! negative regulation of lymphocyte mediated immunity +is_a: GO:0002712 ! regulation of B cell mediated immunity +is_a: GO:0002823 ! negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0019724 ! B cell mediated immunity +relationship: negatively_regulates GO:0019724 ! B cell mediated immunity + +[Term] +id: GO:0002718 +name: regulation of cytokine production involved in immune response +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of cytokine production that contributes to an immune response." [GOC:add] +synonym: "regulation of cytokine production during immune response" RELATED [GOC:dph] +is_a: GO:0001817 ! regulation of cytokine production +is_a: GO:0002700 ! regulation of production of molecular mediator of immune response +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002367 ! cytokine production involved in immune response +relationship: regulates GO:0002367 ! cytokine production involved in immune response + +[Term] +id: GO:0002720 +name: positive regulation of cytokine production involved in immune response +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of cytokine production that contributes to an immune response." [GOC:add] +synonym: "activation of cytokine production during immune response" NARROW [] +synonym: "positive regulation of cytokine production during immune response" RELATED [GOC:dph] +synonym: "stimulation of cytokine production during immune response" NARROW [] +synonym: "up regulation of cytokine production during immune response" RELATED [] +synonym: "up-regulation of cytokine production during immune response" RELATED [] +synonym: "upregulation of cytokine production during immune response" RELATED [] +is_a: GO:0001819 ! positive regulation of cytokine production +is_a: GO:0002702 ! positive regulation of production of molecular mediator of immune response +is_a: GO:0002718 ! regulation of cytokine production involved in immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002367 ! cytokine production involved in immune response +relationship: positively_regulates GO:0002367 ! cytokine production involved in immune response + +[Term] +id: GO:0002739 +name: regulation of cytokine secretion involved in immune response +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of cytokine secretion contributing to an immune response." [GOC:add] +synonym: "regulation of cytokine secretion during immune response" RELATED [GOC:dph] +is_a: GO:0002718 ! regulation of cytokine production involved in immune response +is_a: GO:0050707 ! regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002374 ! cytokine secretion involved in immune response +relationship: regulates GO:0002374 ! cytokine secretion involved in immune response + +[Term] +id: GO:0002741 +name: positive regulation of cytokine secretion involved in immune response +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of cytokine secretion contributing to an immune response." [GOC:add] +synonym: "activation of cytokine secretion during immune response" NARROW [] +synonym: "positive regulation of cytokine secretion during immune response" RELATED [GOC:dph] +synonym: "stimulation of cytokine secretion during immune response" NARROW [] +synonym: "up regulation of cytokine secretion during immune response" RELATED [] +synonym: "up-regulation of cytokine secretion during immune response" RELATED [] +synonym: "upregulation of cytokine secretion during immune response" RELATED [] +is_a: GO:0002739 ! regulation of cytokine secretion involved in immune response +is_a: GO:0050715 ! positive regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002374 ! cytokine secretion involved in immune response +relationship: positively_regulates GO:0002374 ! cytokine secretion involved in immune response + +[Term] +id: GO:0002761 +name: regulation of myeloid leukocyte differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation." [GOC:add] +is_a: GO:0045637 ! regulation of myeloid cell differentiation +is_a: GO:1902105 ! regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002573 ! myeloid leukocyte differentiation +relationship: regulates GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0002762 +name: negative regulation of myeloid leukocyte differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation." [GOC:add] +synonym: "down regulation of myeloid leukocyte differentiation" EXACT [] +synonym: "down-regulation of myeloid leukocyte differentiation" EXACT [] +synonym: "downregulation of myeloid leukocyte differentiation" EXACT [] +synonym: "inhibition of myeloid leukocyte differentiation" NARROW [] +is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation +is_a: GO:0045638 ! negative regulation of myeloid cell differentiation +is_a: GO:1902106 ! negative regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002573 ! myeloid leukocyte differentiation +relationship: negatively_regulates GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0002763 +name: positive regulation of myeloid leukocyte differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation." [GOC:add] +synonym: "activation of myeloid leukocyte differentiation" NARROW [] +synonym: "stimulation of myeloid leukocyte differentiation" NARROW [] +synonym: "up regulation of myeloid leukocyte differentiation" EXACT [] +synonym: "up-regulation of myeloid leukocyte differentiation" EXACT [] +synonym: "upregulation of myeloid leukocyte differentiation" EXACT [] +is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation +is_a: GO:0045639 ! positive regulation of myeloid cell differentiation +is_a: GO:1902107 ! positive regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002573 ! myeloid leukocyte differentiation +relationship: positively_regulates GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0002790 +name: peptide secretion +namespace: biological_process +def: "The controlled release of a peptide from a cell or a tissue." [GOC:add] +is_a: GO:0015833 ! peptide transport +is_a: GO:0046903 ! secretion + +[Term] +id: GO:0002791 +name: regulation of peptide secretion +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of peptide secretion." [GOC:add] +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0090087 ! regulation of peptide transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002790 ! peptide secretion +relationship: regulates GO:0002790 ! peptide secretion + +[Term] +id: GO:0002792 +name: negative regulation of peptide secretion +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion." [GOC:add] +synonym: "down regulation of peptide secretion" EXACT [] +synonym: "down-regulation of peptide secretion" EXACT [] +synonym: "downregulation of peptide secretion" EXACT [] +synonym: "inhibition of peptide secretion" NARROW [] +is_a: GO:0002791 ! regulation of peptide secretion +is_a: GO:0051048 ! negative regulation of secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002790 ! peptide secretion +relationship: negatively_regulates GO:0002790 ! peptide secretion + +[Term] +id: GO:0002819 +name: regulation of adaptive immune response +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of an adaptive immune response." [GOC:add] +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002250 ! adaptive immune response +relationship: regulates GO:0002250 ! adaptive immune response + +[Term] +id: GO:0002820 +name: negative regulation of adaptive immune response +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response." [GOC:add] +synonym: "down regulation of adaptive immune response" EXACT [] +synonym: "down-regulation of adaptive immune response" EXACT [] +synonym: "downregulation of adaptive immune response" EXACT [] +synonym: "inhibition of adaptive immune response" NARROW [] +is_a: GO:0002819 ! regulation of adaptive immune response +is_a: GO:0050777 ! negative regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002250 ! adaptive immune response +relationship: negatively_regulates GO:0002250 ! adaptive immune response + +[Term] +id: GO:0002822 +name: regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata." [GOC:add, GOC:mtg_sensu] +is_a: GO:0002819 ! regulation of adaptive immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +relationship: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + +[Term] +id: GO:0002823 +name: negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata." [GOC:add, GOC:mtg_sensu] +is_a: GO:0002820 ! negative regulation of adaptive immune response +is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +relationship: negatively_regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + +[Term] +id: GO:0002889 +name: regulation of immunoglobulin mediated immune response +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of an immunoglobulin mediated immune response." [GOC:add] +is_a: GO:0002712 ! regulation of B cell mediated immunity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016064 ! immunoglobulin mediated immune response +relationship: regulates GO:0016064 ! immunoglobulin mediated immune response + +[Term] +id: GO:0002890 +name: negative regulation of immunoglobulin mediated immune response +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of an immunoglobulin mediated immune response." [GOC:add] +synonym: "down regulation of immunoglobulin mediated immune response" EXACT [] +synonym: "down-regulation of immunoglobulin mediated immune response" EXACT [] +synonym: "downregulation of immunoglobulin mediated immune response" EXACT [] +synonym: "inhibition of immunoglobulin mediated immune response" NARROW [] +is_a: GO:0002713 ! negative regulation of B cell mediated immunity +is_a: GO:0002889 ! regulation of immunoglobulin mediated immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016064 ! immunoglobulin mediated immune response +relationship: negatively_regulates GO:0016064 ! immunoglobulin mediated immune response + +[Term] +id: GO:0002895 +name: regulation of central B cell tolerance induction +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of central B cell tolerance induction." [GOC:add] +is_a: GO:0002646 ! regulation of central tolerance induction +is_a: GO:0002661 ! regulation of B cell tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002510 ! central B cell tolerance induction +relationship: regulates GO:0002510 ! central B cell tolerance induction + +[Term] +id: GO:0002897 +name: positive regulation of central B cell tolerance induction +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of central B cell tolerance induction." [GOC:add] +synonym: "activation of central B cell tolerance induction" NARROW [] +synonym: "stimulation of central B cell tolerance induction" NARROW [] +synonym: "up regulation of central B cell tolerance induction" EXACT [] +synonym: "up-regulation of central B cell tolerance induction" EXACT [] +synonym: "upregulation of central B cell tolerance induction" EXACT [] +is_a: GO:0002648 ! positive regulation of central tolerance induction +is_a: GO:0002663 ! positive regulation of B cell tolerance induction +is_a: GO:0002895 ! regulation of central B cell tolerance induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002510 ! central B cell tolerance induction +relationship: positively_regulates GO:0002510 ! central B cell tolerance induction + +[Term] +id: GO:0002920 +name: regulation of humoral immune response +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of a humoral immune response." [GOC:add] +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006959 ! humoral immune response +relationship: regulates GO:0006959 ! humoral immune response + +[Term] +id: GO:0002921 +name: negative regulation of humoral immune response +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of a humoral immune response." [GOC:add] +synonym: "down regulation of humoral immune response" EXACT [] +synonym: "down-regulation of humoral immune response" EXACT [] +synonym: "downregulation of humoral immune response" EXACT [] +synonym: "inhibition of humoral immune response" NARROW [] +is_a: GO:0002920 ! regulation of humoral immune response +is_a: GO:0050777 ! negative regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006959 ! humoral immune response +relationship: negatively_regulates GO:0006959 ! humoral immune response + +[Term] +id: GO:0002923 +name: regulation of humoral immune response mediated by circulating immunoglobulin +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of a humoral immune response mediated by circulating immunoglobulin." [GOC:add] +is_a: GO:0002889 ! regulation of immunoglobulin mediated immune response +is_a: GO:0002920 ! regulation of humoral immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002455 ! humoral immune response mediated by circulating immunoglobulin +relationship: regulates GO:0002455 ! humoral immune response mediated by circulating immunoglobulin + +[Term] +id: GO:0002924 +name: negative regulation of humoral immune response mediated by circulating immunoglobulin +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of a humoral immune response mediated by circulating immunoglobulin." [GOC:add] +synonym: "down regulation of humoral immune response mediated by circulating immunoglobulin" EXACT [] +synonym: "down-regulation of humoral immune response mediated by circulating immunoglobulin" EXACT [] +synonym: "downregulation of humoral immune response mediated by circulating immunoglobulin" EXACT [] +synonym: "inhibition of humoral immune response mediated by circulating immunoglobulin" NARROW [] +is_a: GO:0002890 ! negative regulation of immunoglobulin mediated immune response +is_a: GO:0002921 ! negative regulation of humoral immune response +is_a: GO:0002923 ! regulation of humoral immune response mediated by circulating immunoglobulin +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002455 ! humoral immune response mediated by circulating immunoglobulin +relationship: negatively_regulates GO:0002455 ! humoral immune response mediated by circulating immunoglobulin + +[Term] +id: GO:0003002 +name: regionalization +namespace: biological_process +def: "The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment." [GOC:dph, GOC:isa_complete] +synonym: "pattern formation" RELATED [GOC:dph] +is_a: GO:0007389 ! pattern specification process + +[Term] +id: GO:0003006 +name: developmental process involved in reproduction +namespace: biological_process +def: "A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring." [GOC:dph, GOC:isa_complete] +synonym: "reproductive developmental process" RELATED [GOC:dph, GOC:tb] +is_a: GO:0022414 ! reproductive process +is_a: GO:0032502 ! developmental process +intersection_of: GO:0032502 ! developmental process +intersection_of: part_of GO:0000003 ! reproduction + +[Term] +id: GO:0003007 +name: heart morphogenesis +namespace: biological_process +def: "The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC:dph, GOC:isa_complete] +synonym: "cardiac morphogenesis" RELATED [] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0003008 +name: system process +namespace: biological_process +def: "A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective." [GOC:mtg_cardio] +synonym: "organ system process" EXACT [] +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0003013 +name: circulatory system process +namespace: biological_process +def: "A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism." [GOC:mtg_cardio] +subset: goslim_generic +xref: Wikipedia:Circulatory_system +is_a: GO:0003008 ! system process + +[Term] +id: GO:0003015 +name: heart process +namespace: biological_process +def: "A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC:mtg_cardio] +synonym: "cardiac process" RELATED [] +is_a: GO:0003013 ! circulatory system process + +[Term] +id: GO:0003018 +name: vascular process in circulatory system +namespace: biological_process +def: "A circulatory process that occurs at the level of the vasculature." [GOC:mtg_cardio] +synonym: "vasculature process" EXACT [] +is_a: GO:0003013 ! circulatory system process + +[Term] +id: GO:0003128 +name: heart field specification +namespace: biological_process +def: "The process that results in the delineation of a specific region of the lateral mesoderm into the area in which the heart will develop." [GOC:mtg_heart] +is_a: GO:0010092 ! specification of organ identity +relationship: part_of GO:0060914 ! heart formation +created_by: tanyaberardini +creation_date: 2009-09-22T02:56:05Z + +[Term] +id: GO:0003129 +name: heart induction +namespace: biological_process +def: "The close range interaction between mesoderm and endoderm or ectoderm that causes cells to change their fates and specify the development of the heart." [GOC:mtg_heart] +is_a: GO:0001759 ! organ induction +is_a: GO:2000826 ! regulation of heart morphogenesis +relationship: positively_regulates GO:0003128 ! heart field specification +created_by: tanyaberardini +creation_date: 2009-09-22T02:58:41Z + +[Term] +id: GO:0003136 +name: negative regulation of heart induction by canonical Wnt signaling pathway +namespace: biological_process +def: "Any canonical Wnt signaling that decreases the rate, frequency or extent of heart induction." [GOC:mtg_heart, PMID:19862329] +synonym: "negative regulation of cardioblast cell fate specification by Wnt receptor signaling pathway" EXACT [GOC:dph] +synonym: "negative regulation of heart induction by canonical Wnt receptor signaling pathway" EXACT [] +synonym: "negative regulation of heart induction by canonical Wnt receptor signalling pathway" EXACT [GOC:mah] +synonym: "negative regulation of heart induction by canonical Wnt-activated signaling pathway" EXACT [GOC:signaling] +is_a: GO:0009997 ! negative regulation of cardioblast cell fate specification +is_a: GO:0061316 ! canonical Wnt signaling pathway involved in heart development +is_a: GO:1901320 ! negative regulation of heart induction +relationship: negatively_regulates GO:0003129 ! heart induction +created_by: tanyaberardini +creation_date: 2009-09-22T03:26:17Z + +[Term] +id: GO:0003139 +name: secondary heart field specification +namespace: biological_process +def: "The process that results in the delineation of a specific region of the lateral mesoderm into the area which will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract)." [GOC:mtg_heart, GOC:rl, PMID:17276708] +synonym: "anterior heart field specification" NARROW [GOC:mtg_heart] +synonym: "second heart field specification" EXACT [GOC:mtg_heart, PMID:17276708] +synonym: "SHF specification" EXACT [GOC:rl, PMID:22449840] +is_a: GO:0003128 ! heart field specification +created_by: tanyaberardini +creation_date: 2009-09-22T03:47:56Z + +[Term] +id: GO:0003143 +name: embryonic heart tube morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart." [GOC:mtg_heart] +is_a: GO:0048598 ! embryonic morphogenesis +is_a: GO:0060562 ! epithelial tube morphogenesis +relationship: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0035050 ! embryonic heart tube development +relationship: part_of GO:0048562 ! embryonic organ morphogenesis +created_by: tanyaberardini +creation_date: 2009-09-22T04:21:17Z + +[Term] +id: GO:0003151 +name: outflow tract morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries." [GOC:mtg_heart, UBERON:0004145] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0003007 ! heart morphogenesis +created_by: tanyaberardini +creation_date: 2009-09-22T07:59:24Z + +[Term] +id: GO:0003156 +name: regulation of organ formation +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of organ formation. Organ formation is the process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment." [GOC:dph, GOC:mtg_heart, GOC:tb] +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048645 ! organ formation +relationship: regulates GO:0048645 ! organ formation +created_by: tanyaberardini +creation_date: 2009-09-30T11:21:09Z + +[Term] +id: GO:0003158 +name: endothelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of an endothelium over time, from its formation to the mature structure. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities,and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells." [GOC:mtg_heart] +is_a: GO:0009888 ! tissue development +created_by: dph +creation_date: 2009-10-01T12:50:57Z + +[Term] +id: GO:0003159 +name: morphogenesis of an endothelium +namespace: biological_process +def: "The process in which the anatomical structure of an endothelium is generated and organized. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells." [GOC:mtg_heart] +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0003158 ! endothelium development +created_by: dph +creation_date: 2009-10-01T01:34:06Z + +[Term] +id: GO:0003205 +name: cardiac chamber development +namespace: biological_process +def: "The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart." [GOC:mtg_heart] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007507 ! heart development +created_by: dph +creation_date: 2009-10-13T09:11:18Z + +[Term] +id: GO:0003206 +name: cardiac chamber morphogenesis +namespace: biological_process +def: "The process in which a cardiac chamber is generated and organized. A cardiac chamber is an enclosed cavity within the heart." [GOC:mtg_heart] +synonym: "heart chamber morphogenesis" EXACT [GOC:mtg_heart] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0003205 ! cardiac chamber development +created_by: dph +creation_date: 2009-10-13T09:14:51Z + +[Term] +id: GO:0003208 +name: cardiac ventricle morphogenesis +namespace: biological_process +def: "The process in which the cardiac ventricle is generated and organized. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart." [GOC:mtg_heart] +is_a: GO:0003206 ! cardiac chamber morphogenesis +relationship: part_of GO:0003231 ! cardiac ventricle development +created_by: dph +creation_date: 2009-10-13T09:38:44Z + +[Term] +id: GO:0003209 +name: cardiac atrium morphogenesis +namespace: biological_process +def: "The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle." [GOC:mtg_heart] +is_a: GO:0003206 ! cardiac chamber morphogenesis +relationship: part_of GO:0003230 ! cardiac atrium development +created_by: dph +creation_date: 2009-10-13T09:39:44Z + +[Term] +id: GO:0003213 +name: cardiac right atrium morphogenesis +namespace: biological_process +def: "The process in which the right cardiac atrium is generated and organized." [GOC:mtg_heart] +is_a: GO:0003209 ! cardiac atrium morphogenesis +created_by: dph +creation_date: 2009-10-13T09:49:03Z + +[Term] +id: GO:0003214 +name: cardiac left ventricle morphogenesis +namespace: biological_process +def: "The process in which the left cardiac ventricle is generated and organized." [GOC:mtg_heart] +is_a: GO:0003208 ! cardiac ventricle morphogenesis +created_by: dph +creation_date: 2009-10-13T09:50:08Z + +[Term] +id: GO:0003215 +name: cardiac right ventricle morphogenesis +namespace: biological_process +def: "The process in which the right cardiac ventricle is generated and organized." [GOC:mtg_heart] +is_a: GO:0003208 ! cardiac ventricle morphogenesis +created_by: dph +creation_date: 2009-10-13T09:50:57Z + +[Term] +id: GO:0003222 +name: ventricular trabecula myocardium morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the trabecular cardiac ventricle muscle are generated and organized." [GOC:mtg_heart] +synonym: "trabecula carnea morphogenesis" RELATED [GOC:dph] +is_a: GO:0055010 ! ventricular cardiac muscle tissue morphogenesis +is_a: GO:0061384 ! heart trabecula morphogenesis +created_by: dph +creation_date: 2009-10-13T10:33:00Z + +[Term] +id: GO:0003223 +name: ventricular compact myocardium morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the compact cardiac ventricle muscle are generated and organized." [GOC:mtg_heart] +is_a: GO:0055010 ! ventricular cardiac muscle tissue morphogenesis +created_by: dph +creation_date: 2009-10-13T10:34:21Z + +[Term] +id: GO:0003229 +name: ventricular cardiac muscle tissue development +namespace: biological_process +def: "The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure." [GOC:mtg_heart] +synonym: "ventricular myocardium development" EXACT [GOC:mtg_heart] +is_a: GO:0048738 ! cardiac muscle tissue development +created_by: dph +creation_date: 2009-10-13T10:56:01Z + +[Term] +id: GO:0003230 +name: cardiac atrium development +namespace: biological_process +def: "The process whose specific outcome is the progression of a cardiac atrium over time, from its formation to the mature structure. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle." [GOC:mtg_heart] +is_a: GO:0003205 ! cardiac chamber development +created_by: dph +creation_date: 2009-10-13T11:02:07Z + +[Term] +id: GO:0003231 +name: cardiac ventricle development +namespace: biological_process +def: "The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart." [GOC:mtg_heart] +is_a: GO:0003205 ! cardiac chamber development +created_by: dph +creation_date: 2009-10-13T11:03:16Z + +[Term] +id: GO:0003263 +name: cardioblast proliferation +namespace: biological_process +def: "The multiplication or reproduction of cardioblasts, resulting in the expansion of the population in the heart field. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:mtg_heart] +is_a: GO:0061323 ! cell proliferation involved in heart morphogenesis +relationship: part_of GO:0060914 ! heart formation +created_by: dph +creation_date: 2009-10-15T02:13:05Z + +[Term] +id: GO:0003264 +name: regulation of cardioblast proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cardioblast proliferation. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:mtg_heart] +is_a: GO:0003156 ! regulation of organ formation +is_a: GO:2000136 ! regulation of cell proliferation involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003263 ! cardioblast proliferation +relationship: regulates GO:0003263 ! cardioblast proliferation +created_by: dph +creation_date: 2009-10-15T02:19:37Z + +[Term] +id: GO:0003266 +name: regulation of secondary heart field cardioblast proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cardioblast proliferation in the second heart field. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. The secondary heart field is the region of the heart that will form the majority of the mesodermal component of the right ventricle, the arterial pole (outflow tract) and the venous pole (inflow tract)." [GOC:mtg_heart, GOC:rl, PMID:17276708] +synonym: "regulation of second heart field cardioblast proliferation" EXACT [GOC:dph] +synonym: "regulation of SHF cardioblast proliferation " EXACT [GOC:rl] +is_a: GO:0003264 ! regulation of cardioblast proliferation +created_by: dph +creation_date: 2009-10-15T02:26:15Z + +[Term] +id: GO:0003275 +name: apoptotic process involved in outflow tract morphogenesis +namespace: biological_process +def: "Any apoptotic process that contributes to the shaping of the outflow tract. The outflow tract is the portion of the heart through which blood flows into the arteries." [GOC:mtg_apoptosis, GOC:mtg_heart] +synonym: "apoptosis involved in outflow tract morphogenesis" NARROW [] +is_a: GO:0003278 ! apoptotic process involved in heart morphogenesis +intersection_of: GO:0006915 ! apoptotic process +intersection_of: part_of GO:0003151 ! outflow tract morphogenesis +relationship: part_of GO:0003151 ! outflow tract morphogenesis +created_by: dph +creation_date: 2009-10-20T09:30:01Z + +[Term] +id: GO:0003278 +name: apoptotic process involved in heart morphogenesis +namespace: biological_process +def: "Any apoptotic process that contributes to the shaping of the heart." [GOC:mtg_apoptosis, GOC:mtg_heart] +synonym: "apoptosis involved in heart morphogenesis" NARROW [] +is_a: GO:0060561 ! apoptotic process involved in morphogenesis +intersection_of: GO:0006915 ! apoptotic process +intersection_of: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0003007 ! heart morphogenesis +created_by: dph +creation_date: 2009-10-20T09:40:22Z + +[Term] +id: GO:0003279 +name: cardiac septum development +namespace: biological_process +def: "The progression of a cardiac septum over time, from its initial formation to the mature structure." [GOC:mtg_heart] +synonym: "heart septum development" EXACT [GOC:mtg_heart] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0003205 ! cardiac chamber development +created_by: dph +creation_date: 2009-10-20T09:45:13Z + +[Term] +id: GO:0003281 +name: ventricular septum development +namespace: biological_process +def: "The progression of the ventricular septum over time from its formation to the mature structure." [GOC:mtg_heart] +synonym: "interventricular septum development" EXACT [GOC:mtg_heart] +synonym: "septum inferius development" NARROW [GOC:mtg_heart] +is_a: GO:0003279 ! cardiac septum development +relationship: part_of GO:0003231 ! cardiac ventricle development +created_by: dph +creation_date: 2009-10-20T10:04:51Z + +[Term] +id: GO:0003306 +name: Wnt signaling pathway involved in heart development +namespace: biological_process +def: "The series of molecular signals initiated by binding of Wnt protein to a receptor on the surface of the target cell, resulting a change in cell state that contributes to the progression of the heart over time." [GOC:mtg_heart] +synonym: "Wnt receptor signaling pathway involved in heart development" EXACT [] +synonym: "Wnt receptor signalling pathway involved in heart development" EXACT [GOC:mah] +synonym: "Wnt-activated signaling pathway involved in heart development" EXACT [GOC:signaling] +is_a: GO:0016055 ! Wnt signaling pathway +is_a: GO:0061311 ! cell surface receptor signaling pathway involved in heart development +intersection_of: GO:0016055 ! Wnt signaling pathway +intersection_of: part_of GO:0007507 ! heart development +created_by: dph +creation_date: 2009-10-22T12:26:07Z + +[Term] +id: GO:0003307 +name: regulation of Wnt signaling pathway involved in heart development +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell, resulting a change in cell state that contributes to the progression of the heart over time." [GOC:mtg_heart] +synonym: "regulation of Wnt receptor signaling pathway involved in heart development" EXACT [] +synonym: "regulation of Wnt receptor signalling pathway involved in heart development" EXACT [GOC:mah] +synonym: "regulation of Wnt-activated signaling pathway involved in heart development" EXACT [GOC:signaling] +is_a: GO:0030111 ! regulation of Wnt signaling pathway +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003306 ! Wnt signaling pathway involved in heart development +relationship: regulates GO:0003306 ! Wnt signaling pathway involved in heart development +created_by: dph +creation_date: 2009-10-22T12:32:10Z + +[Term] +id: GO:0003308 +name: negative regulation of Wnt signaling pathway involved in heart development +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of the series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell, resulting a change in cell state that contributes to the progression of the heart over time." [GOC:mtg_heart] +synonym: "negative regulation of Wnt receptor signaling pathway involved in heart development" EXACT [] +synonym: "negative regulation of Wnt receptor signalling pathway involved in heart development" EXACT [GOC:mah] +synonym: "negative regulation of Wnt-activated signaling pathway involved in heart development" EXACT [GOC:signaling] +is_a: GO:0003307 ! regulation of Wnt signaling pathway involved in heart development +is_a: GO:0030178 ! negative regulation of Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003306 ! Wnt signaling pathway involved in heart development +relationship: negatively_regulates GO:0003306 ! Wnt signaling pathway involved in heart development +created_by: dph +creation_date: 2009-10-22T12:36:11Z + +[Term] +id: GO:0003309 +name: type B pancreatic cell differentiation +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features of a type B pancreatic cell. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin." [CL:0000169, GOC:dph, PMID:11076772] +synonym: "pancreatic B cell differentiation" EXACT [GOC:mah] +synonym: "pancreatic beta cell differentiation" EXACT [GOC:dph] +is_a: GO:0035883 ! enteroendocrine cell differentiation +relationship: part_of GO:0031018 ! endocrine pancreas development +created_by: dph +creation_date: 2009-10-26T09:27:23Z + +[Term] +id: GO:0003323 +name: type B pancreatic cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin." [CL:0000169, GOC:dph] +synonym: "pancreatic B cell development" EXACT [GOC:mah] +synonym: "pancreatic beta cell development" EXACT [GOC:dph] +is_a: GO:0002068 ! glandular epithelial cell development +relationship: part_of GO:0003309 ! type B pancreatic cell differentiation +created_by: dph +creation_date: 2009-11-02T08:20:11Z + +[Term] +id: GO:0003337 +name: mesenchymal to epithelial transition involved in metanephros morphogenesis +namespace: biological_process +def: "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros." [GOC:dph, GOC:yaf] +synonym: "metanephric mesenchyme to epithelial transition" RELATED [GOC:dph] +is_a: GO:0060231 ! mesenchymal to epithelial transition +intersection_of: GO:0060231 ! mesenchymal to epithelial transition +intersection_of: part_of GO:0003338 ! metanephros morphogenesis +relationship: part_of GO:0072283 ! metanephric renal vesicle morphogenesis +created_by: dph +creation_date: 2009-11-24T09:29:49Z + +[Term] +id: GO:0003338 +name: metanephros morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the metanephros are generated and organized." [GOC:dph, GOC:yaf] +is_a: GO:0060993 ! kidney morphogenesis +relationship: part_of GO:0001656 ! metanephros development +created_by: dph +creation_date: 2009-11-24T09:32:09Z + +[Term] +id: GO:0003344 +name: pericardium morphogenesis +namespace: biological_process +def: "The process in which the anatomical structure of the pericardium is generated and organized." [GOC:dph, PMID:18722343] +is_a: GO:0002011 ! morphogenesis of an epithelial sheet +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0060039 ! pericardium development +created_by: dph +creation_date: 2009-12-01T10:46:34Z + +[Term] +id: GO:0003382 +name: epithelial cell morphogenesis +namespace: biological_process +def: "The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +relationship: part_of GO:0002064 ! epithelial cell development +created_by: dph +creation_date: 2009-12-09T07:21:06Z + +[Term] +id: GO:0003401 +name: axis elongation +namespace: biological_process +def: "The developmental growth that results in the elongation of a line that defines polarity or symmetry in an anatomical structure." [GOC:ascb_2009, GOC:dph, GOC:tb] +synonym: "elongation of an axis" RELATED [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0060560 ! developmental growth involved in morphogenesis +created_by: dph +creation_date: 2009-12-21T01:12:15Z + +[Term] +id: GO:0003402 +name: planar cell polarity pathway involved in axis elongation +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal to modulate cytoskeletal elements and control cell polarity that contributes to axis elongation." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway +intersection_of: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway +intersection_of: part_of GO:0003401 ! axis elongation +relationship: part_of GO:0003401 ! axis elongation +created_by: dph +creation_date: 2009-12-21T01:22:11Z + +[Term] +id: GO:0003674 +name: molecular_function +namespace: molecular_function +alt_id: GO:0005554 +def: "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators] +comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "molecular function" EXACT [] +synonym: "molecular function unknown" NARROW [] +disjoint_from: GO:0005575 ! cellular_component +disjoint_from: GO:0008150 ! biological_process + +[Term] +id: GO:0003676 +name: nucleic acid binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any nucleic acid." [GOC:jl] +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +is_a: GO:0097159 ! organic cyclic compound binding +is_a: GO:1901363 ! heterocyclic compound binding + +[Term] +id: GO:0003677 +name: DNA binding +namespace: molecular_function +def: "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb, GOC:vw] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "microtubule/chromatin interaction" RELATED [] +synonym: "plasmid binding" NARROW [] +is_a: GO:0003676 ! nucleic acid binding + +[Term] +id: GO:0003682 +name: chromatin binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732, PMID:20404130] +subset: goslim_pir +subset: goslim_plant +synonym: "lamin/chromatin binding" BROAD [] +synonym: "microtubule/chromatin interaction" RELATED [] +synonym: "nuclear membrane vesicle binding to chromatin" NARROW [] +is_a: GO:0005488 ! binding + +[Term] +id: GO:0003690 +name: double-stranded DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with double-stranded DNA." [GOC:elh] +subset: gosubset_prok +synonym: "dsDNA binding" EXACT [GOC:elh] +is_a: GO:0043566 ! structure-specific DNA binding + +[Term] +id: GO:0003700 +name: sequence-specific DNA binding transcription factor activity +namespace: molecular_function +alt_id: GO:0000130 +def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:curators, GOC:txnOH] +subset: goslim_plant +subset: gosubset_prok +synonym: "transcription factor activity" BROAD [] +is_a: GO:0001071 ! nucleic acid binding transcription factor activity +relationship: has_part GO:0000976 ! transcription regulatory region sequence-specific DNA binding +relationship: part_of GO:0006355 ! regulation of transcription, DNA-templated + +[Term] +id: GO:0003705 +name: RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II." [GOC:jl, GOC:txnOH] +synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity" EXACT [] +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: has_part GO:0000980 ! RNA polymerase II distal enhancer sequence-specific DNA binding + +[Term] +id: GO:0003707 +name: steroid hormone receptor activity +namespace: molecular_function +def: "Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function." [GOC:signaling, PMID:14708019] +comment: Some steroid hormone receptors reside in the plasma membrane and signal through second messengers or other intracellular signal transduction pathways. For steroid hormone receptors that act in the nucleus to regulate transcription, consider also annotating to the terms: ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity ; GO:0038049' or ligand-activated RNA polymerase II transcription factor binding transcription factor activity ; GO:0038049'. +is_a: GO:0038023 ! signaling receptor activity +relationship: part_of GO:0043401 ! steroid hormone mediated signaling pathway + +[Term] +id: GO:0003712 +name: transcription cofactor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] +subset: gosubset_prok +synonym: "transcriptional co-regulator" EXACT [] +synonym: "transcriptional cofactor activity" EXACT [] +is_a: GO:0000989 ! transcription factor binding transcription factor activity +relationship: has_part GO:0001098 ! basal transcription machinery binding + +[Term] +id: GO:0003713 +name: transcription coactivator activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] +subset: gosubset_prok +synonym: "transcription co-activator activity" EXACT [] +is_a: GO:0003712 ! transcription cofactor activity +relationship: has_part GO:0033613 ! activating transcription factor binding + +[Term] +id: GO:0003714 +name: transcription corepressor activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] +synonym: "transcription co-repressor activity" EXACT [] +is_a: GO:0003712 ! transcription cofactor activity +relationship: has_part GO:0070491 ! repressing transcription factor binding + +[Term] +id: GO:0003824 +name: catalytic activity +namespace: molecular_function +def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN:0198506732] +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] +xref: Wikipedia:Enzyme +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0008152 ! metabolic process + +[Term] +id: GO:0003924 +name: GTPase activity +namespace: molecular_function +def: "Catalysis of the reaction: GTP + H2O = GDP + phosphate." [ISBN:0198547684] +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "ARF small monomeric GTPase activity" NARROW [] +synonym: "dynamin GTPase activity" NARROW [] +synonym: "heterotrimeric G-protein GTPase activity" NARROW [] +synonym: "heterotrimeric G-protein GTPase, alpha-subunit" RELATED [] +synonym: "heterotrimeric G-protein GTPase, beta-subunit" RELATED [] +synonym: "heterotrimeric G-protein GTPase, gamma-subunit" RELATED [] +synonym: "hydrolase activity, acting on acid anhydrides, acting on GTP, involved in cellular and subcellular movement" BROAD [] +synonym: "protein-synthesizing GTPase activity" NARROW [] +synonym: "protein-synthesizing GTPase activity, elongation" NARROW [] +synonym: "protein-synthesizing GTPase activity, initiation" NARROW [] +synonym: "protein-synthesizing GTPase activity, termination" NARROW [] +synonym: "Rab small monomeric GTPase activity" NARROW [] +synonym: "Ran small monomeric GTPase activity" NARROW [] +synonym: "Ras small monomeric GTPase activity" NARROW [] +synonym: "RHEB small monomeric GTPase activity" NARROW [] +synonym: "Rho small monomeric GTPase activity" NARROW [] +synonym: "Sar small monomeric GTPase activity" NARROW [] +synonym: "signal-recognition-particle GTPase activity" NARROW [] +synonym: "small monomeric GTPase activity" NARROW [] +synonym: "tubulin GTPase activity" NARROW [] +xref: Reactome:REACT_100432 "trans-Golgi Network Vesicle Scission, Mus musculus" +xref: Reactome:REACT_100708 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Bos taurus" +xref: Reactome:REACT_101121 "trans-Golgi Network Vesicle Scission, Rattus norvegicus" +xref: Reactome:REACT_101520 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Drosophila melanogaster" +xref: Reactome:REACT_101563 "Loss of Sar1b GTPase, Arabidopsis thaliana" +xref: Reactome:REACT_101678 "G-protein alpha subunit is inactivated, Gallus gallus" +xref: Reactome:REACT_102040 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Xenopus tropicalis" +xref: Reactome:REACT_102208 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Danio rerio" +xref: Reactome:REACT_102307 "Adenylate cyclase increases the GTPase activity of Gi alpha, Gallus gallus" +xref: Reactome:REACT_102371 "Vesicle Uncoating, Oryza sativa" +xref: Reactome:REACT_102510 "trans-Golgi Network Vesicle Scission, Bos taurus" +xref: Reactome:REACT_102532 "Loss of Sar1b GTPase, Danio rerio" +xref: Reactome:REACT_103518 "trans-Golgi Network Lysosomal Vesicle Scission, Sus scrofa" +xref: Reactome:REACT_104081 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_104477 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_104739 "Loss of Sar1b GTPase, Dictyostelium discoideum" +xref: Reactome:REACT_105323 "trans-Golgi Network Vesicle Scission, Canis familiaris" +xref: Reactome:REACT_105697 "G-protein alpha subunit is inactivated, Saccharomyces cerevisiae" +xref: Reactome:REACT_105708 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_105854 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_106121 "Vesicle Uncoating, Saccharomyces cerevisiae" +xref: Reactome:REACT_106217 "Hydrolysis of eEF1A:GTP, Dictyostelium discoideum" +xref: Reactome:REACT_106301 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Mus musculus" +xref: Reactome:REACT_106528 "trans-Golgi Network Lysosomal Vesicle Scission, Canis familiaris" +xref: Reactome:REACT_107176 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_107306 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Rattus norvegicus" +xref: Reactome:REACT_107730 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Saccharomyces cerevisiae" +xref: Reactome:REACT_107820 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Canis familiaris" +xref: Reactome:REACT_108363 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Drosophila melanogaster" +xref: Reactome:REACT_108653 "G-protein alpha subunit is inactivated, Bos taurus" +xref: Reactome:REACT_108825 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Drosophila melanogaster" +xref: Reactome:REACT_108837 "trans-Golgi Network Vesicle Scission, Xenopus tropicalis" +xref: Reactome:REACT_109360 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_109897 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Danio rerio" +xref: Reactome:REACT_110131 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_110443 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_110557 "trans-Golgi Network Vesicle Scission, Danio rerio" +xref: Reactome:REACT_110859 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Caenorhabditis elegans" +xref: Reactome:REACT_110879 "G-protein alpha subunit is inactivated, Canis familiaris" +xref: Reactome:REACT_110931 "G-protein alpha subunit is inactivated, Sus scrofa" +xref: Reactome:REACT_111994 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_112104 "Endocytosis (internalization) of clathrin-coated vesicle, Sus scrofa" +xref: Reactome:REACT_112254 "Endocytosis (internalization) of clathrin-coated vesicle, Xenopus tropicalis" +xref: Reactome:REACT_112389 "Disassembly of COPII coated vesicle, Gallus gallus" +xref: Reactome:REACT_112587 "trans-Golgi Network Vesicle Scission, Schizosaccharomyces pombe" +xref: Reactome:REACT_112651 "Vesicle Uncoating, Xenopus tropicalis" +xref: Reactome:REACT_112671 "Vesicle Uncoating, Plasmodium falciparum" +xref: Reactome:REACT_113058 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Saccharomyces cerevisiae" +xref: Reactome:REACT_113209 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Schizosaccharomyces pombe" +xref: Reactome:REACT_113727 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Saccharomyces cerevisiae" +xref: Reactome:REACT_113832 "Formation of clathrin coated vesicle, Bos taurus" +xref: Reactome:REACT_113952 "Formation of clathrin coated vesicle, Schizosaccharomyces pombe" +xref: Reactome:REACT_113954 "Endocytosis (internalization) of clathrin-coated vesicle, Schizosaccharomyces pombe" +xref: Reactome:REACT_114148 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Schizosaccharomyces pombe" +xref: Reactome:REACT_114153 "Loss of Sar1b GTPase, Xenopus tropicalis" +xref: Reactome:REACT_114188 "Formation of clathrin coated vesicle, Sus scrofa" +xref: Reactome:REACT_114210 "G-protein alpha subunit is inactivated, Schizosaccharomyces pombe" +xref: Reactome:REACT_114331 "trans-Golgi Network Vesicle Scission, Taeniopygia guttata" +xref: Reactome:REACT_114379 "Formation of clathrin coated vesicle, Taeniopygia guttata" +xref: Reactome:REACT_114384 "Hydrolysis of eEF1A:GTP, Gallus gallus" +xref: Reactome:REACT_114532 "Formation of clathrin coated vesicle, Xenopus tropicalis" +xref: Reactome:REACT_114620 "Endocytosis (internalization) of clathrin-coated vesicle, Taeniopygia guttata" +xref: Reactome:REACT_114824 "trans-Golgi Network Lysosomal Vesicle Scission, Taeniopygia guttata" +xref: Reactome:REACT_115229 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Schizosaccharomyces pombe" +xref: Reactome:REACT_115324 "Endocytosis (internalization) of clathrin-coated vesicle, Bos taurus" +xref: Reactome:REACT_12396 "Loss of Sar1b GTPase, Homo sapiens" +xref: Reactome:REACT_12397 "Endocytosis (internalization) of clathrin-coated vesicle, Homo sapiens" +xref: Reactome:REACT_12456 "Vesicle Uncoating, Homo sapiens" +xref: Reactome:REACT_12612 "Endocytosis of clathrin-coated vesicle, Rattus norvegicus" +xref: Reactome:REACT_15316 "G-protein alpha subunit is inactivated, Homo sapiens" +xref: Reactome:REACT_15335 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Homo sapiens" +xref: Reactome:REACT_15449 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Homo sapiens" +xref: Reactome:REACT_15495 "Adenylate cyclase increases the GTPase activity of Gi alpha, Homo sapiens" +xref: Reactome:REACT_19123 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_19178 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_19186 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_19194 "trans-Golgi Network Lysosomal Vesicle Scission, Homo sapiens" +xref: Reactome:REACT_19219 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_19255 "trans-Golgi Network Vesicle Scission, Homo sapiens" +xref: Reactome:REACT_19317 "G alpha (i)1 auto-inactivates by hydrolysing GTP to GDP, Rattus norvegicus" +xref: Reactome:REACT_22359 "Formation of clathrin coated vesicle, Homo sapiens" +xref: Reactome:REACT_28065 "Vesicle Uncoating, Sus scrofa" +xref: Reactome:REACT_28251 "Hydrolysis of eEF1A:GTP, Danio rerio" +xref: Reactome:REACT_28269 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Gallus gallus" +xref: Reactome:REACT_29162 "trans-Golgi Network Lysosomal Vesicle Scission, Mus musculus" +xref: Reactome:REACT_30456 "Hydrolysis of eEF1A:GTP, Plasmodium falciparum" +xref: Reactome:REACT_30463 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Bos taurus" +xref: Reactome:REACT_30562 "Endocytosis (internalization) of clathrin-coated vesicle, Caenorhabditis elegans" +xref: Reactome:REACT_30687 "G-protein alpha subunit is inactivated, Xenopus tropicalis" +xref: Reactome:REACT_30707 "trans-Golgi Network Vesicle Scission, Caenorhabditis elegans" +xref: Reactome:REACT_30942 "Vesicle Uncoating, Rattus norvegicus" +xref: Reactome:REACT_31226 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_31474 "Formation of clathrin coated vesicle, Danio rerio" +xref: Reactome:REACT_31530 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Caenorhabditis elegans" +xref: Reactome:REACT_31599 "trans-Golgi Network Lysosomal Vesicle Scission, Danio rerio" +xref: Reactome:REACT_31709 "Hydrolysis of eEF1A:GTP, Drosophila melanogaster" +xref: Reactome:REACT_31727 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Taeniopygia guttata" +xref: Reactome:REACT_31850 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_32006 "Loss of Sar1b GTPase, Canis familiaris" +xref: Reactome:REACT_32028 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Danio rerio" +xref: Reactome:REACT_32914 "Vesicle Uncoating, Dictyostelium discoideum" +xref: Reactome:REACT_33948 "trans-Golgi Network Lysosomal Vesicle Scission, Rattus norvegicus" +xref: Reactome:REACT_34113 "Vesicle Uncoating, Schizosaccharomyces pombe" +xref: Reactome:REACT_34480 "G-protein alpha subunit is inactivated, Caenorhabditis elegans" +xref: Reactome:REACT_34592 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_34735 "Adenylate cyclase increases the GTPase activity of Gi alpha, Taeniopygia guttata" +xref: Reactome:REACT_348 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Homo sapiens" +xref: Reactome:REACT_36834 "trans-Golgi Network Lysosomal Vesicle Scission, Bos taurus" +xref: Reactome:REACT_37542 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_552 "Hydrolysis of eEF1A:GTP, Homo sapiens" +xref: Reactome:REACT_6171 "Hydrolysis of Ran:GTP to Ran:GDP, Homo sapiens" +xref: Reactome:REACT_712 "Hydrolysis of reEF1A:GTP, Oryctolagus cuniculus" +xref: Reactome:REACT_75799 "Disassembly of COPII coated vesicle, Homo sapiens" +xref: Reactome:REACT_77032 "Hydrolysis of eEF1A:GTP, Canis familiaris" +xref: Reactome:REACT_77303 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Danio rerio" +xref: Reactome:REACT_78069 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Caenorhabditis elegans" +xref: Reactome:REACT_78231 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_78653 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Bos taurus" +xref: Reactome:REACT_78945 "G-protein alpha subunit is inactivated, Rattus norvegicus" +xref: Reactome:REACT_79558 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_79620 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Mus musculus" +xref: Reactome:REACT_80275 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Bos taurus" +xref: Reactome:REACT_80612 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_81304 "Loss of Sar1b GTPase, Taeniopygia guttata" +xref: Reactome:REACT_81448 "Endocytosis (internalization) of clathrin-coated vesicle, Canis familiaris" +xref: Reactome:REACT_81580 "Disassembly of COPII coated vesicle, Mus musculus" +xref: Reactome:REACT_81664 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Caenorhabditis elegans" +xref: Reactome:REACT_81879 "Vesicle Uncoating, Drosophila melanogaster" +xref: Reactome:REACT_82203 "Formation of clathrin coated vesicle, Canis familiaris" +xref: Reactome:REACT_82263 "G-protein alpha subunit is inactivated, Taeniopygia guttata" +xref: Reactome:REACT_82457 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Taeniopygia guttata" +xref: Reactome:REACT_82603 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_82704 "Loss of Sar1b GTPase, Rattus norvegicus" +xref: Reactome:REACT_83308 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Rattus norvegicus" +xref: Reactome:REACT_83403 "G-protein alpha subunit is inactivated, Drosophila melanogaster" +xref: Reactome:REACT_83440 "Hydrolysis of eEF1A:GTP, Schizosaccharomyces pombe" +xref: Reactome:REACT_83730 "Loss of Sar1b GTPase, Plasmodium falciparum" +xref: Reactome:REACT_84204 "Endocytosis (internalization) of clathrin-coated vesicle, Danio rerio" +xref: Reactome:REACT_84553 "Vesicle Uncoating, Canis familiaris" +xref: Reactome:REACT_84696 "G-protein alpha subunit is inactivated, Danio rerio" +xref: Reactome:REACT_84712 "Hydrolysis of eEF1A:GTP, Saccharomyces cerevisiae" +xref: Reactome:REACT_84735 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Rattus norvegicus" +xref: Reactome:REACT_85008 "Vesicle Uncoating, Danio rerio" +xref: Reactome:REACT_85418 "Loss of Sar1b GTPase, Gallus gallus" +xref: Reactome:REACT_85769 "Disassembly of COPII coated vesicle, Danio rerio" +xref: Reactome:REACT_85972 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Canis familiaris" +xref: Reactome:REACT_86227 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Dictyostelium discoideum" +xref: Reactome:REACT_86358 "trans-Golgi Network Lysosomal Vesicle Scission, Caenorhabditis elegans" +xref: Reactome:REACT_86400 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Dictyostelium discoideum" +xref: Reactome:REACT_86630 "Vesicle Uncoating, Mus musculus" +xref: Reactome:REACT_86760 "Adenylate cyclase increases the GTPase activity of G alpha-olf, Gallus gallus" +xref: Reactome:REACT_86972 "Loss of Sar1b GTPase, Mus musculus" +xref: Reactome:REACT_87409 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Dictyostelium discoideum" +xref: Reactome:REACT_87506 "Formation of clathrin coated vesicle, Rattus norvegicus" +xref: Reactome:REACT_87558 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_87653 "Endocytosis (internalization) of clathrin-coated vesicle, Mus musculus" +xref: Reactome:REACT_87661 "Formation of clathrin coated vesicle, Drosophila melanogaster" +xref: Reactome:REACT_88045 "Vesicle Uncoating, Gallus gallus" +xref: Reactome:REACT_88357 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_89231 "Loss of Sar1b GTPase, Bos taurus" +xref: Reactome:REACT_89292 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_89416 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Bos taurus" +xref: Reactome:REACT_89668 "trans-Golgi Network Lysosomal Vesicle Scission, Xenopus tropicalis" +xref: Reactome:REACT_89763 "Vesicle Uncoating, Taeniopygia guttata" +xref: Reactome:REACT_90050 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_90064 "Hydrolysis of eEF1A:GTP, Mus musculus" +xref: Reactome:REACT_90517 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Xenopus tropicalis" +xref: Reactome:REACT_90703 "G-protein alpha subunit is inactivated, Dictyostelium discoideum" +xref: Reactome:REACT_91199 "Adenylate cyclase increases the GTPase activity of Gi alpha, Bos taurus" +xref: Reactome:REACT_91588 "trans-Golgi Network Vesicle Scission, Drosophila melanogaster" +xref: Reactome:REACT_92176 "Endocytosis (internalization) of clathrin-coated vesicle, Drosophila melanogaster" +xref: Reactome:REACT_92197 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Bos taurus" +xref: Reactome:REACT_92198 "Loss of Sar1b GTPase, Oryza sativa" +xref: Reactome:REACT_92450 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Danio rerio" +xref: Reactome:REACT_93249 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Dictyostelium discoideum" +xref: Reactome:REACT_93305 "Loss of Sar1b GTPase, Sus scrofa" +xref: Reactome:REACT_93641 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_93742 "G-protein alpha subunit is inactivated, Mus musculus" +xref: Reactome:REACT_93772 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Gallus gallus" +xref: Reactome:REACT_94019 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_94095 "trans-Golgi Network Vesicle Scission, Sus scrofa" +xref: Reactome:REACT_94305 "Adenylate cyclase increases the GTPase activity of Gi alpha, Xenopus tropicalis" +xref: Reactome:REACT_94760 "Adenylate cyclase increases the GTPase activity of Gi alpha, Danio rerio" +xref: Reactome:REACT_95238 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Rattus norvegicus" +xref: Reactome:REACT_95563 "Adenylate cyclase increases the GTPase activity of Gi alpha, Canis familiaris" +xref: Reactome:REACT_96019 "Loss of Sar1b GTPase, Drosophila melanogaster" +xref: Reactome:REACT_96132 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Drosophila melanogaster" +xref: Reactome:REACT_96223 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_96612 "Adenylate cyclase increases the GTPase activity of Gi alpha, Rattus norvegicus" +xref: Reactome:REACT_96881 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Xenopus tropicalis" +xref: Reactome:REACT_97284 "Loss of Sar1b GTPase, Saccharomyces cerevisiae" +xref: Reactome:REACT_97405 "Adenylaye cyclase increases the GTPase activity of G alpha-olf, Taeniopygia guttata" +xref: Reactome:REACT_97595 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Danio rerio" +xref: Reactome:REACT_97794 "Loss of Sar1b GTPase, Schizosaccharomyces pombe" +xref: Reactome:REACT_98431 "Formation of clathrin coated vesicle, Caenorhabditis elegans" +xref: Reactome:REACT_98556 "Vesicle Uncoating, Bos taurus" +xref: Reactome:REACT_98837 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP, Canis familiaris" +xref: Reactome:REACT_98859 "Adenylate cyclase increases the GTPase activity of Gi alpha, Mus musculus" +xref: Reactome:REACT_99479 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP, Mus musculus" +xref: Reactome:REACT_99533 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP, Sus scrofa" +xref: Reactome:REACT_99616 "Formation of clathrin coated vesicle, Mus musculus" +xref: RHEA:19672 +is_a: GO:0017111 ! nucleoside-triphosphatase activity +relationship: part_of GO:0006184 ! GTP catabolic process + +[Term] +id: GO:0004175 +name: endopeptidase activity +namespace: molecular_function +alt_id: GO:0016809 +def: "Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain." [http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE] +subset: gosubset_prok +synonym: "elastase activity" RELATED [GOC:krc] +synonym: "endoprotease activity" EXACT [] +synonym: "proteasome endopeptidase activity" NARROW [] +synonym: "proteinase" BROAD [] +xref: Reactome:REACT_10017 "Degradation of ubiquitinated -beta catenin by the proteasome, Homo sapiens" +xref: Reactome:REACT_101348 "Degradation of multiubiquitinated Cdh1, Rattus norvegicus" +xref: Reactome:REACT_101866 "Ubiquitinated Cdc6 is degraded by the proteasome, Canis familiaris" +xref: Reactome:REACT_101873 "Degradation of multiubiquitinated cell cycle proteins, Mus musculus" +xref: Reactome:REACT_102952 "Degradation of multiubiquitinated Cdh1, Bos taurus" +xref: Reactome:REACT_103814 "Degradation multiubiquitinated Cyclin A, Xenopus tropicalis" +xref: Reactome:REACT_104331 "Ubiquitinated geminin is degraded by the proteasome, Mus musculus" +xref: Reactome:REACT_104435 "Proteasome mediated degradation of Cyclin D1, Rattus norvegicus" +xref: Reactome:REACT_104684 "Degradation of multiubiquitinated Cdh1, Danio rerio" +xref: Reactome:REACT_104793 "Ubiquitinated Cdc6 is degraded by the proteasome, Mus musculus" +xref: Reactome:REACT_105135 "Degradation of ubiquitinated -beta catenin by the proteasome, Canis familiaris" +xref: Reactome:REACT_105245 "Ubiquitinated Orc1 is degraded by the proteasome, Danio rerio" +xref: Reactome:REACT_105748 "APC/C:Cdh1-mediated degradation of Skp2, Canis familiaris" +xref: Reactome:REACT_106234 "Ubiquitinated Orc1 is degraded by the proteasome, Mus musculus" +xref: Reactome:REACT_106385 "Proteasome mediated degradation of COP1, Xenopus tropicalis" +xref: Reactome:REACT_106617 "gamma-secretase cleaves the p75NTR transmembrane domain, Bos taurus" +xref: Reactome:REACT_106687 "SCF-mediated degradation of Emi1, Bos taurus" +xref: Reactome:REACT_107139 "Ubiquitinated geminin is degraded by the proteasome, Canis familiaris" +xref: Reactome:REACT_107146 "Ubiquitinated Orc1 is degraded by the proteasome, Bos taurus" +xref: Reactome:REACT_108185 "Ubiquitinated Orc1 is degraded by the proteasome, Oryza sativa" +xref: Reactome:REACT_108448 "Proteasome mediated degradation of PAK-2p34, Mus musculus" +xref: Reactome:REACT_108642 "Ubiquitinated geminin is degraded by the proteasome, Xenopus tropicalis" +xref: Reactome:REACT_109047 "Degradation of multiubiquitinated Cdh1, Oryza sativa" +xref: Reactome:REACT_109186 "Ubiquitinated Cdc6 is degraded by the proteasome, Danio rerio" +xref: Reactome:REACT_109261 "Degradation of multiubiquitinated cell cycle proteins, Oryza sativa" +xref: Reactome:REACT_110165 "Degradation of ubiquitinated p27/p21 by the 26S proteasome, Danio rerio" +xref: Reactome:REACT_110191 "26S proteosome degrades ODC holoenzyme complex, Canis familiaris" +xref: Reactome:REACT_110448 "Proteolytic degradation of ubiquitinated-Cdc25A, Xenopus tropicalis" +xref: Reactome:REACT_110469 "gamma-secretase cleaves the p75NTR transmembrane domain, Rattus norvegicus" +xref: Reactome:REACT_110487 "Proteolytic degradation of ubiquitinated-Cdc25A, Danio rerio" +xref: Reactome:REACT_110752 "gamma-secretase cleaves the p75NTR transmembrane domain, Canis familiaris" +xref: Reactome:REACT_111098 "Processing of SCF isoform 1, Homo sapiens" +xref: Reactome:REACT_111104 "Proteasomal cleavage of substrate, Homo sapiens" +xref: Reactome:REACT_111172 "Proteasomal clevage of exogenous antigen, Homo sapiens" +xref: Reactome:REACT_112076 "Ubiquitinated Cdc6 is degraded by the proteasome, Sus scrofa" +xref: Reactome:REACT_113623 "Ubiquitinated geminin is degraded by the proteasome, Sus scrofa" +xref: Reactome:REACT_113749 "Ubiquitinated Orc1 is degraded by the proteasome, Sus scrofa" +xref: Reactome:REACT_114002 "Proteasome mediated degradation of PAK-2p34, Sus scrofa" +xref: Reactome:REACT_114449 "Proteasome mediated degradation of Cyclin D1, Sus scrofa" +xref: Reactome:REACT_114993 "Proteasome mediated degradation of COP1, Sus scrofa" +xref: Reactome:REACT_115363 "Proteasome mediated degradation of Cyclin D1, Oryza sativa" +xref: Reactome:REACT_115913 "Cleavage of ERBB4m80 by gamma-scretase complex, Homo sapiens" +xref: Reactome:REACT_1210 "Ubiquitinated Cdc6 is degraded by the proteasome, Homo sapiens" +xref: Reactome:REACT_13413 "Proteasome mediated degradation of PAK-2p34, Homo sapiens" +xref: Reactome:REACT_13491 "26S proteosome degrades ODC holoenzyme complex, Homo sapiens" +xref: Reactome:REACT_13505 "Proteasome mediated degradation of PAK-2p34, Homo sapiens" +xref: Reactome:REACT_1355 "Insulin degradation, Homo sapiens" +xref: Reactome:REACT_13609 "gamma-secretase cleaves the p75NTR transmembrane domain, Homo sapiens" +xref: Reactome:REACT_1471 "Ubiquitinated geminin is degraded by the proteasome, Homo sapiens" +xref: Reactome:REACT_15476 "Corticotropin cleavage from POMC, Homo sapiens" +xref: Reactome:REACT_1673 "Cytoplasmic phosphorylated Cdc6 is ubiquitinated by the anaphase-promoting complex, Homo sapiens" +xref: Reactome:REACT_20637 "Proteasome mediated degradation of COP1, Homo sapiens" +xref: Reactome:REACT_2142 "Proteasome mediated degradation of Cyclin D1, Homo sapiens" +xref: Reactome:REACT_25343 "Destruction of AUF1 and mRNA, Homo sapiens" +xref: Reactome:REACT_28448 "Ubiquitinated Orc1 is degraded by the proteasome, Dictyostelium discoideum" +xref: Reactome:REACT_28452 "Proteasome mediated degradation of COP1, Bos taurus" +xref: Reactome:REACT_28694 "Proteasome mediated degradation of Cyclin D1, Bos taurus" +xref: Reactome:REACT_29497 "Corticotropin cleavage from POMC, Rattus norvegicus" +xref: Reactome:REACT_29888 "Proteasome mediated degradation of COP1, Dictyostelium discoideum" +xref: Reactome:REACT_30554 "APC/C:Cdh1-mediated degradation of Skp2, Mus musculus" +xref: Reactome:REACT_31644 "Degradation of ubiquitinated -beta catenin by the proteasome, Mus musculus" +xref: Reactome:REACT_32286 "Corticotropin cleavage from POMC, Gallus gallus" +xref: Reactome:REACT_32345 "Proteasome mediated degradation of COP1, Rattus norvegicus" +xref: Reactome:REACT_32454 "Corticotropin cleavage from POMC, Mus musculus" +xref: Reactome:REACT_33103 "26S proteosome degrades ODC holoenzyme complex, Xenopus tropicalis" +xref: Reactome:REACT_33361 "Degradation of multiubiquitinated Securin, Xenopus tropicalis" +xref: Reactome:REACT_33702 "Proteasome mediated degradation of PAK-2p34, Drosophila melanogaster" +xref: Reactome:REACT_34207 "Proteasome mediated degradation of PAK-2p34, Canis familiaris" +xref: Reactome:REACT_34441 "Proteolytic degradation of ubiquitinated-Cdc25A, Rattus norvegicus" +xref: Reactome:REACT_38775 "Ubiquitinated geminin is degraded by the proteasome, Bos taurus" +xref: Reactome:REACT_480 "Ubiquitinated Orc1 is degraded by the proteasome, Homo sapiens" +xref: Reactome:REACT_6715 "Degradation of multiubiquitinated Cdh1, Homo sapiens" +xref: Reactome:REACT_6777 "Degradation of multiubiquitinated Securin, Homo sapiens" +xref: Reactome:REACT_6826 "Degradation of multiubiquitinated cell cycle proteins, Homo sapiens" +xref: Reactome:REACT_6878 "SCF-mediated degradation of Emi1, Homo sapiens" +xref: Reactome:REACT_6937 "Degradation multiubiquitinated Cyclin A, Homo sapiens" +xref: Reactome:REACT_75798 "Trimming of peptides in ER, Homo sapiens" +xref: Reactome:REACT_75871 "Proteasomal cleavage of substrate, Homo sapiens" +xref: Reactome:REACT_78097 "Proteasome mediated degradation of COP1, Canis familiaris" +xref: Reactome:REACT_78726 "gamma-secretase cleaves the p75NTR transmembrane domain, Xenopus tropicalis" +xref: Reactome:REACT_78745 "Proteasome mediated degradation of Cyclin D1, Drosophila melanogaster" +xref: Reactome:REACT_78867 "Degradation multiubiquitinated Cyclin A, Rattus norvegicus" +xref: Reactome:REACT_79225 "Degradation of multiubiquitinated Cdh1, Canis familiaris" +xref: Reactome:REACT_79268 "Degradation of ubiquitinated -beta catenin by the proteasome, Drosophila melanogaster" +xref: Reactome:REACT_79271 "Proteasome mediated degradation of Cyclin D1, Canis familiaris" +xref: Reactome:REACT_79593 "Corticotropin cleavage from POMC, Xenopus tropicalis" +xref: Reactome:REACT_79599 "26S proteosome degrades ODC holoenzyme complex, Danio rerio" +xref: Reactome:REACT_79815 "gamma-secretase cleaves the p75NTR transmembrane domain, Gallus gallus" +xref: Reactome:REACT_79882 "APC/C:Cdh1-mediated degradation of Skp2, Rattus norvegicus" +xref: Reactome:REACT_80109 "gamma-secretase cleaves the p75NTR transmembrane domain, Danio rerio" +xref: Reactome:REACT_80331 "APC/C:Cdh1-mediated degradation of Skp2, Xenopus tropicalis" +xref: Reactome:REACT_80442 "Ubiquitinated Cdc6 is degraded by the proteasome, Drosophila melanogaster" +xref: Reactome:REACT_80463 "Degradation of multiubiquitinated Securin, Danio rerio" +xref: Reactome:REACT_80748 "Degradation multiubiquitinated Cyclin A, Bos taurus" +xref: Reactome:REACT_80774 "Degradation of multiubiquitinated cell cycle proteins, Rattus norvegicus" +xref: Reactome:REACT_80978 "Proteasome mediated degradation of PAK-2p34, Xenopus tropicalis" +xref: Reactome:REACT_81238 "Corticotropin cleavage from POMC, Bos taurus" +xref: Reactome:REACT_81327 "SCF-mediated degradation of Emi1, Mus musculus" +xref: Reactome:REACT_81867 "Ubiquitinated Cdc6 is degraded by the proteasome, Bos taurus" +xref: Reactome:REACT_81958 "Degradation of ubiquitinated p27/p21 by the 26S proteasome, Canis familiaris" +xref: Reactome:REACT_82043 "Ubiquitinated Orc1 is degraded by the proteasome, Canis familiaris" +xref: Reactome:REACT_82474 "Ubiquitinated Cdc6 is degraded by the proteasome, Dictyostelium discoideum" +xref: Reactome:REACT_82600 "Degradation of multiubiquitinated cell cycle proteins, Xenopus tropicalis" +xref: Reactome:REACT_82845 "26S proteosome degrades ODC holoenzyme complex, Rattus norvegicus" +xref: Reactome:REACT_82963 "Degradation of multiubiquitinated cell cycle proteins, Drosophila melanogaster" +xref: Reactome:REACT_83099 "Degradation of ubiquitinated p27/p21 by the 26S proteasome, Bos taurus" +xref: Reactome:REACT_83216 "gamma-secretase cleaves the p75NTR transmembrane domain, Sus scrofa" +xref: Reactome:REACT_83748 "Degradation of multiubiquitinated Cdh1, Drosophila melanogaster" +xref: Reactome:REACT_84139 "Proteasome mediated degradation of COP1, Danio rerio" +xref: Reactome:REACT_85078 "APC/C:Cdh1-mediated degradation of Skp2, Drosophila melanogaster" +xref: Reactome:REACT_86353 "Corticotropin cleavage from POMC, Danio rerio" +xref: Reactome:REACT_86565 "SCF-mediated degradation of Emi1, Rattus norvegicus" +xref: Reactome:REACT_873 "Proteolytic degradation of ubiquitinated-Cdc25A, Homo sapiens" +xref: Reactome:REACT_88382 "Proteasome mediated degradation of COP1, Mus musculus" +xref: Reactome:REACT_88509 "Proteasome mediated degradation of Cyclin D1, Mus musculus" +xref: Reactome:REACT_88535 "Ubiquitinated Orc1 is degraded by the proteasome, Plasmodium falciparum" +xref: Reactome:REACT_88610 "Degradation multiubiquitinated Cyclin A, Canis familiaris" +xref: Reactome:REACT_88818 "Degradation multiubiquitinated Cyclin A, Drosophila melanogaster" +xref: Reactome:REACT_88854 "Corticotropin cleavage from POMC, Taeniopygia guttata" +xref: Reactome:REACT_89011 "Ubiquitinated Orc1 is degraded by the proteasome, Rattus norvegicus" +xref: Reactome:REACT_89036 "Ubiquitinated geminin is degraded by the proteasome, Danio rerio" +xref: Reactome:REACT_89437 "26S proteosome degrades ODC holoenzyme complex, Bos taurus" +xref: Reactome:REACT_89505 "Corticotropin cleavage from POMC, Sus scrofa" +xref: Reactome:REACT_89706 "Degradation of multiubiquitinated Cdh1, Xenopus tropicalis" +xref: Reactome:REACT_90062 "SCF-mediated degradation of Emi1, Canis familiaris" +xref: Reactome:REACT_9018 "Degradation of ubiquitinated CD4, Homo sapiens" +xref: Reactome:REACT_9034 "Degradation of ubiquitinated p27/p21 by the 26S proteasome, Homo sapiens" +xref: Reactome:REACT_9035 "APC/C:Cdh1-mediated degradation of Skp2, Homo sapiens" +xref: Reactome:REACT_90527 "SCF-mediated degradation of Emi1, Drosophila melanogaster" +xref: Reactome:REACT_90608 "Proteasome mediated degradation of Cyclin D1, Danio rerio" +xref: Reactome:REACT_91284 "Degradation of ubiquitinated -beta catenin by the proteasome, Bos taurus" +xref: Reactome:REACT_91685 "Degradation of ubiquitinated -beta catenin by the proteasome, Rattus norvegicus" +xref: Reactome:REACT_91903 "Ubiquitinated Cdc6 is degraded by the proteasome, Rattus norvegicus" +xref: Reactome:REACT_92046 "Corticotropin cleavage from POMC, Canis familiaris" +xref: Reactome:REACT_92221 "Ubiquitinated Cdc6 is degraded by the proteasome, Xenopus tropicalis" +xref: Reactome:REACT_92347 "Proteasome mediated degradation of COP1, Oryza sativa" +xref: Reactome:REACT_92586 "Degradation of ubiquitinated p27/p21 by the 26S proteasome, Xenopus tropicalis" +xref: Reactome:REACT_92969 "Proteolytic degradation of ubiquitinated-Cdc25A, Bos taurus" +xref: Reactome:REACT_93063 "Proteasome mediated degradation of PAK-2p34, Danio rerio" +xref: Reactome:REACT_93174 "SCF-mediated degradation of Emi1, Xenopus tropicalis" +xref: Reactome:REACT_93453 "Degradation of multiubiquitinated Cdh1, Mus musculus" +xref: Reactome:REACT_93935 "gamma-secretase cleaves the p75NTR transmembrane domain, Mus musculus" +xref: Reactome:REACT_94290 "Degradation of ubiquitinated p27/p21 by the 26S proteasome, Rattus norvegicus" +xref: Reactome:REACT_9466 "Proteosome-mediated degradation of APOBEC3G, Homo sapiens" +xref: Reactome:REACT_94694 "Degradation of multiubiquitinated Securin, Canis familiaris" +xref: Reactome:REACT_95326 "Degradation of multiubiquitinated cell cycle proteins, Canis familiaris" +xref: Reactome:REACT_95413 "Degradation of multiubiquitinated cell cycle proteins, Danio rerio" +xref: Reactome:REACT_95513 "Proteolytic degradation of ubiquitinated-Cdc25A, Canis familiaris" +xref: Reactome:REACT_95865 "Proteolytic degradation of ubiquitinated-Cdc25A, Mus musculus" +xref: Reactome:REACT_96387 "Degradation multiubiquitinated Cyclin A, Mus musculus" +xref: Reactome:REACT_96712 "Degradation of multiubiquitinated Securin, Drosophila melanogaster" +xref: Reactome:REACT_96853 "Ubiquitinated Orc1 is degraded by the proteasome, Xenopus tropicalis" +xref: Reactome:REACT_96908 "Ubiquitinated Orc1 is degraded by the proteasome, Drosophila melanogaster" +xref: Reactome:REACT_97049 "Ubiquitinated Cdc6 is degraded by the proteasome, Oryza sativa" +xref: Reactome:REACT_97235 "APC/C:Cdh1-mediated degradation of Skp2, Danio rerio" +xref: Reactome:REACT_97302 "Proteasome mediated degradation of Cyclin D1, Xenopus tropicalis" +xref: Reactome:REACT_97473 "Degradation of ubiquitinated p27/p21 by the 26S proteasome, Mus musculus" +xref: Reactome:REACT_97709 "Degradation multiubiquitinated Cyclin A, Danio rerio" +xref: Reactome:REACT_97826 "Degradation of multiubiquitinated cell cycle proteins, Bos taurus" +xref: Reactome:REACT_97966 "APC/C:Cdh1-mediated degradation of Skp2, Oryza sativa" +xref: Reactome:REACT_98412 "APC/C:Cdh1-mediated degradation of Skp2, Bos taurus" +xref: Reactome:REACT_98429 "Degradation of ubiquitinated -beta catenin by the proteasome, Xenopus tropicalis" +xref: Reactome:REACT_98617 "Degradation of multiubiquitinated Securin, Mus musculus" +xref: Reactome:REACT_98707 "Proteasome mediated degradation of PAK-2p34, Rattus norvegicus" +xref: Reactome:REACT_98822 "Degradation of multiubiquitinated Securin, Rattus norvegicus" +xref: Reactome:REACT_98901 "Degradation of multiubiquitinated Securin, Bos taurus" +xref: Reactome:REACT_98932 "Ubiquitinated geminin is degraded by the proteasome, Rattus norvegicus" +xref: Reactome:REACT_99506 "26S proteosome degrades ODC holoenzyme complex, Mus musculus" +xref: Reactome:REACT_99644 "Proteolytic degradation of ubiquitinated-Cdc25A, Drosophila melanogaster" +is_a: GO:0070011 ! peptidase activity, acting on L-amino acid peptides + +[Term] +id: GO:0004197 +name: cysteine-type endopeptidase activity +namespace: molecular_function +def: "Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile." [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE] +subset: gosubset_prok +synonym: "caspase activity" NARROW [GOC:mtg_apoptosis] +synonym: "lysosomal cysteine-type endopeptidase" NARROW [] +synonym: "metacaspase activity" NARROW [GOC:mtg_apoptosis] +synonym: "thiol endopeptidase activity" EXACT [] +xref: EC:3.4.22 +xref: Reactome:REACT_100050 "Caspase-mediated cleavage of plectin-1, Mus musculus" +xref: Reactome:REACT_100093 "Cleavage of Procaspase-7 by the apoptosome, Danio rerio" +xref: Reactome:REACT_100258 "Caspase-mediated cleavage of PKC theta, Bos taurus" +xref: Reactome:REACT_100371 "Caspase mediated cleavage of HIP-55, Rattus norvegicus" +xref: Reactome:REACT_100591 "Caspase mediated cleavage of C-IAP1, Danio rerio" +xref: Reactome:REACT_100749 "Caspase-mediated cleavage of vimentin at DSVD (85), Sus scrofa" +xref: Reactome:REACT_100786 "Caspase mediated cleavage of BAP31, Sus scrofa" +xref: Reactome:REACT_100806 "Caspase-mediated cleavage of E-Cadherin, Mus musculus" +xref: Reactome:REACT_101275 "Caspase-mediated cleavage of claspin, Bos taurus" +xref: Reactome:REACT_101388 "Caspase-mediated cleavage of Rock-1, Danio rerio" +xref: Reactome:REACT_101482 "Caspase-mediated cleavage of vimentin at TNLD (429), Taeniopygia guttata" +xref: Reactome:REACT_101496 "Caspase-mediated cleavage of Etk, Mus musculus" +xref: Reactome:REACT_101535 "Caspase mediated cleavage of C-IAP1, Xenopus tropicalis" +xref: Reactome:REACT_101617 "Caspase-mediated cleavage of GAS2, Danio rerio" +xref: Reactome:REACT_102211 "Caspase-mediated cleavage of Desmoglein 2, Rattus norvegicus" +xref: Reactome:REACT_102224 "Caspase-mediated cleavage of Lamin B1, Bos taurus" +xref: Reactome:REACT_102308 "Caspase mediated cleavage of HIP-55, Sus scrofa" +xref: Reactome:REACT_102448 "Cleavage of Procaspase-9 to Caspase-9, Gallus gallus" +xref: Reactome:REACT_102624 "Caspase mediated cleavage of C-IAP1, Bos taurus" +xref: Reactome:REACT_102731 "Caspase mediated cleavage of beta-catenin, Mus musculus" +xref: Reactome:REACT_102903 "Caspase-mediated cleavage of FADK 1, Canis familiaris" +xref: Reactome:REACT_103130 "Cleavage of Procaspase-7 by the apoptosome, Xenopus tropicalis" +xref: Reactome:REACT_103265 "Cleavage of Satb1, Taeniopygia guttata" +xref: Reactome:REACT_103288 "Caspase-mediated cleavage of Lamin B1, Xenopus tropicalis" +xref: Reactome:REACT_103478 "Caspase mediated cleavage of APC, Danio rerio" +xref: Reactome:REACT_103480 "Caspase-mediated cleavage of Tau, Sus scrofa" +xref: Reactome:REACT_103527 "Cleavage of PAK-2 at 212, Sus scrofa" +xref: Reactome:REACT_103538 "Caspase mediated cleavage of alpha-II-Fodrin, Gallus gallus" +xref: Reactome:REACT_103796 "Caspase-mediated cleavage of Desmoglein 3, Taeniopygia guttata" +xref: Reactome:REACT_103879 "Cleavage of Satb1, Gallus gallus" +xref: Reactome:REACT_103993 "Cleavage of PAK-2 at 212, Mus musculus" +xref: Reactome:REACT_103997 "Caspase-mediated cleavage of plectin-1, Danio rerio" +xref: Reactome:REACT_104056 "Caspase mediated cleavage of APC, Taeniopygia guttata" +xref: Reactome:REACT_104095 "Caspase-mediated cleavage of alpha adducin, Mus musculus" +xref: Reactome:REACT_104234 "Caspase-mediated cleavage of Desmoglein 1, Mus musculus" +xref: Reactome:REACT_104249 "Caspase mediated cleavage of alpha-II-Fodrin, Danio rerio" +xref: Reactome:REACT_104338 "Legumain degrades DBP, Mus musculus" +xref: Reactome:REACT_104344 "Caspase-mediated cleavage of Tau, Gallus gallus" +xref: Reactome:REACT_104391 "Cleavage of Procaspase-7 by the apoptosome, Taeniopygia guttata" +xref: Reactome:REACT_104407 "Caspase-mediated cleavage of Lamin B1, Danio rerio" +xref: Reactome:REACT_104493 "Caspase-mediated cleavage of E-Cadherin, Rattus norvegicus" +xref: Reactome:REACT_104700 "Caspase 3-mediated cleavage of PKC delta, Canis familiaris" +xref: Reactome:REACT_104895 "Caspase-8 activates BID by cleavage, Mus musculus" +xref: Reactome:REACT_105045 "Caspase-mediated cleavage of E-Cadherin, Gallus gallus" +xref: Reactome:REACT_105170 "Caspase mediated cleavage of alpha-II-Fodrin, Mus musculus" +xref: Reactome:REACT_105481 "Caspase-mediated cleavage of alpha adducin, Gallus gallus" +xref: Reactome:REACT_105581 "Caspase-mediated cleavage of plectin-1, Bos taurus" +xref: Reactome:REACT_105957 "Caspase-mediated cleavage of Rock-1, Rattus norvegicus" +xref: Reactome:REACT_105958 "Caspase-mediated cleavage of MASK, Mus musculus" +xref: Reactome:REACT_106680 "Caspase-mediated cleavage of GAS2, Rattus norvegicus" +xref: Reactome:REACT_107019 "Caspase mediated cleavage of beta-catenin, Taeniopygia guttata" +xref: Reactome:REACT_107128 "Cleavage of Satb1, Danio rerio" +xref: Reactome:REACT_107302 "Caspase-mediated cleavage of Rock-1, Bos taurus" +xref: Reactome:REACT_107511 "Caspase-mediated cleavage of Lamin A, Sus scrofa" +xref: Reactome:REACT_107529 "Caspase-mediated cleavage of Lamin B1, Sus scrofa" +xref: Reactome:REACT_107629 "Caspase-mediated cleavage of Lamin A, Drosophila melanogaster" +xref: Reactome:REACT_107758 "Caspase mediated cleavage of beta-catenin, Danio rerio" +xref: Reactome:REACT_107853 "Caspase-mediated cleavage of GAS2, Bos taurus" +xref: Reactome:REACT_108026 "Caspase mediated cleavage of vimentin at IDVD (259), Taeniopygia guttata" +xref: Reactome:REACT_108198 "Caspase-mediated cleavage of Lamin B1, Rattus norvegicus" +xref: Reactome:REACT_108258 "Caspase-mediated cleavage of FADK 1, Taeniopygia guttata" +xref: Reactome:REACT_108537 "Caspase-mediated cleavage of gelsolin, Mus musculus" +xref: Reactome:REACT_108621 "Caspase mediated cleavage of beta-catenin, Sus scrofa" +xref: Reactome:REACT_108783 "Caspase mediated cleavage of vimentin at IDVD (259), Danio rerio" +xref: Reactome:REACT_108820 "Caspase-mediated cleavage of MASK, Canis familiaris" +xref: Reactome:REACT_108938 "Caspase-mediated cleavage of MASK, Rattus norvegicus" +xref: Reactome:REACT_108946 "Caspase-mediated cleavage of Lamin A, Gallus gallus" +xref: Reactome:REACT_109026 "Caspase-mediated cleavage of PKC theta, Sus scrofa" +xref: Reactome:REACT_109078 "Caspase-mediated cleavage of MASK, Taeniopygia guttata" +xref: Reactome:REACT_109269 "Caspase-mediated cleavage of Etk, Canis familiaris" +xref: Reactome:REACT_109374 "Caspase-mediated cleavage of Desmoglein 1, Danio rerio" +xref: Reactome:REACT_109414 "Caspase mediated cleavage of APC, Xenopus tropicalis" +xref: Reactome:REACT_109547 "Caspase-mediated cleavage of vimentin at DSVD (85), Taeniopygia guttata" +xref: Reactome:REACT_109908 "Activation of caspase-3, Canis familiaris" +xref: Reactome:REACT_110043 "Caspase-mediated cleavage of vimentin at TNLD (429), Danio rerio" +xref: Reactome:REACT_110086 "Caspase-mediated cleavage of Desmoglein 2, Mus musculus" +xref: Reactome:REACT_110544 "Caspase mediated cleavage of BAP31, Canis familiaris" +xref: Reactome:REACT_110842 "Caspase-mediated cleavage of vimentin at DSVD (85), Xenopus tropicalis" +xref: Reactome:REACT_111140 "Antigen processing by cathepsin S in endosoytic vesicle, Homo sapiens" +xref: Reactome:REACT_111954 "Cleavage of Procaspase-7 by the apoptosome, Rattus norvegicus" +xref: Reactome:REACT_112287 "Activation of caspase-3, Xenopus tropicalis" +xref: Reactome:REACT_112363 "Cleavage of Procaspase-9 to Caspase-9, Sus scrofa" +xref: Reactome:REACT_112407 "Caspase mediated cleavage of vimentin at IDVD (259), Caenorhabditis elegans" +xref: Reactome:REACT_112426 "Caspase-mediated cleavage of Desmoglein 1, Xenopus tropicalis" +xref: Reactome:REACT_112597 "Caspase-mediated cleavage of Desmoglein 3, Xenopus tropicalis" +xref: Reactome:REACT_112616 "Cleavage of Procaspase-7 by the apoptosome, Sus scrofa" +xref: Reactome:REACT_112859 "Cleavage of Procaspase-7 by the apoptosome, Canis familiaris" +xref: Reactome:REACT_113141 "Cleavage of Procaspase-9 to Caspase-9, Canis familiaris" +xref: Reactome:REACT_113588 "Caspase-mediated cleavage of Desmoglein 2, Xenopus tropicalis" +xref: Reactome:REACT_114270 "Caspase mediated cleavage of alpha-II-Fodrin, Xenopus tropicalis" +xref: Reactome:REACT_114571 "Cleavage of Procaspase-7 by the apoptosome, Bos taurus" +xref: Reactome:REACT_114579 "Cleavage of Procaspase-9 to Caspase-9, Rattus norvegicus" +xref: Reactome:REACT_114638 "Caspase-mediated cleavage of Acinus, Xenopus tropicalis" +xref: Reactome:REACT_114872 "Caspase mediated cleavage of BAP31, Caenorhabditis elegans" +xref: Reactome:REACT_115070 "Caspase-mediated cleavage of Rock-1, Canis familiaris" +xref: Reactome:REACT_115318 "Caspase-mediated cleavage of plectin-1, Taeniopygia guttata" +xref: Reactome:REACT_115379 "Cleavage of Procaspase-9 to Caspase-9, Bos taurus" +xref: Reactome:REACT_11997 "Caspase-mediated cleavage of Desmoglein 1, Homo sapiens" +xref: Reactome:REACT_12004 "Caspase-mediated cleavage of GAS2, Homo sapiens" +xref: Reactome:REACT_12012 "Caspase mediated cleavage of APC, Homo sapiens" +xref: Reactome:REACT_12014 "Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha, Homo sapiens" +xref: Reactome:REACT_12021 "Caspase-mediated cleavage of FADK 1, Homo sapiens" +xref: Reactome:REACT_12022 "Caspase mediated cleavage of beta-catenin, Homo sapiens" +xref: Reactome:REACT_12024 "Caspase mediated cleavage of alpha-II-Fodrin, Homo sapiens" +xref: Reactome:REACT_12025 "Caspase mediated cleavage of HIP-55, Homo sapiens" +xref: Reactome:REACT_12044 "Caspase-mediated cleavage of alpha adducin, Homo sapiens" +xref: Reactome:REACT_12045 "Caspase mediated cleavage of C-IAP1, Homo sapiens" +xref: Reactome:REACT_12072 "Caspase-mediated cleavage of E-Cadherin, Homo sapiens" +xref: Reactome:REACT_12082 "Caspase-mediated cleavage of Desmoglein 3, Homo sapiens" +xref: Reactome:REACT_12404 "Cleavage of DFF45 (224) by caspase-3, Homo sapiens" +xref: Reactome:REACT_12450 "Caspase-mediated cleavage of Acinus, Homo sapiens" +xref: Reactome:REACT_12471 "Caspase 3-mediated cleavage of PKC delta, Homo sapiens" +xref: Reactome:REACT_12531 "Caspase-mediated cleavage of Rock-1, Homo sapiens" +xref: Reactome:REACT_12544 "Caspase 3-mediated cleavage of DFF45 (117), Homo sapiens" +xref: Reactome:REACT_12638 "Caspase-mediated cleavage of PKC theta, Homo sapiens" +xref: Reactome:REACT_1320 "Caspase-8 activates BID by cleavage, Homo sapiens" +xref: Reactome:REACT_13414 "Caspase-mediated cleavage of Tau, Homo sapiens" +xref: Reactome:REACT_13417 "Caspase-mediated cleavage of Etk, Homo sapiens" +xref: Reactome:REACT_13418 "Caspase-mediated cleavage of plakophilin-1, Homo sapiens" +xref: Reactome:REACT_13428 "Caspase-mediated cleavage of vimentin at DSVD (85), Homo sapiens" +xref: Reactome:REACT_13466 "Cleavage of PAK-2 at 212, Oryctolagus cuniculus" +xref: Reactome:REACT_13468 "Caspase-mediated cleavage of MST3, Homo sapiens" +xref: Reactome:REACT_13476 "Caspase-mediated cleavage of Lamin A, Homo sapiens" +xref: Reactome:REACT_13484 "Caspase-mediated cleavage of Lamin B1, Homo sapiens" +xref: Reactome:REACT_13489 "Caspase mediated cleavage of vimentin at IDVD (259), Homo sapiens" +xref: Reactome:REACT_13519 "Caspase-mediated cleavage of vimentin at TNLD (429), Homo sapiens" +xref: Reactome:REACT_13522 "Caspase-mediated cleavage of plectin-1, Homo sapiens" +xref: Reactome:REACT_13549 "Caspase-mediated cleavage of occludin, Homo sapiens" +xref: Reactome:REACT_13554 "Caspase mediated cleavage of BAP31, Homo sapiens" +xref: Reactome:REACT_13587 "Caspase-mediated cleavage of Z0-1, Homo sapiens" +xref: Reactome:REACT_13598 "Caspase-mediated cleavage of Desmoglein 2, Homo sapiens" +xref: Reactome:REACT_13605 "Caspase-mediated cleavage of Desmoplakin, Homo sapiens" +xref: Reactome:REACT_13636 "Caspase-mediated cleavage of MASK, Homo sapiens" +xref: Reactome:REACT_13652 "Caspase-mediated cleavage of claspin, Homo sapiens" +xref: Reactome:REACT_13664 "Legumain degrades DBP, Homo sapiens" +xref: Reactome:REACT_13747 "Cleavage of PAK-2 at 212, Homo sapiens" +xref: Reactome:REACT_13795 "Caspase-mediated cleavage of gelsolin, Homo sapiens" +xref: Reactome:REACT_13813 "Caspase-mediated cleavage of Z0-2, Homo sapiens" +xref: Reactome:REACT_2116 "Cleavage of Procaspase-9 to Caspase-9, Homo sapiens" +xref: Reactome:REACT_2165 "Cleavage of Procaspase-7 by the apoptosome, Homo sapiens" +xref: Reactome:REACT_22184 "Caspase cleavage of UNC5A, Homo sapiens" +xref: Reactome:REACT_22225 "Cleavage of Satb1, Homo sapiens" +xref: Reactome:REACT_22343 "Caspase cleavage of UNC5B, Homo sapiens" +xref: Reactome:REACT_22367 "Caspase cleavage of Unc5h1, Mus musculus" +xref: Reactome:REACT_22412 "Activation of caspase-3, Homo sapiens" +xref: Reactome:REACT_22420 "Caspase cleavage of Unc5h2, Mus musculus" +xref: Reactome:REACT_22440 "Caspase cleavage of DCC, Homo sapiens" +xref: Reactome:REACT_24999 "Processing of caspases, Homo sapiens" +xref: Reactome:REACT_28312 "Caspase-mediated cleavage of PKC theta, Rattus norvegicus" +xref: Reactome:REACT_28479 "Caspase-mediated cleavage of Etk, Bos taurus" +xref: Reactome:REACT_28628 "Caspase-mediated cleavage of alpha adducin, Canis familiaris" +xref: Reactome:REACT_28846 "Caspase-mediated cleavage of Acinus, Mus musculus" +xref: Reactome:REACT_28869 "Cleavage of Procaspase-7 by the apoptosome, Gallus gallus" +xref: Reactome:REACT_29115 "Caspase-8 activates BID by cleavage, Canis familiaris" +xref: Reactome:REACT_29150 "Caspase mediated cleavage of vimentin at IDVD (259), Canis familiaris" +xref: Reactome:REACT_29160 "Caspase 3-mediated cleavage of DFF45 (117), Sus scrofa" +xref: Reactome:REACT_29351 "Cleavage of Procaspase-9 to Caspase-9, Danio rerio" +xref: Reactome:REACT_29430 "Caspase-mediated cleavage of claspin, Canis familiaris" +xref: Reactome:REACT_29547 "Caspase mediated cleavage of HIP-55, Bos taurus" +xref: Reactome:REACT_29647 "Caspase-mediated cleavage of claspin, Gallus gallus" +xref: Reactome:REACT_29743 "Caspase-mediated cleavage of GAS2, Taeniopygia guttata" +xref: Reactome:REACT_29821 "Caspase-mediated cleavage of Lamin B1, Canis familiaris" +xref: Reactome:REACT_30047 "Caspase mediated cleavage of APC, Mus musculus" +xref: Reactome:REACT_30276 "Legumain degrades DBP, Gallus gallus" +xref: Reactome:REACT_30300 "Caspase mediated cleavage of APC, Sus scrofa" +xref: Reactome:REACT_30513 "Caspase mediated cleavage of APC, Rattus norvegicus" +xref: Reactome:REACT_30561 "Legumain degrades DBP, Canis familiaris" +xref: Reactome:REACT_30860 "Caspase-mediated cleavage of FADK 1, Danio rerio" +xref: Reactome:REACT_31037 "Activation of caspase-3, Danio rerio" +xref: Reactome:REACT_31043 "Caspase mediated cleavage of beta-catenin, Canis familiaris" +xref: Reactome:REACT_31510 "Caspase-mediated cleavage of gelsolin, Bos taurus" +xref: Reactome:REACT_31594 "Caspase mediated cleavage of beta-catenin, Xenopus tropicalis" +xref: Reactome:REACT_31912 "Caspase 3-mediated cleavage of PKC delta, Taeniopygia guttata" +xref: Reactome:REACT_31993 "Cleavage of PAK-2 at 212, Danio rerio" +xref: Reactome:REACT_32081 "Caspase-mediated cleavage of E-Cadherin, Canis familiaris" +xref: Reactome:REACT_32092 "Caspase mediated cleavage of C-IAP1, Canis familiaris" +xref: Reactome:REACT_32303 "Cleavage of Satb1, Canis familiaris" +xref: Reactome:REACT_32343 "Legumain degrades DBP, Danio rerio" +xref: Reactome:REACT_32649 "Caspase mediated cleavage of vimentin at IDVD (259), Mus musculus" +xref: Reactome:REACT_32982 "Caspase-mediated cleavage of Desmoglein 3, Rattus norvegicus" +xref: Reactome:REACT_33284 "Caspase mediated cleavage of HIP-55, Xenopus tropicalis" +xref: Reactome:REACT_33786 "Caspase-mediated cleavage of Desmoglein 2, Danio rerio" +xref: Reactome:REACT_33971 "Caspase-mediated cleavage of FADK 1, Rattus norvegicus" +xref: Reactome:REACT_34082 "Caspase mediated cleavage of alpha-II-Fodrin, Taeniopygia guttata" +xref: Reactome:REACT_34279 "Caspase-mediated cleavage of Desmoglein 2, Taeniopygia guttata" +xref: Reactome:REACT_34342 "Caspase mediated cleavage of vimentin at IDVD (259), Rattus norvegicus" +xref: Reactome:REACT_34469 "Caspase-mediated cleavage of MASK, Danio rerio" +xref: Reactome:REACT_34743 "Cleavage of Procaspase-9 to Caspase-9, Xenopus tropicalis" +xref: Reactome:REACT_34768 "Caspase-mediated cleavage of plectin-1, Rattus norvegicus" +xref: Reactome:REACT_34770 "Caspase 3-mediated cleavage of PKC delta, Bos taurus" +xref: Reactome:REACT_40493 "Caspase 3-mediated cleavage of PKC delta, Mus musculus" +xref: Reactome:REACT_45490 "Caspase 3-mediated cleavage of DFF45 (117), Canis familiaris" +xref: Reactome:REACT_65200 "Caspase mediated cleavage of HIP-55, Mus musculus" +xref: Reactome:REACT_66649 "Caspase-mediated cleavage of FADK 1, Gallus gallus" +xref: Reactome:REACT_69471 "Caspase-mediated cleavage of Lamin B1, Mus musculus" +xref: Reactome:REACT_77064 "Cleavage of DFF45 (224) by caspase-3, Sus scrofa" +xref: Reactome:REACT_77154 "Caspase-mediated cleavage of Lamin A, Bos taurus" +xref: Reactome:REACT_77197 "Caspase 3-mediated cleavage of DFF45 (117), Taeniopygia guttata" +xref: Reactome:REACT_77210 "Caspase-mediated cleavage of FADK 1, Sus scrofa" +xref: Reactome:REACT_77248 "Cleavage of PAK-2 at 212, Taeniopygia guttata" +xref: Reactome:REACT_77301 "Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha, Taeniopygia guttata" +xref: Reactome:REACT_77309 "Caspase mediated cleavage of HIP-55, Canis familiaris" +xref: Reactome:REACT_77343 "Caspase-mediated cleavage of Acinus, Sus scrofa" +xref: Reactome:REACT_77434 "Caspase 3-mediated cleavage of DFF45 (117), Gallus gallus" +xref: Reactome:REACT_77678 "Caspase-mediated cleavage of Rock-1, Mus musculus" +xref: Reactome:REACT_77795 "Cleavage of Satb1, Xenopus tropicalis" +xref: Reactome:REACT_77916 "Caspase-mediated cleavage of vimentin at TNLD (429), Bos taurus" +xref: Reactome:REACT_77921 "Caspase mediated cleavage of APC, Bos taurus" +xref: Reactome:REACT_78072 "Cleavage of DFF45 (224) by caspase-3, Xenopus tropicalis" +xref: Reactome:REACT_78179 "Caspase-8 activates BID by cleavage, Rattus norvegicus" +xref: Reactome:REACT_78180 "Caspase-mediated cleavage of Lamin B1, Gallus gallus" +xref: Reactome:REACT_78322 "Caspase mediated cleavage of C-IAP1, Taeniopygia guttata" +xref: Reactome:REACT_78407 "Caspase mediated cleavage of beta-catenin, Rattus norvegicus" +xref: Reactome:REACT_78676 "Caspase-mediated cleavage of Rock-1, Xenopus tropicalis" +xref: Reactome:REACT_78896 "Caspase-mediated cleavage of Lamin A, Canis familiaris" +xref: Reactome:REACT_78931 "Caspase-mediated cleavage of E-Cadherin, Taeniopygia guttata" +xref: Reactome:REACT_78958 "Caspase 3-mediated cleavage of PKC delta, Xenopus tropicalis" +xref: Reactome:REACT_79257 "Caspase-mediated cleavage of claspin, Xenopus tropicalis" +xref: Reactome:REACT_79283 "Caspase-mediated cleavage of Acinus, Bos taurus" +xref: Reactome:REACT_79470 "Caspase mediated cleavage of BAP31, Rattus norvegicus" +xref: Reactome:REACT_79514 "Cleavage of Satb1, Bos taurus" +xref: Reactome:REACT_79541 "Caspase-mediated cleavage of vimentin at DSVD (85), Canis familiaris" +xref: Reactome:REACT_79778 "Caspase-mediated cleavage of vimentin at TNLD (429), Rattus norvegicus" +xref: Reactome:REACT_79895 "Caspase-mediated cleavage of vimentin at TNLD (429), Xenopus tropicalis" +xref: Reactome:REACT_79950 "Caspase mediated cleavage of APC, Canis familiaris" +xref: Reactome:REACT_80378 "Caspase mediated cleavage of HIP-55, Gallus gallus" +xref: Reactome:REACT_80953 "Caspase-mediated cleavage of Desmoglein 3, Mus musculus" +xref: Reactome:REACT_80998 "Caspase mediated cleavage of C-IAP1, Mus musculus" +xref: Reactome:REACT_81124 "Caspase-mediated cleavage of Desmoglein 2, Gallus gallus" +xref: Reactome:REACT_81156 "Caspase-mediated cleavage of vimentin at TNLD (429), Mus musculus" +xref: Reactome:REACT_81371 "Caspase-mediated cleavage of vimentin at DSVD (85), Mus musculus" +xref: Reactome:REACT_81496 "Caspase-mediated cleavage of GAS2, Canis familiaris" +xref: Reactome:REACT_81521 "Caspase 3-mediated cleavage of DFF45 (117), Mus musculus" +xref: Reactome:REACT_81570 "Caspase-mediated cleavage of Tau, Mus musculus" +xref: Reactome:REACT_81606 "Caspase mediated cleavage of alpha-II-Fodrin, Bos taurus" +xref: Reactome:REACT_81720 "Cleavage of Procaspase-9 to Caspase-9, Mus musculus" +xref: Reactome:REACT_81816 "Cleavage of DFF45 (224) by caspase-3, Danio rerio" +xref: Reactome:REACT_81951 "Caspase mediated cleavage of BAP31, Danio rerio" +xref: Reactome:REACT_82352 "Cleavage of Satb1, Sus scrofa" +xref: Reactome:REACT_82992 "Caspase-mediated cleavage of MASK, Gallus gallus" +xref: Reactome:REACT_83002 "Cleavage of Procaspase-9 to Caspase-9, Taeniopygia guttata" +xref: Reactome:REACT_83106 "Caspase-mediated cleavage of FADK 1, Mus musculus" +xref: Reactome:REACT_83519 "Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha, Mus musculus" +xref: Reactome:REACT_83624 "Caspase-mediated cleavage of MASK, Xenopus tropicalis" +xref: Reactome:REACT_83683 "Caspase-mediated cleavage of vimentin at TNLD (429), Gallus gallus" +xref: Reactome:REACT_84133 "Caspase-mediated cleavage of plectin-1, Canis familiaris" +xref: Reactome:REACT_84494 "Caspase-mediated cleavage of Desmoglein 2, Canis familiaris" +xref: Reactome:REACT_84645 "Caspase 3-mediated cleavage of DFF45 (117), Rattus norvegicus" +xref: Reactome:REACT_84845 "Cleavage of PAK-2 at 212, Canis familiaris" +xref: Reactome:REACT_84872 "Caspase-mediated cleavage of Acinus, Danio rerio" +xref: Reactome:REACT_84905 "Caspase-8 activates BID by cleavage, Taeniopygia guttata" +xref: Reactome:REACT_84967 "Caspase-mediated cleavage of Desmoglein 1, Canis familiaris" +xref: Reactome:REACT_84971 "Cleavage of PAK-2 at 212, Xenopus tropicalis" +xref: Reactome:REACT_85027 "Caspase-mediated cleavage of Tau, Rattus norvegicus" +xref: Reactome:REACT_85032 "Caspase mediated cleavage of HIP-55, Danio rerio" +xref: Reactome:REACT_85270 "Caspase mediated cleavage of BAP31, Mus musculus" +xref: Reactome:REACT_85285 "Caspase-mediated cleavage of alpha adducin, Sus scrofa" +xref: Reactome:REACT_85370 "Caspase-mediated cleavage of vimentin at DSVD (85), Bos taurus" +xref: Reactome:REACT_85432 "Cleavage of PAK-2 at 212, Gallus gallus" +xref: Reactome:REACT_85447 "Caspase-mediated cleavage of Tau, Canis familiaris" +xref: Reactome:REACT_85559 "Caspase-mediated cleavage of Desmoglein 1, Gallus gallus" +xref: Reactome:REACT_85681 "Caspase-mediated cleavage of alpha adducin, Xenopus tropicalis" +xref: Reactome:REACT_85820 "Caspase 3-mediated cleavage of PKC delta, Rattus norvegicus" +xref: Reactome:REACT_85958 "Caspase-mediated cleavage of Etk, Gallus gallus" +xref: Reactome:REACT_86010 "Caspase-mediated cleavage of Desmoglein 3, Gallus gallus" +xref: Reactome:REACT_86094 "Caspase-mediated cleavage of vimentin at TNLD (429), Sus scrofa" +xref: Reactome:REACT_86100 "Caspase-mediated cleavage of Rock-1, Taeniopygia guttata" +xref: Reactome:REACT_86150 "Caspase mediated cleavage of alpha-II-Fodrin, Rattus norvegicus" +xref: Reactome:REACT_86362 "Caspase-mediated cleavage of MASK, Bos taurus" +xref: Reactome:REACT_86384 "Caspase-mediated cleavage of PKC theta, Mus musculus" +xref: Reactome:REACT_86398 "Caspase mediated cleavage of C-IAP1, Rattus norvegicus" +xref: Reactome:REACT_86436 "Caspase-mediated cleavage of claspin, Rattus norvegicus" +xref: Reactome:REACT_86545 "Caspase mediated cleavage of vimentin at IDVD (259), Sus scrofa" +xref: Reactome:REACT_86791 "Caspase-mediated cleavage of Tau, Taeniopygia guttata" +xref: Reactome:REACT_86903 "Caspase mediated cleavage of HIP-55, Taeniopygia guttata" +xref: Reactome:REACT_86932 "Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha, Canis familiaris" +xref: Reactome:REACT_87309 "Legumain degrades DBP, Rattus norvegicus" +xref: Reactome:REACT_87440 "Caspase-mediated cleavage of vimentin at DSVD (85), Gallus gallus" +xref: Reactome:REACT_87658 "Caspase mediated cleavage of vimentin at IDVD (259), Bos taurus" +xref: Reactome:REACT_87895 "Caspase-mediated cleavage of claspin, Mus musculus" +xref: Reactome:REACT_87973 "Caspase-mediated cleavage of FADK 1, Xenopus tropicalis" +xref: Reactome:REACT_88107 "Caspase-mediated cleavage of claspin, Danio rerio" +xref: Reactome:REACT_88165 "Cleavage of DFF45 (224) by caspase-3, Gallus gallus" +xref: Reactome:REACT_88929 "Caspase-8 activates BID by cleavage, Sus scrofa" +xref: Reactome:REACT_89449 "Caspase-mediated cleavage of alpha adducin, Taeniopygia guttata" +xref: Reactome:REACT_89531 "Caspase 3-mediated cleavage of PKC delta, Danio rerio" +xref: Reactome:REACT_89573 "Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha, Rattus norvegicus" +xref: Reactome:REACT_89708 "Cleavage of DFF45 (224) by caspase-3, Rattus norvegicus" +xref: Reactome:REACT_90001 "Caspase-mediated cleavage of FADK 1, Bos taurus" +xref: Reactome:REACT_90025 "Caspase-mediated cleavage of PKC theta, Taeniopygia guttata" +xref: Reactome:REACT_90026 "Caspase-mediated cleavage of vimentin at DSVD (85), Danio rerio" +xref: Reactome:REACT_90780 "Cleavage of Procaspase-7 by the apoptosome, Mus musculus" +xref: Reactome:REACT_90840 "Caspase-mediated cleavage of Desmoglein 3, Danio rerio" +xref: Reactome:REACT_90898 "Caspase-mediated cleavage of Lamin A, Danio rerio" +xref: Reactome:REACT_91339 "Cleavage of Satb1, Rattus norvegicus" +xref: Reactome:REACT_91358 "Caspase 3-mediated cleavage of DFF45 (117), Xenopus tropicalis" +xref: Reactome:REACT_91380 "Caspase-mediated cleavage of gelsolin, Canis familiaris" +xref: Reactome:REACT_91436 "Caspase-mediated cleavage of Lamin A, Xenopus tropicalis" +xref: Reactome:REACT_91694 "Caspase-mediated cleavage of claspin, Sus scrofa" +xref: Reactome:REACT_91811 "Caspase-mediated cleavage of claspin, Taeniopygia guttata" +xref: Reactome:REACT_91825 "Caspase-mediated cleavage of GAS2, Mus musculus" +xref: Reactome:REACT_91992 "Caspase-mediated cleavage of Lamin B1, Taeniopygia guttata" +xref: Reactome:REACT_92095 "Cleavage of DFF45 (224) by caspase-3, Taeniopygia guttata" +xref: Reactome:REACT_92317 "Caspase mediated cleavage of alpha-II-Fodrin, Sus scrofa" +xref: Reactome:REACT_92549 "Caspase-mediated cleavage of Acinus, Rattus norvegicus" +xref: Reactome:REACT_92604 "Caspase mediated cleavage of BAP31, Bos taurus" +xref: Reactome:REACT_92733 "Caspase-mediated cleavage of E-Cadherin, Danio rerio" +xref: Reactome:REACT_93115 "Caspase-mediated cleavage of vimentin at TNLD (429), Canis familiaris" +xref: Reactome:REACT_93215 "Caspase-mediated cleavage of gelsolin, Rattus norvegicus" +xref: Reactome:REACT_93489 "Caspase-mediated cleavage of Acinus, Canis familiaris" +xref: Reactome:REACT_93620 "Caspase-mediated cleavage of E-Cadherin, Bos taurus" +xref: Reactome:REACT_93838 "Cleavage of DFF45 (224) by caspase-3, Bos taurus" +xref: Reactome:REACT_93845 "Caspase-mediated cleavage of Desmoglein 1, Rattus norvegicus" +xref: Reactome:REACT_93876 "Caspase-mediated cleavage of Tau, Danio rerio" +xref: Reactome:REACT_94219 "Cleavage of DFF45 (224) by caspase-3, Canis familiaris" +xref: Reactome:REACT_94280 "Caspase-mediated cleavage of Desmoglein 1, Taeniopygia guttata" +xref: Reactome:REACT_94301 "Caspase-8 activates BID by cleavage, Gallus gallus" +xref: Reactome:REACT_94351 "Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha, Danio rerio" +xref: Reactome:REACT_94538 "Caspase 3-mediated cleavage of PKC delta, Gallus gallus" +xref: Reactome:REACT_94598 "Caspase 3-mediated cleavage of DFF45 (117), Bos taurus" +xref: Reactome:REACT_94641 "Caspase-mediated cleavage of alpha adducin, Rattus norvegicus" +xref: Reactome:REACT_94673 "Caspase-8 activates BID by cleavage, Bos taurus" +xref: Reactome:REACT_94680 "Caspase-mediated cleavage of Tau, Bos taurus" +xref: Reactome:REACT_95121 "Caspase-mediated cleavage of GAS2, Gallus gallus" +xref: Reactome:REACT_95172 "Caspase mediated cleavage of beta-catenin, Gallus gallus" +xref: Reactome:REACT_95220 "Caspase-mediated cleavage of Tau, Xenopus tropicalis" +xref: Reactome:REACT_95222 "Caspase-mediated cleavage of Desmoglein 3, Canis familiaris" +xref: Reactome:REACT_95242 "Caspase mediated cleavage of alpha-II-Fodrin, Canis familiaris" +xref: Reactome:REACT_95283 "Caspase-mediated cleavage of alpha adducin, Bos taurus" +xref: Reactome:REACT_95420 "Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha, Bos taurus" +xref: Reactome:REACT_95652 "Caspase mediated cleavage of APC, Gallus gallus" +xref: Reactome:REACT_95884 "Caspase mediated cleavage of beta-catenin, Bos taurus" +xref: Reactome:REACT_95944 "Caspase-mediated cleavage of PKC theta, Canis familiaris" +xref: Reactome:REACT_95948 "Caspase-mediated cleavage of Rock-1, Gallus gallus" +xref: Reactome:REACT_96025 "Caspase-mediated cleavage of GAS2, Xenopus tropicalis" +xref: Reactome:REACT_96048 "Caspase 3-mediated cleavage of DFF45 (117), Danio rerio" +xref: Reactome:REACT_96146 "Caspase-mediated cleavage of PKC theta, Gallus gallus" +xref: Reactome:REACT_96219 "Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha, Xenopus tropicalis" +xref: Reactome:REACT_96672 "Caspase-mediated cleavage of gelsolin, Danio rerio" +xref: Reactome:REACT_96721 "Caspase-mediated cleavage of farnesyltransferase/geranyl- geranyltransferase subunit alpha, Gallus gallus" +xref: Reactome:REACT_96744 "Caspase-mediated cleavage of vimentin at DSVD (85), Rattus norvegicus" +xref: Reactome:REACT_96941 "Cleavage of Satb1, Mus musculus" +xref: Reactome:REACT_97519 "Cleavage of PAK-2 at 212, Rattus norvegicus" +xref: Reactome:REACT_97541 "Caspase-mediated cleavage of PKC theta, Xenopus tropicalis" +xref: Reactome:REACT_97621 "Caspase mediated cleavage of vimentin at IDVD (259), Gallus gallus" +xref: Reactome:REACT_97639 "Caspase-mediated cleavage of Lamin B1, Drosophila melanogaster" +xref: Reactome:REACT_97875 "Legumain degrades DBP, Xenopus tropicalis" +xref: Reactome:REACT_97995 "Caspase-mediated cleavage of Lamin A, Taeniopygia guttata" +xref: Reactome:REACT_98036 "Activation of caspase-3, Rattus norvegicus" +xref: Reactome:REACT_98139 "Caspase-mediated cleavage of Desmoglein 3, Bos taurus" +xref: Reactome:REACT_98180 "Cleavage of DFF45 (224) by caspase-3, Mus musculus" +xref: Reactome:REACT_98289 "Caspase-mediated cleavage of Lamin A, Mus musculus" +xref: Reactome:REACT_98423 "Caspase-mediated cleavage of Desmoglein 2, Bos taurus" +xref: Reactome:REACT_98483 "Caspase-mediated cleavage of Etk, Rattus norvegicus" +xref: Reactome:REACT_98534 "Caspase-mediated cleavage of Lamin A, Rattus norvegicus" +xref: Reactome:REACT_98703 "Caspase-mediated cleavage of alpha adducin, Danio rerio" +xref: Reactome:REACT_98831 "Caspase mediated cleavage of C-IAP1, Gallus gallus" +xref: Reactome:REACT_98986 "Caspase-mediated cleavage of gelsolin, Gallus gallus" +xref: Reactome:REACT_99229 "Caspase-mediated cleavage of PKC theta, Danio rerio" +xref: Reactome:REACT_99392 "Caspase-mediated cleavage of Etk, Sus scrofa" +xref: Reactome:REACT_99637 "Activation of caspase-3, Mus musculus" +xref: Reactome:REACT_99764 "Caspase-mediated cleavage of Desmoglein 1, Bos taurus" +is_a: GO:0004175 ! endopeptidase activity +is_a: GO:0008234 ! cysteine-type peptidase activity + +[Term] +id: GO:0004340 +name: glucokinase activity +namespace: molecular_function +def: "Catalysis of the reaction: ATP + D-glucose = ADP + D-glucose-6-phosphate." [EC:2.7.1.2] +subset: gosubset_prok +synonym: "ATP:D-glucose 6-phosphotransferase activity" EXACT [EC:2.7.1.2] +synonym: "glucokinase (phosphorylating)" EXACT [EC:2.7.1.2] +synonym: "glucose kinase activity" EXACT [EC:2.7.1.2] +xref: EC:2.7.1.2 +xref: MetaCyc:GLUCOKIN-RXN +xref: Reactome:REACT_109618 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Sus scrofa" +xref: Reactome:REACT_115950 "glucose + ATP => glucose 6-phosphate + ADP, Gallus gallus" +xref: Reactome:REACT_1827 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Homo sapiens" +xref: Reactome:REACT_28331 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Caenorhabditis elegans" +xref: Reactome:REACT_28504 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Taeniopygia guttata" +xref: Reactome:REACT_31619 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Oryza sativa" +xref: Reactome:REACT_33904 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Arabidopsis thaliana" +xref: Reactome:REACT_34118 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Plasmodium falciparum" +xref: Reactome:REACT_80323 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Rattus norvegicus" +xref: Reactome:REACT_81488 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Danio rerio" +xref: Reactome:REACT_82793 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Gallus gallus" +xref: Reactome:REACT_84021 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Bos taurus" +xref: Reactome:REACT_85927 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Schizosaccharomyces pombe" +xref: Reactome:REACT_88172 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Xenopus tropicalis" +xref: Reactome:REACT_90073 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Saccharomyces cerevisiae" +xref: Reactome:REACT_92495 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Mus musculus" +xref: Reactome:REACT_96462 "alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP, Canis familiaris" +xref: RHEA:17828 +is_a: GO:0004396 ! hexokinase activity +relationship: part_of GO:0051156 ! glucose 6-phosphate metabolic process + +[Term] +id: GO:0004396 +name: hexokinase activity +namespace: molecular_function +def: "Catalysis of the reaction: ATP + D-hexose = ADP + D-hexose 6-phosphate." [EC:2.7.1.1] +subset: gosubset_prok +synonym: "ATP-dependent hexokinase activity" EXACT [EC:2.7.1.1] +synonym: "ATP:D-hexose 6-phosphotransferase activity" EXACT [EC:2.7.1.1] +synonym: "glucose ATP phosphotransferase activity" EXACT [EC:2.7.1.1] +synonym: "hexokinase (phosphorylating)" EXACT [EC:2.7.1.1] +synonym: "hexokinase D" RELATED [EC:2.7.1.1] +synonym: "hexokinase type I activity" NARROW [EC:2.7.1.1] +synonym: "hexokinase type II activity" NARROW [EC:2.7.1.1] +synonym: "hexokinase type III activity" NARROW [EC:2.7.1.1] +synonym: "hexokinase type IV" RELATED [EC:2.7.1.1] +synonym: "hexokinase type IV (glucokinase) activity" NARROW [EC:2.7.1.1] +synonym: "hexokinase type IV glucokinase activity" EXACT [EC:2.7.1.1] +xref: EC:2.7.1.1 +xref: MetaCyc:HEXOKINASE-RXN +xref: RHEA:22743 +is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor +is_a: GO:0019200 ! carbohydrate kinase activity + +[Term] +id: GO:0004672 +name: protein kinase activity +namespace: molecular_function +alt_id: GO:0050222 +def: "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP." [MetaCyc:PROTEIN-KINASE-RXN] +comment: Note that triphosphate is used as a phosphate donor by at least one kinase. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "protamine kinase activity" NARROW [] +xref: MetaCyc:PROTEIN-KINASE-RXN +xref: Reactome:REACT_100389 "Phosphorylation and Release of IRF3 or IRF7, Bos taurus" +xref: Reactome:REACT_100723 "Phosphorylation of p130Cas by SRC-FADK1 complex, Canis familiaris" +xref: Reactome:REACT_100866 "Phosphorylation and activation of Ezrin, Gallus gallus" +xref: Reactome:REACT_101171 "Phosphorylation and release of IRF3/IRF7, Rattus norvegicus" +xref: Reactome:REACT_101316 "Autophosphorylation of FADK1 at Y397, Rattus norvegicus" +xref: Reactome:REACT_102340 "Activated Src activates ERK, Danio rerio" +xref: Reactome:REACT_102368 "Phosphorylation and Release of IRF3 or IRF7, Gallus gallus" +xref: Reactome:REACT_104931 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Gallus gallus" +xref: Reactome:REACT_104987 "Phosphorylation of pFADK1 by SRC, Danio rerio" +xref: Reactome:REACT_105344 "Phosphorylation of p130Cas by SRC-FADK1 complex, Sus scrofa" +xref: Reactome:REACT_106425 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Taeniopygia guttata" +xref: Reactome:REACT_106633 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Sus scrofa" +xref: Reactome:REACT_107161 "Phosphorylation and release of IRF3/IRF7, Taeniopygia guttata" +xref: Reactome:REACT_107646 "Phosphorylation and release of IRF3/IRF7, Canis familiaris" +xref: Reactome:REACT_107914 "(Frs2)Rap1-GTP binds to and activates B-Raf, Xenopus tropicalis" +xref: Reactome:REACT_108319 "Activated Src activates ERK, Xenopus tropicalis" +xref: Reactome:REACT_108693 "Phosphorylation and release of IRF3/IRF7, Mus musculus" +xref: Reactome:REACT_109624 "Phosphorylation of p130Cas by SRC-FADK1 complex, Rattus norvegicus" +xref: Reactome:REACT_110105 "Phosphorylation and activation of Ezrin, Canis familiaris" +xref: Reactome:REACT_110177 "Autophosphorylation of FADK1 at Y397, Mus musculus" +xref: Reactome:REACT_110248 "Activated Src activates ERK, Canis familiaris" +xref: Reactome:REACT_111075 "Phosphorylation of LIN52 component of MuvB by DYRK1A, Homo sapiens" +xref: Reactome:REACT_111995 "Phosphorylation of p130Cas by SRC-FADK1 complex, Drosophila melanogaster" +xref: Reactome:REACT_112267 "Autophosphorylation of FADK1 at Y397, Drosophila melanogaster" +xref: Reactome:REACT_112918 "Phosphorylation and activation of Ezrin, Caenorhabditis elegans" +xref: Reactome:REACT_113100 "Activated Src activates ERK, Drosophila melanogaster" +xref: Reactome:REACT_113334 "PKC phosphorylates GRK2, Caenorhabditis elegans" +xref: Reactome:REACT_113440 "Phosphorylation and release of IRF3/IRF7, Xenopus tropicalis" +xref: Reactome:REACT_113589 "Phosphorylation of pFADK1 by SRC, Drosophila melanogaster" +xref: Reactome:REACT_113821 "Activated Src activates ERK, Caenorhabditis elegans" +xref: Reactome:REACT_114093 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Danio rerio" +xref: Reactome:REACT_114693 "Phosphorylation of pFADK1 by SRC, Xenopus tropicalis" +xref: Reactome:REACT_115673 "PIP2 to PIP3 conversion by PI3K bound to GRB2:GAB1 in complex with phosphorylated heterodimer of ERBB2 and EGFR, Homo sapiens" +xref: Reactome:REACT_115712 "Conversion of PIP2 into PIP3 by PI3K bound to p-ERBB4cyt1 homodimers, Homo sapiens" +xref: Reactome:REACT_115868 "Phosphorylation of c-Abl and Arg by ATM, Gallus gallus" +xref: Reactome:REACT_116057 "PIP2 to PIP3 conversion by PI3K bound to phosphorylated heterodimer of ERBB2 and ERBB4 CYT1, Homo sapiens" +xref: Reactome:REACT_116116 "PIP2 to PIP3 conversion by PI3K bound to phosphorylated heterodimer of ERBB2 and ERBB3, Homo sapiens" +xref: Reactome:REACT_12050 "(Frs2)Rap1-GTP binds to and activates B-Raf, Homo sapiens" +xref: Reactome:REACT_1325 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Homo sapiens" +xref: Reactome:REACT_15368 "Phosphorylation of pFADK1 by SRC, Homo sapiens" +xref: Reactome:REACT_15375 "Phosphorylation of p130Cas by SRC-FADK1 complex, Homo sapiens" +xref: Reactome:REACT_15534 "PKC phosphorylates GRK2, Homo sapiens" +xref: Reactome:REACT_15535 "Autophosphorylation of FADK1 at Y397, Homo sapiens" +xref: Reactome:REACT_161 "rLkb-1 (Stk-11) activates AMPK by phosphorylation, Rattus norvegicus" +xref: Reactome:REACT_1825 "INF-gamma induced phosphorylation of L13a, Homo sapiens" +xref: Reactome:REACT_19374 "Phosphorylation of Plexin-A, Mus musculus" +xref: Reactome:REACT_22301 "Phosphorylation and activation of Ezrin, Homo sapiens" +xref: Reactome:REACT_22305 "Phosphorylation of FADK1, Mus musculus" +xref: Reactome:REACT_23900 "Activated Src activates ERK, Homo sapiens" +xref: Reactome:REACT_24935 "Activation of IKK by MEKK1, Homo sapiens" +xref: Reactome:REACT_25200 "IRAK1 phosphorylates Pellino, Homo sapiens" +xref: Reactome:REACT_25213 "Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomer:Mal:activated TLR complex, Homo sapiens" +xref: Reactome:REACT_25241 "IRAK1 phosphorylates Pellino upon TLR7/8 or 9 activation, Homo sapiens" +xref: Reactome:REACT_25327 "Phosphorylation and release of IRF7, Homo sapiens" +xref: Reactome:REACT_25368 "Phosphorylation and release of IRF3/IRF7, Homo sapiens" +xref: Reactome:REACT_27151 "Multiple IRAK1 autophosphorylation within the complex p-IRAK4:oligo MyD88:activated TLR, Homo sapiens" +xref: Reactome:REACT_27163 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR complex, Homo sapiens" +xref: Reactome:REACT_27165 "Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomerl:activated TLR5 or 10 complex, Homo sapiens" +xref: Reactome:REACT_27228 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR, Homo sapiens" +xref: Reactome:REACT_29590 "PKC phosphorylates GRK2, Rattus norvegicus" +xref: Reactome:REACT_29816 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Drosophila melanogaster" +xref: Reactome:REACT_30885 "Phosphorylation of p130Cas by SRC-FADK1 complex, Bos taurus" +xref: Reactome:REACT_31028 "Autophosphorylation of FADK1 at Y397, Sus scrofa" +xref: Reactome:REACT_31157 "Phosphorylation of pFADK1 by SRC, Canis familiaris" +xref: Reactome:REACT_31403 "Autophosphorylation of FADK1 at Y397, Gallus gallus" +xref: Reactome:REACT_32448 "Phosphorylation of pFADK1 by SRC, Bos taurus" +xref: Reactome:REACT_32744 "PKC phosphorylates GRK2, Mus musculus" +xref: Reactome:REACT_33098 "PKC phosphorylates GRK2, Canis familiaris" +xref: Reactome:REACT_33973 "Phosphorylation and Release of IRF3 or IRF7, Canis familiaris" +xref: Reactome:REACT_34630 "(Frs2)Rap1-GTP binds to and activates B-Raf, Danio rerio" +xref: Reactome:REACT_6227 "Activated DTOR also phosphorylates D4EBP, Drosophila melanogaster" +xref: Reactome:REACT_6236 "Activated DTOR phosphorylates DS6K, Drosophila melanogaster" +xref: Reactome:REACT_6842 "Phosphorylation and Release of IRF3 or IRF7, Homo sapiens" +xref: Reactome:REACT_6862 "Multiple IRAK1 autophosphorylation steps, Homo sapiens" +xref: Reactome:REACT_72123 "PKC phosphorylates GRK2, Sus scrofa" +xref: Reactome:REACT_75763 "Phosphorylation and release of IRF3, Gallus gallus" +xref: Reactome:REACT_75767 "Phosphorylation of IKKs complex mediated by MEKK1, Gallus gallus" +xref: Reactome:REACT_77320 "Phosphorylation and release of IRF3/IRF7, Gallus gallus" +xref: Reactome:REACT_77352 "Phosphorylation of p130Cas by SRC-FADK1 complex, Danio rerio" +xref: Reactome:REACT_78568 "Phosphorylation and activation of Ezrin, Danio rerio" +xref: Reactome:REACT_79546 "Activated Src activates ERK, Gallus gallus" +xref: Reactome:REACT_80382 "Phosphorylation and activation of Ezrin, Mus musculus" +xref: Reactome:REACT_81116 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Canis familiaris" +xref: Reactome:REACT_81601 "Autophosphorylation of FADK1 at Y397, Bos taurus" +xref: Reactome:REACT_81960 "PKC phosphorylates GRK2, Drosophila melanogaster" +xref: Reactome:REACT_82440 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Xenopus tropicalis" +xref: Reactome:REACT_82942 "Activated Src activates ERK, Bos taurus" +xref: Reactome:REACT_83498 "Activated Src activates ERK, Taeniopygia guttata" +xref: Reactome:REACT_83992 "(Frs2)Rap1-GTP binds to and activates B-Raf, Mus musculus" +xref: Reactome:REACT_84298 "Autophosphorylation of FADK1 at Y397, Danio rerio" +xref: Reactome:REACT_84426 "Phosphorylation and Release of IRF3 or IRF7, Taeniopygia guttata" +xref: Reactome:REACT_85334 "PKC phosphorylates GRK2, Bos taurus" +xref: Reactome:REACT_85934 "Autophosphorylation of FADK1 at Y397, Canis familiaris" +xref: Reactome:REACT_86784 "Autophosphorylation of FADK1 at Y397, Taeniopygia guttata" +xref: Reactome:REACT_86846 "Activated Src activates ERK, Mus musculus" +xref: Reactome:REACT_87050 "Phosphorylation of pFADK1 by SRC, Mus musculus" +xref: Reactome:REACT_87514 "Phosphorylation and activation of Ezrin, Sus scrofa" +xref: Reactome:REACT_87874 "Phosphorylation of pFADK1 by SRC, Sus scrofa" +xref: Reactome:REACT_87926 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Bos taurus" +xref: Reactome:REACT_88017 "PKC phosphorylates GRK2, Taeniopygia guttata" +xref: Reactome:REACT_88090 "Phosphorylation and release of IRF3/IRF7, Bos taurus" +xref: Reactome:REACT_88178 "Phosphorylation and release of IRF3/IRF7, Sus scrofa" +xref: Reactome:REACT_88344 "(Frs2)Rap1-GTP binds to and activates B-Raf, Sus scrofa" +xref: Reactome:REACT_88685 "Phosphorylation of p130Cas by SRC-FADK1 complex, Xenopus tropicalis" +xref: Reactome:REACT_89390 "(Frs2)Rap1-GTP binds to and activates B-Raf, Bos taurus" +xref: Reactome:REACT_90060 "Autophosphorylation of FADK1 at Y397, Xenopus tropicalis" +xref: Reactome:REACT_90671 "Phosphorylation and activation of Ezrin, Xenopus tropicalis" +xref: Reactome:REACT_90879 "Phosphorylation of p130Cas by SRC-FADK1 complex, Gallus gallus" +xref: Reactome:REACT_91096 "Activated Src activates ERK, Sus scrofa" +xref: Reactome:REACT_93160 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Mus musculus" +xref: Reactome:REACT_93476 "(Frs2)Rap1-GTP binds to and activates B-Raf, Canis familiaris" +xref: Reactome:REACT_93547 "Activated Src activates ERK, Rattus norvegicus" +xref: Reactome:REACT_94091 "Phosphorylation and activation of Ezrin, Bos taurus" +xref: Reactome:REACT_95384 "Phosphorylation and Release of IRF3 or IRF7, Mus musculus" +xref: Reactome:REACT_96044 "Phosphorylation of p130Cas by SRC-FADK1 complex, Mus musculus" +xref: Reactome:REACT_96155 "Phosphorylation and release of IRF3/IRF7, Danio rerio" +xref: Reactome:REACT_96307 "Phosphorylation and Release of IRF3 or IRF7, Danio rerio" +xref: Reactome:REACT_96320 "Phosphorylation and activation of Ezrin, Rattus norvegicus" +xref: Reactome:REACT_96822 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Dictyostelium discoideum" +xref: Reactome:REACT_96873 "LKB1 phosphorylates the alpha subunit of AMPK heterotrimer, Caenorhabditis elegans" +xref: Reactome:REACT_97267 "PKC phosphorylates GRK2, Gallus gallus" +xref: Reactome:REACT_97501 "(Frs2)Rap1-GTP binds to and activates B-Raf, Taeniopygia guttata" +xref: Reactome:REACT_97784 "Phosphorylation and activation of Ezrin, Taeniopygia guttata" +xref: Reactome:REACT_98334 "Phosphorylation of pFADK1 by SRC, Rattus norvegicus" +xref: Reactome:REACT_98994 "(Frs2)Rap1-GTP binds to and activates B-Raf, Gallus gallus" +xref: Reactome:REACT_99274 "Phosphorylation of p130Cas by SRC-FADK1 complex, Taeniopygia guttata" +is_a: GO:0016301 ! kinase activity +is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor +relationship: part_of GO:0006468 ! protein phosphorylation + +[Term] +id: GO:0004674 +name: protein serine/threonine kinase activity +namespace: molecular_function +alt_id: GO:0004695 +alt_id: GO:0004696 +alt_id: GO:0004700 +def: "Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate." [GOC:bf] +subset: gosubset_prok +synonym: "A-kinase activity" NARROW [EC:2.7.11.1] +synonym: "AP50 kinase activity" NARROW [EC:2.7.11.1] +synonym: "ATP-protein transphosphorylase activity" NARROW [EC:2.7.11.1] +synonym: "ATP:protein phosphotransferase (non-specific) activity" NARROW [EC:2.7.11.1] +synonym: "atypical PKC activity" NARROW [] +synonym: "atypical protein kinase C activity" NARROW [] +synonym: "betaIIPKC" RELATED [EC:2.7.11.1] +synonym: "calcium/phospholipid-dependent protein kinase activity" NARROW [EC:2.7.11.1] +synonym: "casein kinase (phosphorylating) activity" NARROW [EC:2.7.11.1] +synonym: "cytidine 3',5'-cyclic monophosphate-responsive protein kinase activity" NARROW [EC:2.7.11.1] +synonym: "dsk1" RELATED [EC:2.7.11.1] +synonym: "epsilon PKC" RELATED [EC:2.7.11.1] +synonym: "galactosyltransferase-associated kinase activity" NARROW [] +synonym: "glycogen synthase A kinase activity" NARROW [EC:2.7.11.1] +synonym: "glycogen synthase kinase 3 activity" NARROW [] +synonym: "glycogen synthase kinase activity" NARROW [EC:2.7.11.1] +synonym: "HIPK2" RELATED [EC:2.7.11.1] +synonym: "Hpr kinase activity" NARROW [EC:2.7.11.1] +synonym: "hydroxyalkyl-protein kinase activity" NARROW [EC:2.7.11.1] +synonym: "M phase-specific cdc2 kinase activity" NARROW [EC:2.7.11.1] +synonym: "MAPK" RELATED [EC:2.7.11.1] +synonym: "mitogen-activated protein kinase activity" BROAD [EC:2.7.11.1] +synonym: "mitogen-activated S6 kinase activity" NARROW [EC:2.7.11.1] +synonym: "non-specific serine/threonine protein kinase activity" NARROW [EC:2.7.11.1] +synonym: "p82 kinase activity" NARROW [EC:2.7.11.1] +synonym: "phosphorylase B kinase kinase activity" NARROW [EC:2.7.11.1] +synonym: "phosphorylase b kinase kinase activity" BROAD [EC:2.7.11.1] +synonym: "PKA" RELATED [EC:2.7.11.1] +synonym: "PKC" RELATED [EC:2.7.11.1] +synonym: "protein glutamyl kinase activity" NARROW [EC:2.7.11.1] +synonym: "protein kinase (phosphorylating) activity" NARROW [EC:2.7.11.1] +synonym: "protein kinase A activity" BROAD [EC:2.7.11.1] +synonym: "protein kinase p58 activity" NARROW [EC:2.7.11.1] +synonym: "protein phosphokinase activity" NARROW [EC:2.7.11.1] +synonym: "protein serine kinase activity" NARROW [EC:2.7.11.1] +synonym: "protein serine-threonine kinase activity" EXACT [EC:2.7.11.1] +synonym: "protein-aspartyl kinase activity" RELATED [EC:2.7.11.1] +synonym: "protein-cysteine kinase activity" NARROW [EC:2.7.11.1] +synonym: "protein-serine kinase activity" NARROW [EC:2.7.11.1] +synonym: "Prp4 protein kinase activity" NARROW [EC:2.7.11.1] +synonym: "Raf kinase activity" NARROW [EC:2.7.11.1] +synonym: "Raf-1" RELATED [EC:2.7.11.1] +synonym: "ribosomal protein S6 kinase II activity" NARROW [EC:2.7.11.1] +synonym: "ribosomal S6 protein kinase activity" NARROW [EC:2.7.11.1] +synonym: "serine kinase activity" NARROW [EC:2.7.11.1] +synonym: "serine protein kinase activity" NARROW [EC:2.7.11.1] +synonym: "serine(threonine) protein kinase activity" EXACT [EC:2.7.11.1] +synonym: "serine-specific protein kinase activity" NARROW [EC:2.7.11.1] +synonym: "serine/threonine protein kinase activity" EXACT [EC:2.7.11.1] +synonym: "STK32" RELATED [EC:2.7.11.1] +synonym: "T-antigen kinase activity" NARROW [EC:2.7.11.1] +synonym: "threonine-specific protein kinase activity" NARROW [EC:2.7.11.1] +synonym: "twitchin kinase activity" NARROW [EC:2.7.11.1] +synonym: "Wee 1-like kinase activity" NARROW [EC:2.7.11.1] +synonym: "Wee-kinase activity" NARROW [EC:2.7.11.1] +synonym: "WEE1Hu" RELATED [EC:2.7.11.1] +xref: EC:2.7.11 +xref: Reactome:REACT_100117 "Phosphorylation of eIF2-alpha by PERK, Xenopus tropicalis" +xref: Reactome:REACT_100192 "AKT phosphorylates IKKalpha, Canis familiaris" +xref: Reactome:REACT_100209 "ERK1/2/5 activate RSK1/2/3, Canis familiaris" +xref: Reactome:REACT_100224 "Activation of cytosolic AMPK by phosphorylation, Bos taurus" +xref: Reactome:REACT_100446 "Activation of cytosolic AMPK by phosphorylation, Rattus norvegicus" +xref: Reactome:REACT_100588 "ERK5 activates the transcription factor MEF2, Xenopus tropicalis" +xref: Reactome:REACT_100590 "AKT phosphorylates IKKalpha, Xenopus tropicalis" +xref: Reactome:REACT_100784 "AKT phosphorylates IKKalpha, Rattus norvegicus" +xref: Reactome:REACT_100870 "Phospho-IKK Complex phosphorylates IkB within the IkB:NFkB Complex, Bos taurus" +xref: Reactome:REACT_100918 "Integrin alpha IIb beta3 T779 phosphorylation blocks SHC binding, Mus musculus" +xref: Reactome:REACT_100989 "Autophosphorylation of IRE1 dimer, Saccharomyces cerevisiae" +xref: Reactome:REACT_101264 "Phosphorylated MAPKs phosphorylate ATF-2, Sus scrofa" +xref: Reactome:REACT_101280 "Activation of claspin, Xenopus tropicalis" +xref: Reactome:REACT_101291 "Phospho-IKK Complex phosphorylates IkB within the IkB:NFkB Complex, Danio rerio" +xref: Reactome:REACT_101497 "Activation of claspin, Bos taurus" +xref: Reactome:REACT_101896 "ERK1/2 phosphorylates MSK1, Canis familiaris" +xref: Reactome:REACT_101920 "Inactivation of MEK1 by p34cdc2, Drosophila melanogaster" +xref: Reactome:REACT_101930 "Inactivation of MEK1 by p34cdc2, Caenorhabditis elegans" +xref: Reactome:REACT_102053 "MEK1 phosphorylates ERK-1, Saccharomyces cerevisiae" +xref: Reactome:REACT_102074 "AKT phosphorylates caspase-9, Mus musculus" +xref: Reactome:REACT_102078 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Canis familiaris" +xref: Reactome:REACT_102096 "Activation of cytosolic AMPK by phosphorylation, Gallus gallus" +xref: Reactome:REACT_102133 "Phosphorylated MAPKs phosphorylate ATF-2, Mus musculus" +xref: Reactome:REACT_102370 "AKT can phosphorylate NUR77, Mus musculus" +xref: Reactome:REACT_102455 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Canis familiaris" +xref: Reactome:REACT_102500 "AKT can phosphorylate RSK, Rattus norvegicus" +xref: Reactome:REACT_102718 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Bos taurus" +xref: Reactome:REACT_102778 "ERK1/2/5 activate RSK1/2/3, Gallus gallus" +xref: Reactome:REACT_102791 "Activation of NF-kB complex, Xenopus tropicalis" +xref: Reactome:REACT_102943 "Phosphorylated MAPKs phosphorylate ATF-2, Rattus norvegicus" +xref: Reactome:REACT_102975 "LIM kinase phosphorylation by ROCK, Danio rerio" +xref: Reactome:REACT_103109 "Phosphorylation of CRMPs by Cdk5, Xenopus tropicalis" +xref: Reactome:REACT_103162 "Myosin regulatory light chain phosphorylation by ROCK, Xenopus tropicalis" +xref: Reactome:REACT_103217 "Phosphorylation of PKC theta, Xenopus tropicalis" +xref: Reactome:REACT_103304 "Phosphorylation of FANCI by ATM/ATR, Danio rerio" +xref: Reactome:REACT_103449 "PDK1 phosphorylates AKT at T308, Caenorhabditis elegans" +xref: Reactome:REACT_103541 "Activated TAK1 mediates phosphorylation of the IKK Complex, Sus scrofa" +xref: Reactome:REACT_103596 "MEK1 phosphorylates ERK-1, Bos taurus" +xref: Reactome:REACT_103658 "Phosphorylation of MARCKS by Protein kinase C, alpha type, Bos taurus" +xref: Reactome:REACT_103882 "Phosphorylation of CRY and PER Proteins, Sus scrofa" +xref: Reactome:REACT_104102 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Mus musculus" +xref: Reactome:REACT_104121 "LIM kinase phosphorylation by ROCK, Drosophila melanogaster" +xref: Reactome:REACT_104145 "PDK1 phosphorylates AKT at T308, Canis familiaris" +xref: Reactome:REACT_104284 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Xenopus tropicalis" +xref: Reactome:REACT_104288 "Phosphorylation of FANCI by ATM/ATR, Drosophila melanogaster" +xref: Reactome:REACT_104416 "ERK1/2 activates ELK1, Canis familiaris" +xref: Reactome:REACT_104521 "MEK1 phosphorylates ERK-1, Mus musculus" +xref: Reactome:REACT_104525 "Phosphorylation of PKC theta, Taeniopygia guttata" +xref: Reactome:REACT_104547 "Recruitment and activation of Chk1, Gallus gallus" +xref: Reactome:REACT_104549 "Phosphorylation of Bcl10, Gallus gallus" +xref: Reactome:REACT_104564 "AKT phosphorylates caspase-9, Bos taurus" +xref: Reactome:REACT_104874 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Mus musculus" +xref: Reactome:REACT_104906 "Myosin regulatory light chain phosphorylation by ROCK, Mus musculus" +xref: Reactome:REACT_104932 "AKT can phosphorylate NUR77, Canis familiaris" +xref: Reactome:REACT_104985 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Rattus norvegicus" +xref: Reactome:REACT_105016 "p38MAPK phosphorylates MSK1, Saccharomyces cerevisiae" +xref: Reactome:REACT_105038 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Sus scrofa" +xref: Reactome:REACT_105077 "Phosphorylation of MARCKS by Protein kinase C, alpha type, Mus musculus" +xref: Reactome:REACT_105298 "Activation of IKK complex, Danio rerio" +xref: Reactome:REACT_105447 "Phosphorylation of CARMA1, Xenopus tropicalis" +xref: Reactome:REACT_105470 "Phosphorylation of FANCD2 by ATR/ATM, Gallus gallus" +xref: Reactome:REACT_105502 "AKT interacts and phosphorylates Cot, Taeniopygia guttata" +xref: Reactome:REACT_105534 "p38MAPK phosphorylates MSK1, Drosophila melanogaster" +xref: Reactome:REACT_105602 "MSK1 activates CREB, Sus scrofa" +xref: Reactome:REACT_105625 "AKT can phosphorylate forkhead box transcription factors, Canis familiaris" +xref: Reactome:REACT_105894 "PKA phosphorylates CREB, Canis familiaris" +xref: Reactome:REACT_106015 "Phosphorylation of Bcl10, Bos taurus" +xref: Reactome:REACT_106033 "ERK1/2/5 activate RSK1/2/3, Danio rerio" +xref: Reactome:REACT_106141 "AKT phosphorylates IKKalpha, Bos taurus" +xref: Reactome:REACT_106200 "PKA phosphorylates CREB, Danio rerio" +xref: Reactome:REACT_106255 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Mus musculus" +xref: Reactome:REACT_106263 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Bos taurus" +xref: Reactome:REACT_106338 "ERK1/2/5 activate RSK1/2/3, Xenopus tropicalis" +xref: Reactome:REACT_106350 "Phosphorylation of CRY and PER Proteins, Xenopus tropicalis" +xref: Reactome:REACT_106414 "CERT + ATP => monophospho-CERT + ADP, Taeniopygia guttata" +xref: Reactome:REACT_106418 "IRAK is activated, Canis familiaris" +xref: Reactome:REACT_106434 "Activation of claspin, Canis familiaris" +xref: Reactome:REACT_106501 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Canis familiaris" +xref: Reactome:REACT_106556 "Activation of TAK1-TAB2 complex, Xenopus tropicalis" +xref: Reactome:REACT_106557 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Taeniopygia guttata" +xref: Reactome:REACT_106566 "Phosphorylation of CARMA1, Rattus norvegicus" +xref: Reactome:REACT_106589 "MEK1 phosphorylates ERK-1, Schizosaccharomyces pombe" +xref: Reactome:REACT_106643 "Autophosphorylation of IRE1 dimer, Danio rerio" +xref: Reactome:REACT_106685 "Myosin regulatory light chain phosphorylation by ROCK, Rattus norvegicus" +xref: Reactome:REACT_106700 "AKT phosphorylates PRAS40, Rattus norvegicus" +xref: Reactome:REACT_106730 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Mus musculus" +xref: Reactome:REACT_106732 "Recruitment and activation of Chk1, Canis familiaris" +xref: Reactome:REACT_106789 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Rattus norvegicus" +xref: Reactome:REACT_106853 "Phosphorylation of MARCKS by Protein kinase C, alpha type, Rattus norvegicus" +xref: Reactome:REACT_106862 "Phosphorylation of MARCKS by Protein kinase C, alpha type, Xenopus tropicalis" +xref: Reactome:REACT_106985 "Phosphorylation of LIMK-1 by PAK, Danio rerio" +xref: Reactome:REACT_107087 "IKKbeta is activated, Bos taurus" +xref: Reactome:REACT_107170 "Phosphorylation of cofilin by LIMK-1, Canis familiaris" +xref: Reactome:REACT_107216 "MSK1 activates CREB, Rattus norvegicus" +xref: Reactome:REACT_107249 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Danio rerio" +xref: Reactome:REACT_107265 "Phosphorylation of eIF2-alpha by PERK, Bos taurus" +xref: Reactome:REACT_107488 "Phosphorylation of L1 by p90rsk, Gallus gallus" +xref: Reactome:REACT_107608 "Phosphorylation of CRMPs by GSK3beta, Sus scrofa" +xref: Reactome:REACT_107764 "Phospho-IKK Complex phosphorylates IkB within the IkB:NFkB Complex, Rattus norvegicus" +xref: Reactome:REACT_107768 "Transphosphorylation of pLIMK1, Mus musculus" +xref: Reactome:REACT_107779 "AKT phosphorylates p21Cip1 and p27Kip1, Rattus norvegicus" +xref: Reactome:REACT_107780 "TORC2 (mTOR) phosphorylates AKT at S473, Canis familiaris" +xref: Reactome:REACT_1078 "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP, Homo sapiens" +xref: Reactome:REACT_108016 "ALOX5 is phosphorylated by MAPKAP2, Gallus gallus" +xref: Reactome:REACT_108133 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Rattus norvegicus" +xref: Reactome:REACT_108154 "Phosphorylation of FANCD2 by ATR/ATM, Oryza sativa" +xref: Reactome:REACT_108328 "Phosphorylation of CRMPs by GSK3beta, Bos taurus" +xref: Reactome:REACT_108433 "Autophosphorylation of PAK, Taeniopygia guttata" +xref: Reactome:REACT_108435 "CERT + ATP => monophospho-CERT + ADP, Gallus gallus" +xref: Reactome:REACT_108461 "Recruitment and activation of Chk1, Bos taurus" +xref: Reactome:REACT_108511 "p38MAPK phosphorylates MSK1, Danio rerio" +xref: Reactome:REACT_108538 "MAPKAPK2 phosphorylates CREB at Serine 133, Sus scrofa" +xref: Reactome:REACT_108605 "PKA phosphorylates CREB, Mus musculus" +xref: Reactome:REACT_108670 "MEK2 phosphorylates ERK-2, Gallus gallus" +xref: Reactome:REACT_108671 "ALOX5 is phosphorylated by MAPKAP2, Mus musculus" +xref: Reactome:REACT_108839 "Transphosphorylation of pLIMK1, Dictyostelium discoideum" +xref: Reactome:REACT_108994 "Phosphorylation of cPLA2 by MAPK p38 alpha, Taeniopygia guttata" +xref: Reactome:REACT_109076 "MEK2 phosphorylates ERK-2, Danio rerio" +xref: Reactome:REACT_109135 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Taeniopygia guttata" +xref: Reactome:REACT_109768 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Rattus norvegicus" +xref: Reactome:REACT_109859 "p38MAPK phosphorylates MSK1, Mus musculus" +xref: Reactome:REACT_110031 "Phosphorylation of L1 by p90rsk, Danio rerio" +xref: Reactome:REACT_110083 "Autophosphorylation of PAK, Gallus gallus" +xref: Reactome:REACT_110087 "MAPKAPK2 phosphorylates CREB at Serine 133, Bos taurus" +xref: Reactome:REACT_110094 "AKT can phosphorylate RSK, Taeniopygia guttata" +xref: Reactome:REACT_110138 "Inactivation of MEK1 by p34cdc2, Taeniopygia guttata" +xref: Reactome:REACT_110166 "AKT can phosphorylate forkhead box transcription factors, Xenopus tropicalis" +xref: Reactome:REACT_110216 "ERK1/2 phosphorylates MSK1, Mus musculus" +xref: Reactome:REACT_110270 "Autophosphorylation of IRE1 dimer, Canis familiaris" +xref: Reactome:REACT_110312 "Phosphorylation of FANCI by ATM/ATR, Mus musculus" +xref: Reactome:REACT_110374 "Phosphorylated MAPKs phosphorylate ATF-2, Gallus gallus" +xref: Reactome:REACT_110431 "Phosphorylation of FANCD2 by ATR/ATM, Sus scrofa" +xref: Reactome:REACT_110457 "Myosin regulatory light chain phosphorylation by ROCK, Danio rerio" +xref: Reactome:REACT_110470 "Phosphorylation of L1 by p90rsk, Canis familiaris" +xref: Reactome:REACT_110479 "AKT phosphorylates TSC2, inhibiting it, Mus musculus" +xref: Reactome:REACT_110532 "Inactivation of MEK1 by p34cdc2, Danio rerio" +xref: Reactome:REACT_110554 "MEK1 phosphorylates ERK-1, Drosophila melanogaster" +xref: Reactome:REACT_110695 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Caenorhabditis elegans" +xref: Reactome:REACT_110719 "Phosphorylation of CARMA1, Gallus gallus" +xref: Reactome:REACT_110757 "Autophosphorylation of PAK, Rattus norvegicus" +xref: Reactome:REACT_110789 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Sus scrofa" +xref: Reactome:REACT_110890 "Phosphorylation of cPLA2 by MAPK p38 alpha, Danio rerio" +xref: Reactome:REACT_110921 "Activation of TAK1-TAB2 complex, Sus scrofa" +xref: Reactome:REACT_110930 "ERK1/2 phosphorylates MSK1, Saccharomyces cerevisiae" +xref: Reactome:REACT_111058 "Phosphorylation of Smad2 by Nodal Receptor, Homo sapiens" +xref: Reactome:REACT_111063 "SPRY2 is phosphorylated by phosphorylated MNK1, Homo sapiens" +xref: Reactome:REACT_111068 "ACVR2A/B (ActRIIA/B) Phosphorylates ACVR1B (ActRIB, ALK4) in Response to Activin, Homo sapiens" +xref: Reactome:REACT_111117 "p-MEK phosphorylates ERK, Homo sapiens" +xref: Reactome:REACT_111130 "Type II Activin Receptor (ActRIIB/ACVR2B) Phosphorylates Type I Activin Receptor (ActRIC/ACVR1C) in Response to NODAL, Homo sapiens" +xref: Reactome:REACT_111131 "Type II Activin Receptor (ActRII/ACVR2) Phosphorylates Type I Activin Receptor (ActRIB/ACVR1B) in Response to NODAL, Homo sapiens" +xref: Reactome:REACT_111138 "Phosphorylation of R-SMAD2/3 by NODAL Receptor, Homo sapiens" +xref: Reactome:REACT_111196 "PKC alpha interacts with and phosphorylates KIT, Homo sapiens" +xref: Reactome:REACT_11174 "Phosphorylation of Cyclin D1 on Thr-286 by GSK-3 beta, Mus musculus" +xref: Reactome:REACT_11183 "Activation of cytosolic AMPK by phosphorylation, Homo sapiens" +xref: Reactome:REACT_111939 "Activated TAK1 mediates phosphorylation of the IKK Complex, Xenopus tropicalis" +xref: Reactome:REACT_111972 "Autophosphorylation of IRE1 dimer, Arabidopsis thaliana" +xref: Reactome:REACT_112003 "Phosphorylation of PKC theta, Saccharomyces cerevisiae" +xref: Reactome:REACT_112061 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Schizosaccharomyces pombe" +xref: Reactome:REACT_112107 "AKT phosphorylates caspase-9, Gallus gallus" +xref: Reactome:REACT_112321 "Phosphorylation of L1 by p90rsk, Schizosaccharomyces pombe" +xref: Reactome:REACT_112392 "AKT phosphorylates FOXO1A, Canis familiaris" +xref: Reactome:REACT_112393 "AKT phosphorylates p21Cip1 and p27Kip1, Gallus gallus" +xref: Reactome:REACT_112404 "Inactivation of MEK1 by p34cdc2, Saccharomyces cerevisiae" +xref: Reactome:REACT_112488 "Inactivation of MEK1 by p34cdc2, Schizosaccharomyces pombe" +xref: Reactome:REACT_112501 "Phosphorylation of L1 by p90rsk, Saccharomyces cerevisiae" +xref: Reactome:REACT_112505 "TORC2 (mTOR) phosphorylates AKT at S473, Schizosaccharomyces pombe" +xref: Reactome:REACT_112514 "Activation of IKK complex, Xenopus tropicalis" +xref: Reactome:REACT_112516 "TORC2 (mTOR) phosphorylates AKT at S473, Saccharomyces cerevisiae" +xref: Reactome:REACT_112550 "AKT phosphorylates GSK3, Schizosaccharomyces pombe" +xref: Reactome:REACT_112561 "AKT phosphorylates FOXO1A, Bos taurus" +xref: Reactome:REACT_112583 "AKT phosphorylates GSK3, Gallus gallus" +xref: Reactome:REACT_112607 "AKT can phosphorylate RSK, Schizosaccharomyces pombe" +xref: Reactome:REACT_112628 "AKT phosphorylates FOXO1A, Taeniopygia guttata" +xref: Reactome:REACT_112928 "Autophosphorylation of IRE1 dimer, Xenopus tropicalis" +xref: Reactome:REACT_112965 "AKT can phosphorylate RSK, Saccharomyces cerevisiae" +xref: Reactome:REACT_113006 "ERK1/2 phosphorylates MSK1, Oryza sativa" +xref: Reactome:REACT_113045 "AKT phosphorylates FOXO1A, Drosophila melanogaster" +xref: Reactome:REACT_113059 "Autophosphorylation of IRE1 dimer, Dictyostelium discoideum" +xref: Reactome:REACT_113062 "CERT + ATP => monophospho-CERT + ADP, Sus scrofa" +xref: Reactome:REACT_113187 "ERK1/2 phosphorylates MSK1, Dictyostelium discoideum" +xref: Reactome:REACT_113199 "Activation of NF-kB complex, Taeniopygia guttata" +xref: Reactome:REACT_113389 "AKT phosphorylates FOXO1A, Mus musculus" +xref: Reactome:REACT_113424 "PDK1 phosphorylates AKT at T308, Gallus gallus" +xref: Reactome:REACT_113479 "ERK1/2 activates ELK1, Taeniopygia guttata" +xref: Reactome:REACT_113486 "AKT phosphorylates TSC2, inhibiting it, Gallus gallus" +xref: Reactome:REACT_113508 "AKT phosphorylates GSK3, Drosophila melanogaster" +xref: Reactome:REACT_113549 "ERK1/2/5 activate RSK1/2/3, Oryza sativa" +xref: Reactome:REACT_113560 "AKT interacts and phosphorylates Cot, Gallus gallus" +xref: Reactome:REACT_113575 "MEK1 phosphorylates ERK-1, Arabidopsis thaliana" +xref: Reactome:REACT_113600 "Phosphorylation of PKC theta, Schizosaccharomyces pombe" +xref: Reactome:REACT_113619 "PDK1 phosphorylates AKT at T308, Saccharomyces cerevisiae" +xref: Reactome:REACT_113634 "Activated TAK1 mediates phosphorylation of the IKK Complex, Drosophila melanogaster" +xref: Reactome:REACT_113693 "MEK1 phosphorylates ERK-1, Oryza sativa" +xref: Reactome:REACT_113717 "AKT can phosphorylate NUR77, Drosophila melanogaster" +xref: Reactome:REACT_113719 "ERK1/2 phosphorylates MSK1, Schizosaccharomyces pombe" +xref: Reactome:REACT_113729 "AKT phosphorylates TSC2, inhibiting it, Schizosaccharomyces pombe" +xref: Reactome:REACT_113732 "p38MAPK phosphorylates MSK1, Arabidopsis thaliana" +xref: Reactome:REACT_113744 "ERK1/2/5 activate RSK1/2/3, Schizosaccharomyces pombe" +xref: Reactome:REACT_113764 "Phosphorylation of cofilin by LIMK-1, Danio rerio" +xref: Reactome:REACT_113794 "Phospho-IKK Complex phosphorylates IkB within the IkB:NFkB Complex, Xenopus tropicalis" +xref: Reactome:REACT_113810 "Phosphorylation of Bcl10, Xenopus tropicalis" +xref: Reactome:REACT_113830 "MEK1 phosphorylates ERK-1, Dictyostelium discoideum" +xref: Reactome:REACT_113835 "Transphosphorylation of pLIMK1, Taeniopygia guttata" +xref: Reactome:REACT_113900 "CERT + ATP => monophospho-CERT + ADP, Caenorhabditis elegans" +xref: Reactome:REACT_113949 "p38MAPK phosphorylates MSK1, Schizosaccharomyces pombe" +xref: Reactome:REACT_114044 "Autophosphorylation of IRE1 dimer, Oryza sativa" +xref: Reactome:REACT_114079 "PDK1 phosphorylates AKT at T308, Schizosaccharomyces pombe" +xref: Reactome:REACT_114092 "AKT phosphorylates CREB, Gallus gallus" +xref: Reactome:REACT_114136 "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP, Caenorhabditis elegans" +xref: Reactome:REACT_114306 "ERK1/2 phosphorylates MSK1, Arabidopsis thaliana" +xref: Reactome:REACT_114321 "AKT phosphorylates IKKalpha, Gallus gallus" +xref: Reactome:REACT_114322 "AKT phosphorylates FOXO1A, Rattus norvegicus" +xref: Reactome:REACT_114335 "MSK1 activates CREB, Xenopus tropicalis" +xref: Reactome:REACT_114476 "p38MAPK phosphorylates MSK1, Dictyostelium discoideum" +xref: Reactome:REACT_114479 "AKT can phosphorylate NUR77, Caenorhabditis elegans" +xref: Reactome:REACT_114548 "AKT phosphorylates MDM2, Gallus gallus" +xref: Reactome:REACT_114581 "AKT can phosphorylate forkhead box transcription factors, Gallus gallus" +xref: Reactome:REACT_114650 "ERK1/2 phosphorylates MSK1, Xenopus tropicalis" +xref: Reactome:REACT_114660 "ERK1/2 activates ELK1, Xenopus tropicalis" +xref: Reactome:REACT_114718 "ERK1/2 activates ELK1, Caenorhabditis elegans" +xref: Reactome:REACT_114782 "ERK1/2/5 activate RSK1/2/3, Dictyostelium discoideum" +xref: Reactome:REACT_114835 "AKT can phosphorylate forkhead box transcription factors, Drosophila melanogaster" +xref: Reactome:REACT_114899 "MSK1 activates ATF1, Xenopus tropicalis" +xref: Reactome:REACT_114971 "Phosphorylation of MARCKS by Protein kinase C, alpha type, Drosophila melanogaster" +xref: Reactome:REACT_115073 "TORC2 (mTOR) phosphorylates AKT at S473, Gallus gallus" +xref: Reactome:REACT_115253 "p38MAPK phosphorylates MSK1, Xenopus tropicalis" +xref: Reactome:REACT_115290 "p38MAPK phosphorylates MSK1, Oryza sativa" +xref: Reactome:REACT_115293 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Saccharomyces cerevisiae" +xref: Reactome:REACT_115340 "AKT phosphorylates FOXO1A, Gallus gallus" +xref: Reactome:REACT_115364 "CERT + ATP => monophospho-CERT + ADP, Drosophila melanogaster" +xref: Reactome:REACT_115391 "ERK1/2/5 activate RSK1/2/3, Arabidopsis thaliana" +xref: Reactome:REACT_115462 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Caenorhabditis elegans" +xref: Reactome:REACT_115474 "AKT phosphorylates BAD, Xenopus tropicalis" +xref: Reactome:REACT_115576 "Phosphorylation of NBS1 by ATM, Gallus gallus" +xref: Reactome:REACT_115647 "Phosphorylation of FANCG at S7, Gallus gallus" +xref: Reactome:REACT_115840 "Phosphorylation of Chk1 by ATM upon DNA damage, Gallus gallus" +xref: Reactome:REACT_115981 "Phosphorylation of RPA2 by CDC2 kinase, Gallus gallus" +xref: Reactome:REACT_115987 "Phosphorylation of Chk1 by ATR, Gallus gallus" +xref: Reactome:REACT_116006 "PKA phosphorylates CREB, Rattus norvegicus" +xref: Reactome:REACT_116016 "Phosphorylation of Chk2 by ATM upon DNA damage, Gallus gallus" +xref: Reactome:REACT_116065 "Phosphorylation of USP8 by P-AKT, Homo sapiens" +xref: Reactome:REACT_1170 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Homo sapiens" +xref: Reactome:REACT_12032 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Homo sapiens" +xref: Reactome:REACT_12383 "AKT phosphorylates PRAS40, Homo sapiens" +xref: Reactome:REACT_12391 "TORC2 (mTOR) phosphorylates AKT at S473, Homo sapiens" +xref: Reactome:REACT_12395 "AKT phosphorylates caspase-9, Homo sapiens" +xref: Reactome:REACT_12399 "Activation of NF-kB complex, Homo sapiens" +xref: Reactome:REACT_12406 "ERK1/2 activates ELK1, Homo sapiens" +xref: Reactome:REACT_12413 "ERK5 activates the transcription factor MEF2, Homo sapiens" +xref: Reactome:REACT_12416 "ERK1/2 activates ELK1, Mus musculus" +xref: Reactome:REACT_12420 "AKT phosphorylates p21Cip1 and p27Kip1, Homo sapiens" +xref: Reactome:REACT_12429 "Akt1 phosphorylates GSK3, Rattus norvegicus" +xref: Reactome:REACT_12430 "AKT phosphorylates FOXO1A, Homo sapiens" +xref: Reactome:REACT_12437 "MSK1 activates ATF1, Homo sapiens" +xref: Reactome:REACT_12461 "AKT phosphorylates IKKalpha, Homo sapiens" +xref: Reactome:REACT_12485 "AKT can phosphorylate RSK, Homo sapiens" +xref: Reactome:REACT_12487 "ERK1/2/5 activate RSK1/2/3, Homo sapiens" +xref: Reactome:REACT_12518 "Activation of TAK1-TAB2 complex, Homo sapiens" +xref: Reactome:REACT_12532 "AKT phosphorylates TSC2, inhibiting it, Homo sapiens" +xref: Reactome:REACT_12537 "AKT phosphorylates MDM2, Homo sapiens" +xref: Reactome:REACT_12546 "p38MAPK phosphorylates MSK1, Homo sapiens" +xref: Reactome:REACT_12549 "AKT phosphorylates GSK3, Homo sapiens" +xref: Reactome:REACT_12557 "Phosphorylation of PKC theta, Homo sapiens" +xref: Reactome:REACT_12565 "AKT phosphorylates BAD, Homo sapiens" +xref: Reactome:REACT_12572 "AKT can phosphorylate forkhead box transcription factors, Homo sapiens" +xref: Reactome:REACT_12573 "Phosphorylation of CARMA1, Homo sapiens" +xref: Reactome:REACT_12576 "ERK1/2 phosphorylates MSK1, Homo sapiens" +xref: Reactome:REACT_12581 "Activation of IKK complex, Homo sapiens" +xref: Reactome:REACT_12584 "PDK1 phosphorylates AKT at T308, Homo sapiens" +xref: Reactome:REACT_12586 "MAPKAPK2 phosphorylates CREB at Serine 133, Homo sapiens" +xref: Reactome:REACT_12597 "AKT phosphorylates CREB, Homo sapiens" +xref: Reactome:REACT_12614 "AKT can phosphorylate NUR77, Homo sapiens" +xref: Reactome:REACT_12619 "Phosphorylation of Bcl10, Homo sapiens" +xref: Reactome:REACT_12622 "RSK1/2/3 phosphorylates CREB at Serine 133, Homo sapiens" +xref: Reactome:REACT_12625 "ERK5 activates the transcription factor MEF2, Rattus norvegicus" +xref: Reactome:REACT_12631 "MSK1 activates CREB, Homo sapiens" +xref: Reactome:REACT_13421 "Irak is activated, Rattus norvegicus" +xref: Reactome:REACT_13502 "IKKbeta phosphorylates IkB causing NF-kB to dissociate, Homo sapiens" +xref: Reactome:REACT_136 "MEK1 phosphorylates ERK-1, Homo sapiens" +xref: Reactome:REACT_13726 "IKKbeta is activated, Homo sapiens" +xref: Reactome:REACT_13775 "IRAK is activated, Homo sapiens" +xref: Reactome:REACT_1469 "perilipin + 3 ATP -> phosphorylated perilipin + 3 ADP, Rattus norvegicus" +xref: Reactome:REACT_15377 "PKA phosphorylates CREB, Homo sapiens" +xref: Reactome:REACT_1621 "perilipin + 3 ATP -> phosphorylated perilipin + 3 ADP, Mus musculus" +xref: Reactome:REACT_1734 "perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP, Homo sapiens" +xref: Reactome:REACT_18263 "Phosphorylation of MARCKS by Protein kinase C, alpha type, Homo sapiens" +xref: Reactome:REACT_18275 "Phosphorylation of eIF2-alpha by PERK, Homo sapiens" +xref: Reactome:REACT_18293 "Phosphorylation of FANCD2 by ATR/ATM, Homo sapiens" +xref: Reactome:REACT_18335 "Phosphorylation of FANCI by ATM/ATR, Homo sapiens" +xref: Reactome:REACT_1836 "Inactivation of MEK1 by p34cdc2, Homo sapiens" +xref: Reactome:REACT_18399 "Autophosphorylation of IRE1 dimer, Homo sapiens" +xref: Reactome:REACT_19152 "CERT + ATP => monophospho-CERT + ADP, Homo sapiens" +xref: Reactome:REACT_19154 "Myosin regulatory light chain phosphorylation by Rock2, Gallus gallus" +xref: Reactome:REACT_19156 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Homo sapiens" +xref: Reactome:REACT_19168 "Transphosphorylation of pLIMK1, Homo sapiens" +xref: Reactome:REACT_19191 "Myosin regulatory light chain phosphorylation by ROCK, Homo sapiens" +xref: Reactome:REACT_19197 "Autophosphorylation of PAK, Homo sapiens" +xref: Reactome:REACT_19221 "Phosphorylation of LIMK-1 by PAK, Homo sapiens" +xref: Reactome:REACT_19232 "AKT interacts and phosphorylates Cot, Homo sapiens" +xref: Reactome:REACT_19276 "Phosphorylation of cofilin by LIMK-1, Homo sapiens" +xref: Reactome:REACT_19282 "LIM kinase phosphorylation by ROCK, Homo sapiens" +xref: Reactome:REACT_19285 "Phosphorylation of CRMPs by Cdk5, Homo sapiens" +xref: Reactome:REACT_19311 "ROCK1 activates LIM kinase 2 (rat), Homo sapiens" +xref: Reactome:REACT_19321 "Phosphorylation of CRMPs by GSK3beta, Homo sapiens" +xref: Reactome:REACT_19361 "Phosphorylation of cofilin by LIMK-1, Mus musculus" +xref: Reactome:REACT_20541 "Phosphorylation of cPLA2 by MAPK p38 alpha, Homo sapiens" +xref: Reactome:REACT_21251 "c-FOS activation by phospho ERK1/2, Homo sapiens" +xref: Reactome:REACT_21276 "Phosphorylation of MEF2 proteins by p38, Homo sapiens" +xref: Reactome:REACT_21321 "Phosphorylation of E proteins by p38 MAPK, Homo sapiens" +xref: Reactome:REACT_21334 "Phosphorylation of E47 by p38 MAPK, Mus musculus" +xref: Reactome:REACT_21338 "activated human TAK1 phosphorylates MKK3/MKK6, Homo sapiens" +xref: Reactome:REACT_21367 "Activated TAK1 phosphorylates MKK4/MKK7, Homo sapiens" +xref: Reactome:REACT_21375 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Homo sapiens" +xref: Reactome:REACT_22101 "Phosphorylation of L1 by p90rsk, Homo sapiens" +xref: Reactome:REACT_22105 "ALOX5 is phosphorylated by MAPKAP2, Homo sapiens" +xref: Reactome:REACT_22125 "IRAK4 phosphorylates IRAK1, Homo sapiens" +xref: Reactome:REACT_22162 "IRAK4-activated IRAK1 autophosphorylates, Homo sapiens" +xref: Reactome:REACT_22240 "Phosphorylation of L1 by p90rsk, Homo sapiens" +xref: Reactome:REACT_22325 "IRAK1 and 4 can phosphorylate Pellino-1 and 2., Homo sapiens" +xref: Reactome:REACT_22371 "Interaction of PAK1 with Rac1-GTP, Homo sapiens" +xref: Reactome:REACT_2247 "MEK2 phosphorylates ERK-2, Homo sapiens" +xref: Reactome:REACT_23849 "PKA/PKG phosphorylate Rap1GAP2, Homo sapiens" +xref: Reactome:REACT_24004 "Integrin alpha IIb beta3 T779 phosphorylation blocks SHC binding, Homo sapiens" +xref: Reactome:REACT_24917 "Phosphorylation of MKK4 by activated TAK1, Gallus gallus" +xref: Reactome:REACT_24948 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Homo sapiens" +xref: Reactome:REACT_24965 "Phosphorylation of KSRP by MAP kinase p38, Homo sapiens" +xref: Reactome:REACT_25002 "Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomer:activated TLR 7/8 or 9, Homo sapiens" +xref: Reactome:REACT_25011 "IRAK4 autophosphorylation in the complex with MyD88:activated TLR 7/8 or 9, Homo sapiens" +xref: Reactome:REACT_25016 "Phosphorylation of HuR by PKCalpha, Homo sapiens" +xref: Reactome:REACT_25040 "Activation of recruited TAK1, Gallus gallus" +xref: Reactome:REACT_25086 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Homo sapiens" +xref: Reactome:REACT_25096 "activated MEK2 phosphorylates ERK2, Gallus gallus" +xref: Reactome:REACT_25097 "IRAK4 autophosphorylation in the complex with activated TLR:MyD88:Mal, Homo sapiens" +xref: Reactome:REACT_25125 "Phosphorylation of CRY and PER Proteins, Homo sapiens" +xref: Reactome:REACT_25161 "phosphorylation of IRAK2 by activated IRAK4, Gallus gallus" +xref: Reactome:REACT_25171 "Phosphorylation of Tristetraproline (TTP) by MK2, Homo sapiens" +xref: Reactome:REACT_25174 "Phosphorylation of IKKs complex by activated TAK1, Gallus gallus" +xref: Reactome:REACT_25184 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Homo sapiens" +xref: Reactome:REACT_25187 "Phosphorylation of KSRP by Protein Kinase B/Akt, Homo sapiens" +xref: Reactome:REACT_25189 "chicken RIP1 facilitates IKKs complex activation, Gallus gallus" +xref: Reactome:REACT_25202 "Phosphorylation of HuR by PKCdelta, Homo sapiens" +xref: Reactome:REACT_25204 "activated IKKs phosphorylates IkB alpha causing the NFkB complex to dissociate from the phospho-IkB, Gallus gallus" +xref: Reactome:REACT_25231 "Phosphorylation of IRF3 by IKK epsilon(IKBKE) complexed with activated TLR3., Gallus gallus" +xref: Reactome:REACT_25285 "Phosphorylation of BRF1 by MK2, Homo sapiens" +xref: Reactome:REACT_25288 "Activation of TAK1 complex bound to activated TLR4:TRAM:TRIF:pUb-TRAF6, Homo sapiens" +xref: Reactome:REACT_25307 "Activation of recruited TAK1 within the complex p-IRAK2: pUb-TRAF6:TAB2/TAB3:TAB1:TAK1, Gallus gallus" +xref: Reactome:REACT_25326 "Phosphorylation of Khsrp by p38 (mouse), Mus musculus" +xref: Reactome:REACT_25335 "Phosphorylation of BRF1 by Protein Kinase B/Akt, Homo sapiens" +xref: Reactome:REACT_25346 "Phosphorylation of IRF3 by TBK1 complexed with activated TLR3, Gallus gallus" +xref: Reactome:REACT_25356 "Phosphorylation of Cry and Per Proteins, Mus musculus" +xref: Reactome:REACT_25369 "Phosphorylation of STAT1 at Ser727, Homo sapiens" +xref: Reactome:REACT_25375 "Auto phosphorylation of TAK1 bound to p-IRAK2:pUb oligo-TRAF6: free K63 pUb:TAB1:TAB2/TAB3, Homo sapiens" +xref: Reactome:REACT_25376 "Phosphorylation of MKK3/MKK6 by activated TAK1, Gallus gallus" +xref: Reactome:REACT_25384 "Activation of JNK by DSCAM, Homo sapiens" +xref: Reactome:REACT_25394 "Autophosphorylation of chicken IRAK4, Gallus gallus" +xref: Reactome:REACT_27158 "IRAK4 binds to activated TLR5 or 15., Gallus gallus" +xref: Reactome:REACT_27180 "IRAK4 autophosphorylation within the complex activated TLR:MyD88, Homo sapiens" +xref: Reactome:REACT_27211 "Activation of recruited TAK1 within the complex p-IRAK2: pUb-TRAF6:TAB2/TAB3:TAB1:TAK1 upon TLR7 or 21 stimulation, Gallus gallus" +xref: Reactome:REACT_27238 "IRAK2 phosphorylation bound to the activated TLR7 (or TLR21) complex, Gallus gallus" +xref: Reactome:REACT_27261 "Autophosphorylation of IRAK4 bound to the activated TLR7 or 21complex., Gallus gallus" +xref: Reactome:REACT_27299 "Activated IRAK4 bound to activated TLR : MyD88 complex phosphorylates IRAK2, Gallus gallus" +xref: Reactome:REACT_28085 "AKT phosphorylates caspase-9, Taeniopygia guttata" +xref: Reactome:REACT_28092 "Phospho-IKK Complex phosphorylates IkB within the IkB:NFkB Complex, Sus scrofa" +xref: Reactome:REACT_28112 "MSK1 activates CREB, Gallus gallus" +xref: Reactome:REACT_28138 "Activation of cytosolic AMPK by phosphorylation, Danio rerio" +xref: Reactome:REACT_28220 "perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP, Sus scrofa" +xref: Reactome:REACT_28367 "AKT phosphorylates caspase-9, Rattus norvegicus" +xref: Reactome:REACT_28572 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Rattus norvegicus" +xref: Reactome:REACT_28620 "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP, Canis familiaris" +xref: Reactome:REACT_28729 "Activation of TAK1-TAB2 complex, Gallus gallus" +xref: Reactome:REACT_28738 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Drosophila melanogaster" +xref: Reactome:REACT_28805 "ERK1/2 activates ELK1, Danio rerio" +xref: Reactome:REACT_28809 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Sus scrofa" +xref: Reactome:REACT_28822 "MEK2 phosphorylates ERK-2, Mus musculus" +xref: Reactome:REACT_28827 "LIM kinase phosphorylation by ROCK, Canis familiaris" +xref: Reactome:REACT_28936 "Activation of NF-kB complex, Bos taurus" +xref: Reactome:REACT_29008 "Phosphorylation of FANCI by ATM/ATR, Oryza sativa" +xref: Reactome:REACT_29035 "IKKbeta phosphorylates IkB causing NF-kB to dissociate, Mus musculus" +xref: Reactome:REACT_29159 "RSK1/2/3 phosphorylates CREB at Serine 133, Canis familiaris" +xref: Reactome:REACT_29403 "Phosphorylation of cPLA2 by MAPK p38 alpha, Gallus gallus" +xref: Reactome:REACT_29503 "Phosphorylation of PKC theta, Caenorhabditis elegans" +xref: Reactome:REACT_29509 "AKT phosphorylates p21Cip1 and p27Kip1, Mus musculus" +xref: Reactome:REACT_29530 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Mus musculus" +xref: Reactome:REACT_29733 "Phosphorylation of FANCI by ATM/ATR, Taeniopygia guttata" +xref: Reactome:REACT_29781 "Phosphorylation of eIF2-alpha by PERK, Taeniopygia guttata" +xref: Reactome:REACT_29936 "Phosphorylation of CRY and PER Proteins, Danio rerio" +xref: Reactome:REACT_29959 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Canis familiaris" +xref: Reactome:REACT_29999 "AKT interacts and phosphorylates Cot, Bos taurus" +xref: Reactome:REACT_30143 "Inactivation of MEK1 by p34cdc2, Bos taurus" +xref: Reactome:REACT_30149 "Activation of claspin, Rattus norvegicus" +xref: Reactome:REACT_30175 "Phosphorylation of FANCI by ATM/ATR, Sus scrofa" +xref: Reactome:REACT_30231 "AKT phosphorylates MDM2, Bos taurus" +xref: Reactome:REACT_30415 "Phospho-IKK Complex phosphorylates IkB within the IkB:NFkB Complex, Canis familiaris" +xref: Reactome:REACT_30432 "Autophosphorylation of IRE1 dimer, Drosophila melanogaster" +xref: Reactome:REACT_30441 "LIM kinase phosphorylation by ROCK, Taeniopygia guttata" +xref: Reactome:REACT_30475 "Activation of cytosolic AMPK by phosphorylation, Taeniopygia guttata" +xref: Reactome:REACT_30512 "ERK1/2/5 activate RSK1/2/3, Rattus norvegicus" +xref: Reactome:REACT_30534 "Phosphorylation of FANCD2 by ATR/ATM, Taeniopygia guttata" +xref: Reactome:REACT_30570 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Xenopus tropicalis" +xref: Reactome:REACT_30575 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Rattus norvegicus" +xref: Reactome:REACT_30766 "MEK1 phosphorylates ERK-1, Canis familiaris" +xref: Reactome:REACT_30848 "ERK1/2/5 activate RSK1/2/3, Sus scrofa" +xref: Reactome:REACT_31008 "Phosphorylation of FANCI by ATM/ATR, Canis familiaris" +xref: Reactome:REACT_31108 "MAPKAPK2 phosphorylates CREB at Serine 133, Xenopus tropicalis" +xref: Reactome:REACT_31283 "Activation of cytosolic AMPK by phosphorylation, Canis familiaris" +xref: Reactome:REACT_31328 "IKKbeta phosphorylates IkB causing NF-kB to dissociate, Bos taurus" +xref: Reactome:REACT_31357 "Inactivation of MEK1 by p34cdc2, Gallus gallus" +xref: Reactome:REACT_31513 "Activation of cytosolic AMPK by phosphorylation, Caenorhabditis elegans" +xref: Reactome:REACT_31523 "Phosphorylation of PKC theta, Mus musculus" +xref: Reactome:REACT_31662 "Phosphorylation of cPLA2 by MAPK p38 alpha, Canis familiaris" +xref: Reactome:REACT_31760 "AKT phosphorylates caspase-9, Xenopus tropicalis" +xref: Reactome:REACT_31783 "Phosphorylation of FANCI by ATM/ATR, Arabidopsis thaliana" +xref: Reactome:REACT_31812 "AKT phosphorylates PRAS40, Canis familiaris" +xref: Reactome:REACT_31857 "Phosphorylation of MARCKS by Protein kinase C, alpha type, Danio rerio" +xref: Reactome:REACT_31893 "IKKbeta is activated, Sus scrofa" +xref: Reactome:REACT_32225 "Phosphorylation of Bcl10, Taeniopygia guttata" +xref: Reactome:REACT_32250 "AKT phosphorylates caspase-9, Canis familiaris" +xref: Reactome:REACT_32384 "Activated TAK1 mediates phosphorylation of the IKK Complex, Bos taurus" +xref: Reactome:REACT_32525 "AKT phosphorylates p21Cip1 and p27Kip1, Bos taurus" +xref: Reactome:REACT_32572 "Activated TAK1 mediates phosphorylation of the IKK Complex, Rattus norvegicus" +xref: Reactome:REACT_32621 "TORC2 (mTOR) phosphorylates AKT at S473, Bos taurus" +xref: Reactome:REACT_32932 "Recruitment and activation of Chk1, Taeniopygia guttata" +xref: Reactome:REACT_32954 "Phosphorylation of eIF2-alpha by PERK, Drosophila melanogaster" +xref: Reactome:REACT_32974 "AKT phosphorylates IKKalpha, Taeniopygia guttata" +xref: Reactome:REACT_33231 "Phosphorylation of cPLA2 by MAPK p38 alpha, Rattus norvegicus" +xref: Reactome:REACT_33306 "p38MAPK phosphorylates MSK1, Rattus norvegicus" +xref: Reactome:REACT_33413 "IKKbeta is activated, Danio rerio" +xref: Reactome:REACT_33562 "Phosphorylation of L1 by p90rsk, Taeniopygia guttata" +xref: Reactome:REACT_33594 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Taeniopygia guttata" +xref: Reactome:REACT_33640 "Phosphorylation of CRY and PER Proteins, Canis familiaris" +xref: Reactome:REACT_33709 "Phosphorylation of eIF2-alpha by PERK, Rattus norvegicus" +xref: Reactome:REACT_33874 "Recruitment and activation of Chk1, Xenopus tropicalis" +xref: Reactome:REACT_33935 "perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP, Canis familiaris" +xref: Reactome:REACT_33943 "PDK1 phosphorylates AKT at T308, Taeniopygia guttata" +xref: Reactome:REACT_34025 "IKKbeta is activated, Rattus norvegicus" +xref: Reactome:REACT_34068 "AKT interacts and phosphorylates Cot, Canis familiaris" +xref: Reactome:REACT_34104 "RSK1/2/3 phosphorylates CREB at Serine 133, Sus scrofa" +xref: Reactome:REACT_34451 "Activation of cytosolic AMPK by phosphorylation, Sus scrofa" +xref: Reactome:REACT_34455 "MEK1 phosphorylates ERK-1, Rattus norvegicus" +xref: Reactome:REACT_34482 "MAPKAPK2 phosphorylates CREB at Serine 133, Danio rerio" +xref: Reactome:REACT_34576 "Phosphorylation of CRY and PER Proteins, Bos taurus" +xref: Reactome:REACT_34701 "AKT can phosphorylate RSK, Bos taurus" +xref: Reactome:REACT_34785 "IKKbeta phosphorylates IkB causing NF-kB to dissociate, Canis familiaris" +xref: Reactome:REACT_38602 "AKT phosphorylates IKKalpha, Mus musculus" +xref: Reactome:REACT_388 "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP, Rattus norvegicus" +xref: Reactome:REACT_40374 "MSK1 activates ATF1, Gallus gallus" +xref: Reactome:REACT_51458 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Gallus gallus" +xref: Reactome:REACT_51558 "AKT can phosphorylate forkhead box transcription factors, Mus musculus" +xref: Reactome:REACT_53247 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Gallus gallus" +xref: Reactome:REACT_54933 "CERT + ATP => monophospho-CERT + ADP, Rattus norvegicus" +xref: Reactome:REACT_60400 "AKT phosphorylates GSK3, Bos taurus" +xref: Reactome:REACT_6197 "Activated DAkt1 phosphorylates TSC2 which inhibits the TSC1/2 complex, Drosophila melanogaster" +xref: Reactome:REACT_6263 "DAkt1-mediated phosphorylation inactivates DFOXO, Drosophila melanogaster" +xref: Reactome:REACT_62985 "Phospho-IKK Complex phosphorylates IkB within the IkB:NFkB Complex, Mus musculus" +xref: Reactome:REACT_6719 "Phosphorylated MAPKs phosphorylate ATF-2, Homo sapiens" +xref: Reactome:REACT_6728 "Phosphorylation of IRF-3/IRF7 and their release from the activated TLR4 complex, Homo sapiens" +xref: Reactome:REACT_6730 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Homo sapiens" +xref: Reactome:REACT_6750 "Activation of claspin, Homo sapiens" +xref: Reactome:REACT_6794 "Second phosphorylation of IRAK1 by IRAK4 bound to activated TLR:MyD88:Mal, Homo sapiens" +xref: Reactome:REACT_6833 "First phosphorylation of IRAK1 by IRAK4 bound to activated TLR:MyD88:Mal, Homo sapiens" +xref: Reactome:REACT_6848 "Phospho-IKK Complex phosphorylates IkB within the IkB:NFkB Complex, Homo sapiens" +xref: Reactome:REACT_6869 "Recruitment and activation of Chk1, Homo sapiens" +xref: Reactome:REACT_69155 "Integrin alpha IIb beta3 T779 phosphorylation blocks SHC binding, Canis familiaris" +xref: Reactome:REACT_6935 "Activated TAK1 mediates phosphorylation of the IKK Complex, Homo sapiens" +xref: Reactome:REACT_75759 "Atr Phosphorylates Histone H2A.X at Unsynapsed Regions, Mus musculus" +xref: Reactome:REACT_75904 "ATR Phosphorylates Histone H2A.X at Unsynapsed Regions, Homo sapiens" +xref: Reactome:REACT_75910 "SMG1 Phosphorylates UPF1 (Enhanced by Exon Junction Complex), Homo sapiens" +xref: Reactome:REACT_77037 "LIM kinase phosphorylation by ROCK, Gallus gallus" +xref: Reactome:REACT_77098 "Phosphorylation of cPLA2 by MAPK p38 alpha, Xenopus tropicalis" +xref: Reactome:REACT_77159 "ALOX5 is phosphorylated by MAPKAP2, Danio rerio" +xref: Reactome:REACT_77220 "ERK1/2 activates ELK1, Rattus norvegicus" +xref: Reactome:REACT_77282 "AKT can phosphorylate NUR77, Xenopus tropicalis" +xref: Reactome:REACT_77423 "AKT phosphorylates TSC2, inhibiting it, Drosophila melanogaster" +xref: Reactome:REACT_77580 "Phosphorylation of MARCKS by Protein kinase C, alpha type, Sus scrofa" +xref: Reactome:REACT_77617 "AKT phosphorylates MDM2, Taeniopygia guttata" +xref: Reactome:REACT_77748 "Myosin regulatory light chain phosphorylation by ROCK, Bos taurus" +xref: Reactome:REACT_77752 "perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP, Danio rerio" +xref: Reactome:REACT_77909 "PKA phosphorylates CREB, Taeniopygia guttata" +xref: Reactome:REACT_77980 "AKT phosphorylates MDM2, Xenopus tropicalis" +xref: Reactome:REACT_78070 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Drosophila melanogaster" +xref: Reactome:REACT_78202 "AKT phosphorylates BAD, Mus musculus" +xref: Reactome:REACT_78246 "Phosphorylation of CRMPs by GSK3beta, Canis familiaris" +xref: Reactome:REACT_78283 "MSK1 activates ATF1, Bos taurus" +xref: Reactome:REACT_78357 "Inactivation of MEK1 by p34cdc2, Rattus norvegicus" +xref: Reactome:REACT_78364 "Phosphorylation of LIMK-1 by PAK, Taeniopygia guttata" +xref: Reactome:REACT_78401 "MEK1 phosphorylates ERK-1, Danio rerio" +xref: Reactome:REACT_78606 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Canis familiaris" +xref: Reactome:REACT_78657 "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP, Bos taurus" +xref: Reactome:REACT_78797 "Phosphorylation of PKC theta, Danio rerio" +xref: Reactome:REACT_78839 "MEK2 phosphorylates ERK-2, Bos taurus" +xref: Reactome:REACT_78999 "TORC2 (mTOR) phosphorylates AKT at S473, Mus musculus" +xref: Reactome:REACT_79009 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Xenopus tropicalis" +xref: Reactome:REACT_79017 "IRAK is activated, Bos taurus" +xref: Reactome:REACT_79041 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Taeniopygia guttata" +xref: Reactome:REACT_79081 "Autophosphorylation of IRE1 dimer, Caenorhabditis elegans" +xref: Reactome:REACT_79082 "Phosphorylation of CRMPs by Cdk5, Danio rerio" +xref: Reactome:REACT_79223 "Activation of IKK complex, Canis familiaris" +xref: Reactome:REACT_79270 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Mus musculus" +xref: Reactome:REACT_79290 "MSK1 activates ATF1, Canis familiaris" +xref: Reactome:REACT_79294 "Autophosphorylation of PAK, Canis familiaris" +xref: Reactome:REACT_79368 "Phosphorylated MAPKs phosphorylate ATF-2, Xenopus tropicalis" +xref: Reactome:REACT_79396 "AKT phosphorylates CREB, Xenopus tropicalis" +xref: Reactome:REACT_79454 "AKT phosphorylates p21Cip1 and p27Kip1, Xenopus tropicalis" +xref: Reactome:REACT_79465 "Phosphorylation of cofilin by LIMK-1, Dictyostelium discoideum" +xref: Reactome:REACT_79487 "MEK1 phosphorylates ERK-1, Caenorhabditis elegans" +xref: Reactome:REACT_79578 "AKT can phosphorylate NUR77, Taeniopygia guttata" +xref: Reactome:REACT_79606 "Phosphorylation of FANCD2 by ATR/ATM, Bos taurus" +xref: Reactome:REACT_79732 "AKT phosphorylates p21Cip1 and p27Kip1, Canis familiaris" +xref: Reactome:REACT_79796 "p38MAPK phosphorylates MSK1, Bos taurus" +xref: Reactome:REACT_79838 "Activation of TAK1-TAB2 complex, Rattus norvegicus" +xref: Reactome:REACT_79875 "LIM kinase phosphorylation by ROCK, Xenopus tropicalis" +xref: Reactome:REACT_79905 "TORC2 (mTOR) phosphorylates AKT at S473, Drosophila melanogaster" +xref: Reactome:REACT_80036 "Phosphorylation of FANCI by ATM/ATR, Gallus gallus" +xref: Reactome:REACT_80060 "PKA phosphorylates CREB, Xenopus tropicalis" +xref: Reactome:REACT_80149 "Phosphorylation of FANCD2 by ATR/ATM, Caenorhabditis elegans" +xref: Reactome:REACT_80188 "p38MAPK phosphorylates MSK1, Sus scrofa" +xref: Reactome:REACT_80214 "AKT phosphorylates TSC2, inhibiting it, Canis familiaris" +xref: Reactome:REACT_80294 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Xenopus tropicalis" +xref: Reactome:REACT_80369 "Activation of NF-kB complex, Rattus norvegicus" +xref: Reactome:REACT_80488 "AKT phosphorylates p21Cip1 and p27Kip1, Taeniopygia guttata" +xref: Reactome:REACT_80566 "RSK1/2/3 phosphorylates CREB at Serine 133, Rattus norvegicus" +xref: Reactome:REACT_80571 "Activation of claspin, Mus musculus" +xref: Reactome:REACT_80638 "MSK1 activates ATF1, Rattus norvegicus" +xref: Reactome:REACT_80833 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Bos taurus" +xref: Reactome:REACT_80847 "perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP, Bos taurus" +xref: Reactome:REACT_80870 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Bos taurus" +xref: Reactome:REACT_80884 "Inactivation of MEK1 by p34cdc2, Xenopus tropicalis" +xref: Reactome:REACT_80885 "Phosphorylation of CARMA1, Danio rerio" +xref: Reactome:REACT_80896 "Recruitment and activation of Chk1, Sus scrofa" +xref: Reactome:REACT_80942 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Canis familiaris" +xref: Reactome:REACT_80981 "Autophosphorylation of PAK, Danio rerio" +xref: Reactome:REACT_80994 "ALOX5 is phosphorylated by MAPKAP2, Xenopus tropicalis" +xref: Reactome:REACT_81006 "Phosphorylated MAPKs phosphorylate ATF-2, Taeniopygia guttata" +xref: Reactome:REACT_81015 "Autophosphorylation of PAK, Mus musculus" +xref: Reactome:REACT_81028 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Mus musculus" +xref: Reactome:REACT_81170 "Phosphorylation of CARMA1, Bos taurus" +xref: Reactome:REACT_81226 "AKT phosphorylates BAD, Bos taurus" +xref: Reactome:REACT_81279 "Activation of TAK1-TAB2 complex, Mus musculus" +xref: Reactome:REACT_81426 "Autophosphorylation of IRE1 dimer, Schizosaccharomyces pombe" +xref: Reactome:REACT_81514 "perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP, Taeniopygia guttata" +xref: Reactome:REACT_81917 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Gallus gallus" +xref: Reactome:REACT_81999 "CERT + ATP => monophospho-CERT + ADP, Mus musculus" +xref: Reactome:REACT_82094 "AKT can phosphorylate RSK, Canis familiaris" +xref: Reactome:REACT_82308 "AKT phosphorylates TSC2, inhibiting it, Taeniopygia guttata" +xref: Reactome:REACT_82341 "MEK2 phosphorylates ERK-2, Sus scrofa" +xref: Reactome:REACT_82426 "Phosphorylation of CRMPs by GSK3beta, Xenopus tropicalis" +xref: Reactome:REACT_82465 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Sus scrofa" +xref: Reactome:REACT_82486 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Danio rerio" +xref: Reactome:REACT_82487 "Transphosphorylation of pLIMK1, Gallus gallus" +xref: Reactome:REACT_82570 "Autophosphorylation of IRE1 dimer, Gallus gallus" +xref: Reactome:REACT_82577 "Phosphorylation of FANCD2 by ATR/ATM, Danio rerio" +xref: Reactome:REACT_82668 "AKT phosphorylates CREB, Taeniopygia guttata" +xref: Reactome:REACT_82929 "Phosphorylated MAPKs phosphorylate ATF-2, Canis familiaris" +xref: Reactome:REACT_82960 "Activation of IKK complex, Rattus norvegicus" +xref: Reactome:REACT_82976 "ALOX5 is phosphorylated by MAPKAP2, Canis familiaris" +xref: Reactome:REACT_82982 "PDK1 phosphorylates AKT at T308, Bos taurus" +xref: Reactome:REACT_83066 "ERK1/2/5 activate RSK1/2/3, Bos taurus" +xref: Reactome:REACT_83075 "Phosphorylation of CARMA1, Taeniopygia guttata" +xref: Reactome:REACT_83134 "IKKbeta phosphorylates IkB causing NF-kB to dissociate, Rattus norvegicus" +xref: Reactome:REACT_83280 "AKT can phosphorylate NUR77, Bos taurus" +xref: Reactome:REACT_83306 "RSK1/2/3 phosphorylates CREB at Serine 133, Gallus gallus" +xref: Reactome:REACT_83327 "Autophosphorylation of PAK, Sus scrofa" +xref: Reactome:REACT_83341 "Phosphorylation of cPLA2 by MAPK p38 alpha, Mus musculus" +xref: Reactome:REACT_83437 "AKT phosphorylates BAD, Rattus norvegicus" +xref: Reactome:REACT_83704 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Sus scrofa" +xref: Reactome:REACT_83820 "Integrin alpha IIb beta3 T779 phosphorylation blocks SHC binding, Rattus norvegicus" +xref: Reactome:REACT_83896 "Phosphorylation of LIMK-1 by PAK, Canis familiaris" +xref: Reactome:REACT_83924 "Phosphorylation of CRMPs by Cdk5, Canis familiaris" +xref: Reactome:REACT_83927 "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP, Sus scrofa" +xref: Reactome:REACT_84390 "Phosphorylation of LIMK-1 by PAK, Rattus norvegicus" +xref: Reactome:REACT_84454 "Phosphorylation of LIMK-1 by PAK, Gallus gallus" +xref: Reactome:REACT_84496 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Sus scrofa" +xref: Reactome:REACT_84727 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Xenopus tropicalis" +xref: Reactome:REACT_84803 "Phosphorylation of CRMPs by GSK3beta, Rattus norvegicus" +xref: Reactome:REACT_84957 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Xenopus tropicalis" +xref: Reactome:REACT_84970 "AKT phosphorylates IKKalpha, Drosophila melanogaster" +xref: Reactome:REACT_85026 "Inactivation of MEK1 by p34cdc2, Mus musculus" +xref: Reactome:REACT_85069 "Phosphorylation of CRMPs by Cdk5, Bos taurus" +xref: Reactome:REACT_85146 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Drosophila melanogaster" +xref: Reactome:REACT_85195 "IRAK is activated, Xenopus tropicalis" +xref: Reactome:REACT_85259 "ALOX5 is phosphorylated by MAPKAP2, Sus scrofa" +xref: Reactome:REACT_85327 "AKT phosphorylates CREB, Mus musculus" +xref: Reactome:REACT_85429 "MAPKAPK2 phosphorylates CREB at Serine 133, Gallus gallus" +xref: Reactome:REACT_85676 "Activation of NF-kB complex, Mus musculus" +xref: Reactome:REACT_85714 "IKKbeta phosphorylates IkB causing NF-kB to dissociate, Sus scrofa" +xref: Reactome:REACT_85726 "perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP, Xenopus tropicalis" +xref: Reactome:REACT_85756 "ERK1/2 phosphorylates MSK1, Bos taurus" +xref: Reactome:REACT_85863 "Phosphorylated MAPKs phosphorylate ATF-2, Danio rerio" +xref: Reactome:REACT_86006 "ERK5 activates the transcription factor MEF2, Oryza sativa" +xref: Reactome:REACT_86021 "Phosphorylation of FANCD2 by ATR/ATM, Drosophila melanogaster" +xref: Reactome:REACT_86110 "Activation of TAK1-TAB2 complex, Canis familiaris" +xref: Reactome:REACT_86121 "Phosphorylation of Bcl10, Danio rerio" +xref: Reactome:REACT_86147 "AKT phosphorylates CREB, Rattus norvegicus" +xref: Reactome:REACT_86151 "Activation of TAK1-TAB2 complex, Taeniopygia guttata" +xref: Reactome:REACT_86231 "TORC2 (mTOR) phosphorylates AKT at S473, Xenopus tropicalis" +xref: Reactome:REACT_86283 "PDK1 phosphorylates AKT at T308, Drosophila melanogaster" +xref: Reactome:REACT_86598 "PKA phosphorylates CREB, Sus scrofa" +xref: Reactome:REACT_86646 "Autophosphorylation of IRE1 dimer, Sus scrofa" +xref: Reactome:REACT_86677 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Danio rerio" +xref: Reactome:REACT_86724 "AKT can phosphorylate forkhead box transcription factors, Bos taurus" +xref: Reactome:REACT_86739 "Recruitment and activation of Chk1, Rattus norvegicus" +xref: Reactome:REACT_86841 "AKT phosphorylates PRAS40, Mus musculus" +xref: Reactome:REACT_86847 "Phosphorylation of FANCI by ATM/ATR, Rattus norvegicus" +xref: Reactome:REACT_86929 "LIM kinase phosphorylation by ROCK, Rattus norvegicus" +xref: Reactome:REACT_86978 "Activated TAK1 mediates phosphorylation of the IKK Complex, Canis familiaris" +xref: Reactome:REACT_86988 "Phosphorylation of FANCD2 by ATR/ATM, Arabidopsis thaliana" +xref: Reactome:REACT_87026 "Phosphorylation of CRMPs by Cdk5, Mus musculus" +xref: Reactome:REACT_87041 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Taeniopygia guttata" +xref: Reactome:REACT_87092 "Phosphorylation of CRY and PER Proteins, Rattus norvegicus" +xref: Reactome:REACT_87111 "ERK1/2 activates ELK1, Bos taurus" +xref: Reactome:REACT_87190 "Activation of IKK complex, Bos taurus" +xref: Reactome:REACT_87348 "Phosphorylation of PKC theta, Gallus gallus" +xref: Reactome:REACT_87421 "Phosphorylation of cofilin by LIMK-1, Drosophila melanogaster" +xref: Reactome:REACT_87451 "AKT interacts and phosphorylates Cot, Rattus norvegicus" +xref: Reactome:REACT_87456 "IRAK is activated, Mus musculus" +xref: Reactome:REACT_87461 "Autophosphorylation of PAK, Xenopus tropicalis" +xref: Reactome:REACT_87481 "Activation of cytosolic AMPK by phosphorylation, Mus musculus" +xref: Reactome:REACT_87543 "AKT phosphorylates CREB, Canis familiaris" +xref: Reactome:REACT_87575 "CERT + ATP => monophospho-CERT + ADP, Xenopus tropicalis" +xref: Reactome:REACT_87625 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Sus scrofa" +xref: Reactome:REACT_87637 "perilipin + 2 ATP -> phosphorylated perilipin + 2 ADP, Gallus gallus" +xref: Reactome:REACT_87667 "AKT interacts and phosphorylates Cot, Xenopus tropicalis" +xref: Reactome:REACT_87833 "PDK1 phosphorylates AKT at T308, Rattus norvegicus" +xref: Reactome:REACT_87846 "ERK1/2/5 activate RSK1/2/3, Saccharomyces cerevisiae" +xref: Reactome:REACT_87861 "Phosphorylation of PKC theta, Rattus norvegicus" +xref: Reactome:REACT_87870 "Phosphorylated MAPKs phosphorylate ATF-2, Schizosaccharomyces pombe" +xref: Reactome:REACT_87896 "ALOX5 is phosphorylated by MAPKAP2, Bos taurus" +xref: Reactome:REACT_88189 "MSK1 activates ATF1, Mus musculus" +xref: Reactome:REACT_88241 "AKT can phosphorylate forkhead box transcription factors, Rattus norvegicus" +xref: Reactome:REACT_88277 "Activation of cytosolic AMPK by phosphorylation, Xenopus tropicalis" +xref: Reactome:REACT_88488 "Phosphorylation of L1 by p90rsk, Bos taurus" +xref: Reactome:REACT_88490 "Myosin regulatory light chain phosphorylation by ROCK, Caenorhabditis elegans" +xref: Reactome:REACT_88529 "Activation of claspin, Gallus gallus" +xref: Reactome:REACT_88559 "Phosphorylation of FANCD2 by ATR/ATM, Xenopus tropicalis" +xref: Reactome:REACT_88591 "Activated TAK1 mediates phosphorylation of the IKK Complex, Danio rerio" +xref: Reactome:REACT_88650 "MSK1 activates ATF1, Taeniopygia guttata" +xref: Reactome:REACT_88937 "IKKbeta is activated, Mus musculus" +xref: Reactome:REACT_88973 "Phosphorylation of L1 by p90rsk, Mus musculus" +xref: Reactome:REACT_89047 "AKT phosphorylates MDM2, Rattus norvegicus" +xref: Reactome:REACT_89054 "RSK1/2/3 phosphorylates CREB at Serine 133, Xenopus tropicalis" +xref: Reactome:REACT_89078 "MSK1 activates CREB, Danio rerio" +xref: Reactome:REACT_89089 "Phosphorylation of L1 by p90rsk, Caenorhabditis elegans" +xref: Reactome:REACT_89170 "Phosphorylation of FANCI by ATM/ATR, Bos taurus" +xref: Reactome:REACT_89266 "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP, Danio rerio" +xref: Reactome:REACT_89355 "Activation of claspin, Danio rerio" +xref: Reactome:REACT_89389 "Transphosphorylation of pLIMK1, Xenopus tropicalis" +xref: Reactome:REACT_89425 "AKT phosphorylates BAD, Canis familiaris" +xref: Reactome:REACT_89433 "Phosphorylated MAPKs phosphorylate ATF-2, Bos taurus" +xref: Reactome:REACT_89557 "RSK1/2/3 phosphorylates CREB at Serine 133, Taeniopygia guttata" +xref: Reactome:REACT_89611 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Mus musculus" +xref: Reactome:REACT_89699 "IRAK is activated, Danio rerio" +xref: Reactome:REACT_89806 "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP, Xenopus tropicalis" +xref: Reactome:REACT_89830 "Activation of TAK1-TAB2 complex, Danio rerio" +xref: Reactome:REACT_89908 "ERK5 activates the transcription factor MEF2, Bos taurus" +xref: Reactome:REACT_89984 "Phosphorylation of PKC theta, Sus scrofa" +xref: Reactome:REACT_90010 "Phosphorylation of eIF2-alpha by PERK, Canis familiaris" +xref: Reactome:REACT_90071 "Phosphorylation of eIF2-alpha by PERK, Gallus gallus" +xref: Reactome:REACT_90165 "Phosphorylation of PKC theta, Canis familiaris" +xref: Reactome:REACT_90173 "TORC2 (mTOR) phosphorylates AKT at S473, Rattus norvegicus" +xref: Reactome:REACT_90268 "p38MAPK phosphorylates MSK1, Taeniopygia guttata" +xref: Reactome:REACT_90319 "PDK1 phosphorylates AKT at T308, Mus musculus" +xref: Reactome:REACT_90333 "AKT phosphorylates GSK3, Canis familiaris" +xref: Reactome:REACT_90350 "Activation of NF-kB complex, Canis familiaris" +xref: Reactome:REACT_90442 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Canis familiaris" +xref: Reactome:REACT_90464 "Phosphorylation of LIMK-1 by PAK, Xenopus tropicalis" +xref: Reactome:REACT_90486 "AKT phosphorylates TSC2, inhibiting it, Rattus norvegicus" +xref: Reactome:REACT_90546 "Active p38 MAPK phosphorylates MAPKAPK2 or 3, Danio rerio" +xref: Reactome:REACT_90590 "MAPKAPK2 phosphorylates CREB at Serine 133, Mus musculus" +xref: Reactome:REACT_90752 "TORC2 (mTOR) phosphorylates AKT at S473, Caenorhabditis elegans" +xref: Reactome:REACT_91042 "Transphosphorylation of pLIMK1, Rattus norvegicus" +xref: Reactome:REACT_91083 "Phosphorylation of PKC theta, Bos taurus" +xref: Reactome:REACT_91184 "Recruitment and activation of Chk1, Danio rerio" +xref: Reactome:REACT_91247 "Phosphorylation of cofilin by LIMK-1, Xenopus tropicalis" +xref: Reactome:REACT_91489 "Autophosphorylation of IRE1 dimer, Taeniopygia guttata" +xref: Reactome:REACT_91679 "Activation of TAK1-TAB2 complex, Bos taurus" +xref: Reactome:REACT_91687 "Phosphorylation of FANCI by ATM/ATR, Xenopus tropicalis" +xref: Reactome:REACT_91695 "AKT phosphorylates GSK3, Taeniopygia guttata" +xref: Reactome:REACT_91715 "AKT phosphorylates GSK3, Mus musculus" +xref: Reactome:REACT_91808 "Autophosphorylation of IRE1 dimer, Mus musculus" +xref: Reactome:REACT_91830 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9, Sus scrofa" +xref: Reactome:REACT_92125 "Activation of IKK complex, Mus musculus" +xref: Reactome:REACT_92263 "TORC2 (mTOR) phosphorylates AKT at S473, Taeniopygia guttata" +xref: Reactome:REACT_92406 "Phosphorylation of CRMPs by Cdk5, Sus scrofa" +xref: Reactome:REACT_92416 "ERK1/2 phosphorylates MSK1, Caenorhabditis elegans" +xref: Reactome:REACT_92486 "AKT phosphorylates CREB, Bos taurus" +xref: Reactome:REACT_92872 "PKA phosphorylates CREB, Bos taurus" +xref: Reactome:REACT_92890 "ERK1/2/5 activate RSK1/2/3, Taeniopygia guttata" +xref: Reactome:REACT_92893 "ERK1/2 phosphorylates MSK1, Sus scrofa" +xref: Reactome:REACT_93044 "MSK1 activates CREB, Mus musculus" +xref: Reactome:REACT_93073 "Autophosphorylation of IRE1 dimer, Rattus norvegicus" +xref: Reactome:REACT_93082 "ERK5 activates the transcription factor MEF2, Danio rerio" +xref: Reactome:REACT_93212 "RSK1/2/3 phosphorylates CREB at Serine 133, Bos taurus" +xref: Reactome:REACT_93229 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Canis familiaris" +xref: Reactome:REACT_93303 "ERK1/2 phosphorylates MSK1, Taeniopygia guttata" +xref: Reactome:REACT_93390 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Gallus gallus" +xref: Reactome:REACT_93505 "Phosphorylation of L1 by p90rsk, Drosophila melanogaster" +xref: Reactome:REACT_93588 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Taeniopygia guttata" +xref: Reactome:REACT_93911 "ERK5 activates the transcription factor MEF2, Canis familiaris" +xref: Reactome:REACT_93914 "LIM kinase phosphorylation by ROCK, Mus musculus" +xref: Reactome:REACT_93919 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Bos taurus" +xref: Reactome:REACT_93998 "AKT can phosphorylate RSK, Caenorhabditis elegans" +xref: Reactome:REACT_94044 "Phosphorylation of CARMA1, Canis familiaris" +xref: Reactome:REACT_94069 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Gallus gallus" +xref: Reactome:REACT_94072 "Phosphorylation of L1 by p90rsk, Rattus norvegicus" +xref: Reactome:REACT_94250 "AKT phosphorylates PRAS40, Bos taurus" +xref: Reactome:REACT_94366 "Phosphorylation of CRMPs by GSK3beta, Danio rerio" +xref: Reactome:REACT_94474 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Danio rerio" +xref: Reactome:REACT_94526 "AKT phosphorylates TSC2, inhibiting it, Bos taurus" +xref: Reactome:REACT_94639 "Autophosphorylation of IRE1 dimer, Bos taurus" +xref: Reactome:REACT_94736 "p38MAPK phosphorylates MSK1, Gallus gallus" +xref: Reactome:REACT_95091 "AKT phosphorylates MDM2, Mus musculus" +xref: Reactome:REACT_95131 "CERT + ATP => monophospho-CERT + ADP, Bos taurus" +xref: Reactome:REACT_95329 "Activation of claspin, Taeniopygia guttata" +xref: Reactome:REACT_95335 "Phosphorylation of Bcl10, Rattus norvegicus" +xref: Reactome:REACT_95356 "MEK2 phosphorylates ERK-2, Taeniopygia guttata" +xref: Reactome:REACT_95369 "AKT phosphorylates PRAS40, Xenopus tropicalis" +xref: Reactome:REACT_95525 "Transphosphorylation of pLIMK1, Canis familiaris" +xref: Reactome:REACT_95566 "Phosphorylation of eIF2-alpha by PERK, Mus musculus" +xref: Reactome:REACT_95602 "hormone-sensitive lipase (HSL) + 2 ATP -> phosphorylated HSL + 2 ADP, Mus musculus" +xref: Reactome:REACT_95622 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Taeniopygia guttata" +xref: Reactome:REACT_95641 "PDK1 phosphorylates AKT at T308, Xenopus tropicalis" +xref: Reactome:REACT_95651 "Transphosphorylation of pLIMK1, Danio rerio" +xref: Reactome:REACT_95762 "Phosphorylation of FANCD2 by ATR/ATM, Dictyostelium discoideum" +xref: Reactome:REACT_95795 "ERK1/2/5 activate RSK1/2/3, Drosophila melanogaster" +xref: Reactome:REACT_95850 "Phosphorylation of L1 by p90rsk, Xenopus tropicalis" +xref: Reactome:REACT_95931 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Bos taurus" +xref: Reactome:REACT_95935 "AKT phosphorylates TSC2, inhibiting it, Xenopus tropicalis" +xref: Reactome:REACT_95951 "AKT can phosphorylate forkhead box transcription factors, Taeniopygia guttata" +xref: Reactome:REACT_95952 "ERK5 activates the transcription factor MEF2, Mus musculus" +xref: Reactome:REACT_96092 "p38MAPK phosphorylates MSK1, Canis familiaris" +xref: Reactome:REACT_96204 "ERK1/2 phosphorylates MSK1, Rattus norvegicus" +xref: Reactome:REACT_96268 "Phosphorylation of FANCD2 by ATR/ATM, Mus musculus" +xref: Reactome:REACT_96340 "MEK2 phosphorylates ERK-2, Rattus norvegicus" +xref: Reactome:REACT_96427 "AKT can phosphorylate RSK, Drosophila melanogaster" +xref: Reactome:REACT_96505 "ERK1/2 phosphorylates MSK1, Gallus gallus" +xref: Reactome:REACT_96534 "Phosphorylation of CRY and PER Proteins, Taeniopygia guttata" +xref: Reactome:REACT_96546 "CERT + ATP => monophospho-CERT + ADP, Danio rerio" +xref: Reactome:REACT_96553 "IKKbeta phosphorylates IkB causing NF-kB to dissociate, Xenopus tropicalis" +xref: Reactome:REACT_96657 "MSK1 activates CREB, Canis familiaris" +xref: Reactome:REACT_96659 "Phosphorylation of CARMA1, Mus musculus" +xref: Reactome:REACT_96804 "Recruitment and activation of Chk1, Mus musculus" +xref: Reactome:REACT_96823 "AKT can phosphorylate NUR77, Rattus norvegicus" +xref: Reactome:REACT_96825 "IRAK is activated, Sus scrofa" +xref: Reactome:REACT_96850 "MAPKAPK2 phosphorylates CREB at Serine 133, Rattus norvegicus" +xref: Reactome:REACT_97199 "Phosphorylation of CRMPs by Cdk5, Rattus norvegicus" +xref: Reactome:REACT_97207 "AKT phosphorylates GSK3, Xenopus tropicalis" +xref: Reactome:REACT_97335 "ERK5 activates the transcription factor MEF2, Arabidopsis thaliana" +xref: Reactome:REACT_97343 "Integrin alpha IIb beta3 T779 phosphorylation blocks SHC binding, Bos taurus" +xref: Reactome:REACT_97347 "ERK1/2/5 activate RSK1/2/3, Caenorhabditis elegans" +xref: Reactome:REACT_97394 "CERT + ATP => monophospho-CERT + ADP, Canis familiaris" +xref: Reactome:REACT_97476 "Phosphorylation of LIMK-1 by PAK, Mus musculus" +xref: Reactome:REACT_97497 "IKKbeta is activated, Xenopus tropicalis" +xref: Reactome:REACT_97544 "MSK1 activates CREB, Taeniopygia guttata" +xref: Reactome:REACT_97593 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Drosophila melanogaster" +xref: Reactome:REACT_97635 "Phosphorylation of cPLA2 by MAPK p38 alpha, Bos taurus" +xref: Reactome:REACT_97792 "Phosphorylation of Bcl10, Mus musculus" +xref: Reactome:REACT_97842 "IKKbeta is activated, Gallus gallus" +xref: Reactome:REACT_97853 "AKT can phosphorylate RSK, Mus musculus" +xref: Reactome:REACT_98007 "ERK1/2 phosphorylates MSK1, Danio rerio" +xref: Reactome:REACT_98032 "Inactivation of MEK1 by p34cdc2, Canis familiaris" +xref: Reactome:REACT_98044 "Phosphorylation of FANCD2 by ATR/ATM, Canis familiaris" +xref: Reactome:REACT_98057 "ALOX5 is phosphorylated by MAPKAP2, Rattus norvegicus" +xref: Reactome:REACT_98110 "ERK1/2 phosphorylates MSK1, Drosophila melanogaster" +xref: Reactome:REACT_98114 "Autophosphorylation of PAK, Bos taurus" +xref: Reactome:REACT_98193 "MSK1 activates ATF1, Danio rerio" +xref: Reactome:REACT_98197 "RSK1/2/3 phosphorylates CREB at Serine 133, Danio rerio" +xref: Reactome:REACT_98215 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Rattus norvegicus" +xref: Reactome:REACT_98244 "Activated TAK1 mediates phosphorylation of the IKK Complex, Mus musculus" +xref: Reactome:REACT_98255 "ERK1/2/5 activate RSK1/2/3, Mus musculus" +xref: Reactome:REACT_98315 "Activation of cytosolic AMPK by phosphorylation, Drosophila melanogaster" +xref: Reactome:REACT_98317 "Phosphorylation of Cdc25C at Ser 216 by Chk1, Bos taurus" +xref: Reactome:REACT_98318 "AKT interacts and phosphorylates Cot, Mus musculus" +xref: Reactome:REACT_98411 "Activation of IKK complex, Sus scrofa" +xref: Reactome:REACT_98629 "MEK2 phosphorylates ERK-2, Canis familiaris" +xref: Reactome:REACT_98897 "RSK1/2/3 phosphorylates CREB at Serine 133, Mus musculus" +xref: Reactome:REACT_98965 "Phosphorylation of L1 by p90rsk, Sus scrofa" +xref: Reactome:REACT_98966 "MSK1 activates CREB, Bos taurus" +xref: Reactome:REACT_99035 "Activation of NF-kB complex, Sus scrofa" +xref: Reactome:REACT_99196 "Phosphorylation of CRMPs by GSK3beta, Mus musculus" +xref: Reactome:REACT_99214 "Phosphorylation of PKC theta, Drosophila melanogaster" +xref: Reactome:REACT_99234 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9, Rattus norvegicus" +xref: Reactome:REACT_99270 "Integrin alpha IIb beta3 T779 phosphorylation blocks SHC binding, Sus scrofa" +xref: Reactome:REACT_99324 "Phosphorylation of eIF2-alpha by PERK, Danio rerio" +xref: Reactome:REACT_99345 "AKT phosphorylates MDM2, Canis familiaris" +xref: Reactome:REACT_99388 "Phosphorylation of FANCD2 by ATR/ATM, Rattus norvegicus" +xref: Reactome:REACT_99466 "monophospho-CERT + 2 ATP => multiphospho-CERT + 2 ADP, Bos taurus" +xref: Reactome:REACT_99563 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Danio rerio" +xref: Reactome:REACT_99566 "IKKbeta is activated, Canis familiaris" +xref: Reactome:REACT_99606 "Phosphorylation of eIF2-alpha by PERK, Sus scrofa" +xref: Reactome:REACT_99613 "PKA phosphorylates CREB, Gallus gallus" +xref: Reactome:REACT_99631 "IRAK is activated, Gallus gallus" +xref: Reactome:REACT_99778 "MAPKAPK2 phosphorylates CREB at Serine 133, Canis familiaris" +xref: Reactome:REACT_99808 "MAP kinase activates MAPKAPK2, MAPKAPK3 and MSK1, Xenopus tropicalis" +xref: Reactome:REACT_99812 "ERK1/2 activates ELK1, Sus scrofa" +xref: Reactome:REACT_99873 "Activation of recruited TAK1 within the complex viral dsRNA:TLR3:TRIF:pUb-TRAF6:TAB1:Ub-TAB2:Ub-TAB3: TAK1, Gallus gallus" +xref: Reactome:REACT_99884 "Phosphorylation of Bcl10, Canis familiaris" +xref: Reactome:REACT_99943 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9, Danio rerio" +is_a: GO:0004672 ! protein kinase activity + +[Term] +id: GO:0004702 +name: receptor signaling protein serine/threonine kinase activity +namespace: molecular_function +def: "Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate." [EC:2.7.11.13, GOC:bf, GOC:mah] +synonym: "receptor signalling protein serine/threonine kinase activity" EXACT [] +xref: EC:2.7.11.- +is_a: GO:0004674 ! protein serine/threonine kinase activity +is_a: GO:0005057 ! receptor signaling protein activity +relationship: part_of GO:0023014 ! signal transduction by phosphorylation + +[Term] +id: GO:0004705 +name: JUN kinase activity +namespace: molecular_function +def: "Catalysis of the reaction: JUN + ATP = JUN phosphate + ADP. This reaction is the phosphorylation and activation of members of the JUN family, a gene family that encodes nuclear transcription factors." [GOC:bf, ISBN:0198506732] +synonym: "c-Jun N-terminal kinase activity" NARROW [] +synonym: "JNK" EXACT [] +synonym: "JNK3alpha1" RELATED [] +synonym: "SAPK1" NARROW [] +xref: EC:2.7.11.- +xref: Reactome:REACT_102468 "Activated JNKs phosphorylate c-JUN, Sus scrofa" +xref: Reactome:REACT_105521 "NRAGE activates JNK, Danio rerio" +xref: Reactome:REACT_107106 "Activated JNKs phosphorylate c-JUN, Canis familiaris" +xref: Reactome:REACT_107943 "NRAGE activates JNK, Mus musculus" +xref: Reactome:REACT_110914 "NRIF and TRAF6 may activate JNK, Danio rerio" +xref: Reactome:REACT_113885 "JNK phosphorylates BIM, BAD and other targets, Xenopus tropicalis" +xref: Reactome:REACT_13422 "NRIF and TRAF6 may activate JNK, Homo sapiens" +xref: Reactome:REACT_13427 "NRAGE activates JNK, Homo sapiens" +xref: Reactome:REACT_13660 "NRIF and TRAF6 may activate JNK, Mus musculus" +xref: Reactome:REACT_13777 "JNK phosphorylates BIM, BAD and other targets, Homo sapiens" +xref: Reactome:REACT_13804 "Nrage activates Jnk1, Rattus norvegicus" +xref: Reactome:REACT_25133 "Activation and dimerization of c-JUN in the nucleus, Gallus gallus" +xref: Reactome:REACT_28274 "NRIF and TRAF6 may activate JNK, Canis familiaris" +xref: Reactome:REACT_28873 "NRAGE activates JNK, Bos taurus" +xref: Reactome:REACT_29090 "JNK phosphorylates BIM, BAD and other targets, Rattus norvegicus" +xref: Reactome:REACT_30421 "NRIF and TRAF6 may activate JNK, Xenopus tropicalis" +xref: Reactome:REACT_31657 "JNK phosphorylates BIM, BAD and other targets, Sus scrofa" +xref: Reactome:REACT_33342 "NRIF and TRAF6 may activate JNK, Bos taurus" +xref: Reactome:REACT_34178 "Activated JNKs phosphorylate c-JUN, Bos taurus" +xref: Reactome:REACT_6716 "Activated JNKs phosphorylate c-JUN, Homo sapiens" +xref: Reactome:REACT_82416 "NRIF and TRAF6 may activate JNK, Gallus gallus" +xref: Reactome:REACT_84873 "Activated JNKs phosphorylate c-JUN, Danio rerio" +xref: Reactome:REACT_89073 "NRIF and TRAF6 may activate JNK, Rattus norvegicus" +xref: Reactome:REACT_89150 "Activated JNKs phosphorylate c-JUN, Taeniopygia guttata" +xref: Reactome:REACT_89326 "Activated JNKs phosphorylate c-JUN, Gallus gallus" +xref: Reactome:REACT_89545 "JNK phosphorylates BIM, BAD and other targets, Mus musculus" +xref: Reactome:REACT_89768 "NRIF and TRAF6 may activate JNK, Taeniopygia guttata" +xref: Reactome:REACT_90609 "Activated JNKs phosphorylate c-JUN, Xenopus tropicalis" +xref: Reactome:REACT_91285 "Activated JNKs phosphorylate c-JUN, Rattus norvegicus" +xref: Reactome:REACT_92150 "NRIF and TRAF6 may activate JNK, Sus scrofa" +xref: Reactome:REACT_92530 "JNK phosphorylates BIM, BAD and other targets, Canis familiaris" +xref: Reactome:REACT_93380 "JNK phosphorylates BIM, BAD and other targets, Bos taurus" +xref: Reactome:REACT_93451 "Activated JNKs phosphorylate c-JUN, Mus musculus" +xref: Reactome:REACT_94744 "NRAGE activates JNK, Xenopus tropicalis" +xref: Reactome:REACT_97463 "NRAGE activates JNK, Canis familiaris" +xref: Reactome:REACT_99495 "NRAGE activates JNK, Sus scrofa" +is_a: GO:0016909 ! SAP kinase activity +relationship: part_of GO:0007258 ! JUN phosphorylation + +[Term] +id: GO:0004707 +name: MAP kinase activity +namespace: molecular_function +alt_id: GO:0008338 +alt_id: GO:0008339 +alt_id: GO:0016908 +def: "Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli." [GOC:ma, ISBN:0198547684] +synonym: "ATP:protein phosphotransferase (MAPKK-activated) activity" EXACT [EC:2.7.11.24] +synonym: "Dp38" RELATED [EC:2.7.11.24] +synonym: "ERK" RELATED [EC:2.7.11.24] +synonym: "ERK1" EXACT [] +synonym: "ERK2" RELATED [] +synonym: "extracellular signal-regulated kinase activity" NARROW [EC:2.7.11.24] +synonym: "LeMPK3" RELATED [EC:2.7.11.24] +synonym: "MAP kinase 1 activity" NARROW [] +synonym: "MAP kinase 2 activity" NARROW [] +synonym: "MAP-2 kinase activity" NARROW [EC:2.7.11.24] +synonym: "MAPK" RELATED [EC:2.7.11.24, PMID:20811974] +synonym: "MBP kinase I activity" NARROW [EC:2.7.11.24] +synonym: "MBP kinase II activity" NARROW [EC:2.7.11.24] +synonym: "mitogen activated kinase activity" EXACT [] +synonym: "mitogen-activated protein kinase activity" EXACT [EC:2.7.11.24] +synonym: "MP kinase activity" NARROW [] +synonym: "Mpk2" NARROW [] +synonym: "myelin basic protein kinase activity" NARROW [EC:2.7.11.24] +synonym: "p38" NARROW [] +synonym: "p38-2" RELATED [EC:2.7.11.24] +synonym: "p38delta" RELATED [EC:2.7.11.24] +synonym: "p42 mitogen-activated protein kinase activity" NARROW [EC:2.7.11.24] +synonym: "p42mapk" RELATED [EC:2.7.11.24] +synonym: "p44mpk" RELATED [EC:2.7.11.24] +synonym: "PMK-1" RELATED [EC:2.7.11.24] +synonym: "PMK-2" RELATED [EC:2.7.11.24] +synonym: "PMK-3" RELATED [EC:2.7.11.24] +synonym: "pp42" RELATED [EC:2.7.11.24] +synonym: "pp44mapk" RELATED [EC:2.7.11.24] +synonym: "SAPK2" NARROW [] +synonym: "STK26" RELATED [EC:2.7.11.24] +xref: EC:2.7.11.24 +xref: KEGG:R00162 +xref: MetaCyc:2.7.11.24-RXN +xref: Reactome:REACT_100829 "ERK5 is activated, Oryza sativa" +xref: Reactome:REACT_104581 "ERK5 is activated, Arabidopsis thaliana" +xref: Reactome:REACT_111161 "Activated ERK1/2 threonine-phosphorylate FRS2alpha., Homo sapiens" +xref: Reactome:REACT_115393 "Phosphorylation of UBF-1:rDNA Promoter, Rattus norvegicus" +xref: Reactome:REACT_12075 "ERK5 is activated, Homo sapiens" +xref: Reactome:REACT_12418 "ERK5 is activated, Rattus norvegicus" +xref: Reactome:REACT_180 "Phosphorylation of UBF-1:rDNA Promoter, Homo sapiens" +xref: Reactome:REACT_25129 "Activation of p38MAPK by DSCAM, Homo sapiens" +xref: Reactome:REACT_29583 "Phosphorylation of UBF-1:rDNA Promoter, Danio rerio" +xref: Reactome:REACT_30765 "Phosphorylation of UBF-1:rDNA Promoter, Canis familiaris" +xref: Reactome:REACT_31584 "Phosphorylation of UBF-1:rDNA Promoter, Bos taurus" +xref: Reactome:REACT_80477 "ERK5 is activated, Danio rerio" +xref: Reactome:REACT_82316 "Activation of p38MAPK by DSCAM, Rattus norvegicus" +xref: Reactome:REACT_83043 "ERK5 is activated, Xenopus tropicalis" +xref: Reactome:REACT_87321 "ERK5 is activated, Mus musculus" +xref: Reactome:REACT_91897 "ERK5 is activated, Bos taurus" +xref: Reactome:REACT_98528 "ERK5 is activated, Canis familiaris" +xref: Reactome:REACT_99483 "ERK5 is activated, Dictyostelium discoideum" +xref: Reactome:REACT_99569 "Phosphorylation of UBF-1:rDNA Promoter, Mus musculus" +is_a: GO:0004702 ! receptor signaling protein serine/threonine kinase activity +relationship: part_of GO:0000165 ! MAPK cascade + +[Term] +id: GO:0004713 +name: protein tyrosine kinase activity +namespace: molecular_function +alt_id: GO:0004718 +def: "Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate." [EC:2.7.10] +subset: gosubset_prok +synonym: "JAK" NARROW [] +synonym: "Janus kinase activity" NARROW [] +synonym: "protein-tyrosine kinase activity" EXACT [] +xref: EC:2.7.10 +xref: Reactome:REACT_100012 "Fyn/Lyn-mediated phosphorylation of FcR1 gamma, Canis familiaris" +xref: Reactome:REACT_100028 "Phosphorylation of DCC by Fyn, Bos taurus" +xref: Reactome:REACT_100038 "Phosphorylation of nephrin by the Src family kinase Fyn, Bos taurus" +xref: Reactome:REACT_100076 "Syk/Lck phosphorylate LAT, Mus musculus" +xref: Reactome:REACT_100084 "Autophosphorylation of NCAM1 bound Fyn, Danio rerio" +xref: Reactome:REACT_100130 "Autophosphorylation of PDGF alpha receptors, Gallus gallus" +xref: Reactome:REACT_100272 "Phosphorylation of PLC-gamma1, Canis familiaris" +xref: Reactome:REACT_100472 "Tyrosine phosphorylation of CRMPs by Fes, Sus scrofa" +xref: Reactome:REACT_100650 "Binding and activation of MAP Kinase, Xenopus tropicalis" +xref: Reactome:REACT_100799 "Phosphorylation of L1 by EPHB2, Mus musculus" +xref: Reactome:REACT_100803 "Activation of Vav1, Mus musculus" +xref: Reactome:REACT_100852 "Phosphorylation of PLC-gamma1, Bos taurus" +xref: Reactome:REACT_100858 "Autocatalytic phosphorylation of FGFR1b, Xenopus tropicalis" +xref: Reactome:REACT_100859 "PLC gamma phosphorylation by FGFR, Sus scrofa" +xref: Reactome:REACT_100890 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Xenopus tropicalis" +xref: Reactome:REACT_100893 "Autophosphorylation of PDGF alpha/beta receptors, Rattus norvegicus" +xref: Reactome:REACT_100943 "Autocatalytic phosphorylation of FGFR2b, Mus musculus" +xref: Reactome:REACT_100947 "EGFR autophosphorylation, Gallus gallus" +xref: Reactome:REACT_101042 "Phosphorylation of EGFR by SRC kinase, Taeniopygia guttata" +xref: Reactome:REACT_101080 "Phosphorylation of CTLA-4, Bos taurus" +xref: Reactome:REACT_101097 "Autocatalytic phosphorylation of FGFR2c, Rattus norvegicus" +xref: Reactome:REACT_101231 "Autocatalytic phosphorylation of FGFR1b, Sus scrofa" +xref: Reactome:REACT_101274 "SEMA4D interacts with Plexin-B1:ErbB2, Xenopus tropicalis" +xref: Reactome:REACT_101384 "Autocatalytic phosphorylation of FGFR2b, Danio rerio" +xref: Reactome:REACT_101466 "Phosphorylation of FRS2-alpha by activated FGFR, Bos taurus" +xref: Reactome:REACT_101595 "Phosphorylation of nephrin by the Src family kinase Fyn, Sus scrofa" +xref: Reactome:REACT_101612 "Phosphorylation of CTLA-4, Rattus norvegicus" +xref: Reactome:REACT_101643 "Phosphorylation of FRS2-alpha by activated FGFR, Rattus norvegicus" +xref: Reactome:REACT_101668 "Phosphorylation of Rob1 by Abl kinase, Canis familiaris" +xref: Reactome:REACT_101714 "Autocatalytic phosphorylation of FGFR4, Bos taurus" +xref: Reactome:REACT_101813 "Autophosphorylation of SRC, Bos taurus" +xref: Reactome:REACT_101985 "Autocatalytic phosphorylation of FGFR3c, Xenopus tropicalis" +xref: Reactome:REACT_102066 "Activation of ZAP-70, Mus musculus" +xref: Reactome:REACT_102080 "Autocatalytic phosphorylation of FGFR1b, Bos taurus" +xref: Reactome:REACT_102206 "Tyrosine phosphorylation of CRMPs by Fes, Xenopus tropicalis" +xref: Reactome:REACT_102366 "Trans-phosphorylation of Tie2, Danio rerio" +xref: Reactome:REACT_102431 "Phosphorylation of DCC by Fyn, Mus musculus" +xref: Reactome:REACT_102446 "Autophosphorylation of PDGF beta receptors, Rattus norvegicus" +xref: Reactome:REACT_102451 "Phosphorylation of FRS2-alpha by activated FGFR, Canis familiaris" +xref: Reactome:REACT_102485 "EGFR activates PLC-gamma1 by phosphorylation, Mus musculus" +xref: Reactome:REACT_102490 "Autophosphorylation of NCAM1 bound Fyn, Xenopus tropicalis" +xref: Reactome:REACT_102575 "FGR binds and phosphorylates ApoER2, Xenopus tropicalis" +xref: Reactome:REACT_102756 "Phosphorylation of FADK1, Sus scrofa" +xref: Reactome:REACT_103001 "Autocatalytic phosphorylation of FGFR3b, Taeniopygia guttata" +xref: Reactome:REACT_103159 "Phosphorylation of nephrin by the Src family kinase Fyn, Rattus norvegicus" +xref: Reactome:REACT_103330 "Phosphorylation of Plexin-A, Taeniopygia guttata" +xref: Reactome:REACT_103364 "Trans-phosphorylation of Tie2, Taeniopygia guttata" +xref: Reactome:REACT_103374 "SEMA4D interacts with Plexin-B1:ErbB2, Mus musculus" +xref: Reactome:REACT_103435 "Autocatalytic phosphorylation of FGFR1c, Sus scrofa" +xref: Reactome:REACT_103496 "Autocatalytic phosphorylation of FGFR1c, Gallus gallus" +xref: Reactome:REACT_103654 "Phosphorylation of Rob1 by Abl kinase, Drosophila melanogaster" +xref: Reactome:REACT_103887 "Trans-phosphorylation of Tie2, Sus scrofa" +xref: Reactome:REACT_103906 "Phosphorylation of PLC-gamma1, Mus musculus" +xref: Reactome:REACT_103917 "Autocatalytic phosphorylation of FGFR2b, Bos taurus" +xref: Reactome:REACT_104292 "Phosphorylation of EGFR by SRC kinase, Danio rerio" +xref: Reactome:REACT_104626 "PLC gamma phosphorylation by FGFR, Rattus norvegicus" +xref: Reactome:REACT_104628 "Phosphorylation of TBSMs in LAT, Rattus norvegicus" +xref: Reactome:REACT_104726 "SYK activation by SRC, Xenopus tropicalis" +xref: Reactome:REACT_104756 "SYK activation by SRC, Bos taurus" +xref: Reactome:REACT_104841 "Activation of SRC by RAL-GTP, Taeniopygia guttata" +xref: Reactome:REACT_104863 "Autocatalytic phosphorylation of FGFR2b, Sus scrofa" +xref: Reactome:REACT_104977 "Autocatalytic phosphorylation of FGFR1b, Rattus norvegicus" +xref: Reactome:REACT_105013 "Phosphorylation of CTLA-4, Mus musculus" +xref: Reactome:REACT_105509 "SHP2 is phosphorylated by activated FGFR, Rattus norvegicus" +xref: Reactome:REACT_105547 "Autocatalytic phosphorylation of FGFR1b, Danio rerio" +xref: Reactome:REACT_105559 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Rattus norvegicus" +xref: Reactome:REACT_105866 "Phosphorylation of Rob1 by Abl kinase, Caenorhabditis elegans" +xref: Reactome:REACT_105876 "SEMA4D interacts with Plexin-B1:ErbB2, Canis familiaris" +xref: Reactome:REACT_105927 "Phosphorylation of CTLA-4, Canis familiaris" +xref: Reactome:REACT_106169 "Autocatalytic phosphorylation of FGFR1b, Canis familiaris" +xref: Reactome:REACT_106379 "Phosphorylation of CBL (EGFR:CBL), Xenopus tropicalis" +xref: Reactome:REACT_106547 "EGFR autophosphorylation, Mus musculus" +xref: Reactome:REACT_106775 "Tyrosine phosphorylation of CRMPs by Fes, Rattus norvegicus" +xref: Reactome:REACT_107007 "SYK activation by SRC, Canis familiaris" +xref: Reactome:REACT_107187 "Phosphorylation of ITAM motifs in CD3 complexes, Mus musculus" +xref: Reactome:REACT_107212 "Phosphorylation of ZAP-70 by Lck, Mus musculus" +xref: Reactome:REACT_107285 "SHP2 is phosphorylated by activated FGFR, Bos taurus" +xref: Reactome:REACT_107298 "EGFR activates PLC-gamma1 by phosphorylation, Gallus gallus" +xref: Reactome:REACT_107312 "Phosphorylation of FRS2-alpha by activated FGFR, Drosophila melanogaster" +xref: Reactome:REACT_107327 "Activation of Vav1, Bos taurus" +xref: Reactome:REACT_107342 "Phosphorylation of FRS2-alpha by activated FGFR, Mus musculus" +xref: Reactome:REACT_107458 "Activation of SRC by RAL-GTP, Bos taurus" +xref: Reactome:REACT_107484 "Phosphorylation of CD28, Bos taurus" +xref: Reactome:REACT_107485 "Phosphorylation of Rob1 by Abl kinase, Xenopus tropicalis" +xref: Reactome:REACT_107535 "SHP2 is phosphorylated by activated FGFR, Xenopus tropicalis" +xref: Reactome:REACT_107546 "Phosphorylation of DCC by Fyn, Rattus norvegicus" +xref: Reactome:REACT_107572 "EGFR autophosphorylation, Taeniopygia guttata" +xref: Reactome:REACT_107798 "Activation of Src, Danio rerio" +xref: Reactome:REACT_107837 "Phosphorylation of FRS2-alpha by activated FGFR, Danio rerio" +xref: Reactome:REACT_107848 "SEMA4D interacts with Plexin-B1:Met, Mus musculus" +xref: Reactome:REACT_107881 "Phosphorylation of DCC by Fyn, Drosophila melanogaster" +xref: Reactome:REACT_108123 "Autocatalytic phosphorylation of FGFR1c, Mus musculus" +xref: Reactome:REACT_108224 "SHP2 is phosphorylated by activated FGFR, Drosophila melanogaster" +xref: Reactome:REACT_108225 "Autocatalytic phosphorylation of FGFR4, Mus musculus" +xref: Reactome:REACT_108245 "Tyrosine phosphorylation of CRMPs by Fes, Bos taurus" +xref: Reactome:REACT_108324 "FGR binds and phosphorylates ApoER2, Canis familiaris" +xref: Reactome:REACT_108410 "Autophosphorylation of NCAM1 bound Fyn, Gallus gallus" +xref: Reactome:REACT_108600 "Autophosphorylation of PDGF alpha receptors, Canis familiaris" +xref: Reactome:REACT_108669 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Xenopus tropicalis" +xref: Reactome:REACT_108733 "Phosphorylation of nephrin by the Src family kinase Fyn, Mus musculus" +xref: Reactome:REACT_108819 "Trans-phosphorylation of Tie2, Canis familiaris" +xref: Reactome:REACT_108838 "Autocatalytic phosphorylation of FGFR4, Sus scrofa" +xref: Reactome:REACT_108934 "Autocatalytic phosphorylation of FGFR2c, Mus musculus" +xref: Reactome:REACT_109237 "Phosphorylation of CBL (EGFR:GRB2:CBL), Mus musculus" +xref: Reactome:REACT_109581 "Syk/Lck phosphorylate LAT, Bos taurus" +xref: Reactome:REACT_109591 "Phosphorylation of L1 by SRC, Canis familiaris" +xref: Reactome:REACT_109753 "Autophosphorylation of NCAM1 bound Fyn, Taeniopygia guttata" +xref: Reactome:REACT_110118 "Binding and activation of MAP Kinase, Sus scrofa" +xref: Reactome:REACT_110259 "Activation of SRC by RAL-GTP, Danio rerio" +xref: Reactome:REACT_110475 "Autocatalytic phosphorylation of FGFR4, Canis familiaris" +xref: Reactome:REACT_111020 "PLC gamma phosphorylation by FGFR, Taeniopygia guttata" +xref: Reactome:REACT_111028 "Phosphorylation of L1 by SRC, Xenopus tropicalis" +xref: Reactome:REACT_111070 "Phosphorylation of JAK2, Homo sapiens" +xref: Reactome:REACT_111072 "Phosphorylation and activation of VAV1, Homo sapiens" +xref: Reactome:REACT_111096 "SRC phosphorylates SPRY2 on Y55 and Y227, Homo sapiens" +xref: Reactome:REACT_111103 "Autophosphorylation of KIT, Homo sapiens" +xref: Reactome:REACT_111110 "SHC1 is phosphorylated, Homo sapiens" +xref: Reactome:REACT_111112 "Phosphorylation of APS, Homo sapiens" +xref: Reactome:REACT_111134 "Phosphorylation of PLCgamma by PDGFR, Homo sapiens" +xref: Reactome:REACT_111147 "JAK2 phosphorylation of GHR, Homo sapiens" +xref: Reactome:REACT_111152 "Phosphorylation of SHP2 by SFKs, Homo sapiens" +xref: Reactome:REACT_111186 "Phosphorylation of GAB2 by SFKs, Homo sapiens" +xref: Reactome:REACT_111201 "Phosphorylation of FRS2-beta by activated FGFR, Homo sapiens" +xref: Reactome:REACT_111218 "STAT5 tyrosine phosphorylation, Homo sapiens" +xref: Reactome:REACT_111244 "Phosphorylation of STATs, Homo sapiens" +xref: Reactome:REACT_111246 "Autocatalytic phosphorylation of BetaKlotho-bound FGFR4, Homo sapiens" +xref: Reactome:REACT_111958 "Phosphorylation of APS, Rattus norvegicus" +xref: Reactome:REACT_112027 "Autophosphorylation of KIT, Xenopus tropicalis" +xref: Reactome:REACT_112044 "Autocatalytic phosphorylation of FGFR2b, Caenorhabditis elegans" +xref: Reactome:REACT_112047 "Phosphorylation of Unc5C, Gallus gallus" +xref: Reactome:REACT_112071 "Phosphorylation and activation of VAV1, Canis familiaris" +xref: Reactome:REACT_112170 "Binding and activation of MAP Kinase, Oryza sativa" +xref: Reactome:REACT_112193 "Autophosphorylation of KIT, Rattus norvegicus" +xref: Reactome:REACT_112269 "Phosphorylation of L1 by SRC, Drosophila melanogaster" +xref: Reactome:REACT_112299 "PLC gamma phosphorylation by FGFR, Drosophila melanogaster" +xref: Reactome:REACT_112349 "SYK activation by SRC, Drosophila melanogaster" +xref: Reactome:REACT_112362 "Phosphorylation of FADK1, Xenopus tropicalis" +xref: Reactome:REACT_112411 "PLC gamma phosphorylation by FGFR, Caenorhabditis elegans" +xref: Reactome:REACT_112557 "Autocatalytic phosphorylation of FGFR4, Caenorhabditis elegans" +xref: Reactome:REACT_112582 "Phosphorylation of FRS2-beta by activated FGFR, Drosophila melanogaster" +xref: Reactome:REACT_112962 "Phosphorylation of APS, Bos taurus" +xref: Reactome:REACT_112967 "Phosphorylation of APS, Canis familiaris" +xref: Reactome:REACT_113016 "Phosphorylation of FRS2-beta by activated FGFR, Gallus gallus" +xref: Reactome:REACT_113054 "Autocatalytic phosphorylation of FGFR3c, Caenorhabditis elegans" +xref: Reactome:REACT_113122 "Autocatalytic phosphorylation of FGFR1c, Caenorhabditis elegans" +xref: Reactome:REACT_113138 "Phosphorylation of FRS2-beta by activated FGFR, Caenorhabditis elegans" +xref: Reactome:REACT_113262 "Phosphorylation of APS, Xenopus tropicalis" +xref: Reactome:REACT_113363 "Phosphorylation of nephrin by the Src family kinase Fyn, Xenopus tropicalis" +xref: Reactome:REACT_113366 "Phosphorylation of nephrin by the Src family kinase Fyn, Caenorhabditis elegans" +xref: Reactome:REACT_113372 "Phosphorylation of L1 by SRC, Caenorhabditis elegans" +xref: Reactome:REACT_113384 "Autophosphorylation of SRC, Xenopus tropicalis" +xref: Reactome:REACT_113409 "Autophosphorylation of KIT, Canis familiaris" +xref: Reactome:REACT_113474 "Autophosphorylation of KIT, Gallus gallus" +xref: Reactome:REACT_113502 "Phosphorylation of FAK by Src kinase, Drosophila melanogaster" +xref: Reactome:REACT_113605 "Phosphorylation and activation of VAV1, Mus musculus" +xref: Reactome:REACT_113630 "Phosphorylation and activation of VAV1, Xenopus tropicalis" +xref: Reactome:REACT_113647 "Autophosphorylation of KIT, Taeniopygia guttata" +xref: Reactome:REACT_113655 "Autophosphorylation of KIT, Mus musculus" +xref: Reactome:REACT_113678 "SHP2 is phosphorylated by activated FGFR, Caenorhabditis elegans" +xref: Reactome:REACT_113688 "Phosphorylation of ITIM in SIRP alpha, Sus scrofa" +xref: Reactome:REACT_113709 "Phosphorylation of CD28, Xenopus tropicalis" +xref: Reactome:REACT_113738 "Autophosphorylation of KIT, Sus scrofa" +xref: Reactome:REACT_113759 "Phosphorylation of ITIM in SIRP alpha, Taeniopygia guttata" +xref: Reactome:REACT_113828 "Autophosphorylation of PDGF beta receptors, Xenopus tropicalis" +xref: Reactome:REACT_113861 "Phosphorylation of APS, Gallus gallus" +xref: Reactome:REACT_113884 "Phosphorylation of APS, Sus scrofa" +xref: Reactome:REACT_113926 "Phosphorylation of APS, Mus musculus" +xref: Reactome:REACT_114012 "Phosphorylation of FRS2-beta by activated FGFR, Canis familiaris" +xref: Reactome:REACT_114045 "Autocatalytic phosphorylation of FGFR1b, Caenorhabditis elegans" +xref: Reactome:REACT_114111 "Phosphorylation of Unc5C, Drosophila melanogaster" +xref: Reactome:REACT_114124 "Phosphorylation of PLC-gamma1, Xenopus tropicalis" +xref: Reactome:REACT_114129 "Phosphorylation of FRS2-alpha by activated FGFR, Caenorhabditis elegans" +xref: Reactome:REACT_114167 "Phosphorylation of APS, Danio rerio" +xref: Reactome:REACT_114185 "Phosphorylation of nephrin by the Src family kinase Fyn, Drosophila melanogaster" +xref: Reactome:REACT_114530 "Phosphorylation of FRS2-beta by activated FGFR, Xenopus tropicalis" +xref: Reactome:REACT_114569 "Phosphorylation of ITIM in SIRP alpha, Bos taurus" +xref: Reactome:REACT_114600 "Binding and activation of MAP Kinase, Dictyostelium discoideum" +xref: Reactome:REACT_114640 "Phosphorylation of APS, Taeniopygia guttata" +xref: Reactome:REACT_114674 "Autophosphorylation of KIT, Bos taurus" +xref: Reactome:REACT_114702 "Autocatalytic phosphorylation of FGFR3b, Caenorhabditis elegans" +xref: Reactome:REACT_114781 "Binding and activation of MAP Kinase, Arabidopsis thaliana" +xref: Reactome:REACT_114786 "Autophosphorylation of KIT, Danio rerio" +xref: Reactome:REACT_114856 "Phosphorylation of FRS2-beta by activated FGFR, Danio rerio" +xref: Reactome:REACT_114870 "Phosphorylation of FRS2-beta by activated FGFR, Rattus norvegicus" +xref: Reactome:REACT_114895 "Activation of SRC by RAL-GTP, Drosophila melanogaster" +xref: Reactome:REACT_114914 "Phosphorylation of FRS2-beta by activated FGFR, Mus musculus" +xref: Reactome:REACT_114996 "Autophosphorylation of NCAM1 bound Fyn, Drosophila melanogaster" +xref: Reactome:REACT_114997 "Phosphorylation and activation of VAV1, Sus scrofa" +xref: Reactome:REACT_115017 "Phosphorylation of FRS2-beta by activated FGFR, Taeniopygia guttata" +xref: Reactome:REACT_115067 "Autocatalytic phosphorylation of FGFR2c, Caenorhabditis elegans" +xref: Reactome:REACT_115068 "Phosphorylation of ITIM in SIRP alpha, Gallus gallus" +xref: Reactome:REACT_115305 "Phosphorylation of DCC by Fyn, Gallus gallus" +xref: Reactome:REACT_115354 "Phosphorylation of FRS2-beta by activated FGFR, Bos taurus" +xref: Reactome:REACT_115375 "Autocatalytic phosphorylation of FGFR1b, Drosophila melanogaster" +xref: Reactome:REACT_115402 "Phosphorylation of FRS2-beta by activated FGFR, Sus scrofa" +xref: Reactome:REACT_115418 "Autocatalytic phosphorylation of FGFR2b, Drosophila melanogaster" +xref: Reactome:REACT_115469 "Autophosphorylation of SRC, Drosophila melanogaster" +xref: Reactome:REACT_115514 "Phosphorylation of Unc5C, Caenorhabditis elegans" +xref: Reactome:REACT_115610 "Trans-autophosphorylation of EGFRvIII mutant dimers, Homo sapiens" +xref: Reactome:REACT_115627 "Phosphorylation of PLC-gamma 1 by p-EGFR mutants, Homo sapiens" +xref: Reactome:REACT_115659 "Trans-autophosphorylation of p-Y877-ERBB2 heterodimers, Homo sapiens" +xref: Reactome:REACT_115772 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Homo sapiens" +xref: Reactome:REACT_115779 "Plcg1 phosphorylation by P-ERBB2:P-EGFR, Homo sapiens" +xref: Reactome:REACT_115796 "Phosphorylation of CBL by ligand-responsive p-6Y-EGFR mutants, Homo sapiens" +xref: Reactome:REACT_115797 "SRC family kinases phosphorylate ERBB2, Homo sapiens" +xref: Reactome:REACT_115817 "Activation of Src by Ral, Rattus norvegicus" +xref: Reactome:REACT_115841 "Phosphorylation of SHC1 by p-EGFR mutants, Homo sapiens" +xref: Reactome:REACT_115849 "Binding and activation of MAP kinase, Rattus norvegicus" +xref: Reactome:REACT_115850 "SHC1 phosphorylation by ERBB2 heterodimers, Homo sapiens" +xref: Reactome:REACT_115882 "PLCG1 phosphorylation by p-EGFR:p-ERBB2, Homo sapiens" +xref: Reactome:REACT_115935 "Phosphorylation of SHC1 by ERBB4 homodimers, Homo sapiens" +xref: Reactome:REACT_115938 "PRLR-bound STAT5 is phosphorylated, Homo sapiens" +xref: Reactome:REACT_115989 "Trans-autophosphorylation of ERBB4 homodimers, Homo sapiens" +xref: Reactome:REACT_116044 "Trans-autophosphorylation of ERBB2 heterodimers, Homo sapiens" +xref: Reactome:REACT_118103 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Gallus gallus" +xref: Reactome:REACT_118164 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Mus musculus" +xref: Reactome:REACT_118258 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Xenopus tropicalis" +xref: Reactome:REACT_118273 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Rattus norvegicus" +xref: Reactome:REACT_118292 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Taeniopygia guttata" +xref: Reactome:REACT_118395 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Caenorhabditis elegans" +xref: Reactome:REACT_118443 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Danio rerio" +xref: Reactome:REACT_118455 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Canis familiaris" +xref: Reactome:REACT_118461 "Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers, Bos taurus" +xref: Reactome:REACT_12016 "Binding and activation of MAP Kinase, Homo sapiens" +xref: Reactome:REACT_12030 "Activation of SRC by RAL-GTP, Homo sapiens" +xref: Reactome:REACT_12394 "Activation of ZAP-70, Homo sapiens" +xref: Reactome:REACT_12408 "Phoshorylation of PECAM-1 by Fyn or Lyn or c-Src, Homo sapiens" +xref: Reactome:REACT_12421 "Phosphorylation of TBSMs in LAT, Homo sapiens" +xref: Reactome:REACT_12424 "Phosphorylation of CBL (EGFR:CBL), Homo sapiens" +xref: Reactome:REACT_12467 "Activation of Lck, Homo sapiens" +xref: Reactome:REACT_12490 "Gab1 phosphorylation by EGFR kinase, Homo sapiens" +xref: Reactome:REACT_12491 "Phosphorylation of CBL (EGFR:GRB2:CBL), Homo sapiens" +xref: Reactome:REACT_12496 "Trans-phosphorylation of Tie2, Homo sapiens" +xref: Reactome:REACT_12498 "Phosphorylation of PLC-gamma1, Homo sapiens" +xref: Reactome:REACT_12538 "Phosphorylation of ZAP-70 by Lck, Homo sapiens" +xref: Reactome:REACT_12566 "Change of PKC theta conformation, Homo sapiens" +xref: Reactome:REACT_12569 "EGFR activates PLC-gamma1 by phosphorylation, Homo sapiens" +xref: Reactome:REACT_12615 "Phosphorylation of SLP-76, Homo sapiens" +xref: Reactome:REACT_12633 "Phosphorylation of ITAM motifs in CD3 complexes, Homo sapiens" +xref: Reactome:REACT_12640 "Inactivation of Lck by Csk, Homo sapiens" +xref: Reactome:REACT_13640 "Trans-phosphorylation of Tie2, Mus musculus" +xref: Reactome:REACT_13767 "Akt phosphorylates Foxo1 in the presence of IRS2, Mus musculus" +xref: Reactome:REACT_15545 "Autophosphorylation of SRC, Homo sapiens" +xref: Reactome:REACT_16926 "Autophosphorylation of PDGF beta receptors, Homo sapiens" +xref: Reactome:REACT_16991 "Activation of Src, Homo sapiens" +xref: Reactome:REACT_16993 "Autophosphorylation of PDGF alpha receptors, Homo sapiens" +xref: Reactome:REACT_17034 "Autophosphorylation of PDGF alpha/beta receptors, Homo sapiens" +xref: Reactome:REACT_18301 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Mus musculus" +xref: Reactome:REACT_18333 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Homo sapiens" +xref: Reactome:REACT_18343 "Autophosphorylation of NCAM1 bound Fyn, Homo sapiens" +xref: Reactome:REACT_18385 "Phosphorylation of FAK by Src kinase, Homo sapiens" +xref: Reactome:REACT_18394 "Phosphorylation of FAK by Src kinases, Mus musculus" +xref: Reactome:REACT_18408 "Autophosphorylation of NCAM1 bound Fyn, Mus musculus" +xref: Reactome:REACT_191 "Fyn/Lyn-mediated phosphorylation of FcR1 gamma, Homo sapiens" +xref: Reactome:REACT_19161 "Tyrosine phosphorylation of CRMPs by Fes, Homo sapiens" +xref: Reactome:REACT_19227 "Phosphorylation of Rob1 by Abl kinase, Homo sapiens" +xref: Reactome:REACT_19264 "Phosphorylation of CD28, Homo sapiens" +xref: Reactome:REACT_19316 "Activation of Vav1, Homo sapiens" +xref: Reactome:REACT_19380 "Phosphorylation of CTLA-4, Homo sapiens" +xref: Reactome:REACT_19381 "SEMA4D interacts with Plexin-B1:ErbB2, Homo sapiens" +xref: Reactome:REACT_19393 "Recruitment and activation of Cdk5, Homo sapiens" +xref: Reactome:REACT_19398 "SEMA4D interacts with Plexin-B1:Met, Homo sapiens" +xref: Reactome:REACT_19420 "Phosphorylation of Plexin-A, Homo sapiens" +xref: Reactome:REACT_21307 "Phosphorylation of FRS2-alpha by activated FGFR, Homo sapiens" +xref: Reactome:REACT_21329 "PLC gamma phosphorylation by FGFR, Homo sapiens" +xref: Reactome:REACT_21372 "SHP2 is phosphorylated by activated FGFR, Homo sapiens" +xref: Reactome:REACT_22163 "Phosphorylation of Unc5C, Mus musculus" +xref: Reactome:REACT_22164 "Phosphorylation of FADK1, Homo sapiens" +xref: Reactome:REACT_22174 "Phosphorylation of Unc5C, Homo sapiens" +xref: Reactome:REACT_22193 "Phosphorylation of L1 by EPHB2, Homo sapiens" +xref: Reactome:REACT_22202 "Phosphorylation of Neurofascin, Homo sapiens" +xref: Reactome:REACT_22213 "Phosphorylation of DCC by Fyn, Homo sapiens" +xref: Reactome:REACT_22229 "Phosphorylation of Y1229 in L1, Homo sapiens" +xref: Reactome:REACT_22236 "Phosphorylation of VAV2, Homo sapiens" +xref: Reactome:REACT_22260 "Phosphorylation of Neurofascin, Rattus norvegicus" +xref: Reactome:REACT_22363 "Phosphorylation of L1 by EPHB2, Gallus gallus" +xref: Reactome:REACT_22408 "Phosphorylation of L1 by SRC, Homo sapiens" +xref: Reactome:REACT_23775 "SYK activation by SRC, Homo sapiens" +xref: Reactome:REACT_23803 "Syk/Lck phosphorylate LAT, Homo sapiens" +xref: Reactome:REACT_23842 "Activation of STAT5a/b by JAK2, Homo sapiens" +xref: Reactome:REACT_23845 "CBL is tyrosine phosphorylated, Homo sapiens" +xref: Reactome:REACT_23897 "Cbl is tyrosine phosphorylated, Rattus norvegicus" +xref: Reactome:REACT_23918 "FGR binds and phosphorylates ApoER2, Homo sapiens" +xref: Reactome:REACT_23920 "Phosphorylation of ITIM in SIRP alpha, Homo sapiens" +xref: Reactome:REACT_23929 "Phosphorylation of nephrin by the Src family kinase Fyn, Homo sapiens" +xref: Reactome:REACT_23953 "Tyrosine kinases phosphorylate the receptor, Homo sapiens" +xref: Reactome:REACT_23957 "Phosphorylation of ITIM in SIRP alpha, Mus musculus" +xref: Reactome:REACT_23971 "SHC1 bound to the common beta chain becomes tyrosine phosphorylated, Homo sapiens" +xref: Reactome:REACT_23997 "Phosphorylation of ITIM in SIRP alpha, Rattus norvegicus" +xref: Reactome:REACT_24928 "Transphosphorylation of JAK1, Homo sapiens" +xref: Reactome:REACT_24933 "Phosphorylation of IFNGR1 by JAK kinases, Homo sapiens" +xref: Reactome:REACT_24993 "Phoshorylation of STAT1 by JAK kinases, Homo sapiens" +xref: Reactome:REACT_25017 "Phosphorylation of STAT1, Homo sapiens" +xref: Reactome:REACT_25105 "Formation of p-STAT1 homodimer, Homo sapiens" +xref: Reactome:REACT_25139 "Phosphorylation of JAK2, Homo sapiens" +xref: Reactome:REACT_25291 "Phosphorylation of STAT2, Homo sapiens" +xref: Reactome:REACT_25383 "Phosphorylation of INFAR1 by TYK2, Homo sapiens" +xref: Reactome:REACT_25401 "Activation of JAK kinases, Homo sapiens" +xref: Reactome:REACT_27150 "SHC1 bound to IL2 receptor is phosphorylated, Homo sapiens" +xref: Reactome:REACT_27154 "Recruited STAT5 is phosphorylated, Homo sapiens" +xref: Reactome:REACT_27196 "JAK1 phosphorylates Y338, Y392 and Y510 of IL2RB, Homo sapiens" +xref: Reactome:REACT_27233 "SYK is a substrate for JAK1, Homo sapiens" +xref: Reactome:REACT_27274 "Within the IL-2R complex JAK3 phosphorylates JAK1, Homo sapiens" +xref: Reactome:REACT_28061 "Activation of SRC by RAL-GTP, Canis familiaris" +xref: Reactome:REACT_28067 "SEMA4D interacts with Plexin-B1:Met, Gallus gallus" +xref: Reactome:REACT_28316 "Autocatalytic phosphorylation of FGFR2c, Taeniopygia guttata" +xref: Reactome:REACT_28323 "Phosphorylation of DCC by Fyn, Xenopus tropicalis" +xref: Reactome:REACT_28460 "Phosphorylation of PLC-gamma1, Gallus gallus" +xref: Reactome:REACT_28552 "Phosphorylation of FAK by Src kinase, Danio rerio" +xref: Reactome:REACT_28638 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Bos taurus" +xref: Reactome:REACT_28674 "Autocatalytic phosphorylation of FGFR3b, Rattus norvegicus" +xref: Reactome:REACT_28866 "Autophosphorylation of SRC, Mus musculus" +xref: Reactome:REACT_29048 "Recruitment and activation of Cdk5, Bos taurus" +xref: Reactome:REACT_29099 "Phosphorylation of Rob1 by Abl kinase, Mus musculus" +xref: Reactome:REACT_29101 "Autophosphorylation of PDGF alpha receptors, Rattus norvegicus" +xref: Reactome:REACT_29123 "Phosphorylation of CBL (EGFR:GRB2:CBL), Bos taurus" +xref: Reactome:REACT_29148 "Phosphorylation of PLC-gamma1, Taeniopygia guttata" +xref: Reactome:REACT_29377 "Phosphorylation of ZAP-70 by Lck, Rattus norvegicus" +xref: Reactome:REACT_29521 "Phosphorylation of FAK by Src kinase, Sus scrofa" +xref: Reactome:REACT_29526 "SEMA4D interacts with Plexin-B1:Met, Danio rerio" +xref: Reactome:REACT_29577 "SEMA4D interacts with Plexin-B1:Met, Taeniopygia guttata" +xref: Reactome:REACT_29615 "Autophosphorylation of PDGF alpha/beta receptors, Taeniopygia guttata" +xref: Reactome:REACT_29693 "Phosphorylation of Plexin-A, Rattus norvegicus" +xref: Reactome:REACT_29769 "Autocatalytic phosphorylation of FGFR1c, Danio rerio" +xref: Reactome:REACT_29899 "Autocatalytic phosphorylation of FGFR1c, Taeniopygia guttata" +xref: Reactome:REACT_29922 "Autophosphorylation of NCAM1 bound Fyn, Sus scrofa" +xref: Reactome:REACT_30299 "Phosphorylation of FAK by Src kinase, Xenopus tropicalis" +xref: Reactome:REACT_30341 "PLC gamma phosphorylation by FGFR, Bos taurus" +xref: Reactome:REACT_30537 "Activation of Lck, Rattus norvegicus" +xref: Reactome:REACT_31235 "Phosphorylation of Plexin-A, Sus scrofa" +xref: Reactome:REACT_31355 "Phosphorylation of PLC-gamma1, Sus scrofa" +xref: Reactome:REACT_31634 "Phosphorylation of CBL (EGFR:GRB2:CBL), Danio rerio" +xref: Reactome:REACT_31682 "Autocatalytic phosphorylation of FGFR1b, Taeniopygia guttata" +xref: Reactome:REACT_31711 "Recruitment and activation of Cdk5, Xenopus tropicalis" +xref: Reactome:REACT_31830 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Rattus norvegicus" +xref: Reactome:REACT_32057 "EGFR activates PLC-gamma1 by phosphorylation, Danio rerio" +xref: Reactome:REACT_32137 "Phosphorylation of CD28, Gallus gallus" +xref: Reactome:REACT_32194 "Binding and activation of MAP Kinase, Bos taurus" +xref: Reactome:REACT_32216 "Phosphorylation of CD28, Taeniopygia guttata" +xref: Reactome:REACT_32277 "Phosphorylation of CD28, Sus scrofa" +xref: Reactome:REACT_32339 "Autophosphorylation of SRC, Sus scrofa" +xref: Reactome:REACT_32399 "Activation of SRC by RAL-GTP, Xenopus tropicalis" +xref: Reactome:REACT_32628 "Phosphorylation of FAK by Src kinase, Rattus norvegicus" +xref: Reactome:REACT_32736 "SHP2 is phosphorylated by activated FGFR, Sus scrofa" +xref: Reactome:REACT_33054 "SEMA4D interacts with Plexin-B1:ErbB2, Rattus norvegicus" +xref: Reactome:REACT_33087 "Autocatalytic phosphorylation of FGFR1c, Canis familiaris" +xref: Reactome:REACT_33105 "Autophosphorylation of PDGF alpha/beta receptors, Gallus gallus" +xref: Reactome:REACT_33138 "Autocatalytic phosphorylation of FGFR2c, Bos taurus" +xref: Reactome:REACT_33216 "Autocatalytic phosphorylation of FGFR2c, Gallus gallus" +xref: Reactome:REACT_33253 "Activation of Vav1, Rattus norvegicus" +xref: Reactome:REACT_33271 "Activation of Vav1, Gallus gallus" +xref: Reactome:REACT_33290 "Activation of SRC by RAL-GTP, Gallus gallus" +xref: Reactome:REACT_33346 "Autophosphorylation of SRC, Rattus norvegicus" +xref: Reactome:REACT_33756 "PLC gamma phosphorylation by FGFR, Danio rerio" +xref: Reactome:REACT_33914 "Phosphorylation of L1 by SRC, Mus musculus" +xref: Reactome:REACT_33926 "Phosphorylation of FADK1, Canis familiaris" +xref: Reactome:REACT_33942 "Activation of Src, Bos taurus" +xref: Reactome:REACT_34221 "FGR binds and phosphorylates ApoER2, Bos taurus" +xref: Reactome:REACT_34603 "FGR binds and phosphorylates ApoER2, Taeniopygia guttata" +xref: Reactome:REACT_34631 "Phosphorylation of CBL (EGFR:CBL), Mus musculus" +xref: Reactome:REACT_34748 "Phosphorylation of FAK by Src kinase, Taeniopygia guttata" +xref: Reactome:REACT_34775 "EGFR activates PLC-gamma1 by phosphorylation, Taeniopygia guttata" +xref: Reactome:REACT_38154 "Autocatalytic phosphorylation of FGFR2c, Canis familiaris" +xref: Reactome:REACT_40535 "Phosphorylation of CD28, Rattus norvegicus" +xref: Reactome:REACT_43352 "Autophosphorylation of PDGF beta receptors, Canis familiaris" +xref: Reactome:REACT_49563 "Phosphorylation of Rob1 by Abl kinase, Rattus norvegicus" +xref: Reactome:REACT_525 "Stabilisation of RAF by further phosphorylation, Homo sapiens" +xref: Reactome:REACT_57922 "Recruitment and activation of Cdk5, Rattus norvegicus" +xref: Reactome:REACT_60196 "Tyrosine phosphorylation of CRMPs by Fes, Gallus gallus" +xref: Reactome:REACT_6329 "Chico is phosphorylated, Drosophila melanogaster" +xref: Reactome:REACT_74834 "Autocatalytic phosphorylation of FGFR2b, Canis familiaris" +xref: Reactome:REACT_77018 "Phosphorylation of Unc5C, Canis familiaris" +xref: Reactome:REACT_77187 "Phosphorylation of CBL (EGFR:GRB2:CBL), Rattus norvegicus" +xref: Reactome:REACT_77310 "Phosphorylation of FAK by Src kinase, Gallus gallus" +xref: Reactome:REACT_77327 "Autocatalytic phosphorylation of FGFR2b, Rattus norvegicus" +xref: Reactome:REACT_77390 "Autocatalytic phosphorylation of FGFR3b, Mus musculus" +xref: Reactome:REACT_77515 "Recruitment and activation of Cdk5, Danio rerio" +xref: Reactome:REACT_77685 "Phosphorylation of TBSMs in LAT, Mus musculus" +xref: Reactome:REACT_77703 "FGR binds and phosphorylates ApoER2, Sus scrofa" +xref: Reactome:REACT_77767 "Phosphorylation of SLP-76, Mus musculus" +xref: Reactome:REACT_77899 "SEMA4D interacts with Plexin-B1:Met, Bos taurus" +xref: Reactome:REACT_78031 "Autocatalytic phosphorylation of FGFR3b, Drosophila melanogaster" +xref: Reactome:REACT_78203 "EGFR autophosphorylation, Canis familiaris" +xref: Reactome:REACT_78352 "PLC gamma phosphorylation by FGFR, Mus musculus" +xref: Reactome:REACT_78358 "SEMA4D interacts with Plexin-B1:Met, Rattus norvegicus" +xref: Reactome:REACT_78386 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Bos taurus" +xref: Reactome:REACT_78434 "Autocatalytic phosphorylation of FGFR3c, Sus scrofa" +xref: Reactome:REACT_78498 "Phosphorylation of L1 by EPHB2, Sus scrofa" +xref: Reactome:REACT_78685 "Autocatalytic phosphorylation of FGFR4, Rattus norvegicus" +xref: Reactome:REACT_78701 "Fyn/Lyn-mediated phosphorylation of FcR1 gamma, Rattus norvegicus" +xref: Reactome:REACT_78868 "Binding and activation of MAP Kinase, Mus musculus" +xref: Reactome:REACT_78902 "Binding and activation of MAP Kinase, Taeniopygia guttata" +xref: Reactome:REACT_78920 "Autophosphorylation of PDGF alpha/beta receptors, Danio rerio" +xref: Reactome:REACT_78933 "Phosphorylation of L1 by EPHB2, Bos taurus" +xref: Reactome:REACT_79167 "Autocatalytic phosphorylation of FGFR1c, Rattus norvegicus" +xref: Reactome:REACT_79338 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Gallus gallus" +xref: Reactome:REACT_79355 "SYK activation by SRC, Sus scrofa" +xref: Reactome:REACT_79394 "Autocatalytic phosphorylation of FGFR2c, Danio rerio" +xref: Reactome:REACT_79407 "SEMA4D interacts with Plexin-B1:ErbB2, Gallus gallus" +xref: Reactome:REACT_79427 "Binding and activation of MAP Kinase, Canis familiaris" +xref: Reactome:REACT_79501 "Inactivation of Lck by Csk, Mus musculus" +xref: Reactome:REACT_79608 "Autocatalytic phosphorylation of FGFR3c, Drosophila melanogaster" +xref: Reactome:REACT_79726 "Phosphorylation of CTLA-4, Taeniopygia guttata" +xref: Reactome:REACT_79900 "Activation of Vav1, Taeniopygia guttata" +xref: Reactome:REACT_79967 "Phosphorylation of L1 by EPHB2, Rattus norvegicus" +xref: Reactome:REACT_80076 "Phosphorylation of Plexin-A, Gallus gallus" +xref: Reactome:REACT_80306 "Phosphorylation of PLC-gamma1, Danio rerio" +xref: Reactome:REACT_80363 "Autocatalytic phosphorylation of FGFR1b, Mus musculus" +xref: Reactome:REACT_80527 "Phosphorylation of ITIM in SIRP alpha, Canis familiaris" +xref: Reactome:REACT_80528 "Autocatalytic phosphorylation of FGFR1c, Bos taurus" +xref: Reactome:REACT_80684 "Activation of Vav1, Sus scrofa" +xref: Reactome:REACT_80829 "EGFR autophosphorylation, Danio rerio" +xref: Reactome:REACT_81084 "Autophosphorylation of PDGF beta receptors, Danio rerio" +xref: Reactome:REACT_81125 "Tyrosine phosphorylation of CRMPs by Fes, Mus musculus" +xref: Reactome:REACT_81165 "Tyrosine phosphorylation of CRMPs by Fes, Danio rerio" +xref: Reactome:REACT_81176 "FGR binds and phosphorylates ApoER2, Mus musculus" +xref: Reactome:REACT_81177 "Autophosphorylation of PDGF alpha receptors, Xenopus tropicalis" +xref: Reactome:REACT_81361 "SYK activation by SRC, Taeniopygia guttata" +xref: Reactome:REACT_81398 "Activation of Src, Xenopus tropicalis" +xref: Reactome:REACT_81445 "Autocatalytic phosphorylation of FGFR1c, Xenopus tropicalis" +xref: Reactome:REACT_81546 "Phosphorylation of ITAM motifs in CD3 complexes, Rattus norvegicus" +xref: Reactome:REACT_81596 "Phosphorylation of Unc5C, Rattus norvegicus" +xref: Reactome:REACT_81637 "Phosphorylation of DCC by Fyn, Danio rerio" +xref: Reactome:REACT_81739 "Gab1 phosphorylation by EGFR kinase, Rattus norvegicus" +xref: Reactome:REACT_81818 "Phosphorylation of L1 by SRC, Rattus norvegicus" +xref: Reactome:REACT_81894 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Taeniopygia guttata" +xref: Reactome:REACT_82030 "Autocatalytic phosphorylation of FGFR3b, Xenopus tropicalis" +xref: Reactome:REACT_82127 "SEMA4D interacts with Plexin-B1:ErbB2, Danio rerio" +xref: Reactome:REACT_82339 "Phosphorylation of Unc5C, Xenopus tropicalis" +xref: Reactome:REACT_82460 "Trans-phosphorylation of Tie2, Gallus gallus" +xref: Reactome:REACT_82503 "EGFR autophosphorylation, Rattus norvegicus" +xref: Reactome:REACT_82597 "Phosphorylation of CBL (EGFR:GRB2:CBL), Xenopus tropicalis" +xref: Reactome:REACT_82628 "Autophosphorylation of PDGF alpha receptors, Bos taurus" +xref: Reactome:REACT_82799 "Tyrosine phosphorylation of CRMPs by Fes, Canis familiaris" +xref: Reactome:REACT_82806 "Autocatalytic phosphorylation of FGFR4, Taeniopygia guttata" +xref: Reactome:REACT_83131 "Activation of ZAP-70, Rattus norvegicus" +xref: Reactome:REACT_83348 "Activation of SRC by RAL-GTP, Mus musculus" +xref: Reactome:REACT_83486 "Binding and activation of MAP Kinase, Drosophila melanogaster" +xref: Reactome:REACT_83804 "Phosphorylation of FRS2-alpha by activated FGFR, Sus scrofa" +xref: Reactome:REACT_83974 "Autophosphorylation of NCAM1 bound Fyn, Canis familiaris" +xref: Reactome:REACT_84259 "Phosphorylation of EGFR by SRC kinase, Rattus norvegicus" +xref: Reactome:REACT_84420 "SEMA4D interacts with Plexin-B1:Met, Xenopus tropicalis" +xref: Reactome:REACT_84487 "Gab1 phosphorylation by EGFR kinase, Xenopus tropicalis" +xref: Reactome:REACT_84530 "SEMA4D interacts with Plexin-B1:Met, Sus scrofa" +xref: Reactome:REACT_84612 "Phosphorylation of Plexin-A, Canis familiaris" +xref: Reactome:REACT_84708 "EGFR activates PLC-gamma1 by phosphorylation, Canis familiaris" +xref: Reactome:REACT_84773 "Binding and activation of MAP Kinase, Danio rerio" +xref: Reactome:REACT_84824 "Phosphorylation of CBL (EGFR:GRB2:CBL), Gallus gallus" +xref: Reactome:REACT_84886 "Phosphorylation of CD28, Canis familiaris" +xref: Reactome:REACT_84961 "Phosphorylation of Unc5C, Sus scrofa" +xref: Reactome:REACT_84986 "Activation of Vav1, Canis familiaris" +xref: Reactome:REACT_85005 "Phosphorylation of DCC by Fyn, Sus scrofa" +xref: Reactome:REACT_85077 "Trans-phosphorylation of Tie2, Bos taurus" +xref: Reactome:REACT_85117 "Autocatalytic phosphorylation of FGFR4, Danio rerio" +xref: Reactome:REACT_85126 "Activation of Src, Mus musculus" +xref: Reactome:REACT_85374 "Autocatalytic phosphorylation of FGFR3c, Taeniopygia guttata" +xref: Reactome:REACT_85443 "Phosphorylation of CBL (EGFR:GRB2:CBL), Taeniopygia guttata" +xref: Reactome:REACT_85500 "Tyrosine phosphorylation of CRMPs by Fes, Taeniopygia guttata" +xref: Reactome:REACT_85722 "Syk/Lck phosphorylate LAT, Sus scrofa" +xref: Reactome:REACT_85785 "Phosphorylation of Rob1 by Abl kinase, Taeniopygia guttata" +xref: Reactome:REACT_85969 "Gab1 phosphorylation by EGFR kinase, Canis familiaris" +xref: Reactome:REACT_86238 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Taeniopygia guttata" +xref: Reactome:REACT_86388 "Phosphorylation of nephrin by the Src family kinase Fyn, Canis familiaris" +xref: Reactome:REACT_86407 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Canis familiaris" +xref: Reactome:REACT_86502 "Autophosphorylation of PDGF alpha/beta receptors, Canis familiaris" +xref: Reactome:REACT_86510 "Phosphorylation of CBL (EGFR:CBL), Canis familiaris" +xref: Reactome:REACT_86579 "Autocatalytic phosphorylation of FGFR2b, Taeniopygia guttata" +xref: Reactome:REACT_86618 "EGFR autophosphorylation, Xenopus tropicalis" +xref: Reactome:REACT_86622 "Phosphorylation of PLC-gamma1, Rattus norvegicus" +xref: Reactome:REACT_86769 "PLC gamma phosphorylation by FGFR, Gallus gallus" +xref: Reactome:REACT_86814 "Activation of Src, Rattus norvegicus" +xref: Reactome:REACT_87052 "Autophosphorylation of NCAM1 bound Fyn, Bos taurus" +xref: Reactome:REACT_87153 "Autophosphorylation of PDGF beta receptors, Taeniopygia guttata" +xref: Reactome:REACT_87252 "Autophosphorylation of PDGF beta receptors, Gallus gallus" +xref: Reactome:REACT_87259 "Autocatalytic phosphorylation of FGFR1c, Drosophila melanogaster" +xref: Reactome:REACT_87371 "Phosphorylation of L1 by SRC, Sus scrofa" +xref: Reactome:REACT_87435 "Phosphorylation of EGFR by SRC kinase, Canis familiaris" +xref: Reactome:REACT_87511 "Fyn/Lyn-mediated phosphorylation of FcR1 gamma, Mus musculus" +xref: Reactome:REACT_87566 "Autocatalytic phosphorylation of FGFR3c, Danio rerio" +xref: Reactome:REACT_87684 "Autocatalytic phosphorylation of FGFR3c, Mus musculus" +xref: Reactome:REACT_87815 "Phosphorylation of Rob1 by Abl kinase, Gallus gallus" +xref: Reactome:REACT_87823 "SHP2 is phosphorylated by activated FGFR, Danio rerio" +xref: Reactome:REACT_87830 "SEMA4D interacts with Plexin-B1:ErbB2, Sus scrofa" +xref: Reactome:REACT_87952 "Phosphorylation of Rob1 by Abl kinase, Danio rerio" +xref: Reactome:REACT_87984 "Autophosphorylation of PDGF alpha/beta receptors, Bos taurus" +xref: Reactome:REACT_88004 "Phosphorylation of EGFR by SRC kinase, Gallus gallus" +xref: Reactome:REACT_88019 "Autophosphorylation of PDGF beta receptors, Bos taurus" +xref: Reactome:REACT_88033 "Trans-phosphorylation of Tie2, Xenopus tropicalis" +xref: Reactome:REACT_88054 "PLC gamma phosphorylation by FGFR, Canis familiaris" +xref: Reactome:REACT_88160 "Autophosphorylation of SRC, Danio rerio" +xref: Reactome:REACT_88281 "Autophosphorylation of PDGF alpha receptors, Taeniopygia guttata" +xref: Reactome:REACT_88379 "Phosphorylation of nephrin by the Src family kinase Fyn, Danio rerio" +xref: Reactome:REACT_88380 "Phosphorylation of FRS2-alpha by activated FGFR, Taeniopygia guttata" +xref: Reactome:REACT_88407 "Autocatalytic phosphorylation of FGFR2c, Sus scrofa" +xref: Reactome:REACT_88554 "Autocatalytic phosphorylation of FGFR1b, Gallus gallus" +xref: Reactome:REACT_88600 "EGFR activates PLC-gamma1 by phosphorylation, Rattus norvegicus" +xref: Reactome:REACT_89014 "SYK activation by SRC, Gallus gallus" +xref: Reactome:REACT_89147 "Autocatalytic phosphorylation of FGFR3c, Gallus gallus" +xref: Reactome:REACT_89172 "SHP2 is phosphorylated by activated FGFR, Mus musculus" +xref: Reactome:REACT_89228 "SHP2 is phosphorylated by activated FGFR, Canis familiaris" +xref: Reactome:REACT_89287 "Gab1 phosphorylation by EGFR kinase, Mus musculus" +xref: Reactome:REACT_89340 "Phosphorylation of FADK1, Danio rerio" +xref: Reactome:REACT_89450 "Phosphorylation of FRS2-alpha by activated FGFR, Gallus gallus" +xref: Reactome:REACT_89463 "Gab1 phosphorylation by EGFR kinase, Bos taurus" +xref: Reactome:REACT_89473 "Autophosphorylation of PDGF beta receptors, Mus musculus" +xref: Reactome:REACT_89616 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Sus scrofa" +xref: Reactome:REACT_89754 "Activation of Src, Sus scrofa" +xref: Reactome:REACT_89762 "Phosphorylation of CBL (EGFR:GRB2:CBL), Canis familiaris" +xref: Reactome:REACT_90297 "Gab1 phosphorylation by EGFR kinase, Danio rerio" +xref: Reactome:REACT_90301 "SEMA4D interacts with Plexin-B1:ErbB2, Bos taurus" +xref: Reactome:REACT_90417 "Autocatalytic phosphorylation of FGFR2c, Drosophila melanogaster" +xref: Reactome:REACT_90496 "Phosphorylation of L1 by SRC, Danio rerio" +xref: Reactome:REACT_90538 "Change of PKC theta conformation, Rattus norvegicus" +xref: Reactome:REACT_90572 "Phosphorylation of Unc5C, Danio rerio" +xref: Reactome:REACT_90657 "Phosphorylation of L1 by EPHB2, Danio rerio" +xref: Reactome:REACT_91164 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Mus musculus" +xref: Reactome:REACT_91188 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Sus scrofa" +xref: Reactome:REACT_91376 "Activation of Src, Gallus gallus" +xref: Reactome:REACT_91467 "Autophosphorylation of NCAM1 bound Fyn, Rattus norvegicus" +xref: Reactome:REACT_91515 "Phosphorylation of FADK1, Drosophila melanogaster" +xref: Reactome:REACT_91538 "Fyn/Lyn-mediated phosphorylation of FcR1 gamma, Sus scrofa" +xref: Reactome:REACT_91883 "Autocatalytic phosphorylation of FGFR3b, Canis familiaris" +xref: Reactome:REACT_91997 "SYK activation by SRC, Rattus norvegicus" +xref: Reactome:REACT_92220 "Syk/Lck phosphorylate LAT, Rattus norvegicus" +xref: Reactome:REACT_92230 "Phosphorylation of EGFR by SRC kinase, Xenopus tropicalis" +xref: Reactome:REACT_92251 "Phosphorylation of L1 by SRC, Bos taurus" +xref: Reactome:REACT_92280 "Phosphorylation of EGFR by SRC kinase, Mus musculus" +xref: Reactome:REACT_92311 "Gab1 phosphorylation by EGFR kinase, Taeniopygia guttata" +xref: Reactome:REACT_92436 "Recruitment and activation of Cdk5, Mus musculus" +xref: Reactome:REACT_92703 "Phosphorylation of FAK by Src kinase, Canis familiaris" +xref: Reactome:REACT_92709 "Change of PKC theta conformation, Mus musculus" +xref: Reactome:REACT_92984 "Phosphorylation of FAK by Src kinase, Bos taurus" +xref: Reactome:REACT_93198 "Activation of Lck, Mus musculus" +xref: Reactome:REACT_93265 "PLC gamma phosphorylation by FGFR, Xenopus tropicalis" +xref: Reactome:REACT_93848 "Phosphorylation of Plexin-A, Danio rerio" +xref: Reactome:REACT_9388 "EGFR autophosphorylation, Homo sapiens" +xref: Reactome:REACT_9401 "Phosphorylation of EGFR by SRC kinase, Homo sapiens" +xref: Reactome:REACT_94058 "Phosphorylation of Unc5C, Bos taurus" +xref: Reactome:REACT_94134 "EGFR activates PLC-gamma1 by phosphorylation, Xenopus tropicalis" +xref: Reactome:REACT_94177 "Autocatalytic phosphorylation of FGFR3c, Rattus norvegicus" +xref: Reactome:REACT_9419 "Autocatalytic phosphorylation of FGFR3c, Homo sapiens" +xref: Reactome:REACT_94210 "Phosphorylation of Plexin-A, Bos taurus" +xref: Reactome:REACT_94240 "Autocatalytic phosphorylation of FGFR3b, Gallus gallus" +xref: Reactome:REACT_9432 "Autocatalytic phosphorylation of FGFR2c, Homo sapiens" +xref: Reactome:REACT_9433 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Homo sapiens" +xref: Reactome:REACT_94384 "Phosphorylation of CBL (EGFR:CBL), Danio rerio" +xref: Reactome:REACT_94446 "Phosphorylation of Rob1 by Abl kinase, Bos taurus" +xref: Reactome:REACT_94605 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Danio rerio" +xref: Reactome:REACT_9474 "Autocatalytic phosphorylation of FGFR4, Homo sapiens" +xref: Reactome:REACT_9476 "Autocatalytic phosphorylation of FGFR2b, Homo sapiens" +xref: Reactome:REACT_94802 "Autophosphorylation of SRC, Canis familiaris" +xref: Reactome:REACT_94886 "Phosphorylation of CD28, Mus musculus" +xref: Reactome:REACT_9493 "Autocatalytic phosphorylation of FGFR1b, Homo sapiens" +xref: Reactome:REACT_9498 "Autocatalytic phosphorylation of FGFR1c, Homo sapiens" +xref: Reactome:REACT_95037 "Phosphorylation of FADK1, Caenorhabditis elegans" +xref: Reactome:REACT_9519 "Autocatalytic phosphorylation of FGFR3b, Homo sapiens" +xref: Reactome:REACT_95415 "Autocatalytic phosphorylation of FGFR3b, Bos taurus" +xref: Reactome:REACT_95734 "Autocatalytic phosphorylation of FGFR3c, Bos taurus" +xref: Reactome:REACT_95742 "Phosphorylation of DCC by Fyn, Caenorhabditis elegans" +xref: Reactome:REACT_95822 "Phosphorylation of L1 by EPHB2, Canis familiaris" +xref: Reactome:REACT_95833 "SHP2 is phosphorylated by activated FGFR, Taeniopygia guttata" +xref: Reactome:REACT_95870 "Recruitment of FAK to NCAM1:Fyn in lipid rafts, Drosophila melanogaster" +xref: Reactome:REACT_95963 "Autocatalytic phosphorylation of FGFR2b, Xenopus tropicalis" +xref: Reactome:REACT_96010 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Canis familiaris" +xref: Reactome:REACT_96018 "Autophosphorylation of PDGF alpha receptors, Mus musculus" +xref: Reactome:REACT_96142 "Phosphorylation of FRS2-alpha by activated FGFR, Xenopus tropicalis" +xref: Reactome:REACT_96362 "Autophosphorylation of PDGF alpha/beta receptors, Mus musculus" +xref: Reactome:REACT_96502 "Autocatalytic phosphorylation of FGFR3b, Sus scrofa" +xref: Reactome:REACT_96514 "Autophosphorylation of PDGF alpha/beta receptors, Xenopus tropicalis" +xref: Reactome:REACT_96580 "Autocatalytic phosphorylation of FGFR4, Drosophila melanogaster" +xref: Reactome:REACT_96596 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Danio rerio" +xref: Reactome:REACT_96705 "Autocatalytic phosphorylation of Klotho-bound FGFR1c, Gallus gallus" +xref: Reactome:REACT_96733 "Trans-phosphorylation of Tie2, Rattus norvegicus" +xref: Reactome:REACT_97087 "Autocatalytic phosphorylation of FGFR3c, Canis familiaris" +xref: Reactome:REACT_97142 "Phosphorylation of DCC by Fyn, Canis familiaris" +xref: Reactome:REACT_97562 "Phosphorylation of CBL (EGFR:CBL), Rattus norvegicus" +xref: Reactome:REACT_97685 "Phosphorylation of Plexin-A, Xenopus tropicalis" +xref: Reactome:REACT_97728 "SYK activation by SRC, Mus musculus" +xref: Reactome:REACT_97810 "SEMA4D interacts with Plexin-B1:ErbB2, Taeniopygia guttata" +xref: Reactome:REACT_97895 "Binding and activation of MAP Kinase, Gallus gallus" +xref: Reactome:REACT_98106 "Recruitment and activation of Cdk5, Canis familiaris" +xref: Reactome:REACT_98221 "Phosphorylation of Rob1 by Abl kinase, Sus scrofa" +xref: Reactome:REACT_98541 "SEMA4D interacts with Plexin-B1:Met, Canis familiaris" +xref: Reactome:REACT_98748 "Activation of Vav1, Xenopus tropicalis" +xref: Reactome:REACT_98850 "Autophosphorylation of PDGF alpha/beta receptors, Sus scrofa" +xref: Reactome:REACT_98862 "Autocatalytic phosphorylation of FGFR3b, Danio rerio" +xref: Reactome:REACT_98867 "FGR binds and phosphorylates ApoER2, Rattus norvegicus" +xref: Reactome:REACT_98878 "Activation of Src, Taeniopygia guttata" +xref: Reactome:REACT_98980 "Phosphorylation of SLP-76, Rattus norvegicus" +xref: Reactome:REACT_98992 "Autocatalytic phosphorylation of FGFR4, Xenopus tropicalis" +xref: Reactome:REACT_99026 "Autocatalytic phosphorylation of FGFR2c, Xenopus tropicalis" +xref: Reactome:REACT_99257 "Autocatalytic phosphorylation of FGFR2b, Gallus gallus" +xref: Reactome:REACT_99293 "Syk/Lck phosphorylate LAT, Canis familiaris" +xref: Reactome:REACT_99500 "Activation of Src, Canis familiaris" +xref: Reactome:REACT_99541 "Fyn/Lyn-mediated phosphorylation of FcR1 gamma, Bos taurus" +xref: Reactome:REACT_99611 "Phosphorylation of FADK1, Rattus norvegicus" +xref: Reactome:REACT_99704 "SHP2 is phosphorylated by activated FGFR, Gallus gallus" +xref: Reactome:REACT_99827 "SYK activation by SRC, Danio rerio" +xref: Reactome:REACT_99888 "Gab1 phosphorylation by EGFR kinase, Gallus gallus" +is_a: GO:0004672 ! protein kinase activity +relationship: part_of GO:0018108 ! peptidyl-tyrosine phosphorylation + +[Term] +id: GO:0004857 +name: enzyme inhibitor activity +namespace: molecular_function +def: "Stops, prevents or reduces the activity of an enzyme." [GOC:ai] +subset: gosubset_prok +is_a: GO:0030234 ! enzyme regulator activity +relationship: part_of GO:0043086 ! negative regulation of catalytic activity + +[Term] +id: GO:0004871 +name: signal transducer activity +namespace: molecular_function +alt_id: GO:0005062 +alt_id: GO:0009369 +alt_id: GO:0009370 +def: "Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:go_curators] +comment: Ligands do NOT have the molecular function 'signal transducer activity'. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "hematopoietin/interferon-class (D200-domain) cytokine receptor signal transducer activity" NARROW [] +synonym: "quorum sensing response regulator activity" NARROW [] +synonym: "quorum sensing signal generator activity" NARROW [] +is_a: GO:0060089 ! molecular transducer activity +relationship: part_of GO:0007165 ! signal transduction + +[Term] +id: GO:0004872 +name: receptor activity +namespace: molecular_function +alt_id: GO:0019041 +def: "Combining with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:ceb, ISBN:0198506732] +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "receptor guanylate cyclase activity" NARROW [] +synonym: "viral antireceptor activity" NARROW [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0004879 +name: ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity +namespace: molecular_function +def: "Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, GOC:txnOH] +comment: GO:0004879 is intended for annotation of nuclear receptors that regulate transcription by binding directly to DNA. When the nuclear receptor functions by binding to other transcription factors or transcription factor complexes, consider instead annotating to 'ligand-activated RNA polymerase II transcription factor binding transcription factor activity ; GO:0038049'. +synonym: "ligand-dependent nuclear receptor activity" RELATED [GOC:bf] +synonym: "ligand-dependent transcription factor activity" RELATED [GOC:bf] +synonym: "nuclear hormone receptor" NARROW [] +synonym: "nuclear receptor activity" RELATED [GOC:bf] +is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity +is_a: GO:0098531 ! direct ligand regulated sequence-specific DNA binding transcription factor activity +relationship: part_of GO:0030522 ! intracellular receptor signaling pathway + +[Term] +id: GO:0004882 +name: androgen receptor activity +namespace: molecular_function +def: "Combining with an androgen and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with an androgen response element in DNA in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:19372015] +synonym: "androgen response element binding" NARROW [GOC:yaf] +is_a: GO:0003707 ! steroid hormone receptor activity +is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity +relationship: has_part GO:0005497 ! androgen binding +relationship: part_of GO:0030521 ! androgen receptor signaling pathway + +[Term] +id: GO:0004888 +name: transmembrane signaling receptor activity +namespace: molecular_function +alt_id: GO:0004926 +def: "Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:go_curators, Wikipedia:Transmembrane_receptor] +comment: 'Transmembrane' in the term name refers to the mechanism of transmitting the signal across the membrane, rather than the subcellular location of the receptor. +subset: gosubset_prok +synonym: "non G protein coupled 7TM receptor activity" NARROW [] +synonym: "non-G-protein coupled 7TM receptor activity" NARROW [] +synonym: "non-G-protein-coupled 7TM receptor activity" NARROW [] +synonym: "transmembrane receptor activity" BROAD [GOC:bf, GOC:signaling] +synonym: "transmembrane signalling receptor activity" EXACT [GOC:mah] +is_a: GO:0038023 ! signaling receptor activity + +[Term] +id: GO:0005041 +name: low-density lipoprotein receptor activity +namespace: molecular_function +alt_id: GO:0008032 +def: "Combining with a low-density lipoprotein particle and delivering the low-density lipoprotein into the cell via endocytosis." [GOC:bf, ISBN:0198506732] +subset: gosubset_prok +synonym: "LDL receptor" EXACT [] +synonym: "LDLR activity" EXACT [GOC:bf] +xref: Wikipedia:LDL_receptor +is_a: GO:0030228 ! lipoprotein particle receptor activity +relationship: has_part GO:0030169 ! low-density lipoprotein particle binding + +[Term] +id: GO:0005057 +name: receptor signaling protein activity +namespace: molecular_function +def: "Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell." [GOC:bf] +comment: This term is intended for annotation of signal transducers that act directly or indirectly downstream of a receptor. For receptors themselves, consider annotating to the term 'receptor activity ; GO:0004872'. +synonym: "intracellular signal transducer activity" EXACT [GOC:bf] +synonym: "receptor signalling protein activity" EXACT [] +is_a: GO:0004871 ! signal transducer activity +intersection_of: GO:0004871 ! signal transducer activity +intersection_of: occurs_in GO:0005622 ! intracellular +relationship: part_of GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0005102 +name: receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:bf, GOC:ceb, ISBN:0198506732] +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "receptor ligand" NARROW [] +synonym: "receptor-associated protein activity" RELATED [] +xref: Wikipedia:Ligand_(biochemistry) +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0005109 +name: frizzled binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with the frizzled (fz) receptor." [GOC:ceb, PR:000001315] +synonym: "frizzled ligand" NARROW [] +synonym: "fz binding" EXACT [] +synonym: "fz ligand" NARROW [] +is_a: GO:0001664 ! G-protein coupled receptor binding + +[Term] +id: GO:0005110 +name: frizzled-2 binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with frizzled-2 (fz2)." [GOC:ceb, PR:000007719] +synonym: "frizzled-2 ligand" NARROW [] +synonym: "fz2 binding" EXACT [] +synonym: "fz2 ligand" NARROW [] +is_a: GO:0005109 ! frizzled binding + +[Term] +id: GO:0005115 +name: receptor tyrosine kinase-like orphan receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with the receptor tyrosine kinase-like orphan receptor (Ror)." [GOC:ceb, GOC:vw] +synonym: "receptor tyrosine kinase-like orphan receptor ligand" NARROW [] +synonym: "Ror binding" BROAD [] +synonym: "Ror ligand" RELATED [] +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0005125 +name: cytokine activity +namespace: molecular_function +def: "Functions to control the survival, growth, differentiation and effector function of tissues and cells." [ISBN:0198599471] +synonym: "autocrine activity" RELATED [GOC:rl] +synonym: "paracrine activity" RELATED [GOC:rl] +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0005198 +name: structural molecule activity +namespace: molecular_function +def: "The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell." [GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0005215 +name: transporter activity +namespace: molecular_function +alt_id: GO:0005478 +def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:ai, GOC:dgf] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "small-molecule carrier or transporter" RELATED [] +xref: Reactome:REACT_6315 "Virion-associated M2 protein mediated ion infusion, Homo sapiens" +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0006810 ! transport + +[Term] +id: GO:0005488 +name: binding +namespace: molecular_function +def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] +comment: For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "ligand" NARROW [] +xref: Wikipedia:Binding_(molecular) +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0005496 +name: steroid binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene." [GOC:jl, ISBN:0198506732] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008289 ! lipid binding +is_a: GO:0097159 ! organic cyclic compound binding + +[Term] +id: GO:0005497 +name: androgen binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any androgen, male sex hormones." [CHEBI:50113, GOC:jl] +is_a: GO:0005496 ! steroid binding +is_a: GO:0042562 ! hormone binding + +[Term] +id: GO:0005509 +name: calcium ion binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with calcium ions (Ca2+)." [GOC:ai] +subset: gosubset_prok +synonym: "calcium ion storage activity" RELATED [] +xref: Reactome:REACT_20509 "Exocytosis of Insulin, Mus musculus" +is_a: GO:0046872 ! metal ion binding + +[Term] +id: GO:0005515 +name: protein binding +namespace: molecular_function +alt_id: GO:0045308 +def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "alpha-2 macroglobulin receptor-associated protein activity" RELATED [] +synonym: "protein amino acid binding" EXACT [] +synonym: "protein degradation tagging activity" RELATED [] +synonym: "protein folding chaperone" NARROW [GOC:dph, GOC:mah, GOC:tb] +synonym: "protein tagging activity" RELATED [] +xref: Reactome:REACT_100287 "Formation of the IGF:IGFBP-4 Complex, Canis familiaris" +xref: Reactome:REACT_101129 "Formation of the IGF:IGFBP-3:ALS Complex, Rattus norvegicus" +xref: Reactome:REACT_102084 "Formation of the IGF:IGFBP-5:ALS Complex, Mus musculus" +xref: Reactome:REACT_102457 "An anchoring protein, SARA, recruits SMAD2/3, Canis familiaris" +xref: Reactome:REACT_103972 "Type II receptor recruits type I receptor, Xenopus tropicalis" +xref: Reactome:REACT_104029 "Formation of the IGF:IGFBP-6 Complex, Bos taurus" +xref: Reactome:REACT_104599 "Type II receptor recruits type I receptor, Sus scrofa" +xref: Reactome:REACT_105776 "Formation of the IGF:IGFBP-3:ALS Complex, Danio rerio" +xref: Reactome:REACT_105895 "Formation of the IGF:IGFBP-4 Complex, Bos taurus" +xref: Reactome:REACT_106168 "Formation of the IGF:IGFBP-2 Complex, Bos taurus" +xref: Reactome:REACT_106189 "Formation of the IGF:IGFBP-5:ALS Complex, Gallus gallus" +xref: Reactome:REACT_107402 "Formation of the IGF:IGFBP-4 Complex, Mus musculus" +xref: Reactome:REACT_108283 "Formation of the IGF:IGFBP-4 Complex, Xenopus tropicalis" +xref: Reactome:REACT_109392 "Formation of the IGF:IGFBP-3:ALS Complex, Gallus gallus" +xref: Reactome:REACT_110419 "Type II receptor recruits type I receptor, Bos taurus" +xref: Reactome:REACT_110570 "Formation of the IGF:IGFBP-3:ALS Complex, Sus scrofa" +xref: Reactome:REACT_15321 "Formation of the IGF:IGFBP-1 Complex, Homo sapiens" +xref: Reactome:REACT_15325 "Formation of the IGF:IGFBP-4 Complex, Homo sapiens" +xref: Reactome:REACT_15355 "Formation of the IGF:IGFBP-5:ALS Complex, Homo sapiens" +xref: Reactome:REACT_15417 "Formation of the IGF:IGFBP-3:ALS Complex, Homo sapiens" +xref: Reactome:REACT_15419 "Formation of the IGF:IGFBP-2 Complex, Homo sapiens" +xref: Reactome:REACT_15506 "Formation of the IGF:IGFBP-6 Complex, Homo sapiens" +xref: Reactome:REACT_15541 "Traversal of the cortical actin network and docking at plasma membrane, Homo sapiens" +xref: Reactome:REACT_20509 "Exocytosis of Insulin, Mus musculus" +xref: Reactome:REACT_20539 "Traversal of the cortical actin network., Mus musculus" +xref: Reactome:REACT_28794 "Formation of the IGF:IGFBP-4 Complex, Sus scrofa" +xref: Reactome:REACT_30571 "Formation of the IGF:IGFBP-6 Complex, Danio rerio" +xref: Reactome:REACT_30672 "Formation of the IGF:IGFBP-2 Complex, Taeniopygia guttata" +xref: Reactome:REACT_31305 "Formation of the IGF:IGFBP-3:ALS Complex, Taeniopygia guttata" +xref: Reactome:REACT_31537 "Formation of the IGF:IGFBP-6 Complex, Rattus norvegicus" +xref: Reactome:REACT_31641 "Type II receptor recruits type I receptor, Danio rerio" +xref: Reactome:REACT_31648 "An anchoring protein, SARA, recruits SMAD2/3, Mus musculus" +xref: Reactome:REACT_32973 "Formation of the IGF:IGFBP-1 Complex, Canis familiaris" +xref: Reactome:REACT_33135 "An anchoring protein, SARA, recruits SMAD2/3, Rattus norvegicus" +xref: Reactome:REACT_34719 "Formation of the IGF:IGFBP-1 Complex, Danio rerio" +xref: Reactome:REACT_6923 "An anchoring protein, SARA, recruits SMAD2/3, Homo sapiens" +xref: Reactome:REACT_6945 "Type II receptor recruits type I receptor, Homo sapiens" +xref: Reactome:REACT_78382 "Formation of the IGF:IGFBP-1 Complex, Mus musculus" +xref: Reactome:REACT_78466 "Formation of the IGF:IGFBP-6 Complex, Canis familiaris" +xref: Reactome:REACT_79634 "Formation of the IGF:IGFBP-5:ALS Complex, Canis familiaris" +xref: Reactome:REACT_80470 "Formation of the IGF:IGFBP-1 Complex, Rattus norvegicus" +xref: Reactome:REACT_80778 "Type II receptor recruits type I receptor, Mus musculus" +xref: Reactome:REACT_83147 "Type II receptor recruits type I receptor, Rattus norvegicus" +xref: Reactome:REACT_83165 "Formation of the IGF:IGFBP-5:ALS Complex, Sus scrofa" +xref: Reactome:REACT_83532 "Formation of the IGF:IGFBP-2 Complex, Xenopus tropicalis" +xref: Reactome:REACT_85250 "Formation of the IGF:IGFBP-2 Complex, Canis familiaris" +xref: Reactome:REACT_85858 "Formation of the IGF:IGFBP-2 Complex, Gallus gallus" +xref: Reactome:REACT_85975 "An anchoring protein, SARA, recruits SMAD2/3, Danio rerio" +xref: Reactome:REACT_87187 "An anchoring protein, SARA, recruits SMAD2/3, Xenopus tropicalis" +xref: Reactome:REACT_87374 "Formation of the IGF:IGFBP-6 Complex, Sus scrofa" +xref: Reactome:REACT_87652 "Formation of the IGF:IGFBP-5:ALS Complex, Bos taurus" +xref: Reactome:REACT_88068 "Formation of the IGF:IGFBP-3:ALS Complex, Canis familiaris" +xref: Reactome:REACT_88138 "Formation of the IGF:IGFBP-5:ALS Complex, Danio rerio" +xref: Reactome:REACT_88223 "Formation of the IGF:IGFBP-1 Complex, Sus scrofa" +xref: Reactome:REACT_89261 "Formation of the IGF:IGFBP-4 Complex, Taeniopygia guttata" +xref: Reactome:REACT_90027 "Formation of the IGF:IGFBP-2 Complex, Rattus norvegicus" +xref: Reactome:REACT_90105 "Formation of the IGF:IGFBP-1 Complex, Xenopus tropicalis" +xref: Reactome:REACT_90666 "An anchoring protein, SARA, recruits SMAD2/3, Sus scrofa" +xref: Reactome:REACT_91560 "Type II receptor recruits type I receptor, Canis familiaris" +xref: Reactome:REACT_92029 "Formation of the IGF:IGFBP-4 Complex, Rattus norvegicus" +xref: Reactome:REACT_93175 "Formation of the IGF:IGFBP-1 Complex, Gallus gallus" +xref: Reactome:REACT_93938 "Formation of the IGF:IGFBP-5:ALS Complex, Rattus norvegicus" +xref: Reactome:REACT_94522 "Formation of the IGF:IGFBP-5:ALS Complex, Taeniopygia guttata" +xref: Reactome:REACT_94808 "Formation of the IGF:IGFBP-6 Complex, Mus musculus" +xref: Reactome:REACT_95241 "Formation of the IGF:IGFBP-3:ALS Complex, Mus musculus" +xref: Reactome:REACT_95561 "Formation of the IGF:IGFBP-5:ALS Complex, Xenopus tropicalis" +xref: Reactome:REACT_95647 "Formation of the IGF:IGFBP-3:ALS Complex, Bos taurus" +xref: Reactome:REACT_96236 "Formation of the IGF:IGFBP-2 Complex, Mus musculus" +xref: Reactome:REACT_96264 "Formation of the IGF:IGFBP-2 Complex, Danio rerio" +xref: Reactome:REACT_98028 "Formation of the IGF:IGFBP-1 Complex, Taeniopygia guttata" +xref: Reactome:REACT_98807 "An anchoring protein, SARA, recruits SMAD2/3, Bos taurus" +is_a: GO:0005488 ! binding + +[Term] +id: GO:0005539 +name: glycosaminoglycan binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues." [GOC:jl, ISBN:0198506732] +subset: gosubset_prok +is_a: GO:0097367 ! carbohydrate derivative binding + +[Term] +id: GO:0005575 +name: cellular_component +namespace: cellular_component +alt_id: GO:0008372 +def: "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators] +comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "cellular component" EXACT [] +synonym: "cellular component unknown" NARROW [] +xref: NIF_Subcellular:sao1337158144 +disjoint_from: GO:0008150 ! biological_process + +[Term] +id: GO:0005576 +name: extracellular region +namespace: cellular_component +def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators] +comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "extracellular" EXACT [] +xref: Wikipedia:Extracellular +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0005578 +name: proteinaceous extracellular matrix +namespace: cellular_component +def: "A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus." [GOC:mtg_sensu, ISBN:0198547684] +subset: goslim_generic +subset: goslim_plant +is_a: GO:0031012 ! extracellular matrix +is_a: GO:0044421 ! extracellular region part + +[Term] +id: GO:0005615 +name: extracellular space +namespace: cellular_component +def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684] +comment: Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. +subset: goslim_generic +subset: goslim_plant +synonym: "intercellular space" RELATED [] +xref: NIF_Subcellular:sao1425028079 +is_a: GO:0044421 ! extracellular region part + +[Term] +id: GO:0005622 +name: intracellular +namespace: cellular_component +def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "internal to cell" EXACT [] +synonym: "nucleocytoplasm" RELATED [GOC:mah] +synonym: "protoplasm" EXACT [] +synonym: "protoplast" RELATED [GOC:mah] +xref: Wikipedia:Intracellular +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0005623 +name: cell +namespace: cellular_component +def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators] +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +xref: NIF_Subcellular:sao1813327414 +xref: Wikipedia:Cell_(biology) +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0005634 +name: nucleus +namespace: cellular_component +def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "cell nucleus" EXACT [] +xref: NIF_Subcellular:sao1702920020 +xref: Wikipedia:Cell_nucleus +is_a: GO:0043231 ! intracellular membrane-bounded organelle + +[Term] +id: GO:0005667 +name: transcription factor complex +namespace: cellular_component +def: "A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription." [GOC:jl] +subset: goslim_metagenomics +subset: goslim_pir +is_a: GO:0043234 ! protein complex +is_a: GO:0044424 ! intracellular part + +[Term] +id: GO:0005694 +name: chromosome +namespace: cellular_component +def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "chromatid" RELATED [] +synonym: "interphase chromosome" NARROW [] +synonym: "prophase chromosome" NARROW [] +xref: Wikipedia:Chromosome +is_a: GO:0043232 ! intracellular non-membrane-bounded organelle + +[Term] +id: GO:0005720 +name: nuclear heterochromatin +namespace: cellular_component +def: "A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin." [ISBN:0198506732] +is_a: GO:0000790 ! nuclear chromatin +is_a: GO:0000792 ! heterochromatin +intersection_of: GO:0000792 ! heterochromatin +intersection_of: part_of GO:0000228 ! nuclear chromosome + +[Term] +id: GO:0005737 +name: cytoplasm +namespace: cellular_component +def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +xref: Wikipedia:Cytoplasm +is_a: GO:0044424 ! intracellular part + +[Term] +id: GO:0005739 +name: mitochondrion +namespace: cellular_component +def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [GOC:giardia, ISBN:0198506732] +comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "mitochondria" EXACT [] +xref: NIF_Subcellular:sao1860313010 +xref: Wikipedia:Mitochondrion +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0005768 +name: endosome +namespace: cellular_component +def: "A membrane-bounded organelle to which materials ingested by endocytosis are delivered." [ISBN:0198506732, PMID:19696797] +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +xref: NIF_Subcellular:sao1720343330 +xref: Wikipedia:Endosome +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part +relationship: part_of GO:0012505 ! endomembrane system + +[Term] +id: GO:0005769 +name: early endosome +namespace: cellular_component +def: "A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways." [GOC:mah, PMID:19696797] +is_a: GO:0005768 ! endosome + +[Term] +id: GO:0005773 +name: vacuole +namespace: cellular_component +def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "vacuolar carboxypeptidase Y" RELATED [] +xref: Wikipedia:Vacuole +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0005783 +name: endoplasmic reticulum +namespace: cellular_component +def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "ER" EXACT [] +xref: NIF_Subcellular:sao1036339110 +xref: Wikipedia:Endoplasmic_reticulum +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part +relationship: part_of GO:0012505 ! endomembrane system + +[Term] +id: GO:0005788 +name: endoplasmic reticulum lumen +namespace: cellular_component +alt_id: GO:0016022 +def: "The volume enclosed by the membranes of the endoplasmic reticulum." [ISBN:0198547684] +synonym: "cisternal lumen" EXACT [] +synonym: "endoplasmic reticulum cisterna" EXACT [] +synonym: "ER cisterna" EXACT [] +synonym: "ER lumen" EXACT [] +is_a: GO:0044432 ! endoplasmic reticulum part +is_a: GO:0070013 ! intracellular organelle lumen + +[Term] +id: GO:0005791 +name: rough endoplasmic reticulum +namespace: cellular_component +def: "The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae." [ISBN:0198506732] +synonym: "RER" EXACT [] +synonym: "rough ER" EXACT [] +xref: NIF_Subcellular:sao1881364067 +xref: Wikipedia:Endoplasmic_reticulum#Rough_endoplasmic_reticulum +is_a: GO:0005783 ! endoplasmic reticulum + +[Term] +id: GO:0005794 +name: Golgi apparatus +namespace: cellular_component +def: "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions." [ISBN:0198506732] +comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +synonym: "Golgi" BROAD [] +synonym: "Golgi complex" EXACT [] +synonym: "Golgi ribbon" NARROW [] +xref: NIF_Subcellular:sao451912436 +xref: Wikipedia:Golgi_apparatus +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part +relationship: part_of GO:0012505 ! endomembrane system + +[Term] +id: GO:0005813 +name: centrosome +namespace: cellular_component +def: "A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle." [GOC:mah, ISBN:0198547684] +subset: goslim_pir +xref: Wikipedia:Centrosome +is_a: GO:0005815 ! microtubule organizing center +is_a: GO:0043232 ! intracellular non-membrane-bounded organelle + +[Term] +id: GO:0005815 +name: microtubule organizing center +namespace: cellular_component +def: "An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides." [GOC:vw, http://en.wikipedia.org/wiki/Microtubule_organizing_center, ISBN:0815316194, PMID:17072892, PMID:17245416] +subset: goslim_candida +subset: goslim_generic +subset: goslim_yeast +synonym: "microtubule organising centre" EXACT [] +synonym: "MTOC" EXACT [] +xref: Wikipedia:Microtubule_organizing_center +is_a: GO:0044430 ! cytoskeletal part +relationship: part_of GO:0015630 ! microtubule cytoskeleton + +[Term] +id: GO:0005829 +name: cytosol +namespace: cellular_component +def: "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC:hgd, GOC:jl] +subset: goslim_aspergillus +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +xref: NIF_Subcellular:sao101633890 +xref: Wikipedia:Cytosol +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0005856 +name: cytoskeleton +namespace: cellular_component +def: "Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:mah, ISBN:0198547684, PMID:16959967] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +xref: Wikipedia:Cytoskeleton +is_a: GO:0043232 ! intracellular non-membrane-bounded organelle + +[Term] +id: GO:0005875 +name: microtubule associated complex +namespace: cellular_component +def: "Any multimeric complex connected to a microtubule." [GOC:jl] +is_a: GO:0043234 ! protein complex +is_a: GO:0044430 ! cytoskeletal part +relationship: part_of GO:0015630 ! microtubule cytoskeleton + +[Term] +id: GO:0005886 +name: plasma membrane +namespace: cellular_component +alt_id: GO:0005904 +def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "bacterial inner membrane" NARROW [] +synonym: "cell membrane" EXACT [] +synonym: "cytoplasmic membrane" EXACT [] +synonym: "inner endospore membrane" NARROW [] +synonym: "juxtamembrane" BROAD [] +synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah] +synonym: "plasmalemma" EXACT [] +xref: NIF_Subcellular:sao1663586795 +xref: Wikipedia:Cell_membrane +is_a: GO:0016020 ! membrane +is_a: GO:0044464 ! cell part +relationship: part_of GO:0071944 ! cell periphery + +[Term] +id: GO:0005901 +name: caveola +namespace: cellular_component +alt_id: GO:0016599 +def: "A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include any of the minute pits or incuppings of the cell membrane formed during pinocytosis. Such caveolae may be pinched off to form free vesicles within the cytoplasm." [GOC:mah, ISBN:0721662544, PMID:16645198] +synonym: "caveolae" EXACT [] +synonym: "caveolar membrane" RELATED [] +xref: Wikipedia:Caveolae +is_a: GO:0044459 ! plasma membrane part +is_a: GO:0045121 ! membrane raft + +[Term] +id: GO:0005902 +name: microvillus +namespace: cellular_component +def: "Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells." [ISBN:0813516194] +comment: Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta. +subset: goslim_pir +synonym: "microvilli" RELATED [] +xref: Wikipedia:Microvillus +is_a: GO:0042995 ! cell projection + +[Term] +id: GO:0005903 +name: brush border +namespace: cellular_component +def: "Dense covering of microvilli on the apical surface of epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell." [GOC:sl, ISBN:0815316194] +subset: goslim_pir +xref: Wikipedia:Brush_border +is_a: GO:0042995 ! cell projection + +[Term] +id: GO:0005905 +name: coated pit +namespace: cellular_component +def: "A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes." [GOC:mah, ISBN:0198506732, PMID:10559856, PMID:17284835] +is_a: GO:0044425 ! membrane part +is_a: GO:0044464 ! cell part +relationship: part_of GO:0012505 ! endomembrane system + +[Term] +id: GO:0005911 +name: cell-cell junction +namespace: cellular_component +def: "A cell junction that forms a connection between two cells; excludes direct cytoplasmic junctions such as ring canals." [GOC:dgh, GOC:hb, GOC:mah] +synonym: "intercellular junction" EXACT [NIF_Subcellular:sao1395777368] +xref: NIF_Subcellular:sao1922892319 +is_a: GO:0030054 ! cell junction + +[Term] +id: GO:0005912 +name: adherens junction +namespace: cellular_component +def: "A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments." [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732] +is_a: GO:0070161 ! anchoring junction + +[Term] +id: GO:0005913 +name: cell-cell adherens junction +namespace: cellular_component +def: "An adherens junction which connects a cell to another cell." [GOC:hb] +is_a: GO:0005911 ! cell-cell junction +is_a: GO:0005912 ! adherens junction + +[Term] +id: GO:0005915 +name: zonula adherens +namespace: cellular_component +def: "A cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells." [ISBN:0815316208] +synonym: "adhesion belt" EXACT [] +synonym: "belt desmosome" EXACT [] +synonym: "fascia adhaerens" EXACT [] +synonym: "intermediate junction" EXACT [] +synonym: "zonula adhaerens" EXACT [] +xref: NIF_Subcellular:sao1400623473 +is_a: GO:0005913 ! cell-cell adherens junction +relationship: part_of GO:0043296 ! apical junction complex + +[Term] +id: GO:0005916 +name: fascia adherens +namespace: cellular_component +def: "A cell-cell adherens junction that contains the transmembrane protein N-cadherin, which interacts with identical molecules from neighboring cells to form a tight mechanical intercellular link; forms a large portion of the intercalated disc, the structure at which myofibrils terminate in cardiomyocytes." [GOC:mtg_muscle, PMID:11732910] +xref: Wikipedia:Fascia_adherens +is_a: GO:0005913 ! cell-cell adherens junction +relationship: part_of GO:0014704 ! intercalated disc + +[Term] +id: GO:0005924 +name: cell-substrate adherens junction +namespace: cellular_component +def: "An adherens junction which connects a cell to the extracellular matrix." [GOC:hb] +synonym: "hemi-adherens junction" RELATED [] +is_a: GO:0005912 ! adherens junction +is_a: GO:0030055 ! cell-substrate junction + +[Term] +id: GO:0005938 +name: cell cortex +namespace: cellular_component +def: "The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins." [GOC:mah, ISBN:0815316194] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_yeast +synonym: "cell periphery" RELATED [] +synonym: "peripheral cytoplasm" RELATED [] +xref: Wikipedia:Cell_cortex +is_a: GO:0044444 ! cytoplasmic part +relationship: part_of GO:0071944 ! cell periphery + +[Term] +id: GO:0005975 +name: carbohydrate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC:mah, ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "carbohydrate metabolism" EXACT [] +xref: Reactome:REACT_102834 "Metabolism of carbohydrates, Mus musculus" +xref: Reactome:REACT_103806 "Metabolism of carbohydrates, Mycobacterium tuberculosis" +xref: Reactome:REACT_104502 "Metabolism of carbohydrates, Gallus gallus" +xref: Reactome:REACT_105321 "Metabolism of carbohydrates, Escherichia coli" +xref: Reactome:REACT_106046 "Metabolism of carbohydrates, Drosophila melanogaster" +xref: Reactome:REACT_107409 "Metabolism of carbohydrates, Caenorhabditis elegans" +xref: Reactome:REACT_115733 "Carbohydrate metabolism, Gallus gallus" +xref: Reactome:REACT_28218 "Metabolism of carbohydrates, Xenopus tropicalis" +xref: Reactome:REACT_32291 "Metabolism of carbohydrates, Staphylococcus aureus N315" +xref: Reactome:REACT_33141 "Metabolism of carbohydrates, Taeniopygia guttata" +xref: Reactome:REACT_33953 "Metabolism of carbohydrates, Rattus norvegicus" +xref: Reactome:REACT_34800 "Metabolism of carbohydrates, Danio rerio" +xref: Reactome:REACT_474 "Metabolism of carbohydrates, Homo sapiens" +xref: Reactome:REACT_77669 "Metabolism of carbohydrates, Plasmodium falciparum" +xref: Reactome:REACT_81945 "Metabolism of carbohydrates, Schizosaccharomyces pombe" +xref: Reactome:REACT_83038 "Metabolism of carbohydrates, Arabidopsis thaliana" +xref: Reactome:REACT_83329 "Metabolism of carbohydrates, Saccharomyces cerevisiae" +xref: Reactome:REACT_88330 "Metabolism of carbohydrates, Bos taurus" +xref: Reactome:REACT_88558 "Metabolism of carbohydrates, Canis familiaris" +xref: Reactome:REACT_90099 "Metabolism of carbohydrates, Sus scrofa" +xref: Reactome:REACT_96375 "Metabolism of carbohydrates, Dictyostelium discoideum" +xref: Reactome:REACT_98394 "Metabolism of carbohydrates, Oryza sativa" +xref: Wikipedia:Carbohydrate_metabolism +is_a: GO:0044238 ! primary metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0005996 +name: monosaccharide metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides." [ISBN:0198506732] +subset: gosubset_prok +synonym: "monosaccharide metabolism" EXACT [] +is_a: GO:0044723 ! single-organism carbohydrate metabolic process + +[Term] +id: GO:0006006 +name: glucose metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides." [ISBN:0198506732] +subset: gosubset_prok +synonym: "cellular glucose metabolic process" EXACT [GOC:vw] +synonym: "glucose metabolism" EXACT [] +xref: Reactome:REACT_101127 "Glucose metabolism, Arabidopsis thaliana" +xref: Reactome:REACT_101310 "Glucose metabolism, Canis familiaris" +xref: Reactome:REACT_102479 "Glucose metabolism, Staphylococcus aureus N315" +xref: Reactome:REACT_102806 "Glucose metabolism, Xenopus tropicalis" +xref: Reactome:REACT_104683 "Glucose metabolism, Danio rerio" +xref: Reactome:REACT_105053 "Glucose metabolism, Plasmodium falciparum" +xref: Reactome:REACT_106618 "Glucose metabolism, Escherichia coli" +xref: Reactome:REACT_29390 "Glucose metabolism, Caenorhabditis elegans" +xref: Reactome:REACT_30713 "Glucose metabolism, Schizosaccharomyces pombe" +xref: Reactome:REACT_30754 "Glucose metabolism, Drosophila melanogaster" +xref: Reactome:REACT_32548 "Glucose metabolism, Sus scrofa" +xref: Reactome:REACT_723 "Glucose metabolism, Homo sapiens" +xref: Reactome:REACT_80637 "Glucose metabolism, Mus musculus" +xref: Reactome:REACT_81545 "Glucose metabolism, Bos taurus" +xref: Reactome:REACT_85067 "Glucose metabolism, Gallus gallus" +xref: Reactome:REACT_85844 "Glucose metabolism, Dictyostelium discoideum" +xref: Reactome:REACT_94241 "Glucose metabolism, Saccharomyces cerevisiae" +xref: Reactome:REACT_97466 "Glucose metabolism, Rattus norvegicus" +xref: Reactome:REACT_98401 "Glucose metabolism, Taeniopygia guttata" +xref: Reactome:REACT_98764 "Glucose metabolism, Oryza sativa" +xref: Reactome:REACT_99558 "Glucose metabolism, Mycobacterium tuberculosis" +is_a: GO:0019318 ! hexose metabolic process + +[Term] +id: GO:0006007 +name: glucose catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose." [GOC:ai] +subset: gosubset_prok +synonym: "glucose breakdown" EXACT [] +synonym: "glucose catabolism" EXACT [] +synonym: "glucose degradation" EXACT [] +is_a: GO:0006006 ! glucose metabolic process +is_a: GO:0019320 ! hexose catabolic process + +[Term] +id: GO:0006022 +name: aminoglycan metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages." [GOC:ai, ISBN:0198506732] +subset: gosubset_prok +synonym: "aminoglycan metabolism" EXACT [] +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process + +[Term] +id: GO:0006029 +name: proteoglycan metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." [GOC:mah, ISBN:0198506732] +subset: gosubset_prok +synonym: "proteoglycan metabolism" EXACT [] +synonym: "proteoglycan sulfate transfer" NARROW [] +is_a: GO:0009100 ! glycoprotein metabolic process + +[Term] +id: GO:0006066 +name: alcohol metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [CHEBI:30879, ISBN:0198506732] +subset: goslim_pir +subset: gosubset_prok +synonym: "alcohol metabolism" EXACT [] +is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:1901615 ! organic hydroxy compound metabolic process + +[Term] +id: GO:0006082 +name: organic acid metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] +subset: goslim_pir +subset: gosubset_prok +synonym: "organic acid metabolism" EXACT [] +is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0006109 +name: regulation of carbohydrate metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of carbohydrate metabolism" EXACT [] +is_a: GO:0080090 ! regulation of primary metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0005975 ! carbohydrate metabolic process +relationship: regulates GO:0005975 ! carbohydrate metabolic process + +[Term] +id: GO:0006139 +name: nucleobase-containing compound metabolic process +namespace: biological_process +alt_id: GO:0055134 +def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] +synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] +synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] +is_a: GO:0006725 ! cellular aromatic compound metabolic process +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +is_a: GO:0044238 ! primary metabolic process +is_a: GO:0046483 ! heterocycle metabolic process +is_a: GO:1901360 ! organic cyclic compound metabolic process + +[Term] +id: GO:0006140 +name: regulation of nucleotide metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleotides." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of nucleotide metabolism" EXACT [] +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +is_a: GO:0019220 ! regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009117 ! nucleotide metabolic process +relationship: regulates GO:0009117 ! nucleotide metabolic process + +[Term] +id: GO:0006152 +name: purine nucleoside catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:go_curators] +subset: gosubset_prok +synonym: "purine nucleoside breakdown" EXACT [] +synonym: "purine nucleoside catabolism" EXACT [] +synonym: "purine nucleoside degradation" EXACT [] +is_a: GO:0009164 ! nucleoside catabolic process +is_a: GO:0042278 ! purine nucleoside metabolic process +is_a: GO:0072523 ! purine-containing compound catabolic process + +[Term] +id: GO:0006163 +name: purine nucleotide metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "purine metabolic process" NARROW [] +synonym: "purine metabolism" NARROW [] +synonym: "purine nucleotide metabolism" EXACT [] +is_a: GO:0009117 ! nucleotide metabolic process +is_a: GO:0072521 ! purine-containing compound metabolic process + +[Term] +id: GO:0006184 +name: GTP catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of GTP, guanosine triphosphate." [ISBN:0198506732] +subset: gosubset_prok +synonym: "GTP breakdown" EXACT [] +synonym: "GTP catabolism" EXACT [] +synonym: "GTP degradation" EXACT [] +synonym: "GTP hydrolysis" NARROW [] +is_a: GO:0009154 ! purine ribonucleotide catabolic process +is_a: GO:0009207 ! purine ribonucleoside triphosphate catabolic process +is_a: GO:0046039 ! GTP metabolic process +is_a: GO:1901069 ! guanosine-containing compound catabolic process + +[Term] +id: GO:0006195 +name: purine nucleotide catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "purine nucleotide breakdown" EXACT [] +synonym: "purine nucleotide catabolism" EXACT [] +synonym: "purine nucleotide degradation" EXACT [] +xref: Reactome:REACT_100331 "Purine catabolism, Dictyostelium discoideum" +xref: Reactome:REACT_104277 "Purine catabolism, Xenopus tropicalis" +xref: Reactome:REACT_105169 "Purine catabolism, Schizosaccharomyces pombe" +xref: Reactome:REACT_105236 "Purine catabolism, Staphylococcus aureus N315" +xref: Reactome:REACT_107505 "Purine catabolism, Oryza sativa" +xref: Reactome:REACT_113844 "Purine catabolism, Plasmodium falciparum" +xref: Reactome:REACT_2086 "Purine catabolism, Homo sapiens" +xref: Reactome:REACT_30574 "Purine catabolism, Saccharomyces cerevisiae" +xref: Reactome:REACT_31958 "Purine catabolism, Drosophila melanogaster" +xref: Reactome:REACT_33664 "Purine catabolism, Mus musculus" +xref: Reactome:REACT_34219 "Purine catabolism, Taeniopygia guttata" +xref: Reactome:REACT_58357 "Purine catabolism, Canis familiaris" +xref: Reactome:REACT_77442 "Purine catabolism, Danio rerio" +xref: Reactome:REACT_77815 "Purine catabolism, Gallus gallus" +xref: Reactome:REACT_78778 "Purine catabolism, Caenorhabditis elegans" +xref: Reactome:REACT_85047 "Purine catabolism, Mycobacterium tuberculosis" +xref: Reactome:REACT_91836 "Purine catabolism, Rattus norvegicus" +xref: Reactome:REACT_95337 "Purine catabolism, Sus scrofa" +xref: Reactome:REACT_95719 "Purine catabolism, Escherichia coli" +xref: Reactome:REACT_98589 "Purine catabolism, Bos taurus" +xref: Reactome:REACT_99571 "Purine catabolism, Arabidopsis thaliana" +is_a: GO:0006163 ! purine nucleotide metabolic process +is_a: GO:0009166 ! nucleotide catabolic process +is_a: GO:0072523 ! purine-containing compound catabolic process + +[Term] +id: GO:0006259 +name: DNA metabolic process +namespace: biological_process +alt_id: GO:0055132 +def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "cellular DNA metabolism" EXACT [] +synonym: "DNA metabolism" EXACT [] +is_a: GO:0044260 ! cellular macromolecule metabolic process +is_a: GO:0090304 ! nucleic acid metabolic process + +[Term] +id: GO:0006308 +name: DNA catabolic process +namespace: biological_process +def: "The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "DNA breakdown" EXACT [] +synonym: "DNA catabolism" EXACT [] +synonym: "DNA degradation" EXACT [] +is_a: GO:0006259 ! DNA metabolic process +is_a: GO:0034655 ! nucleobase-containing compound catabolic process +is_a: GO:0044265 ! cellular macromolecule catabolic process + +[Term] +id: GO:0006309 +name: apoptotic DNA fragmentation +namespace: biological_process +alt_id: GO:0008178 +def: "The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments." [GOC:dph, GOC:mah, GOC:mtg_apoptosis, GOC:tb, ISBN:0721639976] +comment: DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays shows presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. +synonym: "chromatinolysis" BROAD [GOC:mtg_apoptosis] +synonym: "DNA catabolic process during apoptosis" EXACT [] +synonym: "DNA catabolism during apoptosis" EXACT [] +synonym: "DNA fragmentation" BROAD [] +synonym: "DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:cjm, GOC:dph, GOC:tb] +synonym: "endonucleolytic DNA catabolic process involved in apoptosis" EXACT [] +xref: Reactome:REACT_102783 "Apoptosis induced DNA fragmentation, Bos taurus" +xref: Reactome:REACT_105342 "Apoptosis induced DNA fragmentation, Sus scrofa" +xref: Reactome:REACT_110358 "Apoptosis induced DNA fragmentation, Xenopus tropicalis" +xref: Reactome:REACT_113418 "Apoptosis induced DNA fragmentation, Plasmodium falciparum" +xref: Reactome:REACT_1213 "Apoptosis induced DNA fragmentation, Homo sapiens" +xref: Reactome:REACT_28808 "Apoptosis induced DNA fragmentation, Rattus norvegicus" +xref: Reactome:REACT_33113 "Apoptosis induced DNA fragmentation, Mus musculus" +xref: Reactome:REACT_92967 "Apoptosis induced DNA fragmentation, Drosophila melanogaster" +xref: Reactome:REACT_94135 "Apoptosis induced DNA fragmentation, Taeniopygia guttata" +xref: Reactome:REACT_98713 "Apoptosis induced DNA fragmentation, Canis familiaris" +xref: Reactome:REACT_99275 "Apoptosis induced DNA fragmentation, Gallus gallus" +xref: Reactome:REACT_99925 "Apoptosis induced DNA fragmentation, Danio rerio" +is_a: GO:0000737 ! DNA catabolic process, endonucleolytic +intersection_of: GO:0000737 ! DNA catabolic process, endonucleolytic +intersection_of: part_of GO:0030262 ! apoptotic nuclear changes +relationship: part_of GO:0030262 ! apoptotic nuclear changes + +[Term] +id: GO:0006325 +name: chromatin organization +namespace: biological_process +def: "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin." [GOC:mah] +subset: goslim_yeast +synonym: "chromatin organisation" EXACT [GOC:mah] +synonym: "establishment or maintenance of chromatin architecture" EXACT [GOC:mah] +is_a: GO:0051276 ! chromosome organization + +[Term] +id: GO:0006351 +name: transcription, DNA-templated +namespace: biological_process +alt_id: GO:0006350 +alt_id: GO:0061018 +alt_id: GO:0061022 +def: "The cellular synthesis of RNA on a template of DNA." [GOC:jl, GOC:txnOH] +subset: goslim_aspergillus +subset: goslim_metagenomics +subset: goslim_pombe +subset: gosubset_prok +synonym: "cellular transcription" BROAD [] +synonym: "cellular transcription, DNA-dependent" EXACT [] +synonym: "DNA-dependent transcription" EXACT [] +synonym: "transcription" BROAD [] +synonym: "transcription regulator activity" RELATED [] +synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH] +xref: Wikipedia:Transcription_(genetics) +is_a: GO:0032774 ! RNA biosynthetic process +is_a: GO:0034645 ! cellular macromolecule biosynthetic process +relationship: part_of GO:0010467 ! gene expression + +[Term] +id: GO:0006352 +name: DNA-templated transcription, initiation +namespace: biological_process +def: "Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription." [GOC:jid, GOC:txnOH, PMID:18280161] +comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation. +subset: goslim_yeast +subset: gosubset_prok +synonym: "DNA-dependent RNA polymerase complex assembly at promoter" EXACT [] +synonym: "DNA-dependent transcription, initiation" EXACT [GOC:txnOH] +synonym: "initiation of DNA-dependent transcription" EXACT [GOC:jh2] +synonym: "initiation of transcription, DNA-dependent" EXACT [GOC:mah] +synonym: "transcription initiation factor activity" RELATED [] +synonym: "transcription initiation, DNA-dependent" RELATED [GOC:jh2] +is_a: GO:0032774 ! RNA biosynthetic process +relationship: part_of GO:0006351 ! transcription, DNA-templated + +[Term] +id: GO:0006355 +name: regulation of transcription, DNA-templated +namespace: biological_process +alt_id: GO:0032583 +alt_id: GO:0045449 +alt_id: GO:0061019 +def: "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] +subset: goslim_pombe +subset: gosubset_prok +synonym: "regulation of cellular transcription, DNA-dependent" EXACT [] +synonym: "regulation of gene-specific transcription" RELATED [] +synonym: "regulation of transcription, DNA-dependent" EXACT [GOC:txnOH] +synonym: "transcriptional control" BROAD [] +is_a: GO:0010468 ! regulation of gene expression +is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process +is_a: GO:2001141 ! regulation of RNA biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006351 ! transcription, DNA-templated +relationship: regulates GO:0006351 ! transcription, DNA-templated + +[Term] +id: GO:0006357 +name: regulation of transcription from RNA polymerase II promoter +namespace: biological_process +alt_id: GO:0006358 +alt_id: GO:0010551 +def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] +synonym: "global transcription regulation from Pol II promoter" RELATED [] +synonym: "regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] +synonym: "regulation of global transcription from Pol II promoter" RELATED [] +synonym: "regulation of transcription from Pol II promoter" EXACT [] +synonym: "regulation of transcription from RNA polymerase II promoter, global" RELATED [] +is_a: GO:0006355 ! regulation of transcription, DNA-templated +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter +relationship: regulates GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0006359 +name: regulation of transcription from RNA polymerase III promoter +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of transcription from an RNA ploymerase III promoter." [GOC:go_curators] +synonym: "regulation of transcription from Pol III promoter" EXACT [] +is_a: GO:0006355 ! regulation of transcription, DNA-templated +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006383 ! transcription from RNA polymerase III promoter +relationship: regulates GO:0006383 ! transcription from RNA polymerase III promoter + +[Term] +id: GO:0006366 +name: transcription from RNA polymerase II promoter +namespace: biological_process +alt_id: GO:0032568 +alt_id: GO:0032569 +def: "The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC:jl, GOC:txnOH, ISBN:0321000382] +subset: goslim_yeast +synonym: "gene-specific transcription from RNA polymerase II promoter" RELATED [] +synonym: "general transcription from RNA polymerase II promoter" RELATED [] +synonym: "RNA polymerase II transcription factor activity" RELATED [] +synonym: "specific transcription from RNA polymerase II promoter" RELATED [GOC:mah] +synonym: "transcription from Pol II promoter" EXACT [] +xref: Reactome:REACT_105738 "RNA Polymerase II Transcription, Bos taurus" +xref: Reactome:REACT_106213 "RNA Polymerase II Transcription, Caenorhabditis elegans" +xref: Reactome:REACT_108012 "RNA Polymerase II Transcription, Canis familiaris" +xref: Reactome:REACT_109421 "RNA Polymerase II Transcription, Xenopus tropicalis" +xref: Reactome:REACT_1366 "RNA Polymerase II Transcription, Homo sapiens" +xref: Reactome:REACT_31558 "RNA Polymerase II Transcription, Taeniopygia guttata" +xref: Reactome:REACT_32943 "RNA Polymerase II Transcription, Danio rerio" +xref: Reactome:REACT_33538 "RNA Polymerase II Transcription, Rattus norvegicus" +xref: Reactome:REACT_33583 "RNA Polymerase II Transcription, Sus scrofa" +xref: Reactome:REACT_34720 "RNA Polymerase II Transcription, Schizosaccharomyces pombe" +xref: Reactome:REACT_79747 "RNA Polymerase II Transcription, Plasmodium falciparum" +xref: Reactome:REACT_89454 "RNA Polymerase II Transcription, Oryza sativa" +xref: Reactome:REACT_89916 "RNA Polymerase II Transcription, Mus musculus" +xref: Reactome:REACT_97471 "RNA Polymerase II Transcription, Arabidopsis thaliana" +xref: Reactome:REACT_97536 "RNA Polymerase II Transcription, Gallus gallus" +xref: Reactome:REACT_99228 "RNA Polymerase II Transcription, Drosophila melanogaster" +xref: Reactome:REACT_99748 "RNA Polymerase II Transcription, Dictyostelium discoideum" +xref: Reactome:REACT_99950 "RNA Polymerase II Transcription, Saccharomyces cerevisiae" +is_a: GO:0006351 ! transcription, DNA-templated + +[Term] +id: GO:0006367 +name: transcription initiation from RNA polymerase II promoter +namespace: biological_process +def: "Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC:mah, GOC:txnOH] +comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation. +synonym: "transcription initiation from Pol II promoter" EXACT [] +xref: Reactome:REACT_100392 "RNA Polymerase II Transcription Initiation, Dictyostelium discoideum" +xref: Reactome:REACT_101175 "RNA Polymerase II Transcription Initiation, Canis familiaris" +xref: Reactome:REACT_101341 "RNA Polymerase II Transcription Initiation, Danio rerio" +xref: Reactome:REACT_102266 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Canis familiaris" +xref: Reactome:REACT_103457 "RNA Polymerase II Transcription Initiation, Mus musculus" +xref: Reactome:REACT_104036 "RNA Polymerase II Transcription Initiation, Drosophila melanogaster" +xref: Reactome:REACT_104646 "RNA Polymerase II Transcription Initiation, Caenorhabditis elegans" +xref: Reactome:REACT_104707 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Danio rerio" +xref: Reactome:REACT_105389 "RNA Polymerase II Transcription Initiation, Oryza sativa" +xref: Reactome:REACT_1655 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Homo sapiens" +xref: Reactome:REACT_1851 "RNA Polymerase II Transcription Initiation, Homo sapiens" +xref: Reactome:REACT_28862 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Oryza sativa" +xref: Reactome:REACT_31702 "RNA Polymerase II Transcription Initiation, Gallus gallus" +xref: Reactome:REACT_32920 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Bos taurus" +xref: Reactome:REACT_6332 "HIV-1 Transcription Initiation, Homo sapiens" +xref: Reactome:REACT_77736 "RNA Polymerase II Transcription Initiation, Xenopus tropicalis" +xref: Reactome:REACT_79444 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Drosophila melanogaster" +xref: Reactome:REACT_79812 "RNA Polymerase II Transcription Initiation, Rattus norvegicus" +xref: Reactome:REACT_80956 "RNA Polymerase II Transcription Initiation, Schizosaccharomyces pombe" +xref: Reactome:REACT_81703 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Dictyostelium discoideum" +xref: Reactome:REACT_82794 "RNA Polymerase II Transcription Initiation, Bos taurus" +xref: Reactome:REACT_83749 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Saccharomyces cerevisiae" +xref: Reactome:REACT_84134 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Mus musculus" +xref: Reactome:REACT_85783 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Schizosaccharomyces pombe" +xref: Reactome:REACT_85917 "RNA Polymerase II Transcription Initiation, Taeniopygia guttata" +xref: Reactome:REACT_85990 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Xenopus tropicalis" +xref: Reactome:REACT_87429 "RNA Polymerase II Transcription Initiation, Saccharomyces cerevisiae" +xref: Reactome:REACT_87559 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Caenorhabditis elegans" +xref: Reactome:REACT_88340 "RNA Polymerase II Transcription Initiation, Arabidopsis thaliana" +xref: Reactome:REACT_88353 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Gallus gallus" +xref: Reactome:REACT_92769 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Rattus norvegicus" +xref: Reactome:REACT_95808 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Taeniopygia guttata" +xref: Reactome:REACT_98915 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Arabidopsis thaliana" +is_a: GO:0006352 ! DNA-templated transcription, initiation +relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0006383 +name: transcription from RNA polymerase III promoter +namespace: biological_process +def: "The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter." [GOC:jl, GOC:txnOH] +subset: goslim_yeast +subset: gosubset_prok +synonym: "RNA polymerase III transcription factor activity" RELATED [] +synonym: "transcription from Pol III promoter" EXACT [] +xref: Reactome:REACT_100945 "Initiation of RNA Polymerase III Productive Transcription, Schizosaccharomyces pombe" +xref: Reactome:REACT_101038 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Rattus norvegicus" +xref: Reactome:REACT_101551 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Canis familiaris" +xref: Reactome:REACT_101656 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Rattus norvegicus" +xref: Reactome:REACT_101661 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Mus musculus" +xref: Reactome:REACT_101700 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Sus scrofa" +xref: Reactome:REACT_101771 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Gallus gallus" +xref: Reactome:REACT_101901 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Danio rerio" +xref: Reactome:REACT_102138 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Bos taurus" +xref: Reactome:REACT_102603 "RNA Polymerase III Transcription, Gallus gallus" +xref: Reactome:REACT_102683 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Rattus norvegicus" +xref: Reactome:REACT_103091 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Caenorhabditis elegans" +xref: Reactome:REACT_103169 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Taeniopygia guttata" +xref: Reactome:REACT_103226 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Drosophila melanogaster" +xref: Reactome:REACT_103412 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Mus musculus" +xref: Reactome:REACT_103650 "RNA Polymerase III Transcription, Taeniopygia guttata" +xref: Reactome:REACT_103786 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Sus scrofa" +xref: Reactome:REACT_104805 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Schizosaccharomyces pombe" +xref: Reactome:REACT_105112 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Sus scrofa" +xref: Reactome:REACT_105558 "Resumption of RNA Polymerase III Productive Transcription, Dictyostelium discoideum" +xref: Reactome:REACT_105661 "RNA Polymerase III Transcription, Schizosaccharomyces pombe" +xref: Reactome:REACT_106059 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Caenorhabditis elegans" +xref: Reactome:REACT_1061 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Homo sapiens" +xref: Reactome:REACT_106142 "Initiation of RNA Polymerase III Productive Transcription, Gallus gallus" +xref: Reactome:REACT_106447 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Caenorhabditis elegans" +xref: Reactome:REACT_106560 "Initiation of RNA Polymerase III Productive Transcription, Sus scrofa" +xref: Reactome:REACT_106688 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Bos taurus" +xref: Reactome:REACT_106837 "Resumption of RNA Polymerase III Productive Transcription, Mus musculus" +xref: Reactome:REACT_107790 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Taeniopygia guttata" +xref: Reactome:REACT_107815 "RNA Polymerase III Transcription, Saccharomyces cerevisiae" +xref: Reactome:REACT_108150 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Gallus gallus" +xref: Reactome:REACT_108254 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Mus musculus" +xref: Reactome:REACT_108736 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Sus scrofa" +xref: Reactome:REACT_108779 "Initiation of RNA Polymerase III Productive Transcription, Canis familiaris" +xref: Reactome:REACT_109038 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Xenopus tropicalis" +xref: Reactome:REACT_109056 "Resumption of RNA Polymerase III Productive Transcription, Schizosaccharomyces pombe" +xref: Reactome:REACT_109134 "Initiation of RNA Polymerase III Productive Transcription, Drosophila melanogaster" +xref: Reactome:REACT_109293 "RNA Polymerase III Productive Transcription, Mus musculus" +xref: Reactome:REACT_109350 "Resumption of RNA Polymerase III Productive Transcription, Drosophila melanogaster" +xref: Reactome:REACT_109707 "RNA Polymerase III Productive Transcription, Xenopus tropicalis" +xref: Reactome:REACT_109747 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Drosophila melanogaster" +xref: Reactome:REACT_109934 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Drosophila melanogaster" +xref: Reactome:REACT_109938 "Initiation of RNA Polymerase III Productive Transcription, Oryza sativa" +xref: Reactome:REACT_110233 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Taeniopygia guttata" +xref: Reactome:REACT_110354 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Drosophila melanogaster" +xref: Reactome:REACT_110533 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Rattus norvegicus" +xref: Reactome:REACT_110624 "Initiation of RNA Polymerase III Productive Transcription, Danio rerio" +xref: Reactome:REACT_112623 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Drosophila melanogaster" +xref: Reactome:REACT_112804 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Dictyostelium discoideum" +xref: Reactome:REACT_113692 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Dictyostelium discoideum" +xref: Reactome:REACT_114988 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Drosophila melanogaster" +xref: Reactome:REACT_1179 "Initiation of RNA Polymerase III Productive Transcription, Homo sapiens" +xref: Reactome:REACT_118261 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Caenorhabditis elegans" +xref: Reactome:REACT_118310 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Caenorhabditis elegans" +xref: Reactome:REACT_118481 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Caenorhabditis elegans" +xref: Reactome:REACT_1241 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Homo sapiens" +xref: Reactome:REACT_1371 "RNA Polymerase III Transcription, Homo sapiens" +xref: Reactome:REACT_1374 "Resumption of RNA Polymerase III Productive Transcription, Homo sapiens" +xref: Reactome:REACT_1616 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Homo sapiens" +xref: Reactome:REACT_2178 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Homo sapiens" +xref: Reactome:REACT_2210 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Homo sapiens" +xref: Reactome:REACT_2248 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Homo sapiens" +xref: Reactome:REACT_2251 "RNA Polymerase III Productive Transcription, Homo sapiens" +xref: Reactome:REACT_251 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Homo sapiens" +xref: Reactome:REACT_28871 "RNA Polymerase III Productive Transcription, Canis familiaris" +xref: Reactome:REACT_28926 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Xenopus tropicalis" +xref: Reactome:REACT_29249 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Bos taurus" +xref: Reactome:REACT_29589 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Canis familiaris" +xref: Reactome:REACT_30206 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Canis familiaris" +xref: Reactome:REACT_30383 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Taeniopygia guttata" +xref: Reactome:REACT_30530 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Canis familiaris" +xref: Reactome:REACT_30710 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Taeniopygia guttata" +xref: Reactome:REACT_30749 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Rattus norvegicus" +xref: Reactome:REACT_30852 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Drosophila melanogaster" +xref: Reactome:REACT_30868 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Canis familiaris" +xref: Reactome:REACT_31576 "Resumption of RNA Polymerase III Productive Transcription, Xenopus tropicalis" +xref: Reactome:REACT_31708 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Drosophila melanogaster" +xref: Reactome:REACT_32551 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Mus musculus" +xref: Reactome:REACT_32580 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Canis familiaris" +xref: Reactome:REACT_34048 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Bos taurus" +xref: Reactome:REACT_43442 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Bos taurus" +xref: Reactome:REACT_50555 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Bos taurus" +xref: Reactome:REACT_76991 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Rattus norvegicus" +xref: Reactome:REACT_77583 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Gallus gallus" +xref: Reactome:REACT_77734 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Rattus norvegicus" +xref: Reactome:REACT_77763 "RNA Polymerase III Productive Transcription, Rattus norvegicus" +xref: Reactome:REACT_77942 "Initiation of RNA Polymerase III Productive Transcription, Mus musculus" +xref: Reactome:REACT_78034 "Resumption of RNA Polymerase III Productive Transcription, Taeniopygia guttata" +xref: Reactome:REACT_78101 "Resumption of RNA Polymerase III Productive Transcription, Danio rerio" +xref: Reactome:REACT_78330 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Xenopus tropicalis" +xref: Reactome:REACT_78526 "RNA Polymerase III Productive Transcription, Taeniopygia guttata" +xref: Reactome:REACT_79030 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Rattus norvegicus" +xref: Reactome:REACT_79212 "Resumption of RNA Polymerase III Productive Transcription, Rattus norvegicus" +xref: Reactome:REACT_79230 "RNA Polymerase III Transcription, Caenorhabditis elegans" +xref: Reactome:REACT_796 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Homo sapiens" +xref: Reactome:REACT_79674 "RNA Polymerase III Transcription, Xenopus tropicalis" +xref: Reactome:REACT_79928 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Canis familiaris" +xref: Reactome:REACT_80506 "RNA Polymerase III Productive Transcription, Gallus gallus" +xref: Reactome:REACT_80530 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Danio rerio" +xref: Reactome:REACT_80924 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Arabidopsis thaliana" +xref: Reactome:REACT_81033 "RNA Polymerase III Productive Transcription, Schizosaccharomyces pombe" +xref: Reactome:REACT_81681 "Resumption of RNA Polymerase III Productive Transcription, Canis familiaris" +xref: Reactome:REACT_82476 "RNA Polymerase III Productive Transcription, Sus scrofa" +xref: Reactome:REACT_82823 "RNA Polymerase III Transcription, Bos taurus" +xref: Reactome:REACT_82958 "RNA Polymerase III Transcription, Rattus norvegicus" +xref: Reactome:REACT_83072 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Gallus gallus" +xref: Reactome:REACT_83162 "Resumption of RNA Polymerase III Productive Transcription, Gallus gallus" +xref: Reactome:REACT_83237 "RNA Polymerase III Transcription, Danio rerio" +xref: Reactome:REACT_83573 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Danio rerio" +xref: Reactome:REACT_83679 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Mus musculus" +xref: Reactome:REACT_83791 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Taeniopygia guttata" +xref: Reactome:REACT_84005 "RNA Polymerase III Transcription, Sus scrofa" +xref: Reactome:REACT_84052 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Xenopus tropicalis" +xref: Reactome:REACT_84174 "RNA Polymerase III Transcription, Canis familiaris" +xref: Reactome:REACT_84770 "RNA Polymerase III Transcription, Arabidopsis thaliana" +xref: Reactome:REACT_85321 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Gallus gallus" +xref: Reactome:REACT_85665 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Danio rerio" +xref: Reactome:REACT_85700 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Sus scrofa" +xref: Reactome:REACT_85938 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Gallus gallus" +xref: Reactome:REACT_86188 "Initiation of RNA Polymerase III Productive Transcription, Dictyostelium discoideum" +xref: Reactome:REACT_86214 "RNA Polymerase III Productive Transcription, Danio rerio" +xref: Reactome:REACT_86477 "Resumption of RNA Polymerase III Productive Transcription, Sus scrofa" +xref: Reactome:REACT_86680 "RNA Polymerase III Productive Transcription, Bos taurus" +xref: Reactome:REACT_87495 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Danio rerio" +xref: Reactome:REACT_88180 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Canis familiaris" +xref: Reactome:REACT_88328 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Taeniopygia guttata" +xref: Reactome:REACT_89113 "Initiation of RNA Polymerase III Productive Transcription, Bos taurus" +xref: Reactome:REACT_89159 "RNA Polymerase III Productive Transcription, Drosophila melanogaster" +xref: Reactome:REACT_89744 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Mus musculus" +xref: Reactome:REACT_90232 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Mus musculus" +xref: Reactome:REACT_90884 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Sus scrofa" +xref: Reactome:REACT_90929 "Initiation of RNA Polymerase III Productive Transcription, Taeniopygia guttata" +xref: Reactome:REACT_90945 "Initiation of RNA Polymerase III Productive Transcription, Arabidopsis thaliana" +xref: Reactome:REACT_90947 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Danio rerio" +xref: Reactome:REACT_91182 "RNA Polymerase III Transcription, Drosophila melanogaster" +xref: Reactome:REACT_91223 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Taeniopygia guttata" +xref: Reactome:REACT_91433 "Initiation of RNA Polymerase III Productive Transcription, Rattus norvegicus" +xref: Reactome:REACT_92510 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Bos taurus" +xref: Reactome:REACT_92565 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Gallus gallus" +xref: Reactome:REACT_92674 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Sus scrofa" +xref: Reactome:REACT_92814 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Xenopus tropicalis" +xref: Reactome:REACT_92970 "RNA Polymerase III Transcription, Oryza sativa" +xref: Reactome:REACT_93003 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Xenopus tropicalis" +xref: Reactome:REACT_93041 "RNA Polymerase III Productive Transcription, Oryza sativa" +xref: Reactome:REACT_93262 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Oryza sativa" +xref: Reactome:REACT_93305 "Resumption of RNA Polymerase III Productive Transcription, Arabidopsis thaliana" +xref: Reactome:REACT_93548 "RNA Polymerase III Transcription, Dictyostelium discoideum" +xref: Reactome:REACT_93709 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Dictyostelium discoideum" +xref: Reactome:REACT_93754 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Gallus gallus" +xref: Reactome:REACT_93859 "RNA Polymerase III Productive Transcription, Arabidopsis thaliana" +xref: Reactome:REACT_94189 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Xenopus tropicalis" +xref: Reactome:REACT_94421 "RNA Polymerase III Transcription, Mus musculus" +xref: Reactome:REACT_94567 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Xenopus tropicalis" +xref: Reactome:REACT_94753 "Resumption of RNA Polymerase III Productive Transcription, Oryza sativa" +xref: Reactome:REACT_96798 "Resumption of RNA Polymerase III Productive Transcription, Caenorhabditis elegans" +xref: Reactome:REACT_97406 "Initiation of RNA Polymerase III Productive Transcription, Xenopus tropicalis" +xref: Reactome:REACT_97559 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Sus scrofa" +xref: Reactome:REACT_98079 "RNA Polymerase III Productive Transcription, Dictyostelium discoideum" +xref: Reactome:REACT_98254 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Bos taurus" +xref: Reactome:REACT_98466 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Danio rerio" +xref: Reactome:REACT_98470 "Resumption of RNA Polymerase III Productive Transcription, Bos taurus" +xref: Reactome:REACT_98660 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Mus musculus" +xref: Reactome:REACT_98770 "RNA Polymerase III Productive Transcription, Caenorhabditis elegans" +xref: Reactome:REACT_99332 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Danio rerio" +xref: Reactome:REACT_99492 "Initiation of RNA Polymerase III Productive Transcription, Caenorhabditis elegans" +is_a: GO:0006351 ! transcription, DNA-templated + +[Term] +id: GO:0006461 +name: protein complex assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form a protein complex." [GOC:ai] +subset: goslim_generic +subset: goslim_pombe +subset: gosubset_prok +synonym: "chaperone activity" RELATED [] +synonym: "protein complex formation" EXACT [] +is_a: GO:0065003 ! macromolecular complex assembly +is_a: GO:0071822 ! protein complex subunit organization +relationship: part_of GO:0070271 ! protein complex biogenesis + +[Term] +id: GO:0006464 +name: cellular protein modification process +namespace: biological_process +def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:go_curators] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "process resulting in protein modification" RELATED [] +synonym: "protein modification process" BROAD [GOC:bf, GOC:jl] +synonym: "protein tagging activity" RELATED [] +is_a: GO:0036211 ! protein modification process +is_a: GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0006468 +name: protein phosphorylation +namespace: biological_process +def: "The process of introducing a phosphate group on to a protein." [GOC:hb] +subset: goslim_yeast +subset: gosubset_prok +synonym: "protein amino acid phosphorylation" EXACT [GOC:bf] +is_a: GO:0006464 ! cellular protein modification process +is_a: GO:0016310 ! phosphorylation + +[Term] +id: GO:0006469 +name: negative regulation of protein kinase activity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of protein kinase activity" EXACT [] +synonym: "down-regulation of protein kinase activity" EXACT [] +synonym: "downregulation of protein kinase activity" EXACT [] +synonym: "inhibition of protein kinase activity" NARROW [] +is_a: GO:0001933 ! negative regulation of protein phosphorylation +is_a: GO:0033673 ! negative regulation of kinase activity +is_a: GO:0045859 ! regulation of protein kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004672 ! protein kinase activity +relationship: negatively_regulates GO:0004672 ! protein kinase activity + +[Term] +id: GO:0006497 +name: protein lipidation +namespace: biological_process +alt_id: GO:0042050 +def: "The covalent attachment of lipid groups to an amino acid in a protein." [GOC:jl] +comment: For non-covalent interactions with a lipid, consider instead the term 'lipid binding ; GO:0008289' and its children. +subset: goslim_yeast +subset: gosubset_prok +synonym: "lipid:protein modification" EXACT [] +synonym: "protein amino acid lipidation" EXACT [GOC:bf] +xref: RESID:AA0059 +xref: RESID:AA0060 +xref: RESID:AA0077 +xref: RESID:AA0078 +xref: RESID:AA0079 +xref: RESID:AA0080 +xref: RESID:AA0102 +xref: RESID:AA0103 +xref: RESID:AA0104 +xref: RESID:AA0106 +xref: RESID:AA0107 +xref: RESID:AA0158 +xref: RESID:AA0159 +xref: RESID:AA0160 +xref: RESID:AA0161 +xref: RESID:AA0162 +xref: RESID:AA0163 +xref: RESID:AA0166 +xref: RESID:AA0223 +xref: RESID:AA0290 +xref: RESID:AA0307 +xref: RESID:AA0308 +xref: RESID:AA0309 +xref: RESID:AA0316 +is_a: GO:0006464 ! cellular protein modification process +relationship: part_of GO:0042158 ! lipoprotein biosynthetic process + +[Term] +id: GO:0006508 +name: proteolysis +namespace: biological_process +def: "The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds." [GOC:bf, GOC:mah] +comment: This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein maturation. +subset: goslim_pir +subset: gosubset_prok +synonym: "ATP-dependent proteolysis" NARROW [GOC:mah] +synonym: "peptidolysis" EXACT [] +xref: Reactome:REACT_105459 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Gallus gallus" +xref: Reactome:REACT_106013 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Canis familiaris" +xref: Reactome:REACT_106377 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Mus musculus" +xref: Reactome:REACT_107219 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Danio rerio" +xref: Reactome:REACT_110326 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Bos taurus" +xref: Reactome:REACT_733 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Homo sapiens" +xref: Reactome:REACT_84556 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Xenopus tropicalis" +xref: Reactome:REACT_92566 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Sus scrofa" +xref: Reactome:REACT_95969 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Taeniopygia guttata" +xref: Reactome:REACT_98959 "Removal of aminoterminal propeptides from gamma-carboxylated proteins, Rattus norvegicus" +xref: Wikipedia:Proteolysis +is_a: GO:0019538 ! protein metabolic process + +[Term] +id: GO:0006511 +name: ubiquitin-dependent protein catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein." [GOC:go_curators] +synonym: "ubiquitin-dependent protein breakdown" EXACT [] +synonym: "ubiquitin-dependent protein catabolism" EXACT [] +synonym: "ubiquitin-dependent protein degradation" EXACT [] +synonym: "ubiquitin-dependent proteolysis" EXACT [] +is_a: GO:0019941 ! modification-dependent protein catabolic process + +[Term] +id: GO:0006605 +name: protein targeting +namespace: biological_process +def: "The process of targeting specific proteins to particular membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif." [GOC:ma] +comment: Note that protein targeting encompasses the transport of the protein to the specified location, and may also include additional steps such as protein processing. +subset: goslim_generic +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "nascent polypeptide association" RELATED [] +synonym: "protein sorting along secretory pathway" NARROW [] +xref: Wikipedia:Protein_targeting +is_a: GO:0006886 ! intracellular protein transport +is_a: GO:1902582 ! single-organism intracellular transport + +[Term] +id: GO:0006606 +name: protein import into nucleus +namespace: biological_process +def: "The directed movement of a protein from the cytoplasm to the nucleus." [GOC:jl] +synonym: "establishment of protein localization to nucleus" EXACT [GOC:mah] +synonym: "protein import into cell nucleus" EXACT [] +synonym: "protein nucleus import" EXACT [] +synonym: "protein transport from cytoplasm to nucleus" EXACT [] +is_a: GO:0006886 ! intracellular protein transport +is_a: GO:0017038 ! protein import +is_a: GO:0072594 ! establishment of protein localization to organelle +is_a: GO:1902593 ! single-organism nuclear import +relationship: part_of GO:0034504 ! protein localization to nucleus +relationship: part_of GO:0044744 ! protein targeting to nucleus + +[Term] +id: GO:0006629 +name: lipid metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "lipid metabolism" EXACT [] +xref: Reactome:REACT_104930 "Lipid digestion, mobilization, and transport, Drosophila melanogaster" +xref: Reactome:REACT_107479 "Lipid digestion, mobilization, and transport, Xenopus tropicalis" +xref: Reactome:REACT_108775 "Lipid digestion, mobilization, and transport, Canis familiaris" +xref: Reactome:REACT_114669 "Lipid digestion, mobilization, and transport, Staphylococcus aureus N315" +xref: Reactome:REACT_115652 "Lipid metabolism, Gallus gallus" +xref: Reactome:REACT_28745 "Lipid digestion, mobilization, and transport, Saccharomyces cerevisiae" +xref: Reactome:REACT_31395 "Lipid digestion, mobilization, and transport, Sus scrofa" +xref: Reactome:REACT_32539 "Lipid digestion, mobilization, and transport, Bos taurus" +xref: Reactome:REACT_33836 "Lipid digestion, mobilization, and transport, Rattus norvegicus" +xref: Reactome:REACT_602 "Lipid digestion, mobilization, and transport, Homo sapiens" +xref: Reactome:REACT_77176 "Lipid digestion, mobilization, and transport, Danio rerio" +xref: Reactome:REACT_77191 "Lipid digestion, mobilization, and transport, Arabidopsis thaliana" +xref: Reactome:REACT_79244 "Lipid digestion, mobilization, and transport, Plasmodium falciparum" +xref: Reactome:REACT_81778 "Lipid digestion, mobilization, and transport, Oryza sativa" +xref: Reactome:REACT_82512 "Lipid digestion, mobilization, and transport, Taeniopygia guttata" +xref: Reactome:REACT_82723 "Lipid digestion, mobilization, and transport, Escherichia coli" +xref: Reactome:REACT_87884 "Lipid digestion, mobilization, and transport, Caenorhabditis elegans" +xref: Reactome:REACT_90757 "Lipid digestion, mobilization, and transport, Mus musculus" +xref: Reactome:REACT_94607 "Lipid digestion, mobilization, and transport, Mycobacterium tuberculosis" +xref: Reactome:REACT_97906 "Lipid digestion, mobilization, and transport, Gallus gallus" +xref: Reactome:REACT_98129 "Lipid digestion, mobilization, and transport, Schizosaccharomyces pombe" +xref: Reactome:REACT_99706 "Lipid digestion, mobilization, and transport, Dictyostelium discoideum" +xref: Wikipedia:Lipid_metabolism +is_a: GO:0044238 ! primary metabolic process +is_a: GO:0044710 ! single-organism metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0006694 +name: steroid biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification." [GOC:go_curators] +subset: gosubset_prok +synonym: "steroid anabolism" EXACT [] +synonym: "steroid biosynthesis" EXACT [] +synonym: "steroid formation" EXACT [] +synonym: "steroid synthesis" EXACT [] +synonym: "steroidogenesis" EXACT [] +xref: Wikipedia:Steroid_metabolisms#Steroid_biosynthesis +is_a: GO:0008202 ! steroid metabolic process +is_a: GO:0008610 ! lipid biosynthetic process +is_a: GO:1901362 ! organic cyclic compound biosynthetic process + +[Term] +id: GO:0006700 +name: C21-steroid hormone biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones." [GOC:ai] +synonym: "C21-steroid hormone anabolism" EXACT [] +synonym: "C21-steroid hormone biosynthesis" EXACT [] +synonym: "C21-steroid hormone formation" EXACT [] +synonym: "C21-steroid hormone synthesis" EXACT [] +xref: Reactome:REACT_100114 "Pregnenolone biosynthesis, Bos taurus" +xref: Reactome:REACT_107086 "Pregnenolone biosynthesis, Danio rerio" +xref: Reactome:REACT_11038 "Pregnenolone biosynthesis, Homo sapiens" +xref: Reactome:REACT_113158 "Pregnenolone biosynthesis, Dictyostelium discoideum" +xref: Reactome:REACT_115282 "Pregnenolone biosynthesis, Oryza sativa" +xref: Reactome:REACT_115412 "Pregnenolone biosynthesis, Arabidopsis thaliana" +xref: Reactome:REACT_32512 "Pregnenolone biosynthesis, Drosophila melanogaster" +xref: Reactome:REACT_79584 "Pregnenolone biosynthesis, Taeniopygia guttata" +xref: Reactome:REACT_81844 "Pregnenolone biosynthesis, Gallus gallus" +xref: Reactome:REACT_85889 "Pregnenolone biosynthesis, Caenorhabditis elegans" +xref: Reactome:REACT_86180 "Pregnenolone biosynthesis, Xenopus tropicalis" +xref: Reactome:REACT_89702 "Pregnenolone biosynthesis, Rattus norvegicus" +xref: Reactome:REACT_91740 "Pregnenolone biosynthesis, Saccharomyces cerevisiae" +xref: Reactome:REACT_91942 "Pregnenolone biosynthesis, Mus musculus" +xref: Reactome:REACT_96917 "Pregnenolone biosynthesis, Sus scrofa" +xref: Reactome:REACT_98782 "Pregnenolone biosynthesis, Canis familiaris" +is_a: GO:0006694 ! steroid biosynthetic process +is_a: GO:0008207 ! C21-steroid hormone metabolic process +is_a: GO:0042446 ! hormone biosynthetic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0006702 +name: androgen biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics." [ISBN:0198506732] +synonym: "androgen anabolism" EXACT [] +synonym: "androgen biosynthesis" EXACT [] +synonym: "androgen formation" EXACT [] +synonym: "androgen synthesis" EXACT [] +xref: Reactome:REACT_102314 "Androgen biosynthesis, Taeniopygia guttata" +xref: Reactome:REACT_105699 "Androgen biosynthesis, Arabidopsis thaliana" +xref: Reactome:REACT_105813 "Androgen biosynthesis, Sus scrofa" +xref: Reactome:REACT_110320 "Androgen biosynthesis, Oryza sativa" +xref: Reactome:REACT_11059 "Androgen biosynthesis, Homo sapiens" +xref: Reactome:REACT_112163 "Androgen biosynthesis, Escherichia coli" +xref: Reactome:REACT_112753 "Androgen biosynthesis, Mycobacterium tuberculosis" +xref: Reactome:REACT_31255 "Androgen biosynthesis, Canis familiaris" +xref: Reactome:REACT_31731 "Androgen biosynthesis, Drosophila melanogaster" +xref: Reactome:REACT_32074 "Androgen biosynthesis, Schizosaccharomyces pombe" +xref: Reactome:REACT_33719 "Androgen biosynthesis, Plasmodium falciparum" +xref: Reactome:REACT_77502 "Androgen biosynthesis, Xenopus tropicalis" +xref: Reactome:REACT_81567 "Androgen biosynthesis, Bos taurus" +xref: Reactome:REACT_82592 "Androgen biosynthesis, Gallus gallus" +xref: Reactome:REACT_83836 "Androgen biosynthesis, Mus musculus" +xref: Reactome:REACT_93760 "Androgen biosynthesis, Danio rerio" +xref: Reactome:REACT_95083 "Androgen biosynthesis, Rattus norvegicus" +xref: Reactome:REACT_97388 "Androgen biosynthesis, Saccharomyces cerevisiae" +xref: Reactome:REACT_98944 "Androgen biosynthesis, Dictyostelium discoideum" +is_a: GO:0006694 ! steroid biosynthetic process +is_a: GO:0008209 ! androgen metabolic process +is_a: GO:0042446 ! hormone biosynthetic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0006704 +name: glucocorticoid biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol." [ISBN:0198506732] +synonym: "glucocorticoid anabolism" EXACT [] +synonym: "glucocorticoid biosynthesis" EXACT [] +synonym: "glucocorticoid formation" EXACT [] +synonym: "glucocorticoid synthesis" EXACT [] +xref: Reactome:REACT_100413 "Glucocorticoid biosynthesis, Sus scrofa" +xref: Reactome:REACT_101421 "Glucocorticoid biosynthesis, Dictyostelium discoideum" +xref: Reactome:REACT_102866 "Glucocorticoid biosynthesis, Rattus norvegicus" +xref: Reactome:REACT_107330 "Glucocorticoid biosynthesis, Xenopus tropicalis" +xref: Reactome:REACT_107450 "Glucocorticoid biosynthesis, Mus musculus" +xref: Reactome:REACT_107635 "Glucocorticoid biosynthesis, Canis familiaris" +xref: Reactome:REACT_108788 "Glucocorticoid biosynthesis, Mycobacterium tuberculosis" +xref: Reactome:REACT_11036 "Glucocorticoid biosynthesis, Homo sapiens" +xref: Reactome:REACT_112672 "Glucocorticoid biosynthesis, Plasmodium falciparum" +xref: Reactome:REACT_113066 "Glucocorticoid biosynthesis, Escherichia coli" +xref: Reactome:REACT_77995 "Glucocorticoid biosynthesis, Oryza sativa" +xref: Reactome:REACT_79303 "Glucocorticoid biosynthesis, Bos taurus" +xref: Reactome:REACT_84297 "Glucocorticoid biosynthesis, Danio rerio" +xref: Reactome:REACT_85887 "Glucocorticoid biosynthesis, Taeniopygia guttata" +xref: Reactome:REACT_86974 "Glucocorticoid biosynthesis, Drosophila melanogaster" +xref: Reactome:REACT_88537 "Glucocorticoid biosynthesis, Arabidopsis thaliana" +xref: Reactome:REACT_94676 "Glucocorticoid biosynthesis, Gallus gallus" +is_a: GO:0006694 ! steroid biosynthetic process +is_a: GO:0008211 ! glucocorticoid metabolic process + +[Term] +id: GO:0006705 +name: mineralocorticoid biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol." [ISBN:0198506732] +synonym: "mineralocorticoid anabolism" EXACT [] +synonym: "mineralocorticoid biosynthesis" EXACT [] +synonym: "mineralocorticoid formation" EXACT [] +synonym: "mineralocorticoid synthesis" EXACT [] +xref: Reactome:REACT_103517 "Mineralocorticoid biosynthesis, Mus musculus" +xref: Reactome:REACT_108854 "Mineralocorticoid biosynthesis, Gallus gallus" +xref: Reactome:REACT_109273 "Mineralocorticoid biosynthesis, Taeniopygia guttata" +xref: Reactome:REACT_11047 "Mineralocorticoid biosynthesis, Homo sapiens" +xref: Reactome:REACT_112957 "Mineralocorticoid biosynthesis, Escherichia coli" +xref: Reactome:REACT_113805 "Mineralocorticoid biosynthesis, Mycobacterium tuberculosis" +xref: Reactome:REACT_30217 "Mineralocorticoid biosynthesis, Bos taurus" +xref: Reactome:REACT_32293 "Mineralocorticoid biosynthesis, Xenopus tropicalis" +xref: Reactome:REACT_77462 "Mineralocorticoid biosynthesis, Rattus norvegicus" +xref: Reactome:REACT_86556 "Mineralocorticoid biosynthesis, Danio rerio" +xref: Reactome:REACT_88868 "Mineralocorticoid biosynthesis, Drosophila melanogaster" +xref: Reactome:REACT_94686 "Mineralocorticoid biosynthesis, Canis familiaris" +xref: Reactome:REACT_97241 "Mineralocorticoid biosynthesis, Sus scrofa" +is_a: GO:0006694 ! steroid biosynthetic process +is_a: GO:0008212 ! mineralocorticoid metabolic process +is_a: GO:0042446 ! hormone biosynthetic process + +[Term] +id: GO:0006725 +name: cellular aromatic compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732] +subset: goslim_pir +subset: gosubset_prok +synonym: "aromatic compound metabolism" EXACT [] +synonym: "aromatic hydrocarbon metabolic process" NARROW [] +synonym: "aromatic hydrocarbon metabolism" NARROW [] +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0006753 +name: nucleoside phosphate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving any phosphorylated nucleoside." [GOC:mah] +subset: gosubset_prok +synonym: "nucleoside phosphate metabolism" EXACT [] +is_a: GO:0006796 ! phosphate-containing compound metabolic process +is_a: GO:0019637 ! organophosphate metabolic process +is_a: GO:0055086 ! nucleobase-containing small molecule metabolic process + +[Term] +id: GO:0006766 +name: vitamin metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems." [GOC:ai] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_pir +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "vitamin metabolism" EXACT [] +xref: Reactome:REACT_101808 "Metabolism of vitamins and cofactors, Bos taurus" +xref: Reactome:REACT_101968 "Metabolism of vitamins and cofactors, Saccharomyces cerevisiae" +xref: Reactome:REACT_102472 "Vitamins, Xenopus tropicalis" +xref: Reactome:REACT_103646 "Metabolism of vitamins and cofactors, Staphylococcus aureus N315" +xref: Reactome:REACT_104403 "Vitamins, Bos taurus" +xref: Reactome:REACT_105907 "Metabolism of vitamins and cofactors, Danio rerio" +xref: Reactome:REACT_106152 "Metabolism of vitamins and cofactors, Xenopus tropicalis" +xref: Reactome:REACT_108558 "Metabolism of vitamins and cofactors, Rattus norvegicus" +xref: Reactome:REACT_110948 "Metabolism of vitamins and cofactors, Sus scrofa" +xref: Reactome:REACT_11193 "Metabolism of vitamins and cofactors, Homo sapiens" +xref: Reactome:REACT_13450 "Vitamins, Homo sapiens" +xref: Reactome:REACT_30091 "Metabolism of vitamins and cofactors, Oryza sativa" +xref: Reactome:REACT_31562 "Vitamins, Sus scrofa" +xref: Reactome:REACT_33241 "Vitamins, Oryza sativa" +xref: Reactome:REACT_33738 "Metabolism of vitamins and cofactors, Mycobacterium tuberculosis" +xref: Reactome:REACT_34161 "Metabolism of vitamins and cofactors, Mus musculus" +xref: Reactome:REACT_34372 "Vitamins, Taeniopygia guttata" +xref: Reactome:REACT_36524 "Vitamins, Gallus gallus" +xref: Reactome:REACT_78899 "Metabolism of vitamins and cofactors, Caenorhabditis elegans" +xref: Reactome:REACT_79004 "Vitamins, Danio rerio" +xref: Reactome:REACT_80415 "Vitamins, Rattus norvegicus" +xref: Reactome:REACT_81509 "Metabolism of vitamins and cofactors, Gallus gallus" +xref: Reactome:REACT_82129 "Metabolism of vitamins and cofactors, Taeniopygia guttata" +xref: Reactome:REACT_82903 "Vitamins, Canis familiaris" +xref: Reactome:REACT_83508 "Metabolism of vitamins and cofactors, Arabidopsis thaliana" +xref: Reactome:REACT_84128 "Vitamins, Drosophila melanogaster" +xref: Reactome:REACT_87513 "Metabolism of vitamins and cofactors, Schizosaccharomyces pombe" +xref: Reactome:REACT_88847 "Vitamins, Mus musculus" +xref: Reactome:REACT_88850 "Metabolism of vitamins and cofactors, Dictyostelium discoideum" +xref: Reactome:REACT_90099 "Vitamins, Arabidopsis thaliana" +xref: Reactome:REACT_96278 "Metabolism of vitamins and cofactors, Plasmodium falciparum" +xref: Reactome:REACT_96904 "Metabolism of vitamins and cofactors, Drosophila melanogaster" +xref: Reactome:REACT_97734 "Metabolism of vitamins and cofactors, Escherichia coli" +xref: Reactome:REACT_97893 "Metabolism of vitamins and cofactors, Canis familiaris" +is_a: GO:0044281 ! small molecule metabolic process + +[Term] +id: GO:0006790 +name: sulfur compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:ai] +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "sulfur metabolism" EXACT [] +synonym: "sulphur metabolic process" EXACT [] +synonym: "sulphur metabolism" EXACT [] +xref: Reactome:REACT_27247 "Sulfur compound metabolism, Mycobacterium tuberculosis" +xref: Wikipedia:Sulfur_metabolism +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0006793 +name: phosphorus metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4)." [GOC:ai] +subset: goslim_pir +subset: gosubset_prok +synonym: "phosphorus metabolism" EXACT [] +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0006796 +name: phosphate-containing compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid." [GOC:ai] +subset: gosubset_prok +synonym: "phosphate metabolic process" RELATED [] +synonym: "phosphate metabolism" EXACT [] +is_a: GO:0006793 ! phosphorus metabolic process + +[Term] +id: GO:0006807 +name: nitrogen compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [CHEBI:51143, GOC:go_curators, GOC:jl, ISBN:0198506732] +comment: Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node. +subset: goslim_metagenomics +subset: goslim_pir +subset: gosubset_prok +synonym: "nitrogen compound metabolism" EXACT [] +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0006810 +name: transport +namespace: biological_process +alt_id: GO:0015457 +alt_id: GO:0015460 +def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "auxiliary transport protein activity" RELATED [GOC:mah] +synonym: "small molecule transport" NARROW [] +synonym: "solute:solute exchange" NARROW [] +synonym: "transport accessory protein activity" RELATED [GOC:mah] +is_a: GO:0051234 ! establishment of localization + +[Term] +id: GO:0006811 +name: ion transport +namespace: biological_process +def: "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +xref: Reactome:REACT_102356 "Transport of inorganic cations/anions and amino acids/oligopeptides, Xenopus tropicalis" +xref: Reactome:REACT_102895 "Transport of inorganic cations/anions and amino acids/oligopeptides, Staphylococcus aureus N315" +xref: Reactome:REACT_106972 "Transport of inorganic cations/anions and amino acids/oligopeptides, Sus scrofa" +xref: Reactome:REACT_109067 "Transport of inorganic cations/anions and amino acids/oligopeptides, Saccharomyces cerevisiae" +xref: Reactome:REACT_110862 "Transport of inorganic cations/anions and amino acids/oligopeptides, Arabidopsis thaliana" +xref: Reactome:REACT_19397 "Transport of inorganic cations/anions and amino acids/oligopeptides, Homo sapiens" +xref: Reactome:REACT_29110 "Transport of inorganic cations/anions and amino acids/oligopeptides, Oryza sativa" +xref: Reactome:REACT_31978 "Transport of inorganic cations/anions and amino acids/oligopeptides, Mus musculus" +xref: Reactome:REACT_33992 "Transport of inorganic cations/anions and amino acids/oligopeptides, Danio rerio" +xref: Reactome:REACT_34201 "Transport of inorganic cations/anions and amino acids/oligopeptides, Gallus gallus" +xref: Reactome:REACT_79109 "Transport of inorganic cations/anions and amino acids/oligopeptides, Caenorhabditis elegans" +xref: Reactome:REACT_82618 "Transport of inorganic cations/anions and amino acids/oligopeptides, Escherichia coli" +xref: Reactome:REACT_87822 "Transport of inorganic cations/anions and amino acids/oligopeptides, Bos taurus" +xref: Reactome:REACT_91472 "Transport of inorganic cations/anions and amino acids/oligopeptides, Dictyostelium discoideum" +xref: Reactome:REACT_91958 "Transport of inorganic cations/anions and amino acids/oligopeptides, Drosophila melanogaster" +xref: Reactome:REACT_92903 "Transport of inorganic cations/anions and amino acids/oligopeptides, Mycobacterium tuberculosis" +xref: Reactome:REACT_93485 "Transport of inorganic cations/anions and amino acids/oligopeptides, Canis familiaris" +xref: Reactome:REACT_94357 "Transport of inorganic cations/anions and amino acids/oligopeptides, Rattus norvegicus" +xref: Reactome:REACT_96078 "Transport of inorganic cations/anions and amino acids/oligopeptides, Plasmodium falciparum" +xref: Reactome:REACT_96919 "Transport of inorganic cations/anions and amino acids/oligopeptides, Taeniopygia guttata" +xref: Reactome:REACT_98077 "Transport of inorganic cations/anions and amino acids/oligopeptides, Schizosaccharomyces pombe" +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0006812 +name: cation transport +namespace: biological_process +alt_id: GO:0006819 +alt_id: GO:0015674 +def: "The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +subset: gosubset_prok +synonym: "di-, tri-valent inorganic cation transport" NARROW [GOC:mah] +is_a: GO:0006811 ! ion transport + +[Term] +id: GO:0006816 +name: calcium ion transport +namespace: biological_process +def: "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +subset: gosubset_prok +synonym: "calcium transport" EXACT [] +synonym: "mitochondrial sodium/calcium ion exchange" NARROW [] +synonym: "sodium:calcium exchange" NARROW [] +is_a: GO:0070838 ! divalent metal ion transport + +[Term] +id: GO:0006836 +name: neurotransmitter transport +namespace: biological_process +def: "The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [GOC:ai] +subset: goslim_pir +synonym: "sodium:neurotransmitter transport" NARROW [] +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0006869 +name: lipid transport +namespace: biological_process +def: "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732] +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0044765 ! single-organism transport +is_a: GO:0071702 ! organic substance transport +relationship: part_of GO:0010876 ! lipid localization + +[Term] +id: GO:0006873 +name: cellular ion homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of ions at the level of a cell." [GOC:mah] +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0050801 ! ion homeostasis +is_a: GO:0055082 ! cellular chemical homeostasis + +[Term] +id: GO:0006874 +name: cellular calcium ion homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell." [GOC:ceb, GOC:mah] +synonym: "regulation of calcium ion concentration" BROAD [] +is_a: GO:0006875 ! cellular metal ion homeostasis +is_a: GO:0055074 ! calcium ion homeostasis +is_a: GO:0072503 ! cellular divalent inorganic cation homeostasis + +[Term] +id: GO:0006875 +name: cellular metal ion homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of metal ions at the level of a cell." [GOC:ai, GOC:mah] +subset: gosubset_prok +synonym: "cellular heavy metal ion homeostasis" NARROW [] +is_a: GO:0030003 ! cellular cation homeostasis +is_a: GO:0055065 ! metal ion homeostasis + +[Term] +id: GO:0006886 +name: intracellular protein transport +namespace: biological_process +alt_id: GO:0032779 +def: "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." [GOC:mah] +subset: gosubset_prok +synonym: "copper-induced intracellular protein transport" RELATED [GOC:al] +is_a: GO:0015031 ! protein transport +is_a: GO:0046907 ! intracellular transport +intersection_of: GO:0015031 ! protein transport +intersection_of: occurs_in GO:0005622 ! intracellular +relationship: part_of GO:0034613 ! cellular protein localization + +[Term] +id: GO:0006897 +name: endocytosis +namespace: biological_process +alt_id: GO:0016193 +alt_id: GO:0016196 +def: "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363] +subset: goslim_yeast +subset: gosubset_prok +synonym: "nonselective vesicle endocytosis" RELATED [] +synonym: "plasma membrane invagination" EXACT [] +synonym: "vesicle endocytosis" EXACT [] +xref: Wikipedia:Endocytosis +is_a: GO:0016192 ! vesicle-mediated transport +relationship: has_part GO:0010324 ! membrane invagination + +[Term] +id: GO:0006898 +name: receptor-mediated endocytosis +namespace: biological_process +def: "An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles." [GOC:mah, ISBN:0716731363] +synonym: "receptor mediated endocytosis" EXACT [] +xref: Reactome:REACT_100248 "LDL-mediated lipid transport, Gallus gallus" +xref: Reactome:REACT_100330 "chylomicron remnant:apoE:LDLR complex [coated vesicle membrane] => chylomicron remnant:apoE:LDLR complex [endosome membrane], Mus musculus" +xref: Reactome:REACT_103823 "LDLR [endosome membrane] => LDLR [plasma membrane], Sus scrofa" +xref: Reactome:REACT_103978 "LDLR:LDL complex => LDLR + LDL, Danio rerio" +xref: Reactome:REACT_104437 "LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane], Sus scrofa" +xref: Reactome:REACT_105792 "chylomicron remnant:apoE complex + LDLR => chylomicron remnant:apoE:LDLR complex, Danio rerio" +xref: Reactome:REACT_106851 "LDL-mediated lipid transport, Rattus norvegicus" +xref: Reactome:REACT_106981 "LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane], Mus musculus" +xref: Reactome:REACT_107174 "chylomicron remnant:apoE complex + LDLR => chylomicron remnant:apoE:LDLR complex, Sus scrofa" +xref: Reactome:REACT_107413 "LDL + LDLR => LDL:LDLR complex, Danio rerio" +xref: Reactome:REACT_107880 "chylomicron remnant:apoE:LDLR complex => chylomicron remnant:apoE + LDLR, Mus musculus" +xref: Reactome:REACT_109308 "LDLR:LDL complex => LDLR + LDL, Xenopus tropicalis" +xref: Reactome:REACT_110306 "LDL-mediated lipid transport, Canis familiaris" +xref: Reactome:REACT_110472 "LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane], Bos taurus" +xref: Reactome:REACT_110785 "LDLR:LDL complex => LDLR + LDL, Bos taurus" +xref: Reactome:REACT_111177 "Movement of clathrin coated vesicles into early endosome, Homo sapiens" +xref: Reactome:REACT_112262 "LDLR [endosome membrane] => LDLR [plasma membrane], Taeniopygia guttata" +xref: Reactome:REACT_113143 "LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane], Taeniopygia guttata" +xref: Reactome:REACT_113715 "LDLR [endosome membrane] => LDLR [plasma membrane], Drosophila melanogaster" +xref: Reactome:REACT_114061 "LDLR:LDL complex => LDLR + LDL, Taeniopygia guttata" +xref: Reactome:REACT_114157 "chylomicron remnant:apoE complex + LDLR => chylomicron remnant:apoE:LDLR complex, Xenopus tropicalis" +xref: Reactome:REACT_114755 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent), Taeniopygia guttata" +xref: Reactome:REACT_114861 "LDL + LDLR => LDL:LDLR complex, Taeniopygia guttata" +xref: Reactome:REACT_115278 "LDL-mediated lipid transport, Caenorhabditis elegans" +xref: Reactome:REACT_115471 "LDLR [endosome membrane] => LDLR [plasma membrane], Caenorhabditis elegans" +xref: Reactome:REACT_115520 "LDL-mediated lipid transport, Drosophila melanogaster" +xref: Reactome:REACT_28736 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent), Canis familiaris" +xref: Reactome:REACT_29541 "LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane], Canis familiaris" +xref: Reactome:REACT_30278 "LDLR [endosome membrane] => LDLR [plasma membrane], Bos taurus" +xref: Reactome:REACT_30568 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent), Sus scrofa" +xref: Reactome:REACT_30705 "LDLR [endosome membrane] => LDLR [plasma membrane], Rattus norvegicus" +xref: Reactome:REACT_30731 "LDL + LDLR => LDL:LDLR complex, Sus scrofa" +xref: Reactome:REACT_31404 "LDLR:LDL complex => LDLR + LDL, Canis familiaris" +xref: Reactome:REACT_31638 "LDL-mediated lipid transport, Sus scrofa" +xref: Reactome:REACT_33230 "LDLR [endosome membrane] => LDLR [plasma membrane], Mus musculus" +xref: Reactome:REACT_33281 "chylomicron remnant:apoE:LDLR complex => chylomicron remnant:apoE + LDLR, Rattus norvegicus" +xref: Reactome:REACT_34027 "LDLR:LDL complex => LDLR + LDL, Sus scrofa" +xref: Reactome:REACT_50314 "LDL-mediated lipid transport, Mus musculus" +xref: Reactome:REACT_50874 "chylomicron remnant:apoE:LDLR complex [coated vesicle membrane] => chylomicron remnant:apoE:LDLR complex [endosome membrane], Rattus norvegicus" +xref: Reactome:REACT_6720 "chylomicron remnant:apoE:LDLR complex [coated vesicle membrane] => chylomicron remnant:apoE:LDLR complex [endosome membrane], Homo sapiens" +xref: Reactome:REACT_6775 "LDLR:LDL complex => LDLR + LDL, Homo sapiens" +xref: Reactome:REACT_6810 "LDLR [endosome membrane] => LDLR [plasma membrane], Homo sapiens" +xref: Reactome:REACT_6849 "chylomicron remnant:apoE complex + LDLR => chylomicron remnant:apoE:LDLR complex, Homo sapiens" +xref: Reactome:REACT_6860 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-independent), Homo sapiens" +xref: Reactome:REACT_6901 "LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane], Homo sapiens" +xref: Reactome:REACT_6924 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent), Homo sapiens" +xref: Reactome:REACT_6934 "LDL-mediated lipid transport, Homo sapiens" +xref: Reactome:REACT_6940 "LDL + LDLR => LDL:LDLR complex, Homo sapiens" +xref: Reactome:REACT_6951 "chylomicron remnant:apoE:LDLR complex => chylomicron remnant:apoE + LDLR, Homo sapiens" +xref: Reactome:REACT_77527 "LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane], Xenopus tropicalis" +xref: Reactome:REACT_78454 "LDL + LDLR => LDL:LDLR complex, Mus musculus" +xref: Reactome:REACT_78761 "chylomicron remnant:apoE complex + LDLR => chylomicron remnant:apoE:LDLR complex, Rattus norvegicus" +xref: Reactome:REACT_80639 "LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane], Rattus norvegicus" +xref: Reactome:REACT_80964 "LDL-mediated lipid transport, Xenopus tropicalis" +xref: Reactome:REACT_81206 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent), Xenopus tropicalis" +xref: Reactome:REACT_81516 "LDLR [endosome membrane] => LDLR [plasma membrane], Canis familiaris" +xref: Reactome:REACT_81850 "LDL + LDLR => LDL:LDLR complex, Rattus norvegicus" +xref: Reactome:REACT_82541 "chylomicron remnant:apoE complex + LDLR => chylomicron remnant:apoE:LDLR complex, Bos taurus" +xref: Reactome:REACT_82595 "chylomicron remnant:apoE:LDLR complex => chylomicron remnant:apoE + LDLR, Canis familiaris" +xref: Reactome:REACT_83238 "chylomicron remnant:apoE:LDLR complex [coated vesicle membrane] => chylomicron remnant:apoE:LDLR complex [endosome membrane], Sus scrofa" +xref: Reactome:REACT_83320 "LDLR:LDL complex => LDLR + LDL, Mus musculus" +xref: Reactome:REACT_83479 "chylomicron remnant:apoE:LDLR complex => chylomicron remnant:apoE + LDLR, Xenopus tropicalis" +xref: Reactome:REACT_84153 "chylomicron remnant:apoE:LDLR complex => chylomicron remnant:apoE + LDLR, Sus scrofa" +xref: Reactome:REACT_84233 "LDLR [endosome membrane] => LDLR [plasma membrane], Danio rerio" +xref: Reactome:REACT_84451 "LDL + LDLR => LDL:LDLR complex, Canis familiaris" +xref: Reactome:REACT_84602 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent), Danio rerio" +xref: Reactome:REACT_84963 "chylomicron remnant:apoE:LDLR complex [coated vesicle membrane] => chylomicron remnant:apoE:LDLR complex [endosome membrane], Bos taurus" +xref: Reactome:REACT_84978 "LDLR [endosome membrane] => LDLR [plasma membrane], Xenopus tropicalis" +xref: Reactome:REACT_84983 "LDL + LDLR => LDL:LDLR complex, Bos taurus" +xref: Reactome:REACT_85895 "LDL + LDLR => LDL:LDLR complex, Xenopus tropicalis" +xref: Reactome:REACT_86311 "chylomicron remnant:apoE:LDLR complex [coated vesicle membrane] => chylomicron remnant:apoE:LDLR complex [endosome membrane], Danio rerio" +xref: Reactome:REACT_87254 "chylomicron remnant:apoE:LDLR complex [coated vesicle membrane] => chylomicron remnant:apoE:LDLR complex [endosome membrane], Xenopus tropicalis" +xref: Reactome:REACT_87301 "chylomicron remnant:apoE:LDLR complex => chylomicron remnant:apoE + LDLR, Bos taurus" +xref: Reactome:REACT_90065 "chylomicron remnant:apoE:LDLR complex => chylomicron remnant:apoE + LDLR, Danio rerio" +xref: Reactome:REACT_90294 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent), Rattus norvegicus" +xref: Reactome:REACT_90795 "chylomicron remnant:apoE complex + LDLR => chylomicron remnant:apoE:LDLR complex, Canis familiaris" +xref: Reactome:REACT_91303 "LDLR:LDL complex => LDLR + LDL, Rattus norvegicus" +xref: Reactome:REACT_91595 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent), Mus musculus" +xref: Reactome:REACT_93284 "LDL-mediated lipid transport, Bos taurus" +xref: Reactome:REACT_93519 "chylomicron remnant:apoE complex + LDLR => chylomicron remnant:apoE:LDLR complex, Mus musculus" +xref: Reactome:REACT_94912 "LDL-mediated lipid transport, Danio rerio" +xref: Reactome:REACT_95536 "LDL-mediated lipid transport, Taeniopygia guttata" +xref: Reactome:REACT_96679 "LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane], Danio rerio" +xref: Reactome:REACT_98265 "chylomicron remnant:apoE:LDLR complex [coated vesicle membrane] => chylomicron remnant:apoE:LDLR complex [endosome membrane], Canis familiaris" +xref: Reactome:REACT_99018 "LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent), Bos taurus" +xref: Wikipedia:Receptor-mediated_endocytosis +is_a: GO:0006897 ! endocytosis + +[Term] +id: GO:0006913 +name: nucleocytoplasmic transport +namespace: biological_process +alt_id: GO:0000063 +def: "The directed movement of molecules between the nucleus and the cytoplasm." [GOC:go_curators] +comment: Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. +subset: goslim_generic +subset: goslim_pombe +synonym: "nucleocytoplasmic shuttling" NARROW [] +is_a: GO:0016482 ! cytoplasmic transport +is_a: GO:0051169 ! nuclear transport + +[Term] +id: GO:0006915 +name: apoptotic process +namespace: biological_process +alt_id: GO:0006917 +alt_id: GO:0008632 +def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathways) which typically lead to rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. The process ends when the cell has died. The process is divided into a signaling pathway phase, and an execution phase, which is triggered by the former." [GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] +synonym: "activation of apoptosis" NARROW [] +synonym: "apoptosis" NARROW [] +synonym: "apoptosis activator activity" RELATED [] +synonym: "apoptosis signaling" NARROW [] +synonym: "apoptotic cell death" EXACT [GOC:sl] +synonym: "apoptotic program" NARROW [GOC:add] +synonym: "apoptotic programmed cell death" EXACT [] +synonym: "cell suicide" BROAD [] +synonym: "cellular suicide" BROAD [] +synonym: "commitment to apoptosis" RELATED [] +synonym: "induction of apoptosis" RELATED [] +synonym: "induction of apoptosis by p53" RELATED [] +synonym: "programmed cell death by apoptosis" EXACT [] +synonym: "signaling (initiator) caspase activity" RELATED [] +synonym: "type I programmed cell death" NARROW [] +xref: Reactome:REACT_100045 "Apoptosis, Drosophila melanogaster" +xref: Reactome:REACT_100962 "Apoptosis, Mus musculus" +xref: Reactome:REACT_101249 "NRIF signals cell death from the nucleus, Danio rerio" +xref: Reactome:REACT_104187 "NRAGE signals death through JNK, Taeniopygia guttata" +xref: Reactome:REACT_105149 "NADE modulates death signalling, Rattus norvegicus" +xref: Reactome:REACT_106405 "NRAGE signals death through JNK, Xenopus tropicalis" +xref: Reactome:REACT_106672 "NADE modulates death signalling, Sus scrofa" +xref: Reactome:REACT_107264 "NRIF signals cell death from the nucleus, Xenopus tropicalis" +xref: Reactome:REACT_108651 "NRAGE signals death through JNK, Mus musculus" +xref: Reactome:REACT_109165 "NRAGE signals death through JNK, Arabidopsis thaliana" +xref: Reactome:REACT_110081 "NRAGE signals death through JNK, Schizosaccharomyces pombe" +xref: Reactome:REACT_111964 "NRAGE signals death through JNK, Dictyostelium discoideum" +xref: Reactome:REACT_13526 "NADE modulates death signalling, Homo sapiens" +xref: Reactome:REACT_13638 "NRAGE signals death through JNK, Homo sapiens" +xref: Reactome:REACT_13643 "NRIF signals cell death from the nucleus, Homo sapiens" +xref: Reactome:REACT_28087 "Apoptosis, Saccharomyces cerevisiae" +xref: Reactome:REACT_28795 "Apoptosis, Oryza sativa" +xref: Reactome:REACT_28816 "Apoptosis, Danio rerio" +xref: Reactome:REACT_30266 "Apoptosis, Arabidopsis thaliana" +xref: Reactome:REACT_30361 "Apoptosis, Canis familiaris" +xref: Reactome:REACT_30371 "NRAGE signals death through JNK, Saccharomyces cerevisiae" +xref: Reactome:REACT_30548 "NRAGE signals death through JNK, Caenorhabditis elegans" +xref: Reactome:REACT_30763 "NRAGE signals death through JNK, Oryza sativa" +xref: Reactome:REACT_31349 "NRAGE signals death through JNK, Canis familiaris" +xref: Reactome:REACT_34139 "NRAGE signals death through JNK, Gallus gallus" +xref: Reactome:REACT_578 "Apoptosis, Homo sapiens" +xref: Reactome:REACT_77132 "NRAGE signals death through JNK, Drosophila melanogaster" +xref: Reactome:REACT_77313 "NADE modulates death signalling, Bos taurus" +xref: Reactome:REACT_77415 "NRIF signals cell death from the nucleus, Canis familiaris" +xref: Reactome:REACT_78287 "Apoptosis, Gallus gallus" +xref: Reactome:REACT_78802 "NADE modulates death signalling, Canis familiaris" +xref: Reactome:REACT_79809 "Apoptosis, Schizosaccharomyces pombe" +xref: Reactome:REACT_82724 "Apoptosis, Taeniopygia guttata" +xref: Reactome:REACT_83328 "Apoptosis, Sus scrofa" +xref: Reactome:REACT_85877 "NRAGE signals death through JNK, Rattus norvegicus" +xref: Reactome:REACT_86749 "Apoptosis, Rattus norvegicus" +xref: Reactome:REACT_86873 "NRIF signals cell death from the nucleus, Gallus gallus" +xref: Reactome:REACT_87570 "NRIF signals cell death from the nucleus, Rattus norvegicus" +xref: Reactome:REACT_88740 "NRIF signals cell death from the nucleus, Sus scrofa" +xref: Reactome:REACT_88784 "NRIF signals cell death from the nucleus, Mus musculus" +xref: Reactome:REACT_89196 "Apoptosis, Dictyostelium discoideum" +xref: Reactome:REACT_90267 "NRIF signals cell death from the nucleus, Taeniopygia guttata" +xref: Reactome:REACT_91011 "Apoptosis, Caenorhabditis elegans" +xref: Reactome:REACT_91243 "NADE modulates death signalling, Mus musculus" +xref: Reactome:REACT_93937 "Apoptosis, Bos taurus" +xref: Reactome:REACT_94099 "NRAGE signals death through JNK, Danio rerio" +xref: Reactome:REACT_95069 "Apoptosis, Xenopus tropicalis" +xref: Reactome:REACT_95675 "Apoptosis, Plasmodium falciparum" +xref: Reactome:REACT_97627 "NRIF signals cell death from the nucleus, Bos taurus" +xref: Reactome:REACT_99784 "NRAGE signals death through JNK, Bos taurus" +xref: Reactome:REACT_99799 "NRAGE signals death through JNK, Sus scrofa" +xref: Wikipedia:Apoptosis +is_a: GO:0012501 ! programmed cell death + +[Term] +id: GO:0006921 +name: cellular component disassembly involved in execution phase of apoptosis +namespace: biological_process +def: "The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis." [GOC:dph, GOC:mah, GOC:mtg_apoptosis, GOC:tb] +synonym: "cellular component disassembly involved in apoptosis" NARROW [] +synonym: "cellular component disassembly involved in apoptotic process" BROAD [] +synonym: "disassembly of cell structures" BROAD [] +xref: Reactome:REACT_100800 "Apoptotic execution phase, Danio rerio" +xref: Reactome:REACT_108463 "Apoptotic execution phase, Taeniopygia guttata" +xref: Reactome:REACT_29660 "Apoptotic execution phase, Oryza sativa" +xref: Reactome:REACT_77151 "Apoptotic execution phase, Sus scrofa" +xref: Reactome:REACT_78666 "Apoptotic execution phase, Saccharomyces cerevisiae" +xref: Reactome:REACT_79472 "Apoptotic execution phase, Schizosaccharomyces pombe" +xref: Reactome:REACT_79859 "Apoptotic execution phase, Rattus norvegicus" +xref: Reactome:REACT_80493 "Apoptotic execution phase, Dictyostelium discoideum" +xref: Reactome:REACT_81021 "Apoptotic execution phase, Drosophila melanogaster" +xref: Reactome:REACT_81052 "Apoptotic execution phase, Canis familiaris" +xref: Reactome:REACT_84120 "Apoptotic execution phase, Xenopus tropicalis" +xref: Reactome:REACT_89424 "Apoptotic execution phase, Arabidopsis thaliana" +xref: Reactome:REACT_90988 "Apoptotic execution phase, Plasmodium falciparum" +xref: Reactome:REACT_92689 "Apoptotic execution phase, Caenorhabditis elegans" +xref: Reactome:REACT_93576 "Apoptotic execution phase, Gallus gallus" +xref: Reactome:REACT_94230 "Apoptotic execution phase, Bos taurus" +xref: Reactome:REACT_97703 "Apoptotic execution phase, Mus musculus" +xref: Reactome:REACT_995 "Apoptotic execution phase, Homo sapiens" +is_a: GO:0022411 ! cellular component disassembly +intersection_of: GO:0022411 ! cellular component disassembly +intersection_of: part_of GO:0097194 ! execution phase of apoptosis +relationship: part_of GO:0097194 ! execution phase of apoptosis + +[Term] +id: GO:0006928 +name: cellular component movement +namespace: biological_process +def: "The directed, self-propelled movement of a cellular component without the involvement of an external agent such as a transporter or a pore." [GOC:dgh, GOC:dph, GOC:jl, GOC:mlg] +comment: Note that in GO cellular components include whole cells (cell is_a cellular component). +subset: goslim_pir +subset: gosubset_prok +synonym: "cell movement" RELATED [] +synonym: "cellular component motion" EXACT [GOC:dph, GOC:jl] +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0006935 +name: chemotaxis +namespace: biological_process +def: "The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." [ISBN:0198506732] +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "taxis in response to chemical stimulus" EXACT [] +xref: Wikipedia:Chemotaxis +is_a: GO:0042221 ! response to chemical +is_a: GO:0042330 ! taxis + +[Term] +id: GO:0006949 +name: syncytium formation +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732] +subset: goslim_pir +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis + +[Term] +id: GO:0006950 +name: response to stress +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "response to abiotic stress" RELATED [] +synonym: "response to biotic stress" RELATED [] +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0006952 +name: defense response +namespace: biological_process +alt_id: GO:0002217 +alt_id: GO:0042829 +def: "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:go_curators] +subset: gosubset_prok +synonym: "antimicrobial peptide activity" RELATED [] +synonym: "defence response" EXACT [] +synonym: "defense/immunity protein activity" RELATED [] +synonym: "physiological defense response" EXACT [] +is_a: GO:0006950 ! response to stress + +[Term] +id: GO:0006954 +name: inflammatory response +namespace: biological_process +def: "The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages." [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732] +comment: This term was improved by GO_REF:0000022. It was moved. +xref: Wikipedia:Inflammation +is_a: GO:0006952 ! defense response +is_a: GO:0009611 ! response to wounding + +[Term] +id: GO:0006955 +name: immune response +namespace: biological_process +def: "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05] +comment: This term was improved by GO_REF:0000022. It was redefined and moved. +is_a: GO:0002376 ! immune system process +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0006959 +name: humoral immune response +namespace: biological_process +def: "An immune response mediated through a body fluid." [GOC:hb, ISBN:0198506732] +xref: Wikipedia:Humoral_immunity +is_a: GO:0006955 ! immune response + +[Term] +id: GO:0006974 +name: cellular response to DNA damage stimulus +namespace: biological_process +alt_id: GO:0034984 +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC:go_curators] +subset: goslim_yeast +subset: gosubset_prok +synonym: "cellular DNA damage response" EXACT [] +synonym: "DNA damage response" EXACT [] +synonym: "response to DNA damage stimulus" BROAD [] +synonym: "response to genotoxic stress" EXACT [] +is_a: GO:0033554 ! cellular response to stress + +[Term] +id: GO:0006996 +name: organelle organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_pir +subset: gosubset_prok +synonym: "organelle organisation" EXACT [GOC:curators] +synonym: "organelle organization and biogenesis" RELATED [GOC:dph, GOC:jl, GOC:mah] +is_a: GO:0009987 ! cellular process +is_a: GO:0016043 ! cellular component organization + +[Term] +id: GO:0007009 +name: plasma membrane organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_generic +subset: gosubset_prok +synonym: "plasma membrane organisation" EXACT [GOC:curators] +synonym: "plasma membrane organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0044802 ! single-organism membrane organization + +[Term] +id: GO:0007010 +name: cytoskeleton organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "cytoskeletal organization and biogenesis" RELATED [GOC:mah] +synonym: "cytoskeletal regulator activity" RELATED [] +synonym: "cytoskeleton organisation" EXACT [GOC:curators] +synonym: "cytoskeleton organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0006996 ! organelle organization + +[Term] +id: GO:0007015 +name: actin filament organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking." [GOC:mah] +synonym: "actin filament organisation" EXACT [GOC:curators] +synonym: "regulation of actin filament localization" NARROW [] +is_a: GO:0071822 ! protein complex subunit organization +relationship: part_of GO:0030036 ! actin cytoskeleton organization + +[Term] +id: GO:0007016 +name: cytoskeletal anchoring at plasma membrane +namespace: biological_process +def: "A cytoskeleton organization process that directly or indirectly links cytoskeletal filaments to the plasma membrane." [ISBN:0198599323] +synonym: "cytoskeletal anchoring activity" RELATED [] +is_a: GO:0007010 ! cytoskeleton organization +is_a: GO:0032507 ! maintenance of protein location in cell +is_a: GO:1902589 ! single-organism organelle organization + +[Term] +id: GO:0007017 +name: microtubule-based process +namespace: biological_process +def: "Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins." [GOC:mah] +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007044 +name: cell-substrate junction assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form a junction between a cell and its substrate." [GOC:mah] +is_a: GO:0034329 ! cell junction assembly + +[Term] +id: GO:0007045 +name: cell-substrate adherens junction assembly +namespace: biological_process +def: "The aggregation, arrangement, and bonding together of a set of components to form a cell-substrate adherens junction." [GOC:mah] +synonym: "hemi-adherens junction assembly" RELATED [GOC:mah] +is_a: GO:0007044 ! cell-substrate junction assembly +is_a: GO:0034333 ! adherens junction assembly + +[Term] +id: GO:0007049 +name: cell cycle +namespace: biological_process +def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators, GOC:mtg_cell_cycle] +subset: gocheck_do_not_manually_annotate +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "cell-division cycle" EXACT [] +xref: Wikipedia:Cell_cycle +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007059 +name: chromosome segregation +namespace: biological_process +def: "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the alignment of chromosomes at the metaphase plate, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:ai, GOC:mah] +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "chromosome division" EXACT [] +synonym: "chromosome transmission" RELATED [] +xref: Wikipedia:Chromosome_segregation +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007062 +name: sister chromatid cohesion +namespace: biological_process +def: "The cell cycle process in which the sister chromatids of a replicated chromosome are associated with each other." [GOC:jh, GOC:mah, ISBN:0815316194] +synonym: "sister chromatid alignment" RELATED [] +xref: Reactome:REACT_115472 "Phosphorylation of the SA2 Cohesin Complex, Schizosaccharomyces pombe" +xref: Reactome:REACT_118229 "Phosphorylation of the SA2 Cohesin Complex, Taeniopygia guttata" +xref: Reactome:REACT_118307 "Phosphorylation of the SA2 Cohesin Complex, Gallus gallus" +xref: Reactome:REACT_118462 "Phosphorylation of the SA2 Cohesin Complex, Saccharomyces cerevisiae" +xref: Reactome:REACT_1481 "Phosphorylation of the SA2 Cohesin Complex, Homo sapiens" +xref: Reactome:REACT_30230 "Phosphorylation of the SA2 Cohesin Complex, Caenorhabditis elegans" +xref: Reactome:REACT_31519 "Phosphorylation of the SA2 Cohesin Complex, Danio rerio" +xref: Reactome:REACT_33003 "Phosphorylation of the SA2 Cohesin Complex, Dictyostelium discoideum" +xref: Reactome:REACT_82473 "Phosphorylation of the SA2 Cohesin Complex, Canis familiaris" +xref: Reactome:REACT_83187 "Phosphorylation of the SA2 Cohesin Complex, Mus musculus" +xref: Reactome:REACT_84080 "Phosphorylation of the SA2 Cohesin Complex, Xenopus tropicalis" +xref: Reactome:REACT_86014 "Phosphorylation of the SA2 Cohesin Complex, Bos taurus" +xref: Reactome:REACT_91684 "Phosphorylation of the SA2 Cohesin Complex, Drosophila melanogaster" +xref: Reactome:REACT_94817 "Phosphorylation of the SA2 Cohesin Complex, Rattus norvegicus" +is_a: GO:0022402 ! cell cycle process +is_a: GO:0051276 ! chromosome organization +is_a: GO:1902589 ! single-organism organelle organization +relationship: part_of GO:0007059 ! chromosome segregation + +[Term] +id: GO:0007063 +name: regulation of sister chromatid cohesion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of sister chromatid cohesion." [GOC:go_curators] +is_a: GO:0010564 ! regulation of cell cycle process +is_a: GO:0033044 ! regulation of chromosome organization +is_a: GO:0051983 ! regulation of chromosome segregation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007062 ! sister chromatid cohesion +relationship: regulates GO:0007062 ! sister chromatid cohesion + +[Term] +id: GO:0007067 +name: mitosis +namespace: biological_process +def: "A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." [GOC:dph, GOC:ma, GOC:mah, ISBN:0198547684] +subset: goslim_generic +xref: Wikipedia:Mitosis +is_a: GO:0000280 ! nuclear division +is_a: GO:0022402 ! cell cycle process +is_a: GO:1902589 ! single-organism organelle organization +relationship: part_of GO:0000278 ! mitotic cell cycle + +[Term] +id: GO:0007088 +name: regulation of mitosis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of mitosis." [GOC:go_curators] +is_a: GO:0007346 ! regulation of mitotic cell cycle +is_a: GO:0010564 ! regulation of cell cycle process +is_a: GO:0051783 ! regulation of nuclear division +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007067 ! mitosis +relationship: regulates GO:0007067 ! mitosis + +[Term] +id: GO:0007098 +name: centrosome cycle +namespace: biological_process +def: "The cell cycle process in which centrosome duplication and separation takes place. The centrosome cycle can operate with a considerable degree of independence from other processes of the cell cycle." [ISBN:0815316194] +is_a: GO:0022402 ! cell cycle process +is_a: GO:0051297 ! centrosome organization +is_a: GO:1902589 ! single-organism organelle organization + +[Term] +id: GO:0007126 +name: meiosis +namespace: biological_process +def: "A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle. A meiotic cell cycle is the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiotic division occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations." [GOC:dph, GOC:mah, PMID:9334324] +subset: goslim_pombe +xref: Wikipedia:Meiosis +is_a: GO:0022402 ! cell cycle process +is_a: GO:0048610 ! cellular process involved in reproduction +relationship: part_of GO:0051321 ! meiotic cell cycle + +[Term] +id: GO:0007154 +name: cell communication +namespace: biological_process +def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah] +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +xref: Wikipedia:Cell_signaling +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007155 +name: cell adhesion +namespace: biological_process +def: "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC:hb, GOC:pf] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: gosubset_prok +synonym: "cell adhesion molecule activity" RELATED [] +xref: Wikipedia:Cell_adhesion +is_a: GO:0022610 ! biological adhesion +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007160 +name: cell-matrix adhesion +namespace: biological_process +def: "The binding of a cell to the extracellular matrix via adhesion molecules." [GOC:hb] +subset: gosubset_prok +is_a: GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0007162 +name: negative regulation of cell adhesion +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion." [GOC:go_curators] +synonym: "cell adhesion receptor inhibitor activity" RELATED [] +synonym: "down regulation of cell adhesion" EXACT [] +synonym: "down-regulation of cell adhesion" EXACT [] +synonym: "downregulation of cell adhesion" EXACT [] +synonym: "inhibition of cell adhesion" NARROW [] +is_a: GO:0030155 ! regulation of cell adhesion +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007155 ! cell adhesion +relationship: negatively_regulates GO:0007155 ! cell adhesion + +[Term] +id: GO:0007163 +name: establishment or maintenance of cell polarity +namespace: biological_process +alt_id: GO:0030012 +alt_id: GO:0030467 +def: "Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns." [GOC:mah] +subset: goslim_pombe +synonym: "cell polarity" RELATED [GOC:mah, GOC:vw] +synonym: "establishment and/or maintenance of cell polarity" RELATED [] +synonym: "establishment and/or maintenance of cell polarization" RELATED [] +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007164 +name: establishment of tissue polarity +namespace: biological_process +def: "Coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates." [GOC:jid] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0007165 +name: signal transduction +namespace: biological_process +alt_id: GO:0023033 +def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] +comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "signaling cascade" NARROW [] +synonym: "signaling pathway" RELATED [] +synonym: "signalling cascade" NARROW [] +synonym: "signalling pathway" RELATED [GOC:mah] +xref: Reactome:REACT_100624 "EGFR interacts with phospholipase C-gamma, Gallus gallus" +xref: Reactome:REACT_102354 "EGFR interacts with phospholipase C-gamma, Canis familiaris" +xref: Reactome:REACT_112130 "EGFR interacts with phospholipase C-gamma, Oryza sativa" +xref: Reactome:REACT_112549 "EGFR interacts with phospholipase C-gamma, Arabidopsis thaliana" +xref: Reactome:REACT_113151 "EGFR interacts with phospholipase C-gamma, Mycobacterium tuberculosis" +xref: Reactome:REACT_113601 "EGFR interacts with phospholipase C-gamma, Drosophila melanogaster" +xref: Reactome:REACT_113964 "EGFR interacts with phospholipase C-gamma, Bos taurus" +xref: Reactome:REACT_114657 "EGFR interacts with phospholipase C-gamma, Dictyostelium discoideum" +xref: Reactome:REACT_114690 "EGFR interacts with phospholipase C-gamma, Saccharomyces cerevisiae" +xref: Reactome:REACT_114820 "EGFR interacts with phospholipase C-gamma, Sus scrofa" +xref: Reactome:REACT_114910 "EGFR interacts with phospholipase C-gamma, Caenorhabditis elegans" +xref: Reactome:REACT_115037 "EGFR interacts with phospholipase C-gamma, Plasmodium falciparum" +xref: Reactome:REACT_115147 "EGFR interacts with phospholipase C-gamma, Schizosaccharomyces pombe" +xref: Reactome:REACT_12478 "EGFR interacts with phospholipase C-gamma, Homo sapiens" +xref: Reactome:REACT_31232 "EGFR interacts with phospholipase C-gamma, Rattus norvegicus" +xref: Reactome:REACT_78535 "EGFR interacts with phospholipase C-gamma, Xenopus tropicalis" +xref: Reactome:REACT_89740 "EGFR interacts with phospholipase C-gamma, Taeniopygia guttata" +xref: Reactome:REACT_93680 "EGFR interacts with phospholipase C-gamma, Danio rerio" +xref: Reactome:REACT_98872 "EGFR interacts with phospholipase C-gamma, Mus musculus" +xref: Wikipedia:Signal_transduction +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051716 ! cellular response to stimulus +relationship: part_of GO:0007154 ! cell communication +relationship: part_of GO:0044700 ! single organism signaling + +[Term] +id: GO:0007166 +name: cell surface receptor signaling pathway +namespace: biological_process +def: "A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:mah, GOC:pr, GOC:signaling] +subset: gosubset_prok +synonym: "cell surface receptor linked signal transduction" EXACT [] +synonym: "cell surface receptor linked signaling pathway" EXACT [GOC:bf] +synonym: "cell surface receptor linked signalling pathway" EXACT [GOC:mah] +xref: Reactome:REACT_6290 "DILP binds to Drosophila insulin receptor (DINR), Drosophila melanogaster" +is_a: GO:0007165 ! signal transduction + +[Term] +id: GO:0007167 +name: enzyme linked receptor protein signaling pathway +namespace: biological_process +def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, ISBN:0185316194] +synonym: "enzyme linked receptor protein signalling pathway" EXACT [] +is_a: GO:0007166 ! cell surface receptor signaling pathway + +[Term] +id: GO:0007169 +name: transmembrane receptor protein tyrosine kinase signaling pathway +namespace: biological_process +def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling] +synonym: "transmembrane receptor protein tyrosine kinase signalling pathway" EXACT [] +xref: Reactome:REACT_101238 "Activation of TRKA receptors, Bos taurus" +xref: Reactome:REACT_104074 "Activation of TRKA receptors, Rattus norvegicus" +xref: Reactome:REACT_106114 "Activation of TRKA receptors, Sus scrofa" +xref: Reactome:REACT_106720 "Activation of TRKA receptors, Xenopus tropicalis" +xref: Reactome:REACT_108494 "Activation of TRKA receptors, Gallus gallus" +xref: Reactome:REACT_11064 "Activation of TRKA receptors, Homo sapiens" +xref: Reactome:REACT_29786 "Activation of TRKA receptors, Mus musculus" +xref: Reactome:REACT_82296 "Activation of TRKA receptors, Danio rerio" +xref: Reactome:REACT_90767 "Activation of TRKA receptors, Taeniopygia guttata" +xref: Reactome:REACT_97816 "Activation of TRKA receptors, Canis familiaris" +is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway + +[Term] +id: GO:0007178 +name: transmembrane receptor protein serine/threonine kinase signaling pathway +namespace: biological_process +def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling] +synonym: "transmembrane receptor protein serine/threonine kinase signalling pathway" EXACT [] +is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway + +[Term] +id: GO:0007179 +name: transforming growth factor beta receptor signaling pathway +namespace: biological_process +def: "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah, GOC:signaling] +synonym: "TGF-beta receptor signaling pathway" EXACT [] +synonym: "TGF-beta receptor signalling pathway" EXACT [] +synonym: "TGFbeta receptor signaling pathway" EXACT [] +synonym: "TGFbeta receptor signalling pathway" EXACT [] +synonym: "transforming growth factor beta receptor signalling pathway" EXACT [] +xref: Reactome:REACT_101958 "Signaling by TGF beta, Gallus gallus" +xref: Reactome:REACT_106912 "Signaling by TGF beta, Rattus norvegicus" +xref: Reactome:REACT_109530 "Signaling by TGF beta, Canis familiaris" +xref: Reactome:REACT_114882 "Signaling by TGF beta, Caenorhabditis elegans" +xref: Reactome:REACT_28222 "Signaling by TGF beta, Mus musculus" +xref: Reactome:REACT_28776 "Signaling by TGF beta, Taeniopygia guttata" +xref: Reactome:REACT_32950 "Signaling by TGF beta, Danio rerio" +xref: Reactome:REACT_6844 "Signaling by TGF beta, Homo sapiens" +xref: Reactome:REACT_78661 "Signaling by TGF beta, Sus scrofa" +xref: Reactome:REACT_79650 "Signaling by TGF beta, Xenopus tropicalis" +xref: Reactome:REACT_86676 "Signaling by TGF beta, Bos taurus" +xref: Reactome:REACT_96921 "Signaling by TGF beta, Drosophila melanogaster" +is_a: GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0071560 ! cellular response to transforming growth factor beta stimulus + +[Term] +id: GO:0007204 +name: positive regulation of cytosolic calcium ion concentration +namespace: biological_process +def: "Any process that increases the concentration of calcium ions in the cytosol." [GOC:ai] +synonym: "cytoplasmic calcium ion concentration elevation" BROAD [] +synonym: "cytosolic calcium ion concentration elevation" EXACT [] +synonym: "elevation of calcium ion concentration in cytoplasm" BROAD [] +synonym: "elevation of calcium ion concentration in cytosol" EXACT [] +synonym: "elevation of cytoplasmic calcium ion concentration" BROAD [] +synonym: "elevation of cytosolic calcium ion concentration" EXACT [] +is_a: GO:0051480 ! cytosolic calcium ion homeostasis + +[Term] +id: GO:0007219 +name: Notch signaling pathway +namespace: biological_process +alt_id: GO:0030179 +def: "A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, GOC:signaling] +synonym: "N signaling pathway" EXACT [] +synonym: "N signalling pathway" EXACT [] +synonym: "Notch receptor signaling pathway" EXACT [] +synonym: "Notch receptor signalling pathway" EXACT [] +synonym: "Notch signalling pathway" EXACT [] +synonym: "Notch-receptor signaling pathway" EXACT [] +synonym: "Notch-receptor signalling pathway" EXACT [] +xref: Reactome:REACT_105675 "Signaling by Notch, Gallus gallus" +xref: Reactome:REACT_106624 "Signaling by Notch, Taeniopygia guttata" +xref: Reactome:REACT_107006 "Signaling by Notch, Bos taurus" +xref: Reactome:REACT_109213 "Signaling by Notch, Danio rerio" +xref: Reactome:REACT_299 "Signaling by Notch, Homo sapiens" +xref: Reactome:REACT_76949 "Signaling by Notch, Sus scrofa" +xref: Reactome:REACT_77691 "Signaling by Notch, Mus musculus" +xref: Reactome:REACT_78520 "Signaling by Notch, Drosophila melanogaster" +xref: Reactome:REACT_89792 "Signaling by Notch, Xenopus tropicalis" +xref: Reactome:REACT_91210 "Signaling by Notch, Rattus norvegicus" +xref: Reactome:REACT_91671 "Signaling by Notch, Canis familiaris" +xref: Wikipedia:Notch_signaling_pathway +is_a: GO:0007166 ! cell surface receptor signaling pathway + +[Term] +id: GO:0007223 +name: Wnt signaling pathway, calcium modulating pathway +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors leads to an increase in intracellular calcium and activation of protein kinase C (PKC)." [GOC:bf, GOC:dph, GOC:go_curators, PMID:11532397] +synonym: "frizzled-2 signaling pathway" NARROW [] +synonym: "frizzled-2 signalling pathway" NARROW [] +synonym: "non-canonical Wnt signaling pathway" RELATED [] +synonym: "Wnt receptor signaling pathway, calcium modulating pathway" EXACT [] +synonym: "Wnt-activated signaling pathway, calcium modulating pathway" EXACT [GOC:signaling] +is_a: GO:0035567 ! non-canonical Wnt signaling pathway + +[Term] +id: GO:0007224 +name: smoothened signaling pathway +namespace: biological_process +def: "A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened." [GOC:mah, PMID:15205520] +synonym: "hedgehog signaling pathway" EXACT [] +synonym: "hh signaling pathway" NARROW [] +synonym: "hh signalling pathway" NARROW [] +synonym: "Shh signaling pathway" RELATED [GOC:dph] +synonym: "smoothened signalling pathway" EXACT [] +synonym: "Sonic hedgehog signaling pathway" NARROW [GOC:dph] +xref: Wikipedia:Hedgehog_signaling_pathway +is_a: GO:0007166 ! cell surface receptor signaling pathway + +[Term] +id: GO:0007249 +name: I-kappaB kinase/NF-kappaB signaling +namespace: biological_process +def: "The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription." [GOC:bf, GOC:jl, PMID:12773372, Reactome:REACT_13696.1] +synonym: "activation of the inhibitor of kappa kinase" RELATED [] +synonym: "canonical NF-kappaB signaling cascade" EXACT [GOC:bf] +synonym: "I-kappaB kinase/NF-kappaB cascade" RELATED [GOC:signaling] +synonym: "I-kappaB kinase/NF-kappaB signal transduction" EXACT [GOC:signaling] +synonym: "NF-kappaB cascade" BROAD [] +synonym: "p50-dependent NF-kappaB signaling" RELATED [PMID:18292232] +xref: Reactome:REACT_13696.1 "NF-kB is activated and signals survival, Homo sapiens" +xref: Reactome:REACT_25351 "TRAF6 mediated induction of TAK1 complex, Homo sapiens" +is_a: GO:0035556 ! intracellular signal transduction +relationship: has_part GO:0051092 ! positive regulation of NF-kappaB transcription factor activity + +[Term] +id: GO:0007254 +name: JNK cascade +namespace: biological_process +def: "An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell." [GOC:bf, GOC:signaling, PMID:11790549, PMID:20811974] +synonym: "c-Jun N-terminal kinase cascade" EXACT [PMID:20811974] +synonym: "JNK1 cascade" NARROW [GOC:add] +synonym: "JNK2 cascade" NARROW [GOC:add] +synonym: "JNK3 cascade" NARROW [GOC:add] +synonym: "MAPK10 cascade" NARROW [GOC:add] +synonym: "MAPK8 cascade" NARROW [GOC:add] +synonym: "MAPK9 cascade" NARROW [GOC:add] +synonym: "SAPK cascade" BROAD [] +synonym: "stress-activated protein kinase cascade" BROAD [] +xref: Reactome:REACT_107073 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Danio rerio" +xref: Reactome:REACT_107433 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Taeniopygia guttata" +xref: Reactome:REACT_112172 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Arabidopsis thaliana" +xref: Reactome:REACT_114741 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Oryza sativa" +xref: Reactome:REACT_114745 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Dictyostelium discoideum" +xref: Reactome:REACT_21368 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Homo sapiens" +xref: Reactome:REACT_28804 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Canis familiaris" +xref: Reactome:REACT_29903 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Bos taurus" +xref: Reactome:REACT_29906 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Mus musculus" +xref: Reactome:REACT_32441 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Sus scrofa" +xref: Reactome:REACT_79447 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Xenopus tropicalis" +xref: Reactome:REACT_87936 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Gallus gallus" +xref: Reactome:REACT_89698 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Rattus norvegicus" +xref: Reactome:REACT_95448 "JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, Caenorhabditis elegans" +is_a: GO:0051403 ! stress-activated MAPK cascade + +[Term] +id: GO:0007257 +name: activation of JUN kinase activity +namespace: biological_process +def: "The initiation of the activity of the inactive enzyme JUN kinase (JNK)." [GOC:bf] +synonym: "activation of SAPK activity" BROAD [] +xref: Reactome:REACT_25273 "Activated TAK1 mediates Jun kinases (JNK) phosphorylation and activation, Gallus gallus" +is_a: GO:0000187 ! activation of MAPK activity +is_a: GO:0043507 ! positive regulation of JUN kinase activity +relationship: part_of GO:0007254 ! JNK cascade + +[Term] +id: GO:0007258 +name: JUN phosphorylation +namespace: biological_process +def: "The process of introducing a phosphate group into a JUN protein." [GOC:jl] +is_a: GO:0006468 ! protein phosphorylation +relationship: part_of GO:0007254 ! JNK cascade + +[Term] +id: GO:0007264 +name: small GTPase mediated signal transduction +namespace: biological_process +def: "Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals." [GOC:mah] +subset: gosubset_prok +synonym: "small GTPase-mediated signal transduction" EXACT [] +xref: Reactome:REACT_103736 "Signaling by Rho GTPases, Drosophila melanogaster" +xref: Reactome:REACT_104376 "Signalling to p38 via RIT and RIN, Canis familiaris" +xref: Reactome:REACT_104921 "Signaling by Rho GTPases, Sus scrofa" +xref: Reactome:REACT_107228 "Signaling by Rho GTPases, Caenorhabditis elegans" +xref: Reactome:REACT_107412 "Signalling to p38 via RIT and RIN, Saccharomyces cerevisiae" +xref: Reactome:REACT_108043 "Signalling to p38 via RIT and RIN, Danio rerio" +xref: Reactome:REACT_108899 "Signaling by Rho GTPases, Arabidopsis thaliana" +xref: Reactome:REACT_11044 "Signaling by Rho GTPases, Homo sapiens" +xref: Reactome:REACT_113091 "Signalling to p38 via RIT and RIN, Oryza sativa" +xref: Reactome:REACT_114399 "Signalling to p38 via RIT and RIN, Arabidopsis thaliana" +xref: Reactome:REACT_115149 "Signalling to p38 via RIT and RIN, Dictyostelium discoideum" +xref: Reactome:REACT_12077 "Signalling to p38 via RIT and RIN, Homo sapiens" +xref: Reactome:REACT_29744 "Signalling to p38 via RIT and RIN, Xenopus tropicalis" +xref: Reactome:REACT_30245 "Signaling by Rho GTPases, Rattus norvegicus" +xref: Reactome:REACT_30798 "Signalling to p38 via RIT and RIN, Schizosaccharomyces pombe" +xref: Reactome:REACT_32217 "Signaling by Rho GTPases, Gallus gallus" +xref: Reactome:REACT_33280 "Signalling to p38 via RIT and RIN, Taeniopygia guttata" +xref: Reactome:REACT_42108 "Signalling to p38 via RIT and RIN, Caenorhabditis elegans" +xref: Reactome:REACT_77454 "Signaling by Rho GTPases, Mus musculus" +xref: Reactome:REACT_77940 "Signalling to p38 via RIT and RIN, Drosophila melanogaster" +xref: Reactome:REACT_77969 "Signalling to p38 via RIT and RIN, Sus scrofa" +xref: Reactome:REACT_82274 "Signalling to p38 via RIT and RIN, Bos taurus" +xref: Reactome:REACT_85042 "Signaling by Rho GTPases, Saccharomyces cerevisiae" +xref: Reactome:REACT_85386 "Signaling by Rho GTPases, Schizosaccharomyces pombe" +xref: Reactome:REACT_85575 "Signaling by Rho GTPases, Taeniopygia guttata" +xref: Reactome:REACT_85886 "Signaling by Rho GTPases, Dictyostelium discoideum" +xref: Reactome:REACT_86435 "Signaling by Rho GTPases, Xenopus tropicalis" +xref: Reactome:REACT_88164 "Signaling by Rho GTPases, Canis familiaris" +xref: Reactome:REACT_90015 "Signalling to p38 via RIT and RIN, Gallus gallus" +xref: Reactome:REACT_90246 "Signaling by Rho GTPases, Danio rerio" +xref: Reactome:REACT_91397 "Signaling by Rho GTPases, Oryza sativa" +xref: Reactome:REACT_93599 "Signalling to p38 via RIT and RIN, Rattus norvegicus" +xref: Reactome:REACT_94830 "Signaling by Rho GTPases, Bos taurus" +xref: Reactome:REACT_96351 "Signalling to p38 via RIT and RIN, Mus musculus" +is_a: GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0007265 +name: Ras protein signal transduction +namespace: biological_process +def: "A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state." [GOC:bf] +synonym: "Ras mediated signal transduction" EXACT [] +xref: Reactome:REACT_100282 "Signalling to RAS, Saccharomyces cerevisiae" +xref: Reactome:REACT_100832 "Signalling to RAS, Sus scrofa" +xref: Reactome:REACT_102992 "Signalling to RAS, Schizosaccharomyces pombe" +xref: Reactome:REACT_109099 "Signalling to RAS, Gallus gallus" +xref: Reactome:REACT_114204 "Signalling to RAS, Oryza sativa" +xref: Reactome:REACT_114859 "Signalling to RAS, Arabidopsis thaliana" +xref: Reactome:REACT_115010 "Signalling to RAS, Dictyostelium discoideum" +xref: Reactome:REACT_12033 "Signalling to RAS, Homo sapiens" +xref: Reactome:REACT_31921 "Signalling to RAS, Danio rerio" +xref: Reactome:REACT_78554 "Signalling to RAS, Rattus norvegicus" +xref: Reactome:REACT_79426 "Signalling to RAS, Drosophila melanogaster" +xref: Reactome:REACT_79898 "Signalling to RAS, Xenopus tropicalis" +xref: Reactome:REACT_81747 "Signalling to RAS, Caenorhabditis elegans" +xref: Reactome:REACT_82585 "Signalling to RAS, Bos taurus" +xref: Reactome:REACT_89778 "Signalling to RAS, Mus musculus" +xref: Reactome:REACT_93180 "Signalling to RAS, Taeniopygia guttata" +xref: Reactome:REACT_97052 "Signalling to RAS, Canis familiaris" +is_a: GO:0007264 ! small GTPase mediated signal transduction + +[Term] +id: GO:0007266 +name: Rho protein signal transduction +namespace: biological_process +def: "A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state." [GOC:bf] +synonym: "Rho mediated signal transduction" EXACT [] +is_a: GO:0007265 ! Ras protein signal transduction + +[Term] +id: GO:0007267 +name: cell-cell signaling +namespace: biological_process +def: "Any process that mediates the transfer of information from one cell to another." [GOC:mah] +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +synonym: "cell-cell signalling" EXACT [] +is_a: GO:0007154 ! cell communication +is_a: GO:0044700 ! single organism signaling + +[Term] +id: GO:0007268 +name: synaptic transmission +namespace: biological_process +def: "The process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse." [GOC:jl, MeSH:D009435] +synonym: "neurotransmission" RELATED [GOC:dph] +synonym: "regulation of synapse" RELATED [] +synonym: "signal transmission across a synapse" EXACT [] +xref: Reactome:REACT_102443 "Transmission across Chemical Synapses, Mycobacterium tuberculosis" +xref: Reactome:REACT_102748 "Neuronal System, Saccharomyces cerevisiae" +xref: Reactome:REACT_102963 "Transmission across Chemical Synapses, Canis familiaris" +xref: Reactome:REACT_104470 "Transmission across Chemical Synapses, Rattus norvegicus" +xref: Reactome:REACT_104894 "Neuronal System, Xenopus tropicalis" +xref: Reactome:REACT_105301 "Transmission across Chemical Synapses, Caenorhabditis elegans" +xref: Reactome:REACT_106168 "Transmission across Chemical Synapses, Escherichia coli" +xref: Reactome:REACT_106459 "Transmission across Chemical Synapses, Mus musculus" +xref: Reactome:REACT_107151 "Neuronal System, Sus scrofa" +xref: Reactome:REACT_107221 "Transmission across Chemical Synapses, Schizosaccharomyces pombe" +xref: Reactome:REACT_112265 "Transmission across Chemical Synapses, Staphylococcus aureus N315" +xref: Reactome:REACT_113444 "Neuronal System, Staphylococcus aureus N315" +xref: Reactome:REACT_13477 "Transmission across Chemical Synapses, Homo sapiens" +xref: Reactome:REACT_13685 "Neuronal System, Homo sapiens" +xref: Reactome:REACT_29254 "Neuronal System, Danio rerio" +xref: Reactome:REACT_29595 "Neuronal System, Caenorhabditis elegans" +xref: Reactome:REACT_29683 "Transmission across Chemical Synapses, Drosophila melanogaster" +xref: Reactome:REACT_30050 "Transmission across Chemical Synapses, Gallus gallus" +xref: Reactome:REACT_30266 "Transmission across Chemical Synapses, Sus scrofa" +xref: Reactome:REACT_31284 "Transmission across Chemical Synapses, Saccharomyces cerevisiae" +xref: Reactome:REACT_33322 "Neuronal System, Taeniopygia guttata" +xref: Reactome:REACT_33434 "Neuronal System, Escherichia coli" +xref: Reactome:REACT_78038 "Neuronal System, Rattus norvegicus" +xref: Reactome:REACT_78840 "Transmission across Chemical Synapses, Taeniopygia guttata" +xref: Reactome:REACT_79078 "Transmission across Chemical Synapses, Arabidopsis thaliana" +xref: Reactome:REACT_80052 "Neuronal System, Schizosaccharomyces pombe" +xref: Reactome:REACT_82334 "Transmission across Chemical Synapses, Bos taurus" +xref: Reactome:REACT_82746 "Neuronal System, Arabidopsis thaliana" +xref: Reactome:REACT_86563 "Neuronal System, Mus musculus" +xref: Reactome:REACT_86628 "Neuronal System, Canis familiaris" +xref: Reactome:REACT_88599 "Neuronal System, Bos taurus" +xref: Reactome:REACT_88891 "Neuronal System, Mycobacterium tuberculosis" +xref: Reactome:REACT_89065 "Neuronal System, Gallus gallus" +xref: Reactome:REACT_89149 "Neuronal System, Dictyostelium discoideum" +xref: Reactome:REACT_89785 "Neuronal System, Drosophila melanogaster" +xref: Reactome:REACT_90781 "Transmission across Chemical Synapses, Danio rerio" +xref: Reactome:REACT_93592 "Transmission across Chemical Synapses, Xenopus tropicalis" +xref: Reactome:REACT_98546 "Transmission across Chemical Synapses, Dictyostelium discoideum" +xref: Reactome:REACT_99535 "Transmission across Chemical Synapses, Oryza sativa" +xref: Reactome:REACT_99952 "Neuronal System, Oryza sativa" +xref: Wikipedia:Neurotransmission +is_a: GO:0007267 ! cell-cell signaling + +[Term] +id: GO:0007269 +name: neurotransmitter secretion +namespace: biological_process +def: "The regulated release of neurotransmitter into the synaptic cleft. A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin." [CHEBI:25512, GOC:dph] +synonym: "neurotransmitter release" EXACT [] +xref: Reactome:REACT_100716 "Neurotransmitter Release Cycle, Bos taurus" +xref: Reactome:REACT_102134 "Neurotransmitter Release Cycle, Arabidopsis thaliana" +xref: Reactome:REACT_102586 "Neurotransmitter Release Cycle, Xenopus tropicalis" +xref: Reactome:REACT_102743 "Neurotransmitter Release Cycle, Rattus norvegicus" +xref: Reactome:REACT_105010 "Neurotransmitter Release Cycle, Oryza sativa" +xref: Reactome:REACT_105885 "Neurotransmitter Release Cycle, Taeniopygia guttata" +xref: Reactome:REACT_110862 "Neurotransmitter Release Cycle, Sus scrofa" +xref: Reactome:REACT_11184 "Botulinum neurotoxicity, Homo sapiens" +xref: Reactome:REACT_113329 "Neurotransmitter Release Cycle, Staphylococcus aureus N315" +xref: Reactome:REACT_115061 "Neurotransmitter Release Cycle, Dictyostelium discoideum" +xref: Reactome:REACT_13723 "Neurotransmitter Release Cycle, Homo sapiens" +xref: Reactome:REACT_29477 "Neurotransmitter Release Cycle, Danio rerio" +xref: Reactome:REACT_29495 "Neurotransmitter Release Cycle, Drosophila melanogaster" +xref: Reactome:REACT_29928 "Neurotransmitter Release Cycle, Mus musculus" +xref: Reactome:REACT_77375 "Neurotransmitter Release Cycle, Mycobacterium tuberculosis" +xref: Reactome:REACT_85993 "Neurotransmitter Release Cycle, Canis familiaris" +xref: Reactome:REACT_91316 "Neurotransmitter Release Cycle, Caenorhabditis elegans" +xref: Reactome:REACT_95406 "Neurotransmitter Release Cycle, Gallus gallus" +xref: Reactome:REACT_99398 "Neurotransmitter Release Cycle, Escherichia coli" +is_a: GO:0001505 ! regulation of neurotransmitter levels +is_a: GO:0006836 ! neurotransmitter transport +is_a: GO:0023061 ! signal release + +[Term] +id: GO:0007272 +name: ensheathment of neurons +namespace: biological_process +def: "The process in which glial cells envelop neuronal cell bodies and/or axons to form an insulating layer. This can take the form of myelinating or non-myelinating ensheathment." [GOC:dgh, GOC:dph, GOC:tb] +synonym: "ionic insulation of neurons by glial cells" RELATED [] +is_a: GO:0044763 ! single-organism cellular process +relationship: part_of GO:0007399 ! nervous system development +relationship: regulates GO:0019228 ! neuronal action potential + +[Term] +id: GO:0007275 +name: multicellular organismal development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb] +comment: Note that this term was 'developmental process'. +subset: goslim_plant +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0007276 +name: gamete generation +namespace: biological_process +alt_id: GO:0009552 +def: "The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell." [GOC:ems, GOC:mtg_sensu] +synonym: "gametogenesis" RELATED [] +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048609 ! multicellular organismal reproductive process +relationship: part_of GO:0019953 ! sexual reproduction + +[Term] +id: GO:0007281 +name: germ cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism." [GOC:go_curators] +synonym: "germ-cell development" EXACT [] +synonym: "primordial germ cell development" NARROW [] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048468 ! cell development +relationship: part_of GO:0007276 ! gamete generation + +[Term] +id: GO:0007292 +name: female gamete generation +namespace: biological_process +def: "Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction." [GOC:dph, ISBN:0198506732] +is_a: GO:0007276 ! gamete generation + +[Term] +id: GO:0007346 +name: regulation of mitotic cell cycle +namespace: biological_process +def: "Any process that modulates the rate or extent of progress through the mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb] +subset: goslim_pombe +synonym: "control of mitotic cell cycle progression" EXACT [] +synonym: "mitotic cell cycle control" EXACT [] +synonym: "mitotic cell cycle modulation" EXACT [] +synonym: "mitotic cell cycle regulation" EXACT [] +synonym: "mitotic cell cycle regulator" RELATED [] +synonym: "modulation of mitotic cell cycle progression" EXACT [] +synonym: "regulation of mitotic cell cycle progression" EXACT [] +synonym: "regulation of progression through mitotic cell cycle" EXACT [GOC:dph, GOC:tb] +is_a: GO:0051726 ! regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000278 ! mitotic cell cycle +relationship: regulates GO:0000278 ! mitotic cell cycle + +[Term] +id: GO:0007350 +name: blastoderm segmentation +namespace: biological_process +def: "The hierarchical steps resulting in the progressive subdivision of the anterior/posterior axis of the embryo." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238] +is_a: GO:0009880 ! embryonic pattern specification +is_a: GO:0035282 ! segmentation + +[Term] +id: GO:0007351 +name: tripartite regional subdivision +namespace: biological_process +def: "Subdivision of the embryo along the anterior/posterior axis into anterior, posterior and terminal regions." [GOC:dph, GOC:isa_complete, http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238] +is_a: GO:0003002 ! regionalization +relationship: part_of GO:0007350 ! blastoderm segmentation + +[Term] +id: GO:0007368 +name: determination of left/right symmetry +namespace: biological_process +def: "The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry." [GOC:dph, GOC:jid] +synonym: "determination of left/right asymmetry" EXACT [GOC:dph] +is_a: GO:0009855 ! determination of bilateral symmetry + +[Term] +id: GO:0007369 +name: gastrulation +namespace: biological_process +def: "A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm." [GOC:curators, ISBN:9780878933846] +xref: Wikipedia:Gastrulation +is_a: GO:0048598 ! embryonic morphogenesis + +[Term] +id: GO:0007389 +name: pattern specification process +namespace: biological_process +def: "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate." [GOC:go_curators, GOC:isa_complete, ISBN:0521436125] +synonym: "pattern biosynthesis" RELATED [] +synonym: "pattern formation" RELATED [] +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0007398 +name: ectoderm development +namespace: biological_process +def: "The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation." [GOC:dph, GOC:tb] +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0007399 +name: nervous system development +namespace: biological_process +def: "The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state." [GOC:dgh] +synonym: "pan-neural process" RELATED [] +is_a: GO:0048731 ! system development + +[Term] +id: GO:0007403 +name: glial cell fate determination +namespace: biological_process +alt_id: GO:0043361 +def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators, GOC:mtg_sensu] +is_a: GO:0001709 ! cell fate determination +relationship: part_of GO:0021781 ! glial cell fate commitment + +[Term] +id: GO:0007405 +name: neuroblast proliferation +namespace: biological_process +alt_id: GO:0043349 +alt_id: GO:0043350 +def: "The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron." [GOC:ai, GOC:mtg_sensu, GOC:sart] +is_a: GO:0061351 ! neural precursor cell proliferation +is_a: GO:0072089 ! stem cell proliferation +relationship: part_of GO:0048699 ! generation of neurons + +[Term] +id: GO:0007409 +name: axonogenesis +namespace: biological_process +alt_id: GO:0007410 +def: "Generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells." [GOC:jid, ISBN:0198506732] +synonym: "axon growth" NARROW [] +synonym: "neuron long process generation" EXACT systematic_synonym [] +is_a: GO:0048812 ! neuron projection morphogenesis +relationship: part_of GO:0048667 ! cell morphogenesis involved in neuron differentiation +relationship: part_of GO:0061564 ! axon development + +[Term] +id: GO:0007411 +name: axon guidance +namespace: biological_process +alt_id: GO:0008040 +def: "The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues." [ISBN:0878932437] +synonym: "axon chemotaxis" RELATED [GOC:curators] +synonym: "axon growth cone guidance" NARROW [] +synonym: "axon pathfinding" EXACT [GOC:mah] +xref: Reactome:REACT_104226 "Axon guidance, Xenopus tropicalis" +xref: Reactome:REACT_108197 "Axon guidance, Schizosaccharomyces pombe" +xref: Reactome:REACT_110262 "Axon guidance, Drosophila melanogaster" +xref: Reactome:REACT_112315 "Axon guidance, Plasmodium falciparum" +xref: Reactome:REACT_114665 "Axon guidance, Arabidopsis thaliana" +xref: Reactome:REACT_115127 "Axon guidance, Oryza sativa" +xref: Reactome:REACT_18266 "Axon guidance, Homo sapiens" +xref: Reactome:REACT_29678 "Axon guidance, Taeniopygia guttata" +xref: Reactome:REACT_29862 "Axon guidance, Caenorhabditis elegans" +xref: Reactome:REACT_34580 "Axon guidance, Dictyostelium discoideum" +xref: Reactome:REACT_77452 "Axon guidance, Sus scrofa" +xref: Reactome:REACT_77923 "Axon guidance, Danio rerio" +xref: Reactome:REACT_83818 "Axon guidance, Saccharomyces cerevisiae" +xref: Reactome:REACT_86479 "Axon guidance, Gallus gallus" +xref: Reactome:REACT_88453 "Axon guidance, Bos taurus" +xref: Reactome:REACT_92778 "Axon guidance, Mus musculus" +xref: Reactome:REACT_94408 "Axon guidance, Rattus norvegicus" +xref: Reactome:REACT_95076 "Axon guidance, Canis familiaris" +xref: Wikipedia:Axon_guidance +is_a: GO:0097485 ! neuron projection guidance +relationship: part_of GO:0007409 ! axonogenesis + +[Term] +id: GO:0007412 +name: axon target recognition +namespace: biological_process +def: "The process in which an axon recognizes and binds to a set of cells with which it may form stable connections." [ISBN:0878932437] +is_a: GO:0007154 ! cell communication +relationship: part_of GO:0007409 ! axonogenesis + +[Term] +id: GO:0007416 +name: synapse assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form a synapse." [GOC:mah] +synonym: "synapse biogenesis" EXACT [GOC:mah] +synonym: "synaptogenesis" EXACT [GOC:mah] +xref: Wikipedia:Synaptogenesis +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0050808 ! synapse organization +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0007417 +name: central nervous system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord." [GOC:bf, GOC:jid, ISBN:0582227089] +synonym: "CNS development" EXACT [] +xref: Wikipedia:Neural_development +is_a: GO:0048731 ! system development +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0007418 +name: ventral midline development +namespace: biological_process +def: "The process whose specific outcome is the progression of the ventral midline over time, from its formation to the mature structure. In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate." [GOC:bf, GOC:go_curators, PMID:12075342] +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0007420 +name: brain development +namespace: biological_process +def: "The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.)." [GOC:dph, GOC:jid, GOC:tb, UBERON:0000955] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0007422 +name: peripheral nervous system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [GOC:go_curators, UBERON:0000010] +is_a: GO:0048731 ! system development +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0007423 +name: sensory organ development +namespace: biological_process +def: "The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure." [GOC:go_curators] +synonym: "sense organ development" EXACT [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0007440 +name: foregut morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the foregut are generated and organized." [GOC:jid] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048546 ! digestive tract morphogenesis + +[Term] +id: GO:0007442 +name: hindgut morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the hindgut are generated and organized." [GOC:jid] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048546 ! digestive tract morphogenesis +relationship: part_of GO:0061525 ! hindgut development + +[Term] +id: GO:0007492 +name: endoderm development +namespace: biological_process +def: "The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues." [GOC:dph, GOC:tb] +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0007494 +name: midgut development +namespace: biological_process +def: "The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine." [GOC:jid, UBERON:0001045] +is_a: GO:0048565 ! digestive tract development + +[Term] +id: GO:0007498 +name: mesoderm development +namespace: biological_process +def: "The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue." [GOC:dph, GOC:tb] +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0007501 +name: mesodermal cell fate specification +namespace: biological_process +def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a mesoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators] +comment: Note that this term was 'fate specification in mesoderm'. String of term was changed to correspond to format of sibling terms 'endoderm cell fate specification' and 'ectoderm cell fate specification'. +synonym: "mesoderm cell fate specification" EXACT [] +is_a: GO:0001708 ! cell fate specification +relationship: part_of GO:0001710 ! mesodermal cell fate commitment + +[Term] +id: GO:0007507 +name: heart development +namespace: biological_process +alt_id: GO:0007511 +def: "The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC:jid, UBERON:0000948] +synonym: "cardiac development" RELATED [] +synonym: "dorsal vessel development" NARROW [] +xref: Wikipedia:Heart_development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0072358 ! cardiovascular system development + +[Term] +id: GO:0007517 +name: muscle organ development +namespace: biological_process +def: "The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work." [GOC:jid, ISBN:0198506732] +is_a: GO:0048513 ! organ development +is_a: GO:0061061 ! muscle structure development + +[Term] +id: GO:0007519 +name: skeletal muscle tissue development +namespace: biological_process +alt_id: GO:0048637 +def: "The developmental sequence of events leading to the formation of adult muscle that occurs in the anima. In vertebrate skeletal muscle the main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers." [GOC:mtg_muscle] +synonym: "myogenesis" RELATED [] +is_a: GO:0014706 ! striated muscle tissue development +relationship: part_of GO:0060538 ! skeletal muscle organ development + +[Term] +id: GO:0007520 +name: myoblast fusion +namespace: biological_process +def: "A process in which non-proliferating myoblasts fuse to existing fibers or to myotubes to form new fibers. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:mtg_muscle] +is_a: GO:0000768 ! syncytium formation by plasma membrane fusion +relationship: part_of GO:0014902 ! myotube differentiation + +[Term] +id: GO:0007528 +name: neuromuscular junction development +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction." [GOC:mtg_OBO2OWL_2013] +synonym: "neuromuscular junction organization" EXACT [] +synonym: "neuromuscular junction stability" RELATED [GOC:pr] +synonym: "NMJ stability" RELATED [GOC:pr] +is_a: GO:0050808 ! synapse organization + +[Term] +id: GO:0007530 +name: sex determination +namespace: biological_process +def: "Any process that establishes and transmits the specification of sexual status of an individual organism." [ISBN:0198506732] +xref: Wikipedia:Sex-determination_system +is_a: GO:0003006 ! developmental process involved in reproduction + +[Term] +id: GO:0007548 +name: sex differentiation +namespace: biological_process +def: "The establishment of the sex of an organism by physical differentiation." [GOC:ai] +xref: Wikipedia:Sexual_differentiation +is_a: GO:0003006 ! developmental process involved in reproduction + +[Term] +id: GO:0007565 +name: female pregnancy +namespace: biological_process +def: "The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth." [ISBN:0192800825] +synonym: "carrying of young" RELATED [] +synonym: "gestation" EXACT [] +xref: Wikipedia:Gestation +is_a: GO:0044703 ! multi-organism reproductive process +is_a: GO:0044706 ! multi-multicellular organism process + +[Term] +id: GO:0007568 +name: aging +namespace: biological_process +alt_id: GO:0016280 +def: "A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death (GO:0016265) and may succeed developmental maturation (GO:0021700)." [GOC:PO_curators] +subset: goslim_generic +synonym: "ageing" EXACT [] +xref: Wikipedia:Aging +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0007569 +name: cell aging +namespace: biological_process +def: "An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469)." [GOC:PO_curators] +synonym: "cell ageing" EXACT [] +is_a: GO:0007568 ! aging +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0007584 +name: response to nutrient +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus." [GOC:go_curators] +subset: gosubset_prok +synonym: "nutritional response pathway" NARROW [] +synonym: "response to nutrients" EXACT [] +is_a: GO:0031667 ! response to nutrient levels +is_a: GO:0042221 ! response to chemical + +[Term] +id: GO:0007589 +name: body fluid secretion +namespace: biological_process +def: "The controlled release of a fluid by a cell or tissue in an animal." [GOC:ai, GOC:dph, GOC:mah, GOC:tb] +is_a: GO:0046903 ! secretion +is_a: GO:0050878 ! regulation of body fluid levels + +[Term] +id: GO:0007595 +name: lactation +namespace: biological_process +def: "The secretion of milk by the mammary gland." [ISBN:0198506732] +xref: Wikipedia:Lactation +is_a: GO:0007589 ! body fluid secretion +is_a: GO:0032941 ! secretion by tissue +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048609 ! multicellular organismal reproductive process +relationship: part_of GO:0030879 ! mammary gland development + +[Term] +id: GO:0007596 +name: blood coagulation +namespace: biological_process +def: "The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers." [http://www.graylab.ac.uk/omd/, ISBN:0198506732] +synonym: "blood clotting" EXACT [] +xref: Reactome:REACT_101311 "Hemostasis, Plasmodium falciparum" +xref: Reactome:REACT_101372 "Common Pathway, Danio rerio" +xref: Reactome:REACT_102544 "Common Pathway, Rattus norvegicus" +xref: Reactome:REACT_102650 "Common Pathway, Mus musculus" +xref: Reactome:REACT_105166 "Common Pathway, Taeniopygia guttata" +xref: Reactome:REACT_105212 "Common Pathway, Sus scrofa" +xref: Reactome:REACT_107268 "Hemostasis, Saccharomyces cerevisiae" +xref: Reactome:REACT_108583 "Hemostasis, Danio rerio" +xref: Reactome:REACT_113650 "Common Pathway, Drosophila melanogaster" +xref: Reactome:REACT_114152 "Formation of Fibrin Clot (Clotting Cascade), Drosophila melanogaster" +xref: Reactome:REACT_118351 "Hemostasis, Escherichia coli" +xref: Reactome:REACT_1439 "Common Pathway, Homo sapiens" +xref: Reactome:REACT_2051 "Formation of Fibrin Clot (Clotting Cascade), Homo sapiens" +xref: Reactome:REACT_32530 "Hemostasis, Xenopus tropicalis" +xref: Reactome:REACT_32765 "Hemostasis, Mycobacterium tuberculosis" +xref: Reactome:REACT_33270 "Hemostasis, Canis familiaris" +xref: Reactome:REACT_34525 "Hemostasis, Arabidopsis thaliana" +xref: Reactome:REACT_604 "Hemostasis, Homo sapiens" +xref: Reactome:REACT_76944 "Common Pathway, Canis familiaris" +xref: Reactome:REACT_78290 "Hemostasis, Staphylococcus aureus N315" +xref: Reactome:REACT_81054 "Formation of Fibrin Clot (Clotting Cascade), Canis familiaris" +xref: Reactome:REACT_81972 "Formation of Fibrin Clot (Clotting Cascade), Taeniopygia guttata" +xref: Reactome:REACT_82283 "Formation of Fibrin Clot (Clotting Cascade), Mus musculus" +xref: Reactome:REACT_82383 "Hemostasis, Oryza sativa" +xref: Reactome:REACT_82403 "Hemostasis, Rattus norvegicus" +xref: Reactome:REACT_82445 "Formation of Fibrin Clot (Clotting Cascade), Sus scrofa" +xref: Reactome:REACT_82812 "Hemostasis, Bos taurus" +xref: Reactome:REACT_82940 "Common Pathway, Xenopus tropicalis" +xref: Reactome:REACT_83271 "Hemostasis, Dictyostelium discoideum" +xref: Reactome:REACT_84055 "Formation of Fibrin Clot (Clotting Cascade), Danio rerio" +xref: Reactome:REACT_84833 "Formation of Fibrin Clot (Clotting Cascade), Rattus norvegicus" +xref: Reactome:REACT_85674 "Hemostasis, Sus scrofa" +xref: Reactome:REACT_86354 "Common Pathway, Gallus gallus" +xref: Reactome:REACT_89750 "Hemostasis, Mus musculus" +xref: Reactome:REACT_89805 "Formation of Fibrin Clot (Clotting Cascade), Xenopus tropicalis" +xref: Reactome:REACT_90236 "Hemostasis, Taeniopygia guttata" +xref: Reactome:REACT_90805 "Hemostasis, Caenorhabditis elegans" +xref: Reactome:REACT_92318 "Hemostasis, Drosophila melanogaster" +xref: Reactome:REACT_94085 "Hemostasis, Schizosaccharomyces pombe" +xref: Reactome:REACT_94213 "Common Pathway, Bos taurus" +xref: Reactome:REACT_94315 "Formation of Fibrin Clot (Clotting Cascade), Bos taurus" +xref: Reactome:REACT_94798 "Formation of Fibrin Clot (Clotting Cascade), Gallus gallus" +xref: Reactome:REACT_96458 "Hemostasis, Gallus gallus" +xref: Wikipedia:Coagulation +is_a: GO:0007599 ! hemostasis +is_a: GO:0050817 ! coagulation +relationship: part_of GO:0042060 ! wound healing + +[Term] +id: GO:0007599 +name: hemostasis +namespace: biological_process +def: "The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part." [ISBN:0198506732] +xref: Wikipedia:Hemostasis +is_a: GO:0050878 ! regulation of body fluid levels + +[Term] +id: GO:0007610 +name: behavior +namespace: biological_process +def: "The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_plant +subset: gosubset_prok +synonym: "behavioral response to stimulus" EXACT [] +synonym: "behaviour" EXACT [] +synonym: "behavioural response to stimulus" EXACT [] +xref: Wikipedia:Behavior +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0007611 +name: learning or memory +namespace: biological_process +def: "The acquisition and processing of information and/or the storage and retrieval of this information over time." [GOC:jid, PMID:8938125] +is_a: GO:0044708 ! single-organism behavior +is_a: GO:0050890 ! cognition + +[Term] +id: GO:0007612 +name: learning +namespace: biological_process +def: "Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience." [ISBN:0582227089, ISBN:0721662544] +xref: Wikipedia:Learning +is_a: GO:0007611 ! learning or memory + +[Term] +id: GO:0007626 +name: locomotory behavior +namespace: biological_process +def: "The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [GOC:dph] +subset: gosubset_prok +synonym: "behavior via locomotion" EXACT [] +synonym: "locomotion in response to stimulus" EXACT [] +synonym: "locomotory behavioral response to stimulus" EXACT [] +synonym: "locomotory behaviour" EXACT [] +synonym: "locomotory behavioural response to stimulus" EXACT [] +is_a: GO:0007610 ! behavior + +[Term] +id: GO:0007632 +name: visual behavior +namespace: biological_process +def: "The behavior of an organism in response to a visual stimulus." [GOC:jid, GOC:pr] +synonym: "behavioral response to visual stimulus" EXACT [] +synonym: "behavioural response to visual stimulus" EXACT [] +synonym: "visual behaviour" EXACT [] +is_a: GO:0009416 ! response to light stimulus +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044708 ! single-organism behavior + +[Term] +id: GO:0007638 +name: mechanosensory behavior +namespace: biological_process +def: "Behavior that is dependent upon the sensation of a mechanical stimulus." [GOC:go_curators] +synonym: "behavioral response to mechanical stimulus" EXACT [] +synonym: "behavioural response to mechanical stimulus" EXACT [] +synonym: "mechanosensory behaviour" EXACT [] +is_a: GO:0009612 ! response to mechanical stimulus +is_a: GO:0044708 ! single-organism behavior + +[Term] +id: GO:0008013 +name: beta-catenin binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with the beta subunit of the catenin complex." [GOC:bf] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0008015 +name: blood circulation +namespace: biological_process +alt_id: GO:0070261 +def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] +subset: goslim_pir +synonym: "hemolymph circulation" RELATED [] +is_a: GO:0003013 ! circulatory system process + +[Term] +id: GO:0008016 +name: regulation of heart contraction +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body." [GOC:dph, GOC:go_curators, GOC:tb] +synonym: "regulation of cardiac contraction" EXACT [] +is_a: GO:0044057 ! regulation of system process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060047 ! heart contraction +relationship: regulates GO:0060047 ! heart contraction + +[Term] +id: GO:0008022 +name: protein C-terminus binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN:0198506732] +synonym: "C-terminal binding" EXACT [] +synonym: "C-terminal end binding" EXACT [GOC:sl] +synonym: "carboxy-terminal binding" RELATED [GOC:jsg] +synonym: "carboxy-terminus binding" RELATED [GOC:sl] +synonym: "carboxyl-terminal binding" RELATED [GOC:jsg] +synonym: "carboxyl-terminus binding" RELATED [GOC:sl] +synonym: "carboxylate-terminal binding" RELATED [GOC:jsg] +synonym: "carboxylate-terminus binding" NARROW [GOC:jsg] +synonym: "COOH-terminal binding" NARROW [GOC:jsg] +synonym: "COOH-terminus binding" NARROW [GOC:jsg, GOC:sl] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0008035 +name: high-density lipoprotein particle binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with high-density lipoprotein particle, a lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE." [GOC:mah] +synonym: "HDL binding" EXACT [GOC:mah] +is_a: GO:0071813 ! lipoprotein particle binding + +[Term] +id: GO:0008037 +name: cell recognition +namespace: biological_process +def: "The process in which a cell in a multicellular organism interprets its surroundings." [GOC:go_curators] +subset: goslim_pir +synonym: "recognition of surroundings by cell" EXACT [GOC:curators] +is_a: GO:0044763 ! single-organism cellular process +relationship: part_of GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0008038 +name: neuron recognition +namespace: biological_process +def: "The process in which a neuronal cell in a multicellular organism interprets its surroundings." [GOC:go_curators] +synonym: "neuronal cell recognition" EXACT [] +is_a: GO:0008037 ! cell recognition +relationship: part_of GO:0048666 ! neuron development + +[Term] +id: GO:0008047 +name: enzyme activator activity +namespace: molecular_function +def: "Increases the activity of an enzyme." [GOC:mah] +subset: gosubset_prok +is_a: GO:0030234 ! enzyme regulator activity +relationship: part_of GO:0043085 ! positive regulation of catalytic activity + +[Term] +id: GO:0008092 +name: cytoskeletal protein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)." [GOC:mah] +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0008104 +name: protein localization +namespace: biological_process +def: "Any process in which a protein is transported to, or maintained in, a specific location." [GOC:ai] +subset: gosubset_prok +synonym: "establishment and maintenance of protein localization" EXACT [] +synonym: "protein localisation" EXACT [GOC:mah] +is_a: GO:0033036 ! macromolecule localization + +[Term] +id: GO:0008105 +name: asymmetric protein localization +namespace: biological_process +def: "Any process in which a protein is transported to, or maintained in, a specific location such that it is distributed asymmetrically." [GOC:ma] +subset: gosubset_prok +synonym: "asymmetric protein localisation" EXACT [GOC:mah] +synonym: "establishment and maintenance of asymmetric protein localization" EXACT [] +is_a: GO:0008104 ! protein localization + +[Term] +id: GO:0008134 +name: transcription factor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription." [ISBN:0198506732] +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_yeast +subset: gosubset_prok +synonym: "TF binding" EXACT [] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0008144 +name: drug binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease." [GOC:jl, ISBN:0198506732] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0005488 ! binding + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "biological process" EXACT [] +synonym: "biological process unknown" NARROW [] +synonym: "physiological process" EXACT [] +xref: Wikipedia:Biological_process + +[Term] +id: GO:0008152 +name: metabolic process +namespace: biological_process +def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "metabolic process resulting in cell growth" NARROW [] +synonym: "metabolism" EXACT [] +synonym: "metabolism resulting in cell growth" NARROW [] +xref: Wikipedia:Metabolism +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0008201 +name: heparin binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues." [GOC:jl, ISBN:0198506732] +synonym: "heparan sulfate binding" RELATED [] +is_a: GO:0005539 ! glycosaminoglycan binding +is_a: GO:0043168 ! anion binding +is_a: GO:1901681 ! sulfur compound binding + +[Term] +id: GO:0008202 +name: steroid metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." [ISBN:0198547684] +subset: gosubset_prok +synonym: "steroid metabolism" EXACT [] +xref: Reactome:REACT_100535 "Metabolism of steroid hormones and vitamins A and D, Schizosaccharomyces pombe" +xref: Reactome:REACT_104514 "Metabolism of steroid hormones and vitamins A and D, Bos taurus" +xref: Reactome:REACT_104993 "Metabolism of steroid hormones and vitamins A and D, Saccharomyces cerevisiae" +xref: Reactome:REACT_105831 "Metabolism of steroid hormones and vitamins A and D, Dictyostelium discoideum" +xref: Reactome:REACT_108650 "Metabolism of steroid hormones and vitamins A and D, Gallus gallus" +xref: Reactome:REACT_109307 "Metabolism of steroid hormones and vitamins A and D, Mycobacterium tuberculosis" +xref: Reactome:REACT_109504 "Metabolism of steroid hormones and vitamins A and D, Caenorhabditis elegans" +xref: Reactome:REACT_110283 "Metabolism of steroid hormones and vitamins A and D, Danio rerio" +xref: Reactome:REACT_11057 "Metabolism of steroid hormones and vitamins A and D, Homo sapiens" +xref: Reactome:REACT_32683 "Metabolism of steroid hormones and vitamins A and D, Drosophila melanogaster" +xref: Reactome:REACT_34426 "Metabolism of steroid hormones and vitamins A and D, Arabidopsis thaliana" +xref: Reactome:REACT_77930 "Metabolism of steroid hormones and vitamins A and D, Canis familiaris" +xref: Reactome:REACT_81781 "Metabolism of steroid hormones and vitamins A and D, Escherichia coli" +xref: Reactome:REACT_85390 "Metabolism of steroid hormones and vitamins A and D, Oryza sativa" +xref: Reactome:REACT_86063 "Metabolism of steroid hormones and vitamins A and D, Taeniopygia guttata" +xref: Reactome:REACT_86862 "Metabolism of steroid hormones and vitamins A and D, Mus musculus" +xref: Reactome:REACT_90075 "Metabolism of steroid hormones and vitamins A and D, Rattus norvegicus" +xref: Reactome:REACT_93239 "Metabolism of steroid hormones and vitamins A and D, Sus scrofa" +xref: Reactome:REACT_96786 "Metabolism of steroid hormones and vitamins A and D, Xenopus tropicalis" +xref: Reactome:REACT_97355 "Metabolism of steroid hormones and vitamins A and D, Plasmodium falciparum" +xref: Wikipedia:Steroid_metabolism +is_a: GO:0006629 ! lipid metabolic process +is_a: GO:1901360 ! organic cyclic compound metabolic process + +[Term] +id: GO:0008203 +name: cholesterol metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues." [ISBN:0198506732] +subset: gosubset_prok +synonym: "cholesterol metabolism" EXACT [] +is_a: GO:0016125 ! sterol metabolic process + +[Term] +id: GO:0008207 +name: C21-steroid hormone metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones." [GOC:ai] +synonym: "C21-steroid hormone metabolism" EXACT [] +is_a: GO:0008202 ! steroid metabolic process +is_a: GO:0034754 ! cellular hormone metabolic process +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0008209 +name: androgen metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics." [ISBN:0198506732] +synonym: "androgen metabolism" EXACT [] +is_a: GO:0008202 ! steroid metabolic process +is_a: GO:0034754 ! cellular hormone metabolic process +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0008211 +name: glucocorticoid metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects." [ISBN:0198506732] +synonym: "glucocorticoid metabolism" EXACT [] +synonym: "glucocorticosteroid metabolic process" EXACT [] +synonym: "glucocorticosteroid metabolism" EXACT [] +is_a: GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0008212 +name: mineralocorticoid metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Mineralocorticoids act primarily on water and electrolyte balance." [ISBN:0198506732] +synonym: "mineralocorticoid metabolism" EXACT [] +is_a: GO:0008202 ! steroid metabolic process +is_a: GO:0034754 ! cellular hormone metabolic process +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0008217 +name: regulation of blood pressure +namespace: biological_process +def: "Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure." [GOC:dph, GOC:mtg_cardio, ISBN:0721643949] +synonym: "blood pressure homeostasis" RELATED [] +synonym: "blood pressure regulation" EXACT [] +synonym: "control of blood pressure" RELATED [] +xref: Wikipedia:Blood_pressure#Regulation +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0008015 ! blood circulation + +[Term] +id: GO:0008219 +name: cell death +namespace: biological_process +def: "Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as \"apoptotic bodies\"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo." [GOC:mah, GOC:mtg_apoptosis] +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +synonym: "accidental cell death" RELATED [] +synonym: "necrosis" RELATED [] +is_a: GO:0016265 ! death +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0008233 +name: peptidase activity +namespace: molecular_function +def: "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid." [GOC:jl, ISBN:0815332181] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "hydrolase, acting on peptide bonds" EXACT [] +synonym: "peptide hydrolase activity" EXACT [] +synonym: "protease activity" EXACT [] +synonym: "proteinase activity" EXACT [] +xref: EC:3.4 +xref: Reactome:REACT_106748 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Rattus norvegicus" +xref: Reactome:REACT_110349 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Mus musculus" +xref: Reactome:REACT_13710 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Homo sapiens" +xref: Reactome:REACT_19284 "Proteolytic processing of Slit, Homo sapiens" +xref: Reactome:REACT_93020 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Bos taurus" +xref: Reactome:REACT_99630 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6, Gallus gallus" +is_a: GO:0016787 ! hydrolase activity + +[Term] +id: GO:0008234 +name: cysteine-type peptidase activity +namespace: molecular_function +alt_id: GO:0004220 +def: "Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile." [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE] +subset: gosubset_prok +synonym: "cysteine protease activity" EXACT [] +synonym: "thiol protease activity" EXACT [] +xref: EC:3.4.-.- +is_a: GO:0070011 ! peptidase activity, acting on L-amino acid peptides + +[Term] +id: GO:0008283 +name: cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb] +comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0008284 +name: positive regulation of cell proliferation +namespace: biological_process +def: "Any process that activates or increases the rate or extent of cell proliferation." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of cell proliferation" NARROW [] +synonym: "stimulation of cell proliferation" NARROW [] +synonym: "up regulation of cell proliferation" EXACT [] +synonym: "up-regulation of cell proliferation" EXACT [] +synonym: "upregulation of cell proliferation" EXACT [] +is_a: GO:0042127 ! regulation of cell proliferation +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008283 ! cell proliferation +relationship: positively_regulates GO:0008283 ! cell proliferation + +[Term] +id: GO:0008285 +name: negative regulation of cell proliferation +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of cell proliferation." [GOC:go_curators] +synonym: "down regulation of cell proliferation" EXACT [] +synonym: "down-regulation of cell proliferation" EXACT [] +synonym: "downregulation of cell proliferation" EXACT [] +synonym: "inhibition of cell proliferation" NARROW [] +is_a: GO:0042127 ! regulation of cell proliferation +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008283 ! cell proliferation +relationship: negatively_regulates GO:0008283 ! cell proliferation + +[Term] +id: GO:0008286 +name: insulin receptor signaling pathway +namespace: biological_process +def: "The series of molecular signals generated as a consequence of the insulin receptor binding to insulin." [GOC:ceb] +synonym: "daf-2 receptor signaling pathway" NARROW [] +synonym: "insulin receptor signalling pathway" EXACT [] +xref: Reactome:REACT_101230 "Signaling by Insulin receptor, Mus musculus" +xref: Reactome:REACT_101830 "Signaling by Insulin receptor, Oryza sativa" +xref: Reactome:REACT_102947 "Signaling by Insulin receptor, Taeniopygia guttata" +xref: Reactome:REACT_103763 "Signaling by Insulin receptor, Dictyostelium discoideum" +xref: Reactome:REACT_104267 "Signaling by Insulin receptor, Xenopus tropicalis" +xref: Reactome:REACT_109415 "Signaling by Insulin receptor, Canis familiaris" +xref: Reactome:REACT_28335 "Signaling by Insulin receptor, Saccharomyces cerevisiae" +xref: Reactome:REACT_29837 "Signaling by Insulin receptor, Plasmodium falciparum" +xref: Reactome:REACT_498 "Signaling by Insulin receptor, Homo sapiens" +xref: Reactome:REACT_6313 "Signaling by Insulin receptor, Drosophila melanogaster" +xref: Reactome:REACT_67136 "Signaling by Insulin receptor, Bos taurus" +xref: Reactome:REACT_78672 "Signaling by Insulin receptor, Caenorhabditis elegans" +xref: Reactome:REACT_83616 "Signaling by Insulin receptor, Schizosaccharomyces pombe" +xref: Reactome:REACT_90882 "Signaling by Insulin receptor, Sus scrofa" +xref: Reactome:REACT_95985 "Signaling by Insulin receptor, Danio rerio" +xref: Reactome:REACT_97488 "Signaling by Insulin receptor, Arabidopsis thaliana" +xref: Reactome:REACT_99009 "Signaling by Insulin receptor, Rattus norvegicus" +xref: Reactome:REACT_99439 "Signaling by Insulin receptor, Gallus gallus" +is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway +is_a: GO:0032869 ! cellular response to insulin stimulus + +[Term] +id: GO:0008289 +name: lipid binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a lipid." [GOC:ai] +subset: goslim_candida +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0005488 ! binding + +[Term] +id: GO:0008301 +name: DNA binding, bending +namespace: molecular_function +def: "The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence." [GOC:krc, GOC:vw, PMID:10710711, PMID:19037758] +subset: gosubset_prok +synonym: "DNA bending activity" EXACT [] +synonym: "DNA bending involving DNA binding" EXACT [] +is_a: GO:0003677 ! DNA binding + +[Term] +id: GO:0008306 +name: associative learning +namespace: biological_process +def: "Learning by associating a stimulus (the cause) with a particular outcome (the effect)." [ISBN:0582227089] +synonym: "classical conditioning" EXACT [] +synonym: "conditional learning" EXACT [] +synonym: "conditional response" EXACT [] +synonym: "Pavlovian conditioning" EXACT [] +xref: Wikipedia:Learning#Associative_learning +is_a: GO:0007612 ! learning + +[Term] +id: GO:0008344 +name: adult locomotory behavior +namespace: biological_process +def: "Locomotory behavior in a fully developed and mature organism." [GOC:ai] +comment: See also the biological process term 'locomotory behavior ; GO:0007626'. +synonym: "adult locomotory behaviour" EXACT [] +is_a: GO:0007626 ! locomotory behavior +is_a: GO:0030534 ! adult behavior + +[Term] +id: GO:0008354 +name: germ cell migration +namespace: biological_process +def: "The orderly movement of a cell specialized to produce haploid gametes through the embryo from its site of production to the place where the gonads will form." [GOC:bf, GOC:jl] +synonym: "germ-cell migration" EXACT [] +synonym: "primordial germ cell migration" RELATED [] +is_a: GO:0016477 ! cell migration +is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism +relationship: part_of GO:0007276 ! gamete generation + +[Term] +id: GO:0008361 +name: regulation of cell size +namespace: biological_process +def: "Any process that modulates the size of a cell." [GOC:go_curators] +subset: gosubset_prok +synonym: "cell size control" EXACT [] +is_a: GO:0032535 ! regulation of cellular component size + +[Term] +id: GO:0008366 +name: axon ensheathment +namespace: biological_process +alt_id: GO:0042553 +def: "Any process in which the axon of a neuron is insulated, and that insulation maintained, thereby preventing dispersion of the electrical signal." [GOC:jl, ISBN:0878932437] +synonym: "cellular axon ensheathment" EXACT [] +synonym: "cellular nerve ensheathment" RELATED [] +synonym: "nerve ensheathment" RELATED [] +is_a: GO:0007272 ! ensheathment of neurons + +[Term] +id: GO:0008406 +name: gonad development +namespace: biological_process +def: "The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones." [GOC:ems, ISBN:0198506732] +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +is_a: GO:0048608 ! reproductive structure development +relationship: part_of GO:0045137 ! development of primary sexual characteristics + +[Term] +id: GO:0008542 +name: visual learning +namespace: biological_process +def: "Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue." [GOC:jid, ISBN:0582227089] +synonym: "spatial learning" RELATED [] +is_a: GO:0007632 ! visual behavior +is_a: GO:0008306 ! associative learning + +[Term] +id: GO:0008543 +name: fibroblast growth factor receptor signaling pathway +namespace: biological_process +def: "The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands." [GOC:ceb] +synonym: "FGF receptor signaling pathway" EXACT [] +synonym: "FGF receptor signalling pathway" EXACT [] +synonym: "FGFR signaling pathway" EXACT [] +synonym: "fibroblast growth factor receptor signalling pathway" EXACT [] +xref: Reactome:REACT_100065 "FGFR1c ligand binding and activation, Mus musculus" +xref: Reactome:REACT_100193 "FGFR3c ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_100425 "FGFR3c ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_100634 "FGFR2c ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_100821 "FGFR1c and Klotho ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_101067 "Signaling by FGFR, Xenopus tropicalis" +xref: Reactome:REACT_101256 "FGFR1 ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_101261 "FGFR3b ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_101330 "FGFR1b ligand binding and activation, Danio rerio" +xref: Reactome:REACT_101676 "Signaling by FGFR, Gallus gallus" +xref: Reactome:REACT_101991 "FGFR3c ligand binding and activation, Danio rerio" +xref: Reactome:REACT_102813 "Signaling by FGFR, Sus scrofa" +xref: Reactome:REACT_102900 "FGFR1 ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_102940 "FGFR1 ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_102983 "FGFR3c ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_103309 "FGFR1c ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_103577 "Signaling by FGFR, Caenorhabditis elegans" +xref: Reactome:REACT_104466 "FGFR3c ligand binding and activation, Bos taurus" +xref: Reactome:REACT_105552 "Signaling by FGFR, Mus musculus" +xref: Reactome:REACT_105801 "FGFR2 ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_105808 "FGFR2c ligand binding and activation, Danio rerio" +xref: Reactome:REACT_106282 "FGFR2 ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_106586 "FGFR1c and Klotho ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_107516 "FGFR3 ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_107792 "FGFR2b ligand binding and activation, Bos taurus" +xref: Reactome:REACT_108048 "FGFR3 ligand binding and activation, Bos taurus" +xref: Reactome:REACT_108057 "FGFR3b ligand binding and activation, Bos taurus" +xref: Reactome:REACT_108384 "FGFR1c ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_108645 "Signaling by FGFR, Arabidopsis thaliana" +xref: Reactome:REACT_109427 "FGFR1 ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_109441 "FGFR4 ligand binding and activation, Bos taurus" +xref: Reactome:REACT_109874 "FGFR2 ligand binding and activation, Danio rerio" +xref: Reactome:REACT_110057 "Signaling by FGFR, Rattus norvegicus" +xref: Reactome:REACT_110157 "FGFR2b ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_110334 "FGFR3 ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_110540 "FGFR1c and Klotho ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_110592 "FGFR ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_110686 "FGFR3b ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_110991 "FGFR2 ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_112148 "FGFR1b ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_112458 "Signaling by FGFR, Mycobacterium tuberculosis" +xref: Reactome:REACT_112770 "FGFR2 ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_113040 "FGFR1c ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_113367 "Signaling by FGFR, Plasmodium falciparum" +xref: Reactome:REACT_113498 "FGFR3b ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_113682 "FGFR3c ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_114115 "FGFR3 ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_114162 "FGFR2b ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_114328 "Signaling by FGFR, Saccharomyces cerevisiae" +xref: Reactome:REACT_114758 "FGFR2c ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_114804 "FGFR2b ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_115170 "FGFR1 ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_115181 "Signaling by FGFR, Schizosaccharomyces pombe" +xref: Reactome:REACT_115307 "FGFR1b ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_115350 "FGFR4 ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_115356 "FGFR ligand binding and activation, Caenorhabditis elegans" +xref: Reactome:REACT_29132 "FGFR4 ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_29169 "FGFR1b ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_29211 "FGFR1 ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_29608 "FGFR2c ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_30012 "FGFR2 ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_30171 "FGFR ligand binding and activation, Danio rerio" +xref: Reactome:REACT_31565 "FGFR1c and Klotho ligand binding and activation, Danio rerio" +xref: Reactome:REACT_31885 "FGFR1 ligand binding and activation, Bos taurus" +xref: Reactome:REACT_32561 "FGFR2b ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_33067 "FGFR1b ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_33299 "FGFR4 ligand binding and activation, Danio rerio" +xref: Reactome:REACT_33345 "FGFR2b ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_33851 "FGFR2c ligand binding and activation, Bos taurus" +xref: Reactome:REACT_35254 "FGFR3 ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_77367 "FGFR2 ligand binding and activation, Bos taurus" +xref: Reactome:REACT_77757 "FGFR1 ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_77974 "FGFR1b ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_77976 "FGFR3b ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_78827 "FGFR4 ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_80195 "FGFR1c ligand binding and activation, Bos taurus" +xref: Reactome:REACT_80511 "FGFR4 ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_80522 "FGFR1c ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_81030 "FGFR3 ligand binding and activation, Mus musculus" +xref: Reactome:REACT_81325 "FGFR3c ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_81423 "FGFR ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_82006 "FGFR2c ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_82177 "FGFR ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_82322 "FGFR2 ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_82471 "FGFR3 ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_82575 "FGFR ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_83368 "FGFR2c ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_83542 "FGFR1 ligand binding and activation, Mus musculus" +xref: Reactome:REACT_83620 "FGFR1c and Klotho ligand binding and activation, Bos taurus" +xref: Reactome:REACT_83621 "FGFR4 ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_83736 "FGFR2b ligand binding and activation, Danio rerio" +xref: Reactome:REACT_83962 "FGFR1c and Klotho ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_84212 "FGFR2 ligand binding and activation, Mus musculus" +xref: Reactome:REACT_84313 "Signaling by FGFR, Drosophila melanogaster" +xref: Reactome:REACT_84439 "FGFR ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_84550 "FGFR1c ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_84563 "FGFR3b ligand binding and activation, Mus musculus" +xref: Reactome:REACT_84728 "FGFR3b ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_84755 "FGFR ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_85014 "FGFR1 ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_85212 "Signaling by FGFR, Bos taurus" +xref: Reactome:REACT_85655 "FGFR1b ligand binding and activation, Mus musculus" +xref: Reactome:REACT_86158 "FGFR3b ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_86258 "FGFR4 ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_86405 "FGFR3 ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_86768 "FGFR2c ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_86829 "FGFR2 ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_87339 "FGFR1c ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_87721 "FGFR3b ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_87759 "FGFR2c ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_87866 "FGFR3b ligand binding and activation, Danio rerio" +xref: Reactome:REACT_87927 "FGFR3c ligand binding and activation, Mus musculus" +xref: Reactome:REACT_88012 "FGFR2b ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_88057 "FGFR2b ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_88350 "FGFR1c ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_88621 "FGFR2 ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_89576 "Signaling by FGFR, Taeniopygia guttata" +xref: Reactome:REACT_90511 "Signaling by FGFR, Danio rerio" +xref: Reactome:REACT_90558 "FGFR1 ligand binding and activation, Danio rerio" +xref: Reactome:REACT_90759 "FGFR ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_90815 "FGFR ligand binding and activation, Mus musculus" +xref: Reactome:REACT_90948 "FGFR3c ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_91265 "FGFR ligand binding and activation, Bos taurus" +xref: Reactome:REACT_91601 "FGFR1c and Klotho ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_91886 "FGFR2c ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_92480 "FGFR1b ligand binding and activation, Gallus gallus" +xref: Reactome:REACT_92745 "FGFR2c ligand binding and activation, Mus musculus" +xref: Reactome:REACT_93296 "Signaling by FGFR, Canis familiaris" +xref: Reactome:REACT_9390 "FGFR2 ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_9396 "FGFR ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_9400 "FGFR1b ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_9413 "FGFR2c ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_9416 "FGFR2b ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_94238 "FGFR1c ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_94371 "FGFR2b ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_94377 "Signaling by FGFR, Oryza sativa" +xref: Reactome:REACT_9439 "FGFR3 ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_9452 "FGFR4 ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_94582 "Signaling by FGFR, Dictyostelium discoideum" +xref: Reactome:REACT_9470 "Signaling by FGFR, Homo sapiens" +xref: Reactome:REACT_9483 "FGFR1 ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_9484 "FGFR1c and Klotho ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_9508 "FGFR3b ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_9510 "FGFR3c ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_95124 "FGFR1b ligand binding and activation, Bos taurus" +xref: Reactome:REACT_9515 "FGFR1c ligand binding and activation, Homo sapiens" +xref: Reactome:REACT_95314 "FGFR3c ligand binding and activation, Xenopus tropicalis" +xref: Reactome:REACT_96017 "FGFR1c and Klotho ligand binding and activation, Mus musculus" +xref: Reactome:REACT_96035 "FGFR1c ligand binding and activation, Danio rerio" +xref: Reactome:REACT_96057 "FGFR1b ligand binding and activation, Sus scrofa" +xref: Reactome:REACT_96369 "FGFR3c ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_96442 "FGFR3b ligand binding and activation, Rattus norvegicus" +xref: Reactome:REACT_96467 "FGFR3 ligand binding and activation, Danio rerio" +xref: Reactome:REACT_97223 "FGFR1c and Klotho ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_97391 "FGFR1b ligand binding and activation, Canis familiaris" +xref: Reactome:REACT_98666 "FGFR4 ligand binding and activation, Mus musculus" +xref: Reactome:REACT_98769 "FGFR3 ligand binding and activation, Drosophila melanogaster" +xref: Reactome:REACT_98802 "FGFR3 ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_99452 "FGFR4 ligand binding and activation, Taeniopygia guttata" +xref: Reactome:REACT_99507 "FGFR2b ligand binding and activation, Mus musculus" +is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway +is_a: GO:0044344 ! cellular response to fibroblast growth factor stimulus + +[Term] +id: GO:0008544 +name: epidermis development +namespace: biological_process +def: "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of a plant or animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." [GOC:go_curators, UBERON:0001003] +synonym: "hypodermis development" RELATED [GOC:kmv, GOC:rk] +is_a: GO:0009888 ! tissue development +relationship: part_of GO:0043588 ! skin development + +[Term] +id: GO:0008565 +name: protein transporter activity +namespace: molecular_function +alt_id: GO:0015463 +def: "Enables the directed movement of proteins into, out of or within a cell, or between cells." [ISBN:0198506732] +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +synonym: "enzyme transporter activity" NARROW [] +synonym: "holin" RELATED [] +synonym: "protein carrier activity" EXACT [] +synonym: "protein transport chaperone" NARROW [GOC:dph, GOC:mah, GOC:tb] +synonym: "secretin" RELATED [] +is_a: GO:0022892 ! substrate-specific transporter activity +relationship: part_of GO:0015031 ! protein transport + +[Term] +id: GO:0008584 +name: male gonad development +namespace: biological_process +def: "The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure." [GOC:jid] +synonym: "testicular development" EXACT [GOC:sl] +synonym: "testis development" EXACT [GOC:sl] +is_a: GO:0008406 ! gonad development +relationship: part_of GO:0046546 ! development of primary male sexual characteristics + +[Term] +id: GO:0008585 +name: female gonad development +namespace: biological_process +alt_id: GO:0061039 +def: "The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure." [GOC:dph, GOC:jid, GOC:tb] +synonym: "ovarian development" RELATED [GOC:sl] +synonym: "ovary development" RELATED [GOC:sl] +is_a: GO:0008406 ! gonad development +relationship: part_of GO:0046545 ! development of primary female sexual characteristics + +[Term] +id: GO:0008589 +name: regulation of smoothened signaling pathway +namespace: biological_process +alt_id: GO:0007226 +alt_id: GO:0043109 +def: "Any process that modulates the frequency, rate or extent of smoothened signaling." [GOC:go_curators] +synonym: "regulation of hedgehog signaling pathway" EXACT [GOC:bf, GOC:ecd] +synonym: "regulation of hh signaling pathway" EXACT [GOC:bf, GOC:ecd] +synonym: "regulation of smoothened activity" RELATED [] +synonym: "regulation of smoothened by patched" RELATED [] +synonym: "regulation of smoothened receptor activity by patched" RELATED [] +synonym: "regulation of smoothened signalling pathway" EXACT [] +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007224 ! smoothened signaling pathway +relationship: regulates GO:0007224 ! smoothened signaling pathway + +[Term] +id: GO:0008593 +name: regulation of Notch signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the Notch signaling pathway." [GOC:go_curators] +synonym: "regulation of N signaling pathway" EXACT [] +synonym: "regulation of N signalling pathway" EXACT [] +synonym: "regulation of Notch signalling pathway" EXACT [] +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007219 ! Notch signaling pathway +relationship: regulates GO:0007219 ! Notch signaling pathway + +[Term] +id: GO:0008595 +name: anterior/posterior axis specification, embryo +namespace: biological_process +def: "The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238] +synonym: "anterior/posterior axis determination, embryo" RELATED [GOC:dph] +is_a: GO:0000578 ! embryonic axis specification +is_a: GO:0009948 ! anterior/posterior axis specification +relationship: part_of GO:0007351 ! tripartite regional subdivision + +[Term] +id: GO:0008610 +name: lipid biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [GOC:go_curators] +subset: gosubset_prok +synonym: "lipid anabolism" EXACT [] +synonym: "lipid biosynthesis" EXACT [] +synonym: "lipid formation" EXACT [] +synonym: "lipid synthesis" EXACT [] +synonym: "lipogenesis" EXACT [GOC:sl] +is_a: GO:0006629 ! lipid metabolic process +is_a: GO:0044711 ! single-organism biosynthetic process +is_a: GO:1901576 ! organic substance biosynthetic process + +[Term] +id: GO:0008625 +name: extrinsic apoptotic signaling pathway via death domain receptors +namespace: biological_process +def: "A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered." [GOC:mah, GOC:mtg_apoptosis] +comment: Gene products that may be annotated to this term include: 1) ligands such as FASL; 2) receptors such as FAS/CD95 (though care should be taken because FAS can also act as a non-apoptotic signal transducer); 3) signaling molecules such as FADD (FAS-associated protein with a death domain), cIAPs (cellular inhibitor of apoptosis proteins), c-FLIPs and caspases 8 and 10. +synonym: "death receptor-mediated apoptosis" NARROW [] +synonym: "induction of apoptosis via death domain receptors" RELATED [] +synonym: "induction of apoptosis via death receptors" EXACT [GOC:mah] +is_a: GO:0097191 ! extrinsic apoptotic signaling pathway + +[Term] +id: GO:0009056 +name: catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684] +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "breakdown" EXACT [] +synonym: "catabolism" EXACT [] +synonym: "degradation" EXACT [] +xref: Wikipedia:Catabolism +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0009057 +name: macromolecule catabolic process +namespace: biological_process +alt_id: GO:0043285 +def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah] +subset: gosubset_prok +synonym: "biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09] +synonym: "macromolecule breakdown" EXACT [] +synonym: "macromolecule catabolism" EXACT [] +synonym: "macromolecule degradation" EXACT [] +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:1901575 ! organic substance catabolic process + +[Term] +id: GO:0009058 +name: biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: gosubset_prok +synonym: "anabolism" EXACT [] +synonym: "biosynthesis" EXACT [] +synonym: "formation" EXACT [] +synonym: "synthesis" EXACT [] +xref: Wikipedia:Anabolism +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0009059 +name: macromolecule biosynthetic process +namespace: biological_process +alt_id: GO:0043284 +def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah] +subset: gosubset_prok +synonym: "biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09] +synonym: "macromolecule anabolism" EXACT [] +synonym: "macromolecule biosynthesis" EXACT [] +synonym: "macromolecule formation" EXACT [] +synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:1901576 ! organic substance biosynthetic process + +[Term] +id: GO:0009100 +name: glycoprotein metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "glycoprotein metabolism" EXACT [] +is_a: GO:0019538 ! protein metabolic process +is_a: GO:0044260 ! cellular macromolecule metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process + +[Term] +id: GO:0009101 +name: glycoprotein biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "glycoprotein anabolism" EXACT [] +synonym: "glycoprotein biosynthesis" EXACT [] +synonym: "glycoprotein formation" EXACT [] +synonym: "glycoprotein synthesis" EXACT [] +is_a: GO:0009100 ! glycoprotein metabolic process +is_a: GO:0034645 ! cellular macromolecule biosynthetic process +is_a: GO:1901137 ! carbohydrate derivative biosynthetic process + +[Term] +id: GO:0009116 +name: nucleoside metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine)." [GOC:ma] +subset: goslim_pir +subset: gosubset_prok +synonym: "nucleoside metabolism" EXACT [] +is_a: GO:0055086 ! nucleobase-containing small molecule metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process +is_a: GO:1901657 ! glycosyl compound metabolic process + +[Term] +id: GO:0009117 +name: nucleotide metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates)." [GOC:ma] +subset: goslim_metagenomics +subset: goslim_pir +subset: gosubset_prok +synonym: "nucleotide metabolism" EXACT [] +is_a: GO:0006753 ! nucleoside phosphate metabolic process + +[Term] +id: GO:0009118 +name: regulation of nucleoside metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleosides." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of nucleoside metabolism" EXACT [] +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009116 ! nucleoside metabolic process +relationship: regulates GO:0009116 ! nucleoside metabolic process + +[Term] +id: GO:0009119 +name: ribonucleoside metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving any ribonucleoside, a nucleoside in which purine or pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule." [CHEBI:18254, GOC:jl] +subset: gosubset_prok +synonym: "ribonucleoside metabolism" EXACT [] +is_a: GO:0009116 ! nucleoside metabolic process + +[Term] +id: GO:0009141 +name: nucleoside triphosphate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "nucleoside triphosphate metabolism" EXACT [] +is_a: GO:0006753 ! nucleoside phosphate metabolic process + +[Term] +id: GO:0009143 +name: nucleoside triphosphate catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "nucleoside triphosphate breakdown" EXACT [] +synonym: "nucleoside triphosphate catabolism" EXACT [] +synonym: "nucleoside triphosphate degradation" EXACT [] +is_a: GO:0009141 ! nucleoside triphosphate metabolic process +is_a: GO:1901292 ! nucleoside phosphate catabolic process + +[Term] +id: GO:0009144 +name: purine nucleoside triphosphate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "purine nucleoside triphosphate metabolism" EXACT [] +is_a: GO:0009141 ! nucleoside triphosphate metabolic process + +[Term] +id: GO:0009146 +name: purine nucleoside triphosphate catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "purine nucleoside triphosphate breakdown" EXACT [] +synonym: "purine nucleoside triphosphate catabolism" EXACT [] +synonym: "purine nucleoside triphosphate degradation" EXACT [] +is_a: GO:0009143 ! nucleoside triphosphate catabolic process +is_a: GO:0009144 ! purine nucleoside triphosphate metabolic process + +[Term] +id: GO:0009150 +name: purine ribonucleotide metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "purine ribonucleotide metabolism" EXACT [] +is_a: GO:0006163 ! purine nucleotide metabolic process +is_a: GO:0009259 ! ribonucleotide metabolic process + +[Term] +id: GO:0009154 +name: purine ribonucleotide catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "purine ribonucleotide breakdown" EXACT [] +synonym: "purine ribonucleotide catabolism" EXACT [] +synonym: "purine ribonucleotide degradation" EXACT [] +is_a: GO:0006195 ! purine nucleotide catabolic process +is_a: GO:0009150 ! purine ribonucleotide metabolic process +is_a: GO:0009261 ! ribonucleotide catabolic process + +[Term] +id: GO:0009164 +name: nucleoside catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:jl] +subset: gosubset_prok +synonym: "nucleoside breakdown" EXACT [] +synonym: "nucleoside catabolism" EXACT [] +synonym: "nucleoside degradation" EXACT [] +is_a: GO:0009116 ! nucleoside metabolic process +is_a: GO:0034655 ! nucleobase-containing compound catabolic process +is_a: GO:1901136 ! carbohydrate derivative catabolic process +is_a: GO:1901565 ! organonitrogen compound catabolic process +is_a: GO:1901658 ! glycosyl compound catabolic process + +[Term] +id: GO:0009166 +name: nucleotide catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates)." [GOC:go_curators] +subset: gosubset_prok +synonym: "nucleotide breakdown" EXACT [] +synonym: "nucleotide catabolism" EXACT [] +synonym: "nucleotide degradation" EXACT [] +is_a: GO:0009117 ! nucleotide metabolic process +is_a: GO:1901292 ! nucleoside phosphate catabolic process + +[Term] +id: GO:0009187 +name: cyclic nucleotide metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "cyclic nucleotide metabolism" EXACT [] +is_a: GO:0009117 ! nucleotide metabolic process + +[Term] +id: GO:0009199 +name: ribonucleoside triphosphate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "ribonucleoside triphosphate metabolism" EXACT [] +is_a: GO:0009141 ! nucleoside triphosphate metabolic process + +[Term] +id: GO:0009203 +name: ribonucleoside triphosphate catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "ribonucleoside triphosphate breakdown" EXACT [] +synonym: "ribonucleoside triphosphate catabolism" EXACT [] +synonym: "ribonucleoside triphosphate degradation" EXACT [] +is_a: GO:0009143 ! nucleoside triphosphate catabolic process +is_a: GO:0009199 ! ribonucleoside triphosphate metabolic process + +[Term] +id: GO:0009205 +name: purine ribonucleoside triphosphate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "purine ribonucleoside triphosphate metabolism" EXACT [] +is_a: GO:0009144 ! purine nucleoside triphosphate metabolic process +is_a: GO:0009199 ! ribonucleoside triphosphate metabolic process + +[Term] +id: GO:0009207 +name: purine ribonucleoside triphosphate catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "purine ribonucleoside triphosphate breakdown" EXACT [] +synonym: "purine ribonucleoside triphosphate catabolism" EXACT [] +synonym: "purine ribonucleoside triphosphate degradation" EXACT [] +is_a: GO:0009146 ! purine nucleoside triphosphate catabolic process +is_a: GO:0009203 ! ribonucleoside triphosphate catabolic process +is_a: GO:0009205 ! purine ribonucleoside triphosphate metabolic process + +[Term] +id: GO:0009259 +name: ribonucleotide metabolic process +namespace: biological_process +alt_id: GO:0009121 +def: "The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "ribonucleotide metabolism" EXACT [] +is_a: GO:0009117 ! nucleotide metabolic process +is_a: GO:0019693 ! ribose phosphate metabolic process + +[Term] +id: GO:0009261 +name: ribonucleotide catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] +subset: gosubset_prok +synonym: "ribonucleotide breakdown" EXACT [] +synonym: "ribonucleotide catabolism" EXACT [] +synonym: "ribonucleotide degradation" EXACT [] +is_a: GO:0009166 ! nucleotide catabolic process +is_a: GO:0009259 ! ribonucleotide metabolic process +is_a: GO:1901136 ! carbohydrate derivative catabolic process + +[Term] +id: GO:0009306 +name: protein secretion +namespace: biological_process +alt_id: GO:0045166 +alt_id: GO:0045731 +def: "The controlled release of proteins from a cell." [GOC:ai] +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "glycoprotein secretion" NARROW [] +synonym: "protein secretion during cell fate commitment" NARROW [] +synonym: "protein secretion resulting in cell fate commitment" NARROW [] +is_a: GO:0015031 ! protein transport +is_a: GO:0032940 ! secretion by cell + +[Term] +id: GO:0009314 +name: response to radiation +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation." [GOC:jl, Wikipedia:Electromagnetic_radiation] +comment: Note that 'radiation' refers to electromagnetic radiation of any wavelength. +subset: gosubset_prok +synonym: "response to electromagnetic radiation stimulus" EXACT [] +synonym: "response to radiation stimulus" EXACT [] +is_a: GO:0009628 ! response to abiotic stimulus + +[Term] +id: GO:0009416 +name: response to light stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light." [GOC:go_curators, ISBN:0582227089] +subset: gosubset_prok +is_a: GO:0009314 ! response to radiation + +[Term] +id: GO:0009593 +name: detection of chemical stimulus +namespace: biological_process +def: "The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal." [GOC:jl] +synonym: "chemoperception" EXACT [] +synonym: "detection of chemical substance" EXACT [] +synonym: "perception of chemical stimulus" RELATED [] +synonym: "perception of chemical substance" RELATED [] +is_a: GO:0042221 ! response to chemical +is_a: GO:0051606 ! detection of stimulus + +[Term] +id: GO:0009605 +name: response to external stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." [GOC:hb] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_plant +subset: gosubset_prok +synonym: "response to environmental stimulus" EXACT [] +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0009607 +name: response to biotic stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism." [GOC:hb] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_plant +subset: gosubset_prok +synonym: "response to biotic stress" NARROW [] +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0009611 +name: response to wounding +namespace: biological_process +alt_id: GO:0002245 +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism." [GOC:go_curators] +synonym: "physiological response to wounding" EXACT [] +is_a: GO:0006950 ! response to stress + +[Term] +id: GO:0009612 +name: response to mechanical stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus." [GOC:hb] +subset: gosubset_prok +synonym: "chemi-mechanical coupling" RELATED [] +synonym: "mechanical stimulus response" EXACT [] +is_a: GO:0009605 ! response to external stimulus +is_a: GO:0009628 ! response to abiotic stimulus + +[Term] +id: GO:0009617 +name: response to bacterium +namespace: biological_process +alt_id: GO:0009618 +alt_id: GO:0009680 +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium." [GOC:hb] +subset: gosubset_prok +synonym: "response to bacteria" EXACT [] +is_a: GO:0051707 ! response to other organism + +[Term] +id: GO:0009628 +name: response to abiotic stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." [GOC:hb] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_plant +subset: gosubset_prok +synonym: "response to abiotic stress" NARROW [] +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0009653 +name: anatomical structure morphogenesis +namespace: biological_process +def: "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125] +subset: goslim_plant +subset: gosubset_prok +synonym: "anatomical structure organization" EXACT [] +synonym: "embryogenesis and morphogenesis" BROAD [] +synonym: "morphogenesis" EXACT [] +xref: Wikipedia:Morphogenesis +is_a: GO:0032502 ! developmental process +relationship: part_of GO:0048856 ! anatomical structure development + +[Term] +id: GO:0009719 +name: response to endogenous stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism." [GOC:sm] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_plant +subset: gosubset_prok +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0009725 +name: response to hormone +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus." [GOC:jl] +synonym: "growth regulator" RELATED [] +synonym: "response to hormone stimulus" EXACT [GOC:dos] +is_a: GO:0009719 ! response to endogenous stimulus +is_a: GO:0010033 ! response to organic substance + +[Term] +id: GO:0009730 +name: detection of carbohydrate stimulus +namespace: biological_process +def: "The series of events in which a carbohydrate stimulus is received by a cell and converted into a molecular signal." [GOC:sm] +synonym: "perception of carbohydrate stimulus" RELATED [] +is_a: GO:0009593 ! detection of chemical stimulus +is_a: GO:0009743 ! response to carbohydrate + +[Term] +id: GO:0009732 +name: detection of hexose stimulus +namespace: biological_process +def: "The series of events in which a stimulus from a hexose is received and converted into a molecular signal." [GOC:sm] +synonym: "perception of hexose stimulus" RELATED [] +is_a: GO:0009746 ! response to hexose +is_a: GO:0034287 ! detection of monosaccharide stimulus + +[Term] +id: GO:0009743 +name: response to carbohydrate +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus." [GOC:jl] +synonym: "response to carbohydrate stimulus" EXACT [GOC:dos] +is_a: GO:0010033 ! response to organic substance +is_a: GO:1901700 ! response to oxygen-containing compound + +[Term] +id: GO:0009746 +name: response to hexose +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus." [GOC:jl] +synonym: "response to hexose stimulus" EXACT [GOC:dos] +is_a: GO:0034284 ! response to monosaccharide + +[Term] +id: GO:0009749 +name: response to glucose +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus." [GOC:jl] +synonym: "response to glucose stimulus" EXACT [GOC:dos] +is_a: GO:0009746 ! response to hexose + +[Term] +id: GO:0009755 +name: hormone-mediated signaling pathway +namespace: biological_process +def: "A series of molecular signals mediated by the detection of a hormone." [GOC:sm] +synonym: "hormone mediated signalling" EXACT [] +is_a: GO:0007165 ! signal transduction +is_a: GO:0032870 ! cellular response to hormone stimulus + +[Term] +id: GO:0009790 +name: embryo development +namespace: biological_process +alt_id: GO:0009795 +def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] +subset: goslim_generic +subset: goslim_plant +synonym: "embryogenesis" EXACT [] +synonym: "embryogenesis and morphogenesis" BROAD [] +synonym: "embryonal development" EXACT [] +xref: Wikipedia:Embryogenesis +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0009791 +name: post-embryonic development +namespace: biological_process +def: "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." [GOC:go_curators] +subset: goslim_plant +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0009792 +name: embryo development ending in birth or egg hatching +namespace: biological_process +def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] +synonym: "embryogenesis" BROAD [] +is_a: GO:0009790 ! embryo development + +[Term] +id: GO:0009798 +name: axis specification +namespace: biological_process +def: "The establishment, maintenance and elaboration of a pattern along a line or around a point." [GOC:dph, GOC:go_curators, GOC:isa_complete] +synonym: "axis determination" RELATED [] +is_a: GO:0007389 ! pattern specification process + +[Term] +id: GO:0009799 +name: specification of symmetry +namespace: biological_process +def: "The establishment of an organism's body plan or part of an organism such that a similar arrangement in form and relationship of parts around a common axis, or around each side of a plane is created." [GOC:go_curators] +synonym: "determination of symmetry" EXACT [GOC:dph] +is_a: GO:0007389 ! pattern specification process + +[Term] +id: GO:0009855 +name: determination of bilateral symmetry +namespace: biological_process +def: "The establishment of an organism's body plan or part of an organism with respect to a single longitudinal plane. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry." [GOC:go_curators] +synonym: "determination of bilateral asymmetry" EXACT [GOC:dph] +is_a: GO:0009799 ! specification of symmetry + +[Term] +id: GO:0009880 +name: embryonic pattern specification +namespace: biological_process +def: "The process that results in the patterns of cell differentiation that will arise in an embryo." [GOC:go_curators, ISBN:0521436125] +synonym: "embryonic pattern biosynthesis" BROAD [] +synonym: "embryonic pattern formation" BROAD [] +synonym: "ventral/lateral system" RELATED [] +is_a: GO:0007389 ! pattern specification process +relationship: part_of GO:0009790 ! embryo development + +[Term] +id: GO:0009887 +name: organ morphogenesis +namespace: biological_process +def: "Morphogenesis of an organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:dgh, GOC:go_curators, ISBN:0471245208, ISBN:0721662544] +synonym: "histogenesis and organogenesis" BROAD [] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048513 ! organ development + +[Term] +id: GO:0009888 +name: tissue development +namespace: biological_process +def: "The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure." [ISBN:0471245208] +synonym: "histogenesis" EXACT [] +synonym: "histogenesis and organogenesis" BROAD [] +xref: Wikipedia:Histogenesis +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0009889 +name: regulation of biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of anabolism" EXACT [] +synonym: "regulation of biosynthesis" EXACT [] +synonym: "regulation of formation" EXACT [] +synonym: "regulation of synthesis" EXACT [] +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009058 ! biosynthetic process +relationship: regulates GO:0009058 ! biosynthetic process + +[Term] +id: GO:0009890 +name: negative regulation of biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of biosynthetic process" EXACT [] +synonym: "down-regulation of biosynthetic process" EXACT [] +synonym: "downregulation of biosynthetic process" EXACT [] +synonym: "inhibition of biosynthetic process" NARROW [] +synonym: "negative regulation of anabolism" EXACT [] +synonym: "negative regulation of biosynthesis" EXACT [] +synonym: "negative regulation of formation" EXACT [] +synonym: "negative regulation of synthesis" EXACT [] +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0009892 ! negative regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009058 ! biosynthetic process +relationship: negatively_regulates GO:0009058 ! biosynthetic process + +[Term] +id: GO:0009891 +name: positive regulation of biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of biosynthetic process" NARROW [] +synonym: "positive regulation of anabolism" EXACT [] +synonym: "positive regulation of biosynthesis" EXACT [] +synonym: "positive regulation of formation" EXACT [] +synonym: "positive regulation of synthesis" EXACT [] +synonym: "stimulation of biosynthetic process" NARROW [] +synonym: "up regulation of biosynthetic process" EXACT [] +synonym: "up-regulation of biosynthetic process" EXACT [] +synonym: "upregulation of biosynthetic process" EXACT [] +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0009893 ! positive regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009058 ! biosynthetic process +relationship: positively_regulates GO:0009058 ! biosynthetic process + +[Term] +id: GO:0009892 +name: negative regulation of metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of metabolic process" EXACT [] +synonym: "down-regulation of metabolic process" EXACT [] +synonym: "downregulation of metabolic process" EXACT [] +synonym: "inhibition of metabolic process" NARROW [] +synonym: "negative regulation of metabolism" EXACT [] +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008152 ! metabolic process +relationship: negatively_regulates GO:0008152 ! metabolic process + +[Term] +id: GO:0009893 +name: positive regulation of metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of metabolic process" NARROW [] +synonym: "positive regulation of metabolism" EXACT [] +synonym: "stimulation of metabolic process" NARROW [] +synonym: "up regulation of metabolic process" EXACT [] +synonym: "up-regulation of metabolic process" EXACT [] +synonym: "upregulation of metabolic process" EXACT [] +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008152 ! metabolic process +relationship: positively_regulates GO:0008152 ! metabolic process + +[Term] +id: GO:0009894 +name: regulation of catabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of breakdown" EXACT [] +synonym: "regulation of catabolism" EXACT [] +synonym: "regulation of degradation" EXACT [] +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009056 ! catabolic process +relationship: regulates GO:0009056 ! catabolic process + +[Term] +id: GO:0009896 +name: positive regulation of catabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of catabolic process" NARROW [] +synonym: "positive regulation of breakdown" EXACT [] +synonym: "positive regulation of catabolism" EXACT [] +synonym: "positive regulation of degradation" EXACT [] +synonym: "stimulation of catabolic process" NARROW [] +synonym: "up regulation of catabolic process" EXACT [] +synonym: "up-regulation of catabolic process" EXACT [] +synonym: "upregulation of catabolic process" EXACT [] +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0009894 ! regulation of catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009056 ! catabolic process +relationship: positively_regulates GO:0009056 ! catabolic process + +[Term] +id: GO:0009898 +name: cytoplasmic side of plasma membrane +namespace: cellular_component +def: "The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface." [GOC:dos, GOC:tb] +subset: gosubset_prok +synonym: "internal leaflet of plasma membrane" EXACT [GOC:ab] +synonym: "internal side of plasma membrane" EXACT [] +synonym: "juxtamembrane" BROAD [] +is_a: GO:0044459 ! plasma membrane part +is_a: GO:0098562 ! cytoplasmic side of membrane +relationship: part_of GO:0005886 ! plasma membrane + +[Term] +id: GO:0009913 +name: epidermal cell differentiation +namespace: biological_process +alt_id: GO:0043355 +def: "The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis." [GOC:dph, GOC:go_curators, GOC:mtg_sensu, GOC:sdb_2009, GOC:tb] +synonym: "hypodermal cell differentiation" RELATED [GOC:kmv, GOC:rk] +is_a: GO:0030855 ! epithelial cell differentiation +relationship: part_of GO:0008544 ! epidermis development + +[Term] +id: GO:0009914 +name: hormone transport +namespace: biological_process +def: "The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:tb] +subset: goslim_pir +is_a: GO:0010817 ! regulation of hormone levels +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0009948 +name: anterior/posterior axis specification +namespace: biological_process +def: "The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." [GOC:dph, GOC:go_curators, GOC:tb] +synonym: "anterior/posterior axis determination" RELATED [GOC:dph] +is_a: GO:0009798 ! axis specification +relationship: part_of GO:0009952 ! anterior/posterior pattern specification + +[Term] +id: GO:0009950 +name: dorsal/ventral axis specification +namespace: biological_process +def: "The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism." [GOC:dph, GOC:go_curators, GOC:tb] +synonym: "dorsal-ventral axis specification" EXACT [GOC:mah] +synonym: "dorsal/ventral axis determination" RELATED [GOC:dph] +synonym: "dorsoventral axis specification" EXACT [GOC:mah] +is_a: GO:0009798 ! axis specification +relationship: part_of GO:0009953 ! dorsal/ventral pattern formation + +[Term] +id: GO:0009952 +name: anterior/posterior pattern specification +namespace: biological_process +def: "The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb] +synonym: "anterior/posterior pattern formation" RELATED [] +is_a: GO:0003002 ! regionalization + +[Term] +id: GO:0009953 +name: dorsal/ventral pattern formation +namespace: biological_process +def: "The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism." [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb] +synonym: "dorsal-ventral pattern formation" EXACT [GOC:mah] +synonym: "dorsal/ventral pattern specification" NARROW [] +synonym: "dorsoventral pattern formation" EXACT [GOC:mah] +is_a: GO:0003002 ! regionalization + +[Term] +id: GO:0009954 +name: proximal/distal pattern formation +namespace: biological_process +def: "The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end)." [GOC:dph, GOC:go_curators, GOC:isa_complete] +synonym: "proximal/distal pattern specification" NARROW [] +is_a: GO:0003002 ! regionalization + +[Term] +id: GO:0009957 +name: epidermal cell fate specification +namespace: biological_process +alt_id: GO:0043356 +def: "The process in which a cell becomes capable of differentiating autonomously into an epidermal cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:mtg_sensu, GOC:sm] +synonym: "hypodermal cell fate specification" RELATED [GOC:kmv, GOC:rk] +is_a: GO:0001708 ! cell fate specification +relationship: part_of GO:0009913 ! epidermal cell differentiation + +[Term] +id: GO:0009966 +name: regulation of signal transduction +namespace: biological_process +alt_id: GO:0035466 +def: "Any process that modulates the frequency, rate or extent of signal transduction." [GOC:sm] +subset: gosubset_prok +synonym: "regulation of signaling pathway" RELATED [] +synonym: "regulation of signalling pathway" RELATED [GOC:mah] +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0023051 ! regulation of signaling +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007165 ! signal transduction +relationship: regulates GO:0007165 ! signal transduction + +[Term] +id: GO:0009967 +name: positive regulation of signal transduction +namespace: biological_process +alt_id: GO:0035468 +def: "Any process that activates or increases the frequency, rate or extent of signal transduction." [GOC:sm] +subset: gosubset_prok +synonym: "activation of signal transduction" NARROW [] +synonym: "positive regulation of signaling pathway" RELATED [] +synonym: "positive regulation of signalling pathway" RELATED [GOC:mah] +synonym: "stimulation of signal transduction" NARROW [] +synonym: "up regulation of signal transduction" EXACT [] +synonym: "up-regulation of signal transduction" EXACT [] +synonym: "upregulation of signal transduction" EXACT [] +xref: Reactome:REACT_6227 "Activated DTOR also phosphorylates D4EBP, Drosophila melanogaster" +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0010647 ! positive regulation of cell communication +is_a: GO:0023056 ! positive regulation of signaling +is_a: GO:0048584 ! positive regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007165 ! signal transduction +relationship: positively_regulates GO:0007165 ! signal transduction + +[Term] +id: GO:0009968 +name: negative regulation of signal transduction +namespace: biological_process +alt_id: GO:0035467 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction." [GOC:sm] +subset: gosubset_prok +synonym: "down regulation of signal transduction" EXACT [] +synonym: "down-regulation of signal transduction" EXACT [] +synonym: "downregulation of signal transduction" EXACT [] +synonym: "inhibition of signal transduction" NARROW [] +synonym: "negative regulation of signaling pathway" RELATED [] +synonym: "negative regulation of signalling pathway" RELATED [GOC:mah] +xref: Reactome:REACT_6334 "DTSC1 AND DTSC2 form a complex, Drosophila melanogaster" +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0010648 ! negative regulation of cell communication +is_a: GO:0023057 ! negative regulation of signaling +is_a: GO:0048585 ! negative regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007165 ! signal transduction +relationship: negatively_regulates GO:0007165 ! signal transduction + +[Term] +id: GO:0009986 +name: cell surface +namespace: cellular_component +alt_id: GO:0009928 +alt_id: GO:0009929 +def: "The external part of the cell wall and/or plasma membrane." [GOC:jl, GOC:mtg_sensu, GOC:sm] +comment: Note that this term is intended to annotate gene products that are attached (integrated or loosely bound) to the plasma membrane or cell wall. +subset: goslim_pir +subset: gosubset_prok +synonym: "cell associated" EXACT [] +synonym: "cell bound" EXACT [] +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0009987 +name: cellular process +namespace: biological_process +alt_id: GO:0008151 +alt_id: GO:0050875 +def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "cell growth and/or maintenance" NARROW [] +synonym: "cell physiology" EXACT [] +synonym: "cellular physiological process" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0009991 +name: response to extracellular stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus." [GOC:go_curators] +subset: goslim_plant +subset: gosubset_prok +is_a: GO:0009605 ! response to external stimulus + +[Term] +id: GO:0009994 +name: oocyte differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized immature germ cell acquires the specialized features of a mature female gamete." [GOC:go_curators, GOC:mtg_sensu] +synonym: "oocyte cell differentiation" EXACT [] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism +is_a: GO:0030154 ! cell differentiation +is_a: GO:0044702 ! single organism reproductive process +relationship: part_of GO:0048477 ! oogenesis + +[Term] +id: GO:0009996 +name: negative regulation of cell fate specification +namespace: biological_process +def: "Any process that restricts, stops or prevents a cell from adopting a specific cell fate." [GOC:go_curators] +synonym: "down regulation of cell fate specification" EXACT [] +synonym: "down-regulation of cell fate specification" EXACT [] +synonym: "downregulation of cell fate specification" EXACT [] +synonym: "inhibition of cell fate specification" NARROW [] +synonym: "suppression of cell fate" EXACT [] +is_a: GO:0010454 ! negative regulation of cell fate commitment +is_a: GO:0042659 ! regulation of cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001708 ! cell fate specification +relationship: negatively_regulates GO:0001708 ! cell fate specification + +[Term] +id: GO:0009997 +name: negative regulation of cardioblast cell fate specification +namespace: biological_process +alt_id: GO:0042687 +def: "Any process that restricts, stops or prevents a cell from specifying into a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators] +synonym: "down regulation of cardioblast cell fate specification" EXACT [] +synonym: "down-regulation of cardioblast cell fate specification" EXACT [] +synonym: "downregulation of cardioblast cell fate specification" EXACT [] +synonym: "inhibition of cardioblast cell fate specification" NARROW [] +synonym: "suppression of cardioblast cell fate" EXACT [] +is_a: GO:0042686 ! regulation of cardioblast cell fate specification +is_a: GO:2000044 ! negative regulation of cardiac cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042685 ! cardioblast cell fate specification +relationship: negatively_regulates GO:0042685 ! cardioblast cell fate specification + +[Term] +id: GO:0010001 +name: glial cell differentiation +namespace: biological_process +alt_id: GO:0007404 +alt_id: GO:0043360 +def: "The process in which a relatively unspecialized cell acquires the specialized features of a glial cell." [GOC:go_curators, GOC:mtg_sensu] +synonym: "glia cell differentiation" EXACT [] +synonym: "neuroglia differentiation" EXACT [] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0042063 ! gliogenesis + +[Term] +id: GO:0010002 +name: cardioblast differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators] +synonym: "cardiac precursor cell differentiation" EXACT [GOC:mtg_heart] +synonym: "cardioblast cell differentiation" EXACT [] +synonym: "cardiomyocyte generation" RELATED [] +is_a: GO:0035051 ! cardiocyte differentiation +is_a: GO:0048863 ! stem cell differentiation + +[Term] +id: GO:0010033 +name: response to organic substance +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus." [GOC:sm] +subset: gosubset_prok +is_a: GO:0042221 ! response to chemical + +[Term] +id: GO:0010092 +name: specification of organ identity +namespace: biological_process +def: "The regionalization process in which the identity of an organ primordium is specified. Identity is considered to be the aggregate of characteristics by which a structure is recognized." [GOC:tair_curators] +is_a: GO:0003002 ! regionalization +relationship: part_of GO:0048645 ! organ formation + +[Term] +id: GO:0010159 +name: specification of organ position +namespace: biological_process +def: "The regionalization process in which information that determines the correct position at which organ primordia are formed is generated and perceived resulting in correct positioning of the new organ." [PMID:9611175] +is_a: GO:0003002 ! regionalization +relationship: part_of GO:0009887 ! organ morphogenesis + +[Term] +id: GO:0010165 +name: response to X-ray +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz)." [GOC:sm, Wikipedia:X-ray] +synonym: "response to X-ray radiation stimulus" EXACT [] +is_a: GO:0010212 ! response to ionizing radiation + +[Term] +id: GO:0010171 +name: body morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the soma are generated and organized." [GOC:ems, ISBN:0140512888] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0010212 +name: response to ionizing radiation +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID:12509526] +synonym: "response to ionising radiation" EXACT [] +synonym: "response to ionizing radiation stimulus" EXACT [] +is_a: GO:0009314 ! response to radiation + +[Term] +id: GO:0010243 +name: response to organonitrogen compound +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond." [CHEBI:35352, PMID:9869419] +synonym: "response to organic nitrogen" EXACT [] +is_a: GO:0009719 ! response to endogenous stimulus +is_a: GO:0010033 ! response to organic substance +is_a: GO:1901698 ! response to nitrogen compound + +[Term] +id: GO:0010324 +name: membrane invagination +namespace: biological_process +def: "The infolding of a membrane, resulting in formation of a vesicle." [GOC:tb] +subset: goslim_yeast +is_a: GO:0061024 ! membrane organization + +[Term] +id: GO:0010387 +name: COP9 signalosome assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form a COP9 signalosome." [PMID:17307927] +synonym: "signalosome assembly" BROAD [GOC:krc] +is_a: GO:0043623 ! cellular protein complex assembly + +[Term] +id: GO:0010453 +name: regulation of cell fate commitment +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field." [GOC:dph, GOC:tb] +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045165 ! cell fate commitment +relationship: regulates GO:0045165 ! cell fate commitment + +[Term] +id: GO:0010454 +name: negative regulation of cell fate commitment +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field." [GOC:dph, GOC:tb] +is_a: GO:0010453 ! regulation of cell fate commitment +is_a: GO:0045596 ! negative regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0045165 ! cell fate commitment +relationship: negatively_regulates GO:0045165 ! cell fate commitment + +[Term] +id: GO:0010457 +name: centriole-centriole cohesion +namespace: biological_process +def: "The process in which the two centrioles within a centrosome remain tightly paired." [GOC:dph, GOC:tb] +is_a: GO:0051297 ! centrosome organization + +[Term] +id: GO:0010463 +name: mesenchymal cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." [GOC:dph, GOC:tb] +is_a: GO:0072089 ! stem cell proliferation + +[Term] +id: GO:0010464 +name: regulation of mesenchymal cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." [GOC:dph, GOC:tb] +is_a: GO:0072091 ! regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010463 ! mesenchymal cell proliferation +relationship: regulates GO:0010463 ! mesenchymal cell proliferation + +[Term] +id: GO:0010466 +name: negative regulation of peptidase activity +namespace: biological_process +def: "Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins." [GOC:dph, GOC:tb] +is_a: GO:0051346 ! negative regulation of hydrolase activity +is_a: GO:0052547 ! regulation of peptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008233 ! peptidase activity +relationship: negatively_regulates GO:0008233 ! peptidase activity + +[Term] +id: GO:0010467 +name: gene expression +namespace: biological_process +def: "The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] +subset: gosubset_prok +xref: Reactome:REACT_100537 "Gene Expression, Xenopus tropicalis" +xref: Reactome:REACT_101147 "Gene Expression, Danio rerio" +xref: Reactome:REACT_101952 "Gene Expression, Sus scrofa" +xref: Reactome:REACT_105649 "Gene Expression, Drosophila melanogaster" +xref: Reactome:REACT_108313 "Gene Expression, Caenorhabditis elegans" +xref: Reactome:REACT_29068 "Gene Expression, Escherichia coli" +xref: Reactome:REACT_34240 "Gene Expression, Staphylococcus aureus N315" +xref: Reactome:REACT_71 "Gene Expression, Homo sapiens" +xref: Reactome:REACT_78136 "Gene Expression, Mus musculus" +xref: Reactome:REACT_78959 "Gene Expression, Taeniopygia guttata" +xref: Reactome:REACT_79662 "Gene Expression, Plasmodium falciparum" +xref: Reactome:REACT_85241 "Gene Expression, Oryza sativa" +xref: Reactome:REACT_85359 "Gene Expression, Gallus gallus" +xref: Reactome:REACT_86357 "Gene Expression, Canis familiaris" +xref: Reactome:REACT_89816 "Gene Expression, Mycobacterium tuberculosis" +xref: Reactome:REACT_91657 "Gene Expression, Arabidopsis thaliana" +xref: Reactome:REACT_91965 "Gene Expression, Rattus norvegicus" +xref: Reactome:REACT_93586 "Gene Expression, Dictyostelium discoideum" +xref: Reactome:REACT_93968 "Gene Expression, Bos taurus" +xref: Reactome:REACT_94814 "Gene Expression, Schizosaccharomyces pombe" +xref: Reactome:REACT_98256 "Gene Expression, Saccharomyces cerevisiae" +xref: Wikipedia:Gene_expression +is_a: GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0010468 +name: regulation of gene expression +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] +subset: gosubset_prok +synonym: "regulation of gene product expression" RELATED [GOC:curators] +synonym: "regulation of protein expression" NARROW [GOC:curators] +xref: Wikipedia:Regulation_of_gene_expression +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010467 ! gene expression +relationship: regulates GO:0010467 ! gene expression + +[Term] +id: GO:0010469 +name: regulation of receptor activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:dph, GOC:tb] +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004872 ! receptor activity +relationship: regulates GO:0004872 ! receptor activity + +[Term] +id: GO:0010470 +name: regulation of gastrulation +namespace: biological_process +def: "Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals." [GOC:dph, GOC:tb] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0045995 ! regulation of embryonic development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007369 ! gastrulation +relationship: regulates GO:0007369 ! gastrulation + +[Term] +id: GO:0010556 +name: regulation of macromolecule biosynthetic process +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] +subset: gosubset_prok +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009059 ! macromolecule biosynthetic process +relationship: regulates GO:0009059 ! macromolecule biosynthetic process + +[Term] +id: GO:0010557 +name: positive regulation of macromolecule biosynthetic process +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] +is_a: GO:0009891 ! positive regulation of biosynthetic process +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009059 ! macromolecule biosynthetic process +relationship: positively_regulates GO:0009059 ! macromolecule biosynthetic process + +[Term] +id: GO:0010558 +name: negative regulation of macromolecule biosynthetic process +namespace: biological_process +def: "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] +is_a: GO:0009890 ! negative regulation of biosynthetic process +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009059 ! macromolecule biosynthetic process +relationship: negatively_regulates GO:0009059 ! macromolecule biosynthetic process + +[Term] +id: GO:0010559 +name: regulation of glycoprotein biosynthetic process +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb] +subset: gosubset_prok +is_a: GO:0051246 ! regulation of protein metabolic process +is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009101 ! glycoprotein biosynthetic process +relationship: regulates GO:0009101 ! glycoprotein biosynthetic process + +[Term] +id: GO:0010560 +name: positive regulation of glycoprotein biosynthetic process +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb] +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process +is_a: GO:0010559 ! regulation of glycoprotein biosynthetic process +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0051247 ! positive regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009101 ! glycoprotein biosynthetic process +relationship: positively_regulates GO:0009101 ! glycoprotein biosynthetic process + +[Term] +id: GO:0010562 +name: positive regulation of phosphorus metabolic process +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus." [GOC:dph, GOC:tb] +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0051174 ! regulation of phosphorus metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006793 ! phosphorus metabolic process +relationship: positively_regulates GO:0006793 ! phosphorus metabolic process + +[Term] +id: GO:0010563 +name: negative regulation of phosphorus metabolic process +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus." [GOC:dph, GOC:tb] +is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0051174 ! regulation of phosphorus metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006793 ! phosphorus metabolic process +relationship: negatively_regulates GO:0006793 ! phosphorus metabolic process + +[Term] +id: GO:0010564 +name: regulation of cell cycle process +namespace: biological_process +def: "Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events." [GOC:dph, GOC:tb] +is_a: GO:0051726 ! regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0022402 ! cell cycle process +relationship: regulates GO:0022402 ! cell cycle process + +[Term] +id: GO:0010565 +name: regulation of cellular ketone metabolic process +namespace: biological_process +def: "Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:dph, GOC:tb] +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042180 ! cellular ketone metabolic process +relationship: regulates GO:0042180 ! cellular ketone metabolic process + +[Term] +id: GO:0010566 +name: regulation of ketone biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells." [GOC:dph, GOC:tb] +is_a: GO:0010565 ! regulation of cellular ketone metabolic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042181 ! ketone biosynthetic process +relationship: regulates GO:0042181 ! ketone biosynthetic process + +[Term] +id: GO:0010576 +name: metalloenzyme regulator activity +namespace: molecular_function +def: "Modulates the activity of a metalloenzyme. A metalloenzyme is any enzyme that contains metal." [GOC:dph, GOC:tb] +is_a: GO:0030234 ! enzyme regulator activity + +[Term] +id: GO:0010577 +name: metalloenzyme activator activity +namespace: molecular_function +def: "Increases the activity of a metalloenzyme. A metalloenzyme is any enzyme that contains metal." [GOC:dph, GOC:tb] +is_a: GO:0008047 ! enzyme activator activity +is_a: GO:0010576 ! metalloenzyme regulator activity + +[Term] +id: GO:0010591 +name: regulation of lamellipodium assembly +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell." [GOC:dph, GOC:tb] +synonym: "regulation of lamellipodium biogenesis" RELATED [GOC:mah] +is_a: GO:0060491 ! regulation of cell projection assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030032 ! lamellipodium assembly +relationship: regulates GO:0030032 ! lamellipodium assembly + +[Term] +id: GO:0010592 +name: positive regulation of lamellipodium assembly +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell." [GOC:dph, GOC:tb] +synonym: "positive regulation of lamellipodium biogenesis" RELATED [GOC:mah] +is_a: GO:0010591 ! regulation of lamellipodium assembly +is_a: GO:0031346 ! positive regulation of cell projection organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030032 ! lamellipodium assembly +relationship: positively_regulates GO:0030032 ! lamellipodium assembly + +[Term] +id: GO:0010594 +name: regulation of endothelial cell migration +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0010632 ! regulation of epithelial cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043542 ! endothelial cell migration +relationship: regulates GO:0043542 ! endothelial cell migration + +[Term] +id: GO:0010595 +name: positive regulation of endothelial cell migration +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0010594 ! regulation of endothelial cell migration +is_a: GO:0010634 ! positive regulation of epithelial cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0043542 ! endothelial cell migration +relationship: positively_regulates GO:0043542 ! endothelial cell migration + +[Term] +id: GO:0010604 +name: positive regulation of macromolecule metabolic process +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0043170 ! macromolecule metabolic process +relationship: positively_regulates GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0010605 +name: negative regulation of macromolecule metabolic process +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0043170 ! macromolecule metabolic process +relationship: negatively_regulates GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0010623 +name: developmental programmed cell death +namespace: biological_process +def: "The activation of endogenous cellular processes that result in the death of a cell as part of its development." [GOC:dph, GOC:tb] +is_a: GO:0012501 ! programmed cell death +is_a: GO:0048869 ! cellular developmental process +intersection_of: GO:0012501 ! programmed cell death +intersection_of: part_of GO:0048468 ! cell development +relationship: part_of GO:0048468 ! cell development + +[Term] +id: GO:0010628 +name: positive regulation of gene expression +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] +is_a: GO:0010468 ! regulation of gene expression +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010467 ! gene expression +relationship: positively_regulates GO:0010467 ! gene expression + +[Term] +id: GO:0010629 +name: negative regulation of gene expression +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] +is_a: GO:0010468 ! regulation of gene expression +is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010467 ! gene expression +relationship: negatively_regulates GO:0010467 ! gene expression + +[Term] +id: GO:0010631 +name: epithelial cell migration +namespace: biological_process +def: "The orderly movement of an epithelial cell from one site to another, often during the development of a multicellular organism." [GOC:ascb_2009, GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0001667 ! ameboidal cell migration +relationship: part_of GO:0090132 ! epithelium migration + +[Term] +id: GO:0010632 +name: regulation of epithelial cell migration +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of epithelial cell migration." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0030334 ! regulation of cell migration +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010631 ! epithelial cell migration +relationship: regulates GO:0010631 ! epithelial cell migration + +[Term] +id: GO:0010634 +name: positive regulation of epithelial cell migration +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of epithelial cell migration." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0010632 ! regulation of epithelial cell migration +is_a: GO:0030335 ! positive regulation of cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010631 ! epithelial cell migration +relationship: positively_regulates GO:0010631 ! epithelial cell migration + +[Term] +id: GO:0010638 +name: positive regulation of organelle organization +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." [GOC:dph, GOC:tb] +synonym: "positive regulation of organelle organisation" EXACT [GOC:mah] +synonym: "positive regulation of organelle organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0033043 ! regulation of organelle organization +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006996 ! organelle organization +relationship: positively_regulates GO:0006996 ! organelle organization + +[Term] +id: GO:0010646 +name: regulation of cell communication +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb] +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007154 ! cell communication +relationship: regulates GO:0007154 ! cell communication + +[Term] +id: GO:0010647 +name: positive regulation of cell communication +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb] +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007154 ! cell communication +relationship: positively_regulates GO:0007154 ! cell communication + +[Term] +id: GO:0010648 +name: negative regulation of cell communication +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb] +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007154 ! cell communication +relationship: negatively_regulates GO:0007154 ! cell communication + +[Term] +id: GO:0010656 +name: negative regulation of muscle cell apoptotic process +namespace: biological_process +def: "Any process that decreases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death." [GOC:dph, GOC:mtg_apoptosis, GOC:tb] +synonym: "negative regulation of muscle cell apoptosis" NARROW [] +is_a: GO:0010660 ! regulation of muscle cell apoptotic process +is_a: GO:0043066 ! negative regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010657 ! muscle cell apoptotic process +relationship: negatively_regulates GO:0010657 ! muscle cell apoptotic process + +[Term] +id: GO:0010657 +name: muscle cell apoptotic process +namespace: biological_process +def: "A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a muscle cell and result in its death. A muscle cell is a mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle." [CL:0000187, GOC:dph, GOC:mtg_apoptosis, GOC:tb] +synonym: "muscle cell apoptosis" NARROW [] +is_a: GO:0097285 ! cell-type specific apoptotic process + +[Term] +id: GO:0010658 +name: striated muscle cell apoptotic process +namespace: biological_process +def: "A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a striated muscle cell and result in its death. Striated muscle cells make up striated muscle fibers which are divided by transverse bands into striations." [CL:0000737, GOC:dph, GOC:mtg_apoptosis, GOC:tb] +synonym: "striated muscle cell apoptosis" NARROW [] +is_a: GO:0010657 ! muscle cell apoptotic process + +[Term] +id: GO:0010659 +name: cardiac muscle cell apoptotic process +namespace: biological_process +def: "A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a cardiac muscle cell and result in its death. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction." [CL:0000746, GOC:dph, GOC:mtg_apoptosis, GOC:tb] +synonym: "cardiac muscle cell apoptosis" NARROW [] +is_a: GO:0010658 ! striated muscle cell apoptotic process + +[Term] +id: GO:0010660 +name: regulation of muscle cell apoptotic process +namespace: biological_process +def: "Any process that modulates the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death." [GOC:dph, GOC:mtg_apoptosis, GOC:tb] +synonym: "regulation of muscle cell apoptosis" NARROW [] +is_a: GO:0042981 ! regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010657 ! muscle cell apoptotic process +relationship: regulates GO:0010657 ! muscle cell apoptotic process + +[Term] +id: GO:0010662 +name: regulation of striated muscle cell apoptotic process +namespace: biological_process +def: "Any process that modulates the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death." [GOC:dph, GOC:mtg_apoptosis, GOC:tb] +synonym: "regulation of striated muscle cell apoptosis" NARROW [] +is_a: GO:0010660 ! regulation of muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010658 ! striated muscle cell apoptotic process +relationship: regulates GO:0010658 ! striated muscle cell apoptotic process + +[Term] +id: GO:0010664 +name: negative regulation of striated muscle cell apoptotic process +namespace: biological_process +def: "Any process that increases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death." [GOC:BHF, GOC:dph, GOC:mtg_apoptosis, GOC:rl, GOC:tb] +synonym: "down regulation of striated muscle cell apoptosis " EXACT [GOC:dph, GOC:rl, GOC:tb] +synonym: "down-regulation of striated muscle cell apoptosis" EXACT [GOC:dph, GOC:rl, GOC:tb] +synonym: "downregulation of striated muscle cell apoptosis" EXACT [GOC:dph, GOC:rl, GOC:tb] +synonym: "inhibition of striated muscle cell apoptosis " NARROW [GOC:dph, GOC:rl, GOC:tb] +synonym: "negative regulation of striated muscle cell apoptosis" NARROW [] +is_a: GO:0010656 ! negative regulation of muscle cell apoptotic process +is_a: GO:0010662 ! regulation of striated muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010658 ! striated muscle cell apoptotic process +relationship: negatively_regulates GO:0010658 ! striated muscle cell apoptotic process + +[Term] +id: GO:0010665 +name: regulation of cardiac muscle cell apoptotic process +namespace: biological_process +def: "Any process that modulates the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death." [GOC:dph, GOC:mtg_apoptosis, GOC:tb] +synonym: "regulation of cardiac muscle cell apoptosis" NARROW [] +is_a: GO:0010662 ! regulation of striated muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010659 ! cardiac muscle cell apoptotic process +relationship: regulates GO:0010659 ! cardiac muscle cell apoptotic process + +[Term] +id: GO:0010667 +name: negative regulation of cardiac muscle cell apoptotic process +namespace: biological_process +def: "Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death." [GOC:BHF, GOC:dph, GOC:mtg_apoptosis, GOC:rl, GOC:tb] +synonym: "down regulation of cardiac muscle cell apoptosis" EXACT [GOC:dph, GOC:rl, GOC:tb] +synonym: "down-regulation of cardiac muscle cell apoptosis" EXACT [GOC:dph, GOC:rl, GOC:tb] +synonym: "downregulation of cardiac muscle cell apoptosis" EXACT [GOC:dph, GOC:rl, GOC:tb] +synonym: "inhibition of cardiac muscle cell apoptosis " NARROW [GOC:dph, GOC:rl, GOC:tb] +synonym: "negative regulation of cardiac muscle cell apoptosis" NARROW [] +is_a: GO:0010664 ! negative regulation of striated muscle cell apoptotic process +is_a: GO:0010665 ! regulation of cardiac muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010659 ! cardiac muscle cell apoptotic process +relationship: negatively_regulates GO:0010659 ! cardiac muscle cell apoptotic process + +[Term] +id: GO:0010675 +name: regulation of cellular carbohydrate metabolic process +namespace: biological_process +def: "Any process that modulates the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:dph, GOC:tb] +is_a: GO:0006109 ! regulation of carbohydrate metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044262 ! cellular carbohydrate metabolic process +relationship: regulates GO:0044262 ! cellular carbohydrate metabolic process + +[Term] +id: GO:0010712 +name: regulation of collagen metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." [GOC:dph, GOC:tb] +synonym: "regulation of collagen metabolism" EXACT [GOC:dph, GOC:tb] +is_a: GO:0044246 ! regulation of multicellular organismal metabolic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032963 ! collagen metabolic process +relationship: regulates GO:0032963 ! collagen metabolic process + +[Term] +id: GO:0010714 +name: positive regulation of collagen metabolic process +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." [GOC:dph, GOC:tb] +synonym: "positive regulation of collagen metabolism" EXACT [GOC:dph, GOC:tb] +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0010712 ! regulation of collagen metabolic process +is_a: GO:0044253 ! positive regulation of multicellular organismal metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032963 ! collagen metabolic process +relationship: positively_regulates GO:0032963 ! collagen metabolic process + +[Term] +id: GO:0010717 +name: regulation of epithelial to mesenchymal transition +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:2000736 ! regulation of stem cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001837 ! epithelial to mesenchymal transition +relationship: regulates GO:0001837 ! epithelial to mesenchymal transition + +[Term] +id: GO:0010718 +name: positive regulation of epithelial to mesenchymal transition +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0010717 ! regulation of epithelial to mesenchymal transition +is_a: GO:0010770 ! positive regulation of cell morphogenesis involved in differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001837 ! epithelial to mesenchymal transition +relationship: positively_regulates GO:0001837 ! epithelial to mesenchymal transition + +[Term] +id: GO:0010719 +name: negative regulation of epithelial to mesenchymal transition +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0010717 ! regulation of epithelial to mesenchymal transition +is_a: GO:0010771 ! negative regulation of cell morphogenesis involved in differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001837 ! epithelial to mesenchymal transition +relationship: negatively_regulates GO:0001837 ! epithelial to mesenchymal transition + +[Term] +id: GO:0010720 +name: positive regulation of cell development +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048468 ! cell development +relationship: positively_regulates GO:0048468 ! cell development + +[Term] +id: GO:0010721 +name: negative regulation of cell development +namespace: biological_process +def: "Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048468 ! cell development +relationship: negatively_regulates GO:0048468 ! cell development + +[Term] +id: GO:0010769 +name: regulation of cell morphogenesis involved in differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." [GOC:dph, GOC:tb] +is_a: GO:0022604 ! regulation of cell morphogenesis +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000904 ! cell morphogenesis involved in differentiation +relationship: regulates GO:0000904 ! cell morphogenesis involved in differentiation + +[Term] +id: GO:0010770 +name: positive regulation of cell morphogenesis involved in differentiation +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." [GOC:dph, GOC:tb] +is_a: GO:0010720 ! positive regulation of cell development +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0000904 ! cell morphogenesis involved in differentiation +relationship: positively_regulates GO:0000904 ! cell morphogenesis involved in differentiation + +[Term] +id: GO:0010771 +name: negative regulation of cell morphogenesis involved in differentiation +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." [GOC:dph, GOC:tb] +is_a: GO:0010721 ! negative regulation of cell development +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:0051129 ! negative regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0000904 ! cell morphogenesis involved in differentiation +relationship: negatively_regulates GO:0000904 ! cell morphogenesis involved in differentiation + +[Term] +id: GO:0010799 +name: regulation of peptidyl-threonine phosphorylation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine." [GOC:dph, GOC:tb] +is_a: GO:0001932 ! regulation of protein phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0018107 ! peptidyl-threonine phosphorylation +relationship: regulates GO:0018107 ! peptidyl-threonine phosphorylation + +[Term] +id: GO:0010800 +name: positive regulation of peptidyl-threonine phosphorylation +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine." [GOC:dph, GOC:tb] +is_a: GO:0001934 ! positive regulation of protein phosphorylation +is_a: GO:0010799 ! regulation of peptidyl-threonine phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0018107 ! peptidyl-threonine phosphorylation +relationship: positively_regulates GO:0018107 ! peptidyl-threonine phosphorylation + +[Term] +id: GO:0010810 +name: regulation of cell-substrate adhesion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules." [GOC:dph, GOC:pf, GOC:tb] +is_a: GO:0030155 ! regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031589 ! cell-substrate adhesion +relationship: regulates GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0010811 +name: positive regulation of cell-substrate adhesion +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules." [GOC:dph, GOC:pf, GOC:tb] +is_a: GO:0010810 ! regulation of cell-substrate adhesion +is_a: GO:0045785 ! positive regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031589 ! cell-substrate adhesion +relationship: positively_regulates GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0010812 +name: negative regulation of cell-substrate adhesion +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules." [GOC:dph, GOC:pf, GOC:tb] +is_a: GO:0007162 ! negative regulation of cell adhesion +is_a: GO:0010810 ! regulation of cell-substrate adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0031589 ! cell-substrate adhesion +relationship: negatively_regulates GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0010817 +name: regulation of hormone levels +namespace: biological_process +def: "Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0065008 ! regulation of biological quality + +[Term] +id: GO:0010818 +name: T cell chemotaxis +namespace: biological_process +def: "The directed movement of a T cell in response to an external stimulus. A T cell is a type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." [GOC:dph, GOC:tb] +synonym: "T-cell chemotaxis" EXACT [CL:0000084] +is_a: GO:0048247 ! lymphocyte chemotaxis +is_a: GO:0072678 ! T cell migration + +[Term] +id: GO:0010819 +name: regulation of T cell chemotaxis +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus." [GOC:dph, GOC:tb] +is_a: GO:1901623 ! regulation of lymphocyte chemotaxis +is_a: GO:2000404 ! regulation of T cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010818 ! T cell chemotaxis +relationship: regulates GO:0010818 ! T cell chemotaxis + +[Term] +id: GO:0010820 +name: positive regulation of T cell chemotaxis +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0002690 ! positive regulation of leukocyte chemotaxis +is_a: GO:0010819 ! regulation of T cell chemotaxis +is_a: GO:2000406 ! positive regulation of T cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010818 ! T cell chemotaxis +relationship: positively_regulates GO:0010818 ! T cell chemotaxis + +[Term] +id: GO:0010876 +name: lipid localization +namespace: biological_process +def: "Any process in which a lipid is transported to, or maintained in, a specific location." [GOC:BHF, GOC:dph, GOC:tb] +synonym: "lipid localisation" EXACT [GOC:mah] +is_a: GO:0033036 ! macromolecule localization + +[Term] +id: GO:0010893 +name: positive regulation of steroid biosynthetic process +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." [GOC:tb] +is_a: GO:0045940 ! positive regulation of steroid metabolic process +is_a: GO:0046889 ! positive regulation of lipid biosynthetic process +is_a: GO:0050810 ! regulation of steroid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006694 ! steroid biosynthetic process +relationship: positively_regulates GO:0006694 ! steroid biosynthetic process + +[Term] +id: GO:0010894 +name: negative regulation of steroid biosynthetic process +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." [GOC:BHF, GOC:tb] +is_a: GO:0045939 ! negative regulation of steroid metabolic process +is_a: GO:0050810 ! regulation of steroid biosynthetic process +is_a: GO:0051055 ! negative regulation of lipid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006694 ! steroid biosynthetic process +relationship: negatively_regulates GO:0006694 ! steroid biosynthetic process + +[Term] +id: GO:0010906 +name: regulation of glucose metabolic process +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose." [GOC:BHF, GOC:tb] +synonym: "regulation of glucose metabolism" EXACT [GOC:tb] +is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006006 ! glucose metabolic process +relationship: regulates GO:0006006 ! glucose metabolic process + +[Term] +id: GO:0010908 +name: regulation of heparan sulfate proteoglycan biosynthetic process +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis. Heparan sulfate proteoglycan biosynthetic processes are the chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues." [GOC:dph, GOC:tb] +is_a: GO:0010559 ! regulation of glycoprotein biosynthetic process +is_a: GO:0042762 ! regulation of sulfur metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process +relationship: regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process + +[Term] +id: GO:0010909 +name: positive regulation of heparan sulfate proteoglycan biosynthetic process +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis. Heparan sulfate proteoglycan biosynthetic processes are the chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues." [GOC:dph, GOC:tb] +is_a: GO:0010560 ! positive regulation of glycoprotein biosynthetic process +is_a: GO:0010908 ! regulation of heparan sulfate proteoglycan biosynthetic process +is_a: GO:0051176 ! positive regulation of sulfur metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process +relationship: positively_regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process + +[Term] +id: GO:0010915 +name: regulation of very-low-density lipoprotein particle clearance +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of very-low-density lipoprotein particle clearance. Very-low-density lipoprotein particle clearance is the process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." [GOC:BHF, GOC:dph, GOC:tb] +synonym: "regulation of VLDL clearance" EXACT [GOC:dph, GOC:tb] +synonym: "regulation of VLDL particle clearance" EXACT [GOC:dph, GOC:tb] +is_a: GO:0010984 ! regulation of lipoprotein particle clearance +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034447 ! very-low-density lipoprotein particle clearance +relationship: regulates GO:0034447 ! very-low-density lipoprotein particle clearance + +[Term] +id: GO:0010916 +name: negative regulation of very-low-density lipoprotein particle clearance +namespace: biological_process +def: "Any process that decreases the rate, frequency or extent of very-low-density lipoprotein particle clearance. Very-low-density lipoprotein particle clearance is the process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." [GOC:BHF, GOC:dph, GOC:tb] +synonym: "negative regulation of VLDL clearance" EXACT [GOC:dph, GOC:tb] +synonym: "negative regulation of VLDL particle clearance" EXACT [GOC:dph, GOC:tb] +is_a: GO:0010915 ! regulation of very-low-density lipoprotein particle clearance +is_a: GO:0010985 ! negative regulation of lipoprotein particle clearance +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0034447 ! very-low-density lipoprotein particle clearance +relationship: negatively_regulates GO:0034447 ! very-low-density lipoprotein particle clearance + +[Term] +id: GO:0010927 +name: cellular component assembly involved in morphogenesis +namespace: biological_process +def: "The cellular component assembly that is part of the initial shaping of the component during its developmental progression." [GOC:dph, GOC:tb] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis +relationship: part_of GO:0032989 ! cellular component morphogenesis + +[Term] +id: GO:0010934 +name: macrophage cytokine production +namespace: biological_process +def: "The appearance of a macrophage cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb] +is_a: GO:0061082 ! myeloid leukocyte cytokine production + +[Term] +id: GO:0010935 +name: regulation of macrophage cytokine production +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:BHF, GOC:rl] +is_a: GO:0002718 ! regulation of cytokine production involved in immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010934 ! macrophage cytokine production +relationship: regulates GO:0010934 ! macrophage cytokine production + +[Term] +id: GO:0010941 +name: regulation of cell death +namespace: biological_process +def: "Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:dph, GOC:tb] +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008219 ! cell death +relationship: regulates GO:0008219 ! cell death + +[Term] +id: GO:0010942 +name: positive regulation of cell death +namespace: biological_process +def: "Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:dph, GOC:tb] +is_a: GO:0010941 ! regulation of cell death +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008219 ! cell death +relationship: positively_regulates GO:0008219 ! cell death + +[Term] +id: GO:0010950 +name: positive regulation of endopeptidase activity +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins." [GOC:dph, GOC:tb] +is_a: GO:0010952 ! positive regulation of peptidase activity +is_a: GO:0052548 ! regulation of endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004175 ! endopeptidase activity +relationship: positively_regulates GO:0004175 ! endopeptidase activity +created_by: tanyaberardini +creation_date: 2009-04-27T11:45:39Z + +[Term] +id: GO:0010951 +name: negative regulation of endopeptidase activity +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins." [GOC:dph, GOC:tb] +is_a: GO:0010466 ! negative regulation of peptidase activity +is_a: GO:0052548 ! regulation of endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004175 ! endopeptidase activity +relationship: negatively_regulates GO:0004175 ! endopeptidase activity +created_by: tanyaberardini +creation_date: 2009-04-27T11:47:01Z + +[Term] +id: GO:0010952 +name: positive regulation of peptidase activity +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins." [GOC:dph, GOC:tb] +is_a: GO:0051345 ! positive regulation of hydrolase activity +is_a: GO:0052547 ! regulation of peptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008233 ! peptidase activity +relationship: positively_regulates GO:0008233 ! peptidase activity +created_by: tanyaberardini +creation_date: 2009-04-27T11:54:32Z + +[Term] +id: GO:0010959 +name: regulation of metal ion transport +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of metal ion transport. Metal ion transport is the directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb] +is_a: GO:0043269 ! regulation of ion transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030001 ! metal ion transport +relationship: regulates GO:0030001 ! metal ion transport +created_by: tanyaberardini +creation_date: 2009-05-06T11:40:55Z + +[Term] +id: GO:0010975 +name: regulation of neuron projection development +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites)." [GOC:dph, GOC:tb] +synonym: "regulation of neurite biosynthesis" NARROW [GOC:mah] +synonym: "regulation of neurite development" NARROW [GOC:mah] +synonym: "regulation of neurite formation" NARROW [GOC:mah] +synonym: "regulation of neurite growth" NARROW [GOC:mah] +is_a: GO:0031344 ! regulation of cell projection organization +is_a: GO:0045664 ! regulation of neuron differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031175 ! neuron projection development +relationship: regulates GO:0031175 ! neuron projection development +created_by: tanyaberardini +creation_date: 2009-06-01T10:44:45Z + +[Term] +id: GO:0010976 +name: positive regulation of neuron projection development +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites)." [GOC:dph, GOC:tb] +synonym: "positive regulation of neurite biosynthesis" NARROW [GOC:mah] +synonym: "positive regulation of neurite development" NARROW [GOC:mah] +synonym: "positive regulation of neurite formation" NARROW [GOC:mah] +synonym: "positive regulation of neurite growth" NARROW [GOC:mah] +is_a: GO:0010975 ! regulation of neuron projection development +is_a: GO:0031346 ! positive regulation of cell projection organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031175 ! neuron projection development +relationship: positively_regulates GO:0031175 ! neuron projection development +created_by: tanyaberardini +creation_date: 2009-06-01T10:46:44Z + +[Term] +id: GO:0010977 +name: negative regulation of neuron projection development +namespace: biological_process +def: "Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites)." [GOC:dph, GOC:tb] +synonym: "growth cone collapse" RELATED [GOC:pr] +synonym: "negative regulation of neurite biosynthesis" NARROW [GOC:mah] +synonym: "negative regulation of neurite development" NARROW [GOC:mah] +synonym: "negative regulation of neurite formation" NARROW [GOC:mah] +synonym: "negative regulation of neurite growth" NARROW [GOC:mah] +is_a: GO:0010975 ! regulation of neuron projection development +is_a: GO:0031345 ! negative regulation of cell projection organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0031175 ! neuron projection development +relationship: negatively_regulates GO:0031175 ! neuron projection development +created_by: tanyaberardini +creation_date: 2009-06-01T10:47:42Z + +[Term] +id: GO:0010984 +name: regulation of lipoprotein particle clearance +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of lipoprotein particle clearance. Lipoprotein particle clearance is the process in which a lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034381 ! plasma lipoprotein particle clearance +relationship: regulates GO:0034381 ! plasma lipoprotein particle clearance +created_by: tanyaberardini +creation_date: 2009-06-01T12:05:12Z + +[Term] +id: GO:0010985 +name: negative regulation of lipoprotein particle clearance +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of lipoprotein particle clearance. Lipoprotein particle clearance is the process in which a lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0010984 ! regulation of lipoprotein particle clearance +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0034381 ! plasma lipoprotein particle clearance +relationship: negatively_regulates GO:0034381 ! plasma lipoprotein particle clearance +created_by: tanyaberardini +creation_date: 2009-06-01T12:06:59Z + +[Term] +id: GO:0010996 +name: response to auditory stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an auditory stimulus." [GOC:BHF, GOC:dph, GOC:sl, GOC:tb] +synonym: "response to sound" EXACT [GOC:dph, GOC:sl, GOC:tb] +synonym: "response to sound stimulus" EXACT [GOC:dph, GOC:tb] +is_a: GO:0009612 ! response to mechanical stimulus +created_by: tanyaberardini +creation_date: 2009-06-10T11:09:38Z + +[Term] +id: GO:0012501 +name: programmed cell death +namespace: biological_process +alt_id: GO:0016244 +def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] +comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. +synonym: "caspase-independent apoptosis" RELATED [] +synonym: "caspase-independent cell death" NARROW [] +synonym: "non-apoptotic programmed cell death" NARROW [] +synonym: "nonapoptotic programmed cell death" NARROW [] +synonym: "PCD" EXACT [] +synonym: "regulated cell death" RELATED [] +xref: Wikipedia:Programmed_cell_death +is_a: GO:0008219 ! cell death + +[Term] +id: GO:0012505 +name: endomembrane system +namespace: cellular_component +def: "A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles." [GOC:lh] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_yeast +xref: Wikipedia:Endomembrane_system +is_a: GO:0044464 ! cell part +relationship: has_part GO:0005773 ! vacuole +relationship: has_part GO:0005886 ! plasma membrane + +[Term] +id: GO:0014003 +name: oligodendrocyte development +namespace: biological_process +def: "The process aimed at the progression of an oligodendrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An oligodendrocyte is a type of glial cell involved in myelinating the axons in the central nervous system." [GOC:dgh, GOC:ef] +synonym: "oligodendrocyte cell development" EXACT [] +is_a: GO:0021782 ! glial cell development +relationship: part_of GO:0048709 ! oligodendrocyte differentiation + +[Term] +id: GO:0014009 +name: glial cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of glial cells by cell division, resulting in the expansion of their population. Glial cells exist throughout the nervous system, and include Schwann cells, astrocytes, and oligodendrocytes among others." [GOC:ef, ISBN:0878932585] +synonym: "glia proliferation" EXACT [] +is_a: GO:0008283 ! cell proliferation +relationship: part_of GO:0042063 ! gliogenesis + +[Term] +id: GO:0014010 +name: Schwann cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of Schwann cells, resulting in the expansion of their population. Schwann cells are a type of glial cell in the peripheral nervous system." [GOC:ef, ISBN:0878932585] +is_a: GO:0014009 ! glial cell proliferation + +[Term] +id: GO:0014013 +name: regulation of gliogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of gliogenesis, the formation of mature glia." [GOC:ef] +is_a: GO:0050767 ! regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042063 ! gliogenesis +relationship: regulates GO:0042063 ! gliogenesis + +[Term] +id: GO:0014014 +name: negative regulation of gliogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of gliogenesis, the formation of mature glia." [GOC:ef] +synonym: "down regulation of gliogenesis" EXACT [] +synonym: "down-regulation of gliogenesis" EXACT [] +synonym: "downregulation of gliogenesis" EXACT [] +synonym: "inhibition of gliogenesis" NARROW [] +is_a: GO:0014013 ! regulation of gliogenesis +is_a: GO:0050768 ! negative regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042063 ! gliogenesis +relationship: negatively_regulates GO:0042063 ! gliogenesis + +[Term] +id: GO:0014020 +name: primary neural tube formation +namespace: biological_process +def: "The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube." [GOC:ef, ISBN:0878932585] +synonym: "primary neural tube morphogenesis" EXACT [GOC:dph] +synonym: "primary neurulation" EXACT [] +is_a: GO:0001838 ! embryonic epithelial tube formation +relationship: part_of GO:0001841 ! neural tube formation + +[Term] +id: GO:0014029 +name: neural crest formation +namespace: biological_process +def: "The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes." [GOC:dh, GOC:ef] +is_a: GO:0001837 ! epithelial to mesenchymal transition +relationship: part_of GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0014031 +name: mesenchymal cell development +namespace: biological_process +def: "The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." [GOC:dh, GOC:ef] +is_a: GO:0048864 ! stem cell development +relationship: part_of GO:0048762 ! mesenchymal cell differentiation + +[Term] +id: GO:0014032 +name: neural crest cell development +namespace: biological_process +def: "The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." [GOC:dh, GOC:ef] +is_a: GO:0014031 ! mesenchymal cell development +relationship: part_of GO:0014033 ! neural crest cell differentiation + +[Term] +id: GO:0014033 +name: neural crest cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell." [GOC:dh, GOC:ef] +is_a: GO:0048762 ! mesenchymal cell differentiation + +[Term] +id: GO:0014034 +name: neural crest cell fate commitment +namespace: biological_process +def: "The process in which a cell becomes committed to become a neural crest cell." [GOC:dh, GOC:ef] +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0014029 ! neural crest formation +relationship: part_of GO:0014033 ! neural crest cell differentiation + +[Term] +id: GO:0014045 +name: establishment of endothelial blood-brain barrier +namespace: biological_process +def: "Establishment of the endothelial barrier between the blood and the brain. The endothelial cells in the brain capillaries are packed tightly together preventing the passage of most molecules from the blood into the brain. Only lipid soluble molecules or those that are actively transported can pass through the blood-brain barrier." [GOC:dgh, GOC:dph, GOC:sart] +synonym: "establishment of endothelial BBB" EXACT [PMID:20080302] +synonym: "establishment of endothelial blood/brain barrier" EXACT [] +is_a: GO:0060856 ! establishment of blood-brain barrier +is_a: GO:0061028 ! establishment of endothelial barrier +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0014069 +name: postsynaptic density +namespace: cellular_component +def: "The postsynaptic density is a region that lies adjacent to the cytoplasmic face of the postsynaptic membrane at excitatory synapse. It forms a disc that consists of a range of proteins with different functions, some of which contact the cytoplasmic domains of ion channels in the postsynaptic membrane. The proteins making up the disc include receptors, and structural proteins linked to the actin cytoskeleton. They also include signalling machinery, such as protein kinases and phosphatases. The postsynaptic density may be part of a neuron or a muscle cell or a glial cell." [GOC:BHF, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density] +synonym: "post synaptic density" EXACT [] +synonym: "post-synaptic density" EXACT [] +xref: NIF_Subcellular:sao1196688972 +xref: Wikipedia:Postsynaptic_density +is_a: GO:0044430 ! cytoskeletal part +is_a: GO:0044456 ! synapse part + +[Term] +id: GO:0014070 +name: response to organic cyclic compound +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus." [CHEBI:33832, GOC:ef] +synonym: "response to organic cyclic substance" EXACT [GOC:mah] +is_a: GO:0010033 ! response to organic substance + +[Term] +id: GO:0014704 +name: intercalated disc +namespace: cellular_component +def: "A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells." [GOC:mtg_muscle, PMID:11732910] +synonym: "intercalated disk" EXACT [] +xref: Wikipedia:Intercalated_disc +is_a: GO:0044291 ! cell-cell contact zone + +[Term] +id: GO:0014706 +name: striated muscle tissue development +namespace: biological_process +def: "The process whose specific outcome is the progression of a striated muscle over time, from its formation to the mature structure. Striated muscle contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. Skeletal muscle myoblasts fuse to form myotubes and eventually multinucleated muscle fibers. The fusion of cardiac cells is very rare and can only form binucleate cells." [CL:0000737, GOC:dph, GOC:mtg_muscle] +is_a: GO:0060537 ! muscle tissue development + +[Term] +id: GO:0014719 +name: satellite cell activation +namespace: biological_process +def: "A change in the morphology or behavior of a satellite cell resulting from exposure to an activating factor such as a cellular or soluble ligand. Satellite cells are quiescent cells that are located between the basal lamina and the plasmalemma of the muscle fiber, which are the main contributors to postnatal muscle growth. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage." [GOC:mtg_muscle] +is_a: GO:0001775 ! cell activation + +[Term] +id: GO:0014834 +name: satellite cell maintenance involved in skeletal muscle regeneration +namespace: biological_process +def: "The process essential to maintain a ready source of satellite cells. It consists of the return of activated satellite cells to a quiescent state after proliferation to replenish the satellite cell pool. Satellite cells are quiescent cells that are located between the basal lamina and the plasmalemma of the muscle fiber, which are the main contributors to postnatal muscle growth. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage." [GOC:dph, GOC:ef, GOC:mtg_muscle, GOC:tb, PMID:16607119] +synonym: "satellite cell compartment self-renewal involved in skeletal muscle regeneration" EXACT [GOC:dph, GOC:tb] +synonym: "satellite cell population maintenance" EXACT [] +synonym: "satellite cell self-renewal" BROAD [] +is_a: GO:0035019 ! somatic stem cell maintenance +relationship: part_of GO:0043403 ! skeletal muscle tissue regeneration + +[Term] +id: GO:0014855 +name: striated muscle cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of striated muscle cells, resulting in the expansion of a cell population. Striated muscles contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle." [CL:0000737, GOC:ef, GOC:mtg_muscle] +is_a: GO:0033002 ! muscle cell proliferation + +[Term] +id: GO:0014902 +name: myotube differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." [GOC:mtg_muscle] +is_a: GO:0051146 ! striated muscle cell differentiation + +[Term] +id: GO:0015012 +name: heparan sulfate proteoglycan biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues; the former are a mixture of sulfated and nonsulfated D-glucuronic acid and L-iduronic acid; the L-iduronic acid is either sulfated or acetylated on its amino group as well as being sulfated on one of its hydroxyl groups; heparan sulfate chains are covalently linked to peptidyl-serine by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylosyl to serine residues." [GOC:mah, ISBN:0198506732, ISBN:0198547684, RESID:AA0210] +subset: gosubset_prok +synonym: "heparan sulfate proteoglycan anabolism" EXACT [] +synonym: "heparan sulfate proteoglycan biosynthesis" EXACT [] +synonym: "heparan sulfate proteoglycan formation" EXACT [] +synonym: "heparan sulfate proteoglycan synthesis" EXACT [] +synonym: "heparan sulphate proteoglycan biosynthesis" EXACT [] +synonym: "heparan sulphate proteoglycan biosynthetic process" EXACT [] +synonym: "heparin proteoglycan biosynthetic process" RELATED [] +xref: RESID:AA0210 +is_a: GO:0030166 ! proteoglycan biosynthetic process +is_a: GO:0030201 ! heparan sulfate proteoglycan metabolic process +is_a: GO:0044272 ! sulfur compound biosynthetic process +is_a: GO:0044711 ! single-organism biosynthetic process + +[Term] +id: GO:0015026 +name: coreceptor activity +namespace: molecular_function +alt_id: GO:0015027 +alt_id: GO:0015028 +def: "Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity." [GOC:go_curators] +synonym: "coreceptor, insoluble ligand activity" RELATED [GOC:mah] +synonym: "coreceptor, soluble ligand activity" RELATED [GOC:mah] +is_a: GO:0038023 ! signaling receptor activity + +[Term] +id: GO:0015031 +name: protein transport +namespace: biological_process +alt_id: GO:0015831 +def: "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +subset: goslim_pir +subset: gosubset_prok +synonym: "enzyme transport" NARROW [] +is_a: GO:0045184 ! establishment of protein localization +is_a: GO:0071702 ! organic substance transport + +[Term] +id: GO:0015630 +name: microtubule cytoskeleton +namespace: cellular_component +def: "The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins." [GOC:jl, ISBN:0395825172] +subset: goslim_aspergillus +is_a: GO:0005856 ! cytoskeleton + +[Term] +id: GO:0015833 +name: peptide transport +namespace: biological_process +def: "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0042886 ! amide transport +is_a: GO:0071702 ! organic substance transport + +[Term] +id: GO:0015850 +name: organic hydroxy compound transport +namespace: biological_process +def: "The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom." [CHEBI:33822, GOC:ai] +subset: gosubset_prok +synonym: "organic alcohol transport" EXACT [CHEBI:33822] +is_a: GO:0044765 ! single-organism transport +is_a: GO:0071702 ! organic substance transport + +[Term] +id: GO:0015918 +name: sterol transport +namespace: biological_process +def: "The directed movement of sterols into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:ai] +xref: Reactome:REACT_103237 "Trafficking of dietary sterols, Taeniopygia guttata" +xref: Reactome:REACT_105697 "Trafficking of dietary sterols, Danio rerio" +xref: Reactome:REACT_111982 "Trafficking of dietary sterols, Plasmodium falciparum" +xref: Reactome:REACT_114213 "Trafficking of dietary sterols, Mycobacterium tuberculosis" +xref: Reactome:REACT_13781 "Trafficking of dietary sterols, Homo sapiens" +xref: Reactome:REACT_28837 "Trafficking of dietary sterols, Bos taurus" +xref: Reactome:REACT_28881 "Trafficking of dietary sterols, Caenorhabditis elegans" +xref: Reactome:REACT_33323 "Trafficking of dietary sterols, Dictyostelium discoideum" +xref: Reactome:REACT_49006 "Trafficking of dietary sterols, Rattus norvegicus" +xref: Reactome:REACT_81755 "Trafficking of dietary sterols, Sus scrofa" +xref: Reactome:REACT_83389 "Trafficking of dietary sterols, Canis familiaris" +xref: Reactome:REACT_85624 "Trafficking of dietary sterols, Gallus gallus" +xref: Reactome:REACT_90788 "Trafficking of dietary sterols, Saccharomyces cerevisiae" +xref: Reactome:REACT_91234 "Trafficking of dietary sterols, Oryza sativa" +xref: Reactome:REACT_93019 "Trafficking of dietary sterols, Drosophila melanogaster" +xref: Reactome:REACT_93344 "Trafficking of dietary sterols, Mus musculus" +xref: Reactome:REACT_94184 "Trafficking of dietary sterols, Xenopus tropicalis" +xref: Reactome:REACT_96633 "Trafficking of dietary sterols, Arabidopsis thaliana" +is_a: GO:0006869 ! lipid transport +is_a: GO:0015850 ! organic hydroxy compound transport + +[Term] +id: GO:0016020 +name: membrane +namespace: cellular_component +def: "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:mah, ISBN:0815316194] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +xref: Wikipedia:Biological_membrane +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0016021 +name: integral component of membrane +namespace: cellular_component +def: "The component of a membrane consisting of gene products and protein complexes that have some part that penetrates at least one leaflet of the membrane bilayer. This component includes gene products that are buried in the bilayer with no exposure outside the bilayer." [GOC:dos, GOC:go_curators] +subset: gosubset_prok +synonym: "integral to membrane" NARROW [] +synonym: "transmembrane" RELATED [GOC:mah] +xref: Wikipedia:Transmembrane_protein +is_a: GO:0044425 ! membrane part +relationship: part_of GO:0031224 ! intrinsic component of membrane + +[Term] +id: GO:0016023 +name: cytoplasmic membrane-bounded vesicle +namespace: cellular_component +def: "A membrane-bounded vesicle found in the cytoplasm of the cell." [GOC:ai, GOC:mah] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +synonym: "cytoplasmic membrane bounded vesicle" EXACT [] +synonym: "cytoplasmic membrane-enclosed vesicle" EXACT [] +is_a: GO:0031410 ! cytoplasmic vesicle +is_a: GO:0031988 ! membrane-bounded vesicle +is_a: GO:0043231 ! intracellular membrane-bounded organelle +intersection_of: GO:0031988 ! membrane-bounded vesicle +intersection_of: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0016043 +name: cellular component organization +namespace: biological_process +alt_id: GO:0044235 +alt_id: GO:0071842 +def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "cell organisation" EXACT [] +synonym: "cell organization and biogenesis" RELATED [GOC:mah] +synonym: "cellular component organisation at cellular level" EXACT [GOC:mah] +synonym: "cellular component organisation in other organism" EXACT [GOC:mah] +synonym: "cellular component organization at cellular level" EXACT [] +synonym: "cellular component organization in other organism" EXACT [] +is_a: GO:0071840 ! cellular component organization or biogenesis + +[Term] +id: GO:0016049 +name: cell growth +namespace: biological_process +alt_id: GO:0048591 +def: "The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai] +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "cell expansion" RELATED [] +synonym: "cellular growth" EXACT [] +synonym: "growth of cell" EXACT [] +synonym: "metabolic process resulting in cell growth" RELATED [] +synonym: "metabolism resulting in cell growth" RELATED [] +synonym: "non-developmental cell growth" RELATED [GOC:mah] +synonym: "non-developmental growth of a unicellular organism" RELATED [GOC:mah] +is_a: GO:0040007 ! growth +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0016052 +name: carbohydrate catabolic process +namespace: biological_process +alt_id: GO:0006095 +def: "The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [ISBN:0198506732] +subset: gosubset_prok +synonym: "carbohydrate breakdown" EXACT [] +synonym: "carbohydrate catabolism" EXACT [] +synonym: "carbohydrate degradation" EXACT [] +synonym: "catabolic carbohydrate metabolic process" EXACT [] +synonym: "catabolic carbohydrate metabolism" EXACT [] +is_a: GO:0005975 ! carbohydrate metabolic process +is_a: GO:1901575 ! organic substance catabolic process + +[Term] +id: GO:0016055 +name: Wnt signaling pathway +namespace: biological_process +alt_id: GO:0007222 +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state." [GOC:dph, GOC:go_curators, PMID:11532397] +synonym: "frizzled signaling pathway" EXACT [] +synonym: "frizzled signalling pathway" EXACT [] +synonym: "Wg signaling pathway" EXACT [GOC:sart, PMID:8080429] +synonym: "Wg signalling pathway" EXACT [GOC:sart, PMID:8080429] +synonym: "Wingless signaling pathway" EXACT [GOC:sart, PMID:8080429] +synonym: "Wingless signalling pathway" EXACT [GOC:sart, PMID:8080429] +synonym: "Wnt receptor signaling pathway" EXACT [GOC:signaling] +synonym: "Wnt receptor signalling pathway" EXACT [] +synonym: "Wnt-activated signaling pathway" RELATED [] +is_a: GO:0007166 ! cell surface receptor signaling pathway + +[Term] +id: GO:0016064 +name: immunoglobulin mediated immune response +namespace: biological_process +def: "An immune response mediated by immunoglobulins, whether cell-bound or in solution." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was improved by GO_REF:0000022. It was renamed and redefined. +synonym: "antibody-mediated immune response" EXACT [] +is_a: GO:0019724 ! B cell mediated immunity + +[Term] +id: GO:0016070 +name: RNA metabolic process +namespace: biological_process +def: "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_metagenomics +subset: goslim_pir +subset: gosubset_prok +synonym: "RNA metabolism" EXACT [] +xref: Reactome:REACT_107259 "Metabolism of RNA, Sus scrofa" +xref: Reactome:REACT_107652 "Metabolism of RNA, Schizosaccharomyces pombe" +xref: Reactome:REACT_110289 "Metabolism of RNA, Danio rerio" +xref: Reactome:REACT_21257 "Metabolism of RNA, Homo sapiens" +xref: Reactome:REACT_30579 "Metabolism of RNA, Xenopus tropicalis" +xref: Reactome:REACT_31367 "Metabolism of RNA, Dictyostelium discoideum" +xref: Reactome:REACT_33720 "Metabolism of RNA, Plasmodium falciparum" +xref: Reactome:REACT_80071 "Metabolism of RNA, Caenorhabditis elegans" +xref: Reactome:REACT_83630 "Metabolism of RNA, Taeniopygia guttata" +xref: Reactome:REACT_84169 "Metabolism of RNA, Canis familiaris" +xref: Reactome:REACT_85788 "Metabolism of RNA, Oryza sativa" +xref: Reactome:REACT_88316 "Metabolism of RNA, Mus musculus" +xref: Reactome:REACT_89992 "Metabolism of RNA, Saccharomyces cerevisiae" +xref: Reactome:REACT_91556 "Metabolism of RNA, Bos taurus" +xref: Reactome:REACT_92152 "Metabolism of RNA, Drosophila melanogaster" +xref: Reactome:REACT_94876 "Metabolism of RNA, Arabidopsis thaliana" +xref: Reactome:REACT_99403 "Metabolism of RNA, Rattus norvegicus" +xref: Reactome:REACT_99885 "Metabolism of RNA, Gallus gallus" +is_a: GO:0044260 ! cellular macromolecule metabolic process +is_a: GO:0090304 ! nucleic acid metabolic process + +[Term] +id: GO:0016125 +name: sterol metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [ISBN:0198547684] +subset: gosubset_prok +synonym: "sterol metabolism" EXACT [] +is_a: GO:0006066 ! alcohol metabolic process +is_a: GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0016192 +name: vesicle-mediated transport +namespace: biological_process +alt_id: GO:0006899 +def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: gosubset_prok +synonym: "nonselective vesicle transport" NARROW [] +synonym: "protein sorting along secretory pathway" RELATED [] +synonym: "vesicle trafficking" RELATED [] +synonym: "vesicle transport" EXACT [] +synonym: "vesicular transport" EXACT [GOC:mah] +is_a: GO:0006810 ! transport + +[Term] +id: GO:0016197 +name: endosomal transport +namespace: biological_process +def: "The directed movement of substances into, out of or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." [ISBN:0198506732] +subset: goslim_yeast +synonym: "endosome transport" RELATED [GOC:bf] +xref: Reactome:REACT_27258 "Endosomal Sorting Complex Required For Transport (ESCRT), Homo sapiens" +is_a: GO:1902582 ! single-organism intracellular transport + +[Term] +id: GO:0016198 +name: axon choice point recognition +namespace: biological_process +def: "The recognition of molecules at a choice point by an axon growth cone; at a choice point the growth cone determines the direction of its future growth." [PMID:10218152] +is_a: GO:0008038 ! neuron recognition +relationship: part_of GO:0007411 ! axon guidance + +[Term] +id: GO:0016199 +name: axon midline choice point recognition +namespace: biological_process +def: "The recognition of molecules at the central nervous system midline choice point by an axon growth cone; this choice point determines whether the growth cone will cross the midline." [PMID:11376484] +is_a: GO:0016198 ! axon choice point recognition + +[Term] +id: GO:0016202 +name: regulation of striated muscle tissue development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of striated muscle development." [GOC:go_curators] +is_a: GO:0048634 ! regulation of muscle organ development +is_a: GO:1901861 ! regulation of muscle tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0014706 ! striated muscle tissue development +relationship: regulates GO:0014706 ! striated muscle tissue development + +[Term] +id: GO:0016265 +name: death +namespace: biological_process +def: "A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism." [GOC:mah, ISBN:0877797099] +comment: See also the biological process term 'apoptosis ; GO:0006915'. +subset: goslim_plant +subset: gosubset_prok +xref: Wikipedia:Death +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0016301 +name: kinase activity +namespace: molecular_function +def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] +comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "phosphokinase activity" EXACT [] +xref: Reactome:REACT_100073 "Activation of S6K1, Schizosaccharomyces pombe" +xref: Reactome:REACT_100078 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Canis familiaris" +xref: Reactome:REACT_100159 "Inactivation of Myt1 kinase, Mus musculus" +xref: Reactome:REACT_100260 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Taeniopygia guttata" +xref: Reactome:REACT_100298 "Phosphorylation of L1 by CK-II, Rattus norvegicus" +xref: Reactome:REACT_100305 "Regulation of NUDC by phosphorylation, Caenorhabditis elegans" +xref: Reactome:REACT_100311 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Canis familiaris" +xref: Reactome:REACT_100390 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Canis familiaris" +xref: Reactome:REACT_100465 "Phosphorylation and inactivation of eEF2K by activated S6K1, Dictyostelium discoideum" +xref: Reactome:REACT_100495 "Cdc6 protein is phosphorylated by CDK, Xenopus tropicalis" +xref: Reactome:REACT_100519 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Bos taurus" +xref: Reactome:REACT_100636 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Canis familiaris" +xref: Reactome:REACT_100637 "Phosphorylation of the Scc1:Cohesion Complex, Mus musculus" +xref: Reactome:REACT_101024 "Phosphorylation and inactivation of eEF2K by activated S6K1, Bos taurus" +xref: Reactome:REACT_101170 "Phosphorylation of APC component of the destruction complex, Drosophila melanogaster" +xref: Reactome:REACT_101303 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Mus musculus" +xref: Reactome:REACT_101431 "Mcm2-7 is phosphorylated by DDK, Danio rerio" +xref: Reactome:REACT_101543 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Canis familiaris" +xref: Reactome:REACT_101596 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Canis familiaris" +xref: Reactome:REACT_101638 "Phosphorylation and activation of CHK2 by ATM, Bos taurus" +xref: Reactome:REACT_101667 "Down Regulation of Emi1 through Phosphorylation of Emi1, Bos taurus" +xref: Reactome:REACT_101841 "Phosphorylation of Cdc25C at Ser216, Rattus norvegicus" +xref: Reactome:REACT_101862 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Xenopus tropicalis" +xref: Reactome:REACT_101914 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Xenopus tropicalis" +xref: Reactome:REACT_102090 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Taeniopygia guttata" +xref: Reactome:REACT_102093 "Phosphorylation and activation of eIF4G by activated S6K1, Danio rerio" +xref: Reactome:REACT_102154 "Autophosphorylation of PAK-2p34 in the activation loop, Schizosaccharomyces pombe" +xref: Reactome:REACT_102322 "RAF1 phosphorylates MEK2, Danio rerio" +xref: Reactome:REACT_102330 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Xenopus tropicalis" +xref: Reactome:REACT_102380 "Regulation of KIF23 (MKLP1) by phosphorylation, Xenopus tropicalis" +xref: Reactome:REACT_102475 "Inactivation of Myt1 kinase, Rattus norvegicus" +xref: Reactome:REACT_102499 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Canis familiaris" +xref: Reactome:REACT_102552 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Canis familiaris" +xref: Reactome:REACT_102607 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Drosophila melanogaster" +xref: Reactome:REACT_102711 "Phosphorylation of L1 by CK-II, Caenorhabditis elegans" +xref: Reactome:REACT_102729 "RAF1 phosphorylates MEK1, Xenopus tropicalis" +xref: Reactome:REACT_102817 "Phosphorylation of L1 by ERK, Mus musculus" +xref: Reactome:REACT_102887 "Mcm2-7 is phosphorylated by DDK, Rattus norvegicus" +xref: Reactome:REACT_102908 "Phosphorylation of the Scc1:Cohesion Complex, Rattus norvegicus" +xref: Reactome:REACT_102915 "Activation of S6K1, Arabidopsis thaliana" +xref: Reactome:REACT_103060 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Arabidopsis thaliana" +xref: Reactome:REACT_103291 "Phosphorylation of complexed TSC2 by PKB, Drosophila melanogaster" +xref: Reactome:REACT_103327 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Rattus norvegicus" +xref: Reactome:REACT_103359 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Danio rerio" +xref: Reactome:REACT_103468 "Activation of Cdc25C, Drosophila melanogaster" +xref: Reactome:REACT_103691 "Phosphorylation of COP1 at Ser-387 by ATM, Xenopus tropicalis" +xref: Reactome:REACT_103727 "Phosphorylation of NBS1 by ATM, Drosophila melanogaster" +xref: Reactome:REACT_103804 "Phosphorylation of AKT2 by PDK1, Canis familiaris" +xref: Reactome:REACT_103989 "Phosphorylation of NBS1 by ATM, Danio rerio" +xref: Reactome:REACT_104022 "Phosphorylation of p53 at ser-15 by ATM kinase, Xenopus tropicalis" +xref: Reactome:REACT_104044 "Phosphorylation and activation of Chk1 by ATM, Sus scrofa" +xref: Reactome:REACT_104109 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Danio rerio" +xref: Reactome:REACT_104209 "Activation of S6K1, Caenorhabditis elegans" +xref: Reactome:REACT_104323 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Rattus norvegicus" +xref: Reactome:REACT_104386 "Phosphorylation and activation of eIF4B by activated S6K1, Bos taurus" +xref: Reactome:REACT_104523 "Inactivation of Wee1 kinase, Bos taurus" +xref: Reactome:REACT_104644 "Regulation of KIF20A (MKL2) by phosphorylation, Bos taurus" +xref: Reactome:REACT_104687 "Phosphorylation of L1 by CK-II, Canis familiaris" +xref: Reactome:REACT_104730 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Schizosaccharomyces pombe" +xref: Reactome:REACT_104822 "Phosphorylation of COP1 at Ser-387 by ATM, Rattus norvegicus" +xref: Reactome:REACT_104837 "SOS phosphorylation and dissociation (SHC), Mus musculus" +xref: Reactome:REACT_104878 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Xenopus tropicalis" +xref: Reactome:REACT_105254 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Danio rerio" +xref: Reactome:REACT_105274 "Regulation of KIF20A (MKL2) by phosphorylation, Danio rerio" +xref: Reactome:REACT_105345 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Drosophila melanogaster" +xref: Reactome:REACT_105373 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Gallus gallus" +xref: Reactome:REACT_105503 "Phosphorylation of L1 by ERK, Bos taurus" +xref: Reactome:REACT_105561 "Phosphorylation of complexed TSC2 by PKB, Xenopus tropicalis" +xref: Reactome:REACT_105569 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Xenopus tropicalis" +xref: Reactome:REACT_105589 "Phosphorylation of p53 at ser-15 by ATM kinase, Canis familiaris" +xref: Reactome:REACT_105664 "Akt1 phosphorylates BAD protein, Rattus norvegicus" +xref: Reactome:REACT_105700 "Phosphorylation of PDE3B, Rattus norvegicus" +xref: Reactome:REACT_105971 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Xenopus tropicalis" +xref: Reactome:REACT_105976 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Xenopus tropicalis" +xref: Reactome:REACT_106075 "Akt1 phosphorylates BAD protein, Canis familiaris" +xref: Reactome:REACT_106144 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Xenopus tropicalis" +xref: Reactome:REACT_106159 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Canis familiaris" +xref: Reactome:REACT_106186 "Phosphorylation of TSC2 by PKB, Drosophila melanogaster" +xref: Reactome:REACT_106225 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Canis familiaris" +xref: Reactome:REACT_1063 "Phosphorylation of Wee1 kinase by Chk1, Schizosaccharomyces pombe" +xref: Reactome:REACT_106324 "Activation of Cdc25C, Mus musculus" +xref: Reactome:REACT_106383 "Phosphorylation of L1 by ERK, Xenopus tropicalis" +xref: Reactome:REACT_106411 "Phosphorylation and inactivation of eEF2K by activated S6K1, Gallus gallus" +xref: Reactome:REACT_106420 "Regulation of KIF23 (MKLP1) by phosphorylation, Taeniopygia guttata" +xref: Reactome:REACT_106500 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Drosophila melanogaster" +xref: Reactome:REACT_106505 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Rattus norvegicus" +xref: Reactome:REACT_106514 "Phosphorylation of NBS1 by ATM, Mus musculus" +xref: Reactome:REACT_106567 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Mus musculus" +xref: Reactome:REACT_106599 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Xenopus tropicalis" +xref: Reactome:REACT_106681 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Rattus norvegicus" +xref: Reactome:REACT_106722 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Xenopus tropicalis" +xref: Reactome:REACT_106738 "SOS phosphorylation and dissociation (IRS, Crk), Canis familiaris" +xref: Reactome:REACT_106897 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Danio rerio" +xref: Reactome:REACT_107009 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Arabidopsis thaliana" +xref: Reactome:REACT_107055 "Phosphorylation of Cdc25C at Ser216, Bos taurus" +xref: Reactome:REACT_107102 "SOS phosphorylation and dissociation (IRS, Crk), Danio rerio" +xref: Reactome:REACT_107243 "Phosphorylation of APC component of the destruction complex, Mus musculus" +xref: Reactome:REACT_107247 "Phosphorylation of TSC2 by PKB, Mus musculus" +xref: Reactome:REACT_107310 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Danio rerio" +xref: Reactome:REACT_107424 "Inactivation of Myt1 kinase, Canis familiaris" +xref: Reactome:REACT_107623 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Mus musculus" +xref: Reactome:REACT_107685 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Sus scrofa" +xref: Reactome:REACT_107732 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Danio rerio" +xref: Reactome:REACT_107736 "Phosphorylation of Cdc25C at Ser216, Sus scrofa" +xref: Reactome:REACT_107787 "Phosphorylation and activation of CHK2 by ATM, Drosophila melanogaster" +xref: Reactome:REACT_107849 "Phosphorylation of DLC2 by MAPK-8, Bos taurus" +xref: Reactome:REACT_107854 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Canis familiaris" +xref: Reactome:REACT_108002 "Plk1-mediated phosphorylation of Nlp, Bos taurus" +xref: Reactome:REACT_108096 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Rattus norvegicus" +xref: Reactome:REACT_108132 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Gallus gallus" +xref: Reactome:REACT_108362 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Mus musculus" +xref: Reactome:REACT_108394 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Danio rerio" +xref: Reactome:REACT_108520 "Phosphorylation and activation of Chk1 by ATM, Danio rerio" +xref: Reactome:REACT_108578 "Inactivation of Myt1 kinase, Xenopus tropicalis" +xref: Reactome:REACT_108776 "Free APC/C phosphorylated by Plk1, Taeniopygia guttata" +xref: Reactome:REACT_108840 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Canis familiaris" +xref: Reactome:REACT_108871 "Free APC/C phosphorylated by Plk1, Mus musculus" +xref: Reactome:REACT_108971 "Phosphorylation of Cyclin B1 in the CRS domain, Xenopus tropicalis" +xref: Reactome:REACT_108985 "Phosphorylation of cPLA2 by ERK-2, Gallus gallus" +xref: Reactome:REACT_109045 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Danio rerio" +xref: Reactome:REACT_109065 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Taeniopygia guttata" +xref: Reactome:REACT_109117 "Phosphorylation of 4E-BP1 by activated mTORC1, Dictyostelium discoideum" +xref: Reactome:REACT_109197 "SOS phosphorylation and dissociation (IRS), Mus musculus" +xref: Reactome:REACT_109244 "Inactivation of Myt1 kinase, Schizosaccharomyces pombe" +xref: Reactome:REACT_109260 "Free APC/C phosphorylated by Plk1, Xenopus tropicalis" +xref: Reactome:REACT_109264 "SOS phosphorylation and dissociation (IRS), Canis familiaris" +xref: Reactome:REACT_109331 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Drosophila melanogaster" +xref: Reactome:REACT_109367 "Phosphorylation of APC component of the destruction complex, Gallus gallus" +xref: Reactome:REACT_109549 "Regulation of KIF20A (MKL2) by phosphorylation, Xenopus tropicalis" +xref: Reactome:REACT_109641 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Sus scrofa" +xref: Reactome:REACT_109769 "Free APC/C phosphorylated by Plk1, Gallus gallus" +xref: Reactome:REACT_109799 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Mus musculus" +xref: Reactome:REACT_110175 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Mus musculus" +xref: Reactome:REACT_110254 "Phosphorylation of APC component of the destruction complex, Rattus norvegicus" +xref: Reactome:REACT_110296 "Phosphorylation and activation of Chk1 by ATM, Schizosaccharomyces pombe" +xref: Reactome:REACT_110351 "Phosphorylation and inactivation of eEF2K by activated S6K1, Canis familiaris" +xref: Reactome:REACT_110382 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Oryza sativa" +xref: Reactome:REACT_110530 "Down Regulation of Emi1 through Phosphorylation of Emi1, Mus musculus" +xref: Reactome:REACT_110583 "Phosphorylation of DLC2 by MAPK-8, Mus musculus" +xref: Reactome:REACT_110643 "Mcm2-7 is phosphorylated by DDK, Xenopus tropicalis" +xref: Reactome:REACT_110679 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Danio rerio" +xref: Reactome:REACT_110774 "Inactivation of Myt1 kinase, Drosophila melanogaster" +xref: Reactome:REACT_110775 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Rattus norvegicus" +xref: Reactome:REACT_110947 "Regulation of KIF23 (MKLP1) by phosphorylation, Drosophila melanogaster" +xref: Reactome:REACT_110995 "Phosphorylation and activation of eIF4G by activated S6K1, Xenopus tropicalis" +xref: Reactome:REACT_111124 "FGFR associated PI3K phosphorylates PIP2 to PIP3, Homo sapiens" +xref: Reactome:REACT_111171 "FGFR-associated PI3K phosphorylates PIP2 to PIP3, Homo sapiens" +xref: Reactome:REACT_1116 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Homo sapiens" +xref: Reactome:REACT_111930 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Caenorhabditis elegans" +xref: Reactome:REACT_1120 "Regulation of KIF20A (MKL2) by phosphorylation, Homo sapiens" +xref: Reactome:REACT_112075 "Mcm2-7 is phosphorylated by DDK, Drosophila melanogaster" +xref: Reactome:REACT_112101 "Phosphorylation of L1 by CK-II, Xenopus tropicalis" +xref: Reactome:REACT_112156 "Phosphorylation of AKT2 by PDK1, Saccharomyces cerevisiae" +xref: Reactome:REACT_112214 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Schizosaccharomyces pombe" +xref: Reactome:REACT_112270 "Akt1 phosphorylates BAD protein, Xenopus tropicalis" +xref: Reactome:REACT_112298 "Autophosphorylation of DNA-PKcs, Dictyostelium discoideum" +xref: Reactome:REACT_112324 "Phosphorylation and activation of eIF4G by activated S6K1, Oryza sativa" +xref: Reactome:REACT_112360 "Regulation of KIF23 (MKLP1) by phosphorylation, Dictyostelium discoideum" +xref: Reactome:REACT_112413 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Saccharomyces cerevisiae" +xref: Reactome:REACT_112480 "Inactivation of Wee1 kinase, Dictyostelium discoideum" +xref: Reactome:REACT_112545 "Phosphorylation and activation of eIF4G by activated S6K1, Drosophila melanogaster" +xref: Reactome:REACT_112633 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Saccharomyces cerevisiae" +xref: Reactome:REACT_112709 "Phosphorylation of L1 by ERK, Saccharomyces cerevisiae" +xref: Reactome:REACT_112722 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Drosophila melanogaster" +xref: Reactome:REACT_112790 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Caenorhabditis elegans" +xref: Reactome:REACT_112846 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Saccharomyces cerevisiae" +xref: Reactome:REACT_112892 "Phosphorylation of BRCA1 at multiple sites by ATM, Oryza sativa" +xref: Reactome:REACT_112948 "Autophosphorylation of DNA-PKcs, Rattus norvegicus" +xref: Reactome:REACT_113022 "Phosphorylation of Cyclin B1 in the CRS domain, Schizosaccharomyces pombe" +xref: Reactome:REACT_113051 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Arabidopsis thaliana" +xref: Reactome:REACT_113121 "Phosphorylation and activation of eIF4B by activated S6K1, Schizosaccharomyces pombe" +xref: Reactome:REACT_113227 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Saccharomyces cerevisiae" +xref: Reactome:REACT_113244 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Drosophila melanogaster" +xref: Reactome:REACT_113269 "Activation of S6K1, Saccharomyces cerevisiae" +xref: Reactome:REACT_113435 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Oryza sativa" +xref: Reactome:REACT_113527 "Autophosphorylation of DNA-PKcs, Bos taurus" +xref: Reactome:REACT_113569 "Activation of Cdc25C, Saccharomyces cerevisiae" +xref: Reactome:REACT_113811 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Bos taurus" +xref: Reactome:REACT_113820 "Phosphorylation of Cyclin B1 in the CRS domain, Saccharomyces cerevisiae" +xref: Reactome:REACT_113894 "PIP2 conversion to PIP3, Caenorhabditis elegans" +xref: Reactome:REACT_113929 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Caenorhabditis elegans" +xref: Reactome:REACT_113990 "Activation of Cdc25C, Schizosaccharomyces pombe" +xref: Reactome:REACT_114160 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Saccharomyces cerevisiae" +xref: Reactome:REACT_114198 "Phosphorylation of the Scc1:Cohesion Complex, Schizosaccharomyces pombe" +xref: Reactome:REACT_114207 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Schizosaccharomyces pombe" +xref: Reactome:REACT_114227 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Schizosaccharomyces pombe" +xref: Reactome:REACT_114233 "Autophosphorylation of DNA-PKcs, Sus scrofa" +xref: Reactome:REACT_114255 "Autophosphorylation of DNA-PKcs, Mus musculus" +xref: Reactome:REACT_114268 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Schizosaccharomyces pombe" +xref: Reactome:REACT_114280 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Saccharomyces cerevisiae" +xref: Reactome:REACT_114319 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Caenorhabditis elegans" +xref: Reactome:REACT_114323 "Activation of Cdc25C, Caenorhabditis elegans" +xref: Reactome:REACT_114395 "Phosphorylation of DLC1 by MAPK 8, Xenopus tropicalis" +xref: Reactome:REACT_114434 "Autophosphorylation of DNA-PKcs, Taeniopygia guttata" +xref: Reactome:REACT_114461 "Phosphorylation of AKT2 by PDK1, Schizosaccharomyces pombe" +xref: Reactome:REACT_114522 "Phosphorylation of BRCA1 at multiple sites by ATM, Arabidopsis thaliana" +xref: Reactome:REACT_114553 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Saccharomyces cerevisiae" +xref: Reactome:REACT_114599 "Phosphorylation of TSC2 by PKB, Schizosaccharomyces pombe" +xref: Reactome:REACT_114624 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Drosophila melanogaster" +xref: Reactome:REACT_114771 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Canis familiaris" +xref: Reactome:REACT_114906 "Phosphorylation and activation of eIF4G by activated S6K1, Arabidopsis thaliana" +xref: Reactome:REACT_114984 "Autophosphorylation of DNA-PKcs, Xenopus tropicalis" +xref: Reactome:REACT_115006 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Caenorhabditis elegans" +xref: Reactome:REACT_115135 "Phosphorylation and activation of eIF4G by activated S6K1, Dictyostelium discoideum" +xref: Reactome:REACT_115168 "Autophosphorylation of DNA-PKcs, Gallus gallus" +xref: Reactome:REACT_115199 "Autophosphorylation of DNA-PKcs, Canis familiaris" +xref: Reactome:REACT_115358 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Drosophila melanogaster" +xref: Reactome:REACT_115384 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Schizosaccharomyces pombe" +xref: Reactome:REACT_115440 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Danio rerio" +xref: Reactome:REACT_115472 "Phosphorylation of the SA2 Cohesin Complex, Schizosaccharomyces pombe" +xref: Reactome:REACT_115475 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Schizosaccharomyces pombe" +xref: Reactome:REACT_115521 "Autophosphorylation of DNA-PKcs, Danio rerio" +xref: Reactome:REACT_115527 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Schizosaccharomyces pombe" +xref: Reactome:REACT_115747 "Phosphorylation of H2AX at S139 by ATM at the site of DSB, Gallus gallus" +xref: Reactome:REACT_116149 "Phosphorylation of RAD51 by tyrosine kinase Abelson family protein members, Gallus gallus" +xref: Reactome:REACT_118137 "Phosphorylation of the Scc1:Cohesion Complex, Taeniopygia guttata" +xref: Reactome:REACT_118229 "Phosphorylation of the SA2 Cohesin Complex, Taeniopygia guttata" +xref: Reactome:REACT_118284 "Phosphorylation of the Scc1:Cohesion Complex, Saccharomyces cerevisiae" +xref: Reactome:REACT_118307 "Phosphorylation of the SA2 Cohesin Complex, Gallus gallus" +xref: Reactome:REACT_118367 "Phosphorylation of the Scc1:Cohesion Complex, Gallus gallus" +xref: Reactome:REACT_118462 "Phosphorylation of the SA2 Cohesin Complex, Saccharomyces cerevisiae" +xref: Reactome:REACT_1185 "Phosphorylation (Ser5) of RNA pol II CTD, Homo sapiens" +xref: Reactome:REACT_1279 "Cdc6 protein is phosphorylated by CDK, Homo sapiens" +xref: Reactome:REACT_128 "Phosphorylation of Cdc25C at Ser216, Homo sapiens" +xref: Reactome:REACT_132 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Homo sapiens" +xref: Reactome:REACT_1326 "Regulation of NUDC by phosphorylation, Homo sapiens" +xref: Reactome:REACT_13431 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Homo sapiens" +xref: Reactome:REACT_13581 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Oryctolagus cuniculus" +xref: Reactome:REACT_1362 "Phosphorylation of the Scc1:Cohesion Complex, Homo sapiens" +xref: Reactome:REACT_13817 "Autophosphorylation of PAK-2p34, Oryctolagus cuniculus" +xref: Reactome:REACT_1382 "Phosphorylation of PDE3B by AKT-1, Mus musculus" +xref: Reactome:REACT_13820 "Autophosphorylation of PAK-2p34 in the activation loop, Homo sapiens" +xref: Reactome:REACT_1420 "SOS phosphorylation and dissociation (SHC), Homo sapiens" +xref: Reactome:REACT_1481 "Phosphorylation of the SA2 Cohesin Complex, Homo sapiens" +xref: Reactome:REACT_1517 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Homo sapiens" +xref: Reactome:REACT_15386 "Plk1-mediated phosphorylation of Nlp, Homo sapiens" +xref: Reactome:REACT_1603 "Phosphorylation and activation of CHK2 by ATM, Homo sapiens" +xref: Reactome:REACT_1657 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Homo sapiens" +xref: Reactome:REACT_1680 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Homo sapiens" +xref: Reactome:REACT_169 "SOS phosphorylation and dissociation (IRS), Homo sapiens" +xref: Reactome:REACT_1727 "RAF1 phosphorylates MEK2, Homo sapiens" +xref: Reactome:REACT_1756 "Phosphorylation of p53 at ser-15 by ATM kinase, Homo sapiens" +xref: Reactome:REACT_1782 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Homo sapiens" +xref: Reactome:REACT_1808 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Homo sapiens" +xref: Reactome:REACT_1878 "Phosphorylation of PDE3B, Homo sapiens" +xref: Reactome:REACT_188 "Akt1 phosphorylates BAD protein, Homo sapiens" +xref: Reactome:REACT_1888 "Phosphorylation of DLC1 by MAPK 8, Homo sapiens" +xref: Reactome:REACT_1930 "Regulation of KIF23 (MKLP1) by phosphorylation, Homo sapiens" +xref: Reactome:REACT_19312 "Phosphorylation of PD-1, Homo sapiens" +xref: Reactome:REACT_1944 "Inactivation of Wee1 kinase, Homo sapiens" +xref: Reactome:REACT_1981 "Phosphorylation of DLC2 by MAPK-8, Homo sapiens" +xref: Reactome:REACT_2009 "Phosphorylation of NBS1 by ATM, Homo sapiens" +xref: Reactome:REACT_203 "Raf1 phosphorylates MEK1, Rattus norvegicus" +xref: Reactome:REACT_20503 "Phosphorylation of CREB by ribosomal protein S6 kinase, Homo sapiens" +xref: Reactome:REACT_20543 "Phosphorylation of COP1 at Ser-387 by ATM, Homo sapiens" +xref: Reactome:REACT_20562 "Phosphorylation by MAPK/ERK, Homo sapiens" +xref: Reactome:REACT_20578 "Raf activation, Homo sapiens" +xref: Reactome:REACT_20583 "Phosphorylation of CREB by PKA, Homo sapiens" +xref: Reactome:REACT_20631 "Activation of MAPK, Homo sapiens" +xref: Reactome:REACT_20640 "Phophorylation by PDK1, Homo sapiens" +xref: Reactome:REACT_2066 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Homo sapiens" +xref: Reactome:REACT_2111 "Orc1 is phosphorylated by cyclin A/CDK2, Homo sapiens" +xref: Reactome:REACT_2119 "Activation of Cdc25C, Homo sapiens" +xref: Reactome:REACT_215 "Autophosphorylation of DNA-PKcs, Homo sapiens" +xref: Reactome:REACT_22099 "Phosphorylation of L1 by ERK, Homo sapiens" +xref: Reactome:REACT_22378 "Phosphorylation of L1 by CK-II, Homo sapiens" +xref: Reactome:REACT_23976 "Raf1 phosphorylates MEK2, Rattus norvegicus" +xref: Reactome:REACT_23990 "Phosphorylation of cPLA2 by ERK-2, Homo sapiens" +xref: Reactome:REACT_244 "PIP2 conversion to PIP3, Homo sapiens" +xref: Reactome:REACT_26 "SOS phosphorylation and dissociation (IRS, Crk), Homo sapiens" +xref: Reactome:REACT_264 "Phosphorylation of Wee1 kinase by Chk1, Homo sapiens" +xref: Reactome:REACT_28054 "Phosphorylation of BRCA1 at multiple sites by ATM, Mus musculus" +xref: Reactome:REACT_28091 "Inactivation of Wee1 kinase, Canis familiaris" +xref: Reactome:REACT_28113 "RAF1 phosphorylates MEK1, Taeniopygia guttata" +xref: Reactome:REACT_28163 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Canis familiaris" +xref: Reactome:REACT_28264 "Phosphorylation of Wee1 kinase by Chk1, Arabidopsis thaliana" +xref: Reactome:REACT_28480 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Danio rerio" +xref: Reactome:REACT_28555 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Xenopus tropicalis" +xref: Reactome:REACT_28681 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Rattus norvegicus" +xref: Reactome:REACT_28719 "Phosphorylation and activation of eIF4B by activated S6K1, Xenopus tropicalis" +xref: Reactome:REACT_28743 "RAF1 phosphorylates MEK2, Mus musculus" +xref: Reactome:REACT_28746 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Danio rerio" +xref: Reactome:REACT_28824 "Down Regulation of Emi1 through Phosphorylation of Emi1, Danio rerio" +xref: Reactome:REACT_29029 "Phosphorylation of L1 by ERK, Caenorhabditis elegans" +xref: Reactome:REACT_29168 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Canis familiaris" +xref: Reactome:REACT_29201 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Saccharomyces cerevisiae" +xref: Reactome:REACT_29213 "Activation of Cdc25C, Rattus norvegicus" +xref: Reactome:REACT_29277 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Drosophila melanogaster" +xref: Reactome:REACT_29284 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Xenopus tropicalis" +xref: Reactome:REACT_29289 "Activation of S6K1, Gallus gallus" +xref: Reactome:REACT_29300 "Phosphorylation of L1 by ERK, Drosophila melanogaster" +xref: Reactome:REACT_29334 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Rattus norvegicus" +xref: Reactome:REACT_29395 "Phosphorylation of AKT2 by PDK1, Xenopus tropicalis" +xref: Reactome:REACT_29396 "Orc1 is phosphorylated by cyclin A/CDK2, Canis familiaris" +xref: Reactome:REACT_29410 "Regulation of KIF20A (MKL2) by phosphorylation, Rattus norvegicus" +xref: Reactome:REACT_29451 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Bos taurus" +xref: Reactome:REACT_29588 "Phosphorylation of 4E-BP1 by activated mTORC1, Taeniopygia guttata" +xref: Reactome:REACT_29614 "Regulation of NUDC by phosphorylation, Rattus norvegicus" +xref: Reactome:REACT_29689 "Cdc6 protein is phosphorylated by CDK, Bos taurus" +xref: Reactome:REACT_29694 "Phosphorylation of PDE3B, Canis familiaris" +xref: Reactome:REACT_29759 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Bos taurus" +xref: Reactome:REACT_29788 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Xenopus tropicalis" +xref: Reactome:REACT_29873 "Phosphorylation of APC component of the destruction complex, Taeniopygia guttata" +xref: Reactome:REACT_29914 "Down Regulation of Emi1 through Phosphorylation of Emi1, Canis familiaris" +xref: Reactome:REACT_30020 "Phosphorylation (Ser5) of RNA pol II CTD, Rattus norvegicus" +xref: Reactome:REACT_30023 "Phosphorylation (Ser5) of RNA pol II CTD, Xenopus tropicalis" +xref: Reactome:REACT_30052 "Phosphorylation of BRCA1 at multiple sites by ATM, Bos taurus" +xref: Reactome:REACT_30070 "Phosphorylation of L1 by CK-II, Mus musculus" +xref: Reactome:REACT_30084 "PIP2 conversion to PIP3, Canis familiaris" +xref: Reactome:REACT_30113 "SOS phosphorylation and dissociation (IRS, Crk), Drosophila melanogaster" +xref: Reactome:REACT_30116 "Phosphorylation and activation of eIF4B by activated S6K1, Canis familiaris" +xref: Reactome:REACT_30165 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Gallus gallus" +xref: Reactome:REACT_302 "Phosphorylation and activation of Chk1 by ATM, Homo sapiens" +xref: Reactome:REACT_30230 "Phosphorylation of the SA2 Cohesin Complex, Caenorhabditis elegans" +xref: Reactome:REACT_30345 "RAF1 phosphorylates MEK1, Gallus gallus" +xref: Reactome:REACT_30490 "Inactivation of Myt1 kinase, Danio rerio" +xref: Reactome:REACT_30496 "Phosphorylation of the Scc1:Cohesion Complex, Xenopus tropicalis" +xref: Reactome:REACT_30679 "Phosphorylation and inactivation of eEF2K by activated S6K1, Mus musculus" +xref: Reactome:REACT_30700 "Phosphorylation of BRCA1 at multiple sites by ATM, Gallus gallus" +xref: Reactome:REACT_30836 "Inactivation of Myt1 kinase, Bos taurus" +xref: Reactome:REACT_30921 "Phosphorylation and activation of Chk1 by ATM, Xenopus tropicalis" +xref: Reactome:REACT_30938 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Canis familiaris" +xref: Reactome:REACT_30948 "PIP2 conversion to PIP3, Gallus gallus" +xref: Reactome:REACT_30985 "Plk1-mediated phosphorylation of Nlp, Canis familiaris" +xref: Reactome:REACT_30997 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Rattus norvegicus" +xref: Reactome:REACT_31081 "Phosphorylation of TSC2 by PKB, Canis familiaris" +xref: Reactome:REACT_31149 "Phosphorylation of the Scc1:Cohesion Complex, Danio rerio" +xref: Reactome:REACT_31196 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Canis familiaris" +xref: Reactome:REACT_31227 "Regulation of KIF20A (MKL2) by phosphorylation, Gallus gallus" +xref: Reactome:REACT_31273 "Phosphorylation of the Scc1:Cohesion Complex, Canis familiaris" +xref: Reactome:REACT_31290 "Orc1 is phosphorylated by cyclin A/CDK2, Rattus norvegicus" +xref: Reactome:REACT_31293 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Danio rerio" +xref: Reactome:REACT_31449 "Phosphorylation and activation of CHK2 by ATM, Danio rerio" +xref: Reactome:REACT_31466 "Activation of S6K1, Bos taurus" +xref: Reactome:REACT_31519 "Phosphorylation of the SA2 Cohesin Complex, Danio rerio" +xref: Reactome:REACT_31536 "Phosphorylation of NBS1 by ATM, Taeniopygia guttata" +xref: Reactome:REACT_31571 "Autophosphorylation of PAK-2p34 in the activation loop, Gallus gallus" +xref: Reactome:REACT_31625 "Phosphorylation of L1 by ERK, Taeniopygia guttata" +xref: Reactome:REACT_31639 "SOS phosphorylation and dissociation (SHC), Rattus norvegicus" +xref: Reactome:REACT_31868 "Phosphorylation and activation of CHK2 by ATM, Canis familiaris" +xref: Reactome:REACT_31915 "Phosphorylation of L1 by CK-II, Drosophila melanogaster" +xref: Reactome:REACT_31935 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Sus scrofa" +xref: Reactome:REACT_31984 "Phosphorylation (Ser5) of RNA pol II CTD, Arabidopsis thaliana" +xref: Reactome:REACT_32009 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Mus musculus" +xref: Reactome:REACT_32077 "Inactivation of Myt1 kinase, Dictyostelium discoideum" +xref: Reactome:REACT_32079 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Danio rerio" +xref: Reactome:REACT_32145 "Phosphorylation of COP1 at Ser-387 by ATM, Canis familiaris" +xref: Reactome:REACT_32150 "Phosphorylation of NBS1 by ATM, Arabidopsis thaliana" +xref: Reactome:REACT_32271 "Phosphorylation of cPLA2 by ERK-2, Taeniopygia guttata" +xref: Reactome:REACT_32358 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Canis familiaris" +xref: Reactome:REACT_32374 "Mcm2-7 is phosphorylated by DDK, Canis familiaris" +xref: Reactome:REACT_32438 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Sus scrofa" +xref: Reactome:REACT_32492 "Phosphorylation of BRCA1 at multiple sites by ATM, Rattus norvegicus" +xref: Reactome:REACT_32565 "Phosphorylation of NBS1 by ATM, Gallus gallus" +xref: Reactome:REACT_32598 "Phosphorylation and activation of eIF4B by activated S6K1, Taeniopygia guttata" +xref: Reactome:REACT_32620 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Bos taurus" +xref: Reactome:REACT_32845 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Rattus norvegicus" +xref: Reactome:REACT_32906 "Phosphorylation and inactivation of eEF2K by activated S6K1, Sus scrofa" +xref: Reactome:REACT_32956 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Mus musculus" +xref: Reactome:REACT_33003 "Phosphorylation of the SA2 Cohesin Complex, Dictyostelium discoideum" +xref: Reactome:REACT_33009 "Phosphorylation of L1 by ERK, Danio rerio" +xref: Reactome:REACT_33080 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Taeniopygia guttata" +xref: Reactome:REACT_33369 "Phosphorylation of NBS1 by ATM, Rattus norvegicus" +xref: Reactome:REACT_33385 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Canis familiaris" +xref: Reactome:REACT_33519 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Mus musculus" +xref: Reactome:REACT_33532 "Phosphorylation of complexed TSC2 by PKB, Bos taurus" +xref: Reactome:REACT_33692 "Phosphorylation of BRCA1 at multiple sites by ATM, Taeniopygia guttata" +xref: Reactome:REACT_33840 "Regulation of KIF23 (MKLP1) by phosphorylation, Schizosaccharomyces pombe" +xref: Reactome:REACT_33928 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Sus scrofa" +xref: Reactome:REACT_33979 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Rattus norvegicus" +xref: Reactome:REACT_34080 "Phosphorylation of PD-1, Mus musculus" +xref: Reactome:REACT_34111 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Canis familiaris" +xref: Reactome:REACT_34145 "Phosphorylation of cPLA2 by ERK-2, Xenopus tropicalis" +xref: Reactome:REACT_34222 "Phosphorylation of L1 by ERK, Rattus norvegicus" +xref: Reactome:REACT_34285 "Activation of Cdc25C, Bos taurus" +xref: Reactome:REACT_34310 "Phosphorylation and activation of Chk1 by ATM, Bos taurus" +xref: Reactome:REACT_34403 "Phosphorylation (Ser5) of RNA pol II CTD, Danio rerio" +xref: Reactome:REACT_34514 "Phosphorylation and inactivation of eEF2K by activated S6K1, Danio rerio" +xref: Reactome:REACT_34516 "Cdc6 protein is phosphorylated by CDK, Canis familiaris" +xref: Reactome:REACT_34607 "Phosphorylation of 4E-BP1 by activated mTORC1, Bos taurus" +xref: Reactome:REACT_34741 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Rattus norvegicus" +xref: Reactome:REACT_34788 "Phosphorylation and inactivation of eEF2K by activated S6K1, Xenopus tropicalis" +xref: Reactome:REACT_34804 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Gallus gallus" +xref: Reactome:REACT_384 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Homo sapiens" +xref: Reactome:REACT_414 "Inactivation of Myt1 kinase, Homo sapiens" +xref: Reactome:REACT_41715 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Mus musculus" +xref: Reactome:REACT_43 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Homo sapiens" +xref: Reactome:REACT_496 "Down Regulation of Emi1 through Phosphorylation of Emi1, Homo sapiens" +xref: Reactome:REACT_54449 "Phosphorylation and activation of eIF4G by activated S6K1, Mus musculus" +xref: Reactome:REACT_545 "RAF1 phosphorylates MEK1, Homo sapiens" +xref: Reactome:REACT_559 "Phosphorylation and activation of Chk1 by ATM kinase, Mus musculus" +xref: Reactome:REACT_58131 "PIP2 conversion to PIP3, Mus musculus" +xref: Reactome:REACT_6139 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Homo sapiens" +xref: Reactome:REACT_6170 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by the P-TEFb(Cyclin T1:Cdk9) complex, Homo sapiens" +xref: Reactome:REACT_6178 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Homo sapiens" +xref: Reactome:REACT_6234 "Phosphorylation (Ser5) of RNA pol II CTD, Homo sapiens" +xref: Reactome:REACT_6297 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Homo sapiens" +xref: Reactome:REACT_6311 "Phosphorylation of NEFL by the P-TEFb(Cyclin T1:Cdk9) complex, Homo sapiens" +xref: Reactome:REACT_6314 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Homo sapiens" +xref: Reactome:REACT_6316 "Phosphorylation of DSIF by the P-TEFb(Cyclin T1:Cdk9) complex, Human immunodeficiency virus 1" +xref: Reactome:REACT_6327 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Homo sapiens" +xref: Reactome:REACT_6342 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Homo sapiens" +xref: Reactome:REACT_6353 "Phosphorylation of Cyclin B1 in the CRS domain, Homo sapiens" +xref: Reactome:REACT_6725 "Phosphorylation of TSC2 by PKB, Homo sapiens" +xref: Reactome:REACT_6778 "Phosphorylation and activation of eIF4B by activated S6K1, Homo sapiens" +xref: Reactome:REACT_6859 "Free APC/C phosphorylated by Plk1, Homo sapiens" +xref: Reactome:REACT_6861 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Homo sapiens" +xref: Reactome:REACT_6870 "Phosphorylation and activation of eIF4G by activated S6K1, Homo sapiens" +xref: Reactome:REACT_6873 "Phosphorylation of 4E-BP1 by activated mTORC1, Homo sapiens" +xref: Reactome:REACT_6883 "Phosphorylation and inactivation of eEF2K by activated S6K1, Homo sapiens" +xref: Reactome:REACT_6912 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Homo sapiens" +xref: Reactome:REACT_6948 "Activation of S6K1, Homo sapiens" +xref: Reactome:REACT_6952 "Phosphorylation of complexed TSC2 by PKB, Homo sapiens" +xref: Reactome:REACT_76979 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Danio rerio" +xref: Reactome:REACT_77040 "Phosphorylation of COP1 at Ser-387 by ATM, Oryza sativa" +xref: Reactome:REACT_77074 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Mus musculus" +xref: Reactome:REACT_77179 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Bos taurus" +xref: Reactome:REACT_77231 "Phosphorylation of DLC2 by MAPK-8, Gallus gallus" +xref: Reactome:REACT_77234 "Plk1-mediated phosphorylation of Nlp, Gallus gallus" +xref: Reactome:REACT_773 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Homo sapiens" +xref: Reactome:REACT_77326 "RAF1 phosphorylates MEK2, Taeniopygia guttata" +xref: Reactome:REACT_77362 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Rattus norvegicus" +xref: Reactome:REACT_77365 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Xenopus tropicalis" +xref: Reactome:REACT_77397 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Mus musculus" +xref: Reactome:REACT_77407 "Regulation of NUDC by phosphorylation, Bos taurus" +xref: Reactome:REACT_77443 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Danio rerio" +xref: Reactome:REACT_77450 "Phosphorylation of L1 by CK-II, Sus scrofa" +xref: Reactome:REACT_77535 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Mus musculus" +xref: Reactome:REACT_77550 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Drosophila melanogaster" +xref: Reactome:REACT_77566 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Gallus gallus" +xref: Reactome:REACT_77606 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Canis familiaris" +xref: Reactome:REACT_77615 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Gallus gallus" +xref: Reactome:REACT_77654 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Drosophila melanogaster" +xref: Reactome:REACT_77660 "Regulation of KIF23 (MKLP1) by phosphorylation, Caenorhabditis elegans" +xref: Reactome:REACT_77733 "Phosphorylation of PDE3B, Danio rerio" +xref: Reactome:REACT_77834 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Rattus norvegicus" +xref: Reactome:REACT_77857 "Phosphorylation (Ser5) of RNA pol II CTD, Drosophila melanogaster" +xref: Reactome:REACT_77897 "Phosphorylation of Wee1 kinase by Chk1, Taeniopygia guttata" +xref: Reactome:REACT_77911 "Mcm2-7 is phosphorylated by DDK, Taeniopygia guttata" +xref: Reactome:REACT_77928 "Autophosphorylation of PAK-2p34 in the activation loop, Sus scrofa" +xref: Reactome:REACT_77949 "Phosphorylation of Wee1 kinase by Chk1, Drosophila melanogaster" +xref: Reactome:REACT_77977 "Phosphorylation of Cyclin B1 in the CRS domain, Bos taurus" +xref: Reactome:REACT_78014 "Plk1-mediated phosphorylation of Nlp, Taeniopygia guttata" +xref: Reactome:REACT_78035 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Taeniopygia guttata" +xref: Reactome:REACT_78087 "Phosphorylation of TSC2 by PKB, Xenopus tropicalis" +xref: Reactome:REACT_78121 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Gallus gallus" +xref: Reactome:REACT_78226 "Regulation of NUDC by phosphorylation, Xenopus tropicalis" +xref: Reactome:REACT_78281 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Rattus norvegicus" +xref: Reactome:REACT_78427 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Danio rerio" +xref: Reactome:REACT_78450 "Phosphorylation and activation of eIF4B by activated S6K1, Drosophila melanogaster" +xref: Reactome:REACT_78451 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Taeniopygia guttata" +xref: Reactome:REACT_78503 "Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB, Bos taurus" +xref: Reactome:REACT_78533 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Danio rerio" +xref: Reactome:REACT_78539 "Down Regulation of Emi1 through Phosphorylation of Emi1, Xenopus tropicalis" +xref: Reactome:REACT_78556 "Free APC/C phosphorylated by Plk1, Drosophila melanogaster" +xref: Reactome:REACT_78625 "Phosphorylation and inactivation of eEF2K by activated S6K1, Caenorhabditis elegans" +xref: Reactome:REACT_78651 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Rattus norvegicus" +xref: Reactome:REACT_78696 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Xenopus tropicalis" +xref: Reactome:REACT_78748 "Cdc6 protein is phosphorylated by CDK, Drosophila melanogaster" +xref: Reactome:REACT_78901 "Phosphorylation (Ser5) of RNA pol II CTD, Mus musculus" +xref: Reactome:REACT_79012 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Schizosaccharomyces pombe" +xref: Reactome:REACT_79039 "Autophosphorylation of PAK-2p34 in the activation loop, Caenorhabditis elegans" +xref: Reactome:REACT_79087 "Phosphorylation of Wee1 kinase by Chk1, Oryza sativa" +xref: Reactome:REACT_79125 "SOS phosphorylation and dissociation (IRS), Bos taurus" +xref: Reactome:REACT_79182 "Phosphorylation of Cyclin B1 in the CRS domain, Canis familiaris" +xref: Reactome:REACT_79208 "Mcm2-7 is phosphorylated by DDK, Bos taurus" +xref: Reactome:REACT_79220 "Phosphorylation of 4E-BP1 by activated mTORC1, Canis familiaris" +xref: Reactome:REACT_79255 "Phosphorylation of p53 at ser-15 by ATM kinase, Danio rerio" +xref: Reactome:REACT_79372 "Cdc6 protein is phosphorylated by CDK, Danio rerio" +xref: Reactome:REACT_79573 "Phosphorylation of p53 at ser-15 by ATM kinase, Mus musculus" +xref: Reactome:REACT_79686 "Phosphorylation of the Scc1:Cohesion Complex, Drosophila melanogaster" +xref: Reactome:REACT_79694 "Autophosphorylation of PAK-2p34 in the activation loop, Xenopus tropicalis" +xref: Reactome:REACT_79700 "Activation of S6K1, Taeniopygia guttata" +xref: Reactome:REACT_79709 "Orc1 is phosphorylated by cyclin A/CDK2, Mus musculus" +xref: Reactome:REACT_79720 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Danio rerio" +xref: Reactome:REACT_80110 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Drosophila melanogaster" +xref: Reactome:REACT_80144 "Phosphorylation of complexed TSC2 by PKB, Sus scrofa" +xref: Reactome:REACT_80185 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Mus musculus" +xref: Reactome:REACT_80213 "Activation of S6K1, Canis familiaris" +xref: Reactome:REACT_80218 "Phosphorylation of the Scc1:Cohesion Complex, Dictyostelium discoideum" +xref: Reactome:REACT_80239 "Regulation of KIF20A (MKL2) by phosphorylation, Dictyostelium discoideum" +xref: Reactome:REACT_80255 "Mcm2-7 is phosphorylated by DDK, Mus musculus" +xref: Reactome:REACT_80591 "Regulation of KIF20A (MKL2) by phosphorylation, Drosophila melanogaster" +xref: Reactome:REACT_80606 "Phosphorylation of NBS1 by ATM, Oryza sativa" +xref: Reactome:REACT_80617 "Inactivation of Wee1 kinase, Xenopus tropicalis" +xref: Reactome:REACT_80632 "Phosphorylation of L1 by ERK, Schizosaccharomyces pombe" +xref: Reactome:REACT_80665 "Down Regulation of Emi1 through Phosphorylation of Emi1, Taeniopygia guttata" +xref: Reactome:REACT_80684 "Phosphorylation of COP1 at Ser-387 by ATM, Arabidopsis thaliana" +xref: Reactome:REACT_80689 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Oryza sativa" +xref: Reactome:REACT_80699 "PIP2 conversion to PIP3, Danio rerio" +xref: Reactome:REACT_80700 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Sus scrofa" +xref: Reactome:REACT_80714 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Rattus norvegicus" +xref: Reactome:REACT_80804 "Phosphorylation of PDE3B, Bos taurus" +xref: Reactome:REACT_80853 "Phosphorylation (Ser5) of RNA pol II CTD, Dictyostelium discoideum" +xref: Reactome:REACT_80860 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Rattus norvegicus" +xref: Reactome:REACT_80909 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Drosophila melanogaster" +xref: Reactome:REACT_81027 "PIP2 conversion to PIP3, Sus scrofa" +xref: Reactome:REACT_81148 "Phosphorylation and activation of CHK2 by ATM, Taeniopygia guttata" +xref: Reactome:REACT_81218 "Phosphorylation and activation of CHK2 by ATM, Rattus norvegicus" +xref: Reactome:REACT_81439 "Phosphorylation of APC component of the destruction complex, Xenopus tropicalis" +xref: Reactome:REACT_81458 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Bos taurus" +xref: Reactome:REACT_81490 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Xenopus tropicalis" +xref: Reactome:REACT_81590 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Bos taurus" +xref: Reactome:REACT_81616 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Canis familiaris" +xref: Reactome:REACT_81647 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Rattus norvegicus" +xref: Reactome:REACT_81652 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Rattus norvegicus" +xref: Reactome:REACT_81693 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Drosophila melanogaster" +xref: Reactome:REACT_81715 "Orc1 is phosphorylated by cyclin A/CDK2, Drosophila melanogaster" +xref: Reactome:REACT_81727 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Danio rerio" +xref: Reactome:REACT_81864 "Phosphorylation of Cx43 by c-src, Bos taurus" +xref: Reactome:REACT_81941 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Bos taurus" +xref: Reactome:REACT_82037 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Mus musculus" +xref: Reactome:REACT_82115 "Phosphorylation and activation of Chk1 by ATM, Saccharomyces cerevisiae" +xref: Reactome:REACT_82125 "Phosphorylation of complexed TSC2 by PKB, Danio rerio" +xref: Reactome:REACT_82128 "PIP2 conversion to PIP3, Taeniopygia guttata" +xref: Reactome:REACT_82261 "Phosphorylation of DLC2 by MAPK-8, Xenopus tropicalis" +xref: Reactome:REACT_82270 "Autophosphorylation of PAK-2p34 in the activation loop, Rattus norvegicus" +xref: Reactome:REACT_82303 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Xenopus tropicalis" +xref: Reactome:REACT_82310 "Phosphorylation and activation of Chk1 by ATM, Gallus gallus" +xref: Reactome:REACT_82361 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Canis familiaris" +xref: Reactome:REACT_82456 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Bos taurus" +xref: Reactome:REACT_82473 "Phosphorylation of the SA2 Cohesin Complex, Canis familiaris" +xref: Reactome:REACT_82616 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Mus musculus" +xref: Reactome:REACT_82678 "Phosphorylation of complexed TSC2 by PKB, Rattus norvegicus" +xref: Reactome:REACT_82728 "Plk1-mediated phosphorylation of Nlp, Mus musculus" +xref: Reactome:REACT_82751 "Down Regulation of Emi1 through Phosphorylation of Emi1, Rattus norvegicus" +xref: Reactome:REACT_82824 "Inactivation of Wee1 kinase, Rattus norvegicus" +xref: Reactome:REACT_82901 "Phosphorylation of DLC2 by MAPK-8, Canis familiaris" +xref: Reactome:REACT_82927 "PIP2 conversion to PIP3, Rattus norvegicus" +xref: Reactome:REACT_83006 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Caenorhabditis elegans" +xref: Reactome:REACT_83089 "Inactivation of Myt1 kinase, Saccharomyces cerevisiae" +xref: Reactome:REACT_83110 "Phosphorylation (Ser5) of RNA pol II CTD, Schizosaccharomyces pombe" +xref: Reactome:REACT_83178 "Phosphorylation and activation of Chk1 by ATM, Oryza sativa" +xref: Reactome:REACT_83187 "Phosphorylation of the SA2 Cohesin Complex, Mus musculus" +xref: Reactome:REACT_83239 "Phosphorylation and activation of eIF4G by activated S6K1, Gallus gallus" +xref: Reactome:REACT_83279 "Phosphorylation of NBS1 by ATM, Canis familiaris" +xref: Reactome:REACT_83297 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Danio rerio" +xref: Reactome:REACT_83436 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Arabidopsis thaliana" +xref: Reactome:REACT_83476 "Phosphorylation and activation of CHK2 by ATM, Mus musculus" +xref: Reactome:REACT_83529 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Drosophila melanogaster" +xref: Reactome:REACT_83533 "Phosphorylation and activation of Chk1 by ATM, Rattus norvegicus" +xref: Reactome:REACT_83579 "Phosphorylation of Wee1 kinase by Chk1, Gallus gallus" +xref: Reactome:REACT_83582 "Plk1-mediated phosphorylation of Nlp, Danio rerio" +xref: Reactome:REACT_83671 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Taeniopygia guttata" +xref: Reactome:REACT_83696 "Free APC/C phosphorylated by Plk1, Bos taurus" +xref: Reactome:REACT_83709 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Mus musculus" +xref: Reactome:REACT_83727 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Gallus gallus" +xref: Reactome:REACT_83899 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Sus scrofa" +xref: Reactome:REACT_83979 "Phosphorylation of COP1 at Ser-387 by ATM, Mus musculus" +xref: Reactome:REACT_84080 "Phosphorylation of the SA2 Cohesin Complex, Xenopus tropicalis" +xref: Reactome:REACT_84082 "Phosphorylation of Wee1 kinase by Chk1, Rattus norvegicus" +xref: Reactome:REACT_84208 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Mus musculus" +xref: Reactome:REACT_84273 "Phosphorylation of L1 by ERK, Sus scrofa" +xref: Reactome:REACT_84348 "Phosphorylation of COP1 at Ser-387 by ATM, Taeniopygia guttata" +xref: Reactome:REACT_84405 "Phosphorylation of p53 at ser-15 by ATM kinase, Rattus norvegicus" +xref: Reactome:REACT_845 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Homo sapiens" +xref: Reactome:REACT_84560 "Cdc6 protein is phosphorylated by CDK, Saccharomyces cerevisiae" +xref: Reactome:REACT_84656 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Bos taurus" +xref: Reactome:REACT_84932 "Phosphorylation of Wee1 kinase by Chk1, Sus scrofa" +xref: Reactome:REACT_85009 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Taeniopygia guttata" +xref: Reactome:REACT_85017 "Activation of S6K1, Dictyostelium discoideum" +xref: Reactome:REACT_85044 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Canis familiaris" +xref: Reactome:REACT_85066 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Taeniopygia guttata" +xref: Reactome:REACT_85256 "Phosphorylation of Cdc25C at Ser216, Mus musculus" +xref: Reactome:REACT_85328 "Regulation of KIF20A (MKL2) by phosphorylation, Mus musculus" +xref: Reactome:REACT_85379 "Phosphorylation of Cx43 by c-src, Sus scrofa" +xref: Reactome:REACT_85449 "Phosphorylation and activation of eIF4G by activated S6K1, Bos taurus" +xref: Reactome:REACT_85586 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Gallus gallus" +xref: Reactome:REACT_85699 "Phosphorylation of Cyclin B1 in the CRS domain, Rattus norvegicus" +xref: Reactome:REACT_85720 "Phosphorylation of L1 by ERK, Canis familiaris" +xref: Reactome:REACT_85745 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Xenopus tropicalis" +xref: Reactome:REACT_85751 "Phosphorylation of BRCA1 at multiple sites by ATM, Canis familiaris" +xref: Reactome:REACT_85812 "Phosphorylation and activation of Chk1 by ATM, Drosophila melanogaster" +xref: Reactome:REACT_85836 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Gallus gallus" +xref: Reactome:REACT_85871 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Mus musculus" +xref: Reactome:REACT_86014 "Phosphorylation of the SA2 Cohesin Complex, Bos taurus" +xref: Reactome:REACT_86033 "Phosphorylation and activation of CHK2 by ATM, Schizosaccharomyces pombe" +xref: Reactome:REACT_86061 "Phosphorylation of Cyclin E1:Cdk2 complexes by Myt1, Bos taurus" +xref: Reactome:REACT_86092 "Phosphorylation of COP1 at Ser-387 by ATM, Bos taurus" +xref: Reactome:REACT_86211 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Saccharomyces cerevisiae" +xref: Reactome:REACT_86252 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Drosophila melanogaster" +xref: Reactome:REACT_86261 "Regulation of NUDC by phosphorylation, Dictyostelium discoideum" +xref: Reactome:REACT_86277 "Phosphorylation of TSC2 by PKB, Bos taurus" +xref: Reactome:REACT_86365 "Phosphorylation and activation of eIF4G by activated S6K1, Rattus norvegicus" +xref: Reactome:REACT_86372 "Akt1 phosphorylates BAD protein, Mus musculus" +xref: Reactome:REACT_86415 "Phosphorylation of Cx43 by c-src, Xenopus tropicalis" +xref: Reactome:REACT_86422 "Phosphorylation of PD-1, Rattus norvegicus" +xref: Reactome:REACT_86533 "Cdc6 protein is phosphorylated by CDK, Sus scrofa" +xref: Reactome:REACT_86736 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Rattus norvegicus" +xref: Reactome:REACT_86800 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Danio rerio" +xref: Reactome:REACT_86867 "Phosphorylation of p53 at ser-15 by ATM kinase, Bos taurus" +xref: Reactome:REACT_86952 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Sus scrofa" +xref: Reactome:REACT_86967 "Phosphorylation (Ser5) of RNA pol II CTD, Gallus gallus" +xref: Reactome:REACT_87010 "Regulation of NUDC by phosphorylation, Danio rerio" +xref: Reactome:REACT_87121 "Phosphorylation of cPLA2 by ERK-2, Bos taurus" +xref: Reactome:REACT_87149 "Phosphorylation of L1 by CK-II, Danio rerio" +xref: Reactome:REACT_87212 "Phosphorylation of Cx43 by c-src, Mus musculus" +xref: Reactome:REACT_87222 "Cdc6 protein is phosphorylated by CDK, Schizosaccharomyces pombe" +xref: Reactome:REACT_87298 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Sus scrofa" +xref: Reactome:REACT_87329 "Regulation of KIF23 (MKLP1) by phosphorylation, Mus musculus" +xref: Reactome:REACT_87391 "Phosphorylation of Cx43 by c-src, Rattus norvegicus" +xref: Reactome:REACT_87424 "SOS phosphorylation and dissociation (SHC), Danio rerio" +xref: Reactome:REACT_87437 "Phosphorylation of AKT2 by PDK1, Caenorhabditis elegans" +xref: Reactome:REACT_87485 "Activation of S6K1, Xenopus tropicalis" +xref: Reactome:REACT_87497 "Akt1 phosphorylates BAD protein, Bos taurus" +xref: Reactome:REACT_87503 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Xenopus tropicalis" +xref: Reactome:REACT_87523 "Phosphorylation of Cyclin B1 in the CRS domain, Mus musculus" +xref: Reactome:REACT_87534 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Gallus gallus" +xref: Reactome:REACT_87593 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Gallus gallus" +xref: Reactome:REACT_87650 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Xenopus tropicalis" +xref: Reactome:REACT_87679 "Phosphorylation of PDE3B, Xenopus tropicalis" +xref: Reactome:REACT_87753 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Bos taurus" +xref: Reactome:REACT_87880 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes, Danio rerio" +xref: Reactome:REACT_87967 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Xenopus tropicalis" +xref: Reactome:REACT_88025 "Activation of S6K1, Mus musculus" +xref: Reactome:REACT_88055 "Phosphorylation of NBS1 by ATM, Sus scrofa" +xref: Reactome:REACT_88091 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Xenopus tropicalis" +xref: Reactome:REACT_88220 "Regulation of KIF23 (MKLP1) by phosphorylation, Rattus norvegicus" +xref: Reactome:REACT_88298 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Taeniopygia guttata" +xref: Reactome:REACT_88326 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Canis familiaris" +xref: Reactome:REACT_88374 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Xenopus tropicalis" +xref: Reactome:REACT_88421 "Phosphorylation and inactivation of eEF2K by activated S6K1, Rattus norvegicus" +xref: Reactome:REACT_88430 "Orc1 is phosphorylated by cyclin A/CDK2, Bos taurus" +xref: Reactome:REACT_88440 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Caenorhabditis elegans" +xref: Reactome:REACT_88458 "Phosphorylation of cPLA2 by ERK-2, Danio rerio" +xref: Reactome:REACT_88486 "Inactivation of Wee1 kinase, Taeniopygia guttata" +xref: Reactome:REACT_88516 "Cdc6 protein is phosphorylated by CDK, Rattus norvegicus" +xref: Reactome:REACT_88548 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Taeniopygia guttata" +xref: Reactome:REACT_88564 "Plk1-mediated phosphorylation of Nlp, Xenopus tropicalis" +xref: Reactome:REACT_88590 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Rattus norvegicus" +xref: Reactome:REACT_88665 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Danio rerio" +xref: Reactome:REACT_88668 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Drosophila melanogaster" +xref: Reactome:REACT_88766 "Phosphorylation (Ser5) of RNA pol II CTD, Oryza sativa" +xref: Reactome:REACT_88871 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex, Rattus norvegicus" +xref: Reactome:REACT_88928 "Autophosphorylation of PAK-2p34 in the activation loop, Drosophila melanogaster" +xref: Reactome:REACT_88987 "Free APC/C phosphorylated by Plk1, Canis familiaris" +xref: Reactome:REACT_89001 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Gallus gallus" +xref: Reactome:REACT_89026 "Phosphorylation of PD-1, Gallus gallus" +xref: Reactome:REACT_89122 "Activation of Cdc25C, Canis familiaris" +xref: Reactome:REACT_89366 "Phosphorylation of APC component of the destruction complex, Canis familiaris" +xref: Reactome:REACT_89427 "Phosphorylation of AKT2 by PDK1, Bos taurus" +xref: Reactome:REACT_89464 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Taeniopygia guttata" +xref: Reactome:REACT_89547 "Phosphorylation of NBS1 by ATM, Xenopus tropicalis" +xref: Reactome:REACT_89579 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Xenopus tropicalis" +xref: Reactome:REACT_89769 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Taeniopygia guttata" +xref: Reactome:REACT_89794 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Mus musculus" +xref: Reactome:REACT_89879 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Mus musculus" +xref: Reactome:REACT_89988 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Schizosaccharomyces pombe" +xref: Reactome:REACT_9007 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Homo sapiens" +xref: Reactome:REACT_90132 "Phosphorylation of AKT2 by PDK1, Sus scrofa" +xref: Reactome:REACT_90167 "Phosphorylation of Wee1 kinase by Chk1, Bos taurus" +xref: Reactome:REACT_90220 "Wee1- mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes, Rattus norvegicus" +xref: Reactome:REACT_90227 "Phosphorylation of AKT2 by PDK1, Mus musculus" +xref: Reactome:REACT_90290 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Taeniopygia guttata" +xref: Reactome:REACT_90364 "Regulation of NUDC by phosphorylation, Canis familiaris" +xref: Reactome:REACT_90426 "Phosphorylation of Wee1 kinase by Chk1, Mus musculus" +xref: Reactome:REACT_90449 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Canis familiaris" +xref: Reactome:REACT_90562 "Regulation of NUDC by phosphorylation, Drosophila melanogaster" +xref: Reactome:REACT_9057 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Homo sapiens" +xref: Reactome:REACT_9067 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Homo sapiens" +xref: Reactome:REACT_90675 "Phosphorylation (Ser5) of RNA pol II CTD, Caenorhabditis elegans" +xref: Reactome:REACT_907 "Mcm2-7 is phosphorylated by DDK, Homo sapiens" +xref: Reactome:REACT_9070 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Homo sapiens" +xref: Reactome:REACT_908 "Phosphorylation of AKT2 by PDK1, Homo sapiens" +xref: Reactome:REACT_90917 "Phosphorylation of Wee1 kinase by Chk1, Canis familiaris" +xref: Reactome:REACT_91050 "SOS phosphorylation and dissociation (IRS, Crk), Mus musculus" +xref: Reactome:REACT_91062 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Bos taurus" +xref: Reactome:REACT_91085 "Inactivation of Wee1 kinase, Danio rerio" +xref: Reactome:REACT_91156 "Phosphorylation and activation of CHK2 by ATM, Gallus gallus" +xref: Reactome:REACT_91157 "Phosphorylation (Ser5) of RNA pol II CTD, Saccharomyces cerevisiae" +xref: Reactome:REACT_91196 "Phosphorylation of 4E-BP1 by activated mTORC1, Mus musculus" +xref: Reactome:REACT_91197 "Phosphorylation and activation of eIF4B by activated S6K1, Mus musculus" +xref: Reactome:REACT_91240 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Xenopus tropicalis" +xref: Reactome:REACT_91263 "Down Regulation of Emi1 through Phosphorylation of Emi1, Gallus gallus" +xref: Reactome:REACT_91382 "SOS phosphorylation and dissociation (IRS), Danio rerio" +xref: Reactome:REACT_91470 "Regulation of KIF20A (MKL2) by phosphorylation, Canis familiaris" +xref: Reactome:REACT_91501 "PIP2 conversion to PIP3, Bos taurus" +xref: Reactome:REACT_91541 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Rattus norvegicus" +xref: Reactome:REACT_91574 "Phosphorylation of DLC2 by MAPK-8, Rattus norvegicus" +xref: Reactome:REACT_91643 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Drosophila melanogaster" +xref: Reactome:REACT_91684 "Phosphorylation of the SA2 Cohesin Complex, Drosophila melanogaster" +xref: Reactome:REACT_91760 "Regulation of KIF23 (MKLP1) by phosphorylation, Danio rerio" +xref: Reactome:REACT_91937 "Phosphorylation of APC component of the destruction complex, Bos taurus" +xref: Reactome:REACT_92033 "Inactivation of Myt1 kinase, Caenorhabditis elegans" +xref: Reactome:REACT_92108 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Rattus norvegicus" +xref: Reactome:REACT_92126 "Activation of S6K1, Oryza sativa" +xref: Reactome:REACT_92148 "Autophosphorylation of PAK-2p34 in the activation loop, Danio rerio" +xref: Reactome:REACT_92219 "Phosphorylation of PDE3B, Caenorhabditis elegans" +xref: Reactome:REACT_92247 "Phosphorylation of the Emi1 DSGxxS degron by Plk1, Canis familiaris" +xref: Reactome:REACT_92407 "Regulation of KIF23 (MKLP1) by phosphorylation, Canis familiaris" +xref: Reactome:REACT_92735 "Autophosphorylation of PAK-2p34 in the activation loop, Taeniopygia guttata" +xref: Reactome:REACT_92736 "Phosphorylation of L1 by ERK, Gallus gallus" +xref: Reactome:REACT_92804 "Phosphorylation of Wee1 kinase by Chk1, Danio rerio" +xref: Reactome:REACT_92852 "SOS phosphorylation and dissociation (SHC), Canis familiaris" +xref: Reactome:REACT_92889 "Phosphorylation of TSC2 by PKB, Sus scrofa" +xref: Reactome:REACT_92915 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Danio rerio" +xref: Reactome:REACT_92929 "RAF1 phosphorylates MEK1, Danio rerio" +xref: Reactome:REACT_92951 "Phosphorylation and activation of Chk1 by ATM, Canis familiaris" +xref: Reactome:REACT_93018 "RAF1 phosphorylates MEK1, Bos taurus" +xref: Reactome:REACT_93105 "Phosphorylation of cPLA2 by ERK-2, Rattus norvegicus" +xref: Reactome:REACT_93124 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes, Mus musculus" +xref: Reactome:REACT_93149 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Dictyostelium discoideum" +xref: Reactome:REACT_93166 "Phosphorylation and activation of Chk1 by ATM, Taeniopygia guttata" +xref: Reactome:REACT_93219 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Xenopus tropicalis" +xref: Reactome:REACT_93221 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Xenopus tropicalis" +xref: Reactome:REACT_93346 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Mus musculus" +xref: Reactome:REACT_93366 "Phosphorylation of cPLA2 by ERK-2, Canis familiaris" +xref: Reactome:REACT_93414 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Drosophila melanogaster" +xref: Reactome:REACT_93440 "Regulation of KIF20A (MKL2) by phosphorylation, Taeniopygia guttata" +xref: Reactome:REACT_93441 "Regulation of KIF23 (MKLP1) by phosphorylation, Gallus gallus" +xref: Reactome:REACT_93613 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Rattus norvegicus" +xref: Reactome:REACT_93615 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Bos taurus" +xref: Reactome:REACT_937 "Phosphorylation of BRCA1 at multiple sites by ATM, Homo sapiens" +xref: Reactome:REACT_93706 "RAF1 phosphorylates MEK1, Canis familiaris" +xref: Reactome:REACT_93746 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Mus musculus" +xref: Reactome:REACT_93878 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Gallus gallus" +xref: Reactome:REACT_94017 "SOS phosphorylation and dissociation (IRS, Crk), Bos taurus" +xref: Reactome:REACT_94113 "Phosphorylation of Cx43 by c-src, Canis familiaris" +xref: Reactome:REACT_94151 "Phosphorylation of Wee1 kinase by Chk1, Xenopus tropicalis" +xref: Reactome:REACT_94248 "SOS phosphorylation and dissociation (SHC), Bos taurus" +xref: Reactome:REACT_94258 "Phosphorylation of p53 at ser-15 by ATM kinase, Sus scrofa" +xref: Reactome:REACT_94298 "Phosphorylation of Cyclin B1 in the CRS domain, Danio rerio" +xref: Reactome:REACT_94397 "Orc1 is phosphorylated by cyclin A/CDK2, Danio rerio" +xref: Reactome:REACT_94428 "Phosphorylation of PD-1, Bos taurus" +xref: Reactome:REACT_94452 "Phosphorylation of MDC1/NFBD1 by ATM (within 2 c-term BRCT domains), Bos taurus" +xref: Reactome:REACT_94464 "Phosphorylation and activation of eIF4B by activated S6K1, Danio rerio" +xref: Reactome:REACT_94562 "Phosphorylation of the Scc1:Cohesion Complex, Caenorhabditis elegans" +xref: Reactome:REACT_94615 "SOS phosphorylation and dissociation (IRS, Crk), Rattus norvegicus" +xref: Reactome:REACT_94784 "Phosphorylation of Cyclin D1 at T286 by glycogen synthase kinase-3 beta, Rattus norvegicus" +xref: Reactome:REACT_94817 "Phosphorylation of the SA2 Cohesin Complex, Rattus norvegicus" +xref: Reactome:REACT_94947 "Autophosphorylation of PAK-2p34 in the activation loop, Canis familiaris" +xref: Reactome:REACT_95052 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Oryza sativa" +xref: Reactome:REACT_95087 "Phosphorylation of the Scc1:Cohesion Complex, Bos taurus" +xref: Reactome:REACT_95088 "Inactivation of Wee1 kinase, Mus musculus" +xref: Reactome:REACT_95089 "Phosphorylation of Cyclin E:Cdk2 complexes by Wee-1, Bos taurus" +xref: Reactome:REACT_95155 "Regulation of NUDC by phosphorylation, Taeniopygia guttata" +xref: Reactome:REACT_95163 "CAK-mediated phosphorylation of Cyclin A:Cdk2, Mus musculus" +xref: Reactome:REACT_95437 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Drosophila melanogaster" +xref: Reactome:REACT_95461 "Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2, Bos taurus" +xref: Reactome:REACT_95504 "Phosphorylation of Cdc25C at Ser216, Xenopus tropicalis" +xref: Reactome:REACT_95769 "PIP2 conversion to PIP3, Xenopus tropicalis" +xref: Reactome:REACT_96 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Homo sapiens" +xref: Reactome:REACT_96039 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Canis familiaris" +xref: Reactome:REACT_96088 "Phosphorylation of PDE3B, Sus scrofa" +xref: Reactome:REACT_96097 "SOS phosphorylation and dissociation (IRS), Rattus norvegicus" +xref: Reactome:REACT_96102 "Phosphorylation of Cx43 by c-src, Gallus gallus" +xref: Reactome:REACT_96129 "Phosphorylation and activation of eIF4G by activated S6K1, Taeniopygia guttata" +xref: Reactome:REACT_96200 "Regulation of NUDC by phosphorylation, Gallus gallus" +xref: Reactome:REACT_96208 "Phosphorylation of COP1 at Ser-387 by ATM, Sus scrofa" +xref: Reactome:REACT_96218 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes, Drosophila melanogaster" +xref: Reactome:REACT_96356 "Free APC/C phosphorylated by Plk1, Rattus norvegicus" +xref: Reactome:REACT_96461 "Phosphorylation of L1 by CK-II, Bos taurus" +xref: Reactome:REACT_96468 "Autophosphorylation of PAK-2p34 in the activation loop, Mus musculus" +xref: Reactome:REACT_96483 "Phosphorylation of COP1 at Ser-387 by ATM, Gallus gallus" +xref: Reactome:REACT_96500 "RAF1 phosphorylates MEK2, Gallus gallus" +xref: Reactome:REACT_96524 "Activation of Cdc25C, Xenopus tropicalis" +xref: Reactome:REACT_96656 "Plk1-mediated phosphorylation of Nlp, Rattus norvegicus" +xref: Reactome:REACT_96666 "Phosphorylation and activation of CHK2 by ATM, Saccharomyces cerevisiae" +xref: Reactome:REACT_96758 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Canis familiaris" +xref: Reactome:REACT_96793 "Activation of S6K1, Danio rerio" +xref: Reactome:REACT_96797 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Rattus norvegicus" +xref: Reactome:REACT_96877 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Sus scrofa" +xref: Reactome:REACT_96899 "Phosphorylation of TSC2 by PKB, Rattus norvegicus" +xref: Reactome:REACT_96968 "Cdc6 protein is phosphorylated by CDK, Mus musculus" +xref: Reactome:REACT_97193 "Phosphorylation and activation of eIF4G by activated S6K1, Canis familiaris" +xref: Reactome:REACT_97218 "Orc1 is phosphorylated by cyclin A/CDK2, Xenopus tropicalis" +xref: Reactome:REACT_97282 "Activation of S6K1, Sus scrofa" +xref: Reactome:REACT_97299 "Phosphorylation of Cyclin E2:Cdk2 complexes by Myt1, Mus musculus" +xref: Reactome:REACT_97458 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Dictyostelium discoideum" +xref: Reactome:REACT_97577 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Bos taurus" +xref: Reactome:REACT_97661 "Mcm2-7 is phosphorylated by DDK, Gallus gallus" +xref: Reactome:REACT_97667 "Phosphorylation of complexed TSC2 by PKB, Canis familiaris" +xref: Reactome:REACT_97748 "Phosphorylation of cPLA2 by ERK-2, Mus musculus" +xref: Reactome:REACT_97759 "Phosphorylation of Cx43 by c-src, Danio rerio" +xref: Reactome:REACT_97847 "Phosphorylation of Cdc25A at Ser-123 by Chk2, Mus musculus" +xref: Reactome:REACT_97905 "Phosphorylation of BRCA1 at multiple sites by ATM, Xenopus tropicalis" +xref: Reactome:REACT_98024 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Mus musculus" +xref: Reactome:REACT_98050 "Phosphorylation of Cdc25C at Ser216, Canis familiaris" +xref: Reactome:REACT_98066 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Saccharomyces cerevisiae" +xref: Reactome:REACT_98109 "Regulation of NUDC by phosphorylation, Mus musculus" +xref: Reactome:REACT_98176 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Bos taurus" +xref: Reactome:REACT_98213 "Phosphorylation of Cdc25A at Ser-123 in response to DNA damage, Xenopus tropicalis" +xref: Reactome:REACT_98253 "RAF1 phosphorylates MEK2, Bos taurus" +xref: Reactome:REACT_98296 "Phosphorylation of Cyclin B1 in the CRS domain, Drosophila melanogaster" +xref: Reactome:REACT_98373 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2, Drosophila melanogaster" +xref: Reactome:REACT_98378 "Phosphorylation of COP1 at Ser-387 by ATM, Danio rerio" +xref: Reactome:REACT_98395 "Phosphorylation and activation of Chk1 by ATM, Arabidopsis thaliana" +xref: Reactome:REACT_98434 "Phosphorylation and inactivation of eEF2K by activated S6K1, Taeniopygia guttata" +xref: Reactome:REACT_98436 "Phosphorylation of 4E-BP1 by activated mTORC1, Gallus gallus" +xref: Reactome:REACT_98443 "Inactivation of Wee1 kinase, Gallus gallus" +xref: Reactome:REACT_98493 "Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197, Drosophila melanogaster" +xref: Reactome:REACT_98558 "Autophosphorylation of PAK-2p34 in the activation loop, Saccharomyces cerevisiae" +xref: Reactome:REACT_98560 "Phosphorylation and activation of CHK2 by ATM, Xenopus tropicalis" +xref: Reactome:REACT_98663 "Regulation of KIF23 (MKLP1) by phosphorylation, Bos taurus" +xref: Reactome:REACT_98708 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Drosophila melanogaster" +xref: Reactome:REACT_98731 "Phosphorylation of Cdc25A at Ser-123 by Chk1, Danio rerio" +xref: Reactome:REACT_98738 "Phosphorylation of TSC2 by PKB, Danio rerio" +xref: Reactome:REACT_98741 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Bos taurus" +xref: Reactome:REACT_98779 "Phosphorylation of Cx43 by c-src, Taeniopygia guttata" +xref: Reactome:REACT_988 "Phosphorylation of MDM2 at serine-395 by ATM kinase, Homo sapiens" +xref: Reactome:REACT_98847 "Phosphorylation of complexed TSC2 by PKB, Mus musculus" +xref: Reactome:REACT_98908 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Rattus norvegicus" +xref: Reactome:REACT_98913 "Phosphorylation of PD-1, Canis familiaris" +xref: Reactome:REACT_98971 "Phosphorylation of AKT2 by PDK1, Rattus norvegicus" +xref: Reactome:REACT_98996 "Free APC/C phosphorylated by Plk1, Danio rerio" +xref: Reactome:REACT_99025 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Taeniopygia guttata" +xref: Reactome:REACT_99053 "CAK-mediated phosphorylation of Cyclin E:Cdk2, Sus scrofa" +xref: Reactome:REACT_99141 "Phosphorylation of NBS1 by ATM, Bos taurus" +xref: Reactome:REACT_99158 "Inactivation of Wee1 kinase, Drosophila melanogaster" +xref: Reactome:REACT_99207 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Taeniopygia guttata" +xref: Reactome:REACT_99231 "Phosphorylation of AKT2 by PDK1, Danio rerio" +xref: Reactome:REACT_99266 "Activation of the Anaphase Promoting Complex (APC) by PLK1, Caenorhabditis elegans" +xref: Reactome:REACT_99302 "Phosphorylation of Cyclin D:Cdk4/6 complexes, Sus scrofa" +xref: Reactome:REACT_99311 "RAF1 phosphorylates MEK1, Mus musculus" +xref: Reactome:REACT_9955 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Homo sapiens" +xref: Reactome:REACT_99556 "Phosphorylation of Ribosomal protein S6 by activated S6K1, Mus musculus" +xref: Reactome:REACT_99560 "RAF1 phosphorylates MEK2, Canis familiaris" +xref: Reactome:REACT_9959 "Phosphoryation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3, Homo sapiens" +xref: Reactome:REACT_99595 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15, Bos taurus" +xref: Reactome:REACT_99713 "Phosphorylation of DLC2 by MAPK-8, Taeniopygia guttata" +xref: Reactome:REACT_9978 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Homo sapiens" +xref: Reactome:REACT_99785 "Phosphorylation of phospho-(Ser45 ) at Thr 41 by GSK-3, Canis familiaris" +xref: Reactome:REACT_9983 "Phosphorylation of APC component of the destruction complex, Homo sapiens" +xref: Reactome:REACT_9987 "Phosphorylation of phospho-(Ser45,Thr41,Ser37) at Ser33 by GSK-3, Homo sapiens" +xref: Reactome:REACT_99929 "Phosphorylation of beta-catenin at Ser45 by CK1 alpha, Gallus gallus" +xref: Reactome:REACT_99966 "Intermolecular autophosphorylation of ATM within dimeric ATM complexes, Schizosaccharomyces pombe" +xref: Reactome:REACT_9997 "Phosphorylation of Cx43 by c-src, Homo sapiens" +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups +relationship: part_of GO:0016310 ! phosphorylation + +[Term] +id: GO:0016310 +name: phosphorylation +namespace: biological_process +def: "The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide." [ISBN:0198506732] +subset: goslim_metagenomics +subset: gosubset_prok +xref: Wikipedia:Phosphorylation +is_a: GO:0006796 ! phosphate-containing compound metabolic process + +[Term] +id: GO:0016323 +name: basolateral plasma membrane +namespace: cellular_component +def: "The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." [GOC:go_curators] +is_a: GO:0044459 ! plasma membrane part + +[Term] +id: GO:0016324 +name: apical plasma membrane +namespace: cellular_component +def: "The region of the plasma membrane located at the apical end of the cell." [GOC:curators] +is_a: GO:0044459 ! plasma membrane part +relationship: part_of GO:0045177 ! apical part of cell + +[Term] +id: GO:0016328 +name: lateral plasma membrane +namespace: cellular_component +def: "The membranes on the sides of epithelial cells which lie at the interface of adjacent cells." [GOC:hb] +is_a: GO:0044459 ! plasma membrane part + +[Term] +id: GO:0016331 +name: morphogenesis of embryonic epithelium +namespace: biological_process +def: "The process in which the anatomical structures of embryonic epithelia are generated and organized." [GOC:jl] +is_a: GO:0002009 ! morphogenesis of an epithelium +is_a: GO:0048598 ! embryonic morphogenesis + +[Term] +id: GO:0016332 +name: establishment or maintenance of polarity of embryonic epithelium +namespace: biological_process +def: "Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization of epithelial cells in an embryo." [GOC:isa_complete, GOC:mah] +is_a: GO:0007163 ! establishment or maintenance of cell polarity +relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium + +[Term] +id: GO:0016337 +name: cell-cell adhesion +namespace: biological_process +def: "The attachment of one cell to another cell via adhesion molecules." [GOC:hb] +subset: gosubset_prok +is_a: GO:0007155 ! cell adhesion + +[Term] +id: GO:0016342 +name: catenin complex +namespace: cellular_component +def: "Complex of peripheral cytoplasmic proteins (alpha-, beta- and gamma-catenin) that interact with the cytoplasmic region of uvomorulin/E-cadherin to connect it to the actin cytoskeleton." [ISBN:0198599323] +is_a: GO:0043234 ! protein complex +is_a: GO:0044459 ! plasma membrane part +relationship: part_of GO:0019897 ! extrinsic component of plasma membrane + +[Term] +id: GO:0016358 +name: dendrite development +namespace: biological_process +def: "The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell." [GOC:jl, ISBN:0198506732] +is_a: GO:0031175 ! neuron projection development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0016462 +name: pyrophosphatase activity +namespace: molecular_function +def: "Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments." [EC:3.6.1.-, GOC:curators] +subset: gosubset_prok +xref: EC:3.6.1.- +is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides + +[Term] +id: GO:0016477 +name: cell migration +namespace: biological_process +def: "The orderly movement of a cell from one site to another, often during the development of a multicellular organism or multicellular structure." [GOC:ems, GOC:pf] +xref: Wikipedia:Cell_migration +is_a: GO:0048870 ! cell motility + +[Term] +id: GO:0016482 +name: cytoplasmic transport +namespace: biological_process +def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, or within the cytoplasm of a cell." [GOC:ai] +synonym: "cytoplasmic streaming" NARROW [] +is_a: GO:0046907 ! intracellular transport + +[Term] +id: GO:0016504 +name: peptidase activator activity +namespace: molecular_function +def: "Increases the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds." [GOC:ai] +subset: gosubset_prok +synonym: "protease activator activity" EXACT [GOC:mah] +xref: Reactome:REACT_6229 "NA activation of TGF-beta, Homo sapiens" +is_a: GO:0008047 ! enzyme activator activity +is_a: GO:0061134 ! peptidase regulator activity +relationship: part_of GO:0010952 ! positive regulation of peptidase activity +relationship: positively_regulates GO:0008233 ! peptidase activity + +[Term] +id: GO:0016567 +name: protein ubiquitination +namespace: biological_process +def: "The process in which one or more ubiquitin groups are added to a protein." [GOC:ai] +synonym: "protein ubiquitinylation" EXACT [] +synonym: "protein ubiquitylation" EXACT [] +is_a: GO:0032446 ! protein modification by small protein conjugation + +[Term] +id: GO:0016568 +name: chromatin modification +namespace: biological_process +def: "The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure." [GOC:mah, PMID:20404130] +subset: goslim_pombe +is_a: GO:0006325 ! chromatin organization + +[Term] +id: GO:0016740 +name: transferase activity +namespace: molecular_function +def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +xref: EC:2 +xref: Reactome:REACT_25050 "Molybdenum ion transfer onto molybdopterin, Homo sapiens" +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +namespace: molecular_function +def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] +comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. +subset: gosubset_prok +xref: EC:2.7 +is_a: GO:0016740 ! transferase activity + +[Term] +id: GO:0016773 +name: phosphotransferase activity, alcohol group as acceptor +namespace: molecular_function +def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor)." [GOC:jl] +subset: gosubset_prok +xref: EC:2.7.1 +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups + +[Term] +id: GO:0016787 +name: hydrolase activity +namespace: molecular_function +def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +xref: EC:3 +xref: Reactome:REACT_110436 "Hydrolysis of phosphatidylcholine, Bos taurus" +xref: Reactome:REACT_111159 "Partial proteolysis of antigen in phagolysosomes, Homo sapiens" +xref: Reactome:REACT_15331 "Hydrolysis of phosphatidylcholine, Homo sapiens" +xref: Reactome:REACT_83734 "Hydrolysis of phosphatidylcholine, Danio rerio" +xref: Reactome:REACT_84047 "Hydrolysis of phosphatidylcholine, Xenopus tropicalis" +xref: Reactome:REACT_87959 "Hydrolysis of phosphatidylcholine, Gallus gallus" +xref: Reactome:REACT_88159 "Hydrolysis of phosphatidylcholine, Canis familiaris" +xref: Reactome:REACT_90118 "Hydrolysis of phosphatidylcholine, Mus musculus" +xref: Reactome:REACT_91045 "Hydrolysis of phosphatidylcholine, Taeniopygia guttata" +xref: Reactome:REACT_98572 "Hydrolysis of phosphatidylcholine, Rattus norvegicus" +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0016817 +name: hydrolase activity, acting on acid anhydrides +namespace: molecular_function +def: "Catalysis of the hydrolysis of any acid anhydride." [GOC:jl] +subset: gosubset_prok +synonym: "hydrolase activity, acting on acid anhydrides, involved in cellular and subcellular movement" NARROW [] +xref: EC:3.6 +is_a: GO:0016787 ! hydrolase activity + +[Term] +id: GO:0016818 +name: hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides +namespace: molecular_function +def: "Catalysis of the hydrolysis of any acid anhydride which contains phosphorus." [GOC:jl] +subset: gosubset_prok +xref: EC:3.6.1 +is_a: GO:0016817 ! hydrolase activity, acting on acid anhydrides + +[Term] +id: GO:0016909 +name: SAP kinase activity +namespace: molecular_function +def: "Catalysis of the phosphorylation of proteins. A family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. Strongly activated by stress signals such as heat or osmotic shock, DNA-damaging agents, inhibitors of protein synthesis and pro-inflammatory cytokines." [GOC:ma] +synonym: "SAPK" EXACT [] +synonym: "stress-activated kinase activity" EXACT [] +synonym: "stress-activated protein kinase activity" EXACT [] +xref: EC:2.7.11.- +is_a: GO:0004707 ! MAP kinase activity + +[Term] +id: GO:0016925 +name: protein sumoylation +namespace: biological_process +alt_id: GO:0006485 +alt_id: GO:0016927 +def: "The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein." [GOC:jl, PMID:11265250] +synonym: "protein sumolation" EXACT [] +synonym: "small ubiquitin-related protein 1 conjugation" EXACT [] +synonym: "SUMO-protein conjugation" EXACT [] +synonym: "sumoylation" EXACT [] +xref: Wikipedia:SUMO_protein +is_a: GO:0032446 ! protein modification by small protein conjugation + +[Term] +id: GO:0017015 +name: regulation of transforming growth factor beta receptor signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of activity of any TGF-beta receptor signaling pathway." [GOC:mah] +synonym: "regulation of TGF-beta receptor signaling pathway" EXACT [] +synonym: "regulation of TGFbeta receptor signaling pathway" EXACT [] +synonym: "regulation of transforming growth factor beta receptor signalling pathway" EXACT [] +is_a: GO:0090092 ! regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0090287 ! regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007179 ! transforming growth factor beta receptor signaling pathway +relationship: regulates GO:0007179 ! transforming growth factor beta receptor signaling pathway + +[Term] +id: GO:0017038 +name: protein import +namespace: biological_process +def: "The directed movement of proteins into a cell or organelle." [GOC:ai] +subset: gosubset_prok +synonym: "protein uptake" EXACT [] +is_a: GO:0015031 ! protein transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0017111 +name: nucleoside-triphosphatase activity +namespace: molecular_function +def: "Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate." [EC:3.6.1.15] +subset: gosubset_prok +synonym: "apyrase activity" BROAD [] +synonym: "NTPase activity" EXACT [EC:3.6.1.15] +synonym: "nucleoside 5-triphosphatase activity" EXACT [EC:3.6.1.15] +synonym: "nucleoside triphosphatase activity" EXACT [] +synonym: "nucleoside triphosphate hydrolase activity" EXACT [EC:3.6.1.15] +synonym: "nucleoside triphosphate phosphohydrolase activity" EXACT [EC:3.6.1.15] +synonym: "nucleoside-5-triphosphate phosphohydrolase activity" EXACT [EC:3.6.1.15] +synonym: "unspecific diphosphate phosphohydrolase activity" EXACT [EC:3.6.1.15] +xref: EC:3.6.1.15 +xref: MetaCyc:NUCLEOSIDE-TRIPHOSPHATASE-RXN +xref: RHEA:23683 +is_a: GO:0016462 ! pyrophosphatase activity + +[Term] +id: GO:0017124 +name: SH3 domain binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins." [GOC:go_curators, Pfam:PF00018] +is_a: GO:0019904 ! protein domain specific binding + +[Term] +id: GO:0017145 +name: stem cell division +namespace: biological_process +def: "The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types." [GOC:jid, ISBN:0582227089] +synonym: "stem cell renewal" EXACT [] +is_a: GO:0051301 ! cell division + +[Term] +id: GO:0017147 +name: Wnt-protein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling." [GOC:jl] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0018105 +name: peptidyl-serine phosphorylation +namespace: biological_process +def: "The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine." [RESID:AA0037] +subset: gosubset_prok +xref: RESID:AA0037 +is_a: GO:0006468 ! protein phosphorylation +is_a: GO:0018209 ! peptidyl-serine modification + +[Term] +id: GO:0018107 +name: peptidyl-threonine phosphorylation +namespace: biological_process +def: "The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine." [RESID:AA0038] +subset: gosubset_prok +xref: RESID:AA0038 +is_a: GO:0006468 ! protein phosphorylation +is_a: GO:0018210 ! peptidyl-threonine modification + +[Term] +id: GO:0018108 +name: peptidyl-tyrosine phosphorylation +namespace: biological_process +def: "The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine." [RESID:AA0039] +subset: gosubset_prok +xref: RESID:AA0039 +is_a: GO:0006468 ! protein phosphorylation +is_a: GO:0018212 ! peptidyl-tyrosine modification + +[Term] +id: GO:0018130 +name: heterocycle biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [ISBN:0198547684] +subset: gosubset_prok +synonym: "heterocycle anabolism" EXACT [] +synonym: "heterocycle biosynthesis" EXACT [] +synonym: "heterocycle formation" EXACT [] +synonym: "heterocycle synthesis" EXACT [] +is_a: GO:0044249 ! cellular biosynthetic process +is_a: GO:0046483 ! heterocycle metabolic process + +[Term] +id: GO:0018193 +name: peptidyl-amino acid modification +namespace: biological_process +def: "The alteration of an amino acid residue in a peptide." [GOC:mah] +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0018209 +name: peptidyl-serine modification +namespace: biological_process +def: "The modification of peptidyl-serine." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0018193 ! peptidyl-amino acid modification + +[Term] +id: GO:0018210 +name: peptidyl-threonine modification +namespace: biological_process +def: "The modification of peptidyl-threonine." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0018193 ! peptidyl-amino acid modification + +[Term] +id: GO:0018212 +name: peptidyl-tyrosine modification +namespace: biological_process +def: "The modification of peptidyl-tyrosine." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0018193 ! peptidyl-amino acid modification + +[Term] +id: GO:0018345 +name: protein palmitoylation +namespace: biological_process +alt_id: GO:0018318 +alt_id: GO:0018349 +def: "The covalent attachment of a palmitoyl group to a protein." [GOC:jl, PMID:15520806] +subset: gosubset_prok +synonym: "protein amino acid palmitoylation" EXACT [GOC:bf] +is_a: GO:0006497 ! protein lipidation +is_a: GO:0043543 ! protein acylation + +[Term] +id: GO:0019200 +name: carbohydrate kinase activity +namespace: molecular_function +def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a carbohydrate substrate molecule." [GOC:jl] +subset: gosubset_prok +is_a: GO:0016301 ! kinase activity +relationship: part_of GO:0046835 ! carbohydrate phosphorylation + +[Term] +id: GO:0019207 +name: kinase regulator activity +namespace: molecular_function +def: "Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:ai] +subset: gosubset_prok +is_a: GO:0030234 ! enzyme regulator activity +relationship: has_part GO:0019900 ! kinase binding +relationship: part_of GO:0042325 ! regulation of phosphorylation +relationship: regulates GO:0016301 ! kinase activity + +[Term] +id: GO:0019210 +name: kinase inhibitor activity +namespace: molecular_function +def: "Stops, prevents or reduces the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] +subset: gosubset_prok +is_a: GO:0004857 ! enzyme inhibitor activity +is_a: GO:0019207 ! kinase regulator activity +relationship: negatively_regulates GO:0016301 ! kinase activity +relationship: part_of GO:0042326 ! negative regulation of phosphorylation + +[Term] +id: GO:0019216 +name: regulation of lipid metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of lipid metabolism" EXACT [] +is_a: GO:0080090 ! regulation of primary metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006629 ! lipid metabolic process +relationship: regulates GO:0006629 ! lipid metabolic process + +[Term] +id: GO:0019218 +name: regulation of steroid metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of steroid metabolism" EXACT [] +is_a: GO:0019216 ! regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008202 ! steroid metabolic process +relationship: regulates GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0019219 +name: regulation of nucleobase-containing compound metabolic process +namespace: biological_process +def: "Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] +synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0051171 ! regulation of nitrogen compound metabolic process +is_a: GO:0080090 ! regulation of primary metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006139 ! nucleobase-containing compound metabolic process +relationship: regulates GO:0006139 ! nucleobase-containing compound metabolic process + +[Term] +id: GO:0019220 +name: regulation of phosphate metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of phosphate metabolism" EXACT [] +is_a: GO:0051174 ! regulation of phosphorus metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006796 ! phosphate-containing compound metabolic process +relationship: regulates GO:0006796 ! phosphate-containing compound metabolic process + +[Term] +id: GO:0019221 +name: cytokine-mediated signaling pathway +namespace: biological_process +def: "A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:19295629] +synonym: "cytokine and chemokine mediated signaling pathway" EXACT [] +synonym: "cytokine mediated signalling pathway" EXACT [] +xref: Reactome:REACT_25229 "Interferon Signaling, Homo sapiens" +is_a: GO:0007166 ! cell surface receptor signaling pathway +is_a: GO:0071345 ! cellular response to cytokine stimulus + +[Term] +id: GO:0019222 +name: regulation of metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of metabolism" EXACT [] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008152 ! metabolic process +relationship: regulates GO:0008152 ! metabolic process + +[Term] +id: GO:0019226 +name: transmission of nerve impulse +namespace: biological_process +def: "The neurological system process in which a signal is transmitted through the nervous system by synaptic transmission and the sequential electrochemical polarization and depolarization that travels across the membrane of a nerve cell (neuron) in response to stimulation." [GOC:curators, ISBN:0815316194] +synonym: "signal transmission along a neuron" EXACT [] +is_a: GO:0035637 ! multicellular organismal signaling +is_a: GO:0050877 ! neurological system process +relationship: part_of GO:0007154 ! cell communication + +[Term] +id: GO:0019228 +name: neuronal action potential +namespace: biological_process +def: "An action potential that occurs in a neuron." [GOC:dph, GOC:isa_complete, GOC:tb] +synonym: "generation of action potential" RELATED [GOC:dph, GOC:tb] +is_a: GO:0001508 ! action potential +relationship: part_of GO:0019226 ! transmission of nerve impulse + +[Term] +id: GO:0019318 +name: hexose metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule." [ISBN:0198506732] +subset: gosubset_prok +synonym: "hexose metabolism" EXACT [] +is_a: GO:0005996 ! monosaccharide metabolic process + +[Term] +id: GO:0019320 +name: hexose catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule." [ISBN:0198506732] +subset: gosubset_prok +synonym: "hexose breakdown" EXACT [] +synonym: "hexose catabolism" EXACT [] +synonym: "hexose degradation" EXACT [] +is_a: GO:0019318 ! hexose metabolic process +is_a: GO:0046365 ! monosaccharide catabolic process + +[Term] +id: GO:0019438 +name: aromatic compound biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai] +subset: gosubset_prok +synonym: "aromatic compound anabolism" EXACT [] +synonym: "aromatic compound biosynthesis" EXACT [] +synonym: "aromatic compound formation" EXACT [] +synonym: "aromatic compound synthesis" EXACT [] +synonym: "aromatic hydrocarbon biosynthesis" NARROW [] +synonym: "aromatic hydrocarbon biosynthetic process" NARROW [] +is_a: GO:0006725 ! cellular aromatic compound metabolic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0019439 +name: aromatic compound catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai] +subset: gosubset_prok +synonym: "aromatic compound breakdown" EXACT [] +synonym: "aromatic compound catabolism" EXACT [] +synonym: "aromatic compound degradation" EXACT [] +synonym: "aromatic hydrocarbon catabolic process" NARROW [] +synonym: "aromatic hydrocarbon catabolism" NARROW [] +is_a: GO:0006725 ! cellular aromatic compound metabolic process +is_a: GO:0044248 ! cellular catabolic process + +[Term] +id: GO:0019534 +name: toxin transporter activity +namespace: molecular_function +def: "Enables the directed movement of a toxin into, out of or within a cell, or between cells. A toxin is a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism." [ISBN:0198506732] +subset: gosubset_prok +is_a: GO:0005215 ! transporter activity +relationship: part_of GO:1901998 ! toxin transport + +[Term] +id: GO:0019538 +name: protein metabolic process +namespace: biological_process +alt_id: GO:0006411 +def: "The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification." [GOC:ma] +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "protein metabolic process and modification" EXACT [] +synonym: "protein metabolism" EXACT [] +synonym: "protein metabolism and modification" EXACT [] +xref: Wikipedia:Protein_metabolism +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0044238 ! primary metabolic process + +[Term] +id: GO:0019637 +name: organophosphate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound." [ISBN:0198506732] +subset: gosubset_prok +synonym: "organophosphate metabolism" EXACT [] +is_a: GO:0006793 ! phosphorus metabolic process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0019693 +name: ribose phosphate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar." [GOC:ai] +subset: gosubset_prok +synonym: "ribose phosphate metabolism" EXACT [] +is_a: GO:0006796 ! phosphate-containing compound metabolic process +is_a: GO:0019637 ! organophosphate metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process + +[Term] +id: GO:0019724 +name: B cell mediated immunity +namespace: biological_process +def: "Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] +comment: This term was improved by GO_REF:0000022. It was moved. +synonym: "B lymphocyte mediated immune effector process" EXACT [] +synonym: "B lymphocyte mediated immunity" EXACT [] +synonym: "B-cell mediated immune effector process" EXACT [] +synonym: "B-cell mediated immunity" EXACT [] +synonym: "B-lymphocyte mediated immune effector process" EXACT [] +synonym: "B-lymphocyte mediated immunity" EXACT [] +is_a: GO:0002449 ! lymphocyte mediated immunity +is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + +[Term] +id: GO:0019725 +name: cellular homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state at the level of the cell." [GOC:isa_complete, GOC:jl, ISBN:0395825172] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_plant +subset: gosubset_prok +is_a: GO:0042592 ! homeostatic process +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0019827 +name: stem cell maintenance +namespace: biological_process +def: "The process in which an organism retains a population of stem cells, preventing the commitment of all stem cell progeny to a differentiated cell fate." [GOC:mah, ISBN:0878932437] +synonym: "maintenance of pluripotency" RELATED [GOC:vk] +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0045596 ! negative regulation of cell differentiation +relationship: part_of GO:0048864 ! stem cell development + +[Term] +id: GO:0019894 +name: kinesin binding +namespace: molecular_function +def: "Interacting selectively and non-covalently and stoichiometrically with kinesin, a member of a superfamily of microtubule-based motor proteins that perform force-generating tasks such as organelle transport and chromosome segregation." [GOC:curators, PMID:8606779] +is_a: GO:0008092 ! cytoskeletal protein binding + +[Term] +id: GO:0019897 +name: extrinsic component of plasma membrane +namespace: cellular_component +alt_id: GO:0000157 +def: "The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:curators, GOC:dos] +subset: gosubset_prok +synonym: "extrinsic to plasma membrane" EXACT [] +synonym: "juxtamembrane" BROAD [] +synonym: "peripheral plasma membrane protein" EXACT [] +is_a: GO:0019898 ! extrinsic component of membrane +is_a: GO:0044459 ! plasma membrane part +intersection_of: GO:0019898 ! extrinsic component of membrane +intersection_of: part_of GO:0005886 ! plasma membrane + +[Term] +id: GO:0019898 +name: extrinsic component of membrane +namespace: cellular_component +alt_id: GO:0030396 +def: "The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos, GOC:jl, GOC:mah] +comment: Note that proteins extrinsic to membranes can be removed by treatments that do not disrupt the membrane, such as salt solutions. +subset: gosubset_prok +synonym: "extrinsic to membrane" EXACT [] +synonym: "peripheral membrane protein" EXACT [] +xref: Wikipedia:Peripheral_membrane_protein +is_a: GO:0044425 ! membrane part + +[Term] +id: GO:0019899 +name: enzyme binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any enzyme." [GOC:jl] +subset: goslim_generic +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0019900 +name: kinase binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group." [GOC:jl] +is_a: GO:0019899 ! enzyme binding + +[Term] +id: GO:0019901 +name: protein kinase binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate." [GOC:jl] +is_a: GO:0019900 ! kinase binding + +[Term] +id: GO:0019902 +name: phosphatase binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any phosphatase." [GOC:jl] +subset: gosubset_prok +is_a: GO:0019899 ! enzyme binding + +[Term] +id: GO:0019903 +name: protein phosphatase binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any protein phosphatase." [GOC:jl] +subset: gosubset_prok +is_a: GO:0019902 ! phosphatase binding + +[Term] +id: GO:0019904 +name: protein domain specific binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a specific domain of a protein." [GOC:go_curators] +subset: gosubset_prok +synonym: "protein domain-specific binding" EXACT [] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0019941 +name: modification-dependent protein catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein." [GOC:go_curators] +subset: gosubset_prok +synonym: "modification-dependent protein breakdown" EXACT [] +synonym: "modification-dependent protein catabolism" EXACT [] +synonym: "modification-dependent protein degradation" EXACT [] +synonym: "modification-dependent proteolysis" EXACT [GOC:rl] +synonym: "modification-initiated protein catabolic process" EXACT [GOC:rl] +synonym: "modification-initiated protein catabolism" EXACT [GOC:rl] +synonym: "modification-initiated proteolysis" EXACT [GOC:rl] +synonym: "protein degradation tagging activity" RELATED [] +synonym: "protein-ligand-dependent protein catabolic process" NARROW [] +synonym: "protein-ligand-dependent protein catabolism" NARROW [] +is_a: GO:0043632 ! modification-dependent macromolecule catabolic process +is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process + +[Term] +id: GO:0019953 +name: sexual reproduction +namespace: biological_process +def: "A reproduction process that creates a new organism by combining the genetic material of two organisms. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two different individuals (parents) join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny." [GOC:jl, http://en.wikipedia.org/wiki/Sexual_reproduction, ISBN:0387520546] +comment: Sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times. +xref: Wikipedia:Sexual_reproduction +is_a: GO:0000003 ! reproduction +is_a: GO:0044703 ! multi-organism reproductive process + +[Term] +id: GO:0020028 +name: hemoglobin import +namespace: biological_process +def: "The directed movement into a tissue, cell or organelle of externally available hemoglobin." [GOC:mb] +synonym: "haemoglobin uptake" EXACT [] +synonym: "hemoglobin uptake" EXACT [] +is_a: GO:0017038 ! protein import + +[Term] +id: GO:0021508 +name: floor plate formation +namespace: biological_process +def: "The formation of a ventral region of glial cells in the neural tube that provides inductive signals for the specification of neuronal cell types. The floor plate is evident at the ventral midline by the neural fold stage." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0007418 ! ventral midline development +relationship: part_of GO:0033505 ! floor plate morphogenesis + +[Term] +id: GO:0021510 +name: spinal cord development +namespace: biological_process +def: "The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0021515 +name: cell differentiation in spinal cord +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the spinal cord. Differentiation includes the processes involved in commitment of a cell to a specific fate." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] +comment: This term was added by GO_REF:0000021. +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0021510 ! spinal cord development + +[Term] +id: GO:0021516 +name: dorsal spinal cord development +namespace: biological_process +def: "The process whose specific outcome is the progression of the dorsal region of the spinal cord over time, from its formation to the mature structure. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11179871] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021510 ! spinal cord development + +[Term] +id: GO:0021527 +name: spinal cord association neuron differentiation +namespace: biological_process +def: "The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of association neurons. Association neurons are cells located in the dorsal portion of the spinal cord that integrate sensory input. Differentiation includes the processes involved in commitment of a cell to a specific fate." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] +comment: This term was added by GO_REF:0000021. +synonym: "spinal cord dorsal interneuron differentiation" EXACT [GOC:dph] +is_a: GO:0021515 ! cell differentiation in spinal cord +is_a: GO:0021953 ! central nervous system neuron differentiation +relationship: part_of GO:0021516 ! dorsal spinal cord development + +[Term] +id: GO:0021532 +name: neural tube patterning +namespace: biological_process +def: "The regionalization process that regulates the coordinated growth that establishes the non-random spatial arrangement of the neural tube." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0003002 ! regionalization +relationship: part_of GO:0021915 ! neural tube development + +[Term] +id: GO:0021533 +name: cell differentiation in hindbrain +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mature cells of the hindbrain. Differentiation includes the processes involved in commitment of a cell to a specific fate." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030902 ! hindbrain development + +[Term] +id: GO:0021535 +name: cell migration in hindbrain +namespace: biological_process +def: "The orderly movement of a cell that will reside in the hindbrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0016477 ! cell migration +relationship: part_of GO:0030902 ! hindbrain development + +[Term] +id: GO:0021536 +name: diencephalon development +namespace: biological_process +def: "The process whose specific outcome is the progression of the diencephalon over time, from its formation to the mature structure. The diencephalon is the paired caudal parts of the prosencephalon from which the thalamus, hypothalamus, epithalamus and subthalamus are derived; these regions regulate autonomic, visceral and endocrine function, and process information directed to the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021537 +name: telencephalon development +namespace: biological_process +def: "The process whose specific outcome is the progression of the telencephalon over time, from its formation to the mature structure. The telencephalon is the paired anteriolateral division of the prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] +comment: This term was added by GO_REF:0000021. +synonym: "cerebrum development" EXACT [GOC:sl, PMID:22331407] +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021541 +name: ammon gyrus development +namespace: biological_process +def: "The process whose specific outcome is the progression of the ammon gyrus over time, from its formation to the mature structure. The ammon gyrus, often subdivided into the CA1 and CA3 regions, is one of the two interlocking gyri of the hippocampus that is rich in large pyramidal neurons." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +synonym: "Ammon's horn development" RELATED [GOC:cls] +synonym: "cornu ammonis development" RELATED [GOC:cls] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021766 ! hippocampus development + +[Term] +id: GO:0021543 +name: pallium development +namespace: biological_process +def: "The process whose specific outcome is the progression of the pallium over time, from its formation to the mature structure. The pallium is the roof region of the telencephalon." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021537 ! telencephalon development + +[Term] +id: GO:0021544 +name: subpallium development +namespace: biological_process +def: "The process whose specific outcome is the progression of the subpallium over time, from its formation to the mature structure. The subpallium is the base region of the telencephalon." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021537 ! telencephalon development + +[Term] +id: GO:0021545 +name: cranial nerve development +namespace: biological_process +def: "The process whose specific outcome is the progression of the cranial nerves over time, from its formation to the mature structure. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0021675 ! nerve development + +[Term] +id: GO:0021549 +name: cerebellum development +namespace: biological_process +def: "The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0022037 ! metencephalon development + +[Term] +id: GO:0021551 +name: central nervous system morphogenesis +namespace: biological_process +def: "The process in which the anatomical structure of the central nervous system is generated and organized. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0582227089] +comment: This term was added by GO_REF:0000021. +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0021575 +name: hindbrain morphogenesis +namespace: biological_process +def: "The process in which the anatomical structure of the hindbrain is generated and organized. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +synonym: "rhombencephalon morphogenesis" RELATED [] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0030902 ! hindbrain development + +[Term] +id: GO:0021576 +name: hindbrain formation +namespace: biological_process +def: "The process that gives rise to the hindbrain. This process pertains to the initial formation of a structure from unspecified parts. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021575 ! hindbrain morphogenesis + +[Term] +id: GO:0021587 +name: cerebellum morphogenesis +namespace: biological_process +def: "The process in which the anatomical structure of the cerebellum is generated and organized. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. The cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021549 ! cerebellum development +relationship: part_of GO:0021575 ! hindbrain morphogenesis + +[Term] +id: GO:0021588 +name: cerebellum formation +namespace: biological_process +def: "The process that gives rise to the cerebellum. This process pertains to the initial formation of a structure from unspecified parts. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. The cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021576 ! hindbrain formation +relationship: part_of GO:0021587 ! cerebellum morphogenesis + +[Term] +id: GO:0021675 +name: nerve development +namespace: biological_process +def: "The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0021681 +name: cerebellar granular layer development +namespace: biological_process +def: "The process whose specific outcome is the progression of the cerebellar granule layer over time, from its formation to the mature structure. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021695 ! cerebellar cortex development + +[Term] +id: GO:0021683 +name: cerebellar granular layer morphogenesis +namespace: biological_process +def: "The process in which the anatomical structure of the cerebellar granular layer is generated and organized. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021681 ! cerebellar granular layer development +relationship: part_of GO:0021696 ! cerebellar cortex morphogenesis + +[Term] +id: GO:0021684 +name: cerebellar granular layer formation +namespace: biological_process +def: "The process that gives rise to the cerebellar granule layer. This process pertains to the initial formation of a structure from unspecified parts. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021683 ! cerebellar granular layer morphogenesis +relationship: part_of GO:0021697 ! cerebellar cortex formation + +[Term] +id: GO:0021695 +name: cerebellar cortex development +namespace: biological_process +def: "The process whose specific outcome is the progression of the cerebellar cortex over time, from its formation to the mature structure. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021549 ! cerebellum development + +[Term] +id: GO:0021696 +name: cerebellar cortex morphogenesis +namespace: biological_process +def: "The process in which the anatomical structure of the cranial nerves are generated and organized. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021587 ! cerebellum morphogenesis +relationship: part_of GO:0021695 ! cerebellar cortex development + +[Term] +id: GO:0021697 +name: cerebellar cortex formation +namespace: biological_process +def: "The process that gives rise to the cerebellar cortex. This process pertains to the initial formation of a structure from unspecified parts. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0838580343] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021696 ! cerebellar cortex morphogenesis + +[Term] +id: GO:0021700 +name: developmental maturation +namespace: biological_process +def: "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +subset: goslim_generic +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0021707 +name: cerebellar granule cell differentiation +namespace: biological_process +def: "The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar granule cell. Differentiation includes the processes involved in commitment of a neuroblast to a granule cell fate. A granule cell is a glutamatergic interneuron found in the cerebellar cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15157725] +comment: This term was added by GO_REF:0000021. +is_a: GO:0021533 ! cell differentiation in hindbrain +is_a: GO:0021953 ! central nervous system neuron differentiation +relationship: part_of GO:0021684 ! cerebellar granular layer formation + +[Term] +id: GO:0021732 +name: midbrain-hindbrain boundary maturation +namespace: biological_process +def: "A developmental process, independent of morphogenetic (shape) change, that is required for the midbrain-hindbrain boundary to attain its fully functional state. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15541513] +comment: This term was added by GO_REF:0000021. +synonym: "isthmus maturation" RELATED [] +synonym: "MHB maturation" RELATED [] +is_a: GO:0071695 ! anatomical structure maturation +relationship: part_of GO:0030917 ! midbrain-hindbrain boundary development + +[Term] +id: GO:0021756 +name: striatum development +namespace: biological_process +def: "The progression of the striatum over time from its initial formation until its mature state. The striatum is a region of the forebrain consisting of the caudate nucleus, putamen and fundus striati." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420] +comment: This term was added by GO_REF:0000021. +synonym: "neostriatum development" EXACT [] +synonym: "striate nucleus development" EXACT [] +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021544 ! subpallium development + +[Term] +id: GO:0021757 +name: caudate nucleus development +namespace: biological_process +def: "The progression of the caudate nucleus over time from its initial formation until its mature state. The caudate nucleus is the C-shaped structures of the striatum containing input neurons involved with control of voluntary movement in the brain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048857 ! neural nucleus development +relationship: part_of GO:0021756 ! striatum development + +[Term] +id: GO:0021758 +name: putamen development +namespace: biological_process +def: "The progression of the putamen over time from its initial formation until its mature state. The putamen is the lens-shaped basal ganglion involved with control of voluntary movement in the brain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021756 ! striatum development + +[Term] +id: GO:0021761 +name: limbic system development +namespace: biological_process +def: "The progression of the limbic system over time from its initial formation until its mature state. The limbic system is a collection of structures in the brain involved in emotion, motivation and emotional aspects of memory." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048731 ! system development +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021766 +name: hippocampus development +namespace: biological_process +def: "The progression of the hippocampus over time from its initial formation until its mature state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420, UBERON:0002421] +comment: This term was added by GO_REF:0000021. +synonym: "hippocampal formation development" EXACT [ABA:HPF] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021543 ! pallium development +relationship: part_of GO:0021761 ! limbic system development + +[Term] +id: GO:0021767 +name: mammillary body development +namespace: biological_process +def: "The progression of the mammillary body over time from its initial formation until its mature state. The mammillary body is a protrusion at the posterior end of the hypothalamus that contains hypothalamic nuclei." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021536 ! diencephalon development +relationship: part_of GO:0021761 ! limbic system development + +[Term] +id: GO:0021772 +name: olfactory bulb development +namespace: biological_process +def: "The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, ISBN:0878937420] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021988 ! olfactory lobe development + +[Term] +id: GO:0021779 +name: oligodendrocyte cell fate commitment +namespace: biological_process +def: "The process in which the developmental fate of a cell becomes restricted such that it will develop into an oligodendrocyte." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0021781 ! glial cell fate commitment +is_a: GO:0048709 ! oligodendrocyte differentiation + +[Term] +id: GO:0021781 +name: glial cell fate commitment +namespace: biological_process +def: "The process in which the developmental fate of a cell becomes restricted such that it will develop into a glial cell." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0021782 +name: glial cell development +namespace: biological_process +def: "The process aimed at the progression of a glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048468 ! cell development +relationship: part_of GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0021794 +name: thalamus development +namespace: biological_process +def: "The process in which the thalamus changes over time, from its initial formation to its mature state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021536 ! diencephalon development + +[Term] +id: GO:0021795 +name: cerebral cortex cell migration +namespace: biological_process +def: "The orderly movement of cells from one site to another in the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0022029 ! telencephalon cell migration +relationship: part_of GO:0021987 ! cerebral cortex development + +[Term] +id: GO:0021797 +name: forebrain anterior/posterior pattern specification +namespace: biological_process +def: "The creation of specific areas of progenitor domains along the anterior-posterior axis of the developing forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +synonym: "forebrain anterior-posterior pattern specification" EXACT [] +is_a: GO:0009952 ! anterior/posterior pattern specification +relationship: part_of GO:0021871 ! forebrain regionalization + +[Term] +id: GO:0021799 +name: cerebral cortex radially oriented cell migration +namespace: biological_process +def: "The migration of cells in the developing cerebral cortex in which cells move from the ventricular and/or subventricular zone toward the surface of the brain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] +comment: This term was added by GO_REF:0000021. +is_a: GO:0021795 ! cerebral cortex cell migration + +[Term] +id: GO:0021801 +name: cerebral cortex radial glia guided migration +namespace: biological_process +def: "The radial migration of neuronal or glial precursor cells along radial glial cells during the development of the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] +comment: This term was added by GO_REF:0000021. +synonym: "glial-guided locomotion" RELATED [PMID:12626695] +is_a: GO:0021799 ! cerebral cortex radially oriented cell migration + +[Term] +id: GO:0021819 +name: layer formation in cerebral cortex +namespace: biological_process +def: "The detachment of cells from radial glial fibers at the appropriate time when they cease to migrate and form distinct layer in the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] +comment: This term was added by GO_REF:0000021. +synonym: "cerebral cortex lamination" RELATED [PMID:12626695] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0021801 ! cerebral cortex radial glia guided migration + +[Term] +id: GO:0021846 +name: cell proliferation in forebrain +namespace: biological_process +def: "The creation of greater cell numbers in the forebrain due to cell division of progenitor cells." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0061351 ! neural precursor cell proliferation +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021852 +name: pyramidal neuron migration +namespace: biological_process +def: "The migration of pyramidal a neuron precursor from the ventricular zone to the correct layer of the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] +comment: This term was added by GO_REF:0000021. +synonym: "projection neuron migration" RELATED [PMID:12626695] +is_a: GO:0001764 ! neuron migration +is_a: GO:0021801 ! cerebral cortex radial glia guided migration +relationship: part_of GO:0021860 ! pyramidal neuron development + +[Term] +id: GO:0021854 +name: hypothalamus development +namespace: biological_process +def: "The progression of the hypothalamus region of the forebrain, from its initial formation to its mature state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021536 ! diencephalon development +relationship: part_of GO:0021761 ! limbic system development + +[Term] +id: GO:0021855 +name: hypothalamus cell migration +namespace: biological_process +def: "The directed movement of a cell into the hypothalamus region of the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0016477 ! cell migration +relationship: part_of GO:0021854 ! hypothalamus development + +[Term] +id: GO:0021859 +name: pyramidal neuron differentiation +namespace: biological_process +def: "The process in which a neuroblast or one of its progeny commits to a pyramidal neuron fate, migrates from the ventricular zone to the appropriate layer in the cortex and develops into a mature neuron." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +synonym: "projection neuron differentiation" BROAD [PMID:16226447] +is_a: GO:0030182 ! neuron differentiation + +[Term] +id: GO:0021860 +name: pyramidal neuron development +namespace: biological_process +def: "The progression of a pyramidal neuron from its initial formation to its mature state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +synonym: "projection neuron development" BROAD [PMID:16226447] +is_a: GO:0021884 ! forebrain neuron development +relationship: part_of GO:0021859 ! pyramidal neuron differentiation + +[Term] +id: GO:0021861 +name: forebrain radial glial cell differentiation +namespace: biological_process +def: "The process in which neuroepithelial cells of the neural tube give rise to radial glial cells, specialized bipotential progenitors cells of the forebrain. Differentiation includes the processes involved in commitment of a cell to a specific fate." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:16226447] +comment: This term was added by GO_REF:0000021. +synonym: "radial glial cell differentiation in forebrain" EXACT [GOC:curators] +is_a: GO:0060019 ! radial glial cell differentiation +relationship: part_of GO:0021872 ! forebrain generation of neurons + +[Term] +id: GO:0021871 +name: forebrain regionalization +namespace: biological_process +def: "The regionalization process resulting in the creation of areas within the forebrain that will direct the behavior of cell migration in differentiation as the forebrain develops." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:isa_complete, GOC:jid, GOC:mtg_15jun06, PMID:16226447] +comment: This term was added by GO_REF:0000021. +is_a: GO:0003002 ! regionalization +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021872 +name: forebrain generation of neurons +namespace: biological_process +def: "The process in which nerve cells are generated in the forebrain. This includes the production of neuroblasts from and their differentiation into neurons." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +synonym: "generation of neurons in forebrain" EXACT [GOC:curators] +is_a: GO:0048699 ! generation of neurons +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021873 +name: forebrain neuroblast division +namespace: biological_process +def: "The division of a neuroblast located in the forebrain. Neuroblast division gives rise to at least another neuroblast." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0055057 ! neuroblast division +relationship: part_of GO:0021872 ! forebrain generation of neurons + +[Term] +id: GO:0021874 +name: Wnt signaling pathway involved in forebrain neuroblast division +namespace: biological_process +def: "The series of molecular signals initiated by binding of Wnt protein to a receptor on the surface of the target cell that contributes to the self renewal of neuroblasts in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:16226447] +comment: This term was added by GO_REF:0000021. +synonym: "Wnt receptor signaling pathway involved in forebrain neuroblast division" EXACT [] +synonym: "Wnt receptor signalling pathway in forebrain neuroblast division" EXACT [] +synonym: "Wnt-activated signaling pathway involved in forebrain neuroblast division" EXACT [GOC:signaling] +is_a: GO:0016055 ! Wnt signaling pathway +intersection_of: GO:0016055 ! Wnt signaling pathway +intersection_of: part_of GO:0021873 ! forebrain neuroblast division +relationship: part_of GO:0021873 ! forebrain neuroblast division + +[Term] +id: GO:0021879 +name: forebrain neuron differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a neuron that will reside in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:16226447] +comment: This term was added by GO_REF:0000021. +is_a: GO:0021953 ! central nervous system neuron differentiation +relationship: part_of GO:0021872 ! forebrain generation of neurons + +[Term] +id: GO:0021884 +name: forebrain neuron development +namespace: biological_process +def: "The process whose specific outcome is the progression of a neuron that resides in the forebrain, from its initial commitment to its fate, to the fully functional differentiated cell." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0021954 ! central nervous system neuron development +relationship: part_of GO:0021879 ! forebrain neuron differentiation + +[Term] +id: GO:0021885 +name: forebrain cell migration +namespace: biological_process +def: "The orderly movement of a cell from one site to another at least one of which is located in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0016477 ! cell migration +relationship: part_of GO:0030900 ! forebrain development + +[Term] +id: GO:0021889 +name: olfactory bulb interneuron differentiation +namespace: biological_process +def: "The process in which a neuroblast acquires specialized features of an interneuron residing in the olfactory bulb." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] +comment: This term was added by GO_REF:0000021. +is_a: GO:0021879 ! forebrain neuron differentiation +relationship: part_of GO:0021772 ! olfactory bulb development + +[Term] +id: GO:0021891 +name: olfactory bulb interneuron development +namespace: biological_process +def: "The process whose specific outcome is the progression of an interneuron residing in the olfactory bulb, from its initial commitment, to the fully functional differentiated cell." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048666 ! neuron development +relationship: part_of GO:0021889 ! olfactory bulb interneuron differentiation + +[Term] +id: GO:0021903 +name: rostrocaudal neural tube patterning +namespace: biological_process +def: "The process in which the neural tube is divided into specific regions along the rostrocaudal axis." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] +comment: This term was added by GO_REF:0000021. +synonym: "anterior-posterior neural tube patterning" RELATED [GOC:dph] +is_a: GO:0009952 ! anterior/posterior pattern specification +relationship: part_of GO:0021532 ! neural tube patterning + +[Term] +id: GO:0021904 +name: dorsal/ventral neural tube patterning +namespace: biological_process +def: "The process in which the neural tube is regionalized in the dorsoventral axis." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] +comment: This term was added by GO_REF:0000021. +synonym: "dorsal-ventral neural tube patterning" EXACT [GOC:dph] +synonym: "dorsoventral neural tube patterning" EXACT [GOC:mah] +is_a: GO:0009953 ! dorsal/ventral pattern formation +relationship: part_of GO:0021532 ! neural tube patterning + +[Term] +id: GO:0021915 +name: neural tube development +namespace: biological_process +def: "The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007399 ! nervous system development +relationship: part_of GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0021932 +name: hindbrain radial glia guided cell migration +namespace: biological_process +def: "The radially directed movement of a cell along radial glial cells in the hindbrain. Radial migration refers to a directed movement from the internal ventricular area to the outer surface of the hindbrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15157725] +comment: This term was added by GO_REF:0000021. +is_a: GO:0021535 ! cell migration in hindbrain + +[Term] +id: GO:0021943 +name: formation of radial glial scaffolds +namespace: biological_process +def: "The formation of scaffolds from a radial glial cell. The scaffolds are used as a substrate for the radial migration of cells." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15157725] +comment: This term was added by GO_REF:0000021. +synonym: "Bergmann fiber biosynthesis" RELATED [PMID:15157725] +synonym: "Bergmann fiber formation" RELATED [PMID:15157725] +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +relationship: part_of GO:0021932 ! hindbrain radial glia guided cell migration + +[Term] +id: GO:0021953 +name: central nervous system neuron differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the central nervous system." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0030182 ! neuron differentiation +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0021954 +name: central nervous system neuron development +namespace: biological_process +def: "The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0048666 ! neuron development +relationship: part_of GO:0021953 ! central nervous system neuron differentiation + +[Term] +id: GO:0021983 +name: pituitary gland development +namespace: biological_process +def: "The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +synonym: "hypophysis development" RELATED [GOC:dph] +is_a: GO:0048732 ! gland development +relationship: part_of GO:0021536 ! diencephalon development +relationship: part_of GO:0035270 ! endocrine system development + +[Term] +id: GO:0021984 +name: adenohypophysis development +namespace: biological_process +def: "The progression of the adenohypophysis over time from its initial formation until its mature state. The adenohypophysis is the anterior part of the pituitary. It secretes a variety of hormones and its function is regulated by the hypothalamus." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +synonym: "adenophysis development" EXACT [] +synonym: "anterior pituitary development" EXACT [] +synonym: "anterior pituitary gland development" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021983 ! pituitary gland development + +[Term] +id: GO:0021987 +name: cerebral cortex development +namespace: biological_process +def: "The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +synonym: "neocortex development" RELATED [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021543 ! pallium development + +[Term] +id: GO:0021988 +name: olfactory lobe development +namespace: biological_process +def: "The progression of the olfactory lobe over time from its initial formation until its mature state. The olfactory lobe is the area of the brain that process the neural inputs for the sense of smell." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021537 ! telencephalon development + +[Term] +id: GO:0022004 +name: midbrain-hindbrain boundary maturation during brain development +namespace: biological_process +def: "A developmental process occurring after the brain has been specified along the neural axis that is required for the midbrain-hindbrain boundary to attain its fully functional state. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:15541513] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021732 ! midbrain-hindbrain boundary maturation + +[Term] +id: GO:0022008 +name: neurogenesis +namespace: biological_process +def: "Generation of cells within the nervous system." [GO_REF:0000021, GOC:cls, GOC:curators, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +synonym: "nervous system cell generation" EXACT systematic_synonym [] +synonym: "neural cell differentiation" RELATED [GOC:BHF, GOC:dph] +xref: Wikipedia:Neurogenesis +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0022009 +name: central nervous system vasculogenesis +namespace: biological_process +def: "The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes in the central nervous system. The capillary endothelial cells in the brain are specialized to form the blood-brain barrier." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0001570 ! vasculogenesis +relationship: part_of GO:0014045 ! establishment of endothelial blood-brain barrier + +[Term] +id: GO:0022010 +name: central nervous system myelination +namespace: biological_process +def: "The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of oligodendrocytes in the central nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +synonym: "myelination in central nervous system" EXACT [] +is_a: GO:0032291 ! axon ensheathment in central nervous system +is_a: GO:0042552 ! myelination +relationship: part_of GO:0014003 ! oligodendrocyte development + +[Term] +id: GO:0022029 +name: telencephalon cell migration +namespace: biological_process +def: "The orderly movement of a cell from one site to another at least one of which is located in the telencephalon." [GO_REF:0000021, GOC:cls, GOC:curators, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0021885 ! forebrain cell migration +relationship: part_of GO:0021537 ! telencephalon development + +[Term] +id: GO:0022037 +name: metencephalon development +namespace: biological_process +def: "The process whose specific outcome is the progression of the metencephalon over time, from its formation to the mature structure." [GO_REF:0000021, GOC:cls, GOC:curators, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030902 ! hindbrain development + +[Term] +id: GO:0022402 +name: cell cycle process +namespace: biological_process +def: "The cellular process that ensures successive accurate and complete genome replication and chromosome segregation." [GOC:isa_complete, GOC:mtg_cell_cycle] +subset: gocheck_do_not_manually_annotate +subset: gosubset_prok +is_a: GO:0044763 ! single-organism cellular process +intersection_of: GO:0044763 ! single-organism cellular process +intersection_of: part_of GO:0007049 ! cell cycle +relationship: part_of GO:0007049 ! cell cycle + +[Term] +id: GO:0022404 +name: molting cycle process +namespace: biological_process +def: "A multicellular organismal process involved in the periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin." [GOC:isa_complete] +is_a: GO:0044707 ! single-multicellular organism process +relationship: part_of GO:0042303 ! molting cycle + +[Term] +id: GO:0022405 +name: hair cycle process +namespace: biological_process +def: "A multicellular organismal process involved in the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:isa_complete] +is_a: GO:0022404 ! molting cycle process +relationship: part_of GO:0042633 ! hair cycle + +[Term] +id: GO:0022407 +name: regulation of cell-cell adhesion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of attachment of a cell to another cell." [GOC:isa_complete] +is_a: GO:0030155 ! regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016337 ! cell-cell adhesion +relationship: regulates GO:0016337 ! cell-cell adhesion + +[Term] +id: GO:0022408 +name: negative regulation of cell-cell adhesion +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell." [GOC:isa_complete] +synonym: "down regulation of cell-cell adhesion" EXACT [] +synonym: "down-regulation of cell-cell adhesion" EXACT [] +synonym: "downregulation of cell-cell adhesion" EXACT [] +synonym: "inhibition of cell-cell adhesion" NARROW [] +is_a: GO:0007162 ! negative regulation of cell adhesion +is_a: GO:0022407 ! regulation of cell-cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016337 ! cell-cell adhesion +relationship: negatively_regulates GO:0016337 ! cell-cell adhesion + +[Term] +id: GO:0022409 +name: positive regulation of cell-cell adhesion +namespace: biological_process +def: "Any process that activates or increases the rate or extent of cell adhesion to another cell." [GOC:isa_complete] +synonym: "activation of cell-cell adhesion" NARROW [] +synonym: "stimulation of cell-cell adhesion" NARROW [] +synonym: "up regulation of cell-cell adhesion" EXACT [] +synonym: "up-regulation of cell-cell adhesion" EXACT [] +synonym: "upregulation of cell-cell adhesion" EXACT [] +is_a: GO:0022407 ! regulation of cell-cell adhesion +is_a: GO:0045785 ! positive regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016337 ! cell-cell adhesion +relationship: positively_regulates GO:0016337 ! cell-cell adhesion + +[Term] +id: GO:0022411 +name: cellular component disassembly +namespace: biological_process +alt_id: GO:0071845 +def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] +subset: goslim_pir +subset: gosubset_prok +synonym: "cell structure disassembly" EXACT [] +synonym: "cellular component disassembly at cellular level" EXACT [] +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0022412 +name: cellular process involved in reproduction in multicellular organism +namespace: biological_process +def: "A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism." [GOC:isa_complete] +synonym: "reproductive cellular process in multicellular organism" EXACT [GOC:curators] +is_a: GO:0048610 ! cellular process involved in reproduction +intersection_of: GO:0044763 ! single-organism cellular process +intersection_of: part_of GO:0032504 ! multicellular organism reproduction +relationship: part_of GO:0032504 ! multicellular organism reproduction + +[Term] +id: GO:0022414 +name: reproductive process +namespace: biological_process +def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] +subset: gosubset_prok +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0000003 ! reproduction + +[Term] +id: GO:0022602 +name: ovulation cycle process +namespace: biological_process +def: "A process involved in the sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years." [GOC:isa_complete] +synonym: "estrous cycle process" RELATED [] +synonym: "menstrual cycle process" RELATED [] +is_a: GO:0044699 ! single-organism process +is_a: GO:0048511 ! rhythmic process +relationship: part_of GO:0042698 ! ovulation cycle + +[Term] +id: GO:0022603 +name: regulation of anatomical structure morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of morphogenesis" EXACT [] +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009653 ! anatomical structure morphogenesis +relationship: regulates GO:0009653 ! anatomical structure morphogenesis + +[Term] +id: GO:0022604 +name: regulation of cell morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized." [GOC:isa_complete] +subset: gosubset_prok +synonym: "negative regulation of cell shape and cell size" RELATED [GOC:dph, GOC:tb] +synonym: "positive regulation of cell shape and cell size" RELATED [GOC:dph, GOC:tb] +synonym: "regulation of cell shape and cell size" RELATED [GOC:dph, GOC:tb] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000902 ! cell morphogenesis +relationship: regulates GO:0000902 ! cell morphogenesis + +[Term] +id: GO:0022607 +name: cellular component assembly +namespace: biological_process +alt_id: GO:0071844 +def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +synonym: "cell structure assembly" EXACT [] +synonym: "cellular component assembly at cellular level" EXACT [] +is_a: GO:0016043 ! cellular component organization +relationship: part_of GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0022610 +name: biological adhesion +namespace: biological_process +def: "The attachment of a cell or organism to a substrate or other organism." [GOC:isa_complete] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0022612 +name: gland morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a gland are generated and organized." [GOC:isa_complete] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048732 ! gland development + +[Term] +id: GO:0022892 +name: substrate-specific transporter activity +namespace: molecular_function +def: "Enables the directed movement of a specific substance or group of related substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:mtg_transport] +subset: gosubset_prok +is_a: GO:0005215 ! transporter activity + +[Term] +id: GO:0023014 +name: signal transduction by phosphorylation +namespace: biological_process +def: "A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate." [GOC:mtg_signal, GOC:signaling] +comment: For annotation of intracellular kinases, consider also annotating to 'signal transduction by phosphorylation ; GO:0023014'. +synonym: "signal transduction via phosphorylation event" RELATED [GOC:bf] +synonym: "signal transmission via phosphorylation event" RELATED [GOC:bf] +is_a: GO:0007165 ! signal transduction +is_a: GO:0016310 ! phosphorylation +is_a: GO:0044710 ! single-organism metabolic process +creation_date: 2010-02-16T09:30:50Z + +[Term] +id: GO:0023019 +name: signal transduction involved in regulation of gene expression +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another." [GOC:mtg_signal] +synonym: "regulation of gene expression as a consequence of signal transmission" RELATED [GOC:bf] +is_a: GO:0007165 ! signal transduction +intersection_of: GO:0007165 ! signal transduction +intersection_of: part_of GO:0010468 ! regulation of gene expression +relationship: part_of GO:0010468 ! regulation of gene expression +creation_date: 2010-02-16T09:30:50Z + +[Term] +id: GO:0023051 +name: regulation of signaling +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a signaling process." [GOC:mtg_signal] +synonym: "regulation of signaling process" RELATED [GOC:bf] +synonym: "regulation of signalling process" RELATED [GOC:mah] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0023052 ! signaling +relationship: regulates GO:0044700 ! single organism signaling +creation_date: 2010-02-16T09:30:50Z + +[Term] +id: GO:0023052 +name: signaling +namespace: biological_process +alt_id: GO:0023046 +def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] +comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological signaling" EXACT [] +synonym: "signaling process" EXACT [] +synonym: "signalling" EXACT [] +synonym: "signalling process" RELATED [GOC:mah] +is_a: GO:0008150 ! biological_process +creation_date: 2010-02-16T09:30:50Z + +[Term] +id: GO:0023056 +name: positive regulation of signaling +namespace: biological_process +def: "Any process that activates, maintains or increases the frequency, rate or extent of a signaling process." [GOC:mtg_signal] +synonym: "positive regulation of signaling process" RELATED [GOC:bf] +synonym: "positive regulation of signalling process" EXACT [GOC:mah] +is_a: GO:0023051 ! regulation of signaling +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0023052 ! signaling +relationship: positively_regulates GO:0044700 ! single organism signaling +creation_date: 2010-02-16T09:30:50Z + +[Term] +id: GO:0023057 +name: negative regulation of signaling +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process." [GOC:mtg_signal] +synonym: "negative regulation of signaling process" RELATED [GOC:bf] +synonym: "negative regulation of signalling process" RELATED [GOC:mah] +is_a: GO:0023051 ! regulation of signaling +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0023052 ! signaling +relationship: negatively_regulates GO:0044700 ! single organism signaling +creation_date: 2010-02-16T09:30:50Z + +[Term] +id: GO:0023061 +name: signal release +namespace: biological_process +def: "The process in which a signal is secreted or discharged into the extracellular medium from a cellular source." [GOC:mtg_signal] +synonym: "signal secretion" EXACT [GOC:bf] +is_a: GO:0032940 ! secretion by cell +relationship: part_of GO:0007267 ! cell-cell signaling +creation_date: 2010-02-16T09:30:50Z + +[Term] +id: GO:0030001 +name: metal ion transport +namespace: biological_process +def: "The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +subset: gosubset_prok +synonym: "heavy metal ion transport" NARROW [] +is_a: GO:0006812 ! cation transport + +[Term] +id: GO:0030003 +name: cellular cation homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of cations at the level of a cell." [GOC:ceb, GOC:mah] +subset: gosubset_prok +is_a: GO:0006873 ! cellular ion homeostasis +is_a: GO:0055080 ! cation homeostasis + +[Term] +id: GO:0030010 +name: establishment of cell polarity +namespace: biological_process +alt_id: GO:0000283 +alt_id: GO:0030468 +def: "The specification and formation of anisotropic intracellular organization or cell growth patterns." [GOC:mah] +synonym: "bud site selection/establishment of cell polarity" NARROW [] +synonym: "cell polarization" EXACT [] +is_a: GO:0007163 ! establishment or maintenance of cell polarity + +[Term] +id: GO:0030016 +name: myofibril +namespace: cellular_component +def: "The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism." [ISBN:0815316194] +synonym: "striated muscle fiber" RELATED [] +synonym: "striated muscle fibre" RELATED [] +xref: Wikipedia:Myofibril +is_a: GO:0043292 ! contractile fiber + +[Term] +id: GO:0030017 +name: sarcomere +namespace: cellular_component +def: "The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." [ISBN:0815316194] +xref: Wikipedia:Sarcomere +is_a: GO:0044449 ! contractile fiber part +relationship: part_of GO:0030016 ! myofibril + +[Term] +id: GO:0030018 +name: Z disc +namespace: cellular_component +def: "Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached." [GOC:mtg_muscle, ISBN:0815316194] +synonym: "Z band" EXACT [] +synonym: "Z disk" EXACT [] +synonym: "Z line" EXACT [] +is_a: GO:0044449 ! contractile fiber part +relationship: part_of GO:0031674 ! I band + +[Term] +id: GO:0030027 +name: lamellipodium +namespace: cellular_component +def: "A thin sheetlike process extended by the leading edge of a crawling fibroblast; contains a dense meshwork of actin filaments." [ISBN:0815316194] +xref: Wikipedia:Lamellipodia +is_a: GO:0042995 ! cell projection +relationship: part_of GO:0031252 ! cell leading edge + +[Term] +id: GO:0030029 +name: actin filament-based process +namespace: biological_process +def: "Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins." [GOC:mah] +synonym: "microfilament-based process" RELATED [] +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0030030 +name: cell projection organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +subset: gosubset_prok +synonym: "cell projection organisation" EXACT [GOC:curators] +synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] +synonym: "cell surface structure organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0030031 +name: cell projection assembly +namespace: biological_process +def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "cell projection biogenesis" RELATED [GOC:mah] +synonym: "formation of a cell surface projection" EXACT [] +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0030030 ! cell projection organization + +[Term] +id: GO:0030032 +name: lamellipodium assembly +namespace: biological_process +def: "Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell." [GOC:mah, ISBN:0815316194] +synonym: "lamellipodium biogenesis" RELATED [GOC:mah] +synonym: "lamellipodium biosynthesis" EXACT [] +synonym: "lamellipodium formation" EXACT [] +is_a: GO:0030031 ! cell projection assembly + +[Term] +id: GO:0030036 +name: actin cytoskeleton organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins." [GOC:dph, GOC:jl, GOC:mah] +synonym: "actin cytoskeleton organisation" EXACT [GOC:curators] +synonym: "actin cytoskeleton organization and biogenesis" RELATED [GOC:mah] +synonym: "actin modulating activity" RELATED [] +is_a: GO:0007010 ! cytoskeleton organization +is_a: GO:0030029 ! actin filament-based process +is_a: GO:1902589 ! single-organism organelle organization + +[Term] +id: GO:0030054 +name: cell junction +namespace: cellular_component +def: "A cellular component that forms a specialized region of connection between two cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix." [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732] +xref: Wikipedia:Cell_junction +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0030055 +name: cell-substrate junction +namespace: cellular_component +def: "A cell junction that forms a connection between a cell and the extracellular matrix." [GOC:hb, GOC:mah] +synonym: "cell-matrix junction" EXACT [] +is_a: GO:0030054 ! cell junction + +[Term] +id: GO:0030057 +name: desmosome +namespace: cellular_component +def: "A cell-cell junction in which: on the cytoplasmic surface of each interacting plasma membrane is a dense plaque composed of a mixture of intracellular anchor proteins; a bundle of keratin intermediate filaments is attached to the surface of each plaque; transmembrane adhesion proteins of the cadherin family bind to the plaques and interact through their extracellular domains to hold the adjacent membranes together by a Ca2+-dependent mechanism." [GOC:mah, GOC:mtg_muscle, ISBN:0815332181] +synonym: "macula adherens" EXACT [] +synonym: "spot desmosome" EXACT [] +xref: Wikipedia:Desmosome +is_a: GO:0005911 ! cell-cell junction +is_a: GO:0070161 ! anchoring junction + +[Term] +id: GO:0030072 +name: peptide hormone secretion +namespace: biological_process +def: "The regulated release of a peptide hormone from a cell." [GOC:mah] +is_a: GO:0002790 ! peptide secretion +is_a: GO:0046879 ! hormone secretion + +[Term] +id: GO:0030073 +name: insulin secretion +namespace: biological_process +def: "The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin." [GOC:mah, ISBN:0198506732] +is_a: GO:0030072 ! peptide hormone secretion + +[Term] +id: GO:0030097 +name: hemopoiesis +namespace: biological_process +def: "The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates." [GOC:dgh, ISBN:0198506732] +synonym: "blood cell biosynthesis" EXACT [] +synonym: "blood cell formation" EXACT [] +synonym: "haemopoiesis" EXACT [] +synonym: "hematopoiesis" EXACT [] +xref: Wikipedia:Haematopoiesis +is_a: GO:0048534 ! hematopoietic or lymphoid organ development + +[Term] +id: GO:0030098 +name: lymphocyte differentiation +namespace: biological_process +alt_id: GO:0046650 +def: "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:go_curators] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "lymphocyte cell differentiation" EXACT [] +synonym: "lymphocyte development" RELATED [GOC:add] +synonym: "lymphocytic blood cell differentiation" EXACT [] +is_a: GO:0002521 ! leukocyte differentiation +is_a: GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0030099 +name: myeloid cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages." [GOC:add, ISBN:0781735149] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030097 ! hemopoiesis + +[Term] +id: GO:0030100 +name: regulation of endocytosis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of endocytosis." [GOC:go_curators] +is_a: GO:0051128 ! regulation of cellular component organization +is_a: GO:0060627 ! regulation of vesicle-mediated transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006897 ! endocytosis +relationship: regulates GO:0006897 ! endocytosis + +[Term] +id: GO:0030111 +name: regulation of Wnt signaling pathway +namespace: biological_process +alt_id: GO:0008590 +def: "Any process that modulates the frequency, rate or extent of the activity of the Wnt signal transduction pathway." [GOC:dph, GOC:mah, GOC:tb] +synonym: "regulation of frizzled signaling pathway" EXACT [] +synonym: "regulation of frizzled signalling pathway" EXACT [] +synonym: "regulation of Wnt receptor signaling pathway" EXACT [] +synonym: "regulation of Wnt receptor signalling pathway" EXACT [] +synonym: "regulation of Wnt-activated signaling pathway" EXACT [GOC:signaling] +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016055 ! Wnt signaling pathway +relationship: regulates GO:0016055 ! Wnt signaling pathway + +[Term] +id: GO:0030139 +name: endocytic vesicle +namespace: cellular_component +def: "A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting." [GOC:go_curators, PMID:19696797] +subset: gosubset_prok +synonym: "endocytotic transport vesicle" EXACT [] +synonym: "endocytotic vesicle" EXACT [] +xref: NIF_Subcellular:sao1362520468 +is_a: GO:0016023 ! cytoplasmic membrane-bounded vesicle + +[Term] +id: GO:0030154 +name: cell differentiation +namespace: biological_process +def: "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732] +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +xref: Wikipedia:Cellular_differentiation +is_a: GO:0048869 ! cellular developmental process + +[Term] +id: GO:0030155 +name: regulation of cell adhesion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix." [GOC:mah] +subset: gosubset_prok +synonym: "cell adhesion receptor regulator activity" RELATED [] +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007155 ! cell adhesion +relationship: regulates GO:0007155 ! cell adhesion + +[Term] +id: GO:0030162 +name: regulation of proteolysis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of peptidolysis" EXACT [] +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006508 ! proteolysis +relationship: regulates GO:0006508 ! proteolysis + +[Term] +id: GO:0030163 +name: protein catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:mah] +comment: This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_pombe +subset: gosubset_prok +synonym: "pheromone catabolic process" RELATED [] +synonym: "pheromone catabolism" RELATED [] +synonym: "protein breakdown" EXACT [] +synonym: "protein catabolism" EXACT [] +synonym: "protein degradation" EXACT [] +xref: Wikipedia:Protein_catabolism +is_a: GO:0009057 ! macromolecule catabolic process +is_a: GO:0019538 ! protein metabolic process + +[Term] +id: GO:0030165 +name: PDZ domain binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins." [GOC:go_curators, Pfam:PF00595] +synonym: "DHR-domain binding" EXACT [] +synonym: "GLGF-domain binding" EXACT [] +is_a: GO:0019904 ! protein domain specific binding + +[Term] +id: GO:0030166 +name: proteoglycan biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." [GOC:mah, ISBN:0198506732] +subset: gosubset_prok +synonym: "proteoglycan anabolism" EXACT [] +synonym: "proteoglycan biosynthesis" EXACT [] +synonym: "proteoglycan formation" EXACT [] +synonym: "proteoglycan synthesis" EXACT [] +is_a: GO:0006029 ! proteoglycan metabolic process +is_a: GO:0009101 ! glycoprotein biosynthetic process + +[Term] +id: GO:0030168 +name: platelet activation +namespace: biological_process +def: "A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug." [http://www.graylab.ac.uk/omd/] +synonym: "blood coagulation, platelet activation" EXACT [GOC:add, GOC:pde] +xref: Reactome:REACT_103583 "Platelet activation, signaling and aggregation, Mus musculus" +xref: Reactome:REACT_105599 "Platelet activation, signaling and aggregation, Danio rerio" +xref: Reactome:REACT_108920 "Platelet activation, signaling and aggregation, Saccharomyces cerevisiae" +xref: Reactome:REACT_109042 "Platelet activation, signaling and aggregation, Arabidopsis thaliana" +xref: Reactome:REACT_118465 "Platelet activation, signaling and aggregation, Escherichia coli" +xref: Reactome:REACT_28166 "Platelet activation, signaling and aggregation, Rattus norvegicus" +xref: Reactome:REACT_29092 "Platelet activation, signaling and aggregation, Caenorhabditis elegans" +xref: Reactome:REACT_29357 "Platelet activation, signaling and aggregation, Staphylococcus aureus N315" +xref: Reactome:REACT_32211 "Platelet activation, signaling and aggregation, Bos taurus" +xref: Reactome:REACT_798 "Platelet activation, signaling and aggregation, Homo sapiens" +xref: Reactome:REACT_82375 "Platelet activation, signaling and aggregation, Sus scrofa" +xref: Reactome:REACT_82964 "Platelet activation, signaling and aggregation, Mycobacterium tuberculosis" +xref: Reactome:REACT_83720 "Platelet activation, signaling and aggregation, Dictyostelium discoideum" +xref: Reactome:REACT_85922 "Platelet activation, signaling and aggregation, Canis familiaris" +xref: Reactome:REACT_86767 "Platelet activation, signaling and aggregation, Taeniopygia guttata" +xref: Reactome:REACT_86968 "Platelet activation, signaling and aggregation, Xenopus tropicalis" +xref: Reactome:REACT_88667 "Platelet activation, signaling and aggregation, Drosophila melanogaster" +xref: Reactome:REACT_88938 "Platelet activation, signaling and aggregation, Gallus gallus" +xref: Reactome:REACT_92635 "Platelet activation, signaling and aggregation, Oryza sativa" +xref: Reactome:REACT_96250 "Platelet activation, signaling and aggregation, Schizosaccharomyces pombe" +xref: Reactome:REACT_97013 "Platelet activation, signaling and aggregation, Plasmodium falciparum" +is_a: GO:0001775 ! cell activation +relationship: part_of GO:0007596 ! blood coagulation + +[Term] +id: GO:0030169 +name: low-density lipoprotein particle binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a low-density lipoprotein particle, a lipoprotein particle that is rich in cholesterol esters and low in triglycerides, is typically composed of APOB100 and APOE, and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm." [GOC:mah] +synonym: "LDL binding" EXACT [] +is_a: GO:0071813 ! lipoprotein particle binding + +[Term] +id: GO:0030177 +name: positive regulation of Wnt signaling pathway +namespace: biological_process +alt_id: GO:0045811 +def: "Any process that activates or increases the frequency, rate or extent of Wnt signal transduction." [GOC:dph, GOC:go_curators, GOC:tb] +synonym: "activation of frizzled signaling pathway" NARROW [] +synonym: "activation of Wnt receptor signaling pathway" NARROW [] +synonym: "positive regulation of frizzled signaling pathway" EXACT [] +synonym: "positive regulation of frizzled signalling pathway" EXACT [] +synonym: "positive regulation of Wnt receptor signaling pathway" EXACT [] +synonym: "positive regulation of Wnt receptor signalling pathway" EXACT [] +synonym: "positive regulation of Wnt-activated signaling pathway" EXACT [GOC:signaling] +synonym: "stimulation of frizzled signaling pathway" NARROW [] +synonym: "stimulation of Wnt receptor signaling pathway" NARROW [] +synonym: "up regulation of frizzled signaling pathway" EXACT [] +synonym: "up regulation of Wnt receptor signaling pathway" EXACT [] +synonym: "up-regulation of frizzled signaling pathway" EXACT [] +synonym: "up-regulation of Wnt receptor signaling pathway" EXACT [] +synonym: "upregulation of frizzled signaling pathway" EXACT [] +synonym: "upregulation of Wnt receptor signaling pathway" EXACT [] +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0030111 ! regulation of Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016055 ! Wnt signaling pathway +relationship: positively_regulates GO:0016055 ! Wnt signaling pathway + +[Term] +id: GO:0030178 +name: negative regulation of Wnt signaling pathway +namespace: biological_process +alt_id: GO:0045810 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway." [GOC:dph, GOC:go_curators, GOC:tb] +synonym: "down regulation of frizzled signaling pathway" EXACT [] +synonym: "down regulation of Wnt receptor signaling pathway" EXACT [] +synonym: "down-regulation of frizzled signaling pathway" EXACT [] +synonym: "down-regulation of Wnt receptor signaling pathway" EXACT [] +synonym: "downregulation of frizzled signaling pathway" EXACT [] +synonym: "downregulation of Wnt receptor signaling pathway" EXACT [] +synonym: "inhibition of frizzled signaling pathway" NARROW [] +synonym: "inhibition of Wnt receptor signaling pathway" NARROW [] +synonym: "negative regulation of frizzled signaling pathway" EXACT [] +synonym: "negative regulation of frizzled signalling pathway" EXACT [] +synonym: "negative regulation of Wnt receptor signaling pathway" EXACT [] +synonym: "negative regulation of Wnt receptor signalling pathway" EXACT [] +synonym: "negative regulation of Wnt-activated signaling pathway" EXACT [GOC:signaling] +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:0030111 ! regulation of Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016055 ! Wnt signaling pathway +relationship: negatively_regulates GO:0016055 ! Wnt signaling pathway + +[Term] +id: GO:0030182 +name: neuron differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a neuron." [GOC:mah] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0048699 ! generation of neurons + +[Term] +id: GO:0030183 +name: B cell differentiation +namespace: biological_process +alt_id: GO:0042115 +def: "The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." [GO_REF:0000022, GOC:mah, GOC:mtg_15nov05] +comment: This term was improved by GO_REF:0000022. It was moved. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "B cell development" RELATED [GOC:add] +synonym: "B lymphocyte differentiation" EXACT [] +synonym: "B-cell differentiation" EXACT [] +synonym: "B-lymphocyte differentiation" EXACT [] +is_a: GO:0030098 ! lymphocyte differentiation +is_a: GO:0042113 ! B cell activation + +[Term] +id: GO:0030193 +name: regulation of blood coagulation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of blood coagulation." [GOC:mah] +is_a: GO:0032101 ! regulation of response to external stimulus +is_a: GO:0050818 ! regulation of coagulation +is_a: GO:0061041 ! regulation of wound healing +is_a: GO:1900046 ! regulation of hemostasis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007596 ! blood coagulation +relationship: regulates GO:0007596 ! blood coagulation + +[Term] +id: GO:0030198 +name: extracellular matrix organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix." [GOC:mah] +subset: goslim_generic +subset: gosubset_prok +synonym: "extracellular matrix organisation" EXACT [GOC:curators] +synonym: "extracellular matrix organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0043062 ! extracellular structure organization + +[Term] +id: GO:0030199 +name: collagen fibril organization +namespace: biological_process +def: "Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix." [GOC:mah, ISBN:0815316194] +synonym: "collagen fibril organisation" EXACT [GOC:curators] +synonym: "fibrillar collagen organization" EXACT [GOC:mah] +is_a: GO:0030198 ! extracellular matrix organization + +[Term] +id: GO:0030201 +name: heparan sulfate proteoglycan metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving any proteoglycan containing heparan sulfate, any member of a group of glycosaminoglycans that have repeat units consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues, the former being a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids, and the latter being either sulfated or acetylated on its amino group as well as sulfated on one of its hydroxyl groups." [GOC:mah, ISBN:0198506732] +subset: gosubset_prok +synonym: "heparan sulfate proteoglycan metabolism" EXACT [] +synonym: "heparan sulphate proteoglycan metabolic process" EXACT [] +synonym: "heparan sulphate proteoglycan metabolism" EXACT [] +synonym: "heparin proteoglycan metabolic process" RELATED [] +is_a: GO:0006029 ! proteoglycan metabolic process +is_a: GO:0006790 ! sulfur compound metabolic process +is_a: GO:0043436 ! oxoacid metabolic process + +[Term] +id: GO:0030203 +name: glycosaminoglycan metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties." [ISBN:0192800981] +subset: gosubset_prok +synonym: "glycosaminoglycan metabolism" EXACT [] +is_a: GO:0006022 ! aminoglycan metabolic process + +[Term] +id: GO:0030217 +name: T cell differentiation +namespace: biological_process +alt_id: GO:0042112 +alt_id: GO:0046652 +def: "The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex." [GO_REF:0000022, GOC:jid, GOC:mah, GOC:mtg_15nov05] +comment: This term was improved by GO_REF:0000022. It was moved. Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "T cell development" RELATED [GOC:add] +synonym: "T lymphocyte differentiation" EXACT [] +synonym: "T-cell differentiation" EXACT [] +synonym: "T-lymphocyte differentiation" EXACT [] +is_a: GO:0030098 ! lymphocyte differentiation +is_a: GO:0042110 ! T cell activation + +[Term] +id: GO:0030224 +name: monocyte differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte." [GOC:mah] +synonym: "monocyte cell differentiation" EXACT [] +is_a: GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0030228 +name: lipoprotein particle receptor activity +namespace: molecular_function +def: "Combining with a lipoprotein particle and delivering the lipoprotein particle into the cell via endocytosis. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids." [CHEBI:6495, GOC:bf, GOC:mah, PMID:12827279] +comment: This term is intended for cell surface receptors that bind and internalize a lipoprotein particle. For members of the lipoprotein receptor family that transduce a signal rather than endocytose their ligand, consider instead the terms 'signaling receptor activity ; GO:0038023' and its children, or 'reelin receptor activity ; GO:0038025'. +subset: gosubset_prok +synonym: "lipoprotein receptor activity" EXACT [GOC:dph] +synonym: "plasma lipoprotein particle receptor activity" EXACT [GOC:BHF] +is_a: GO:0038024 ! cargo receptor activity +relationship: has_part GO:0071813 ! lipoprotein particle binding + +[Term] +id: GO:0030229 +name: very-low-density lipoprotein particle receptor activity +namespace: molecular_function +def: "Combining with a very-low-density lipoprotein particle and delivering the very-low-density lipoprotein into the cell via endocytosis." [GOC:bf, ISBN:0198506732] +synonym: "apolipoprotein E receptor activity" RELATED [GOC:rl] +synonym: "very-low-density lipoprotein receptor activity" EXACT [GOC:dph] +synonym: "VLDL receptor" EXACT [] +xref: Wikipedia:VLDL_receptor +is_a: GO:0030228 ! lipoprotein particle receptor activity +relationship: has_part GO:0034189 ! very-low-density lipoprotein particle binding + +[Term] +id: GO:0030234 +name: enzyme regulator activity +namespace: molecular_function +def: "Binds to and modulates the activity of an enzyme." [GOC:mah] +comment: GO:0030234 is reserved for cases when the regulator directly interacts with the enzyme. When regulation of enzyme activity is achieved without enzyme binding, or when the mechanism of regulation is unknown, instead annotate to 'regulation of catalytic activity ; GO:0050790'. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "catalytic regulator activity" EXACT [GOC:dph] +synonym: "enzyme modulator" EXACT [] +is_a: GO:0003674 ! molecular_function +relationship: has_part GO:0019899 ! enzyme binding +relationship: part_of GO:0050790 ! regulation of catalytic activity +relationship: regulates GO:0003824 ! catalytic activity + +[Term] +id: GO:0030237 +name: female sex determination +namespace: biological_process +def: "The specification of female sex of an individual organism." [GOC:mah, ISBN:0198506732] +is_a: GO:0007530 ! sex determination +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0030262 +name: apoptotic nuclear changes +namespace: biological_process +def: "Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis." [GOC:mah, GOC:mtg_apoptosis] +synonym: "apoptotic nuclear change" NARROW [] +is_a: GO:0006921 ! cellular component disassembly involved in execution phase of apoptosis + +[Term] +id: GO:0030278 +name: regulation of ossification +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of bone formation." [GOC:go_curators] +synonym: "regulation of bone biosynthesis" EXACT [] +synonym: "regulation of bone formation" EXACT [] +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001503 ! ossification +relationship: regulates GO:0001503 ! ossification + +[Term] +id: GO:0030279 +name: negative regulation of ossification +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of bone formation." [GOC:go_curators] +synonym: "down regulation of ossification" EXACT [] +synonym: "down-regulation of ossification" EXACT [] +synonym: "downregulation of ossification" EXACT [] +synonym: "inhibition of ossification" NARROW [] +synonym: "negative regulation of bone biosynthesis" EXACT [] +synonym: "negative regulation of bone formation" EXACT [] +is_a: GO:0030278 ! regulation of ossification +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001503 ! ossification +relationship: negatively_regulates GO:0001503 ! ossification + +[Term] +id: GO:0030282 +name: bone mineralization +namespace: biological_process +def: "The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue." [GOC:mah, PMID:22936354] +synonym: "bone calcification" NARROW [] +is_a: GO:0031214 ! biomineral tissue development +relationship: part_of GO:0001503 ! ossification + +[Term] +id: GO:0030301 +name: cholesterol transport +namespace: biological_process +def: "The directed movement of cholesterol, cholest-5-en-3-beta-ol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah, ISBN:0198506732] +is_a: GO:0015918 ! sterol transport + +[Term] +id: GO:0030307 +name: positive regulation of cell growth +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, extent or direction of cell growth." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of cell growth" NARROW [] +synonym: "stimulation of cell growth" NARROW [] +synonym: "up regulation of cell growth" EXACT [] +synonym: "up-regulation of cell growth" EXACT [] +synonym: "upregulation of cell growth" EXACT [] +is_a: GO:0001558 ! regulation of cell growth +is_a: GO:0045927 ! positive regulation of growth +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016049 ! cell growth +relationship: positively_regulates GO:0016049 ! cell growth + +[Term] +id: GO:0030308 +name: negative regulation of cell growth +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of cell growth" EXACT [] +synonym: "down-regulation of cell growth" EXACT [] +synonym: "downregulation of cell growth" EXACT [] +synonym: "inhibition of cell growth" NARROW [] +xref: Reactome:REACT_6328 "DRheb is inhibited by the TSC1/2 complex, Drosophila melanogaster" +is_a: GO:0001558 ! regulation of cell growth +is_a: GO:0045926 ! negative regulation of growth +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016049 ! cell growth +relationship: negatively_regulates GO:0016049 ! cell growth + +[Term] +id: GO:0030316 +name: osteoclast differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue." [CL:0000092, GOC:add, ISBN:0781735149, PMID:12161749] +synonym: "osteoclast cell differentiation" EXACT [] +is_a: GO:0002573 ! myeloid leukocyte differentiation + +[Term] +id: GO:0030318 +name: melanocyte differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a melanocyte." [GOC:mah] +synonym: "melanocyte cell differentiation" EXACT [] +synonym: "melanophore differentiation" EXACT [] +is_a: GO:0050931 ! pigment cell differentiation +is_a: GO:0060563 ! neuroepithelial cell differentiation + +[Term] +id: GO:0030323 +name: respiratory tube development +namespace: biological_process +def: "The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract." [GOC:jid] +is_a: GO:0035295 ! tube development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0030324 +name: lung development +namespace: biological_process +def: "The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax." [GOC:jid, UBERON:0002048] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0030323 ! respiratory tube development +relationship: part_of GO:0060541 ! respiratory system development + +[Term] +id: GO:0030326 +name: embryonic limb morphogenesis +namespace: biological_process +def: "The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping." [GOC:bf, GOC:jl, ISBN:0395825172] +is_a: GO:0035108 ! limb morphogenesis +is_a: GO:0035113 ! embryonic appendage morphogenesis + +[Term] +id: GO:0030331 +name: estrogen receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an estrogen receptor." [GOC:ai] +is_a: GO:0035258 ! steroid hormone receptor binding + +[Term] +id: GO:0030334 +name: regulation of cell migration +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell migration." [GOC:go_curators] +is_a: GO:2000145 ! regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016477 ! cell migration +relationship: regulates GO:0016477 ! cell migration + +[Term] +id: GO:0030335 +name: positive regulation of cell migration +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell migration." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of cell migration" NARROW [] +synonym: "stimulation of cell migration" NARROW [] +synonym: "up regulation of cell migration" EXACT [] +synonym: "up-regulation of cell migration" EXACT [] +synonym: "upregulation of cell migration" EXACT [] +is_a: GO:0030334 ! regulation of cell migration +is_a: GO:2000147 ! positive regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016477 ! cell migration +relationship: positively_regulates GO:0016477 ! cell migration + +[Term] +id: GO:0030336 +name: negative regulation of cell migration +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration." [GOC:go_curators] +synonym: "down regulation of cell migration" EXACT [] +synonym: "down-regulation of cell migration" EXACT [] +synonym: "downregulation of cell migration" EXACT [] +synonym: "inhibition of cell migration" NARROW [] +is_a: GO:0030334 ! regulation of cell migration +is_a: GO:2000146 ! negative regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016477 ! cell migration +relationship: negatively_regulates GO:0016477 ! cell migration + +[Term] +id: GO:0030424 +name: axon +namespace: cellular_component +def: "The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter." [GOC:nln, ISBN:0198506732] +xref: NIF_Subcellular:sao1770195789 +xref: Wikipedia:Axon +is_a: GO:0043005 ! neuron projection + +[Term] +id: GO:0030425 +name: dendrite +namespace: cellular_component +def: "A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body." [GOC:dos, GOC:mah, GOC:nln, ISBN:0198506732] +xref: NIF_Subcellular:sao1211023249 +xref: Wikipedia:Dendrite +is_a: GO:0043005 ! neuron projection + +[Term] +id: GO:0030492 +name: hemoglobin binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin." [CHEBI:35143, GOC:jl] +synonym: "globin binding" NARROW [] +synonym: "haemoglobin binding" EXACT [] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0030500 +name: regulation of bone mineralization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of bone mineralization." [GOC:go_curators] +is_a: GO:0030278 ! regulation of ossification +is_a: GO:0070167 ! regulation of biomineral tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030282 ! bone mineralization +relationship: regulates GO:0030282 ! bone mineralization + +[Term] +id: GO:0030501 +name: positive regulation of bone mineralization +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of bone mineralization." [GOC:go_curators] +synonym: "activation of bone mineralization" NARROW [] +synonym: "stimulation of bone mineralization" NARROW [] +synonym: "up regulation of bone mineralization" EXACT [] +synonym: "up-regulation of bone mineralization" EXACT [] +synonym: "upregulation of bone mineralization" EXACT [] +is_a: GO:0030500 ! regulation of bone mineralization +is_a: GO:0045778 ! positive regulation of ossification +is_a: GO:0070169 ! positive regulation of biomineral tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030282 ! bone mineralization +relationship: positively_regulates GO:0030282 ! bone mineralization + +[Term] +id: GO:0030509 +name: BMP signaling pathway +namespace: biological_process +def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:0878932437, PR:000000034] +synonym: "BMP receptor signaling pathway" RELATED [] +synonym: "BMP signalling pathway" EXACT [] +synonym: "bone morphogenetic protein signaling pathway" EXACT [] +synonym: "bone morphogenetic protein signalling pathway" EXACT [] +xref: Reactome:REACT_105000 "Signaling by BMP, Mus musculus" +xref: Reactome:REACT_107332 "Signaling by BMP, Bos taurus" +xref: Reactome:REACT_12034 "Signaling by BMP, Homo sapiens" +xref: Reactome:REACT_28579 "Signaling by BMP, Sus scrofa" +xref: Reactome:REACT_31763 "Signaling by BMP, Taeniopygia guttata" +xref: Reactome:REACT_77157 "Signaling by BMP, Gallus gallus" +xref: Reactome:REACT_79322 "Signaling by BMP, Drosophila melanogaster" +xref: Reactome:REACT_80158 "Signaling by BMP, Rattus norvegicus" +xref: Reactome:REACT_81213 "Signaling by BMP, Xenopus tropicalis" +xref: Reactome:REACT_86022 "Signaling by BMP, Canis familiaris" +xref: Reactome:REACT_96139 "Signaling by BMP, Danio rerio" +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway + +[Term] +id: GO:0030510 +name: regulation of BMP signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the activity of any BMP receptor signaling pathway." [GOC:mah] +synonym: "regulation of BMP receptor signaling pathway" RELATED [] +synonym: "regulation of BMP signalling pathway" EXACT [] +synonym: "regulation of bone morphogenetic protein signaling pathway" EXACT [] +synonym: "regulation of bone morphogenetic protein signalling pathway" EXACT [] +is_a: GO:0090092 ! regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030509 ! BMP signaling pathway +relationship: regulates GO:0030509 ! BMP signaling pathway + +[Term] +id: GO:0030512 +name: negative regulation of transforming growth factor beta receptor signaling pathway +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway." [GOC:mah] +synonym: "down regulation of transforming growth factor beta receptor signaling pathway" EXACT [] +synonym: "down-regulation of transforming growth factor beta receptor signaling pathway" EXACT [] +synonym: "downregulation of transforming growth factor beta receptor signaling pathway" EXACT [] +synonym: "inhibition of transforming growth factor beta receptor signaling pathway" NARROW [] +synonym: "negative regulation of TGF-beta receptor signaling pathway" EXACT [] +synonym: "negative regulation of TGFbeta receptor signaling pathway" EXACT [] +synonym: "negative regulation of transforming growth factor beta receptor signalling pathway" EXACT [] +xref: Reactome:REACT_105250 "I-SMAD competes with SMAD2/3 for type I receptor (TGFBR1), Danio rerio" +xref: Reactome:REACT_113798 "SKI complexes with the SMAD complex, suppressing TGF-beta signaling, Danio rerio" +xref: Reactome:REACT_6887 "SKI complexes with the SMAD complex, suppressing TGF-beta signaling, Homo sapiens" +xref: Reactome:REACT_6909 "I-SMAD competes with SMAD2/3 for type I receptor (TGFBR1), Homo sapiens" +xref: Reactome:REACT_78193 "SKI complexes with the SMAD complex, suppressing TGF-beta signaling, Xenopus tropicalis" +xref: Reactome:REACT_79577 "SKI complexes with the SMAD complex, suppressing TGF-beta signaling, Bos taurus" +xref: Reactome:REACT_81179 "I-SMAD competes with SMAD2/3 for type I receptor (TGFBR1), Mus musculus" +xref: Reactome:REACT_82804 "I-SMAD competes with SMAD2/3 for type I receptor (TGFBR1), Canis familiaris" +xref: Reactome:REACT_86702 "SKI complexes with the SMAD complex, suppressing TGF-beta signaling, Rattus norvegicus" +xref: Reactome:REACT_87642 "SKI complexes with the SMAD complex, suppressing TGF-beta signaling, Drosophila melanogaster" +xref: Reactome:REACT_88145 "SKI complexes with the SMAD complex, suppressing TGF-beta signaling, Mus musculus" +xref: Reactome:REACT_90968 "I-SMAD competes with SMAD2/3 for type I receptor (TGFBR1), Rattus norvegicus" +xref: Reactome:REACT_91943 "SKI complexes with the SMAD complex, suppressing TGF-beta signaling, Canis familiaris" +xref: Reactome:REACT_93061 "I-SMAD competes with SMAD2/3 for type I receptor (TGFBR1), Xenopus tropicalis" +xref: Reactome:REACT_93800 "I-SMAD competes with SMAD2/3 for type I receptor (TGFBR1), Bos taurus" +xref: Reactome:REACT_95269 "I-SMAD competes with SMAD2/3 for type I receptor (TGFBR1), Sus scrofa" +is_a: GO:0017015 ! regulation of transforming growth factor beta receptor signaling pathway +is_a: GO:0090101 ! negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +is_a: GO:0090288 ! negative regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007179 ! transforming growth factor beta receptor signaling pathway +relationship: negatively_regulates GO:0007179 ! transforming growth factor beta receptor signaling pathway + +[Term] +id: GO:0030513 +name: positive regulation of BMP signaling pathway +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity." [GOC:go_curators] +synonym: "activation of BMP signaling pathway" NARROW [] +synonym: "positive regulation of BMP receptor signaling pathway" RELATED [] +synonym: "positive regulation of BMP signalling pathway" EXACT [] +synonym: "positive regulation of bone morphogenetic protein signaling pathway" EXACT [] +synonym: "positive regulation of bone morphogenetic protein signalling pathway" EXACT [] +synonym: "stimulation of BMP signaling pathway" NARROW [] +synonym: "up regulation of BMP signaling pathway" EXACT [] +synonym: "up-regulation of BMP signaling pathway" EXACT [] +synonym: "upregulation of BMP signaling pathway" EXACT [] +is_a: GO:0030510 ! regulation of BMP signaling pathway +is_a: GO:0090100 ! positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030509 ! BMP signaling pathway +relationship: positively_regulates GO:0030509 ! BMP signaling pathway + +[Term] +id: GO:0030514 +name: negative regulation of BMP signaling pathway +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway." [GOC:go_curators] +synonym: "down regulation of BMP signaling pathway" EXACT [] +synonym: "down-regulation of BMP signaling pathway" EXACT [] +synonym: "downregulation of BMP signaling pathway" EXACT [] +synonym: "inhibition of BMP signaling pathway" NARROW [] +synonym: "negative regulation of BMP receptor signaling pathway" RELATED [] +synonym: "negative regulation of BMP signalling pathway" EXACT [] +synonym: "negative regulation of bone morphogenetic protein signaling pathway" EXACT [] +synonym: "negative regulation of bone morphogenetic protein signalling pathway" EXACT [] +is_a: GO:0030510 ! regulation of BMP signaling pathway +is_a: GO:0090101 ! negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030509 ! BMP signaling pathway +relationship: negatively_regulates GO:0030509 ! BMP signaling pathway + +[Term] +id: GO:0030516 +name: regulation of axon extension +namespace: biological_process +def: "Any process that modulates the rate, direction or extent of axon extension." [GOC:go_curators] +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:0050770 ! regulation of axonogenesis +is_a: GO:0061387 ! regulation of extent of cell growth +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048675 ! axon extension +relationship: regulates GO:0048675 ! axon extension + +[Term] +id: GO:0030517 +name: negative regulation of axon extension +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of axon outgrowth." [GOC:mah] +synonym: "down regulation of axon extension" EXACT [] +synonym: "down-regulation of axon extension" EXACT [] +synonym: "downregulation of axon extension" EXACT [] +synonym: "inhibition of axon extension" NARROW [] +is_a: GO:0030308 ! negative regulation of cell growth +is_a: GO:0030516 ! regulation of axon extension +is_a: GO:0048640 ! negative regulation of developmental growth +is_a: GO:0050771 ! negative regulation of axonogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048675 ! axon extension +relationship: negatively_regulates GO:0048675 ! axon extension + +[Term] +id: GO:0030518 +name: intracellular steroid hormone receptor signaling pathway +namespace: biological_process +def: "A series of molecular signals generated as a consequence of a intracellular steroid hormone receptor binding to one of its physiological ligands." [GOC:mah, GOC:signaling] +synonym: "steroid hormone receptor signaling pathway" BROAD [GOC:bf] +synonym: "steroid hormone receptor signalling pathway" BROAD [GOC:bf] +is_a: GO:0030522 ! intracellular receptor signaling pathway + +[Term] +id: GO:0030520 +name: intracellular estrogen receptor signaling pathway +namespace: biological_process +def: "Any series of molecular signals generated as a consequence of an intracellular estrogen receptor binding to one of its physiological ligands. The pathway begins with receptor-ligand binding, and ends with regulation of a downstream cellular process (e.g. transcription)." [GOC:mah, GOC:signaling] +synonym: "estrogen receptor signaling pathway" BROAD [GOC:bf] +synonym: "estrogen receptor signalling pathway" BROAD [GOC:bf] +is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway + +[Term] +id: GO:0030521 +name: androgen receptor signaling pathway +namespace: biological_process +def: "Any series of molecular signals generated as a consequence of an androgen binding to its receptor." [GOC:mah] +synonym: "androgen receptor signalling pathway" EXACT [] +is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway + +[Term] +id: GO:0030522 +name: intracellular receptor signaling pathway +namespace: biological_process +def: "Any series of molecular signals initiated by a ligand binding to an receptor located within a cell." [GOC:bf, GOC:mah] +synonym: "intracellular receptor mediated signaling pathway" EXACT [] +synonym: "intracellular receptor-mediated signaling pathway" EXACT [] +synonym: "intracellular receptor-mediated signalling pathway" EXACT [] +is_a: GO:0007165 ! signal transduction + +[Term] +id: GO:0030534 +name: adult behavior +namespace: biological_process +def: "Behavior in a fully developed and mature organism." [GOC:mah, ISBN:0877797099] +comment: See also the biological process term 'behavior ; GO:0007610'. +synonym: "adult behavioral response to stimulus" EXACT [] +synonym: "adult behaviour" EXACT [] +synonym: "adult behavioural response to stimulus" EXACT [] +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044708 ! single-organism behavior + +[Term] +id: GO:0030539 +name: male genitalia development +namespace: biological_process +def: "The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure." [GOC:ems, ISBN:0140512888] +synonym: "male genital development" EXACT [] +is_a: GO:0048806 ! genitalia development +relationship: part_of GO:0046546 ! development of primary male sexual characteristics + +[Term] +id: GO:0030540 +name: female genitalia development +namespace: biological_process +def: "The process whose specific outcome is the progression of the female genitalia over time, from formation to the mature structure." [GOC:mah] +synonym: "female genital development" EXACT [] +is_a: GO:0048806 ! genitalia development +relationship: part_of GO:0046545 ! development of primary female sexual characteristics + +[Term] +id: GO:0030545 +name: receptor regulator activity +namespace: molecular_function +def: "The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed." [GOC:ceb] +is_a: GO:0003674 ! molecular_function +relationship: part_of GO:0010469 ! regulation of receptor activity +relationship: regulates GO:0004872 ! receptor activity + +[Term] +id: GO:0030546 +name: receptor activator activity +namespace: molecular_function +def: "The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased." [GOC:ceb] +is_a: GO:0030545 ! receptor regulator activity +relationship: part_of GO:2000273 ! positive regulation of receptor activity +relationship: positively_regulates GO:0004872 ! receptor activity + +[Term] +id: GO:0030547 +name: receptor inhibitor activity +namespace: molecular_function +def: "The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is decreased." [GOC:ceb] +is_a: GO:0030545 ! receptor regulator activity +relationship: negatively_regulates GO:0004872 ! receptor activity +relationship: part_of GO:2000272 ! negative regulation of receptor activity + +[Term] +id: GO:0030579 +name: ubiquitin-dependent SMAD protein catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of SMAD signaling proteins by ubiquitination and targeting to the proteasome." [GOC:go_curators] +synonym: "ubiquitin-dependent SMAD protein breakdown" EXACT [] +synonym: "ubiquitin-dependent SMAD protein catabolism" EXACT [] +synonym: "ubiquitin-dependent SMAD protein degradation" EXACT [] +is_a: GO:0006511 ! ubiquitin-dependent protein catabolic process +relationship: part_of GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway + +[Term] +id: GO:0030595 +name: leukocyte chemotaxis +namespace: biological_process +def: "The movement of a leukocyte in response to an external stimulus." [GOC:add, GOC:jl] +synonym: "immune cell chemotaxis" EXACT [] +synonym: "leucocyte chemotaxis" EXACT [] +is_a: GO:0050900 ! leukocyte migration +is_a: GO:0060326 ! cell chemotaxis + +[Term] +id: GO:0030799 +name: regulation of cyclic nucleotide metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cyclic nucleotides." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of cyclic nucleotide metabolism" EXACT [] +is_a: GO:0006140 ! regulation of nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009187 ! cyclic nucleotide metabolic process +relationship: regulates GO:0009187 ! cyclic nucleotide metabolic process + +[Term] +id: GO:0030801 +name: positive regulation of cyclic nucleotide metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving cyclic nucleotides." [GOC:mah] +subset: gosubset_prok +synonym: "activation of cyclic nucleotide metabolic process" NARROW [] +synonym: "positive regulation of cyclic nucleotide metabolism" EXACT [] +synonym: "stimulation of cyclic nucleotide metabolic process" NARROW [] +synonym: "up regulation of cyclic nucleotide metabolic process" EXACT [] +synonym: "up-regulation of cyclic nucleotide metabolic process" EXACT [] +synonym: "upregulation of cyclic nucleotide metabolic process" EXACT [] +is_a: GO:0030799 ! regulation of cyclic nucleotide metabolic process +is_a: GO:0045981 ! positive regulation of nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009187 ! cyclic nucleotide metabolic process +relationship: positively_regulates GO:0009187 ! cyclic nucleotide metabolic process + +[Term] +id: GO:0030811 +name: regulation of nucleotide catabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of nucleotide breakdown" EXACT [] +synonym: "regulation of nucleotide catabolism" EXACT [] +synonym: "regulation of nucleotide degradation" EXACT [] +is_a: GO:0006140 ! regulation of nucleotide metabolic process +is_a: GO:0031329 ! regulation of cellular catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009166 ! nucleotide catabolic process +relationship: regulates GO:0009166 ! nucleotide catabolic process + +[Term] +id: GO:0030823 +name: regulation of cGMP metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cGMP." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of cGMP metabolism" EXACT [] +is_a: GO:0030799 ! regulation of cyclic nucleotide metabolic process +is_a: GO:1900542 ! regulation of purine nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046068 ! cGMP metabolic process +relationship: regulates GO:0046068 ! cGMP metabolic process + +[Term] +id: GO:0030825 +name: positive regulation of cGMP metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving cGMP." [GOC:mah] +subset: gosubset_prok +synonym: "activation of cGMP metabolic process" NARROW [] +synonym: "positive regulation of cGMP metabolism" EXACT [] +synonym: "stimulation of cGMP metabolic process" NARROW [] +synonym: "up regulation of cGMP metabolic process" EXACT [] +synonym: "up-regulation of cGMP metabolic process" EXACT [] +synonym: "upregulation of cGMP metabolic process" EXACT [] +is_a: GO:0030801 ! positive regulation of cyclic nucleotide metabolic process +is_a: GO:0030823 ! regulation of cGMP metabolic process +is_a: GO:1900544 ! positive regulation of purine nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046068 ! cGMP metabolic process +relationship: positively_regulates GO:0046068 ! cGMP metabolic process + +[Term] +id: GO:0030850 +name: prostate gland development +namespace: biological_process +def: "The process whose specific outcome is the progression of the prostate gland over time, from its formation to the mature structure. The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid." [PMID:11839751] +synonym: "prostate development" EXACT [] +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048608 ! reproductive structure development +is_a: GO:0048732 ! gland development +relationship: part_of GO:0001655 ! urogenital system development + +[Term] +id: GO:0030855 +name: epithelial cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium." [GOC:ecd, PMID:11839751] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0060429 ! epithelium development + +[Term] +id: GO:0030856 +name: regulation of epithelial cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of epithelial cell differentiation." [GOC:mah] +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030855 ! epithelial cell differentiation +relationship: regulates GO:0030855 ! epithelial cell differentiation + +[Term] +id: GO:0030858 +name: positive regulation of epithelial cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of epithelial cell differentiation." [GOC:mah] +synonym: "activation of epithelial cell differentiation" NARROW [] +synonym: "stimulation of epithelial cell differentiation" NARROW [] +synonym: "up regulation of epithelial cell differentiation" EXACT [] +synonym: "up-regulation of epithelial cell differentiation" EXACT [] +synonym: "upregulation of epithelial cell differentiation" EXACT [] +is_a: GO:0030856 ! regulation of epithelial cell differentiation +is_a: GO:0045597 ! positive regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030855 ! epithelial cell differentiation +relationship: positively_regulates GO:0030855 ! epithelial cell differentiation + +[Term] +id: GO:0030877 +name: beta-catenin destruction complex +namespace: cellular_component +alt_id: GO:0034742 +alt_id: GO:0034747 +def: "A cytoplasmic protein complex containing glycogen synthase kinase-3-beta (GSK-3-beta), the adenomatous polyposis coli protein (APC), and the scaffolding protein axin, among others; phosphorylates beta-catenin, targets it for degradation by the proteasome." [PMID:14600025] +comment: Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'. +synonym: "23S APC complex" NARROW [] +synonym: "APC-Axin-1-beta-catenin complex" EXACT [] +synonym: "Axin-APC-beta-catenin-GSK3B complex" EXACT [] +synonym: "beta-catenin degradation complex" EXACT [] +is_a: GO:0043234 ! protein complex +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0030879 +name: mammary gland development +namespace: biological_process +def: "The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages." [PMID:9576833] +synonym: "mammogenesis" NARROW [GOC:dph] +is_a: GO:0048732 ! gland development + +[Term] +id: GO:0030888 +name: regulation of B cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of B cell proliferation." [GOC:mah] +synonym: "regulation of B lymphocyte proliferation" EXACT [] +synonym: "regulation of B-cell proliferation" EXACT [] +synonym: "regulation of B-lymphocyte proliferation" EXACT [] +is_a: GO:0050670 ! regulation of lymphocyte proliferation +is_a: GO:0050864 ! regulation of B cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042100 ! B cell proliferation +relationship: regulates GO:0042100 ! B cell proliferation + +[Term] +id: GO:0030890 +name: positive regulation of B cell proliferation +namespace: biological_process +def: "Any process that activates or increases the rate or extent of B cell proliferation." [GOC:mah] +synonym: "activation of B cell proliferation" NARROW [] +synonym: "positive regulation of B lymphocyte proliferation" EXACT [] +synonym: "positive regulation of B-cell proliferation" EXACT [] +synonym: "positive regulation of B-lymphocyte proliferation" EXACT [] +synonym: "stimulation of B cell proliferation" NARROW [] +synonym: "up regulation of B cell proliferation" EXACT [] +synonym: "up-regulation of B cell proliferation" EXACT [] +synonym: "upregulation of B cell proliferation" EXACT [] +is_a: GO:0030888 ! regulation of B cell proliferation +is_a: GO:0050671 ! positive regulation of lymphocyte proliferation +is_a: GO:0050871 ! positive regulation of B cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042100 ! B cell proliferation +relationship: positively_regulates GO:0042100 ! B cell proliferation + +[Term] +id: GO:0030900 +name: forebrain development +namespace: biological_process +def: "The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions)." [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=forebrain] +synonym: "prosencephalon development" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007420 ! brain development + +[Term] +id: GO:0030901 +name: midbrain development +namespace: biological_process +def: "The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)." [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=midbrain] +synonym: "mesencephalon development" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007420 ! brain development + +[Term] +id: GO:0030902 +name: hindbrain development +namespace: biological_process +def: "The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium)." [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=hindbrain] +synonym: "rhombencephalon development" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007420 ! brain development + +[Term] +id: GO:0030916 +name: otic vesicle formation +namespace: biological_process +def: "The process resulting in the transition of the otic placode into the otic vesicle, a transient embryonic structure formed during development of the vertebrate inner ear." [GOC:dgh] +synonym: "otocyst biosynthesis" EXACT [] +synonym: "otocyst formation" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0071600 ! otic vesicle morphogenesis + +[Term] +id: GO:0030917 +name: midbrain-hindbrain boundary development +namespace: biological_process +def: "The process whose specific outcome is the progression of the midbrain-hindbrain boundary over time, from its formation to the mature structure. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages." [GOC:dgh] +synonym: "isthmic organizer development" EXACT [] +synonym: "isthmomesencephalic boundary development" EXACT [] +synonym: "isthmus development" EXACT [] +synonym: "MHB development" EXACT [] +synonym: "midbrain-hindbrain orgainizer development" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007420 ! brain development +relationship: part_of GO:0021903 ! rostrocaudal neural tube patterning + +[Term] +id: GO:0030971 +name: receptor tyrosine kinase binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity." [GOC:mah] +synonym: "transmembrane receptor protein tyrosine kinase ligand binding" RELATED [] +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0030997 +name: regulation of centriole-centriole cohesion +namespace: biological_process +def: "Any process that modulates the extent to which the two centrioles within a centrosome remain tightly paired; may be mediated by the assembly and disassembly of a proteinaceous linker." [PMID:11076968] +is_a: GO:0070507 ! regulation of microtubule cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010457 ! centriole-centriole cohesion +relationship: part_of GO:0007098 ! centrosome cycle +relationship: regulates GO:0010457 ! centriole-centriole cohesion + +[Term] +id: GO:0031012 +name: extracellular matrix +namespace: cellular_component +def: "A structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals and bacteria) or be part of the cell (as in plants)." [GOC:mah] +subset: goslim_metagenomics +subset: goslim_pir +subset: gosubset_prok +xref: Wikipedia:Extracellular_matrix +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0031016 +name: pancreas development +namespace: biological_process +def: "The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes." [GOC:cvs] +xref: Wikipedia:Pancreas +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0031018 +name: endocrine pancreas development +namespace: biological_process +def: "The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin." [GOC:cvs] +xref: Reactome:REACT_100172 "Regulation of beta-cell development, Staphylococcus aureus N315" +xref: Reactome:REACT_100239 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Canis familiaris" +xref: Reactome:REACT_101492 "Regulation of gene expression in beta cells, Canis familiaris" +xref: Reactome:REACT_102188 "Regulation of beta-cell development, Escherichia coli" +xref: Reactome:REACT_102956 "Regulation of beta-cell development, Sus scrofa" +xref: Reactome:REACT_105131 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Sus scrofa" +xref: Reactome:REACT_105242 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Taeniopygia guttata" +xref: Reactome:REACT_105455 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Mus musculus" +xref: Reactome:REACT_105798 "Regulation of gene expression in early pancreatic precursor cells, Drosophila melanogaster" +xref: Reactome:REACT_106781 "Regulation of beta-cell development, Gallus gallus" +xref: Reactome:REACT_107233 "Regulation of beta-cell development, Caenorhabditis elegans" +xref: Reactome:REACT_107418 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Rattus norvegicus" +xref: Reactome:REACT_108013 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Xenopus tropicalis" +xref: Reactome:REACT_108544 "Regulation of gene expression in early pancreatic precursor cells, Xenopus tropicalis" +xref: Reactome:REACT_111030 "Regulation of gene expression in beta cells, Danio rerio" +xref: Reactome:REACT_112937 "Regulation of gene expression in beta cells, Mycobacterium tuberculosis" +xref: Reactome:REACT_114067 "Regulation of beta-cell development, Mycobacterium tuberculosis" +xref: Reactome:REACT_13641 "Regulation of Beta-Cell Development, Mus musculus" +xref: Reactome:REACT_13650 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Homo sapiens" +xref: Reactome:REACT_13673 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Homo sapiens" +xref: Reactome:REACT_13698 "Regulation of beta-cell development, Homo sapiens" +xref: Reactome:REACT_13778 "Regulation of gene expression in early pancreatic precursor cells, Homo sapiens" +xref: Reactome:REACT_13819 "Regulation of gene expression in beta cells, Homo sapiens" +xref: Reactome:REACT_28720 "Regulation of gene expression in beta cells, Caenorhabditis elegans" +xref: Reactome:REACT_29082 "Regulation of gene expression in beta cells, Gallus gallus" +xref: Reactome:REACT_29825 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Canis familiaris" +xref: Reactome:REACT_30048 "Regulation of gene expression in early pancreatic precursor cells, Canis familiaris" +xref: Reactome:REACT_31811 "Regulation of gene expression in early pancreatic precursor cells, Bos taurus" +xref: Reactome:REACT_33149 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Drosophila melanogaster" +xref: Reactome:REACT_33362 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Caenorhabditis elegans" +xref: Reactome:REACT_33643 "Regulation of beta-cell development, Bos taurus" +xref: Reactome:REACT_33882 "Regulation of gene expression in beta cells, Arabidopsis thaliana" +xref: Reactome:REACT_33965 "Regulation of gene expression in beta cells, Rattus norvegicus" +xref: Reactome:REACT_34484 "Regulation of beta-cell development, Schizosaccharomyces pombe" +xref: Reactome:REACT_77445 "Regulation of beta-cell development, Oryza sativa" +xref: Reactome:REACT_77538 "Regulation of gene expression in beta cells, Bos taurus" +xref: Reactome:REACT_78194 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Rattus norvegicus" +xref: Reactome:REACT_78480 "Regulation of gene expression in beta cells, Saccharomyces cerevisiae" +xref: Reactome:REACT_79238 "Regulation of beta-cell development, Danio rerio" +xref: Reactome:REACT_79240 "Regulation of gene expression in early pancreatic precursor cells, Gallus gallus" +xref: Reactome:REACT_79285 "Regulation of gene expression in beta cells, Dictyostelium discoideum" +xref: Reactome:REACT_80121 "Regulation of beta-cell development, Plasmodium falciparum" +xref: Reactome:REACT_80317 "Regulation of gene expression in early pancreatic precursor cells, Mus musculus" +xref: Reactome:REACT_82017 "Regulation of beta-cell development, Xenopus tropicalis" +xref: Reactome:REACT_82782 "Regulation of gene expression in beta cells, Xenopus tropicalis" +xref: Reactome:REACT_82897 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Danio rerio" +xref: Reactome:REACT_83026 "Regulation of gene expression in beta cells, Oryza sativa" +xref: Reactome:REACT_83105 "Regulation of gene expression in beta cells, Escherichia coli" +xref: Reactome:REACT_83129 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Bos taurus" +xref: Reactome:REACT_83414 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Sus scrofa" +xref: Reactome:REACT_85060 "Regulation of gene expression in early pancreatic precursor cells, Taeniopygia guttata" +xref: Reactome:REACT_85721 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Gallus gallus" +xref: Reactome:REACT_86199 "Regulation of gene expression in beta cells, Mus musculus" +xref: Reactome:REACT_86989 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Xenopus tropicalis" +xref: Reactome:REACT_87974 "Regulation of beta-cell development, Rattus norvegicus" +xref: Reactome:REACT_88048 "Regulation of gene expression in beta cells, Taeniopygia guttata" +xref: Reactome:REACT_89334 "Regulation of gene expression in beta cells, Schizosaccharomyces pombe" +xref: Reactome:REACT_89352 "Regulation of beta-cell development, Arabidopsis thaliana" +xref: Reactome:REACT_89883 "Regulation of beta-cell development, Mus musculus" +xref: Reactome:REACT_89999 "Regulation of beta-cell development, Taeniopygia guttata" +xref: Reactome:REACT_90418 "Regulation of beta-cell development, Saccharomyces cerevisiae" +xref: Reactome:REACT_90603 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Danio rerio" +xref: Reactome:REACT_91799 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Bos taurus" +xref: Reactome:REACT_92191 "Regulation of gene expression in early pancreatic precursor cells, Caenorhabditis elegans" +xref: Reactome:REACT_92743 "Regulation of gene expression in beta cells, Staphylococcus aureus N315" +xref: Reactome:REACT_93408 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Mus musculus" +xref: Reactome:REACT_93479 "Regulation of beta-cell development, Drosophila melanogaster" +xref: Reactome:REACT_93693 "Regulation of beta-cell development, Dictyostelium discoideum" +xref: Reactome:REACT_94334 "Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, Taeniopygia guttata" +xref: Reactome:REACT_94430 "Regulation of gene expression in early pancreatic precursor cells, Danio rerio" +xref: Reactome:REACT_95482 "Regulation of gene expression in early pancreatic precursor cells, Sus scrofa" +xref: Reactome:REACT_95696 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Gallus gallus" +xref: Reactome:REACT_97083 "Regulation of gene expression in beta cells, Drosophila melanogaster" +xref: Reactome:REACT_97526 "Regulation of gene expression in early pancreatic precursor cells, Rattus norvegicus" +xref: Reactome:REACT_97545 "Regulation of gene expression in beta cells, Plasmodium falciparum" +xref: Reactome:REACT_98354 "Regulation of beta-cell development, Canis familiaris" +xref: Reactome:REACT_99516 "Regulation of gene expression in beta cells, Sus scrofa" +xref: Reactome:REACT_99600 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Caenorhabditis elegans" +xref: Reactome:REACT_99890 "Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells, Drosophila melanogaster" +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0031016 ! pancreas development +relationship: part_of GO:0035270 ! endocrine system development + +[Term] +id: GO:0031023 +name: microtubule organizing center organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microtubule organizing center, a structure from which microtubules grow." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_pir +synonym: "microtubule organising center organisation" EXACT [GOC:curators] +synonym: "microtubule organizing center organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0006996 ! organelle organization +relationship: part_of GO:0000226 ! microtubule cytoskeleton organization + +[Term] +id: GO:0031069 +name: hair follicle morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the hair follicle are generated and organized." [GOC:ln] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0022405 ! hair cycle process +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001942 ! hair follicle development +relationship: part_of GO:0048730 ! epidermis morphogenesis + +[Term] +id: GO:0031076 +name: embryonic camera-type eye development +namespace: biological_process +def: "The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure." [GOC:mah, GOC:mtg_sensu] +synonym: "embryonic eye development" EXACT [] +is_a: GO:0043010 ! camera-type eye development +is_a: GO:0048568 ! embryonic organ development + +[Term] +id: GO:0031098 +name: stress-activated protein kinase signaling cascade +namespace: biological_process +def: "A series of molecular signals in which a stress-activated protein kinase (SAPK) cascade relays one or more of the signals." [GOC:mah] +synonym: "JNK signaling pathway" NARROW [] +synonym: "JNK signalling pathway" NARROW [] +synonym: "SAPK signaling pathway" EXACT [] +synonym: "SAPK signalling pathway" EXACT [] +synonym: "stress-activated protein kinase signaling pathway" EXACT [] +synonym: "stress-activated protein kinase signalling pathway" EXACT [] +is_a: GO:0033554 ! cellular response to stress +is_a: GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0031099 +name: regeneration +namespace: biological_process +def: "The regrowth of a lost or destroyed body part, such as an organ or tissue." [GOC:mah] +xref: Wikipedia:Regeneration_(biology) +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0031100 +name: organ regeneration +namespace: biological_process +def: "The regrowth of a lost or destroyed organ." [GOC:mah] +is_a: GO:0031099 ! regeneration +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0031128 +name: developmental induction +namespace: biological_process +def: "Signaling at short range between cells or tissues of different ancestry and developmental potential that results in one cell or tissue effecting a developmental change in the other." [GOC:mah] +is_a: GO:0045168 ! cell-cell signaling involved in cell fate commitment + +[Term] +id: GO:0031133 +name: regulation of axon diameter +namespace: biological_process +def: "Any process that modulates the rate, direction or extent of axon growth such that the correct diameter is attained and maintained." [GOC:dph, GOC:mah, GOC:tb] +is_a: GO:0032536 ! regulation of cell projection size +is_a: GO:0050770 ! regulation of axonogenesis + +[Term] +id: GO:0031175 +name: neuron projection development +namespace: biological_process +def: "The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites)." [GOC:mah] +synonym: "neurite biosynthesis" NARROW [] +synonym: "neurite development" NARROW [GOC:dph] +synonym: "neurite formation" NARROW [] +synonym: "neurite growth" NARROW [] +synonym: "neurite outgrowth" NARROW [] +is_a: GO:0030030 ! cell projection organization +relationship: part_of GO:0048666 ! neuron development + +[Term] +id: GO:0031214 +name: biomineral tissue development +namespace: biological_process +def: "Formation of hard tissues that consist mainly of inorganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation." [PMID:15132736] +synonym: "biomineral formation" RELATED [GOC:dph, GOC:tb] +synonym: "biomineralization" EXACT [] +synonym: "mineralization" EXACT [] +xref: Wikipedia:Biomineralisation +is_a: GO:0009888 ! tissue development +relationship: part_of GO:0048513 ! organ development + +[Term] +id: GO:0031223 +name: auditory behavior +namespace: biological_process +def: "The behavior of an organism in response to a sound." [GOC:pr, GOC:rc] +synonym: "auditory behaviour" EXACT [] +synonym: "behavioral response to sound" EXACT [] +synonym: "behavioural response to sound" EXACT [] +is_a: GO:0007638 ! mechanosensory behavior +is_a: GO:0010996 ! response to auditory stimulus + +[Term] +id: GO:0031224 +name: intrinsic component of membrane +namespace: cellular_component +def: "The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane." [GOC:mah] +comment: Note that proteins intrinsic to membranes cannot be removed without disrupting the membrane, e.g. by detergent. +subset: gosubset_prok +synonym: "intrinsic to membrane" NARROW [] +is_a: GO:0044425 ! membrane part + +[Term] +id: GO:0031252 +name: cell leading edge +namespace: cellular_component +def: "The area of a motile cell closest to the direction of movement." [GOC:pg] +subset: goslim_pir +synonym: "front of cell" EXACT [] +synonym: "leading edge of cell" EXACT [] +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0031253 +name: cell projection membrane +namespace: cellular_component +def: "The portion of the plasma membrane surrounding a cell surface projection." [GOC:mah] +synonym: "membrane extension" RELATED [] +synonym: "membrane projection" RELATED [] +is_a: GO:0044459 ! plasma membrane part +is_a: GO:0044463 ! cell projection part + +[Term] +id: GO:0031323 +name: regulation of cellular metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of cellular metabolism" EXACT [] +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044237 ! cellular metabolic process +relationship: regulates GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0031324 +name: negative regulation of cellular metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] +subset: gosubset_prok +synonym: "down regulation of cellular metabolic process" EXACT [] +synonym: "down-regulation of cellular metabolic process" EXACT [] +synonym: "downregulation of cellular metabolic process" EXACT [] +synonym: "inhibition of cellular metabolic process" NARROW [] +synonym: "negative regulation of cellular metabolism" EXACT [] +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044237 ! cellular metabolic process +relationship: negatively_regulates GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0031325 +name: positive regulation of cellular metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] +subset: gosubset_prok +synonym: "activation of cellular metabolic process" NARROW [] +synonym: "positive regulation of cellular metabolism" EXACT [] +synonym: "stimulation of cellular metabolic process" NARROW [] +synonym: "up regulation of cellular metabolic process" EXACT [] +synonym: "up-regulation of cellular metabolic process" EXACT [] +synonym: "upregulation of cellular metabolic process" EXACT [] +xref: Reactome:REACT_101225 "ChREBP activates metabolic gene expression, Mus musculus" +xref: Reactome:REACT_102187 "ChREBP activates metabolic gene expression, Escherichia coli" +xref: Reactome:REACT_102331 "ChREBP activates metabolic gene expression, Caenorhabditis elegans" +xref: Reactome:REACT_105293 "ChREBP activates metabolic gene expression, Plasmodium falciparum" +xref: Reactome:REACT_108571 "ChREBP activates metabolic gene expression, Drosophila melanogaster" +xref: Reactome:REACT_109170 "ChREBP activates metabolic gene expression, Xenopus tropicalis" +xref: Reactome:REACT_2122 "ChREBP activates metabolic gene expression, Homo sapiens" +xref: Reactome:REACT_28360 "ChREBP activates metabolic gene expression, Arabidopsis thaliana" +xref: Reactome:REACT_31270 "ChREBP activates metabolic gene expression, Mycobacterium tuberculosis" +xref: Reactome:REACT_79603 "ChREBP activates metabolic gene expression, Canis familiaris" +xref: Reactome:REACT_80902 "ChREBP activates metabolic gene expression, Saccharomyces cerevisiae" +xref: Reactome:REACT_83058 "ChREBP activates metabolic gene expression, Taeniopygia guttata" +xref: Reactome:REACT_84314 "ChREBP activates metabolic gene expression, Oryza sativa" +xref: Reactome:REACT_86633 "ChREBP activates metabolic gene expression, Dictyostelium discoideum" +xref: Reactome:REACT_87840 "ChREBP activates metabolic gene expression, Danio rerio" +xref: Reactome:REACT_88060 "ChREBP activates metabolic gene expression, Rattus norvegicus" +xref: Reactome:REACT_91293 "ChREBP activates metabolic gene expression, Staphylococcus aureus N315" +xref: Reactome:REACT_91429 "ChREBP activates metabolic gene expression, Gallus gallus" +xref: Reactome:REACT_91906 "ChREBP activates metabolic gene expression, Schizosaccharomyces pombe" +xref: Reactome:REACT_92487 "ChREBP activates metabolic gene expression, Bos taurus" +xref: Reactome:REACT_99393 "ChREBP activates metabolic gene expression, Sus scrofa" +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044237 ! cellular metabolic process +relationship: positively_regulates GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0031326 +name: regulation of cellular biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of cellular anabolism" EXACT [] +synonym: "regulation of cellular biosynthesis" EXACT [] +synonym: "regulation of cellular formation" EXACT [] +synonym: "regulation of cellular synthesis" EXACT [] +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044249 ! cellular biosynthetic process +relationship: regulates GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0031327 +name: negative regulation of cellular biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] +subset: gosubset_prok +synonym: "down regulation of cellular biosynthetic process" EXACT [] +synonym: "down-regulation of cellular biosynthetic process" EXACT [] +synonym: "downregulation of cellular biosynthetic process" EXACT [] +synonym: "inhibition of cellular biosynthetic process" NARROW [] +synonym: "negative regulation of cellular anabolism" EXACT [] +synonym: "negative regulation of cellular biosynthesis" EXACT [] +synonym: "negative regulation of cellular formation" EXACT [] +synonym: "negative regulation of cellular synthesis" EXACT [] +is_a: GO:0009890 ! negative regulation of biosynthetic process +is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044249 ! cellular biosynthetic process +relationship: negatively_regulates GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0031328 +name: positive regulation of cellular biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] +subset: gosubset_prok +synonym: "activation of cellular biosynthetic process" NARROW [] +synonym: "positive regulation of cellular anabolism" EXACT [] +synonym: "positive regulation of cellular biosynthesis" EXACT [] +synonym: "positive regulation of cellular formation" EXACT [] +synonym: "positive regulation of cellular synthesis" EXACT [] +synonym: "stimulation of cellular biosynthetic process" NARROW [] +synonym: "up regulation of cellular biosynthetic process" EXACT [] +synonym: "up-regulation of cellular biosynthetic process" EXACT [] +synonym: "upregulation of cellular biosynthetic process" EXACT [] +is_a: GO:0009891 ! positive regulation of biosynthetic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044249 ! cellular biosynthetic process +relationship: positively_regulates GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0031329 +name: regulation of cellular catabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of cellular breakdown" EXACT [] +synonym: "regulation of cellular catabolism" EXACT [] +synonym: "regulation of cellular degradation" EXACT [] +is_a: GO:0009894 ! regulation of catabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044248 ! cellular catabolic process +relationship: regulates GO:0044248 ! cellular catabolic process + +[Term] +id: GO:0031333 +name: negative regulation of protein complex assembly +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly." [GOC:mah] +subset: gosubset_prok +synonym: "down regulation of protein complex assembly" EXACT [] +synonym: "down-regulation of protein complex assembly" EXACT [] +synonym: "downregulation of protein complex assembly" EXACT [] +synonym: "inhibition of protein complex assembly" NARROW [] +is_a: GO:0043254 ! regulation of protein complex assembly +is_a: GO:0051129 ! negative regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006461 ! protein complex assembly +relationship: negatively_regulates GO:0006461 ! protein complex assembly + +[Term] +id: GO:0031334 +name: positive regulation of protein complex assembly +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of protein complex assembly." [GOC:mah] +subset: gosubset_prok +synonym: "activation of protein complex assembly" NARROW [] +synonym: "stimulation of protein complex assembly" NARROW [] +synonym: "up regulation of protein complex assembly" EXACT [] +synonym: "up-regulation of protein complex assembly" EXACT [] +synonym: "upregulation of protein complex assembly" EXACT [] +is_a: GO:0043254 ! regulation of protein complex assembly +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006461 ! protein complex assembly +relationship: positively_regulates GO:0006461 ! protein complex assembly + +[Term] +id: GO:0031344 +name: regulation of cell projection organization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of cell projection organisation" EXACT [GOC:curators] +synonym: "regulation of cell projection organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030030 ! cell projection organization +relationship: regulates GO:0030030 ! cell projection organization + +[Term] +id: GO:0031345 +name: negative regulation of cell projection organization +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." [GOC:mah] +synonym: "down regulation of cell projection organization" EXACT [GOC:mah] +synonym: "down-regulation of cell projection organization" EXACT [] +synonym: "downregulation of cell projection organization" EXACT [] +synonym: "inhibition of cell projection organization" NARROW [] +synonym: "negative regulation of cell projection organisation" EXACT [GOC:curators] +synonym: "negative regulation of cell projection organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0031344 ! regulation of cell projection organization +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051129 ! negative regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030030 ! cell projection organization +relationship: negatively_regulates GO:0030030 ! cell projection organization + +[Term] +id: GO:0031346 +name: positive regulation of cell projection organization +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." [GOC:mah] +synonym: "activation of cell projection organization" NARROW [] +synonym: "positive regulation of cell projection organisation" EXACT [GOC:curators] +synonym: "positive regulation of cell projection organization and biogenesis" RELATED [GOC:mah] +synonym: "stimulation of cell projection organization" NARROW [] +synonym: "up regulation of cell projection organization" EXACT [] +synonym: "up-regulation of cell projection organization" EXACT [] +synonym: "upregulation of cell projection organization" EXACT [] +is_a: GO:0031344 ! regulation of cell projection organization +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030030 ! cell projection organization +relationship: positively_regulates GO:0030030 ! cell projection organization + +[Term] +id: GO:0031347 +name: regulation of defense response +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a defense response." [GOC:mah] +is_a: GO:0080134 ! regulation of response to stress +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006952 ! defense response +relationship: regulates GO:0006952 ! defense response + +[Term] +id: GO:0031349 +name: positive regulation of defense response +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of a defense response." [GOC:mah] +synonym: "activation of defense response" NARROW [] +synonym: "stimulation of defense response" NARROW [] +synonym: "up regulation of defense response" EXACT [] +synonym: "up-regulation of defense response" EXACT [] +synonym: "upregulation of defense response" EXACT [] +is_a: GO:0031347 ! regulation of defense response +is_a: GO:0048584 ! positive regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006952 ! defense response +relationship: positively_regulates GO:0006952 ! defense response + +[Term] +id: GO:0031396 +name: regulation of protein ubiquitination +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the addition of ubiquitin groups to a protein." [GOC:mah] +is_a: GO:0031399 ! regulation of protein modification process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016567 ! protein ubiquitination +relationship: regulates GO:0016567 ! protein ubiquitination + +[Term] +id: GO:0031397 +name: negative regulation of protein ubiquitination +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein." [GOC:mah] +synonym: "down regulation of protein ubiquitination" EXACT [] +synonym: "down-regulation of protein ubiquitination" EXACT [] +synonym: "downregulation of protein ubiquitination" EXACT [] +synonym: "inhibition of protein ubiquitination" NARROW [] +is_a: GO:0031396 ! regulation of protein ubiquitination +is_a: GO:0031400 ! negative regulation of protein modification process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016567 ! protein ubiquitination +relationship: negatively_regulates GO:0016567 ! protein ubiquitination + +[Term] +id: GO:0031399 +name: regulation of protein modification process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." [GOC:mah, GOC:tb] +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0032268 ! regulation of cellular protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006464 ! cellular protein modification process +relationship: regulates GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0031400 +name: negative regulation of protein modification process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." [GOC:mah, GOC:tb] +synonym: "down regulation of protein modification" EXACT [] +synonym: "down-regulation of protein modification" EXACT [] +synonym: "downregulation of protein modification" EXACT [] +synonym: "inhibition of protein modification" NARROW [] +is_a: GO:0031399 ! regulation of protein modification process +is_a: GO:0032269 ! negative regulation of cellular protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006464 ! cellular protein modification process +relationship: negatively_regulates GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0031401 +name: positive regulation of protein modification process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." [GOC:mah, GOC:tb] +synonym: "activation of protein modification" NARROW [] +synonym: "stimulation of protein modification" NARROW [] +synonym: "up regulation of protein modification" EXACT [] +synonym: "up-regulation of protein modification" EXACT [] +synonym: "upregulation of protein modification" EXACT [] +is_a: GO:0031399 ! regulation of protein modification process +is_a: GO:0032270 ! positive regulation of cellular protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006464 ! cellular protein modification process +relationship: positively_regulates GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0031410 +name: cytoplasmic vesicle +namespace: cellular_component +def: "A vesicle formed of membrane or protein, found in the cytoplasm of a cell." [GOC:mah] +subset: gosubset_prok +xref: NIF_Subcellular:sao180601769 +is_a: GO:0031982 ! vesicle +is_a: GO:0043229 ! intracellular organelle +is_a: GO:0044444 ! cytoplasmic part +intersection_of: GO:0031982 ! vesicle +intersection_of: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0031490 +name: chromatin DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with DNA that is assembled into chromatin." [GOC:mah] +is_a: GO:0003682 ! chromatin binding +is_a: GO:0043566 ! structure-specific DNA binding + +[Term] +id: GO:0031526 +name: brush border membrane +namespace: cellular_component +def: "The portion of the plasma membrane surrounding the brush border." [GOC:mah] +is_a: GO:0031253 ! cell projection membrane +relationship: part_of GO:0005903 ! brush border + +[Term] +id: GO:0031528 +name: microvillus membrane +namespace: cellular_component +def: "The portion of the plasma membrane surrounding a microvillus." [GOC:mah] +is_a: GO:0031253 ! cell projection membrane +relationship: part_of GO:0005902 ! microvillus + +[Term] +id: GO:0031589 +name: cell-substrate adhesion +namespace: biological_process +def: "The attachment of a cell to the underlying substrate via adhesion molecules." [GOC:mah, GOC:pf] +subset: gosubset_prok +is_a: GO:0007155 ! cell adhesion + +[Term] +id: GO:0031623 +name: receptor internalization +namespace: biological_process +def: "A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane." [GOC:bf, GOC:mah, GOC:signaling, PMID:15006537, PMID:19643732] +is_a: GO:0006898 ! receptor-mediated endocytosis +is_a: GO:0043112 ! receptor metabolic process +is_a: GO:0044710 ! single-organism metabolic process +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0031624 +name: ubiquitin conjugating enzyme binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a ubiquitin conjugating enzyme, any of the E2 proteins." [GOC:vp] +is_a: GO:0044390 ! small protein conjugating enzyme binding + +[Term] +id: GO:0031641 +name: regulation of myelination +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the formation of a myelin sheath around nerve axons." [GOC:mah] +is_a: GO:0051960 ! regulation of nervous system development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042552 ! myelination +relationship: regulates GO:0042552 ! myelination + +[Term] +id: GO:0031667 +name: response to nutrient levels +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients." [GOC:mah] +subset: gosubset_prok +is_a: GO:0009991 ! response to extracellular stimulus + +[Term] +id: GO:0031668 +name: cellular response to extracellular stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus." [GOC:mah] +subset: gosubset_prok +is_a: GO:0007154 ! cell communication +is_a: GO:0009991 ! response to extracellular stimulus +is_a: GO:0051716 ! cellular response to stimulus +is_a: GO:0071496 ! cellular response to external stimulus + +[Term] +id: GO:0031669 +name: cellular response to nutrient levels +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients." [GOC:mah] +subset: gosubset_prok +is_a: GO:0031667 ! response to nutrient levels +is_a: GO:0031668 ! cellular response to extracellular stimulus + +[Term] +id: GO:0031670 +name: cellular response to nutrient +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus." [GOC:mah] +is_a: GO:0007584 ! response to nutrient +is_a: GO:0031669 ! cellular response to nutrient levels +is_a: GO:0070887 ! cellular response to chemical stimulus + +[Term] +id: GO:0031674 +name: I band +namespace: cellular_component +def: "A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end." [ISBN:0321204131] +synonym: "I disc" EXACT [] +synonym: "isotropic disc" EXACT [] +synonym: "J disc" EXACT [] +xref: Wikipedia:Sarcomere#bands +is_a: GO:0044449 ! contractile fiber part +relationship: part_of GO:0030017 ! sarcomere + +[Term] +id: GO:0031943 +name: regulation of glucocorticoid metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids." [GOC:mah] +synonym: "regulation of glucocorticoid metabolism" EXACT [] +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008211 ! glucocorticoid metabolic process +relationship: regulates GO:0008211 ! glucocorticoid metabolic process + +[Term] +id: GO:0031945 +name: positive regulation of glucocorticoid metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids." [GOC:mah] +synonym: "activation of glucocorticoid metabolic process" NARROW [] +synonym: "positive regulation of glucocorticoid metabolism" EXACT [] +synonym: "stimulation of glucocorticoid metabolic process" NARROW [] +synonym: "up regulation of glucocorticoid metabolic process" EXACT [] +synonym: "up-regulation of glucocorticoid metabolic process" EXACT [] +synonym: "upregulation of glucocorticoid metabolic process" EXACT [] +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0031943 ! regulation of glucocorticoid metabolic process +is_a: GO:0032352 ! positive regulation of hormone metabolic process +is_a: GO:0045940 ! positive regulation of steroid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008211 ! glucocorticoid metabolic process +relationship: positively_regulates GO:0008211 ! glucocorticoid metabolic process + +[Term] +id: GO:0031946 +name: regulation of glucocorticoid biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids." [GOC:mah] +is_a: GO:0031943 ! regulation of glucocorticoid metabolic process +is_a: GO:0090030 ! regulation of steroid hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006704 ! glucocorticoid biosynthetic process +relationship: regulates GO:0006704 ! glucocorticoid biosynthetic process + +[Term] +id: GO:0031948 +name: positive regulation of glucocorticoid biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids." [GOC:mah] +synonym: "activation of glucocorticoid biosynthetic process" NARROW [] +synonym: "stimulation of glucocorticoid biosynthetic process" NARROW [] +synonym: "up regulation of glucocorticoid biosynthetic process" EXACT [] +synonym: "up-regulation of glucocorticoid biosynthetic process" EXACT [] +synonym: "upregulation of glucocorticoid biosynthetic process" EXACT [] +is_a: GO:0031945 ! positive regulation of glucocorticoid metabolic process +is_a: GO:0031946 ! regulation of glucocorticoid biosynthetic process +is_a: GO:0090031 ! positive regulation of steroid hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006704 ! glucocorticoid biosynthetic process +relationship: positively_regulates GO:0006704 ! glucocorticoid biosynthetic process + +[Term] +id: GO:0031974 +name: membrane-enclosed lumen +namespace: cellular_component +def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0031981 +name: nuclear lumen +namespace: cellular_component +def: "The volume enclosed by the nuclear inner membrane." [GOC:mah, GOC:pz] +is_a: GO:0044428 ! nuclear part +is_a: GO:0070013 ! intracellular organelle lumen + +[Term] +id: GO:0031982 +name: vesicle +namespace: cellular_component +def: "Any small, fluid-filled, spherical organelle enclosed by membrane or protein." [GOC:mah, GOC:pz] +subset: goslim_metagenomics +subset: goslim_pir +subset: gosubset_prok +xref: NIF_Subcellular:sao221389602 +xref: Wikipedia:Vesicle_(biology) +is_a: GO:0043226 ! organelle + +[Term] +id: GO:0031988 +name: membrane-bounded vesicle +namespace: cellular_component +def: "Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer." [GOC:mah] +subset: gosubset_prok +synonym: "membrane-enclosed vesicle" EXACT [] +is_a: GO:0031982 ! vesicle + +[Term] +id: GO:0032088 +name: negative regulation of NF-kappaB transcription factor activity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB." [GOC:dph, GOC:rl, GOC:tb] +synonym: "inhibition of NF-kappaB transcription factor" EXACT [GOC:dph, GOC:tb] +synonym: "NF-kappaB inhibitor" RELATED [] +is_a: GO:0043433 ! negative regulation of sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0032091 +name: negative regulation of protein binding +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding." [GOC:mah] +subset: gosubset_prok +synonym: "down regulation of protein binding" EXACT [] +synonym: "down-regulation of protein binding" EXACT [] +synonym: "downregulation of protein binding" EXACT [] +synonym: "inhibition of protein binding" NARROW [] +is_a: GO:0043393 ! regulation of protein binding +is_a: GO:0051100 ! negative regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0005515 ! protein binding +relationship: negatively_regulates GO:0005515 ! protein binding + +[Term] +id: GO:0032092 +name: positive regulation of protein binding +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of protein binding." [GOC:mah] +subset: gosubset_prok +synonym: "activation of protein binding" NARROW [] +synonym: "stimulation of protein binding" NARROW [] +synonym: "up regulation of protein binding" EXACT [] +synonym: "up-regulation of protein binding" EXACT [] +synonym: "upregulation of protein binding" EXACT [] +is_a: GO:0043393 ! regulation of protein binding +is_a: GO:0051099 ! positive regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0005515 ! protein binding +relationship: positively_regulates GO:0005515 ! protein binding + +[Term] +id: GO:0032101 +name: regulation of response to external stimulus +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a response to an external stimulus." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009605 ! response to external stimulus +relationship: regulates GO:0009605 ! response to external stimulus + +[Term] +id: GO:0032102 +name: negative regulation of response to external stimulus +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +synonym: "down regulation of response to external stimulus" EXACT [] +synonym: "down-regulation of response to external stimulus" EXACT [] +synonym: "downregulation of response to external stimulus" EXACT [] +synonym: "inhibition of response to external stimulus" NARROW [] +is_a: GO:0032101 ! regulation of response to external stimulus +is_a: GO:0048585 ! negative regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009605 ! response to external stimulus +relationship: negatively_regulates GO:0009605 ! response to external stimulus + +[Term] +id: GO:0032103 +name: positive regulation of response to external stimulus +namespace: biological_process +def: "Any process that activates, maintains or increases the rate of a response to an external stimulus." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +synonym: "activation of response to external stimulus" NARROW [] +synonym: "stimulation of response to external stimulus" NARROW [] +synonym: "up regulation of response to external stimulus" EXACT [] +synonym: "up-regulation of response to external stimulus" EXACT [] +synonym: "upregulation of response to external stimulus" EXACT [] +is_a: GO:0032101 ! regulation of response to external stimulus +is_a: GO:0048584 ! positive regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009605 ! response to external stimulus +relationship: positively_regulates GO:0009605 ! response to external stimulus + +[Term] +id: GO:0032147 +name: activation of protein kinase activity +namespace: biological_process +def: "Any process that initiates the activity of an inactive protein kinase." [GOC:mah] +synonym: "protein kinase activation" RELATED [] +is_a: GO:0045860 ! positive regulation of protein kinase activity + +[Term] +id: GO:0032148 +name: activation of protein kinase B activity +namespace: biological_process +def: "Any process that initiates the activity of the inactive enzyme protein kinase B." [GOC:pg] +synonym: "protein kinase B activation" EXACT [] +is_a: GO:0032147 ! activation of protein kinase activity + +[Term] +id: GO:0032231 +name: regulation of actin filament bundle assembly +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the assembly of actin filament bundles." [GOC:mah] +synonym: "regulation of actin cable assembly" EXACT [GOC:dph, GOC:tb] +synonym: "regulation of actin filament bundle formation" RELATED [GOC:dph] +is_a: GO:0032956 ! regulation of actin cytoskeleton organization +is_a: GO:0044087 ! regulation of cellular component biogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051017 ! actin filament bundle assembly +relationship: regulates GO:0051017 ! actin filament bundle assembly + +[Term] +id: GO:0032233 +name: positive regulation of actin filament bundle assembly +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles." [GOC:mah] +synonym: "activation of actin filament bundle formation" NARROW [] +synonym: "stimulation of actin filament bundle formation" NARROW [] +synonym: "up regulation of actin filament bundle formation" EXACT [] +synonym: "up-regulation of actin filament bundle formation" EXACT [] +synonym: "upregulation of actin filament bundle formation" EXACT [] +is_a: GO:0032231 ! regulation of actin filament bundle assembly +is_a: GO:0051495 ! positive regulation of cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0051017 ! actin filament bundle assembly +relationship: positively_regulates GO:0051017 ! actin filament bundle assembly + +[Term] +id: GO:0032268 +name: regulation of cellular protein metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of cellular protein metabolism" EXACT [] +is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044267 ! cellular protein metabolic process +relationship: regulates GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0032269 +name: negative regulation of cellular protein metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah] +synonym: "down regulation of cellular protein metabolic process" EXACT [] +synonym: "down-regulation of cellular protein metabolic process" EXACT [] +synonym: "downregulation of cellular protein metabolic process" EXACT [] +synonym: "inhibition of cellular protein metabolic process" NARROW [] +synonym: "negative regulation of cellular protein metabolism" EXACT [] +is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0032268 ! regulation of cellular protein metabolic process +is_a: GO:0051248 ! negative regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044267 ! cellular protein metabolic process +relationship: negatively_regulates GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0032270 +name: positive regulation of cellular protein metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah] +synonym: "activation of cellular protein metabolic process" NARROW [] +synonym: "positive regulation of cellular protein metabolism" EXACT [] +synonym: "stimulation of cellular protein metabolic process" NARROW [] +synonym: "up regulation of cellular protein metabolic process" EXACT [] +synonym: "up-regulation of cellular protein metabolic process" EXACT [] +synonym: "upregulation of cellular protein metabolic process" EXACT [] +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0032268 ! regulation of cellular protein metabolic process +is_a: GO:0051247 ! positive regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044267 ! cellular protein metabolic process +relationship: positively_regulates GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0032288 +name: myelin assembly +namespace: biological_process +def: "The process in which the wraps of cell membrane that constitute myelin are laid down around an axon in the central or peripheral nervous system." [GOC:dgh, GOC:dph, GOC:tb] +synonym: "myelin formation" RELATED [GOC:dph, GOC:tb] +is_a: GO:0010927 ! cellular component assembly involved in morphogenesis +relationship: part_of GO:0042552 ! myelination + +[Term] +id: GO:0032289 +name: central nervous system myelin formation +namespace: biological_process +def: "The process in which the wraps of cell membrane that constitute myelin are laid down around an axon by an oligodendrocyte in the central nervous system." [GOC:dgh] +synonym: "myelin formation in central nervous system" EXACT [GOC:curators] +is_a: GO:0032288 ! myelin assembly +relationship: part_of GO:0022010 ! central nervous system myelination + +[Term] +id: GO:0032291 +name: axon ensheathment in central nervous system +namespace: biological_process +def: "The process in which a glial cell membrane closes around an axon in the central nervous system. This can be a myelinating or a non-myelinating neuron-glial interaction." [GOC:dgh] +synonym: "ensheathment of axons in central nervous system" EXACT [GOC:curators] +is_a: GO:0008366 ! axon ensheathment + +[Term] +id: GO:0032318 +name: regulation of Ras GTPase activity +namespace: biological_process +def: "Any process that modulates the activity of a GTPase of the Ras superfamily." [GOC:mah] +is_a: GO:0043087 ! regulation of GTPase activity +relationship: part_of GO:0046578 ! regulation of Ras protein signal transduction + +[Term] +id: GO:0032319 +name: regulation of Rho GTPase activity +namespace: biological_process +def: "Any process that modulates the activity of a GTPase of the Rho family." [GOC:mah] +is_a: GO:0032318 ! regulation of Ras GTPase activity +relationship: part_of GO:0035023 ! regulation of Rho protein signal transduction + +[Term] +id: GO:0032320 +name: positive regulation of Ras GTPase activity +namespace: biological_process +def: "Any process that activates or increases the activity of a GTPase of the Ras superfamily." [GOC:mah] +synonym: "stimulation of Ras GTPase activity" NARROW [] +synonym: "up regulation of Ras GTPase activity" EXACT [] +synonym: "up-regulation of Ras GTPase activity" EXACT [] +synonym: "upregulation of Ras GTPase activity" EXACT [] +is_a: GO:0032318 ! regulation of Ras GTPase activity +is_a: GO:0043547 ! positive regulation of GTPase activity + +[Term] +id: GO:0032321 +name: positive regulation of Rho GTPase activity +namespace: biological_process +def: "Any process that activates or increases the activity of a GTPase of the Rho family." [GOC:mah] +synonym: "stimulation of Rho GTPase activity" NARROW [] +synonym: "up regulation of Rho GTPase activity" EXACT [] +synonym: "up-regulation of Rho GTPase activity" EXACT [] +synonym: "upregulation of Rho GTPase activity" EXACT [] +is_a: GO:0032319 ! regulation of Rho GTPase activity +is_a: GO:0032320 ! positive regulation of Ras GTPase activity + +[Term] +id: GO:0032330 +name: regulation of chondrocyte differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of chondrocyte differentiation." [GOC:mah] +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0061035 ! regulation of cartilage development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002062 ! chondrocyte differentiation +relationship: regulates GO:0002062 ! chondrocyte differentiation + +[Term] +id: GO:0032331 +name: negative regulation of chondrocyte differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation." [GOC:mah] +synonym: "down regulation of chondrocyte differentiation" EXACT [] +synonym: "down-regulation of chondrocyte differentiation" EXACT [] +synonym: "downregulation of chondrocyte differentiation" EXACT [] +synonym: "inhibition of chondrocyte differentiation" NARROW [] +is_a: GO:0032330 ! regulation of chondrocyte differentiation +is_a: GO:0045596 ! negative regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002062 ! chondrocyte differentiation +relationship: negatively_regulates GO:0002062 ! chondrocyte differentiation + +[Term] +id: GO:0032341 +name: aldosterone metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving aldosterone, a corticosteroid hormone that is produced by the zona glomerulosa of the adrenal cortex and regulates salt (sodium and potassium) and water balance." [PMID:16527843] +synonym: "aldosterone metabolism" EXACT [] +is_a: GO:0006066 ! alcohol metabolic process +is_a: GO:0008207 ! C21-steroid hormone metabolic process +is_a: GO:0008212 ! mineralocorticoid metabolic process +is_a: GO:0042180 ! cellular ketone metabolic process + +[Term] +id: GO:0032342 +name: aldosterone biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of aldosterone, a corticosteroid hormone that is produced by the zona glomerulosa of the adrenal cortex and regulates salt (sodium and potassium) and water balance." [PMID:16527843] +is_a: GO:0006700 ! C21-steroid hormone biosynthetic process +is_a: GO:0006705 ! mineralocorticoid biosynthetic process +is_a: GO:0032341 ! aldosterone metabolic process +is_a: GO:0042181 ! ketone biosynthetic process +is_a: GO:0046165 ! alcohol biosynthetic process + +[Term] +id: GO:0032344 +name: regulation of aldosterone metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving aldosterone." [GOC:mah] +synonym: "regulation of aldosterone metabolism" EXACT [] +is_a: GO:0010565 ! regulation of cellular ketone metabolic process +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032341 ! aldosterone metabolic process +relationship: regulates GO:0032341 ! aldosterone metabolic process + +[Term] +id: GO:0032346 +name: positive regulation of aldosterone metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving aldosterone." [GOC:mah] +synonym: "activation of aldosterone metabolic process" NARROW [] +synonym: "positive regulation of aldosterone metabolism" EXACT [] +synonym: "stimulation of aldosterone metabolic process" NARROW [] +synonym: "up regulation of aldosterone metabolic process" EXACT [] +synonym: "up-regulation of aldosterone metabolic process" EXACT [] +synonym: "upregulation of aldosterone metabolic process" EXACT [] +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0032344 ! regulation of aldosterone metabolic process +is_a: GO:0032352 ! positive regulation of hormone metabolic process +is_a: GO:0045940 ! positive regulation of steroid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032341 ! aldosterone metabolic process +relationship: positively_regulates GO:0032341 ! aldosterone metabolic process + +[Term] +id: GO:0032347 +name: regulation of aldosterone biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of aldosterone." [GOC:mah] +is_a: GO:0010566 ! regulation of ketone biosynthetic process +is_a: GO:0032344 ! regulation of aldosterone metabolic process +is_a: GO:0090030 ! regulation of steroid hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032342 ! aldosterone biosynthetic process +relationship: regulates GO:0032342 ! aldosterone biosynthetic process + +[Term] +id: GO:0032349 +name: positive regulation of aldosterone biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of aldosterone." [GOC:mah] +synonym: "activation of aldosterone biosynthetic process" NARROW [] +synonym: "stimulation of aldosterone biosynthetic process" NARROW [] +synonym: "up regulation of aldosterone biosynthetic process" EXACT [] +synonym: "up-regulation of aldosterone biosynthetic process" EXACT [] +synonym: "upregulation of aldosterone biosynthetic process" EXACT [] +is_a: GO:0032346 ! positive regulation of aldosterone metabolic process +is_a: GO:0032347 ! regulation of aldosterone biosynthetic process +is_a: GO:0090031 ! positive regulation of steroid hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032342 ! aldosterone biosynthetic process +relationship: positively_regulates GO:0032342 ! aldosterone biosynthetic process + +[Term] +id: GO:0032350 +name: regulation of hormone metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving any hormone." [GOC:mah] +synonym: "regulation of hormone metabolism" EXACT [] +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042445 ! hormone metabolic process +relationship: regulates GO:0042445 ! hormone metabolic process + +[Term] +id: GO:0032351 +name: negative regulation of hormone metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving any hormone." [GOC:mah] +synonym: "down regulation of hormone metabolic process" EXACT [] +synonym: "down-regulation of hormone metabolic process" EXACT [] +synonym: "downregulation of hormone metabolic process" EXACT [] +synonym: "inhibition of hormone metabolic process" NARROW [] +synonym: "negative regulation of hormone metabolism" EXACT [] +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042445 ! hormone metabolic process +relationship: negatively_regulates GO:0042445 ! hormone metabolic process + +[Term] +id: GO:0032352 +name: positive regulation of hormone metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving any hormone." [GOC:mah] +synonym: "activation of hormone metabolic process" NARROW [] +synonym: "positive regulation of hormone metabolism" EXACT [] +synonym: "stimulation of hormone metabolic process" NARROW [] +synonym: "up regulation of hormone metabolic process" EXACT [] +synonym: "up-regulation of hormone metabolic process" EXACT [] +synonym: "upregulation of hormone metabolic process" EXACT [] +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042445 ! hormone metabolic process +relationship: positively_regulates GO:0042445 ! hormone metabolic process + +[Term] +id: GO:0032353 +name: negative regulation of hormone biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones." [GOC:ai] +synonym: "down regulation of hormone biosynthetic process" EXACT [] +synonym: "down-regulation of hormone biosynthetic process" EXACT [] +synonym: "downregulation of hormone biosynthetic process" EXACT [] +synonym: "inhibition of hormone biosynthetic process" NARROW [] +is_a: GO:0031327 ! negative regulation of cellular biosynthetic process +is_a: GO:0032351 ! negative regulation of hormone metabolic process +is_a: GO:0046885 ! regulation of hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042446 ! hormone biosynthetic process +relationship: negatively_regulates GO:0042446 ! hormone biosynthetic process + +[Term] +id: GO:0032355 +name: response to estradiol +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen." [GOC:mah, ISBN:0911910123] +synonym: "response to E2 stimulus" EXACT [] +synonym: "response to estradiol stimulus" EXACT [GOC:dos] +is_a: GO:0043627 ! response to estrogen +is_a: GO:0097305 ! response to alcohol + +[Term] +id: GO:0032364 +name: oxygen homeostasis +namespace: biological_process +def: "A homeostatic process involved in the maintenance of an internal steady state of oxygen within an organism or cell." [GOC:rph] +is_a: GO:0033483 ! gas homeostasis + +[Term] +id: GO:0032365 +name: intracellular lipid transport +namespace: biological_process +def: "The directed movement of lipids within cells." [GOC:mah] +is_a: GO:0006869 ! lipid transport +is_a: GO:1902582 ! single-organism intracellular transport +intersection_of: GO:0006869 ! lipid transport +intersection_of: occurs_in GO:0005622 ! intracellular +relationship: occurs_in GO:0005622 ! intracellular + +[Term] +id: GO:0032366 +name: intracellular sterol transport +namespace: biological_process +def: "The directed movement of sterols within cells." [GOC:mah] +is_a: GO:0015918 ! sterol transport +is_a: GO:0032365 ! intracellular lipid transport +intersection_of: GO:0015918 ! sterol transport +intersection_of: occurs_in GO:0005622 ! intracellular + +[Term] +id: GO:0032367 +name: intracellular cholesterol transport +namespace: biological_process +def: "The directed movement of cholesterol, cholest-5-en-3-beta-ol, within cells." [GOC:mah] +is_a: GO:0030301 ! cholesterol transport +is_a: GO:0032366 ! intracellular sterol transport +intersection_of: GO:0030301 ! cholesterol transport +intersection_of: occurs_in GO:0005622 ! intracellular + +[Term] +id: GO:0032386 +name: regulation of intracellular transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of substances within cells." [GOC:mah] +is_a: GO:0051049 ! regulation of transport +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046907 ! intracellular transport +relationship: regulates GO:0046907 ! intracellular transport + +[Term] +id: GO:0032387 +name: negative regulation of intracellular transport +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells." [GOC:mah] +synonym: "down regulation of intracellular transport" EXACT [] +synonym: "down-regulation of intracellular transport" EXACT [] +synonym: "downregulation of intracellular transport" EXACT [] +synonym: "inhibition of intracellular transport" NARROW [] +is_a: GO:0032386 ! regulation of intracellular transport +is_a: GO:0051051 ! negative regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046907 ! intracellular transport +relationship: negatively_regulates GO:0046907 ! intracellular transport + +[Term] +id: GO:0032388 +name: positive regulation of intracellular transport +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells." [GOC:mah] +synonym: "activation of intracellular transport" NARROW [] +synonym: "stimulation of intracellular transport" NARROW [] +synonym: "up regulation of intracellular transport" EXACT [] +synonym: "up-regulation of intracellular transport" EXACT [] +synonym: "upregulation of intracellular transport" EXACT [] +is_a: GO:0032386 ! regulation of intracellular transport +is_a: GO:0051050 ! positive regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046907 ! intracellular transport +relationship: positively_regulates GO:0046907 ! intracellular transport + +[Term] +id: GO:0032403 +name: protein complex binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:mah] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0032444 +name: activin responsive factor complex +namespace: cellular_component +def: "A transcriptionally active complex that binds to an activin response element (ARE) in the promoter of target genes, and is composed of two SMAD2 proteins, one SMAD4 protein and a Forkhead activin signal transducer (FAST) transcription factor." [PMID:12374795, PMID:9288972] +comment: Note that this term should not be confused with any of the molecular function and biological process terms that refer to the small GTPase ARF (ADP-ribosylation factor). +synonym: "ARF complex" EXACT [] +is_a: GO:0044798 ! nuclear transcription factor complex + +[Term] +id: GO:0032446 +name: protein modification by small protein conjugation +namespace: biological_process +def: "A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to a target protein." [GOC:mah] +is_a: GO:0070647 ! protein modification by small protein conjugation or removal + +[Term] +id: GO:0032501 +name: multicellular organismal process +namespace: biological_process +alt_id: GO:0050874 +def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] +subset: goslim_pir +synonym: "organismal physiological process" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0032502 +name: developmental process +namespace: biological_process +def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] +subset: goslim_aspergillus +subset: goslim_pir +subset: gosubset_prok +synonym: "development" NARROW [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0032504 +name: multicellular organism reproduction +namespace: biological_process +def: "The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:isa_complete, GOC:jid] +is_a: GO:0000003 ! reproduction +is_a: GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0032507 +name: maintenance of protein location in cell +namespace: biological_process +def: "Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere." [GOC:isa_complete, GOC:mah] +synonym: "maintenance of protein localization in cell" RELATED [GOC:dph, GOC:tb] +is_a: GO:0045185 ! maintenance of protein location +is_a: GO:0051651 ! maintenance of location in cell +intersection_of: GO:0045185 ! maintenance of protein location +intersection_of: occurs_in GO:0005623 ! cell +relationship: part_of GO:0034613 ! cellular protein localization + +[Term] +id: GO:0032525 +name: somite rostral/caudal axis specification +namespace: biological_process +def: "The establishment, maintenance and elaboration of the rostro-caudal axis of a somite, prior to the morphological formation of a somite boundary." [GOC:bf, PMID:16326386, PMID:17360776] +synonym: "somite rostrocaudal axis specification" EXACT [] +synonym: "somite rostrocaudal polarity" RELATED [] +is_a: GO:0000578 ! embryonic axis specification +is_a: GO:0009948 ! anterior/posterior axis specification +relationship: part_of GO:0001756 ! somitogenesis + +[Term] +id: GO:0032535 +name: regulation of cellular component size +namespace: biological_process +def: "A process that modulates the size of a cellular component." [GOC:mah] +subset: gosubset_prok +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0090066 ! regulation of anatomical structure size + +[Term] +id: GO:0032536 +name: regulation of cell projection size +namespace: biological_process +def: "A process that modulates the size of a cell projection." [GOC:mah] +is_a: GO:0032535 ! regulation of cellular component size + +[Term] +id: GO:0032602 +name: chemokine production +namespace: biological_process +def: "The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032609 +name: interferon-gamma production +namespace: biological_process +def: "The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah] +synonym: "IFNG production" EXACT [GOC:mah] +synonym: "type II IFN production" BROAD [GOC:mah] +synonym: "type II interferon production" BROAD [] +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032611 +name: interleukin-1 beta production +namespace: biological_process +def: "The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] +synonym: "IL-1 beta production" EXACT [] +is_a: GO:0032612 ! interleukin-1 production + +[Term] +id: GO:0032612 +name: interleukin-1 production +namespace: biological_process +def: "The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] +synonym: "IL-1 production" EXACT [] +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032635 +name: interleukin-6 production +namespace: biological_process +def: "The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] +synonym: "IL-6 production" EXACT [] +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032637 +name: interleukin-8 production +namespace: biological_process +def: "The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] +synonym: "IL-8 production" EXACT [] +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0032642 +name: regulation of chemokine production +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of chemokine production." [GOC:mah] +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032602 ! chemokine production +relationship: regulates GO:0032602 ! chemokine production + +[Term] +id: GO:0032649 +name: regulation of interferon-gamma production +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah] +synonym: "regulation of type II interferon production" BROAD [] +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032609 ! interferon-gamma production +relationship: regulates GO:0032609 ! interferon-gamma production + +[Term] +id: GO:0032651 +name: regulation of interleukin-1 beta production +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of interleukin-1 beta production." [GOC:mah] +synonym: "regulation of IL-1 beta production" EXACT [] +is_a: GO:0032652 ! regulation of interleukin-1 production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032611 ! interleukin-1 beta production +relationship: regulates GO:0032611 ! interleukin-1 beta production + +[Term] +id: GO:0032652 +name: regulation of interleukin-1 production +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of interleukin-1 production." [GOC:mah] +synonym: "regulation of IL-1 production" EXACT [] +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032612 ! interleukin-1 production +relationship: regulates GO:0032612 ! interleukin-1 production + +[Term] +id: GO:0032675 +name: regulation of interleukin-6 production +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of interleukin-6 production." [GOC:mah] +synonym: "regulation of IL-6 production" EXACT [] +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032635 ! interleukin-6 production +relationship: regulates GO:0032635 ! interleukin-6 production + +[Term] +id: GO:0032677 +name: regulation of interleukin-8 production +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of interleukin-8 production." [GOC:mah] +synonym: "regulation of IL-8 production" EXACT [] +is_a: GO:0001817 ! regulation of cytokine production +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032637 ! interleukin-8 production +relationship: regulates GO:0032637 ! interleukin-8 production + +[Term] +id: GO:0032729 +name: positive regulation of interferon-gamma production +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah] +synonym: "activation of interferon-gamma production" NARROW [] +synonym: "positive regulation of type II interferon production" BROAD [] +synonym: "stimulation of interferon-gamma production" NARROW [] +synonym: "up regulation of interferon-gamma production" EXACT [] +synonym: "up-regulation of interferon-gamma production" EXACT [] +synonym: "upregulation of interferon-gamma production" EXACT [] +is_a: GO:0001819 ! positive regulation of cytokine production +is_a: GO:0032649 ! regulation of interferon-gamma production +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032609 ! interferon-gamma production +relationship: positively_regulates GO:0032609 ! interferon-gamma production + +[Term] +id: GO:0032731 +name: positive regulation of interleukin-1 beta production +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of interleukin-1 beta production." [GOC:mah] +synonym: "activation of interleukin-1 beta production" NARROW [] +synonym: "positive regulation of IL-1 beta production" EXACT [] +synonym: "stimulation of interleukin-1 beta production" NARROW [] +synonym: "up regulation of interleukin-1 beta production" EXACT [] +synonym: "up-regulation of interleukin-1 beta production" EXACT [] +synonym: "upregulation of interleukin-1 beta production" EXACT [] +is_a: GO:0032651 ! regulation of interleukin-1 beta production +is_a: GO:0032732 ! positive regulation of interleukin-1 production +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032611 ! interleukin-1 beta production +relationship: positively_regulates GO:0032611 ! interleukin-1 beta production + +[Term] +id: GO:0032732 +name: positive regulation of interleukin-1 production +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of interleukin-1 production." [GOC:mah] +synonym: "activation of interleukin-1 production" NARROW [] +synonym: "positive regulation of IL-1 production" EXACT [] +synonym: "stimulation of interleukin-1 production" NARROW [] +synonym: "up regulation of interleukin-1 production" EXACT [] +synonym: "up-regulation of interleukin-1 production" EXACT [] +synonym: "upregulation of interleukin-1 production" EXACT [] +is_a: GO:0001819 ! positive regulation of cytokine production +is_a: GO:0032652 ! regulation of interleukin-1 production +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032612 ! interleukin-1 production +relationship: positively_regulates GO:0032612 ! interleukin-1 production + +[Term] +id: GO:0032755 +name: positive regulation of interleukin-6 production +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of interleukin-6 production." [GOC:mah] +synonym: "activation of interleukin-6 production" NARROW [] +synonym: "positive regulation of IL-6 production" EXACT [] +synonym: "stimulation of interleukin-6 production" NARROW [] +synonym: "up regulation of interleukin-6 production" EXACT [] +synonym: "up-regulation of interleukin-6 production" EXACT [] +synonym: "upregulation of interleukin-6 production" EXACT [] +is_a: GO:0001819 ! positive regulation of cytokine production +is_a: GO:0032675 ! regulation of interleukin-6 production +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032635 ! interleukin-6 production +relationship: positively_regulates GO:0032635 ! interleukin-6 production + +[Term] +id: GO:0032774 +name: RNA biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers." [GOC:mah] +synonym: "RNA anabolism" EXACT [] +synonym: "RNA biosynthesis" EXACT [] +synonym: "RNA formation" EXACT [] +synonym: "RNA synthesis" EXACT [] +is_a: GO:0009059 ! macromolecule biosynthetic process +is_a: GO:0016070 ! RNA metabolic process +is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process + +[Term] +id: GO:0032793 +name: positive regulation of CREB transcription factor activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of activity of the transcription factor CREB." [GOC:dph, GOC:ecd, GOC:tb] +synonym: "activation of CREB" EXACT [] +synonym: "activation of CREB transcription factor" EXACT [GOC:dph, GOC:tb] +synonym: "CREB activator" RELATED [] +is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0032808 +name: lacrimal gland development +namespace: biological_process +def: "The process whose specific outcome is the progression of the lacrimal gland over time, from its formation to the mature structure. The lacrimal gland produces secretions that lubricate and protect the cornea of the eye." [GOC:ln] +is_a: GO:0048732 ! gland development +relationship: part_of GO:0035272 ! exocrine system development + +[Term] +id: GO:0032835 +name: glomerulus development +namespace: biological_process +def: "The progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney. The glomerulus is part of the nephron and is restricted to one body segment." [GOC:mah, GOC:mtg_kidney_jan10] +synonym: "glomerular development" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0072006 ! nephron development + +[Term] +id: GO:0032844 +name: regulation of homeostatic process +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of a homeostatic process." [GOC:mah] +subset: gosubset_prok +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042592 ! homeostatic process +relationship: regulates GO:0042592 ! homeostatic process + +[Term] +id: GO:0032846 +name: positive regulation of homeostatic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of a homeostatic process." [GOC:mah] +synonym: "activation of homeostatic process" NARROW [] +synonym: "stimulation of homeostatic process" NARROW [] +synonym: "up regulation of homeostatic process" EXACT [] +synonym: "up-regulation of homeostatic process" EXACT [] +synonym: "upregulation of homeostatic process" EXACT [] +is_a: GO:0032844 ! regulation of homeostatic process +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042592 ! homeostatic process +relationship: positively_regulates GO:0042592 ! homeostatic process + +[Term] +id: GO:0032856 +name: activation of Ras GTPase activity +namespace: biological_process +def: "Any process that initiates the activity of an inactive GTPase of the Ras superfamily through the replacement of GDP by GTP." [GOC:dph, GOC:mah, GOC:tb] +comment: Note that this term should not be confused with the molecular function term 'Ras GTPase activator activity ; GO:0005099', which refers specifically to the activity of Ras GAPs. +synonym: "Ras GTPase activation" EXACT [] +is_a: GO:0032320 ! positive regulation of Ras GTPase activity + +[Term] +id: GO:0032862 +name: activation of Rho GTPase activity +namespace: biological_process +def: "Any process that initiates the activity of an inactive GTPase of the Rho family through the replacement of GDP by GTP." [GOC:dph, GOC:mah, GOC:tb] +comment: Note that this term should not be confused with the molecular function term 'Rho GTPase activator activity ; GO:0005100', which refers specifically to the activity of Rho GAPs. +synonym: "Rho GTPase activation" EXACT [] +is_a: GO:0032321 ! positive regulation of Rho GTPase activity +is_a: GO:0032856 ! activation of Ras GTPase activity + +[Term] +id: GO:0032868 +name: response to insulin +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." [GOC:mah, ISBN:0198506732] +synonym: "response to insulin stimulus" EXACT [GOC:dos] +is_a: GO:0043434 ! response to peptide hormone + +[Term] +id: GO:0032869 +name: cellular response to insulin stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." [GOC:mah, ISBN:0198506732] +is_a: GO:0032868 ! response to insulin +is_a: GO:0071375 ! cellular response to peptide hormone stimulus + +[Term] +id: GO:0032870 +name: cellular response to hormone stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus." [GOC:mah] +is_a: GO:0009725 ! response to hormone +is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:0071495 ! cellular response to endogenous stimulus + +[Term] +id: GO:0032872 +name: regulation of stress-activated MAPK cascade +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade." [GOC:mah] +synonym: "regulation of p38 MAPK signaling" EXACT [] +synonym: "regulation of p38 MAPK signalling" EXACT [] +synonym: "regulation of stress-activated MAPK signaling pathway" EXACT [] +synonym: "regulation of stress-activated MAPK signalling pathway" EXACT [] +synonym: "regulation of stress-activated MAPKKK cascade" EXACT [] +synonym: "regulation of stress-activated MAPKKK signaling pathway" EXACT [] +synonym: "regulation of stress-activated MAPKKK signalling pathway" EXACT [] +is_a: GO:0043408 ! regulation of MAPK cascade +is_a: GO:0070302 ! regulation of stress-activated protein kinase signaling cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051403 ! stress-activated MAPK cascade +relationship: regulates GO:0051403 ! stress-activated MAPK cascade + +[Term] +id: GO:0032874 +name: positive regulation of stress-activated MAPK cascade +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade." [GOC:mah] +synonym: "activation of stress-activated MAPK cascade" NARROW [] +synonym: "positive regulation of p38 MAPK signaling" EXACT [] +synonym: "positive regulation of p38 MAPK signalling" EXACT [] +synonym: "positive regulation of stress-activated MAPK signaling pathway" EXACT [] +synonym: "positive regulation of stress-activated MAPK signalling pathway" EXACT [] +synonym: "positive regulation of stress-activated MAPKKK cascade" EXACT [] +synonym: "positive regulation of stress-activated MAPKKK signaling pathway" EXACT [] +synonym: "positive regulation of stress-activated MAPKKK signalling pathway" EXACT [] +synonym: "stimulation of stress-activated MAPK cascade" NARROW [] +synonym: "up regulation of stress-activated MAPK cascade" EXACT [] +synonym: "up-regulation of stress-activated MAPK cascade" EXACT [] +synonym: "upregulation of stress-activated MAPK cascade" EXACT [] +is_a: GO:0032872 ! regulation of stress-activated MAPK cascade +is_a: GO:0043410 ! positive regulation of MAPK cascade +is_a: GO:0070304 ! positive regulation of stress-activated protein kinase signaling cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0051403 ! stress-activated MAPK cascade +relationship: positively_regulates GO:0051403 ! stress-activated MAPK cascade + +[Term] +id: GO:0032879 +name: regulation of localization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location." [GOC:mah] +subset: gosubset_prok +synonym: "regulation of localisation" EXACT [GOC:mah] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051179 ! localization +relationship: regulates GO:0051179 ! localization + +[Term] +id: GO:0032880 +name: regulation of protein localization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location." [GOC:dph, GOC:mah, GOC:tb] +subset: gosubset_prok +synonym: "regulation of protein localisation" EXACT [GOC:mah] +is_a: GO:0032879 ! regulation of localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008104 ! protein localization +relationship: regulates GO:0008104 ! protein localization + +[Term] +id: GO:0032886 +name: regulation of microtubule-based process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton." [GOC:mah] +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007017 ! microtubule-based process +relationship: regulates GO:0007017 ! microtubule-based process + +[Term] +id: GO:0032940 +name: secretion by cell +namespace: biological_process +def: "The controlled release of a substance by a cell." [GOC:mah] +synonym: "cellular secretion" EXACT [] +xref: Wikipedia:Secretion +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0046903 ! secretion +is_a: GO:0051649 ! establishment of localization in cell + +[Term] +id: GO:0032941 +name: secretion by tissue +namespace: biological_process +def: "The controlled release of a substance by a tissue." [GOC:mah] +synonym: "expulsion of gland contents" RELATED [GOC:mah] +synonym: "tissue secretion" EXACT [] +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0046903 ! secretion + +[Term] +id: GO:0032943 +name: mononuclear cell proliferation +namespace: biological_process +def: "The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] +synonym: "PBMC proliferation" NARROW [] +synonym: "peripheral blood mononuclear cell proliferation" NARROW [] +is_a: GO:0070661 ! leukocyte proliferation + +[Term] +id: GO:0032944 +name: regulation of mononuclear cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of mononuclear cell proliferation." [GOC:add] +synonym: "regulation of PBMC proliferation" NARROW [] +synonym: "regulation of peripheral blood mononuclear cell proliferation" NARROW [] +is_a: GO:0070663 ! regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032943 ! mononuclear cell proliferation +relationship: regulates GO:0032943 ! mononuclear cell proliferation + +[Term] +id: GO:0032945 +name: negative regulation of mononuclear cell proliferation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation." [GOC:add] +synonym: "negative regulation of PBMC proliferation" NARROW [] +synonym: "negative regulation of peripheral blood mononuclear cell proliferation" NARROW [] +is_a: GO:0032944 ! regulation of mononuclear cell proliferation +is_a: GO:0070664 ! negative regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032943 ! mononuclear cell proliferation +relationship: negatively_regulates GO:0032943 ! mononuclear cell proliferation + +[Term] +id: GO:0032946 +name: positive regulation of mononuclear cell proliferation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of mononuclear cell proliferation." [GOC:add] +synonym: "activation of mononuclear cell proliferation" NARROW [] +synonym: "positive regulation of PBMC proliferation" NARROW [] +synonym: "positive regulation of peripheral blood mononuclear cell proliferation" NARROW [] +synonym: "stimulation of mononuclear cell proliferation" NARROW [] +synonym: "up regulation of mononuclear cell proliferation" EXACT [] +synonym: "up-regulation of mononuclear cell proliferation" EXACT [] +synonym: "upregulation of mononuclear cell proliferation" EXACT [] +is_a: GO:0032944 ! regulation of mononuclear cell proliferation +is_a: GO:0070665 ! positive regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032943 ! mononuclear cell proliferation +relationship: positively_regulates GO:0032943 ! mononuclear cell proliferation + +[Term] +id: GO:0032956 +name: regulation of actin cytoskeleton organization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins." [GOC:mah] +synonym: "regulation of actin cytoskeleton organisation" EXACT [GOC:mah] +synonym: "regulation of actin cytoskeleton organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0032970 ! regulation of actin filament-based process +is_a: GO:0051493 ! regulation of cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030036 ! actin cytoskeleton organization +relationship: regulates GO:0030036 ! actin cytoskeleton organization + +[Term] +id: GO:0032963 +name: collagen metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%)." [GOC:mah, ISBN:0198506732] +synonym: "collagen metabolism" EXACT [] +is_a: GO:0044259 ! multicellular organismal macromolecule metabolic process + +[Term] +id: GO:0032964 +name: collagen biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%)." [GOC:mah, ISBN:0198506732] +synonym: "collagen anabolism" EXACT [] +synonym: "collagen biosynthesis" EXACT [] +synonym: "collagen formation" EXACT [] +synonym: "collagen synthesis" EXACT [] +is_a: GO:0009059 ! macromolecule biosynthetic process +is_a: GO:0032963 ! collagen metabolic process +is_a: GO:0044711 ! single-organism biosynthetic process + +[Term] +id: GO:0032965 +name: regulation of collagen biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." [GOC:mah] +synonym: "regulation of collagen anabolism" EXACT [] +synonym: "regulation of collagen biosynthesis" EXACT [] +synonym: "regulation of collagen formation" EXACT [] +synonym: "regulation of collagen synthesis" EXACT [] +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0010712 ! regulation of collagen metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032964 ! collagen biosynthetic process +relationship: regulates GO:0032964 ! collagen biosynthetic process + +[Term] +id: GO:0032967 +name: positive regulation of collagen biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." [GOC:mah] +synonym: "positive regulation of collagen anabolism" EXACT [] +synonym: "positive regulation of collagen biosynthesis" EXACT [] +synonym: "positive regulation of collagen formation" EXACT [] +synonym: "positive regulation of collagen synthesis" EXACT [] +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process +is_a: GO:0010714 ! positive regulation of collagen metabolic process +is_a: GO:0032965 ! regulation of collagen biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032964 ! collagen biosynthetic process +relationship: positively_regulates GO:0032964 ! collagen biosynthetic process + +[Term] +id: GO:0032970 +name: regulation of actin filament-based process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton." [GOC:mah] +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030029 ! actin filament-based process +relationship: regulates GO:0030029 ! actin filament-based process + +[Term] +id: GO:0032984 +name: macromolecular complex disassembly +namespace: biological_process +alt_id: GO:0034623 +def: "The disaggregation of a macromolecular complex into its constituent components." [GOC:mah] +subset: gosubset_prok +synonym: "cellular macromolecular complex disassembly" EXACT [] +synonym: "cellular macromolecule complex disassembly" EXACT [] +synonym: "macromolecule complex disassembly" EXACT [] +is_a: GO:0022411 ! cellular component disassembly +is_a: GO:0043933 ! macromolecular complex subunit organization + +[Term] +id: GO:0032987 +name: protein-lipid complex disassembly +namespace: biological_process +def: "The disaggregation of a protein-lipid complex into its constituent components." [GOC:mah] +is_a: GO:0032984 ! macromolecular complex disassembly +is_a: GO:0071825 ! protein-lipid complex subunit organization + +[Term] +id: GO:0032989 +name: cellular component morphogenesis +namespace: biological_process +def: "The process in which cellular structures, including whole cells or cell parts, are generated and organized." [GOC:dph, GOC:mah, GOC:tb] +subset: goslim_pir +subset: gosubset_prok +synonym: "cellular structure morphogenesis" EXACT [GOC:dph, GOC:tb] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0016043 ! cellular component organization +is_a: GO:0048869 ! cellular developmental process + +[Term] +id: GO:0032990 +name: cell part morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a cell part are generated and organized." [GOC:mah] +is_a: GO:0032989 ! cellular component morphogenesis + +[Term] +id: GO:0032991 +name: macromolecular complex +namespace: cellular_component +def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together." [GOC:mah] +subset: goslim_pir +subset: gosubset_prok +synonym: "macromolecule complex" EXACT [] +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0032993 +name: protein-DNA complex +namespace: cellular_component +def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] +subset: gosubset_prok +synonym: "DNA-protein complex" EXACT [GOC:mah] +is_a: GO:0032991 ! macromolecular complex + +[Term] +id: GO:0033002 +name: muscle cell proliferation +namespace: biological_process +def: "The expansion of a muscle cell population by cell division." [CL:0000187, GOC:mah] +synonym: "myocyte proliferation" EXACT [] +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0033036 +name: macromolecule localization +namespace: biological_process +def: "Any process in which a macromolecule is transported to, or maintained in, a specific location." [GOC:mah] +subset: gosubset_prok +synonym: "macromolecule localisation" EXACT [GOC:mah] +is_a: GO:0051179 ! localization + +[Term] +id: GO:0033043 +name: regulation of organelle organization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." [GOC:mah] +subset: goslim_yeast +synonym: "regulation of organelle organisation" EXACT [GOC:mah] +synonym: "regulation of organelle organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006996 ! organelle organization +relationship: regulates GO:0006996 ! organelle organization + +[Term] +id: GO:0033044 +name: regulation of chromosome organization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome." [GOC:mah] +synonym: "regulation of chromosome organisation" EXACT [GOC:mah] +synonym: "regulation of chromosome organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0033043 ! regulation of organelle organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051276 ! chromosome organization +relationship: regulates GO:0051276 ! chromosome organization + +[Term] +id: GO:0033077 +name: T cell differentiation in thymus +namespace: biological_process +def: "The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus." [GOC:add, ISBN:0781735149] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "T cell development in thymus" RELATED [GOC:add] +synonym: "thymic T cell differentiation" EXACT [] +synonym: "thymocyte cell differentiation" EXACT [] +synonym: "thymocyte differentiation" EXACT [] +is_a: GO:0030217 ! T cell differentiation + +[Term] +id: GO:0033079 +name: immature T cell proliferation +namespace: biological_process +def: "The expansion of an immature T cell population by cell division." [GOC:add, ISBN:0781735149] +is_a: GO:0042098 ! T cell proliferation + +[Term] +id: GO:0033080 +name: immature T cell proliferation in thymus +namespace: biological_process +def: "The expansion of an immature T cell population by cell division in the thymus." [GOC:add, ISBN:0781735149] +synonym: "thymic T cell proliferation" EXACT [] +synonym: "thymocyte cell proliferation" EXACT [] +synonym: "thymocyte proliferation" EXACT [] +is_a: GO:0033079 ! immature T cell proliferation +relationship: part_of GO:0033077 ! T cell differentiation in thymus + +[Term] +id: GO:0033081 +name: regulation of T cell differentiation in thymus +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of T cell differentiation in the thymus." [GOC:add, GOC:mah] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "regulation of T cell development in thymus" RELATED [GOC:add] +synonym: "regulation of thymic T cell differentiation" EXACT [] +synonym: "regulation of thymocyte cell differentiation" EXACT [] +synonym: "regulation of thymocyte differentiation" EXACT [] +is_a: GO:0045580 ! regulation of T cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033077 ! T cell differentiation in thymus +relationship: regulates GO:0033077 ! T cell differentiation in thymus + +[Term] +id: GO:0033085 +name: negative regulation of T cell differentiation in thymus +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation in the thymus." [GOC:add, GOC:mah] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "negative regulation of T cell development in thymus" RELATED [GOC:add] +synonym: "negative regulation of thymic T cell differentiation" EXACT [] +synonym: "negative regulation of thymocyte cell differentiation" EXACT [] +synonym: "negative regulation of thymocyte differentiation" EXACT [] +is_a: GO:0033081 ! regulation of T cell differentiation in thymus +is_a: GO:0045581 ! negative regulation of T cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0033077 ! T cell differentiation in thymus +relationship: negatively_regulates GO:0033077 ! T cell differentiation in thymus + +[Term] +id: GO:0033121 +name: regulation of purine nucleotide catabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides." [GOC:mah] +synonym: "regulation of purine nucleotide breakdown" EXACT [] +synonym: "regulation of purine nucleotide catabolism" EXACT [] +synonym: "regulation of purine nucleotide degradation" EXACT [] +is_a: GO:0030811 ! regulation of nucleotide catabolic process +is_a: GO:1900542 ! regulation of purine nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006195 ! purine nucleotide catabolic process +relationship: regulates GO:0006195 ! purine nucleotide catabolic process + +[Term] +id: GO:0033124 +name: regulation of GTP catabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of GTP, guanosine triphosphate." [GOC:mah] +synonym: "regulation of GTP breakdown" EXACT [] +synonym: "regulation of GTP catabolism" EXACT [] +synonym: "regulation of GTP degradation" EXACT [] +is_a: GO:0009118 ! regulation of nucleoside metabolic process +is_a: GO:0033121 ! regulation of purine nucleotide catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006184 ! GTP catabolic process +relationship: regulates GO:0006184 ! GTP catabolic process + +[Term] +id: GO:0033131 +name: regulation of glucokinase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of glucokinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a glucose molecule." [GOC:mah] +synonym: "glucokinase regulator" NARROW [] +is_a: GO:0010906 ! regulation of glucose metabolic process +is_a: GO:0043549 ! regulation of kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004340 ! glucokinase activity +relationship: regulates GO:0004340 ! glucokinase activity + +[Term] +id: GO:0033132 +name: negative regulation of glucokinase activity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of glucokinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a glucose molecule." [GOC:mah] +synonym: "down regulation of glucokinase activity" EXACT [] +synonym: "down-regulation of glucokinase activity" EXACT [] +synonym: "downregulation of glucokinase activity" EXACT [] +synonym: "glucokinase inhibitor" NARROW [] +synonym: "inhibition of glucokinase activity" NARROW [] +is_a: GO:0033131 ! regulation of glucokinase activity +is_a: GO:0033673 ! negative regulation of kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004340 ! glucokinase activity +relationship: negatively_regulates GO:0004340 ! glucokinase activity + +[Term] +id: GO:0033135 +name: regulation of peptidyl-serine phosphorylation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-serine." [GOC:mah] +subset: gosubset_prok +is_a: GO:0001932 ! regulation of protein phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0018105 ! peptidyl-serine phosphorylation +relationship: regulates GO:0018105 ! peptidyl-serine phosphorylation + +[Term] +id: GO:0033138 +name: positive regulation of peptidyl-serine phosphorylation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine." [GOC:mah] +is_a: GO:0001934 ! positive regulation of protein phosphorylation +is_a: GO:0033135 ! regulation of peptidyl-serine phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0018105 ! peptidyl-serine phosphorylation +relationship: positively_regulates GO:0018105 ! peptidyl-serine phosphorylation + +[Term] +id: GO:0033143 +name: regulation of intracellular steroid hormone receptor signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." [GOC:mah] +synonym: "regulation of steroid hormone receptor signaling pathway" BROAD [GOC:bf] +synonym: "regulation of steroid hormone receptor signalling pathway" BROAD [] +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway +relationship: regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway + +[Term] +id: GO:0033144 +name: negative regulation of intracellular steroid hormone receptor signaling pathway +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." [GOC:mah] +synonym: "negative regulation of steroid hormone receptor signaling pathway" BROAD [GOC:bf] +synonym: "negative regulation of steroid hormone receptor signalling pathway" BROAD [GOC:bf] +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway +relationship: negatively_regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway + +[Term] +id: GO:0033146 +name: regulation of intracellular estrogen receptor signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the activity of an intracellular estrogen receptor signaling pathway." [GOC:mah] +synonym: "regulation of estrogen receptor signaling pathway" BROAD [GOC:bf] +synonym: "regulation of estrogen receptor signalling pathway" EXACT [] +is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030520 ! intracellular estrogen receptor signaling pathway +relationship: regulates GO:0030520 ! intracellular estrogen receptor signaling pathway + +[Term] +id: GO:0033147 +name: negative regulation of intracellular estrogen receptor signaling pathway +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of an intracellular estrogen receptor signaling pathway." [GOC:mah] +synonym: "negative regulation of estrogen receptor signaling pathway" BROAD [GOC:bf] +synonym: "negative regulation of estrogen receptor signalling pathway" EXACT [] +is_a: GO:0033144 ! negative regulation of intracellular steroid hormone receptor signaling pathway +is_a: GO:0033146 ! regulation of intracellular estrogen receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030520 ! intracellular estrogen receptor signaling pathway +relationship: negatively_regulates GO:0030520 ! intracellular estrogen receptor signaling pathway + +[Term] +id: GO:0033157 +name: regulation of intracellular protein transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells." [GOC:mah] +is_a: GO:0032386 ! regulation of intracellular transport +is_a: GO:0051223 ! regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006886 ! intracellular protein transport +relationship: regulates GO:0006886 ! intracellular protein transport + +[Term] +id: GO:0033233 +name: regulation of protein sumoylation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the addition of SUMO groups to a protein." [GOC:mah] +synonym: "regulation of sumoylation" EXACT [] +is_a: GO:0031399 ! regulation of protein modification process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016925 ! protein sumoylation +relationship: regulates GO:0016925 ! protein sumoylation + +[Term] +id: GO:0033234 +name: negative regulation of protein sumoylation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of SUMO groups to a protein." [GOC:mah] +synonym: "negative regulation of sumoylation" EXACT [] +is_a: GO:0031400 ! negative regulation of protein modification process +is_a: GO:0033233 ! regulation of protein sumoylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016925 ! protein sumoylation +relationship: negatively_regulates GO:0016925 ! protein sumoylation + +[Term] +id: GO:0033267 +name: axon part +namespace: cellular_component +def: "A part of an axon, a cell projection of a neuron." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +xref: NIF_Subcellular:sao280355188 +is_a: GO:0044463 ! cell projection part +is_a: GO:0097458 ! neuron part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0030424 ! axon +relationship: part_of GO:0030424 ! axon + +[Term] +id: GO:0033273 +name: response to vitamin +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin stimulus." [GOC:sl] +is_a: GO:0007584 ! response to nutrient + +[Term] +id: GO:0033365 +name: protein localization to organelle +namespace: biological_process +def: "A process in which a protein is transported to, or maintained in, a location within an organelle." [GOC:mah] +synonym: "protein localisation to organelle" EXACT [GOC:mah] +synonym: "protein localization in organelle" EXACT [GOC:mah] +is_a: GO:0034613 ! cellular protein localization + +[Term] +id: GO:0033483 +name: gas homeostasis +namespace: biological_process +def: "A homeostatic process involved in the maintenance of an internal steady state of a gas within an organism or cell." [GOC:mah] +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0033500 +name: carbohydrate homeostasis +namespace: biological_process +def: "A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell." [GOC:mah] +subset: gosubset_prok +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0033504 +name: floor plate development +namespace: biological_process +def: "The progression of the floor plate over time from its initial formation until its mature state." [GOC:dh] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021915 ! neural tube development + +[Term] +id: GO:0033505 +name: floor plate morphogenesis +namespace: biological_process +def: "The process in which the anatomical structure of the floor plate is generated and organized." [GOC:dh] +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0033504 ! floor plate development + +[Term] +id: GO:0033554 +name: cellular response to stress +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +is_a: GO:0006950 ! response to stress +is_a: GO:0051716 ! cellular response to stimulus + +[Term] +id: GO:0033598 +name: mammary gland epithelial cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of mammary gland epithelial cells, resulting in the expansion of a cell population. Mammary gland epithelial cells make up the covering of surfaces of the mammary gland. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." [GOC:dph, GOC:mah] +is_a: GO:0050673 ! epithelial cell proliferation +relationship: part_of GO:0061180 ! mammary gland epithelium development + +[Term] +id: GO:0033613 +name: activating transcription factor binding +namespace: molecular_function +alt_id: GO:0001107 +def: "Interacting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription." [GOC:mah, GOC:txnOH] +synonym: "transcription activator binding" EXACT [] +is_a: GO:0008134 ! transcription factor binding + +[Term] +id: GO:0033622 +name: integrin activation +namespace: biological_process +def: "The aggregation, arrangement and bonding together of an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits, that lead to the increased affinity of the integrin for its extracellular ligands." [GOC:add, PMID:12213832, PMID:14754902] +synonym: "integrin complex activation" EXACT [] +synonym: "integrin complex assembly" EXACT [] +is_a: GO:0006461 ! protein complex assembly + +[Term] +id: GO:0033623 +name: regulation of integrin activation +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of integrin activation." [GOC:add] +synonym: "regulation of integrin complex activation" EXACT [] +is_a: GO:0043254 ! regulation of protein complex assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033622 ! integrin activation +relationship: regulates GO:0033622 ! integrin activation + +[Term] +id: GO:0033625 +name: positive regulation of integrin activation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of integrin activation." [GOC:add] +synonym: "positive regulation of integrin complex activation" EXACT [] +is_a: GO:0031334 ! positive regulation of protein complex assembly +is_a: GO:0033623 ! regulation of integrin activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0033622 ! integrin activation +relationship: positively_regulates GO:0033622 ! integrin activation + +[Term] +id: GO:0033627 +name: cell adhesion mediated by integrin +namespace: biological_process +def: "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits." [GOC:add, PMID:12213832, PMID:14754902] +synonym: "cell adhesion mediated by integrin complex" EXACT [] +is_a: GO:0007155 ! cell adhesion + +[Term] +id: GO:0033628 +name: regulation of cell adhesion mediated by integrin +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of cell adhesion mediated by integrin." [GOC:add] +synonym: "regulation of cell adhesion mediated by integrin complex" EXACT [] +is_a: GO:0030155 ! regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033627 ! cell adhesion mediated by integrin +relationship: regulates GO:0033627 ! cell adhesion mediated by integrin + +[Term] +id: GO:0033630 +name: positive regulation of cell adhesion mediated by integrin +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin." [GOC:add] +synonym: "positive regulation of cell adhesion mediated by integrin complex" EXACT [] +is_a: GO:0033628 ! regulation of cell adhesion mediated by integrin +is_a: GO:0045785 ! positive regulation of cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0033627 ! cell adhesion mediated by integrin +relationship: positively_regulates GO:0033627 ! cell adhesion mediated by integrin + +[Term] +id: GO:0033673 +name: negative regulation of kinase activity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] +synonym: "down regulation of kinase activity" EXACT [] +synonym: "down-regulation of kinase activity" EXACT [] +synonym: "downregulation of kinase activity" EXACT [] +synonym: "inhibition of kinase activity" NARROW [] +synonym: "kinase inhibitor" NARROW [] +is_a: GO:0043549 ! regulation of kinase activity +is_a: GO:0051348 ! negative regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016301 ! kinase activity +relationship: negatively_regulates GO:0016301 ! kinase activity + +[Term] +id: GO:0033674 +name: positive regulation of kinase activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] +synonym: "kinase activator" NARROW [] +synonym: "stimulation of kinase activity" NARROW [] +synonym: "up regulation of kinase activity" EXACT [] +synonym: "up-regulation of kinase activity" EXACT [] +synonym: "upregulation of kinase activity" EXACT [] +is_a: GO:0043549 ! regulation of kinase activity +is_a: GO:0051347 ! positive regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016301 ! kinase activity +relationship: positively_regulates GO:0016301 ! kinase activity + +[Term] +id: GO:0033687 +name: osteoblast proliferation +namespace: biological_process +def: "The multiplication or reproduction of osteoblasts, resulting in the expansion of an osteoblast cell population. An osteoblast is a bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone." [GOC:mah] +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0033688 +name: regulation of osteoblast proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of osteoblast proliferation." [GOC:mah] +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033687 ! osteoblast proliferation +relationship: regulates GO:0033687 ! osteoblast proliferation + +[Term] +id: GO:0033689 +name: negative regulation of osteoblast proliferation +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of osteoblast proliferation." [GOC:mah] +synonym: "down regulation of osteoblast proliferation" EXACT [] +synonym: "down-regulation of osteoblast proliferation" EXACT [] +synonym: "downregulation of osteoblast proliferation" EXACT [] +synonym: "inhibition of osteoblast proliferation" NARROW [] +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0033688 ! regulation of osteoblast proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0033687 ! osteoblast proliferation +relationship: negatively_regulates GO:0033687 ! osteoblast proliferation + +[Term] +id: GO:0033690 +name: positive regulation of osteoblast proliferation +namespace: biological_process +def: "Any process that activates or increases the rate or extent of osteoblast proliferation." [GOC:mah] +synonym: "activation of osteoblast proliferation" NARROW [] +synonym: "stimulation of osteoblast proliferation" NARROW [] +synonym: "up regulation of osteoblast proliferation" EXACT [] +synonym: "up-regulation of osteoblast proliferation" EXACT [] +synonym: "upregulation of osteoblast proliferation" EXACT [] +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0033688 ! regulation of osteoblast proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0033687 ! osteoblast proliferation +relationship: positively_regulates GO:0033687 ! osteoblast proliferation + +[Term] +id: GO:0033993 +name: response to lipid +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus." [GOC:sl] +is_a: GO:0010033 ! response to organic substance + +[Term] +id: GO:0034097 +name: response to cytokine +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus." [GOC:sl] +synonym: "response to cytokine stimulus" EXACT [GOC:dos] +is_a: GO:0010033 ! response to organic substance + +[Term] +id: GO:0034103 +name: regulation of tissue remodeling +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of tissue remodeling." [GOC:add] +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048771 ! tissue remodeling +relationship: regulates GO:0048771 ! tissue remodeling + +[Term] +id: GO:0034104 +name: negative regulation of tissue remodeling +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of tissue remodeling." [GOC:add] +is_a: GO:0034103 ! regulation of tissue remodeling +is_a: GO:0051241 ! negative regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048771 ! tissue remodeling +relationship: negatively_regulates GO:0048771 ! tissue remodeling + +[Term] +id: GO:0034105 +name: positive regulation of tissue remodeling +namespace: biological_process +def: "Any process that activates or increases the frequency, rate, or extent of tissue remodeling." [GOC:add] +is_a: GO:0034103 ! regulation of tissue remodeling +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048771 ! tissue remodeling +relationship: positively_regulates GO:0048771 ! tissue remodeling + +[Term] +id: GO:0034109 +name: homotypic cell-cell adhesion +namespace: biological_process +def: "The attachment of a cell to a second cell of the identical type via adhesion molecules." [GOC:add] +comment: Note that this term is not synonymous with 'homophilic cell adhesion ; GO:0007156'; the process may occur by homophilic or heterophilic mechanisms. +is_a: GO:0016337 ! cell-cell adhesion + +[Term] +id: GO:0034185 +name: apolipoprotein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an apolipoprotein, the protein component of a lipoprotein complex." [GOC:BHF, GOC:rl] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0034189 +name: very-low-density lipoprotein particle binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a very-low-density lipoprotein particle, a triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm." [GOC:BHF, GOC:mah] +synonym: "very-low-density lipoprotein binding" EXACT [GOC:bf, GOC:dph] +synonym: "VLDL binding" EXACT [] +is_a: GO:0071813 ! lipoprotein particle binding + +[Term] +id: GO:0034220 +name: ion transmembrane transport +namespace: biological_process +def: "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC:mah] +comment: Note that this term is not intended for use in annotating lateral movement within membranes. +synonym: "ion membrane transport" EXACT [] +synonym: "transmembrane ion transport" EXACT [GOC:dph, GOC:tb] +xref: Reactome:REACT_100497 "Ion channel transport, Rattus norvegicus" +xref: Reactome:REACT_101721 "Ion transport by P-type ATPases, Canis familiaris" +xref: Reactome:REACT_103924 "Ion transport by P-type ATPases, Taeniopygia guttata" +xref: Reactome:REACT_107347 "Ion channel transport, Caenorhabditis elegans" +xref: Reactome:REACT_108844 "Ion transport by P-type ATPases, Drosophila melanogaster" +xref: Reactome:REACT_109050 "Ion channel transport, Gallus gallus" +xref: Reactome:REACT_25149 "Ion transport by P-type ATPases, Homo sapiens" +xref: Reactome:REACT_25300 "Ion channel transport, Homo sapiens" +xref: Reactome:REACT_25387 "Ligand-gated ion channel transport, Homo sapiens" +xref: Reactome:REACT_28672 "Ion transport by P-type ATPases, Arabidopsis thaliana" +xref: Reactome:REACT_30601 "Ion channel transport, Danio rerio" +xref: Reactome:REACT_31166 "Ion channel transport, Sus scrofa" +xref: Reactome:REACT_32763 "Ion channel transport, Plasmodium falciparum" +xref: Reactome:REACT_33389 "Ion channel transport, Mycobacterium tuberculosis" +xref: Reactome:REACT_34584 "Ion channel transport, Oryza sativa" +xref: Reactome:REACT_77153 "Ion channel transport, Arabidopsis thaliana" +xref: Reactome:REACT_77267 "Ion channel transport, Taeniopygia guttata" +xref: Reactome:REACT_78982 "Ion transport by P-type ATPases, Bos taurus" +xref: Reactome:REACT_79679 "Ion transport by P-type ATPases, Xenopus tropicalis" +xref: Reactome:REACT_81685 "Ion channel transport, Bos taurus" +xref: Reactome:REACT_82102 "Ion channel transport, Canis familiaris" +xref: Reactome:REACT_89671 "Ion channel transport, Xenopus tropicalis" +xref: Reactome:REACT_89674 "Ion transport by P-type ATPases, Caenorhabditis elegans" +xref: Reactome:REACT_89758 "Ion transport by P-type ATPases, Sus scrofa" +xref: Reactome:REACT_89890 "Ion transport by P-type ATPases, Oryza sativa" +xref: Reactome:REACT_92146 "Ion transport by P-type ATPases, Mus musculus" +xref: Reactome:REACT_93475 "Ion transport by P-type ATPases, Rattus norvegicus" +xref: Reactome:REACT_94109 "Ion channel transport, Mus musculus" +xref: Reactome:REACT_94939 "Ion transport by P-type ATPases, Mycobacterium tuberculosis" +xref: Reactome:REACT_94986 "Ion transport by P-type ATPases, Plasmodium falciparum" +xref: Reactome:REACT_97506 "Ion transport by P-type ATPases, Danio rerio" +xref: Reactome:REACT_97619 "Ion channel transport, Drosophila melanogaster" +xref: Reactome:REACT_98518 "Ion transport by P-type ATPases, Gallus gallus" +is_a: GO:0006811 ! ion transport +is_a: GO:0055085 ! transmembrane transport + +[Term] +id: GO:0034284 +name: response to monosaccharide +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus." [GOC:mah] +synonym: "response to monosaccharide stimulus" EXACT [GOC:dos] +is_a: GO:0009743 ! response to carbohydrate + +[Term] +id: GO:0034287 +name: detection of monosaccharide stimulus +namespace: biological_process +def: "The series of events in which a stimulus from a monosaccharide is received and converted into a molecular signal." [GOC:mah] +synonym: "perception of monosaccharide stimulus" RELATED [] +is_a: GO:0009730 ! detection of carbohydrate stimulus +is_a: GO:0034284 ! response to monosaccharide + +[Term] +id: GO:0034329 +name: cell junction assembly +namespace: biological_process +def: "A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction." [GOC:mah] +xref: Reactome:REACT_102961 "Cell junction organization, Canis familiaris" +xref: Reactome:REACT_103254 "Cell junction organization, Bos taurus" +xref: Reactome:REACT_20676 "Cell junction organization, Homo sapiens" +xref: Reactome:REACT_30673 "Cell junction organization, Danio rerio" +xref: Reactome:REACT_81158 "Cell junction organization, Taeniopygia guttata" +xref: Reactome:REACT_82932 "Cell junction organization, Mus musculus" +xref: Reactome:REACT_84768 "Cell junction organization, Drosophila melanogaster" +xref: Reactome:REACT_92671 "Cell junction organization, Caenorhabditis elegans" +xref: Reactome:REACT_94741 "Cell junction organization, Rattus norvegicus" +xref: Reactome:REACT_96353 "Cell junction organization, Gallus gallus" +xref: Reactome:REACT_96361 "Cell junction organization, Xenopus tropicalis" +xref: Reactome:REACT_98047 "Cell junction organization, Sus scrofa" +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0034330 ! cell junction organization + +[Term] +id: GO:0034330 +name: cell junction organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_generic +synonym: "cell junction assembly and maintenance" EXACT [] +synonym: "cell junction biogenesis" RELATED [] +synonym: "cell junction organisation" EXACT [GOC:mah] +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0034332 +name: adherens junction organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments." [GOC:dph, GOC:jl, GOC:mah] +synonym: "adherens junction assembly and maintenance" EXACT [] +synonym: "adherens junction organisation" EXACT [GOC:curators] +xref: Reactome:REACT_106603 "Adherens junctions interactions, Xenopus tropicalis" +xref: Reactome:REACT_108185 "Adherens junctions interactions, Sus scrofa" +xref: Reactome:REACT_110805 "Adherens junctions interactions, Gallus gallus" +xref: Reactome:REACT_115366 "Adherens junctions interactions, Drosophila melanogaster" +xref: Reactome:REACT_19195 "Adherens junctions interactions, Homo sapiens" +xref: Reactome:REACT_28088 "Adherens junctions interactions, Canis familiaris" +xref: Reactome:REACT_28998 "Adherens junctions interactions, Mus musculus" +xref: Reactome:REACT_32787 "Adherens junctions interactions, Danio rerio" +xref: Reactome:REACT_86794 "Adherens junctions interactions, Bos taurus" +xref: Reactome:REACT_90289 "Adherens junctions interactions, Taeniopygia guttata" +xref: Reactome:REACT_92943 "Adherens junctions interactions, Rattus norvegicus" +is_a: GO:0045216 ! cell-cell junction organization + +[Term] +id: GO:0034333 +name: adherens junction assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments." [GOC:mah] +synonym: "adherens junction formation" EXACT [] +is_a: GO:0034329 ! cell junction assembly +is_a: GO:0034332 ! adherens junction organization + +[Term] +id: GO:0034340 +name: response to type I interferon +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a type I interferon stimulus. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, ISBN:0126896631, PMID:15546383, PMID:16681834] +synonym: "response to type I IFN" EXACT [] +is_a: GO:0034097 ! response to cytokine +relationship: part_of GO:0045087 ! innate immune response + +[Term] +id: GO:0034381 +name: plasma lipoprotein particle clearance +namespace: biological_process +def: "The process in which a lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." [GOC:ascb_2009, GOC:BHF, GOC:dph, GOC:mah, GOC:tb] +synonym: "lipoprotein particle clearance" EXACT [GOC:mah] +is_a: GO:0044707 ! single-multicellular organism process +relationship: has_part GO:0006898 ! receptor-mediated endocytosis +relationship: has_part GO:0071829 ! plasma lipoprotein particle disassembly +relationship: part_of GO:0097006 ! regulation of plasma lipoprotein particle levels + +[Term] +id: GO:0034383 +name: low-density lipoprotein particle clearance +namespace: biological_process +def: "The process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." [GOC:BHF, GOC:mah] +synonym: "LDL clearance" EXACT [] +is_a: GO:0034381 ! plasma lipoprotein particle clearance +relationship: has_part GO:0090495 ! low-density lipoprotein particle disassembly + +[Term] +id: GO:0034390 +name: smooth muscle cell apoptotic process +namespace: biological_process +def: "Any apoptotic process in a smooth muscle cell. Smooth muscle consists of non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels." [CL:0000192, GOC:BHF, GOC:mah, GOC:mtg_apoptosis, GOC:rl] +synonym: "apoptosis of smooth muscle cells" EXACT [] +synonym: "programmed cell death of smooth muscle cells by apoptosis" EXACT [] +synonym: "programmed cell death, smooth muscle cells" EXACT [] +synonym: "SMC apoptosis" EXACT [] +synonym: "smooth muscle cell apoptosis" NARROW [] +synonym: "smooth muscle cell programmed cell death by apoptosis" EXACT [] +is_a: GO:0010657 ! muscle cell apoptotic process + +[Term] +id: GO:0034391 +name: regulation of smooth muscle cell apoptotic process +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of smooth muscle cell apoptotic process." [GOC:BHF, GOC:mtg_apoptosis, GOC:rl] +synonym: "regulation of SMC apoptosis" EXACT [] +synonym: "regulation of smooth muscle cell apoptosis" NARROW [] +is_a: GO:0010660 ! regulation of muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034390 ! smooth muscle cell apoptotic process +relationship: regulates GO:0034390 ! smooth muscle cell apoptotic process + +[Term] +id: GO:0034392 +name: negative regulation of smooth muscle cell apoptotic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process." [GOC:BHF, GOC:mtg_apoptosis, GOC:rl] +synonym: "down regulation of smooth muscle cell apoptosis" EXACT [] +synonym: "down-regulation of smooth muscle cell apoptosis" EXACT [] +synonym: "downregulation of smooth muscle cell apoptosis" EXACT [] +synonym: "inhibition of smooth muscle cell apoptosis" NARROW [] +synonym: "negative regulation of SMC apoptosis" EXACT [] +synonym: "negative regulation of smooth muscle cell apoptosis" NARROW [] +is_a: GO:0010656 ! negative regulation of muscle cell apoptotic process +is_a: GO:0034391 ! regulation of smooth muscle cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0034390 ! smooth muscle cell apoptotic process +relationship: negatively_regulates GO:0034390 ! smooth muscle cell apoptotic process + +[Term] +id: GO:0034394 +name: protein localization to cell surface +namespace: biological_process +def: "A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane." [GOC:mah] +synonym: "protein localisation at cell surface" EXACT [GOC:mah] +synonym: "protein localization at cell surface" EXACT [GOC:curators] +is_a: GO:0034613 ! cellular protein localization + +[Term] +id: GO:0034446 +name: substrate adhesion-dependent cell spreading +namespace: biological_process +def: "The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate." [GOC:mah, GOC:pf, PMID:17050732] +synonym: "cell spreading during cell substrate adhesion" EXACT [] +synonym: "substrate adhesion dependent cell spreading" EXACT [] +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +is_a: GO:0031589 ! cell-substrate adhesion + +[Term] +id: GO:0034447 +name: very-low-density lipoprotein particle clearance +namespace: biological_process +def: "The process in which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." [GOC:BHF, GOC:rl] +synonym: "VLDL clearance" EXACT [] +is_a: GO:0034381 ! plasma lipoprotein particle clearance + +[Term] +id: GO:0034504 +name: protein localization to nucleus +namespace: biological_process +def: "A process in which a protein is transported to, or maintained in, a location within the nucleus." [GOC:ecd] +synonym: "protein localisation to nucleus" EXACT [GOC:mah] +synonym: "protein localization in cell nucleus" EXACT [] +synonym: "protein localization in nucleus" EXACT [GOC:mah] +is_a: GO:0033365 ! protein localization to organelle + +[Term] +id: GO:0034612 +name: response to tumor necrosis factor +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus." [GOC:mah] +synonym: "response to TNF" EXACT [] +is_a: GO:0034097 ! response to cytokine + +[Term] +id: GO:0034613 +name: cellular protein localization +namespace: biological_process +alt_id: GO:0016249 +def: "Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah] +synonym: "cellular protein localisation" EXACT [GOC:mah] +synonym: "channel localizer activity" NARROW [GOC:mah] +is_a: GO:0008104 ! protein localization +is_a: GO:0070727 ! cellular macromolecule localization + +[Term] +id: GO:0034622 +name: cellular macromolecular complex assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level." [GOC:mah] +subset: goslim_pir +subset: gosubset_prok +synonym: "cellular macromolecule complex assembly" EXACT [] +is_a: GO:0065003 ! macromolecular complex assembly + +[Term] +id: GO:0034641 +name: cellular nitrogen compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] +subset: goslim_generic +subset: gosubset_prok +synonym: "cellular nitrogen compound metabolism" EXACT [] +xref: Reactome:REACT_102000 "Metabolism of amino acids and derivatives, Mycobacterium tuberculosis" +xref: Reactome:REACT_103710 "Metabolism of amino acids and derivatives, Escherichia coli" +xref: Reactome:REACT_107293 "Metabolism of amino acids and derivatives, Arabidopsis thaliana" +xref: Reactome:REACT_108179 "Metabolism of amino acids and derivatives, Xenopus tropicalis" +xref: Reactome:REACT_109042 "Metabolism of amino acids and derivatives, Sus scrofa" +xref: Reactome:REACT_13 "Metabolism of amino acids and derivatives, Homo sapiens" +xref: Reactome:REACT_28699 "Metabolism of amino acids and derivatives, Saccharomyces cerevisiae" +xref: Reactome:REACT_29108 "Metabolism of amino acids and derivatives, Caenorhabditis elegans" +xref: Reactome:REACT_32429 "Metabolism of amino acids and derivatives, Rattus norvegicus" +xref: Reactome:REACT_33347 "Metabolism of amino acids and derivatives, Mus musculus" +xref: Reactome:REACT_34326 "Metabolism of amino acids and derivatives, Staphylococcus aureus N315" +xref: Reactome:REACT_55564 "Metabolism of amino acids and derivatives, Gallus gallus" +xref: Reactome:REACT_77741 "Metabolism of amino acids and derivatives, Taeniopygia guttata" +xref: Reactome:REACT_82379 "Metabolism of amino acids and derivatives, Bos taurus" +xref: Reactome:REACT_86268 "Metabolism of amino acids and derivatives, Drosophila melanogaster" +xref: Reactome:REACT_90299 "Metabolism of amino acids and derivatives, Oryza sativa" +xref: Reactome:REACT_91959 "Metabolism of amino acids and derivatives, Plasmodium falciparum" +xref: Reactome:REACT_93580 "Metabolism of amino acids and derivatives, Danio rerio" +xref: Reactome:REACT_95666 "Metabolism of amino acids and derivatives, Canis familiaris" +xref: Reactome:REACT_98086 "Metabolism of amino acids and derivatives, Dictyostelium discoideum" +xref: Reactome:REACT_99241 "Metabolism of amino acids and derivatives, Schizosaccharomyces pombe" +is_a: GO:0006807 ! nitrogen compound metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0034645 +name: cellular macromolecule biosynthetic process +namespace: biological_process +alt_id: GO:0034961 +def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells." [CHEBI:33694, GOC:mah] +synonym: "cellular biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09] +synonym: "cellular macromolecule anabolism" EXACT [GOC:mah] +synonym: "cellular macromolecule biosynthesis" EXACT [GOC:mah] +synonym: "cellular macromolecule formation" EXACT [GOC:mah] +synonym: "cellular macromolecule synthesis" EXACT [GOC:mah] +is_a: GO:0009059 ! macromolecule biosynthetic process +is_a: GO:0044249 ! cellular biosynthetic process +is_a: GO:0044260 ! cellular macromolecule metabolic process + +[Term] +id: GO:0034650 +name: cortisol metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving cortisol, the steroid hormone 11-beta-17,21-trihydroxypregn-4-ene-3,20-dione. Cortisol is synthesized from cholesterol in the adrenal gland and controls carbohydrate, fat and protein metabolism and has anti-inflammatory properties." [CHEBI:17650, GOC:BHF, GOC:mah, GOC:rl] +synonym: "cortisol metabolism" EXACT [] +is_a: GO:0006066 ! alcohol metabolic process +is_a: GO:0008211 ! glucocorticoid metabolic process +is_a: GO:0042180 ! cellular ketone metabolic process + +[Term] +id: GO:0034651 +name: cortisol biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of cortisol, the steroid hormone 11-beta-17,21-trihydroxypregn-4-ene-3,20-dione. Cortisol is synthesized from cholesterol in the adrenal gland and controls carbohydrate, fat and protein metabolism and has anti-inflammatory properties." [CHEBI:17650, GOC:BHF, GOC:mah, GOC:rl] +synonym: "cortisol anabolism" NARROW [] +synonym: "cortisol biosynthesis" EXACT [] +synonym: "cortisol formation" EXACT [] +synonym: "cortisol synthesis" EXACT [] +is_a: GO:0006704 ! glucocorticoid biosynthetic process +is_a: GO:0034650 ! cortisol metabolic process +is_a: GO:0042181 ! ketone biosynthetic process +is_a: GO:0046165 ! alcohol biosynthetic process + +[Term] +id: GO:0034654 +name: nucleobase-containing compound biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] +subset: gosubset_prok +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid anabolism" EXACT [] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis" EXACT [] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid formation" EXACT [] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid synthesis" NARROW [] +is_a: GO:0006139 ! nucleobase-containing compound metabolic process +is_a: GO:0018130 ! heterocycle biosynthetic process +is_a: GO:0019438 ! aromatic compound biosynthetic process +is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process +is_a: GO:1901362 ! organic cyclic compound biosynthetic process + +[Term] +id: GO:0034655 +name: nucleobase-containing compound catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] +subset: goslim_generic +subset: gosubset_prok +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" EXACT [] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process" RELATED [GOC:dph, GOC:tb] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolism" EXACT [] +synonym: "nucleobase, nucleoside, nucleotide and nucleic acid degradation" EXACT [] +is_a: GO:0006139 ! nucleobase-containing compound metabolic process +is_a: GO:0019439 ! aromatic compound catabolic process +is_a: GO:0044270 ! cellular nitrogen compound catabolic process +is_a: GO:0046700 ! heterocycle catabolic process +is_a: GO:1901361 ! organic cyclic compound catabolic process + +[Term] +id: GO:0034750 +name: Scrib-APC-beta-catenin complex +namespace: cellular_component +def: "A protein complex that contains the Scribble protein (a cell polarity determinant), the tumor suppressor protein adenomatous polyposis coli (APC), and beta-catenin; may be involved in the control of cell proliferation." [PMID:16611247] +comment: Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'. +synonym: "hScrib-APC-beta-catenin complex" NARROW [] +is_a: GO:0043234 ! protein complex +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0034754 +name: cellular hormone metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone, as carried out by individual cells." [GOC:mah] +is_a: GO:0042445 ! hormone metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0034762 +name: regulation of transmembrane transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other." [GOC:mah] +synonym: "regulation of membrane transport" EXACT [] +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0055085 ! transmembrane transport +relationship: regulates GO:0055085 ! transmembrane transport + +[Term] +id: GO:0034765 +name: regulation of ion transmembrane transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." [GOC:mah] +synonym: "regulation of ion membrane transport" EXACT [] +synonym: "regulation of transmembrane ion transport" EXACT [GOC:dph, GOC:tb] +is_a: GO:0034762 ! regulation of transmembrane transport +is_a: GO:0043269 ! regulation of ion transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034220 ! ion transmembrane transport +relationship: regulates GO:0034220 ! ion transmembrane transport + +[Term] +id: GO:0035019 +name: somatic stem cell maintenance +namespace: biological_process +def: "The process in which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line." [GOC:bf, ISBN:0582227089] +is_a: GO:0019827 ! stem cell maintenance + +[Term] +id: GO:0035023 +name: regulation of Rho protein signal transduction +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of Rho protein signal transduction." [GOC:bf] +is_a: GO:0046578 ! regulation of Ras protein signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007266 ! Rho protein signal transduction +relationship: regulates GO:0007266 ! Rho protein signal transduction + +[Term] +id: GO:0035050 +name: embryonic heart tube development +namespace: biological_process +def: "The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field." [GOC:go_curators] +is_a: GO:0035295 ! tube development +relationship: part_of GO:0007507 ! heart development +relationship: part_of GO:0009790 ! embryo development +relationship: part_of GO:0048568 ! embryonic organ development + +[Term] +id: GO:0035051 +name: cardiocyte differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell that will form part of the cardiac organ of an individual." [GOC:bf] +synonym: "cardiac cell differentiation" EXACT [] +synonym: "heart cell differentiation" EXACT [] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0035054 +name: embryonic heart tube anterior/posterior pattern specification +namespace: biological_process +def: "The establishment, maintenance and elaboration of cell differentiation that results in the anterior/posterior subdivision of the embryonic heart tube. In Drosophila this results in subdivision of the dorsal vessel into to the posterior heart proper and the anterior aorta." [GOC:bf, PMID:12435360] +is_a: GO:0009952 ! anterior/posterior pattern specification +relationship: part_of GO:0035050 ! embryonic heart tube development + +[Term] +id: GO:0035058 +name: nonmotile primary cilium assembly +namespace: biological_process +def: "The assembly of a primary cilium which contains a variable array of axonemal microtubules but does not contain molecular motors. Nonmotile primary cilia are found on many different cell types and function as sensory organelles that concentrate and organize sensory signaling molecules." [GOC:kmv, PMID:14521833, PMID:14521834] +synonym: "immotile primary cilium assembly" EXACT [GOC:bf] +synonym: "nonmotile primary cilia assembly" RELATED [GOC:bf] +synonym: "sensory cilium assembly" EXACT [GOC:kmv] +synonym: "sensory cilium biogenesis" RELATED [GOC:mah] +is_a: GO:0042384 ! cilium assembly + +[Term] +id: GO:0035088 +name: establishment or maintenance of apical/basal cell polarity +namespace: biological_process +def: "Any cellular process that results in the specification, formation or maintenance polarization of a cell's architecture along its apical/basal axis so that the apical and basal regions of the cell have different membrane, extracellular matrix and sub-membrane cellular components." [GOC:bf, GOC:mah, PMID:10934483] +is_a: GO:0061245 ! establishment or maintenance of bipolar cell polarity + +[Term] +id: GO:0035089 +name: establishment of apical/basal cell polarity +namespace: biological_process +def: "The specification and formation of the polarity of a cell along its apical/basal axis." [GOC:bf] +is_a: GO:0035088 ! establishment or maintenance of apical/basal cell polarity +is_a: GO:0061162 ! establishment of monopolar cell polarity + +[Term] +id: GO:0035107 +name: appendage morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of appendages are generated and organized. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch." [ISBN:0582227089] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048736 ! appendage development + +[Term] +id: GO:0035108 +name: limb morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping." [UBERON:0002101] +synonym: "limb bud morphogenesis" NARROW [GOC:dph] +is_a: GO:0035107 ! appendage morphogenesis +relationship: part_of GO:0060173 ! limb development + +[Term] +id: GO:0035112 +name: genitalia morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of genitalia are generated and organized. The genitalia are the organs of reproduction or generation, external and internal." [GOC:bf] +synonym: "genital morphogenesis" RELATED [] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0009887 ! organ morphogenesis +is_a: GO:0044702 ! single organism reproductive process +relationship: part_of GO:0048806 ! genitalia development + +[Term] +id: GO:0035113 +name: embryonic appendage morphogenesis +namespace: biological_process +def: "The process, occurring in the embryo, by which the anatomical structures of the appendage are generated and organized. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch." [ISBN:0582227089] +is_a: GO:0035107 ! appendage morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis + +[Term] +id: GO:0035115 +name: embryonic forelimb morphogenesis +namespace: biological_process +alt_id: GO:0035117 +def: "The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human." [ISBN:0198612001] +synonym: "embryonic arm morphogenesis" NARROW [GOC:bf, GOC:cjm] +is_a: GO:0030326 ! embryonic limb morphogenesis +is_a: GO:0035136 ! forelimb morphogenesis + +[Term] +id: GO:0035116 +name: embryonic hindlimb morphogenesis +namespace: biological_process +def: "The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal." [ISBN:0198612001] +is_a: GO:0030326 ! embryonic limb morphogenesis +is_a: GO:0035137 ! hindlimb morphogenesis + +[Term] +id: GO:0035136 +name: forelimb morphogenesis +namespace: biological_process +alt_id: GO:0035140 +def: "The process in which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human." [GOC:go_curators] +synonym: "arm morphogenesis" NARROW [GOC:bf, GOC:cjm] +is_a: GO:0035108 ! limb morphogenesis + +[Term] +id: GO:0035137 +name: hindlimb morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the hindlimb are generated and organized." [GOC:go_curators] +is_a: GO:0035108 ! limb morphogenesis + +[Term] +id: GO:0035148 +name: tube formation +namespace: biological_process +def: "Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow." [GOC:bf] +synonym: "lumen formation in an anatomical structure" RELATED [GOC:dph, GOC:mah] +synonym: "tube lumen formation" EXACT [GOC:dph, GOC:mah] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0035239 ! tube morphogenesis + +[Term] +id: GO:0035150 +name: regulation of tube size +namespace: biological_process +def: "Ensuring that a tube is of the correct length and diameter. Tube size must be maintained not only during tube formation, but also throughout development and in some physiological processes." [PMID:10887083] +is_a: GO:0090066 ! regulation of anatomical structure size + +[Term] +id: GO:0035239 +name: tube morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [GOC:bf, PMID:14624839] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0035295 ! tube development + +[Term] +id: GO:0035254 +name: glutamate receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a glutamate receptor." [GOC:bf] +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0035255 +name: ionotropic glutamate receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels." [GOC:bf, ISBN:0198506732] +is_a: GO:0035254 ! glutamate receptor binding + +[Term] +id: GO:0035257 +name: nuclear hormone receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a nuclear hormone receptor, a ligand-dependent receptor found in the nucleus of the cell." [GOC:bf] +is_a: GO:0051427 ! hormone receptor binding + +[Term] +id: GO:0035258 +name: steroid hormone receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a steroid hormone receptor." [GOC:bf] +is_a: GO:0035257 ! nuclear hormone receptor binding + +[Term] +id: GO:0035261 +name: external genitalia morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the external genitalia are generated and organized. The external genitalia are the outer sex organs, such as the penis or vulva in mammals." [http://www.ndif.org/Terms/genitalia.html] +is_a: GO:0035112 ! genitalia morphogenesis + +[Term] +id: GO:0035265 +name: organ growth +namespace: biological_process +def: "The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function." [GOC:bf, ISBN:0471245208, ISBN:0721662544] +is_a: GO:0040007 ! growth +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0035270 +name: endocrine system development +namespace: biological_process +def: "Progression of the endocrine system over time, from its formation to a mature structure. The endocrine system is a system of hormones and ductless glands, where the glands release hormones directly into the blood, lymph or other intercellular fluid, and the hormones circulate within the body to affect distant organs. The major glands that make up the human endocrine system are the hypothalamus, pituitary, thyroid, parathryoids, adrenals, pineal body, and the reproductive glands which include the ovaries and testes." [GOC:bf, http://encyclopedia.thefreedictionary.com/Endocrine+sytem, ISBN:0198506732] +is_a: GO:0048731 ! system development + +[Term] +id: GO:0035272 +name: exocrine system development +namespace: biological_process +def: "Progression of the exocrine system over time, from its formation to a mature structure. The exocrine system is a system of hormones and glands, where the glands secrete straight to a target site via ducts or tubes. The human exocrine system includes the salivary glands, sweat glands and many glands of the digestive system." [GOC:bf, http://encyclopedia.thefreedictionary.com/Exocrine+gland, ISBN:0198506732] +is_a: GO:0048731 ! system development + +[Term] +id: GO:0035282 +name: segmentation +namespace: biological_process +def: "The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis." [PMID:10611687, PMID:9706689] +xref: Wikipedia:Segmentation_(biology) +is_a: GO:0003002 ! regionalization + +[Term] +id: GO:0035295 +name: tube development +namespace: biological_process +def: "The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts." [PMID:12526790] +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0035313 +name: wound healing, spreading of epidermal cells +namespace: biological_process +def: "The migration of an epidermal cell along or through a wound gap that contributes to the reestablishment of a continuous epidermis." [GOC:bf, PMID:15269788] +is_a: GO:0044319 ! wound healing, spreading of cells + +[Term] +id: GO:0035326 +name: enhancer binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter." [GOC:sart, GOC:txnOH, SO:0000165] +is_a: GO:0044212 ! transcription regulatory region DNA binding +created_by: rfoulger +creation_date: 2010-02-26T10:17:00Z + +[Term] +id: GO:0035411 +name: catenin import into nucleus +namespace: biological_process +def: "The directed movement of a catenin protein from the cytoplasm into the nucleus." [GOC:BHF] +comment: Note that 'translocation' is sometimes used in the literature to refer to the entire process of protein import into the nucleus, but in GO refers specifically to the step in which a cargo-carrier protein complex moves through the nuclear pore complex. +synonym: "catenin protein nuclear translocation" NARROW [GOC:mah] +is_a: GO:0006606 ! protein import into nucleus +created_by: rfoulger +creation_date: 2010-03-24T02:51:42Z + +[Term] +id: GO:0035412 +name: regulation of catenin import into nucleus +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus." [GOC:BHF] +synonym: "regulation of catenin protein nuclear translocation" NARROW [GOC:mah] +is_a: GO:0042306 ! regulation of protein import into nucleus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035411 ! catenin import into nucleus +relationship: regulates GO:0035411 ! catenin import into nucleus +created_by: rfoulger +creation_date: 2010-03-24T02:52:33Z + +[Term] +id: GO:0035413 +name: positive regulation of catenin import into nucleus +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus." [GOC:BHF] +synonym: "positive regulation of catenin protein nuclear translocation" NARROW [GOC:mah] +is_a: GO:0035412 ! regulation of catenin import into nucleus +is_a: GO:0042307 ! positive regulation of protein import into nucleus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0035411 ! catenin import into nucleus +relationship: positively_regulates GO:0035411 ! catenin import into nucleus +created_by: rfoulger +creation_date: 2010-03-24T02:53:38Z + +[Term] +id: GO:0035414 +name: negative regulation of catenin import into nucleus +namespace: biological_process +def: "Any process that decreases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus." [GOC:BHF] +synonym: "negative regulation of catenin protein nuclear translocation" NARROW [GOC:mah] +is_a: GO:0035412 ! regulation of catenin import into nucleus +is_a: GO:0042308 ! negative regulation of protein import into nucleus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0035411 ! catenin import into nucleus +relationship: negatively_regulates GO:0035411 ! catenin import into nucleus +created_by: rfoulger +creation_date: 2010-03-24T02:54:21Z + +[Term] +id: GO:0035426 +name: extracellular matrix-cell signaling +namespace: biological_process +def: "Any process that mediates the transfer of information between the extracellular matrix and a cell." [GOC:bf] +synonym: "cell-extracellular matrix signalling" EXACT [] +synonym: "extracellular matrix-cell signalling" EXACT [] +is_a: GO:0007154 ! cell communication +is_a: GO:0044700 ! single organism signaling +created_by: rfoulger +creation_date: 2010-03-29T02:26:54Z + +[Term] +id: GO:0035470 +name: positive regulation of vascular wound healing +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature." [GOC:rph] +is_a: GO:0045766 ! positive regulation of angiogenesis +is_a: GO:0061043 ! regulation of vascular wound healing +is_a: GO:0090303 ! positive regulation of wound healing +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061042 ! vascular wound healing +relationship: positively_regulates GO:0061042 ! vascular wound healing +created_by: rfoulger +creation_date: 2010-04-22T10:49:09Z + +[Term] +id: GO:0035473 +name: lipase binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any lipase." [GOC:BHF] +is_a: GO:0019899 ! enzyme binding +created_by: rfoulger +creation_date: 2010-04-22T05:28:52Z + +[Term] +id: GO:0035556 +name: intracellular signal transduction +namespace: biological_process +alt_id: GO:0007242 +alt_id: GO:0007243 +alt_id: GO:0023013 +alt_id: GO:0023034 +def: "The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell." [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782] +synonym: "intracellular protein kinase cascade" NARROW [GOC:signaling] +synonym: "intracellular signal transduction pathway" NARROW [] +synonym: "intracellular signaling cascade" RELATED [GOC:signaling] +synonym: "intracellular signaling chain" EXACT [ISBN:3527303782] +synonym: "intracellular signaling pathway" RELATED [] +synonym: "protein kinase cascade" NARROW [GOC:signaling] +synonym: "signal transduction via intracellular signaling cascade" RELATED [] +synonym: "signal transmission via intracellular cascade" NARROW [] +xref: Reactome:REACT_100795 "PKA-mediated phosphorylation of key metabolic factors, Saccharomyces cerevisiae" +xref: Reactome:REACT_102462 "PKA-mediated phosphorylation of key metabolic factors, Canis familiaris" +xref: Reactome:REACT_104200 "PKA-mediated phosphorylation of key metabolic factors, Taeniopygia guttata" +xref: Reactome:REACT_108216 "PKA-mediated phosphorylation of key metabolic factors, Dictyostelium discoideum" +xref: Reactome:REACT_1525 "PKA-mediated phosphorylation of key metabolic factors, Homo sapiens" +xref: Reactome:REACT_80030 "PKA-mediated phosphorylation of key metabolic factors, Sus scrofa" +xref: Reactome:REACT_83068 "PKA-mediated phosphorylation of key metabolic factors, Gallus gallus" +xref: Reactome:REACT_83869 "PKA-mediated phosphorylation of key metabolic factors, Xenopus tropicalis" +xref: Reactome:REACT_87453 "PKA-mediated phosphorylation of key metabolic factors, Bos taurus" +xref: Reactome:REACT_89085 "PKA-mediated phosphorylation of key metabolic factors, Rattus norvegicus" +xref: Reactome:REACT_89983 "PKA-mediated phosphorylation of key metabolic factors, Danio rerio" +xref: Reactome:REACT_90740 "PKA-mediated phosphorylation of key metabolic factors, Schizosaccharomyces pombe" +xref: Reactome:REACT_99938 "PKA-mediated phosphorylation of key metabolic factors, Mus musculus" +is_a: GO:0007165 ! signal transduction +intersection_of: GO:0007165 ! signal transduction +intersection_of: occurs_in GO:0005622 ! intracellular +created_by: rfoulger +creation_date: 2010-05-14T01:14:37Z + +[Term] +id: GO:0035567 +name: non-canonical Wnt signaling pathway +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via effectors other than beta-catenin." [GOC:signaling] +comment: This term should only be used when Wnt receptor signaling occurs via a beta-catenin-independent route but the downstream effectors are unknown. If the downstream effectors are known, consider instead annotating to one of the children, or requesting a new term. +synonym: "beta-catenin-independent Wnt receptor signaling pathway" EXACT [GOC:signaling] +synonym: "non-canonical Wnt receptor signaling pathway" EXACT [] +synonym: "non-canonical Wnt receptor signalling pathway" EXACT [GOC:mah] +synonym: "non-canonical Wnt-activated signaling pathway" EXACT [GOC:signaling] +is_a: GO:0016055 ! Wnt signaling pathway +created_by: rfoulger +creation_date: 2010-07-23T02:26:01Z + +[Term] +id: GO:0035637 +name: multicellular organismal signaling +namespace: biological_process +def: "The transfer of information occurring at the level of a multicellular organism." [GOC:go_curators] +synonym: "multicellular organismal signalling" EXACT [GOC:bf] +is_a: GO:0044700 ! single organism signaling +is_a: GO:0044707 ! single-multicellular organism process +created_by: rfoulger +creation_date: 2011-01-14T10:13:50Z + +[Term] +id: GO:0035659 +name: Wnt signaling pathway involved in wound healing, spreading of epidermal cells +namespace: biological_process +def: "The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of a cell in the epidermis that contributes to the migration of an epidermal cell along or through a wound gap to reestablish a continuous epidermis." [GOC:BHF] +synonym: "Wnt receptor signaling pathway involved in wound healing, spreading of epidermal cells" EXACT [] +synonym: "Wnt receptor signalling pathway involved in wound healing, spreading of epidermal cells" EXACT [GOC:mah] +synonym: "Wnt-activated signaling pathway involved in wound healing, spreading of epidermal cells" EXACT [GOC:signaling] +is_a: GO:0016055 ! Wnt signaling pathway +intersection_of: GO:0016055 ! Wnt signaling pathway +intersection_of: part_of GO:0035313 ! wound healing, spreading of epidermal cells +relationship: part_of GO:0035313 ! wound healing, spreading of epidermal cells +created_by: rfoulger +creation_date: 2011-01-28T11:34:02Z + +[Term] +id: GO:0035773 +name: insulin secretion involved in cellular response to glucose stimulus +namespace: biological_process +def: "The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin, in response to a glucose stimulus." [GOC:bf, GOC:yaf, PMID:8492079] +synonym: "insulin secretion involved in cellular response to glucose" EXACT [GOC:bf] +is_a: GO:0030073 ! insulin secretion +intersection_of: GO:0030073 ! insulin secretion +intersection_of: part_of GO:0071333 ! cellular response to glucose stimulus +relationship: part_of GO:0071333 ! cellular response to glucose stimulus +created_by: rfoulger +creation_date: 2011-04-01T01:14:40Z + +[Term] +id: GO:0035850 +name: epithelial cell differentiation involved in kidney development +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an epithelial cell that characterize the cells of the kidney as it progresses from its formation to the mature state." [GOC:bf, GOC:mtg_kidney_jan10, GOC:yaf, PMID:16216236] +is_a: GO:0030855 ! epithelial cell differentiation +is_a: GO:0061005 ! cell differentiation involved in kidney development +intersection_of: GO:0030855 ! epithelial cell differentiation +intersection_of: part_of GO:0001822 ! kidney development +relationship: part_of GO:0001822 ! kidney development +created_by: rfoulger +creation_date: 2011-05-11T11:34:21Z + +[Term] +id: GO:0035883 +name: enteroendocrine cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an enteroendocrine cell. Enteroendocrine cells are hormonally active epithelial cells in the gut that constitute the diffuse neuroendocrine system." [CL:0000164, GOC:bf] +is_a: GO:0002067 ! glandular epithelial cell differentiation +created_by: rfoulger +creation_date: 2011-06-06T11:48:51Z + +[Term] +id: GO:0035886 +name: vascular smooth muscle cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a vascular smooth muscle cell." [GOC:sl, PMID:16151017, PMID:18267954] +synonym: "vascular associated smooth muscle cell differentiation" EXACT [CL:0000359] +synonym: "VSMC differentiation" EXACT [PMID:16151017] +is_a: GO:0051145 ! smooth muscle cell differentiation +relationship: part_of GO:0001944 ! vasculature development +created_by: rfoulger +creation_date: 2011-06-08T11:23:52Z + +[Term] +id: GO:0035904 +name: aorta development +namespace: biological_process +def: "The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body." [GOC:bf, GOC:dgh, MA:0000062, UBERON:0000947, Wikipedia:Aorta] +is_a: GO:0060840 ! artery development +created_by: rfoulger +creation_date: 2011-06-24T11:00:07Z + +[Term] +id: GO:0035909 +name: aorta morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of an aorta are generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body." [GOC:bf, GOC:dgh, MA:0000062, UBERON:0000947, Wikipedia:Aorta] +is_a: GO:0048844 ! artery morphogenesis +relationship: part_of GO:0035904 ! aorta development +created_by: rfoulger +creation_date: 2011-06-24T11:11:11Z + +[Term] +id: GO:0035914 +name: skeletal muscle cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle." [CL:0000188, GOC:BHF, GOC:vk] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0007519 ! skeletal muscle tissue development +created_by: rfoulger +creation_date: 2011-06-24T02:36:19Z + +[Term] +id: GO:0035987 +name: endodermal cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo." [CL:0000223, GOC:yaf, PMID:17624332] +synonym: "endoderm cell differentiation" EXACT [CL:0000223] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0001706 ! endoderm formation +created_by: rfoulger +creation_date: 2011-08-25T04:50:36Z + +[Term] +id: GO:0036022 +name: limb joint morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a limb joint are generated and organized. A limb joint is a flexible region that separates the rigid sections of a limb to allow movement in a controlled manner." [GOC:bf] +synonym: "knee morphogenesis" NARROW [GOC:bf] +synonym: "leg joint morphogenesis" NARROW [GOC:bf] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0035108 ! limb morphogenesis +created_by: rfoulger +creation_date: 2011-10-13T04:52:59Z + +[Term] +id: GO:0036023 +name: embryonic skeletal limb joint morphogenesis +namespace: biological_process +def: "The process, occurring in the embryo, in which the anatomical structures of a skeletal limb joint are generated and organized. A skeletal limb joint is the connecting structure between the bones of a limb." [GOC:bf, Wikipedia:Joint] +is_a: GO:0036022 ! limb joint morphogenesis +is_a: GO:0060272 ! embryonic skeletal joint morphogenesis +relationship: part_of GO:0030326 ! embryonic limb morphogenesis +created_by: rfoulger +creation_date: 2011-10-13T04:57:39Z + +[Term] +id: GO:0036211 +name: protein modification process +namespace: biological_process +def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:bf, GOC:jl] +synonym: "protein modification" EXACT [GOC:bf] +is_a: GO:0019538 ! protein metabolic process +is_a: GO:0043412 ! macromolecule modification +created_by: rfoulger +creation_date: 2012-04-26T01:47:12Z + +[Term] +id: GO:0036303 +name: lymph vessel morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of lymph vessels are generated and organized. The lymph vessel is the vasculature carrying lymph." [GOC:BHF, GOC:gr, PMID:18093989] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001945 ! lymph vessel development +created_by: rfoulger +creation_date: 2012-08-08T10:08:47Z + +[Term] +id: GO:0036314 +name: response to sterol +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a sterol stimulus." [CHEBI:15889, GOC:bf] +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0033993 ! response to lipid +is_a: GO:0097305 ! response to alcohol +created_by: rfoulger +creation_date: 2012-08-21T14:50:14Z + +[Term] +id: GO:0036315 +name: cellular response to sterol +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a sterol stimulus." [CHEBI:15889, GOC:bf] +is_a: GO:0036314 ! response to sterol +is_a: GO:0071396 ! cellular response to lipid +is_a: GO:0071407 ! cellular response to organic cyclic compound +is_a: GO:0097306 ! cellular response to alcohol +created_by: rfoulger +creation_date: 2012-08-21T14:51:21Z + +[Term] +id: GO:0036342 +name: post-anal tail morphogenesis +namespace: biological_process +def: "The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance." [GOC:bf, GOC:kmv, Wikipedia:Chordate] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +created_by: rfoulger +creation_date: 2012-09-11T13:54:49Z + +[Term] +id: GO:0036445 +name: neuronal stem cell division +namespace: biological_process +def: "The self-renewing division of a neuronal stem cell." [CL:0000047, GOC:nhn] +synonym: " NSC division" EXACT [CL:0000047] +is_a: GO:0048103 ! somatic stem cell division +created_by: rfoulger +creation_date: 2013-10-30T10:03:27Z + +[Term] +id: GO:0038023 +name: signaling receptor activity +namespace: molecular_function +def: "Receiving a signal and transmitting the signal in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:bf, GOC:signaling] +comment: Note that this term and its child terms are intended for receptors that are directly coupled to a signal transduction pathway. This term should therefore not be used to annotate decoy receptors and other proteins that bind a signal but do not pass the signal on. This term can be used to annotate dependence receptors that transduce a signal when a ligand is withdrawn (in this case, signal withdrawal is considered to be the initiating signal), or receptors that signal at a basal level in the absence of a bound agonist. For receptors that mediate transport of a substance into the cell by receptor-mediated endocytosis, consider instead the term 'cargo receptor activity ; GO:0038024' and its children. +synonym: "receptor activity involved in signal transduction" EXACT [GOC:bf] +synonym: "signalling receptor activity" EXACT [GOC:mah] +is_a: GO:0004871 ! signal transducer activity +is_a: GO:0004872 ! receptor activity +intersection_of: GO:0004872 ! receptor activity +intersection_of: part_of GO:0007165 ! signal transduction +created_by: rfoulger +creation_date: 2011-08-01T02:45:27Z + +[Term] +id: GO:0038024 +name: cargo receptor activity +namespace: molecular_function +def: "Combining selectively with an extracellular macromolecule and delivering the macromolecule into the cell via endocytosis." [GOC:bf, GOC:signaling, PMID:15239958] +comment: Note that this term and its child terms are intended for receptors that bind to and internalize molecules by receptor-mediated endocytosis. For receptors that are coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. +synonym: "endocytic receptor activity" RELATED [GOC:signaling, ISBN:0123645387, PMID:12671190] +synonym: "receptor activity involved in ligand uptake" EXACT [PMID:12671190] +synonym: "receptor activity involved in receptor-mediated endocytosis" EXACT [GOC:bf] +synonym: "transport receptor activity" RELATED [GOC:signaling] +is_a: GO:0004872 ! receptor activity +intersection_of: GO:0004872 ! receptor activity +intersection_of: part_of GO:0006898 ! receptor-mediated endocytosis +relationship: part_of GO:0006898 ! receptor-mediated endocytosis +created_by: rfoulger +creation_date: 2011-08-01T02:50:45Z + +[Term] +id: GO:0038025 +name: reelin receptor activity +namespace: molecular_function +def: "Combining with the secreted glycoprotein reelin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:bf, PMID:12827279, PMID:20223215, PR:000013879] +synonym: "reeler receptor activity" EXACT [PR:000013879] +is_a: GO:0004888 ! transmembrane signaling receptor activity +relationship: part_of GO:0038026 ! reelin-mediated signaling pathway +created_by: rfoulger +creation_date: 2011-08-02T12:01:25Z + +[Term] +id: GO:0038026 +name: reelin-mediated signaling pathway +namespace: biological_process +def: "A series of molecular signals initiated by the binding of reelin (a secreted glycoprotein) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, PMID:12827279, PMID:20223215, PR:000013879] +synonym: "reeler-mediated signaling pathway" EXACT [GOC:bf, PR:000013879] +synonym: "reelin-mediated signal transduction pathway" EXACT [GOC:bf] +synonym: "reelin-mediated signalling pathway" EXACT [GOC:bf] +is_a: GO:0007166 ! cell surface receptor signaling pathway +created_by: rfoulger +creation_date: 2011-08-02T02:06:18Z + +[Term] +id: GO:0038030 +name: non-canonical Wnt signaling pathway via MAPK cascade +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, where the signal is passed on via the MAPKKK cascade." [GOC:BHF, GOC:signaling, GOC:vk, PMID:17720811] +synonym: "non-canonical Wnt receptor signaling pathway via MAPK cascade" EXACT [] +synonym: "non-canonical Wnt receptor signaling pathway via MAPK signaling" EXACT [GOC:bf] +synonym: "non-canonical Wnt receptor signaling pathway via MAPKKK cascade" EXACT [GOC:signaling] +synonym: "non-canonical Wnt receptor signalling pathway via MAPKKK cascade" EXACT [GOC:bf] +synonym: "non-canonical Wnt-activated signaling pathway via MAPK cascade" EXACT [GOC:signaling] +is_a: GO:0035567 ! non-canonical Wnt signaling pathway +relationship: has_part GO:0000165 ! MAPK cascade +created_by: rfoulger +creation_date: 2011-09-08T01:46:07Z + +[Term] +id: GO:0038031 +name: non-canonical Wnt signaling pathway via JNK cascade +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, where the signal is passed on via the JNK cascade." [GOC:BHF, GPC:rl, PMID:19137009, PMID:20032469] +synonym: "non-canonical Wnt receptor signaling pathway via JNK cascade" EXACT [] +synonym: "non-canonical Wnt receptor signalling pathway via JNK cascade" EXACT [GOC:bf] +synonym: "non-canonical Wnt-activated signaling pathway via JNK cascade" EXACT [GOC:signaling] +is_a: GO:0038030 ! non-canonical Wnt signaling pathway via MAPK cascade +relationship: has_part GO:0007254 ! JNK cascade +created_by: rfoulger +creation_date: 2011-09-08T01:57:10Z + +[Term] +id: GO:0040007 +name: growth +namespace: biological_process +alt_id: GO:0048590 +def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] +comment: See also the biological process term 'cell growth ; GO:0016049'. +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "growth pattern" RELATED [] +synonym: "non-developmental growth" RELATED [GOC:mah] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0040008 +name: regulation of growth +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development." [GOC:ems, GOC:mah] +subset: gosubset_prok +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0040007 ! growth +relationship: regulates GO:0040007 ! growth + +[Term] +id: GO:0040011 +name: locomotion +namespace: biological_process +def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh] +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0040012 +name: regulation of locomotion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of locomotion of a cell or organism." [GOC:ems] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0040011 ! locomotion +relationship: regulates GO:0040011 ! locomotion + +[Term] +id: GO:0040013 +name: negative regulation of locomotion +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism." [GOC:go_curators] +synonym: "down regulation of locomotion" EXACT [] +synonym: "down-regulation of locomotion" EXACT [] +synonym: "downregulation of locomotion" EXACT [] +synonym: "inhibition of locomotion" NARROW [] +is_a: GO:0040012 ! regulation of locomotion +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0040011 ! locomotion +relationship: negatively_regulates GO:0040011 ! locomotion + +[Term] +id: GO:0040017 +name: positive regulation of locomotion +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism." [GOC:go_curators] +synonym: "activation of locomotion" NARROW [] +synonym: "stimulation of locomotion" NARROW [] +synonym: "up regulation of locomotion" EXACT [] +synonym: "up-regulation of locomotion" EXACT [] +synonym: "upregulation of locomotion" EXACT [] +is_a: GO:0040012 ! regulation of locomotion +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0040011 ! locomotion +relationship: positively_regulates GO:0040011 ! locomotion + +[Term] +id: GO:0040019 +name: positive regulation of embryonic development +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of embryonic development." [GOC:go_curators] +synonym: "activation of embryonic development" NARROW [] +synonym: "stimulation of embryonic development" NARROW [] +synonym: "up regulation of embryonic development" EXACT [] +synonym: "up-regulation of embryonic development" EXACT [] +synonym: "upregulation of embryonic development" EXACT [] +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009790 ! embryo development +relationship: positively_regulates GO:0009790 ! embryo development + +[Term] +id: GO:0040020 +name: regulation of meiosis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of meiosis, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes." [GOC:ems, GOC:ma] +is_a: GO:0010564 ! regulation of cell cycle process +is_a: GO:0051445 ! regulation of meiotic cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007126 ! meiosis +relationship: regulates GO:0007126 ! meiosis + +[Term] +id: GO:0040036 +name: regulation of fibroblast growth factor receptor signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:go_curators] +synonym: "regulation of FGF receptor signaling pathway" EXACT [] +synonym: "regulation of FGF receptor signalling pathway" EXACT [] +synonym: "regulation of FGFR signaling pathway" EXACT [] +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0090287 ! regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway +relationship: regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway + +[Term] +id: GO:0040037 +name: negative regulation of fibroblast growth factor receptor signaling pathway +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:go_curators] +synonym: "down regulation of fibroblast growth factor receptor signaling pathway" EXACT [] +synonym: "down-regulation of fibroblast growth factor receptor signaling pathway" EXACT [] +synonym: "downregulation of fibroblast growth factor receptor signaling pathway" EXACT [] +synonym: "inhibition of fibroblast growth factor receptor signaling pathway" NARROW [] +synonym: "negative regulation of FGF receptor signaling pathway" EXACT [] +synonym: "negative regulation of FGF receptor signalling pathway" EXACT [] +synonym: "negative regulation of FGFR signaling pathway" EXACT [] +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:0040036 ! regulation of fibroblast growth factor receptor signaling pathway +is_a: GO:0090288 ! negative regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway +relationship: negatively_regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway + +[Term] +id: GO:0042033 +name: chemokine biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of chemokines, any member of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria." [GOC:BHF, GOC:rl, http://en.wikipedia.org/wiki/Chemokine, ISBN:0198506732, PMID:12183377] +synonym: "chemokine anabolism" EXACT [] +synonym: "chemokine biosynthesis" EXACT [] +synonym: "chemokine formation" EXACT [] +synonym: "chemokine synthesis" EXACT [] +is_a: GO:0042089 ! cytokine biosynthetic process +is_a: GO:0050755 ! chemokine metabolic process +relationship: part_of GO:0032602 ! chemokine production + +[Term] +id: GO:0042035 +name: regulation of cytokine biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines." [GOC:go_curators] +synonym: "regulation of cytokine anabolism" EXACT [] +synonym: "regulation of cytokine biosynthesis" EXACT [] +synonym: "regulation of cytokine formation" EXACT [] +synonym: "regulation of cytokine synthesis" EXACT [] +is_a: GO:0001817 ! regulation of cytokine production +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042089 ! cytokine biosynthetic process +relationship: regulates GO:0042089 ! cytokine biosynthetic process + +[Term] +id: GO:0042036 +name: negative regulation of cytokine biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines." [GOC:go_curators] +synonym: "down regulation of cytokine biosynthetic process" EXACT [] +synonym: "down-regulation of cytokine biosynthetic process" EXACT [] +synonym: "downregulation of cytokine biosynthetic process" EXACT [] +synonym: "inhibition of cytokine biosynthetic process" NARROW [] +synonym: "negative regulation of cytokine anabolism" EXACT [] +synonym: "negative regulation of cytokine biosynthesis" EXACT [] +synonym: "negative regulation of cytokine formation" EXACT [] +synonym: "negative regulation of cytokine synthesis" EXACT [] +is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process +is_a: GO:0031327 ! negative regulation of cellular biosynthetic process +is_a: GO:0042035 ! regulation of cytokine biosynthetic process +is_a: GO:0051248 ! negative regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042089 ! cytokine biosynthetic process +relationship: negatively_regulates GO:0042089 ! cytokine biosynthetic process + +[Term] +id: GO:0042060 +name: wound healing +namespace: biological_process +def: "The series of events that restore integrity to a damaged tissue, following an injury." [GOC:bf, PMID:15269788] +xref: Wikipedia:Wound_healing +is_a: GO:0009611 ! response to wounding + +[Term] +id: GO:0042063 +name: gliogenesis +namespace: biological_process +def: "The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia." [GOC:dgh, GOC:jid] +synonym: "glial cell generation" EXACT systematic_synonym [] +is_a: GO:0022008 ! neurogenesis + +[Term] +id: GO:0042074 +name: cell migration involved in gastrulation +namespace: biological_process +def: "The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression)." [GOC:jl, http://www.cellmigration.org/, ISBN:0878932437] +is_a: GO:0001667 ! ameboidal cell migration +intersection_of: GO:0016477 ! cell migration +intersection_of: part_of GO:0007369 ! gastrulation +relationship: part_of GO:0007369 ! gastrulation + +[Term] +id: GO:0042089 +name: cytokine biosynthetic process +namespace: biological_process +alt_id: GO:0042032 +def: "The chemical reactions and pathways resulting in the formation of cytokines, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity." [GOC:bf, ISBN:0198506732, ISBN:0198599471] +synonym: "cytokine anabolism" EXACT [] +synonym: "cytokine biosynthesis" EXACT [] +synonym: "cytokine formation" EXACT [] +synonym: "cytokine synthesis" EXACT [] +synonym: "induction of cytokines" NARROW [] +is_a: GO:0042107 ! cytokine metabolic process +relationship: part_of GO:0001816 ! cytokine production + +[Term] +id: GO:0042098 +name: T cell proliferation +namespace: biological_process +alt_id: GO:0042111 +def: "The expansion of a T cell population by cell division. Follows T cell activation." [GOC:jl] +synonym: "T lymphocyte proliferation" EXACT [] +synonym: "T-cell proliferation" EXACT [] +synonym: "T-lymphocyte proliferation" EXACT [] +is_a: GO:0042110 ! T cell activation +is_a: GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0042100 +name: B cell proliferation +namespace: biological_process +alt_id: GO:0042114 +def: "The expansion of a B cell population by cell division. Follows B cell activation." [GOC:jl] +synonym: "B lymphocyte proliferation" EXACT [] +synonym: "B-cell proliferation" EXACT [] +synonym: "B-lymphocyte proliferation" EXACT [] +is_a: GO:0042113 ! B cell activation +is_a: GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0042107 +name: cytokine metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving cytokines, any of a group of proteins or glycoproteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity." [GO_REF:0000022, GOC:bf, GOC:BHF, GOC:go_curators, GOC:mtg_15nov05, ISBN:0198599471] +comment: This term was improved by GO_REF:0000022. It was moved. +synonym: "cytokine metabolism" EXACT [] +is_a: GO:0019538 ! protein metabolic process + +[Term] +id: GO:0042108 +name: positive regulation of cytokine biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines." [GOC:go_curators] +synonym: "activation of cytokine biosynthetic process" NARROW [] +synonym: "positive regulation of cytokine anabolism" EXACT [] +synonym: "positive regulation of cytokine biosynthesis" EXACT [] +synonym: "positive regulation of cytokine formation" EXACT [] +synonym: "positive regulation of cytokine synthesis" EXACT [] +synonym: "stimulation of cytokine biosynthetic process" NARROW [] +synonym: "up regulation of cytokine biosynthetic process" EXACT [] +synonym: "up-regulation of cytokine biosynthetic process" EXACT [] +synonym: "upregulation of cytokine biosynthetic process" EXACT [] +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0042035 ! regulation of cytokine biosynthetic process +is_a: GO:0051247 ! positive regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042089 ! cytokine biosynthetic process +relationship: positively_regulates GO:0042089 ! cytokine biosynthetic process + +[Term] +id: GO:0042110 +name: T cell activation +namespace: biological_process +def: "The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [GOC:mgi_curators, ISBN:0781735140] +synonym: "T lymphocyte activation" EXACT [] +synonym: "T-cell activation" EXACT [] +synonym: "T-lymphocyte activation" EXACT [] +is_a: GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0042113 +name: B cell activation +namespace: biological_process +def: "The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [GOC:mgi_curators, ISBN:0781735140] +synonym: "B lymphocyte activation" EXACT [] +synonym: "B-cell activation" EXACT [] +synonym: "B-lymphocyte activation" EXACT [] +is_a: GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0042116 +name: macrophage activation +namespace: biological_process +def: "A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735149, PMID:14506301] +is_a: GO:0002274 ! myeloid leukocyte activation + +[Term] +id: GO:0042127 +name: regulation of cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell proliferation." [GOC:jl] +subset: gosubset_prok +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008283 ! cell proliferation +relationship: regulates GO:0008283 ! cell proliferation + +[Term] +id: GO:0042129 +name: regulation of T cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of T cell proliferation." [GOC:jl] +synonym: "regulation of T lymphocyte proliferation" EXACT [] +synonym: "regulation of T-cell proliferation" EXACT [] +synonym: "regulation of T-lymphocyte proliferation" EXACT [] +is_a: GO:0050670 ! regulation of lymphocyte proliferation +is_a: GO:0050863 ! regulation of T cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042098 ! T cell proliferation +relationship: regulates GO:0042098 ! T cell proliferation + +[Term] +id: GO:0042130 +name: negative regulation of T cell proliferation +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of T cell proliferation." [GOC:jl] +synonym: "down regulation of T cell proliferation" EXACT [] +synonym: "down-regulation of T cell proliferation" EXACT [] +synonym: "downregulation of T cell proliferation" EXACT [] +synonym: "inhibition of T cell proliferation" NARROW [] +synonym: "negative regulation of T lymphocyte proliferation" EXACT [] +synonym: "negative regulation of T-cell proliferation" EXACT [] +synonym: "negative regulation of T-lymphocyte proliferation" EXACT [] +is_a: GO:0042129 ! regulation of T cell proliferation +is_a: GO:0050672 ! negative regulation of lymphocyte proliferation +is_a: GO:0050868 ! negative regulation of T cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042098 ! T cell proliferation +relationship: negatively_regulates GO:0042098 ! T cell proliferation + +[Term] +id: GO:0042157 +name: lipoprotein metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." [ISBN:0198506732] +subset: gosubset_prok +synonym: "lipoprotein metabolism" EXACT [] +xref: Reactome:REACT_101960 "apolipoprotein(a) + LDL => Lp(a), Gallus gallus" +xref: Reactome:REACT_102413 "HDL-mediated lipid transport, Caenorhabditis elegans" +xref: Reactome:REACT_102496 "Chylomicron-mediated lipid transport, Sus scrofa" +xref: Reactome:REACT_103493 "Chylomicron-mediated lipid transport, Taeniopygia guttata" +xref: Reactome:REACT_105868 "Chylomicron-mediated lipid transport, Mus musculus" +xref: Reactome:REACT_107056 "Lipoprotein metabolism, Oryza sativa" +xref: Reactome:REACT_110247 "HDL-mediated lipid transport, Danio rerio" +xref: Reactome:REACT_110573 "Lipoprotein metabolism, Taeniopygia guttata" +xref: Reactome:REACT_112911 "apolipoprotein(a) + LDL => Lp(a), Xenopus tropicalis" +xref: Reactome:REACT_13621 "HDL-mediated lipid transport, Homo sapiens" +xref: Reactome:REACT_28841 "Lipoprotein metabolism, Drosophila melanogaster" +xref: Reactome:REACT_29288 "Chylomicron-mediated lipid transport, Rattus norvegicus" +xref: Reactome:REACT_33886 "HDL-mediated lipid transport, Arabidopsis thaliana" +xref: Reactome:REACT_59602 "Lipoprotein metabolism, Rattus norvegicus" +xref: Reactome:REACT_6823 "Lipoprotein metabolism, Homo sapiens" +xref: Reactome:REACT_6841 "Chylomicron-mediated lipid transport, Homo sapiens" +xref: Reactome:REACT_6958 "apolipoprotein(a) + LDL => Lp(a), Homo sapiens" +xref: Reactome:REACT_73884 "HDL-mediated lipid transport, Canis familiaris" +xref: Reactome:REACT_78284 "apolipoprotein(a) + LDL => Lp(a), Rattus norvegicus" +xref: Reactome:REACT_79032 "HDL-mediated lipid transport, Xenopus tropicalis" +xref: Reactome:REACT_79044 "HDL-mediated lipid transport, Mus musculus" +xref: Reactome:REACT_79237 "Lipoprotein metabolism, Arabidopsis thaliana" +xref: Reactome:REACT_80334 "HDL-mediated lipid transport, Gallus gallus" +xref: Reactome:REACT_80616 "apolipoprotein(a) + LDL => Lp(a), Mus musculus" +xref: Reactome:REACT_82187 "Lipoprotein metabolism, Sus scrofa" +xref: Reactome:REACT_82188 "Lipoprotein metabolism, Bos taurus" +xref: Reactome:REACT_82533 "Chylomicron-mediated lipid transport, Gallus gallus" +xref: Reactome:REACT_83113 "HDL-mediated lipid transport, Bos taurus" +xref: Reactome:REACT_83971 "HDL-mediated lipid transport, Drosophila melanogaster" +xref: Reactome:REACT_84211 "HDL-mediated lipid transport, Sus scrofa" +xref: Reactome:REACT_84712 "Lipoprotein metabolism, Danio rerio" +xref: Reactome:REACT_85446 "Chylomicron-mediated lipid transport, Danio rerio" +xref: Reactome:REACT_85688 "Lipoprotein metabolism, Canis familiaris" +xref: Reactome:REACT_85772 "HDL-mediated lipid transport, Taeniopygia guttata" +xref: Reactome:REACT_85867 "apolipoprotein(a) + LDL => Lp(a), Taeniopygia guttata" +xref: Reactome:REACT_86142 "Lipoprotein metabolism, Xenopus tropicalis" +xref: Reactome:REACT_87119 "Chylomicron-mediated lipid transport, Canis familiaris" +xref: Reactome:REACT_88173 "Lipoprotein metabolism, Mus musculus" +xref: Reactome:REACT_88824 "Lipoprotein metabolism, Plasmodium falciparum" +xref: Reactome:REACT_90523 "apolipoprotein(a) + LDL => Lp(a), Danio rerio" +xref: Reactome:REACT_90792 "HDL-mediated lipid transport, Oryza sativa" +xref: Reactome:REACT_91134 "Lipoprotein metabolism, Gallus gallus" +xref: Reactome:REACT_91166 "apolipoprotein(a) + LDL => Lp(a), Sus scrofa" +xref: Reactome:REACT_92373 "apolipoprotein(a) + LDL => Lp(a), Bos taurus" +xref: Reactome:REACT_92731 "apolipoprotein(a) + LDL => Lp(a), Canis familiaris" +xref: Reactome:REACT_93774 "HDL-mediated lipid transport, Rattus norvegicus" +xref: Reactome:REACT_96211 "HDL-mediated lipid transport, Plasmodium falciparum" +xref: Reactome:REACT_96602 "Chylomicron-mediated lipid transport, Bos taurus" +xref: Reactome:REACT_97927 "Lipoprotein metabolism, Caenorhabditis elegans" +xref: Reactome:REACT_98591 "Chylomicron-mediated lipid transport, Xenopus tropicalis" +is_a: GO:0019538 ! protein metabolic process + +[Term] +id: GO:0042158 +name: lipoprotein biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." [ISBN:0198506732] +subset: gosubset_prok +synonym: "lipoprotein anabolism" EXACT [] +synonym: "lipoprotein biosynthesis" EXACT [] +synonym: "lipoprotein formation" EXACT [] +synonym: "lipoprotein synthesis" EXACT [] +xref: Reactome:REACT_100834 "nascent chylomicron [endoplasmic reticulum lumen] => nascent chylomicron [extracellular], Mus musculus" +xref: Reactome:REACT_101820 "nascent chylomicron [endoplasmic reticulum lumen] => nascent chylomicron [extracellular], Bos taurus" +xref: Reactome:REACT_103581 "nascent chylomicron [endoplasmic reticulum lumen] => nascent chylomicron [extracellular], Gallus gallus" +xref: Reactome:REACT_107441 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex, Danio rerio" +xref: Reactome:REACT_110066 "ApoB-48:TG:PL complex + 100 triacylglycerols + ApoA-I + ApoA-IV => nascent chylomicron, Canis familiaris" +xref: Reactome:REACT_30241 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex, Rattus norvegicus" +xref: Reactome:REACT_30451 "ApoB-48:TG:PL complex + 100 triacylglycerols + ApoA-I + ApoA-IV => nascent chylomicron, Mus musculus" +xref: Reactome:REACT_31956 "ApoB-48:TG:PL complex + 100 triacylglycerols + ApoA-I + ApoA-IV => nascent chylomicron, Bos taurus" +xref: Reactome:REACT_34229 "nascent chylomicron [endoplasmic reticulum lumen] => nascent chylomicron [extracellular], Canis familiaris" +xref: Reactome:REACT_6813 "nascent chylomicron [endoplasmic reticulum lumen] => nascent chylomicron [extracellular], Homo sapiens" +xref: Reactome:REACT_6908 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex, Homo sapiens" +xref: Reactome:REACT_6915 "ApoB-48:TG:PL complex + 100 triacylglycerols + ApoA-I + ApoA-IV => nascent chylomicron, Homo sapiens" +xref: Reactome:REACT_79155 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex, Canis familiaris" +xref: Reactome:REACT_81934 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex, Xenopus tropicalis" +xref: Reactome:REACT_84235 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex, Mus musculus" +xref: Reactome:REACT_89204 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex, Gallus gallus" +xref: Reactome:REACT_93001 "nascent chylomicron [endoplasmic reticulum lumen] => nascent chylomicron [extracellular], Xenopus tropicalis" +xref: Reactome:REACT_95479 "nascent chylomicron [endoplasmic reticulum lumen] => nascent chylomicron [extracellular], Sus scrofa" +xref: Reactome:REACT_95856 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex, Bos taurus" +xref: Reactome:REACT_98397 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex, Taeniopygia guttata" +is_a: GO:0034645 ! cellular macromolecule biosynthetic process +is_a: GO:0042157 ! lipoprotein metabolic process + +[Term] +id: GO:0042176 +name: regulation of protein catabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators, GOC:jl] +subset: gosubset_prok +synonym: "regulation of protein breakdown" EXACT [] +synonym: "regulation of protein catabolism" EXACT [] +synonym: "regulation of protein degradation" EXACT [] +is_a: GO:0009894 ! regulation of catabolic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030163 ! protein catabolic process +relationship: regulates GO:0030163 ! protein catabolic process + +[Term] +id: GO:0042180 +name: cellular ketone metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:jl, ISBN:0787650153] +subset: goslim_pir +subset: gosubset_prok +synonym: "ketone metabolism" EXACT [] +is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0042181 +name: ketone biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:go_curators] +subset: gosubset_prok +synonym: "ketone anabolism" EXACT [] +synonym: "ketone biosynthesis" EXACT [] +synonym: "ketone formation" EXACT [] +synonym: "ketone synthesis" EXACT [] +is_a: GO:0042180 ! cellular ketone metabolic process +is_a: GO:0044249 ! cellular biosynthetic process +is_a: GO:0044283 ! small molecule biosynthetic process +is_a: GO:1901576 ! organic substance biosynthetic process + +[Term] +id: GO:0042221 +name: response to chemical +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_yeast +subset: gosubset_prok +synonym: "response to chemical stimulus" EXACT [GOC:dos] +synonym: "response to chemical substance" EXACT [] +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0042226 +name: interleukin-6 biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of interleukin-6." [GOC:go_curators] +synonym: "IL-6 biosynthesis" EXACT [] +synonym: "IL-6 biosynthetic process" EXACT [] +synonym: "interleukin-6 anabolism" EXACT [] +synonym: "interleukin-6 biosynthesis" EXACT [] +synonym: "interleukin-6 formation" EXACT [] +synonym: "interleukin-6 synthesis" EXACT [] +is_a: GO:0042089 ! cytokine biosynthetic process +relationship: part_of GO:0032635 ! interleukin-6 production + +[Term] +id: GO:0042246 +name: tissue regeneration +namespace: biological_process +def: "The regrowth of lost or destroyed tissues." [GOC:curators] +is_a: GO:0009888 ! tissue development +is_a: GO:0031099 ! regeneration +is_a: GO:0048589 ! developmental growth +relationship: part_of GO:0042060 ! wound healing + +[Term] +id: GO:0042249 +name: establishment of planar polarity of embryonic epithelium +namespace: biological_process +def: "Coordinated organization of groups of cells in the plane of an embryonic epithelium, such that they all orient to similar coordinates." [GOC:ascb_2009, GOC:dph, GOC:jl, GOC:tb] +is_a: GO:0001736 ! establishment of planar polarity + +[Term] +id: GO:0042278 +name: purine nucleoside metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:jl, ISBN:0140512713] +subset: gosubset_prok +synonym: "purine metabolic process" BROAD [] +synonym: "purine metabolism" BROAD [] +synonym: "purine nucleoside metabolism" EXACT [] +is_a: GO:0009116 ! nucleoside metabolic process +is_a: GO:0072521 ! purine-containing compound metabolic process + +[Term] +id: GO:0042297 +name: vocal learning +namespace: biological_process +def: "A behavioral process whose outcome is a relatively long-lasting adaptive behavioral change whereby an organism modifies innate vocalizations to imitate or create new sounds." [PMID:16418265, PMID:17035521] +xref: Wikipedia:Vocal_learning +is_a: GO:0007612 ! learning +is_a: GO:0031223 ! auditory behavior + +[Term] +id: GO:0042303 +name: molting cycle +namespace: biological_process +def: "The periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin, etc." [GOC:jl, ISBN:0198506732] +subset: goslim_pir +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0042306 +name: regulation of protein import into nucleus +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of movement of proteins from the cytoplasm to the nucleus." [GOC:jl] +synonym: "regulation of protein import into cell nucleus" EXACT [] +synonym: "regulation of protein transport from cytoplasm to nucleus" EXACT [] +synonym: "regulation of protein-nucleus import" EXACT [] +is_a: GO:0033157 ! regulation of intracellular protein transport +is_a: GO:0046822 ! regulation of nucleocytoplasmic transport +is_a: GO:1900180 ! regulation of protein localization to nucleus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006606 ! protein import into nucleus +relationship: regulates GO:0006606 ! protein import into nucleus + +[Term] +id: GO:0042307 +name: positive regulation of protein import into nucleus +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus." [GOC:jl] +synonym: "activation of protein import into nucleus" NARROW [] +synonym: "positive regulation of protein import into cell nucleus" EXACT [] +synonym: "positive regulation of protein transport from cytoplasm to nucleus" EXACT [] +synonym: "positive regulation of protein-nucleus import" EXACT [] +synonym: "stimulation of protein import into nucleus" NARROW [] +synonym: "up regulation of protein import into nucleus" EXACT [] +synonym: "up-regulation of protein import into nucleus" EXACT [] +synonym: "upregulation of protein import into nucleus" EXACT [] +is_a: GO:0042306 ! regulation of protein import into nucleus +is_a: GO:0046824 ! positive regulation of nucleocytoplasmic transport +is_a: GO:0090316 ! positive regulation of intracellular protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006606 ! protein import into nucleus +relationship: positively_regulates GO:0006606 ! protein import into nucleus + +[Term] +id: GO:0042308 +name: negative regulation of protein import into nucleus +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus." [GOC:jl] +synonym: "down regulation of protein import into nucleus" EXACT [] +synonym: "down-regulation of protein import into nucleus" EXACT [] +synonym: "downregulation of protein import into nucleus" EXACT [] +synonym: "inhibition of protein import into nucleus" NARROW [] +synonym: "negative regulation of protein import into cell nucleus" EXACT [] +synonym: "negative regulation of protein transport from cytoplasm to nucleus" EXACT [] +synonym: "negative regulation of protein-nucleus import" EXACT [] +is_a: GO:0042306 ! regulation of protein import into nucleus +is_a: GO:0046823 ! negative regulation of nucleocytoplasmic transport +is_a: GO:0090317 ! negative regulation of intracellular protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006606 ! protein import into nucleus +relationship: negatively_regulates GO:0006606 ! protein import into nucleus + +[Term] +id: GO:0042325 +name: regulation of phosphorylation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule." [GOC:jl] +subset: gosubset_prok +is_a: GO:0019220 ! regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016310 ! phosphorylation +relationship: regulates GO:0016310 ! phosphorylation + +[Term] +id: GO:0042326 +name: negative regulation of phosphorylation +namespace: biological_process +def: "Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule." [GOC:jl] +subset: gosubset_prok +synonym: "down regulation of phosphorylation" EXACT [] +synonym: "down-regulation of phosphorylation" EXACT [] +synonym: "downregulation of phosphorylation" EXACT [] +synonym: "inhibition of phosphorylation" NARROW [] +is_a: GO:0042325 ! regulation of phosphorylation +is_a: GO:0045936 ! negative regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016310 ! phosphorylation +relationship: negatively_regulates GO:0016310 ! phosphorylation + +[Term] +id: GO:0042327 +name: positive regulation of phosphorylation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule." [GOC:jl] +subset: gosubset_prok +synonym: "activation of phosphorylation" NARROW [] +synonym: "stimulation of phosphorylation" NARROW [] +synonym: "up regulation of phosphorylation" EXACT [] +synonym: "up-regulation of phosphorylation" EXACT [] +synonym: "upregulation of phosphorylation" EXACT [] +is_a: GO:0042325 ! regulation of phosphorylation +is_a: GO:0045937 ! positive regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016310 ! phosphorylation +relationship: positively_regulates GO:0016310 ! phosphorylation + +[Term] +id: GO:0042330 +name: taxis +namespace: biological_process +def: "The directed movement of a motile cell or organism in response to an external stimulus." [GOC:jl, ISBN:0192801023] +subset: gosubset_prok +synonym: "directed movement in response to stimulus" EXACT [] +xref: Wikipedia:Taxis +is_a: GO:0009605 ! response to external stimulus +is_a: GO:0040011 ! locomotion + +[Term] +id: GO:0042384 +name: cilium assembly +namespace: biological_process +def: "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:kmv, ISBN:0198506732] +comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. +synonym: "ciliogenesis" EXACT [] +synonym: "cilium biogenesis" RELATED [GOC:mah] +synonym: "microtubule-based flagellum assembly" EXACT [] +is_a: GO:0010927 ! cellular component assembly involved in morphogenesis +is_a: GO:0030031 ! cell projection assembly +is_a: GO:0044782 ! cilium organization +is_a: GO:0070925 ! organelle assembly +relationship: part_of GO:0060271 ! cilium morphogenesis + +[Term] +id: GO:0042391 +name: regulation of membrane potential +namespace: biological_process +def: "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732] +subset: gosubset_prok +is_a: GO:0065008 ! regulation of biological quality + +[Term] +id: GO:0042445 +name: hormone metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [CHEBI:24621, GOC:jl] +subset: goslim_pir +subset: gosubset_prok +synonym: "hormone metabolism" EXACT [] +is_a: GO:0008152 ! metabolic process +is_a: GO:0010817 ! regulation of hormone levels + +[Term] +id: GO:0042446 +name: hormone biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [CHEBI:24621, GOC:jl] +subset: gosubset_prok +synonym: "hormone anabolism" EXACT [] +synonym: "hormone biosynthesis" EXACT [] +synonym: "hormone formation" EXACT [] +synonym: "hormone synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0042445 ! hormone metabolic process + +[Term] +id: GO:0042454 +name: ribonucleoside catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of any ribonucleoside, a nucleoside in which purine or pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule." [CHEBI:18254, GOC:jl] +subset: gosubset_prok +synonym: "ribonucleoside breakdown" EXACT [] +synonym: "ribonucleoside catabolism" EXACT [] +synonym: "ribonucleoside degradation" EXACT [] +is_a: GO:0009119 ! ribonucleoside metabolic process +is_a: GO:0009164 ! nucleoside catabolic process + +[Term] +id: GO:0042471 +name: ear morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the ear are generated and organized. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." [GOC:jl, ISBN:0192801023] +synonym: "hearing organ morphogenesis" EXACT [] +is_a: GO:0048562 ! embryonic organ morphogenesis +relationship: part_of GO:0043583 ! ear development + +[Term] +id: GO:0042472 +name: inner ear morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively." [GOC:jl, ISBN:0192801023] +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0042471 ! ear morphogenesis +relationship: part_of GO:0048839 ! inner ear development + +[Term] +id: GO:0042475 +name: odontogenesis of dentin-containing tooth +namespace: biological_process +def: "The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel." [GOC:cjm, GOC:mah, GOC:mtg_sensu, PMID:10333884, PMID:15355794] +comment: Note that placoid scales found in the cartilaginous fishes presumably develop through the same processes, but are found on the dermis, rather than in the mouth or pharynx. See http://en.wikipedia.org/wiki/Placoid_scale#Placoid_scales. +synonym: "odontogenesis of dentine-containing teeth" EXACT [] +synonym: "odontogenesis of dentine-containing tooth" EXACT [GOC:mah] +synonym: "odontogeny" BROAD [] +synonym: "odontosis" BROAD [] +synonym: "tooth development" BROAD [] +is_a: GO:0042476 ! odontogenesis + +[Term] +id: GO:0042476 +name: odontogenesis +namespace: biological_process +alt_id: GO:0042477 +def: "The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food." [GOC:jl, GOC:mah] +synonym: "odontogenesis of calcareous or chitinous tooth" NARROW [] +synonym: "odontogeny" EXACT [] +synonym: "odontosis" EXACT [] +synonym: "tooth development" EXACT [] +xref: Wikipedia:Odontogenesis +is_a: GO:0009887 ! organ morphogenesis + +[Term] +id: GO:0042493 +name: response to drug +namespace: biological_process +alt_id: GO:0017035 +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease." [GOC:jl] +subset: goslim_candida +subset: gosubset_prok +synonym: "drug resistance" RELATED [] +synonym: "drug susceptibility/resistance" RELATED [] +is_a: GO:0042221 ! response to chemical + +[Term] +id: GO:0042552 +name: myelination +namespace: biological_process +def: "The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier." [GOC:dgh, GOC:mah] +xref: Wikipedia:Myelin +is_a: GO:0008366 ! axon ensheathment + +[Term] +id: GO:0042562 +name: hormone binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of other cells possessing functional receptors for the hormone." [CHEBI:24621, GOC:jl] +subset: goslim_pir +is_a: GO:0005488 ! binding + +[Term] +id: GO:0042592 +name: homeostatic process +namespace: biological_process +def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "homeostasis" RELATED [] +is_a: GO:0065008 ! regulation of biological quality + +[Term] +id: GO:0042593 +name: glucose homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of glucose within an organism or cell." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0033500 ! carbohydrate homeostasis + +[Term] +id: GO:0042632 +name: cholesterol homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell." [GOC:go_curators] +is_a: GO:0055092 ! sterol homeostasis + +[Term] +id: GO:0042633 +name: hair cycle +namespace: biological_process +def: "The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:go_curators, PMID:12230507] +is_a: GO:0042303 ! molting cycle + +[Term] +id: GO:0042659 +name: regulation of cell fate specification +namespace: biological_process +def: "Any process that mediates the adoption of a specific fate by a cell." [GOC:go_curators] +is_a: GO:0010453 ! regulation of cell fate commitment +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001708 ! cell fate specification +relationship: regulates GO:0001708 ! cell fate specification + +[Term] +id: GO:0042660 +name: positive regulation of cell fate specification +namespace: biological_process +def: "Any process that activates or enables a cell to adopt a specific fate." [GOC:go_curators] +synonym: "activation of cell fate specification" NARROW [] +synonym: "stimulation of cell fate specification" NARROW [] +synonym: "up regulation of cell fate specification" EXACT [] +synonym: "up-regulation of cell fate specification" EXACT [] +synonym: "upregulation of cell fate specification" EXACT [] +is_a: GO:0042659 ! regulation of cell fate specification +is_a: GO:0045597 ! positive regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001708 ! cell fate specification +relationship: positively_regulates GO:0001708 ! cell fate specification + +[Term] +id: GO:0042661 +name: regulation of mesodermal cell fate specification +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of mesoderm cell fate specification." [GOC:go_curators] +is_a: GO:0010470 ! regulation of gastrulation +is_a: GO:0042659 ! regulation of cell fate specification +is_a: GO:2000027 ! regulation of organ morphogenesis +is_a: GO:2000380 ! regulation of mesoderm development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007501 ! mesodermal cell fate specification +relationship: regulates GO:0007501 ! mesodermal cell fate specification + +[Term] +id: GO:0042662 +name: negative regulation of mesodermal cell fate specification +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mesoderm cell fate specification." [GOC:go_curators] +synonym: "down regulation of mesodermal cell fate specification" EXACT [] +synonym: "down-regulation of mesodermal cell fate specification" EXACT [] +synonym: "downregulation of mesodermal cell fate specification" EXACT [] +synonym: "inhibition of mesodermal cell fate specification" NARROW [] +synonym: "suppression of mesodermal cell fate" EXACT [] +is_a: GO:0009996 ! negative regulation of cell fate specification +is_a: GO:0042661 ! regulation of mesodermal cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007501 ! mesodermal cell fate specification +relationship: negatively_regulates GO:0007501 ! mesodermal cell fate specification + +[Term] +id: GO:0042684 +name: cardioblast cell fate commitment +namespace: biological_process +def: "The process in which a cell becomes committed to becoming a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators] +is_a: GO:0060911 ! cardiac cell fate commitment +relationship: part_of GO:0010002 ! cardioblast differentiation + +[Term] +id: GO:0042685 +name: cardioblast cell fate specification +namespace: biological_process +def: "The process in which a cell becomes capable of differentiating autonomously into a cardioblast cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators] +is_a: GO:0060912 ! cardiac cell fate specification +relationship: part_of GO:0042684 ! cardioblast cell fate commitment + +[Term] +id: GO:0042686 +name: regulation of cardioblast cell fate specification +namespace: biological_process +def: "Any process that mediates the specification of a cell into a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators] +is_a: GO:0051890 ! regulation of cardioblast differentiation +is_a: GO:2000043 ! regulation of cardiac cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042685 ! cardioblast cell fate specification +relationship: regulates GO:0042685 ! cardioblast cell fate specification + +[Term] +id: GO:0042692 +name: muscle cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a muscle cell." [CL:0000187, GOC:go_curators] +xref: Reactome:REACT_109683 "Myogenesis, Rattus norvegicus" +xref: Reactome:REACT_113484 "Myogenesis, Caenorhabditis elegans" +xref: Reactome:REACT_21303 "Myogenesis, Homo sapiens" +xref: Reactome:REACT_32665 "Myogenesis, Danio rerio" +xref: Reactome:REACT_34056 "Myogenesis, Canis familiaris" +xref: Reactome:REACT_77596 "Myogenesis, Sus scrofa" +xref: Reactome:REACT_84060 "Myogenesis, Gallus gallus" +xref: Reactome:REACT_84715 "Myogenesis, Drosophila melanogaster" +xref: Reactome:REACT_85310 "Myogenesis, Taeniopygia guttata" +xref: Reactome:REACT_90630 "Myogenesis, Bos taurus" +xref: Reactome:REACT_95727 "Myogenesis, Mus musculus" +xref: Reactome:REACT_95839 "Myogenesis, Xenopus tropicalis" +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0061061 ! muscle structure development + +[Term] +id: GO:0042693 +name: muscle cell fate commitment +namespace: biological_process +def: "The process in which the cellular identity of muscle cells is acquired and determined." [CL:0000187, GOC:go_curators] +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0042695 +name: thelarche +namespace: biological_process +def: "The beginning of development of the breasts in the female." [GOC:curators, PMID:19117864] +xref: Wikipedia:Thelarche +is_a: GO:0046543 ! development of secondary female sexual characteristics +relationship: part_of GO:0030879 ! mammary gland development + +[Term] +id: GO:0042698 +name: ovulation cycle +namespace: biological_process +def: "The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years." [ISBN:0721662544] +synonym: "estrous cycle" RELATED [] +synonym: "menstrual cycle" RELATED [] +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048511 ! rhythmic process +is_a: GO:0048609 ! multicellular organismal reproductive process + +[Term] +id: GO:0042733 +name: embryonic digit morphogenesis +namespace: biological_process +def: "The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe." [GOC:bf, GOC:jl, UBERON:0002544] +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0030326 ! embryonic limb morphogenesis + +[Term] +id: GO:0042762 +name: regulation of sulfur metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of sulfur metabolism" EXACT [] +synonym: "regulation of sulphur metabolic process" EXACT [] +synonym: "regulation of sulphur metabolism" EXACT [] +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006790 ! sulfur compound metabolic process +relationship: regulates GO:0006790 ! sulfur compound metabolic process + +[Term] +id: GO:0042770 +name: signal transduction in response to DNA damage +namespace: biological_process +def: "A cascade of processes induced by the detection of DNA damage within a cell." [GOC:go_curators] +synonym: "DNA damage response, signal transduction" EXACT [GOC:curators] +synonym: "response to DNA damage stimulus by intracellular signaling cascade" EXACT [GOC:dph, GOC:tb] +is_a: GO:0006974 ! cellular response to DNA damage stimulus +is_a: GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0042787 +name: protein ubiquitination involved in ubiquitin-dependent protein catabolic process +namespace: biological_process +alt_id: GO:0043432 +def: "The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein." [GOC:go_curators] +synonym: "myofibrillar protein ubiquitination during ubiquitin-dependent protein breakdown" NARROW [] +synonym: "myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolic process" NARROW [] +synonym: "myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolism" NARROW [] +synonym: "myofibrillar protein ubiquitination during ubiquitin-dependent protein degradation" NARROW [] +synonym: "protein degradation tagging activity" RELATED [] +synonym: "protein ubiquitination during ubiquitin-dependent protein breakdown" EXACT [] +synonym: "protein ubiquitination during ubiquitin-dependent protein catabolic process" RELATED [GOC:dph, GOC:tb] +synonym: "protein ubiquitination during ubiquitin-dependent protein catabolism" EXACT [] +synonym: "protein ubiquitination during ubiquitin-dependent protein degradation" EXACT [] +synonym: "protein ubiquitinylation during ubiquitin-dependent protein catabolic process" EXACT [] +synonym: "protein ubiquitinylation during ubiquitin-dependent protein catabolism" EXACT [] +synonym: "protein ubiquitylation during ubiquitin-dependent protein catabolic process" EXACT [] +synonym: "protein ubiquitylation during ubiquitin-dependent protein catabolism" EXACT [] +xref: Reactome:REACT_100004 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Canis familiaris" +xref: Reactome:REACT_100823 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Mus musculus" +xref: Reactome:REACT_101110 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Mus musculus" +xref: Reactome:REACT_103809 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Xenopus tropicalis" +xref: Reactome:REACT_104518 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Taeniopygia guttata" +xref: Reactome:REACT_105370 "Multiubiquitination of APC/C-associated Cdh1, Danio rerio" +xref: Reactome:REACT_105620 "Multiubiquitination of APC/C-associated Cdh1, Taeniopygia guttata" +xref: Reactome:REACT_106156 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Rattus norvegicus" +xref: Reactome:REACT_106906 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Xenopus tropicalis" +xref: Reactome:REACT_107379 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Xenopus tropicalis" +xref: Reactome:REACT_107829 "Multiubiquitination of APC/C-associated Cdh1, Rattus norvegicus" +xref: Reactome:REACT_108446 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Danio rerio" +xref: Reactome:REACT_108589 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Mus musculus" +xref: Reactome:REACT_109071 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Drosophila melanogaster" +xref: Reactome:REACT_110158 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Gallus gallus" +xref: Reactome:REACT_114376 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Oryza sativa" +xref: Reactome:REACT_28669 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Drosophila melanogaster" +xref: Reactome:REACT_30747 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Bos taurus" +xref: Reactome:REACT_31985 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Danio rerio" +xref: Reactome:REACT_32728 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Gallus gallus" +xref: Reactome:REACT_32748 "Multiubiquitination of APC/C-associated Cdh1, Mus musculus" +xref: Reactome:REACT_33468 "Multiubiquitination of APC/C-associated Cdh1, Bos taurus" +xref: Reactome:REACT_6723 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Homo sapiens" +xref: Reactome:REACT_6735 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Homo sapiens" +xref: Reactome:REACT_6791 "Multiubiquitination of APC/C-associated Cdh1, Homo sapiens" +xref: Reactome:REACT_6824 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Homo sapiens" +xref: Reactome:REACT_6914 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Homo sapiens" +xref: Reactome:REACT_77058 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Bos taurus" +xref: Reactome:REACT_78216 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Rattus norvegicus" +xref: Reactome:REACT_78475 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Taeniopygia guttata" +xref: Reactome:REACT_79393 "Multiubiquitination of APC/C-associated Cdh1, Drosophila melanogaster" +xref: Reactome:REACT_79773 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Xenopus tropicalis" +xref: Reactome:REACT_79781 "Multiubiquitination of APC/C-associated Cdh1, Oryza sativa" +xref: Reactome:REACT_80157 "Multiubiquitination of APC/C-associated Cdh1, Xenopus tropicalis" +xref: Reactome:REACT_80243 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Taeniopygia guttata" +xref: Reactome:REACT_81796 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Canis familiaris" +xref: Reactome:REACT_81809 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Gallus gallus" +xref: Reactome:REACT_85194 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Drosophila melanogaster" +xref: Reactome:REACT_86043 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Danio rerio" +xref: Reactome:REACT_87217 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Gallus gallus" +xref: Reactome:REACT_87349 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Taeniopygia guttata" +xref: Reactome:REACT_89066 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex, Mus musculus" +xref: Reactome:REACT_91216 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Oryza sativa" +xref: Reactome:REACT_91336 "Multiubiquitination of APC/C-associated Cdh1, Gallus gallus" +xref: Reactome:REACT_91686 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Bos taurus" +xref: Reactome:REACT_91885 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Rattus norvegicus" +xref: Reactome:REACT_92341 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Dictyostelium discoideum" +xref: Reactome:REACT_92878 "Multiubiquitination of APC/C-associated Cdh1, Canis familiaris" +xref: Reactome:REACT_94687 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Bos taurus" +xref: Reactome:REACT_94864 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex, Canis familiaris" +xref: Reactome:REACT_95501 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex, Canis familiaris" +xref: Reactome:REACT_97971 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Drosophila melanogaster" +xref: Reactome:REACT_98894 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Rattus norvegicus" +xref: Reactome:REACT_99825 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex, Danio rerio" +is_a: GO:0016567 ! protein ubiquitination +intersection_of: GO:0016567 ! protein ubiquitination +intersection_of: part_of GO:0006511 ! ubiquitin-dependent protein catabolic process +relationship: part_of GO:0006511 ! ubiquitin-dependent protein catabolic process + +[Term] +id: GO:0042802 +name: identical protein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an identical protein or proteins." [GOC:jl] +subset: gosubset_prok +synonym: "isoform-specific homophilic binding" EXACT [PMID:17889655] +synonym: "protein homopolymerization" RELATED [] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0042803 +name: protein homodimerization activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC:jl] +subset: gosubset_prok +synonym: "dimerization activity" BROAD [] +is_a: GO:0042802 ! identical protein binding +is_a: GO:0046983 ! protein dimerization activity + +[Term] +id: GO:0042813 +name: Wnt-activated receptor activity +namespace: molecular_function +def: "Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:go_curators] +synonym: "frizzled receptor activity" RELATED [] +synonym: "frizzled-2 receptor activity" RELATED [] +synonym: "Wnt receptor activity" EXACT [GOC:bf, GOC:signaling] +is_a: GO:0004888 ! transmembrane signaling receptor activity +relationship: has_part GO:0017147 ! Wnt-protein binding + +[Term] +id: GO:0042886 +name: amide transport +namespace: biological_process +def: "The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0198506732] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0044765 ! single-organism transport +is_a: GO:0071705 ! nitrogen compound transport + +[Term] +id: GO:0042953 +name: lipoprotein transport +namespace: biological_process +def: "The directed movement of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0198506732] +subset: gosubset_prok +is_a: GO:0015031 ! protein transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0042954 +name: lipoprotein transporter activity +namespace: molecular_function +def: "Enables the directed movement of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids, into, out of or within a cell, or between cells." [GOC:jl, ISBN:0198506732] +subset: gosubset_prok +is_a: GO:0008565 ! protein transporter activity +relationship: part_of GO:0042953 ! lipoprotein transport + +[Term] +id: GO:0042981 +name: regulation of apoptotic process +namespace: biological_process +def: "Any process that modulates the occurrence or rate of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] +comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. +synonym: "apoptosis regulator activity" RELATED [] +synonym: "regulation of apoptosis" NARROW [] +xref: Reactome:REACT_106248 "Regulation of Apoptosis, Mus musculus" +xref: Reactome:REACT_109234 "Regulation of Apoptosis, Rattus norvegicus" +xref: Reactome:REACT_109339 "Regulation of Apoptosis, Sus scrofa" +xref: Reactome:REACT_13648 "Regulation of Apoptosis, Homo sapiens" +xref: Reactome:REACT_29911 "Regulation of Apoptosis, Danio rerio" +xref: Reactome:REACT_30641 "Regulation of Apoptosis, Drosophila melanogaster" +xref: Reactome:REACT_79698 "Regulation of Apoptosis, Taeniopygia guttata" +xref: Reactome:REACT_85908 "Regulation of Apoptosis, Bos taurus" +xref: Reactome:REACT_86575 "Regulation of Apoptosis, Xenopus tropicalis" +xref: Reactome:REACT_95946 "Regulation of Apoptosis, Caenorhabditis elegans" +xref: Reactome:REACT_96201 "Regulation of Apoptosis, Canis familiaris" +xref: Reactome:REACT_99944 "Regulation of Apoptosis, Gallus gallus" +is_a: GO:0043067 ! regulation of programmed cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006915 ! apoptotic process +relationship: regulates GO:0006915 ! apoptotic process + +[Term] +id: GO:0042995 +name: cell projection +namespace: cellular_component +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +subset: goslim_pir +subset: gosubset_prok +synonym: "cell process" BROAD [] +synonym: "cellular process" BROAD [] +synonym: "cellular projection" EXACT [] +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0043005 +name: neuron projection +namespace: cellular_component +def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +subset: goslim_pir +synonym: "neurite" NARROW [] +synonym: "neuron process" EXACT [] +synonym: "neuron protrusion" EXACT [] +synonym: "neuronal cell projection" EXACT [] +xref: NIF_Subcellular:sao-867568886 +is_a: GO:0042995 ! cell projection +is_a: GO:0097458 ! neuron part + +[Term] +id: GO:0043009 +name: chordate embryonic development +namespace: biological_process +def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] +is_a: GO:0009792 ! embryo development ending in birth or egg hatching + +[Term] +id: GO:0043010 +name: camera-type eye development +namespace: biological_process +alt_id: GO:0001747 +alt_id: GO:0031075 +def: "The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field." [GOC:go_curators, GOC:mtg_sensu] +is_a: GO:0001654 ! eye development + +[Term] +id: GO:0043025 +name: neuronal cell body +namespace: cellular_component +def: "The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites." [GOC:go_curators] +comment: Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections. +subset: goslim_pir +synonym: "neuron cell body" EXACT [] +synonym: "neuronal cell soma" EXACT [] +xref: NIF_Subcellular:sao1044911821 +xref: Wikipedia:Soma_(biology) +is_a: GO:0044297 ! cell body +is_a: GO:0097458 ! neuron part + +[Term] +id: GO:0043028 +name: cysteine-type endopeptidase regulator activity involved in apoptotic process +namespace: molecular_function +def: "Modulates the activity of a cysteine-type endopeptidase involved in the apoptotic process." [GOC:jl, GOC:mtg_apoptosis, PMID:14744432, Wikipedia:Caspase] +synonym: "caspase regulator activity" BROAD [] +xref: Reactome:REACT_102937 "p75NTR:NADE promotes caspase2/3 activation, Rattus norvegicus" +xref: Reactome:REACT_103522 "p75NTR:NADE promotes caspase2/3 activation, Mus musculus" +xref: Reactome:REACT_108417 "p75NTR:NADE promotes caspase2/3 activation, Canis familiaris" +xref: Reactome:REACT_13533 "p75NTR:NADE promotes caspase2/3 activation, Homo sapiens" +xref: Reactome:REACT_32934 "p75NTR:NADE promotes caspase2/3 activation, Sus scrofa" +xref: Reactome:REACT_89561 "p75NTR:NADE promotes caspase2/3 activation, Bos taurus" +is_a: GO:0030234 ! enzyme regulator activity +relationship: part_of GO:0043281 ! regulation of cysteine-type endopeptidase activity involved in apoptotic process + +[Term] +id: GO:0043030 +name: regulation of macrophage activation +namespace: biological_process +def: "Any process that modulates the frequency or rate of macrophage activation." [GOC:jl] +is_a: GO:0002694 ! regulation of leukocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042116 ! macrophage activation +relationship: regulates GO:0042116 ! macrophage activation + +[Term] +id: GO:0043032 +name: positive regulation of macrophage activation +namespace: biological_process +def: "Any process that stimulates, induces or increases the rate of macrophage activation." [GOC:jl] +synonym: "activation of macrophage activation" NARROW [] +synonym: "stimulation of macrophage activation" NARROW [] +synonym: "up regulation of macrophage activation" EXACT [] +synonym: "up-regulation of macrophage activation" EXACT [] +synonym: "upregulation of macrophage activation" EXACT [] +is_a: GO:0002696 ! positive regulation of leukocyte activation +is_a: GO:0043030 ! regulation of macrophage activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042116 ! macrophage activation +relationship: positively_regulates GO:0042116 ! macrophage activation + +[Term] +id: GO:0043049 +name: otic placode formation +namespace: biological_process +def: "The initial developmental process that will lead to the formation of the vertebrate inner ear. The otic placode forms as a thickening of the head ectoderm adjacent to the developing hindbrain." [GOC:go_curators, PMID:12668634] +is_a: GO:0060788 ! ectodermal placode formation +relationship: part_of GO:0030916 ! otic vesicle formation + +[Term] +id: GO:0043062 +name: extracellular structure organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] +subset: goslim_pir +subset: gosubset_prok +synonym: "extracellular structure organisation" EXACT [GOC:curators] +synonym: "extracellular structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0043065 +name: positive regulation of apoptotic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] +comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is positively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. +synonym: "activation of apoptosis" NARROW [] +synonym: "positive regulation of apoptosis" NARROW [] +synonym: "pro-apoptosis" RELATED [] +synonym: "stimulation of apoptosis" NARROW [] +synonym: "up regulation of apoptosis" EXACT [] +synonym: "up-regulation of apoptosis" EXACT [] +synonym: "upregulation of apoptosis" EXACT [] +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:0043068 ! positive regulation of programmed cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006915 ! apoptotic process +relationship: positively_regulates GO:0006915 ! apoptotic process + +[Term] +id: GO:0043066 +name: negative regulation of apoptotic process +namespace: biological_process +alt_id: GO:0006916 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] +comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. +synonym: "anti-apoptosis" EXACT [] +synonym: "apoptosis inhibitor activity" RELATED [] +synonym: "down regulation of apoptosis" EXACT [] +synonym: "down-regulation of apoptosis" EXACT [] +synonym: "downregulation of apoptosis" EXACT [] +synonym: "inhibition of apoptosis" NARROW [] +synonym: "negative regulation of apoptosis" NARROW [] +synonym: "pro-survival" RELATED [] +xref: Reactome:REACT_13537 "p75NTR signals via NF-kB, Homo sapiens" +xref: Reactome:REACT_29981 "p75NTR signals via NF-kB, Canis familiaris" +xref: Reactome:REACT_77563 "p75NTR signals via NF-kB, Sus scrofa" +xref: Reactome:REACT_81263 "p75NTR signals via NF-kB, Taeniopygia guttata" +xref: Reactome:REACT_83278 "p75NTR signals via NF-kB, Drosophila melanogaster" +xref: Reactome:REACT_84567 "p75NTR signals via NF-kB, Gallus gallus" +xref: Reactome:REACT_91585 "p75NTR signals via NF-kB, Danio rerio" +xref: Reactome:REACT_93662 "p75NTR signals via NF-kB, Rattus norvegicus" +xref: Reactome:REACT_95215 "p75NTR signals via NF-kB, Mus musculus" +xref: Reactome:REACT_95867 "p75NTR signals via NF-kB, Xenopus tropicalis" +xref: Reactome:REACT_98500 "p75NTR signals via NF-kB, Bos taurus" +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:0043069 ! negative regulation of programmed cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006915 ! apoptotic process +relationship: negatively_regulates GO:0006915 ! apoptotic process + +[Term] +id: GO:0043067 +name: regulation of programmed cell death +namespace: biological_process +alt_id: GO:0043070 +def: "Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] +synonym: "regulation of non-apoptotic programmed cell death" NARROW [] +is_a: GO:0010941 ! regulation of cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0012501 ! programmed cell death +relationship: regulates GO:0012501 ! programmed cell death + +[Term] +id: GO:0043068 +name: positive regulation of programmed cell death +namespace: biological_process +alt_id: GO:0043071 +def: "Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] +synonym: "activation of programmed cell death" NARROW [] +synonym: "positive regulation of non-apoptotic programmed cell death" NARROW [] +synonym: "stimulation of programmed cell death" NARROW [] +synonym: "up regulation of programmed cell death" EXACT [] +synonym: "up-regulation of programmed cell death" EXACT [] +synonym: "upregulation of programmed cell death" EXACT [] +is_a: GO:0010942 ! positive regulation of cell death +is_a: GO:0043067 ! regulation of programmed cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0012501 ! programmed cell death +relationship: positively_regulates GO:0012501 ! programmed cell death + +[Term] +id: GO:0043069 +name: negative regulation of programmed cell death +namespace: biological_process +alt_id: GO:0043072 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] +synonym: "down regulation of programmed cell death" EXACT [] +synonym: "down-regulation of programmed cell death" EXACT [] +synonym: "downregulation of programmed cell death" EXACT [] +synonym: "inhibition of programmed cell death" NARROW [] +synonym: "negative regulation of non-apoptotic programmed cell death" NARROW [] +is_a: GO:0043067 ! regulation of programmed cell death +is_a: GO:0060548 ! negative regulation of cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0012501 ! programmed cell death +relationship: negatively_regulates GO:0012501 ! programmed cell death + +[Term] +id: GO:0043085 +name: positive regulation of catalytic activity +namespace: biological_process +def: "Any process that activates or increases the activity of an enzyme." [GOC:jl, GOC:tb] +subset: gosubset_prok +synonym: "activation of enzyme activity" NARROW [] +synonym: "positive regulation of enzyme activity" EXACT [GOC:tb] +synonym: "stimulation of enzyme activity" NARROW [] +synonym: "up regulation of enzyme activity" EXACT [] +synonym: "up-regulation of enzyme activity" EXACT [] +synonym: "upregulation of enzyme activity" EXACT [] +is_a: GO:0044093 ! positive regulation of molecular function +is_a: GO:0050790 ! regulation of catalytic activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0003824 ! catalytic activity +relationship: positively_regulates GO:0003824 ! catalytic activity + +[Term] +id: GO:0043086 +name: negative regulation of catalytic activity +namespace: biological_process +def: "Any process that stops or reduces the activity of an enzyme." [GOC:jl, GOC:tb] +subset: gosubset_prok +synonym: "down regulation of enzyme activity" EXACT [] +synonym: "down-regulation of enzyme activity" EXACT [] +synonym: "downregulation of enzyme activity" EXACT [] +synonym: "inhibition of enzyme activity" NARROW [] +synonym: "negative regulation of enzyme activity" EXACT [GOC:tb] +is_a: GO:0044092 ! negative regulation of molecular function +is_a: GO:0050790 ! regulation of catalytic activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003824 ! catalytic activity +relationship: negatively_regulates GO:0003824 ! catalytic activity + +[Term] +id: GO:0043087 +name: regulation of GTPase activity +namespace: biological_process +def: "Any process that modulates the rate of GTP hydrolysis by a GTPase." [GOC:jl] +subset: gosubset_prok +is_a: GO:0033124 ! regulation of GTP catabolic process +is_a: GO:0051336 ! regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003924 ! GTPase activity +relationship: regulates GO:0003924 ! GTPase activity + +[Term] +id: GO:0043112 +name: receptor metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:jl] +subset: gosubset_prok +synonym: "receptor metabolism" EXACT [] +is_a: GO:0044260 ! cellular macromolecule metabolic process + +[Term] +id: GO:0043113 +name: receptor clustering +namespace: biological_process +def: "The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response." [GOC:bf, GOC:jl, GOC:pr, PMID:19747931, PMID:21453460] +is_a: GO:0072657 ! protein localization to membrane + +[Term] +id: GO:0043114 +name: regulation of vascular permeability +namespace: biological_process +def: "Any process that modulates the extent to which blood vessels can be pervaded by fluid." [GOC:jl] +is_a: GO:0003018 ! vascular process in circulatory system +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0008015 ! blood circulation + +[Term] +id: GO:0043122 +name: regulation of I-kappaB kinase/NF-kappaB signaling +namespace: biological_process +def: "Any process that modulates I-kappaB kinase/NF-kappaB signaling." [GOC:jl, PMID:12773372] +synonym: "regulation of I-kappaB kinase/NF-kappaB cascade" RELATED [GOC:signaling] +is_a: GO:1902531 ! regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007249 ! I-kappaB kinase/NF-kappaB signaling +relationship: regulates GO:0007249 ! I-kappaB kinase/NF-kappaB signaling + +[Term] +id: GO:0043123 +name: positive regulation of I-kappaB kinase/NF-kappaB signaling +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling." [GOC:jl] +synonym: "activation of I-kappaB kinase/NF-kappaB cascade" RELATED [] +synonym: "positive regulation of I-kappaB kinase/NF-kappaB cascade" RELATED [GOC:signaling] +synonym: "stimulation of I-kappaB kinase/NF-kappaB cascade" NARROW [] +synonym: "up regulation of I-kappaB kinase/NF-kappaB cascade" RELATED [] +synonym: "up-regulation of I-kappaB kinase/NF-kappaB cascade" RELATED [] +synonym: "upregulation of I-kappaB kinase/NF-kappaB cascade" RELATED [] +xref: Reactome:REACT_24918 "IRAK1 recruits IKK complex, Homo sapiens" +is_a: GO:0043122 ! regulation of I-kappaB kinase/NF-kappaB signaling +is_a: GO:1902533 ! positive regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007249 ! I-kappaB kinase/NF-kappaB signaling +relationship: positively_regulates GO:0007249 ! I-kappaB kinase/NF-kappaB signaling + +[Term] +id: GO:0043149 +name: stress fiber assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form a stress fiber. A stress fiber is a contractile actin filament bundle that consists of short actin filaments with alternating polarity." [GOC:go_curators, GOC:mah, PMID:16651381] +synonym: "actin cable assembly" RELATED [GOC:mah] +synonym: "actin cable formation" RELATED [GOC:mah] +synonym: "stress fibre biosynthesis" RELATED [] +synonym: "stress fibre formation" RELATED [] +is_a: GO:0051017 ! actin filament bundle assembly + +[Term] +id: GO:0043154 +name: negative regulation of cysteine-type endopeptidase activity involved in apoptotic process +namespace: biological_process +alt_id: GO:0001719 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process." [GOC:jl, GOC:mtg_apoptosis] +synonym: "down regulation of caspase activity" EXACT [] +synonym: "down-regulation of caspase activity" EXACT [] +synonym: "downregulation of caspase activity" EXACT [] +synonym: "inhibition of caspase activation" NARROW [] +synonym: "inhibition of caspase activity" NARROW [] +synonym: "negative regulation of caspase activation" EXACT [] +synonym: "negative regulation of caspase activity" BROAD [] +is_a: GO:0043281 ! regulation of cysteine-type endopeptidase activity involved in apoptotic process +is_a: GO:2000117 ! negative regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097153 ! cysteine-type endopeptidase activity involved in apoptotic process +relationship: part_of GO:0006915 ! apoptotic process + +[Term] +id: GO:0043167 +name: ion binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with ions, charged atoms or groups of atoms." [GOC:jl] +subset: goslim_generic +subset: goslim_pir +subset: goslim_yeast +subset: gosubset_prok +synonym: "atom binding" RELATED [] +is_a: GO:0005488 ! binding + +[Term] +id: GO:0043168 +name: anion binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with anions, charged atoms or groups of atoms with a net negative charge." [GOC:jl] +subset: gosubset_prok +is_a: GO:0043167 ! ion binding + +[Term] +id: GO:0043169 +name: cation binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge." [GOC:jl] +subset: gosubset_prok +is_a: GO:0043167 ! ion binding + +[Term] +id: GO:0043170 +name: macromolecule metabolic process +namespace: biological_process +alt_id: GO:0043283 +def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah] +subset: goslim_pir +subset: gosubset_prok +synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] +synonym: "macromolecule metabolism" EXACT [] +is_a: GO:0071704 ! organic substance metabolic process + +[Term] +id: GO:0043198 +name: dendritic shaft +namespace: cellular_component +def: "Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines." [GOC:nln] +synonym: "trunk" RELATED [NIF_Subcellular:sao1078172392] +xref: NIF_Subcellular:sao2034472720 +is_a: GO:0044463 ! cell projection part +is_a: GO:0097458 ! neuron part +relationship: part_of GO:0030425 ! dendrite + +[Term] +id: GO:0043200 +name: response to amino acid +namespace: biological_process +alt_id: GO:0010237 +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups." [CHEBI:33709, GOC:ef, GOC:mlg] +synonym: "response to amino acid stimulus" EXACT [GOC:dos] +is_a: GO:0001101 ! response to acid +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:1901700 ! response to oxygen-containing compound + +[Term] +id: GO:0043207 +name: response to external biotic stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0009605 ! response to external stimulus +is_a: GO:0009607 ! response to biotic stimulus + +[Term] +id: GO:0043226 +name: organelle +namespace: cellular_component +def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators] +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +xref: NIF_Subcellular:sao1539965131 +xref: Wikipedia:Organelle +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0043227 +name: membrane-bounded organelle +namespace: cellular_component +def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gosubset_prok +synonym: "membrane-enclosed organelle" EXACT [] +xref: NIF_Subcellular:sao414196390 +is_a: GO:0043226 ! organelle + +[Term] +id: GO:0043228 +name: non-membrane-bounded organelle +namespace: cellular_component +def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gosubset_prok +synonym: "non-membrane-enclosed organelle" EXACT [] +xref: NIF_Subcellular:sao1456184038 +is_a: GO:0043226 ! organelle + +[Term] +id: GO:0043229 +name: intracellular organelle +namespace: cellular_component +def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0043226 ! organelle +is_a: GO:0044424 ! intracellular part + +[Term] +id: GO:0043231 +name: intracellular membrane-bounded organelle +namespace: cellular_component +def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: goslim_pir +subset: gosubset_prok +synonym: "intracellular membrane-enclosed organelle" EXACT [] +is_a: GO:0043227 ! membrane-bounded organelle +is_a: GO:0043229 ! intracellular organelle + +[Term] +id: GO:0043232 +name: intracellular non-membrane-bounded organelle +namespace: cellular_component +def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: goslim_pir +subset: gosubset_prok +synonym: "intracellular non-membrane-enclosed organelle" EXACT [] +is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043229 ! intracellular organelle + +[Term] +id: GO:0043233 +name: organelle lumen +namespace: cellular_component +def: "The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen." [GOC:jl, GOC:mah] +is_a: GO:0031974 ! membrane-enclosed lumen +is_a: GO:0044422 ! organelle part + +[Term] +id: GO:0043234 +name: protein complex +namespace: cellular_component +def: "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules." [GOC:go_curators] +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +synonym: "protein-protein complex" EXACT [] +xref: Wikipedia:Protein_complex +is_a: GO:0032991 ! macromolecular complex + +[Term] +id: GO:0043235 +name: receptor complex +namespace: cellular_component +def: "Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:go_curators] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0043234 ! protein complex + +[Term] +id: GO:0043254 +name: regulation of protein complex assembly +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of protein complex assembly." [GOC:jl] +subset: gosubset_prok +is_a: GO:0044087 ! regulation of cellular component biogenesis +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006461 ! protein complex assembly +relationship: regulates GO:0006461 ! protein complex assembly + +[Term] +id: GO:0043269 +name: regulation of ion transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl] +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006811 ! ion transport +relationship: regulates GO:0006811 ! ion transport + +[Term] +id: GO:0043280 +name: positive regulation of cysteine-type endopeptidase activity involved in apoptotic process +namespace: biological_process +def: "Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process." [GOC:jl, GOC:mtg_apoptosis] +synonym: "activation of caspase activity" NARROW [] +synonym: "positive regulation of caspase activity" BROAD [] +synonym: "stimulation of caspase activity" NARROW [] +synonym: "up regulation of caspase activity" EXACT [] +synonym: "up-regulation of caspase activity" EXACT [] +synonym: "upregulation of caspase activity" EXACT [] +is_a: GO:0043281 ! regulation of cysteine-type endopeptidase activity involved in apoptotic process +is_a: GO:2001056 ! positive regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0097153 ! cysteine-type endopeptidase activity involved in apoptotic process +relationship: part_of GO:0006915 ! apoptotic process + +[Term] +id: GO:0043281 +name: regulation of cysteine-type endopeptidase activity involved in apoptotic process +namespace: biological_process +alt_id: GO:0043026 +def: "Any process that modulates the activity of a cysteine-type endopeptidase involved in apoptosis." [GOC:jl, GOC:mtg_apoptosis] +synonym: "regulation of caspase activation" NARROW [] +synonym: "regulation of caspase activity" BROAD [] +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:2000116 ! regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097153 ! cysteine-type endopeptidase activity involved in apoptotic process +relationship: part_of GO:0006915 ! apoptotic process + +[Term] +id: GO:0043292 +name: contractile fiber +namespace: cellular_component +def: "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle." [GOC:go_curators, ISBN:0815316194] +synonym: "contractile fibre" EXACT [] +synonym: "muscle fiber" BROAD [] +synonym: "muscle fibre" BROAD [] +is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0043296 +name: apical junction complex +namespace: cellular_component +def: "A functional unit located near the cell apex at the points of contact between epithelial cells, which in vertebrates is composed of the tight junction, the zonula adherens, and desmosomes and in some invertebrates, such as Drosophila, is composed of the subapical complex (SAC), the zonula adherens and the septate junction. Functions in the regulation of cell polarity, tissue integrity and intercellular adhesion and permeability." [GOC:go_curators, GOC:kmv, PMID:12525486, PMID:15196556] +synonym: "apical cell junction complex" EXACT [GOC:mah] +synonym: "apical junction" EXACT [] +is_a: GO:0005911 ! cell-cell junction + +[Term] +id: GO:0043392 +name: negative regulation of DNA binding +namespace: biological_process +def: "Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb] +subset: gosubset_prok +synonym: "down regulation of DNA binding" EXACT [] +synonym: "down-regulation of DNA binding" EXACT [] +synonym: "downregulation of DNA binding" EXACT [] +synonym: "inhibition of DNA binding" NARROW [] +is_a: GO:0051100 ! negative regulation of binding +is_a: GO:0051101 ! regulation of DNA binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003677 ! DNA binding +relationship: negatively_regulates GO:0003677 ! DNA binding + +[Term] +id: GO:0043393 +name: regulation of protein binding +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of protein binding." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0051098 ! regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0005515 ! protein binding +relationship: regulates GO:0005515 ! protein binding + +[Term] +id: GO:0043401 +name: steroid hormone mediated signaling pathway +namespace: biological_process +def: "A series of molecular signals mediated by a steroid hormone binding to a receptor." [PMID:12606724] +synonym: "steroid hormone mediated signalling" EXACT [] +is_a: GO:0009755 ! hormone-mediated signaling pathway +is_a: GO:0071383 ! cellular response to steroid hormone stimulus + +[Term] +id: GO:0043403 +name: skeletal muscle tissue regeneration +namespace: biological_process +def: "The regrowth of skeletal muscle tissue to repair injured or damaged muscle fibers in the postnatal stage." [GOC:ef, GOC:mtg_muscle, PMID:12021255, PMID:16607119] +synonym: "myofiber turnover" RELATED [] +is_a: GO:0042246 ! tissue regeneration + +[Term] +id: GO:0043405 +name: regulation of MAP kinase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of MAP kinase activity." [GOC:dph, GOC:go_curators] +synonym: "Regulation of MAPK activity" EXACT [GOC:dph] +synonym: "regulation of mitogen activated protein kinase activity" EXACT [] +synonym: "regulation of mitogen-activated protein kinase activity" EXACT [] +is_a: GO:0043408 ! regulation of MAPK cascade +is_a: GO:0071900 ! regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004707 ! MAP kinase activity +relationship: regulates GO:0004707 ! MAP kinase activity + +[Term] +id: GO:0043406 +name: positive regulation of MAP kinase activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of MAP kinase activity." [GOC:dph, GOC:go_curators] +synonym: "positive regulation of mitogen activated protein kinase activity" EXACT [] +synonym: "positive regulation of mitogen-activated protein kinase activity" EXACT [] +synonym: "stimulation of MAPK activity" NARROW [] +synonym: "up regulation of MAPK activity" EXACT [] +synonym: "up-regulation of MAPK activity" EXACT [] +synonym: "upregulation of MAPK activity" EXACT [] +is_a: GO:0043405 ! regulation of MAP kinase activity +is_a: GO:0043410 ! positive regulation of MAPK cascade +is_a: GO:0071902 ! positive regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004707 ! MAP kinase activity +relationship: positively_regulates GO:0004707 ! MAP kinase activity + +[Term] +id: GO:0043407 +name: negative regulation of MAP kinase activity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity." [GOC:dph, GOC:go_curators] +synonym: "down regulation of MAPK activity" EXACT [] +synonym: "down-regulation of MAPK activity" EXACT [] +synonym: "downregulation of MAPK activity" EXACT [] +synonym: "inhibition of MAPK activity" NARROW [] +synonym: "negative regulation of mitogen activated protein kinase activity" EXACT [] +synonym: "negative regulation of mitogen-activated protein kinase activity" EXACT [] +is_a: GO:0043405 ! regulation of MAP kinase activity +is_a: GO:0043409 ! negative regulation of MAPK cascade +is_a: GO:0071901 ! negative regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004707 ! MAP kinase activity +relationship: negatively_regulates GO:0004707 ! MAP kinase activity + +[Term] +id: GO:0043408 +name: regulation of MAPK cascade +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade." [GOC:go_curators] +synonym: "regulation of MAP kinase cascade" EXACT [GOC:signaling] +synonym: "regulation of MAP kinase kinase kinase cascade" EXACT [] +synonym: "regulation of MAPKKK cascade" EXACT [GOC:signaling] +synonym: "regulation of mitogen activated protein kinase cascade" EXACT [GOC:signaling] +synonym: "regulation of mitogen activated protein kinase kinase kinase cascade" EXACT [] +synonym: "regulation of mitogen-activated protein kinase cascade" EXACT [GOC:signaling] +synonym: "regulation of mitogen-activated protein kinase kinase kinase cascade" EXACT [] +is_a: GO:0042325 ! regulation of phosphorylation +is_a: GO:1902531 ! regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000165 ! MAPK cascade +relationship: regulates GO:0000165 ! MAPK cascade + +[Term] +id: GO:0043409 +name: negative regulation of MAPK cascade +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade." [GOC:go_curators] +synonym: "down regulation of MAPK cascade" EXACT [GOC:signaling] +synonym: "down regulation of MAPKKK cascade" EXACT [] +synonym: "down-regulation of MAPK cascade" EXACT [GOC:signaling] +synonym: "down-regulation of MAPKKK cascade" EXACT [] +synonym: "downregulation of MAPK cascade" EXACT [GOC:signaling] +synonym: "downregulation of MAPKKK cascade" EXACT [] +synonym: "inhibition of MAPK cascade" NARROW [GOC:signaling] +synonym: "inhibition of MAPKKK cascade" NARROW [] +synonym: "negative regulation of MAP kinase cascade" EXACT [GOC:signaling] +synonym: "negative regulation of MAP kinase kinase kinase cascade" EXACT [] +synonym: "negative regulation of MAPKKK cascade" EXACT [GOC:signaling] +synonym: "negative regulation of mitogen activated protein kinase cascade" EXACT [GOC:signaling] +synonym: "negative regulation of mitogen activated protein kinase kinase kinase cascade" EXACT [] +synonym: "negative regulation of mitogen-activated protein kinase cascade" EXACT [GOC:signaling] +synonym: "negative regulation of mitogen-activated protein kinase kinase kinase cascade" EXACT [] +is_a: GO:0042326 ! negative regulation of phosphorylation +is_a: GO:0043408 ! regulation of MAPK cascade +is_a: GO:1902532 ! negative regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0000165 ! MAPK cascade +relationship: negatively_regulates GO:0000165 ! MAPK cascade + +[Term] +id: GO:0043410 +name: positive regulation of MAPK cascade +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade." [GOC:go_curators] +synonym: "activation of MAPK cascade" NARROW [GOC:signaling] +synonym: "activation of MAPKKK cascade" NARROW [] +synonym: "positive regulation of MAP kinase cascade" EXACT [GOC:signaling] +synonym: "positive regulation of MAP kinase kinase kinase cascade" EXACT [] +synonym: "positive regulation of MAPKKK cascade" EXACT [GOC:signaling] +synonym: "positive regulation of mitogen activated protein kinase kinase kinase cascade" EXACT [] +synonym: "positive regulation of mitogen-activated protein kinase cascade" EXACT [GOC:signaling] +synonym: "positive regulation of mitogen-activated protein kinase kinase kinase cascade" EXACT [] +synonym: "stimulation of MAPK cascade" EXACT [GOC:signaling] +synonym: "stimulation of MAPKKK cascade" NARROW [] +synonym: "up regulation of MAPKKK cascade" EXACT [] +synonym: "up-regulation of MAPK cascade" EXACT [GOC:signaling] +synonym: "up-regulation of MAPKKK cascade" EXACT [] +synonym: "upregulation of MAPK cascade" EXACT [GOC:signaling] +synonym: "upregulation of MAPKKK cascade" EXACT [] +is_a: GO:0042327 ! positive regulation of phosphorylation +is_a: GO:0043408 ! regulation of MAPK cascade +is_a: GO:1902533 ! positive regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0000165 ! MAPK cascade +relationship: positively_regulates GO:0000165 ! MAPK cascade + +[Term] +id: GO:0043412 +name: macromolecule modification +namespace: biological_process +def: "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties." [GOC:go_curators] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0043433 +name: negative regulation of sequence-specific DNA binding transcription factor activity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:jl] +synonym: "down regulation of transcription factor activity" EXACT [] +synonym: "down-regulation of transcription factor activity" EXACT [] +synonym: "downregulation of transcription factor activity" EXACT [] +synonym: "inhibition of transcription factor activity" NARROW [] +synonym: "negative regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb] +is_a: GO:0044092 ! negative regulation of molecular function +is_a: GO:0051090 ! regulation of sequence-specific DNA binding transcription factor activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity +relationship: negatively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0043434 +name: response to peptide hormone +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals." [PMID:11027914, PMID:15134857, Wikipedia:Peptide_hormone] +synonym: "response to peptide hormone stimulus" EXACT [GOC:dos] +synonym: "response to polypeptide hormone stimulus" EXACT [] +is_a: GO:0009725 ! response to hormone +is_a: GO:1901652 ! response to peptide + +[Term] +id: GO:0043436 +name: oxoacid metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons)." [CHEBI:24833] +subset: gosubset_prok +synonym: "keto acid metabolic process" EXACT [] +synonym: "keto acid metabolism" EXACT [] +synonym: "ketoacid metabolic process" EXACT [] +synonym: "ketoacid metabolism" EXACT [] +synonym: "oxo acid metabolic process" EXACT [] +synonym: "oxo acid metabolism" EXACT [] +synonym: "oxoacid metabolism" EXACT [] +is_a: GO:0006082 ! organic acid metabolic process + +[Term] +id: GO:0043473 +name: pigmentation +namespace: biological_process +def: "The deposition or aggregation of coloring matter in an organism, tissue or cell." [GOC:jl] +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0044699 ! single-organism process + +[Term] +id: GO:0043491 +name: protein kinase B signaling +namespace: biological_process +def: "A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound." [GOC:bf, PMID:20517722] +synonym: "AKT signal transduction" EXACT [GOC:signaling] +synonym: "AKT signaling" EXACT [GOC:signaling] +synonym: "AKT signaling cascade" RELATED [] +synonym: "AKT signalling cascade" EXACT [] +synonym: "PKB signal transduction" EXACT [GOC:signaling] +synonym: "PKB signaling" EXACT [GOC:signaling] +synonym: "PKB signaling cascade" RELATED [] +synonym: "PKB signalling cascade" RELATED [] +synonym: "protein kinase B signal transduction" EXACT [GOC:signaling] +synonym: "protein kinase B signaling cascade" RELATED [GOC:signaling] +synonym: "protein kinase B signalling cascade" RELATED [] +is_a: GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0043506 +name: regulation of JUN kinase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of JUN kinase activity." [GOC:jl] +synonym: "regulation of JUNK activity" EXACT [] +is_a: GO:0043405 ! regulation of MAP kinase activity +is_a: GO:0046328 ! regulation of JNK cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004705 ! JUN kinase activity +relationship: regulates GO:0004705 ! JUN kinase activity + +[Term] +id: GO:0043507 +name: positive regulation of JUN kinase activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of JUN kinase activity." [GOC:jl] +synonym: "positive regulation of JUNK activity" EXACT [] +synonym: "stimulation of JNK activity" NARROW [] +synonym: "up regulation of JNK activity" EXACT [] +synonym: "up-regulation of JNK activity" EXACT [] +synonym: "upregulation of JNK activity" EXACT [] +is_a: GO:0043406 ! positive regulation of MAP kinase activity +is_a: GO:0043506 ! regulation of JUN kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004705 ! JUN kinase activity +relationship: positively_regulates GO:0004705 ! JUN kinase activity + +[Term] +id: GO:0043508 +name: negative regulation of JUN kinase activity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of JUN kinase activity." [GOC:jl] +synonym: "down regulation of JNK activity" EXACT [] +synonym: "down-regulation of JNK activity" EXACT [] +synonym: "downregulation of JNK activity" EXACT [] +synonym: "inhibition of JNK activity" NARROW [] +synonym: "negative regulation of JUNK activity" EXACT [] +is_a: GO:0043407 ! negative regulation of MAP kinase activity +is_a: GO:0043506 ! regulation of JUN kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004705 ! JUN kinase activity +relationship: negatively_regulates GO:0004705 ! JUN kinase activity + +[Term] +id: GO:0043523 +name: regulation of neuron apoptotic process +namespace: biological_process +def: "Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons." [GOC:go_curators, GOC:mtg_apoptosis] +synonym: "regulation of apoptosis of neuronal cells" EXACT [] +synonym: "regulation of apoptosis of neurons" EXACT [] +synonym: "regulation of neuron apoptosis" NARROW [] +synonym: "regulation of neuron programmed cell death" EXACT [] +synonym: "regulation of neuronal cell programmed cell death" EXACT [] +synonym: "regulation of programmed cell death of neuronal cells" EXACT [] +synonym: "regulation of programmed cell death, neurons" EXACT [] +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:1901214 ! regulation of neuron death +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051402 ! neuron apoptotic process +relationship: regulates GO:0051402 ! neuron apoptotic process + +[Term] +id: GO:0043524 +name: negative regulation of neuron apoptotic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons." [GOC:go_curators, GOC:mtg_apoptosis] +synonym: "down regulation of neuron apoptosis" EXACT [] +synonym: "down-regulation of neuron apoptosis" EXACT [] +synonym: "downregulation of neuron apoptosis" EXACT [] +synonym: "inhibition of neuron apoptosis" NARROW [] +synonym: "negative regulation of neuron apoptosis" NARROW [] +synonym: "negative regulation of programmed cell death, neurons" EXACT [] +synonym: "neuron survival" NARROW [] +is_a: GO:0043066 ! negative regulation of apoptotic process +is_a: GO:0043523 ! regulation of neuron apoptotic process +is_a: GO:1901215 ! negative regulation of neuron death +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0051402 ! neuron apoptotic process +relationship: negatively_regulates GO:0051402 ! neuron apoptotic process + +[Term] +id: GO:0043534 +name: blood vessel endothelial cell migration +namespace: biological_process +def: "The orderly movement of an endothelial cell into the extracellular matrix in order to form new blood vessels during angiogenesis." [PMID:11166264] +is_a: GO:0043542 ! endothelial cell migration + +[Term] +id: GO:0043535 +name: regulation of blood vessel endothelial cell migration +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the migration of the endothelial cells of blood vessels." [GOC:go_curators] +is_a: GO:0010594 ! regulation of endothelial cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043534 ! blood vessel endothelial cell migration +relationship: regulates GO:0043534 ! blood vessel endothelial cell migration + +[Term] +id: GO:0043536 +name: positive regulation of blood vessel endothelial cell migration +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the migration of the endothelial cells of blood vessels." [GOC:go_curators] +synonym: "activation of blood vessel endothelial cell migration" NARROW [] +synonym: "stimulation of blood vessel endothelial cell migration" NARROW [] +synonym: "up regulation of blood vessel endothelial cell migration" EXACT [] +synonym: "up-regulation of blood vessel endothelial cell migration" EXACT [] +synonym: "upregulation of blood vessel endothelial cell migration" EXACT [] +is_a: GO:0010595 ! positive regulation of endothelial cell migration +is_a: GO:0043535 ! regulation of blood vessel endothelial cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0043534 ! blood vessel endothelial cell migration +relationship: positively_regulates GO:0043534 ! blood vessel endothelial cell migration + +[Term] +id: GO:0043542 +name: endothelial cell migration +namespace: biological_process +def: "The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." [GOC:go_curators] +is_a: GO:0010631 ! epithelial cell migration + +[Term] +id: GO:0043543 +name: protein acylation +namespace: biological_process +def: "The addition of an acyl group, any group or radical of the form RCO- where R is an organic group, to a protein amino acid." [GOC:jl] +subset: goslim_yeast +subset: gosubset_prok +synonym: "protein amino acid acylation" EXACT [GOC:bf] +is_a: GO:0006464 ! cellular protein modification process + +[Term] +id: GO:0043547 +name: positive regulation of GTPase activity +namespace: biological_process +def: "Any process that activates or increases the activity of a GTPase." [GOC:jl] +synonym: "activation of GTPase activity" NARROW [] +synonym: "stimulation of GTPase activity" NARROW [] +synonym: "up regulation of GTPase activity" EXACT [] +synonym: "up-regulation of GTPase activity" EXACT [] +synonym: "upregulation of GTPase activity" EXACT [] +is_a: GO:0043087 ! regulation of GTPase activity +is_a: GO:0051345 ! positive regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0003924 ! GTPase activity +relationship: positively_regulates GO:0003924 ! GTPase activity + +[Term] +id: GO:0043549 +name: regulation of kinase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:bf] +subset: gosubset_prok +is_a: GO:0042325 ! regulation of phosphorylation +is_a: GO:0051338 ! regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016301 ! kinase activity +relationship: regulates GO:0016301 ! kinase activity + +[Term] +id: GO:0043565 +name: sequence-specific DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding." [GOC:jl] +subset: gosubset_prok +synonym: "sequence specific DNA binding" EXACT [] +is_a: GO:0003677 ! DNA binding + +[Term] +id: GO:0043566 +name: structure-specific DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with DNA of a specific structure or configuration e.g. triplex DNA binding or bent DNA binding." [GOC:jl] +subset: gosubset_prok +synonym: "structure specific DNA binding" EXACT [] +is_a: GO:0003677 ! DNA binding + +[Term] +id: GO:0043567 +name: regulation of insulin-like growth factor receptor signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of insulin-like growth factor receptor signaling." [GOC:bf] +synonym: "regulation of IGF receptor signaling pathway" EXACT [] +synonym: "regulation of IGF receptor signalling pathway" EXACT [] +synonym: "regulation of insulin-like growth factor receptor signalling pathway" EXACT [] +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048009 ! insulin-like growth factor receptor signaling pathway +relationship: regulates GO:0048009 ! insulin-like growth factor receptor signaling pathway + +[Term] +id: GO:0043568 +name: positive regulation of insulin-like growth factor receptor signaling pathway +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of insulin-like growth factor receptor signaling." [GOC:bf] +synonym: "activation of insulin-like growth factor receptor signaling pathway" NARROW [] +synonym: "positive regulation of IGF receptor signaling pathway" EXACT [] +synonym: "positive regulation of IGF receptor signalling pathway" EXACT [] +synonym: "positive regulation of insulin-like growth factor receptor signalling pathway" EXACT [] +synonym: "stimulation of insulin-like growth factor receptor signaling pathway" NARROW [] +synonym: "up regulation of insulin-like growth factor receptor signaling pathway" EXACT [] +synonym: "up-regulation of insulin-like growth factor receptor signaling pathway" EXACT [] +synonym: "upregulation of insulin-like growth factor receptor signaling pathway" EXACT [] +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0043567 ! regulation of insulin-like growth factor receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048009 ! insulin-like growth factor receptor signaling pathway +relationship: positively_regulates GO:0048009 ! insulin-like growth factor receptor signaling pathway + +[Term] +id: GO:0043583 +name: ear development +namespace: biological_process +def: "The process whose specific outcome is the progression of the ear over time, from its formation to the mature structure. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." [GOC:jl, ISBN:0192801023] +synonym: "hearing organ development" EXACT [] +is_a: GO:0007423 ! sensory organ development + +[Term] +id: GO:0043584 +name: nose development +namespace: biological_process +def: "The process whose specific outcome is the progression of the nose over time, from its formation to the mature structure. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)." [GOC:jl, http://www.mercksource.com/] +synonym: "nasus development" EXACT [] +is_a: GO:0007423 ! sensory organ development +relationship: part_of GO:0060541 ! respiratory system development + +[Term] +id: GO:0043586 +name: tongue development +namespace: biological_process +def: "The process whose specific outcome is the progression of the tongue over time, from its formation to the mature structure. The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech." [GOC:jl, UBERON:0001723] +synonym: "glossa development" NARROW [] +synonym: "lingua development" NARROW [] +is_a: GO:0007423 ! sensory organ development + +[Term] +id: GO:0043587 +name: tongue morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the tongue are generated and organized. The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in man other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech." [GOC:jl, UBERON:0001723] +synonym: "glossa morphogenesis" NARROW [] +synonym: "lingua morphogenesis" EXACT [] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0043586 ! tongue development + +[Term] +id: GO:0043588 +name: skin development +namespace: biological_process +def: "The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue." [GOC:jl, UBERON:0002097] +synonym: "animal skin development" EXACT [] +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0043589 +name: skin morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the skin are generated and organized. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner, sensitive and vascular dermis (cutis, corium or true skin) composed mostly of connective tissue." [GOC:jl, UBERON:0002097] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0043588 ! skin development + +[Term] +id: GO:0043623 +name: cellular protein complex assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell." [GOC:jl] +subset: gosubset_prok +is_a: GO:0006461 ! protein complex assembly +is_a: GO:0034622 ! cellular macromolecular complex assembly + +[Term] +id: GO:0043627 +name: response to estrogen +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics." [GOC:jl, ISBN:0198506732] +synonym: "response to estrogen stimulus" EXACT [GOC:dos] +synonym: "response to oestrogen stimulus" EXACT [] +is_a: GO:0048545 ! response to steroid hormone + +[Term] +id: GO:0043632 +name: modification-dependent macromolecule catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, initiated by covalent modification of the target molecule." [GOC:jl] +subset: gosubset_prok +is_a: GO:0044265 ! cellular macromolecule catabolic process + +[Term] +id: GO:0043933 +name: macromolecular complex subunit organization +namespace: biological_process +alt_id: GO:0034600 +alt_id: GO:0034621 +def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex." [GOC:mtg_mpo] +subset: gosubset_prok +synonym: "cellular macromolecular complex organization" EXACT [] +synonym: "cellular macromolecular complex subunit organisation" EXACT [GOC:curators] +synonym: "cellular macromolecular complex subunit organization" EXACT [] +synonym: "macromolecular complex organization" EXACT [] +synonym: "macromolecular complex subunit organisation" EXACT [GOC:curators] +is_a: GO:0016043 ! cellular component organization + +[Term] +id: GO:0044057 +name: regulation of system process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system." [GOC:jl] +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003008 ! system process +relationship: regulates GO:0003008 ! system process + +[Term] +id: GO:0044085 +name: cellular component biogenesis +namespace: biological_process +alt_id: GO:0071843 +def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gosubset_prok +synonym: "cellular component biogenesis at cellular level" EXACT [] +is_a: GO:0071840 ! cellular component organization or biogenesis + +[Term] +id: GO:0044087 +name: regulation of cellular component biogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component." [GOC:jl] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044085 ! cellular component biogenesis +relationship: regulates GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0044089 +name: positive regulation of cellular component biogenesis +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component." [GOC:jl] +is_a: GO:0044087 ! regulation of cellular component biogenesis +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044085 ! cellular component biogenesis +relationship: positively_regulates GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0044092 +name: negative regulation of molecular function +namespace: biological_process +def: "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003674 ! molecular_function +relationship: negatively_regulates GO:0003674 ! molecular_function +created_by: jane +creation_date: 2009-04-21T04:07:27Z + +[Term] +id: GO:0044093 +name: positive regulation of molecular function +namespace: biological_process +def: "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0003674 ! molecular_function +relationship: positively_regulates GO:0003674 ! molecular_function +created_by: jane +creation_date: 2009-04-21T04:11:06Z + +[Term] +id: GO:0044212 +name: transcription regulatory region DNA binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:jl, GOC:txnOH, SO:0005836] +comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". +is_a: GO:0000975 ! regulatory region DNA binding +created_by: jane +creation_date: 2009-11-04T12:58:25Z + +[Term] +id: GO:0044236 +name: multicellular organismal metabolic process +namespace: biological_process +def: "The chemical reactions and pathways in a single multicellular organism that occur at the tissue, organ, or organismal level. These processes, unlike cellular metabolism, can include transport of substances between cells when that transport is required." [GOC:go_curators] +synonym: "multicellular organismal metabolism" EXACT [] +synonym: "single multicellular organismal metabolic process" EXACT [] +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0044710 ! single-organism metabolic process + +[Term] +id: GO:0044237 +name: cellular metabolic process +namespace: biological_process +def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] +subset: goslim_pir +subset: gosubset_prok +synonym: "cellular metabolism" EXACT [] +synonym: "intermediary metabolism" RELATED [GOC:mah] +is_a: GO:0008152 ! metabolic process +is_a: GO:0009987 ! cellular process + +[Term] +id: GO:0044238 +name: primary metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] +subset: goslim_pir +subset: gosubset_prok +synonym: "primary metabolism" EXACT [] +is_a: GO:0008152 ! metabolic process + +[Term] +id: GO:0044246 +name: regulation of multicellular organismal metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of chemical reactions and pathways in multicellular organisms that occur at the tissue, organ, or organismal level." [GOC:go_curators, GOC:tb] +synonym: "regulation of organismal metabolic process" EXACT [GOC:tb] +synonym: "regulation of organismal metabolism" EXACT [] +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044236 ! multicellular organismal metabolic process +relationship: regulates GO:0044236 ! multicellular organismal metabolic process + +[Term] +id: GO:0044248 +name: cellular catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:jl] +subset: gosubset_prok +synonym: "cellular breakdown" EXACT [] +synonym: "cellular catabolism" EXACT [] +synonym: "cellular degradation" EXACT [] +is_a: GO:0009056 ! catabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0044249 +name: cellular biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] +subset: gosubset_prok +synonym: "cellular anabolism" EXACT [] +synonym: "cellular biosynthesis" EXACT [] +synonym: "cellular formation" EXACT [] +synonym: "cellular synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0044253 +name: positive regulation of multicellular organismal metabolic process +namespace: biological_process +def: "Any process that activates or increases frequency, rate or extent of chemical reactions and pathways in multicellular organisms that occur at the tissue, organ, or organismal level." [GOC:jl] +synonym: "activation of organismal metabolic process" NARROW [] +synonym: "positive regulation of organismal metabolism" EXACT [] +synonym: "stimulation of organismal metabolic process" NARROW [] +synonym: "up regulation of organismal metabolic process" EXACT [] +synonym: "up-regulation of organismal metabolic process" EXACT [] +synonym: "upregulation of organismal metabolic process" EXACT [] +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0044246 ! regulation of multicellular organismal metabolic process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044236 ! multicellular organismal metabolic process +relationship: positively_regulates GO:0044236 ! multicellular organismal metabolic process + +[Term] +id: GO:0044257 +name: cellular protein catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a protein by individual cells." [GOC:jl] +subset: gosubset_prok +synonym: "cellular protein breakdown" EXACT [] +synonym: "cellular protein catabolism" EXACT [] +synonym: "cellular protein degradation" EXACT [] +xref: Reactome:REACT_104979 "Degradation of newly synthesized ApoB-48, Rattus norvegicus" +xref: Reactome:REACT_105668 "Degradation of newly synthesized ApoB-48, Mus musculus" +xref: Reactome:REACT_107565 "Degradation of newly synthesized ApoB-48, Xenopus tropicalis" +xref: Reactome:REACT_28414 "Degradation of newly synthesized ApoB-48, Canis familiaris" +xref: Reactome:REACT_30520 "Degradation of newly synthesized ApoB-48, Gallus gallus" +xref: Reactome:REACT_34532 "Degradation of newly synthesized ApoB-48, Taeniopygia guttata" +xref: Reactome:REACT_6829 "Degradation of newly synthesized ApoB-48, Homo sapiens" +xref: Reactome:REACT_77105 "Degradation of newly synthesized ApoB-48, Danio rerio" +xref: Reactome:REACT_79506 "Degradation of newly synthesized ApoB-48, Sus scrofa" +xref: Reactome:REACT_86672 "Degradation of newly synthesized ApoB-48, Bos taurus" +is_a: GO:0030163 ! protein catabolic process +is_a: GO:0044265 ! cellular macromolecule catabolic process +is_a: GO:0044267 ! cellular protein metabolic process + +[Term] +id: GO:0044259 +name: multicellular organismal macromolecule metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving macromolecules, large molecules including proteins, nucleic acids and carbohydrates, in multicellular organisms occurring at the tissue, organ, or organismal level." [GOC:jl] +synonym: "organismal macromolecule metabolism" EXACT [] +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0044236 ! multicellular organismal metabolic process + +[Term] +id: GO:0044260 +name: cellular macromolecule metabolic process +namespace: biological_process +alt_id: GO:0034960 +def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells." [CHEBI:33694, GOC:mah] +subset: gosubset_prok +synonym: "cellular biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] +synonym: "cellular macromolecule metabolism" EXACT [] +is_a: GO:0043170 ! macromolecule metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0044262 +name: cellular carbohydrate metabolic process +namespace: biological_process +alt_id: GO:0006092 +def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:jl] +subset: gosubset_prok +synonym: "cellular carbohydrate metabolism" EXACT [] +synonym: "main pathways of carbohydrate metabolic process" NARROW [] +synonym: "main pathways of carbohydrate metabolism" NARROW [] +is_a: GO:0005975 ! carbohydrate metabolic process +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0044265 +name: cellular macromolecule catabolic process +namespace: biological_process +alt_id: GO:0034962 +def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells." [CHEBI:33694, GOC:jl] +subset: gosubset_prok +synonym: "cellular biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09] +synonym: "cellular macromolecule breakdown" EXACT [] +synonym: "cellular macromolecule catabolism" EXACT [] +synonym: "cellular macromolecule degradation" EXACT [] +is_a: GO:0009057 ! macromolecule catabolic process +is_a: GO:0044248 ! cellular catabolic process +is_a: GO:0044260 ! cellular macromolecule metabolic process + +[Term] +id: GO:0044267 +name: cellular protein metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification." [GOC:jl] +subset: gosubset_prok +synonym: "cellular protein metabolism" EXACT [] +xref: Reactome:REACT_101554 "Metabolism of proteins, Gallus gallus" +xref: Reactome:REACT_102155 "Metabolism of proteins, Arabidopsis thaliana" +xref: Reactome:REACT_105825 "Metabolism of proteins, Dictyostelium discoideum" +xref: Reactome:REACT_106151 "Metabolism of proteins, Xenopus tropicalis" +xref: Reactome:REACT_108005 "Metabolism of proteins, Bos taurus" +xref: Reactome:REACT_109022 "Metabolism of proteins, Schizosaccharomyces pombe" +xref: Reactome:REACT_17015 "Metabolism of proteins, Homo sapiens" +xref: Reactome:REACT_32904 "Metabolism of proteins, Canis familiaris" +xref: Reactome:REACT_34473 "Metabolism of proteins, Taeniopygia guttata" +xref: Reactome:REACT_80561 "Metabolism of proteins, Escherichia coli" +xref: Reactome:REACT_81994 "Metabolism of proteins, Sus scrofa" +xref: Reactome:REACT_82523 "Metabolism of proteins, Danio rerio" +xref: Reactome:REACT_85873 "Metabolism of proteins, Saccharomyces cerevisiae" +xref: Reactome:REACT_86658 "Metabolism of proteins, Drosophila melanogaster" +xref: Reactome:REACT_89852 "Metabolism of proteins, Rattus norvegicus" +xref: Reactome:REACT_91052 "Metabolism of proteins, Caenorhabditis elegans" +xref: Reactome:REACT_93132 "Metabolism of proteins, Mus musculus" +xref: Reactome:REACT_96466 "Metabolism of proteins, Plasmodium falciparum" +xref: Reactome:REACT_99179 "Metabolism of proteins, Oryza sativa" +is_a: GO:0019538 ! protein metabolic process +is_a: GO:0044260 ! cellular macromolecule metabolic process + +[Term] +id: GO:0044270 +name: cellular nitrogen compound catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds." [GOC:jl, ISBN:0198506732] +subset: gosubset_prok +synonym: "nitrogen compound breakdown" BROAD [] +synonym: "nitrogen compound catabolism" BROAD [] +synonym: "nitrogen compound degradation" BROAD [] +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +is_a: GO:0044248 ! cellular catabolic process + +[Term] +id: GO:0044271 +name: cellular nitrogen compound biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds." [GOC:jl, ISBN:0198506732] +subset: gosubset_prok +synonym: "nitrogen compound anabolism" BROAD [] +synonym: "nitrogen compound biosynthesis" BROAD [] +synonym: "nitrogen compound formation" BROAD [] +synonym: "nitrogen compound synthesis" BROAD [] +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0044272 +name: sulfur compound biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:jl] +subset: gosubset_prok +synonym: "sulfur biosynthesis" NARROW [] +synonym: "sulfur biosynthetic process" NARROW [] +synonym: "sulfur compound anabolism" EXACT [] +synonym: "sulfur compound biosynthesis" EXACT [] +synonym: "sulfur compound formation" EXACT [] +synonym: "sulfur compound synthesis" EXACT [] +is_a: GO:0006790 ! sulfur compound metabolic process +is_a: GO:0044249 ! cellular biosynthetic process + +[Term] +id: GO:0044281 +name: small molecule metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] +comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. +subset: goslim_generic +subset: goslim_metagenomics +synonym: "small molecule metabolism" EXACT [] +xref: Reactome:REACT_111217 "Metabolism, Homo sapiens" +xref: Reactome:REACT_112077 "Metabolism, Xenopus tropicalis" +xref: Reactome:REACT_112140 "Metabolism, Dictyostelium discoideum" +xref: Reactome:REACT_112621 "Metabolism, Mus musculus" +xref: Reactome:REACT_112912 "Metabolism, Arabidopsis thaliana" +xref: Reactome:REACT_113131 "Metabolism, Schizosaccharomyces pombe" +xref: Reactome:REACT_113305 "Metabolism, Canis familiaris" +xref: Reactome:REACT_113457 "Metabolism, Mycobacterium tuberculosis" +xref: Reactome:REACT_113568 "Metabolism, Rattus norvegicus" +xref: Reactome:REACT_113610 "Metabolism, Caenorhabditis elegans" +xref: Reactome:REACT_113934 "Metabolism, Escherichia coli" +xref: Reactome:REACT_114081 "Metabolism, Gallus gallus" +xref: Reactome:REACT_114137 "Metabolism, Sus scrofa" +xref: Reactome:REACT_114421 "Metabolism, Saccharomyces cerevisiae" +xref: Reactome:REACT_114473 "Metabolism, Danio rerio" +xref: Reactome:REACT_114495 "Metabolism, Staphylococcus aureus N315" +xref: Reactome:REACT_114668 "Metabolism, Plasmodium falciparum" +xref: Reactome:REACT_114983 "Metabolism, Drosophila melanogaster" +xref: Reactome:REACT_115063 "Metabolism, Taeniopygia guttata" +xref: Reactome:REACT_115388 "Metabolism, Oryza sativa" +xref: Reactome:REACT_115420 "Metabolism, Bos taurus" +xref: Reactome:REACT_115655 "Metabolism, Gallus gallus" +is_a: GO:0044710 ! single-organism metabolic process +created_by: jane +creation_date: 2010-01-26T12:05:20Z + +[Term] +id: GO:0044283 +name: small molecule biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] +comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. +synonym: "small molecule biosynthesis" EXACT [] +is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:0044711 ! single-organism biosynthetic process +created_by: jane +creation_date: 2010-01-26T12:06:49Z + +[Term] +id: GO:0044291 +name: cell-cell contact zone +namespace: cellular_component +def: "Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle." [NIF_Subcellular:sao1299635018] +synonym: "cell cell contact zone" EXACT [] +xref: NIF_Subcellular:sao1299635018 +is_a: GO:0005911 ! cell-cell junction +created_by: jane +creation_date: 2010-02-04T02:42:54Z + +[Term] +id: GO:0044297 +name: cell body +namespace: cellular_component +def: "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections." [GOC:go_curators] +comment: Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections. +subset: goslim_pir +synonym: "cell soma" EXACT [] +is_a: GO:0044464 ! cell part +created_by: jane +creation_date: 2010-02-05T10:37:16Z + +[Term] +id: GO:0044319 +name: wound healing, spreading of cells +namespace: biological_process +def: "The migration of a cell along or through a wound gap that contributes to the reestablishment of a continuous surface." [GOC:jl] +synonym: "cell migration involved in wound healing epiboly" EXACT [] +is_a: GO:0016477 ! cell migration +intersection_of: GO:0016477 ! cell migration +intersection_of: part_of GO:0090505 ! epiboly involved in wound healing +relationship: part_of GO:0090505 ! epiboly involved in wound healing +created_by: jane +creation_date: 2010-07-14T02:10:01Z + +[Term] +id: GO:0044325 +name: ion channel binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient." [GOC:BHF, GOC:jl] +is_a: GO:0005515 ! protein binding +created_by: janelomax +creation_date: 2010-08-04T12:52:59Z + +[Term] +id: GO:0044331 +name: cell-cell adhesion mediated by cadherin +namespace: biological_process +def: "The attachment of one cell to another cell via a cadherin, transmembrane proteins having repeating extracellular calcium ion binding domains." [GOC:ha, GOC:hgd, GOC:jl, PMID:10923970] +is_a: GO:0016337 ! cell-cell adhesion +created_by: janelomax +creation_date: 2010-08-20T10:24:54Z + +[Term] +id: GO:0044332 +name: Wnt signaling pathway involved in dorsal/ventral axis specification +namespace: biological_process +def: "The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell contributing to the establishment, maintenance and elaboration of the dorsal/ventral axis." [GOC:jl, GOC:yaf] +synonym: "Wnt receptor signaling pathway involved in dorsal/ventral axis specification" EXACT [] +synonym: "Wnt receptor signalling pathway involved in dorsal/ventral axis specification" EXACT [GOC:mah] +synonym: "Wnt-activated signaling pathway involved in dorsal/ventral axis specification" EXACT [GOC:signaling] +is_a: GO:0016055 ! Wnt signaling pathway +intersection_of: GO:0016055 ! Wnt signaling pathway +intersection_of: part_of GO:0009950 ! dorsal/ventral axis specification +relationship: part_of GO:0009950 ! dorsal/ventral axis specification +created_by: janelomax +creation_date: 2010-08-20T11:30:30Z + +[Term] +id: GO:0044333 +name: Wnt signaling pathway involved in digestive tract morphogenesis +namespace: biological_process +def: "The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell contributing to the generation and the organization of the digestive tract." [GOC:BHF, GOC:jl] +synonym: "Wnt receptor signaling pathway involved in digestive tract morphogenesis" EXACT [] +synonym: "Wnt receptor signalling pathway involved in digestive tract morphogenesis" EXACT [GOC:mah] +synonym: "Wnt-activated signaling pathway involved in digestive tract morphogenesis" RELATED [GOC:signaling] +is_a: GO:0016055 ! Wnt signaling pathway +intersection_of: GO:0016055 ! Wnt signaling pathway +intersection_of: part_of GO:0048546 ! digestive tract morphogenesis +relationship: part_of GO:0048546 ! digestive tract morphogenesis +created_by: janelomax +creation_date: 2010-08-20T11:36:23Z + +[Term] +id: GO:0044334 +name: canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in the positive regulation of epithelial cell to mesenchymal cell transition." [GOC:BHF, GOC:jl] +synonym: "canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition" EXACT [] +synonym: "canonical Wnt receptor signalling pathway involved in positive regulation of epithelial to mesenchymal transition" EXACT [GOC:mah] +synonym: "canonical Wnt-activated signaling pathway involved in positive regulation of epithelial to mesenchymal transition" EXACT [GOC:signaling] +is_a: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: part_of GO:0010718 ! positive regulation of epithelial to mesenchymal transition +relationship: part_of GO:0010718 ! positive regulation of epithelial to mesenchymal transition +created_by: janelomax +creation_date: 2010-08-20T02:35:17Z + +[Term] +id: GO:0044335 +name: canonical Wnt signaling pathway involved in neural crest cell differentiation +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in neural crest cell differentiation." [GOC:BHF, GOC:jl] +synonym: "canonical Wnt receptor signaling pathway involved in neural crest cell differentiation" EXACT [] +synonym: "canonical Wnt receptor signalling pathway involved in neural crest cell differentiation" EXACT [GOC:mah] +synonym: "canonical Wnt-activated signaling pathway involved in neural crest cell differentiation" EXACT [GOC:signaling] +is_a: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: part_of GO:0014033 ! neural crest cell differentiation +relationship: part_of GO:0014033 ! neural crest cell differentiation +created_by: janelomax +creation_date: 2010-08-20T03:02:34Z + +[Term] +id: GO:0044336 +name: canonical Wnt signaling pathway involved in negative regulation of apoptotic process +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in the negative regulation of apoptotic process." [GOC:BHF, GOC:jl, GOC:mtg_apoptosis] +synonym: "canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis" NARROW [] +synonym: "canonical Wnt receptor signaling pathway involved in negative regulation of apoptotic process" EXACT [GOC:signaling] +synonym: "canonical Wnt receptor signalling pathway involved in negative regulation of apoptosis" EXACT [GOC:mah] +is_a: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: part_of GO:0043066 ! negative regulation of apoptotic process +relationship: part_of GO:0043066 ! negative regulation of apoptotic process +created_by: janelomax +creation_date: 2010-08-20T03:07:53Z + +[Term] +id: GO:0044340 +name: canonical Wnt signaling pathway involved in regulation of cell proliferation +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contributes to modulating the rate or frequency of cell proliferation." [GOC:BHF, GOC:jl] +synonym: "canonical Wnt receptor signaling pathway involved in regulation of cell proliferation" EXACT [] +synonym: "canonical Wnt receptor signalling pathway involved in regulation of cell proliferation" EXACT [GOC:mah] +synonym: "canonical Wnt-activated signaling pathway involved in regulation of cell proliferation" EXACT [GOC:signaling] +is_a: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: part_of GO:0008283 ! cell proliferation +relationship: part_of GO:0042127 ! regulation of cell proliferation +created_by: janelomax +creation_date: 2010-08-20T03:57:25Z + +[Term] +id: GO:0044342 +name: type B pancreatic cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin." [GOC:jl, GOC:yaf] +synonym: "pancreatic B cell proliferation" EXACT [GOC:mah] +synonym: "pancreatic beta cell proliferation" EXACT [] +is_a: GO:0008283 ! cell proliferation +created_by: janelomax +creation_date: 2010-08-25T01:44:51Z + +[Term] +id: GO:0044343 +name: canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that modulates the rate or frequency of pancreatic B cell proliferation. Pancreatic B cell are cells of the pancreas that secrete insulin." [GOC:jl, GOC:yaf] +synonym: "canonical Wnt receptor signaling pathway involved in pancreatic beta cell proliferation" RELATED [] +synonym: "canonical Wnt receptor signaling pathway involved in regulation of pancreatic B cell proliferation" EXACT [GOC:mah] +synonym: "canonical Wnt receptor signaling pathway involved in regulation of type B pancreatic cell proliferation" EXACT [] +synonym: "canonical Wnt receptor signalling pathway involved in regulation of pancreatic B cell proliferation" EXACT [GOC:mah] +synonym: "canonical Wnt receptor signalling pathway involved in regulation of type B pancreatic cell proliferation" EXACT [GOC:mah] +synonym: "canonical Wnt-activated signaling pathway involved in regulation of type B pancreatic cell proliferation" EXACT [GOC:signaling] +is_a: GO:0044340 ! canonical Wnt signaling pathway involved in regulation of cell proliferation +intersection_of: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: part_of GO:0061469 ! regulation of type B pancreatic cell proliferation +relationship: part_of GO:0061469 ! regulation of type B pancreatic cell proliferation +created_by: janelomax +creation_date: 2010-08-25T01:53:22Z + +[Term] +id: GO:0044344 +name: cellular response to fibroblast growth factor stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an fibroblast growth factor stimulus." [GOC:jl, GOC:yaf] +synonym: "cellular response to FGF stimulus" EXACT [] +is_a: GO:0071363 ! cellular response to growth factor stimulus +is_a: GO:0071495 ! cellular response to endogenous stimulus +is_a: GO:0071774 ! response to fibroblast growth factor +created_by: janelomax +creation_date: 2010-08-25T02:00:51Z + +[Term] +id: GO:0044346 +name: fibroblast apoptotic process +namespace: biological_process +def: "Any apoptotic process in a fibroblast, a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules." [CL:0000057, GOC:jl, GOC:mtg_apoptosis, GOC:yaf] +synonym: "fibroblast apoptosis" NARROW [] +is_a: GO:0097285 ! cell-type specific apoptotic process +created_by: janelomax +creation_date: 2010-09-23T11:33:38Z + +[Term] +id: GO:0044390 +name: small protein conjugating enzyme binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a small protein conjugating enzyme such as ubiquitin conjugating enzyme." [GOC:jl] +synonym: "E2 protein ligase binding" EXACT [] +is_a: GO:0019899 ! enzyme binding +created_by: janelomax +creation_date: 2011-12-15T04:38:44Z + +[Term] +id: GO:0044421 +name: extracellular region part +namespace: cellular_component +def: "Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: gosubset_prok +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005576 ! extracellular region +relationship: part_of GO:0005576 ! extracellular region + +[Term] +id: GO:0044422 +name: organelle part +namespace: cellular_component +def: "Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: gosubset_prok +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0043226 ! organelle +relationship: part_of GO:0043226 ! organelle + +[Term] +id: GO:0044424 +name: intracellular part +namespace: cellular_component +def: "Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: gosubset_prok +is_a: GO:0044464 ! cell part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005622 ! intracellular +relationship: part_of GO:0005622 ! intracellular + +[Term] +id: GO:0044425 +name: membrane part +namespace: cellular_component +def: "Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: gosubset_prok +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0016020 ! membrane +relationship: part_of GO:0016020 ! membrane + +[Term] +id: GO:0044427 +name: chromosomal part +namespace: cellular_component +def: "Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: gosubset_prok +synonym: "chromosomal component" EXACT [] +synonym: "chromosome component" EXACT [] +synonym: "chromosome part" EXACT [] +is_a: GO:0044446 ! intracellular organelle part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005694 ! chromosome +relationship: part_of GO:0005694 ! chromosome + +[Term] +id: GO:0044428 +name: nuclear part +namespace: cellular_component +def: "Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +synonym: "nucleus component" EXACT [] +is_a: GO:0044446 ! intracellular organelle part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005634 ! nucleus +relationship: part_of GO:0005634 ! nucleus + +[Term] +id: GO:0044430 +name: cytoskeletal part +namespace: cellular_component +def: "Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +synonym: "cytoskeleton component" EXACT [] +is_a: GO:0044446 ! intracellular organelle part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005856 ! cytoskeleton +relationship: part_of GO:0005856 ! cytoskeleton + +[Term] +id: GO:0044432 +name: endoplasmic reticulum part +namespace: cellular_component +def: "Any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +synonym: "ER component" EXACT [] +is_a: GO:0044444 ! cytoplasmic part +is_a: GO:0044446 ! intracellular organelle part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005783 ! endoplasmic reticulum +relationship: part_of GO:0005783 ! endoplasmic reticulum + +[Term] +id: GO:0044444 +name: cytoplasmic part +namespace: cellular_component +def: "Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: gosubset_prok +synonym: "cytoplasm component" EXACT [] +is_a: GO:0044424 ! intracellular part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005737 ! cytoplasm +relationship: part_of GO:0005737 ! cytoplasm + +[Term] +id: GO:0044446 +name: intracellular organelle part +namespace: cellular_component +def: "A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: gosubset_prok +is_a: GO:0044422 ! organelle part +is_a: GO:0044424 ! intracellular part +relationship: part_of GO:0043229 ! intracellular organelle + +[Term] +id: GO:0044449 +name: contractile fiber part +namespace: cellular_component +def: "Any constituent part of a contractile fiber, a fiber composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +synonym: "contractile fibre component" EXACT [] +synonym: "muscle fiber component" BROAD [] +synonym: "muscle fibre component" BROAD [] +is_a: GO:0044422 ! organelle part +is_a: GO:0044444 ! cytoplasmic part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0043292 ! contractile fiber +relationship: part_of GO:0043292 ! contractile fiber + +[Term] +id: GO:0044454 +name: nuclear chromosome part +namespace: cellular_component +def: "Any constituent part of a nuclear chromosome, a chromosome found in the nucleus of a eukaryotic cell." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +is_a: GO:0044427 ! chromosomal part +is_a: GO:0044428 ! nuclear part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0000228 ! nuclear chromosome +relationship: part_of GO:0000228 ! nuclear chromosome + +[Term] +id: GO:0044456 +name: synapse part +namespace: cellular_component +def: "Any constituent part of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0045202 ! synapse +relationship: part_of GO:0045202 ! synapse + +[Term] +id: GO:0044459 +name: plasma membrane part +namespace: cellular_component +def: "Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: gosubset_prok +is_a: GO:0044425 ! membrane part +is_a: GO:0044464 ! cell part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005886 ! plasma membrane +relationship: part_of GO:0005886 ! plasma membrane + +[Term] +id: GO:0044463 +name: cell projection part +namespace: cellular_component +def: "Any constituent part of a cell projection, a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: gosubset_prok +is_a: GO:0044464 ! cell part +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0042995 ! cell projection +relationship: part_of GO:0042995 ! cell projection + +[Term] +id: GO:0044464 +name: cell part +namespace: cellular_component +def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: goslim_pir +subset: gosubset_prok +synonym: "protoplast" RELATED [GOC:mah] +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005623 ! cell +relationship: part_of GO:0005623 ! cell + +[Term] +id: GO:0044699 +name: single-organism process +namespace: biological_process +def: "A biological process that involves only one organism." [GOC:jl] +synonym: "single organism process" EXACT [] +is_a: GO:0008150 ! biological_process +created_by: janelomax +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0044700 +name: single organism signaling +namespace: biological_process +def: "A signaling process occurring within a single organism." [GOC:jl] +is_a: GO:0023052 ! signaling +is_a: GO:0044699 ! single-organism process +created_by: janelomax +creation_date: 2012-09-19T15:12:49Z + +[Term] +id: GO:0044702 +name: single organism reproductive process +namespace: biological_process +def: "A biological process that directly contributes to the process of producing new individuals, involving a single organism." [GOC:jl] +is_a: GO:0022414 ! reproductive process +is_a: GO:0044699 ! single-organism process +created_by: janelomax +creation_date: 2012-09-19T15:56:06Z + +[Term] +id: GO:0044703 +name: multi-organism reproductive process +namespace: biological_process +def: "A biological process that directly contributes to the process of producing new individuals, involving another organism." [GOC:jl] +is_a: GO:0022414 ! reproductive process +is_a: GO:0051704 ! multi-organism process +created_by: janelomax +creation_date: 2012-09-19T15:56:30Z + +[Term] +id: GO:0044706 +name: multi-multicellular organism process +namespace: biological_process +def: "A multicellular organism process which involves another multicellular organism of the same or different species." [GOC:jl] +is_a: GO:0032501 ! multicellular organismal process +is_a: GO:0051704 ! multi-organism process +created_by: janelomax +creation_date: 2012-09-19T16:06:16Z + +[Term] +id: GO:0044707 +name: single-multicellular organism process +namespace: biological_process +def: "A biological process occurring within a single, multicellular organism." [GOC:jl] +is_a: GO:0032501 ! multicellular organismal process +is_a: GO:0044699 ! single-organism process +created_by: janelomax +creation_date: 2012-09-19T16:07:47Z + +[Term] +id: GO:0044708 +name: single-organism behavior +namespace: biological_process +def: "The specific behavior of a single organism in response to external or internal stimuli." [GOC:jl, GOC:pr] +is_a: GO:0007610 ! behavior +is_a: GO:0044699 ! single-organism process +created_by: janelomax +creation_date: 2012-09-20T14:06:08Z + +[Term] +id: GO:0044710 +name: single-organism metabolic process +namespace: biological_process +def: "A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism." [GOC:jl] +is_a: GO:0008152 ! metabolic process +is_a: GO:0044699 ! single-organism process +created_by: janelomax +creation_date: 2012-10-17T15:46:40Z + +[Term] +id: GO:0044711 +name: single-organism biosynthetic process +namespace: biological_process +def: "A biosynthetic process - chemical reactions and pathways resulting in the formation of substances - involving a single organism." [GOC:jl] +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0044710 ! single-organism metabolic process +created_by: janelomax +creation_date: 2012-10-17T15:52:18Z + +[Term] +id: GO:0044712 +name: single-organism catabolic process +namespace: biological_process +def: "A catabolic process - chemical reactions and pathways resulting in the breakdown of substances - which involves a single organism." [GOC:jl] +is_a: GO:0009056 ! catabolic process +is_a: GO:0044710 ! single-organism metabolic process +created_by: janelomax +creation_date: 2012-10-17T15:52:35Z + +[Term] +id: GO:0044723 +name: single-organism carbohydrate metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving carbohydrates, occurring within a single organism." [GOC:jl] +is_a: GO:0005975 ! carbohydrate metabolic process +is_a: GO:0044710 ! single-organism metabolic process +created_by: janelomax +creation_date: 2012-10-23T15:40:34Z + +[Term] +id: GO:0044724 +name: single-organism carbohydrate catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of carbohydrates, occurring within a single organism." [GOC:jl] +is_a: GO:0016052 ! carbohydrate catabolic process +is_a: GO:0044712 ! single-organism catabolic process +is_a: GO:0044723 ! single-organism carbohydrate metabolic process +created_by: janelomax +creation_date: 2012-10-23T16:34:39Z + +[Term] +id: GO:0044744 +name: protein targeting to nucleus +namespace: biological_process +def: "The process of directing proteins towards the nucleus, usually using signals contained within the protein." [GOC:jl] +is_a: GO:0006605 ! protein targeting +is_a: GO:0051169 ! nuclear transport +is_a: GO:0072594 ! establishment of protein localization to organelle +created_by: janelomax +creation_date: 2012-11-07T15:45:54Z + +[Term] +id: GO:0044763 +name: single-organism cellular process +namespace: biological_process +def: "Any process that is carried out at the cellular level, occurring within a single organism." [GOC:jl] +is_a: GO:0009987 ! cellular process +is_a: GO:0044699 ! single-organism process +created_by: janelomax +creation_date: 2012-12-11T16:56:55Z + +[Term] +id: GO:0044765 +name: single-organism transport +namespace: biological_process +def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism." [GOC:jl] +is_a: GO:0006810 ! transport +is_a: GO:0044699 ! single-organism process +created_by: janelomax +creation_date: 2012-12-13T16:25:32Z + +[Term] +id: GO:0044767 +name: single-organism developmental process +namespace: biological_process +def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism." [GOC:jl] +is_a: GO:0032502 ! developmental process +is_a: GO:0044699 ! single-organism process +created_by: janelomax +creation_date: 2012-12-19T12:21:31Z + +[Term] +id: GO:0044782 +name: cilium organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:jl] +comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. +synonym: "microtubule-based flagellum organization" EXACT [] +is_a: GO:0030030 ! cell projection organization +created_by: janelomax +creation_date: 2013-03-27T15:09:58Z + +[Term] +id: GO:0044798 +name: nuclear transcription factor complex +namespace: cellular_component +def: "A protein complex, located in the nucleus, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription." [GOC:jl] +is_a: GO:0005667 ! transcription factor complex +is_a: GO:0044428 ! nuclear part +intersection_of: GO:0005667 ! transcription factor complex +intersection_of: part_of GO:0005634 ! nucleus +created_by: janelomax +creation_date: 2013-08-28T12:12:27Z + +[Term] +id: GO:0044801 +name: single-organism membrane fusion +namespace: biological_process +def: "The membrane organization process that joins two lipid bilayers to form a single membrane, involving only one organism." [GOC:jl] +is_a: GO:0044802 ! single-organism membrane organization +is_a: GO:0061025 ! membrane fusion +created_by: janelomax +creation_date: 2013-09-10T15:08:20Z + +[Term] +id: GO:0044802 +name: single-organism membrane organization +namespace: biological_process +def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane, involving only one organism." [GOC:jl] +is_a: GO:0044699 ! single-organism process +is_a: GO:0061024 ! membrane organization +created_by: janelomax +creation_date: 2013-09-10T15:11:17Z + +[Term] +id: GO:0045013 +name: carbon catabolite repression of transcription +namespace: biological_process +def: "A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances." [GOC:mah, ISBN:0198506732, PMID:11018147, PMID:18359269, PMID:9618445] +subset: gosubset_prok +synonym: "carbon catabolite repression" EXACT [] +synonym: "negative regulation of transcription by carbon catabolites" EXACT [GOC:mah] +is_a: GO:0045892 ! negative regulation of transcription, DNA-templated +is_a: GO:0045990 ! carbon catabolite regulation of transcription + +[Term] +id: GO:0045014 +name: negative regulation of transcription by glucose +namespace: biological_process +def: "Any process involving glucose that stops, prevents or reduces the rate of transcription. The presence of glucose in the growth medium inhibits the synthesis of certain enzymes in bacteria growing on the medium. For example, transcription of some catabolic operons is under negative control by specific repressors and glucose is an anti-inducer of xylose utilization and glycerol kinase." [ISBN:0198506732, PMID:11018147] +subset: gosubset_prok +synonym: "down regulation of transcription by glucose" EXACT [] +synonym: "down-regulation of transcription by glucose" EXACT [] +synonym: "downregulation of transcription by glucose" EXACT [] +synonym: "glucose effect" EXACT [] +synonym: "glucose repression" EXACT [] +synonym: "inhibition of transcription by glucose" NARROW [] +is_a: GO:0045013 ! carbon catabolite repression of transcription +is_a: GO:0046015 ! regulation of transcription by glucose + +[Term] +id: GO:0045026 +name: plasma membrane fusion +namespace: biological_process +alt_id: GO:0006947 +def: "The joining of two or more lipid bilayer membranes that surround a cell." [GOC:elh, GOC:mtg_muscle] +synonym: "cell fusion" BROAD [] +synonym: "cell-cell fusion" BROAD [] +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0044801 ! single-organism membrane fusion + +[Term] +id: GO:0045056 +name: transcytosis +namespace: biological_process +def: "The directed movement of endocytosed material through the cell and its exocytosis from the plasma membrane at the opposite side." [ISBN:0716731363] +xref: Wikipedia:Transcytosis +is_a: GO:0016192 ! vesicle-mediated transport +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0045073 +name: regulation of chemokine biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of chemokines." [GOC:go_curators] +synonym: "regulation of chemokine anabolism" EXACT [] +synonym: "regulation of chemokine biosynthesis" EXACT [] +synonym: "regulation of chemokine formation" EXACT [] +synonym: "regulation of chemokine synthesis" EXACT [] +is_a: GO:0032642 ! regulation of chemokine production +is_a: GO:0042035 ! regulation of cytokine biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042033 ! chemokine biosynthetic process +relationship: regulates GO:0042033 ! chemokine biosynthetic process + +[Term] +id: GO:0045080 +name: positive regulation of chemokine biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of chemokines." [GOC:go_curators] +synonym: "activation of chemokine biosynthetic process" NARROW [] +synonym: "positive regulation of chemokine anabolism" EXACT [] +synonym: "positive regulation of chemokine biosynthesis" EXACT [] +synonym: "positive regulation of chemokine formation" EXACT [] +synonym: "positive regulation of chemokine synthesis" EXACT [] +synonym: "stimulation of chemokine biosynthetic process" NARROW [] +synonym: "up regulation of chemokine biosynthetic process" EXACT [] +synonym: "up-regulation of chemokine biosynthetic process" EXACT [] +synonym: "upregulation of chemokine biosynthetic process" EXACT [] +is_a: GO:0042108 ! positive regulation of cytokine biosynthetic process +is_a: GO:0045073 ! regulation of chemokine biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042033 ! chemokine biosynthetic process +relationship: positively_regulates GO:0042033 ! chemokine biosynthetic process + +[Term] +id: GO:0045087 +name: innate immune response +namespace: biological_process +alt_id: GO:0002226 +def: "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu] +comment: This term was improved by GO_REF:0000022. It was moved. +synonym: "innate immunity" EXACT [GOC:pg] +synonym: "nonspecific immune response" EXACT [] +xref: Reactome:REACT_101086 "Innate Immune System, Bos taurus" +xref: Reactome:REACT_108180 "Innate Immune System, Arabidopsis thaliana" +xref: Reactome:REACT_110518 "Innate Immune System, Taeniopygia guttata" +xref: Reactome:REACT_31297 "Innate Immune System, Xenopus tropicalis" +xref: Reactome:REACT_32992 "Innate Immune System, Gallus gallus" +xref: Reactome:REACT_6802 "Innate Immune System, Homo sapiens" +xref: Reactome:REACT_78575 "Innate Immune System, Canis familiaris" +xref: Reactome:REACT_81815 "Innate Immune System, Saccharomyces cerevisiae" +xref: Reactome:REACT_81962 "Innate Immune System, Dictyostelium discoideum" +xref: Reactome:REACT_86987 "Innate Immune System, Mus musculus" +xref: Reactome:REACT_88681 "Innate Immune System, Drosophila melanogaster" +xref: Reactome:REACT_90618 "Innate Immune System, Caenorhabditis elegans" +xref: Reactome:REACT_90753 "Innate Immune System, Schizosaccharomyces pombe" +xref: Reactome:REACT_94451 "Innate Immune System, Rattus norvegicus" +xref: Reactome:REACT_95471 "Innate Immune System, Sus scrofa" +xref: Reactome:REACT_95642 "Innate Immune System, Oryza sativa" +xref: Reactome:REACT_99610 "Innate Immune System, Danio rerio" +xref: Wikipedia:Innate_immune_system +is_a: GO:0006952 ! defense response +is_a: GO:0006955 ! immune response + +[Term] +id: GO:0045088 +name: regulation of innate immune response +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection." [GOC:ebc] +is_a: GO:0031347 ! regulation of defense response +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045087 ! innate immune response +relationship: regulates GO:0045087 ! innate immune response + +[Term] +id: GO:0045121 +name: membrane raft +namespace: cellular_component +def: "Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions." [PMID:16645198] +synonym: "GEM domain" RELATED [] +synonym: "glycolipid-enriched membrane domain" RELATED [] +synonym: "lipid raft" EXACT [] +xref: Wikipedia:Lipid_raft +is_a: GO:0044425 ! membrane part + +[Term] +id: GO:0045124 +name: regulation of bone resorption +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of bone tissue loss (resorption)." [GOC:ai] +is_a: GO:0032844 ! regulation of homeostatic process +is_a: GO:0046850 ! regulation of bone remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045453 ! bone resorption +relationship: regulates GO:0045453 ! bone resorption + +[Term] +id: GO:0045136 +name: development of secondary sexual characteristics +namespace: biological_process +def: "The process whose specific outcome is the progression of the secondary sexual characteristics over time, from their formation to the mature structures. In humans, these include growth of axillary, chest, and pubic hair, voice changes, testicular/penile enlargement, breast development and menstrual periods. Development occurs in response to sex hormone secretion." [GOC:ai] +is_a: GO:0003006 ! developmental process involved in reproduction +relationship: part_of GO:0007275 ! multicellular organismal development +relationship: part_of GO:0007548 ! sex differentiation + +[Term] +id: GO:0045137 +name: development of primary sexual characteristics +namespace: biological_process +def: "The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion." [GOC:ai] +is_a: GO:0003006 ! developmental process involved in reproduction +relationship: part_of GO:0007275 ! multicellular organismal development +relationship: part_of GO:0007548 ! sex differentiation + +[Term] +id: GO:0045165 +name: cell fate commitment +namespace: biological_process +def: "The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field." [ISBN:0716731185] +comment: Note that this term was 'cell fate determination' but the term name was changed to better match its existing definition and the child term 'cell fate determination; GO:0001709' was also created. +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0030154 ! cell differentiation + +[Term] +id: GO:0045168 +name: cell-cell signaling involved in cell fate commitment +namespace: biological_process +def: "Signaling at long or short range between cells that results in the commitment of a cell to a certain fate." [GOC:dph, GOC:go_curators, GOC:tb] +synonym: "cell fate commitment, cell-cell signaling" EXACT [] +synonym: "cell fate commitment, cell-cell signalling" EXACT [] +synonym: "cell-cell signaling during in cell fate commitment" EXACT [] +synonym: "cell-cell signaling resulting in cell fate commitment" EXACT [] +synonym: "cell-cell signalling during cell fate commitment" EXACT [] +synonym: "cell-cell signalling involved in cell fate specification" NARROW [GOC:dph, GOC:tb] +synonym: "cell-cell signalling resulting in cell fate commitment" EXACT [] +is_a: GO:0007267 ! cell-cell signaling +intersection_of: GO:0007267 ! cell-cell signaling +intersection_of: part_of GO:0045165 ! cell fate commitment +relationship: part_of GO:0045165 ! cell fate commitment + +[Term] +id: GO:0045177 +name: apical part of cell +namespace: cellular_component +def: "The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue." [GOC:mah, ISBN:0815316194] +subset: goslim_pir +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0045184 +name: establishment of protein localization +namespace: biological_process +def: "The directed movement of a protein to a specific location." [GOC:bf] +subset: gosubset_prok +synonym: "establishment of protein localisation" EXACT [GOC:mah] +synonym: "protein positioning" EXACT [] +synonym: "protein recruitment" EXACT [] +is_a: GO:0051234 ! establishment of localization +relationship: part_of GO:0008104 ! protein localization + +[Term] +id: GO:0045185 +name: maintenance of protein location +namespace: biological_process +def: "Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away." [GOC:bf] +subset: gosubset_prok +synonym: "active protein retrieval" NARROW [] +synonym: "maintenance of protein localization" RELATED [GOC:dph, GOC:tb] +synonym: "protein retention" NARROW [] +synonym: "protein sequestering" NARROW [] +is_a: GO:0051235 ! maintenance of location +relationship: part_of GO:0008104 ! protein localization + +[Term] +id: GO:0045202 +name: synapse +namespace: cellular_component +def: "The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [ISBN:0198506732] +subset: goslim_pir +synonym: "electrotonic synapse" RELATED [NIF_Subcellular:sao1311109124] +synonym: "mixed synapse" NARROW [NIF_Subcellular:sao1506103497] +synonym: "synaptic junction" EXACT [] +xref: NIF_Subcellular:sao914572699 +xref: Wikipedia:Chemical_synapse +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0045216 +name: cell-cell junction organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] +synonym: "cell-cell junction assembly and maintenance" EXACT [] +synonym: "cell-cell junction biogenesis" RELATED [] +synonym: "cell-cell junction organisation" EXACT [GOC:mah] +synonym: "intercellular junction assembly and maintenance" EXACT [] +xref: Reactome:REACT_103817 "Cell-cell junction organization, Sus scrofa" +xref: Reactome:REACT_107288 "Cell-cell junction organization, Gallus gallus" +xref: Reactome:REACT_108264 "Cell-cell junction organization, Canis familiaris" +xref: Reactome:REACT_114636 "Cell-cell junction organization, Drosophila melanogaster" +xref: Reactome:REACT_19331 "Cell-cell junction organization, Homo sapiens" +xref: Reactome:REACT_30769 "Cell-cell junction organization, Danio rerio" +xref: Reactome:REACT_81733 "Cell-cell junction organization, Rattus norvegicus" +xref: Reactome:REACT_87932 "Cell-cell junction organization, Mus musculus" +xref: Reactome:REACT_88224 "Cell-cell junction organization, Bos taurus" +xref: Reactome:REACT_94850 "Cell-cell junction organization, Taeniopygia guttata" +xref: Reactome:REACT_95996 "Cell-cell junction organization, Xenopus tropicalis" +is_a: GO:0034330 ! cell junction organization + +[Term] +id: GO:0045294 +name: alpha-catenin binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with the alpha subunit of the catenin complex." [GOC:bf] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0045296 +name: cadherin binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion." [GOC:bf] +is_a: GO:0050839 ! cell adhesion molecule binding + +[Term] +id: GO:0045321 +name: leukocyte activation +namespace: biological_process +def: "A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor." [GOC:add] +synonym: "immune cell activation" EXACT [] +synonym: "leucocyte activation" EXACT [] +xref: Wikipedia:Immunologic_activation +is_a: GO:0001775 ! cell activation +is_a: GO:0002376 ! immune system process + +[Term] +id: GO:0045408 +name: regulation of interleukin-6 biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-6." [GOC:go_curators] +synonym: "regulation of IL-6 biosynthesis" EXACT [] +synonym: "regulation of IL-6 biosynthetic process" EXACT [] +synonym: "regulation of interleukin-6 anabolism" EXACT [] +synonym: "regulation of interleukin-6 biosynthesis" EXACT [] +synonym: "regulation of interleukin-6 formation" EXACT [] +synonym: "regulation of interleukin-6 synthesis" EXACT [] +is_a: GO:0032675 ! regulation of interleukin-6 production +is_a: GO:0042035 ! regulation of cytokine biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042226 ! interleukin-6 biosynthetic process +relationship: regulates GO:0042226 ! interleukin-6 biosynthetic process + +[Term] +id: GO:0045409 +name: negative regulation of interleukin-6 biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-6." [GOC:go_curators] +synonym: "down regulation of interleukin-6 biosynthetic process" EXACT [] +synonym: "down-regulation of interleukin-6 biosynthetic process" EXACT [] +synonym: "downregulation of interleukin-6 biosynthetic process" EXACT [] +synonym: "inhibition of interleukin-6 biosynthetic process" NARROW [] +synonym: "negative regulation of IL-6 biosynthesis" EXACT [] +synonym: "negative regulation of IL-6 biosynthetic process" EXACT [] +synonym: "negative regulation of interleukin-6 anabolism" EXACT [] +synonym: "negative regulation of interleukin-6 biosynthesis" EXACT [] +synonym: "negative regulation of interleukin-6 formation" EXACT [] +synonym: "negative regulation of interleukin-6 synthesis" EXACT [] +is_a: GO:0042036 ! negative regulation of cytokine biosynthetic process +is_a: GO:0045408 ! regulation of interleukin-6 biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042226 ! interleukin-6 biosynthetic process +relationship: negatively_regulates GO:0042226 ! interleukin-6 biosynthetic process + +[Term] +id: GO:0045444 +name: fat cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat." [CL:0000136, GOC:go_curators] +synonym: "adipocyte cell differentiation" EXACT [] +synonym: "adipocyte differentiation" EXACT [] +synonym: "adipogenesis" RELATED [] +synonym: "adipose cell differentiation" EXACT [] +is_a: GO:0030154 ! cell differentiation + +[Term] +id: GO:0045446 +name: endothelial cell differentiation +namespace: biological_process +def: "The process in which a mesodermal, bone marrow or neural crest cell acquires specialized features of an endothelial cell, a thin flattened cell. A layer of such cells lines the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium." [CL:0000115, GOC:go_curators] +is_a: GO:0030855 ! epithelial cell differentiation +relationship: part_of GO:0003158 ! endothelium development + +[Term] +id: GO:0045453 +name: bone resorption +namespace: biological_process +def: "The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products." [GOC:mah, PMID:10968780] +xref: Wikipedia:Bone_resorption +is_a: GO:0001894 ! tissue homeostasis +relationship: part_of GO:0046849 ! bone remodeling + +[Term] +id: GO:0045577 +name: regulation of B cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of B cell differentiation." [GOC:go_curators] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "regulation of B cell development" RELATED [GOC:add] +synonym: "regulation of B lymphocyte differentiation" EXACT [] +synonym: "regulation of B-cell differentiation" EXACT [] +synonym: "regulation of B-lymphocyte differentiation" EXACT [] +is_a: GO:0045619 ! regulation of lymphocyte differentiation +is_a: GO:0050864 ! regulation of B cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030183 ! B cell differentiation +relationship: regulates GO:0030183 ! B cell differentiation + +[Term] +id: GO:0045578 +name: negative regulation of B cell differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation." [GOC:go_curators] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "down regulation of B cell differentiation" EXACT [] +synonym: "down-regulation of B cell differentiation" EXACT [] +synonym: "downregulation of B cell differentiation" EXACT [] +synonym: "inhibition of B cell differentiation" NARROW [] +synonym: "negative regulation of B cell development" RELATED [GOC:add] +synonym: "negative regulation of B lymphocyte differentiation" EXACT [] +synonym: "negative regulation of B-cell differentiation" EXACT [] +synonym: "negative regulation of B-lymphocyte differentiation" EXACT [] +is_a: GO:0045577 ! regulation of B cell differentiation +is_a: GO:0045620 ! negative regulation of lymphocyte differentiation +is_a: GO:0050869 ! negative regulation of B cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030183 ! B cell differentiation +relationship: negatively_regulates GO:0030183 ! B cell differentiation + +[Term] +id: GO:0045580 +name: regulation of T cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of T cell differentiation." [GOC:go_curators] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "regulation of T cell development" RELATED [GOC:add] +synonym: "regulation of T lymphocyte differentiation" EXACT [] +synonym: "regulation of T-cell differentiation" EXACT [] +synonym: "regulation of T-lymphocyte differentiation" EXACT [] +is_a: GO:0045619 ! regulation of lymphocyte differentiation +is_a: GO:0050863 ! regulation of T cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030217 ! T cell differentiation +relationship: regulates GO:0030217 ! T cell differentiation + +[Term] +id: GO:0045581 +name: negative regulation of T cell differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation." [GOC:go_curators] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "down regulation of T cell differentiation" EXACT [] +synonym: "down-regulation of T cell differentiation" EXACT [] +synonym: "downregulation of T cell differentiation" EXACT [] +synonym: "inhibition of T cell differentiation" NARROW [] +synonym: "negative regulation of T cell development" RELATED [GOC:add] +synonym: "negative regulation of T lymphocyte differentiation" EXACT [] +synonym: "negative regulation of T-cell differentiation" EXACT [] +synonym: "negative regulation of T-lymphocyte differentiation" EXACT [] +is_a: GO:0045580 ! regulation of T cell differentiation +is_a: GO:0045620 ! negative regulation of lymphocyte differentiation +is_a: GO:0050868 ! negative regulation of T cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030217 ! T cell differentiation +relationship: negatively_regulates GO:0030217 ! T cell differentiation + +[Term] +id: GO:0045595 +name: regulation of cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030154 ! cell differentiation +relationship: regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045596 +name: negative regulation of cell differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of cell differentiation" EXACT [] +synonym: "down-regulation of cell differentiation" EXACT [] +synonym: "downregulation of cell differentiation" EXACT [] +synonym: "inhibition of cell differentiation" NARROW [] +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051093 ! negative regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030154 ! cell differentiation +relationship: negatively_regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045597 +name: positive regulation of cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell differentiation." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of cell differentiation" NARROW [] +synonym: "stimulation of cell differentiation" NARROW [] +synonym: "up regulation of cell differentiation" EXACT [] +synonym: "up-regulation of cell differentiation" EXACT [] +synonym: "upregulation of cell differentiation" EXACT [] +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030154 ! cell differentiation +relationship: positively_regulates GO:0030154 ! cell differentiation + +[Term] +id: GO:0045598 +name: regulation of fat cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of adipocyte differentiation." [GOC:go_curators] +synonym: "regulation of adipocyte cell differentiation" EXACT [] +synonym: "regulation of adipocyte differentiation" EXACT [] +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045444 ! fat cell differentiation +relationship: regulates GO:0045444 ! fat cell differentiation + +[Term] +id: GO:0045599 +name: negative regulation of fat cell differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation." [GOC:go_curators] +synonym: "down regulation of fat cell differentiation" EXACT [] +synonym: "down-regulation of fat cell differentiation" EXACT [] +synonym: "downregulation of fat cell differentiation" EXACT [] +synonym: "inhibition of fat cell differentiation" NARROW [] +synonym: "negative regulation of adipocyte cell differentiation" EXACT [] +synonym: "negative regulation of adipocyte differentiation" EXACT [] +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0045598 ! regulation of fat cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0045444 ! fat cell differentiation +relationship: negatively_regulates GO:0045444 ! fat cell differentiation + +[Term] +id: GO:0045600 +name: positive regulation of fat cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of adipocyte differentiation." [GOC:go_curators] +synonym: "activation of fat cell differentiation" NARROW [] +synonym: "positive regulation of adipocyte cell differentiation" EXACT [] +synonym: "positive regulation of adipocyte differentiation" EXACT [] +synonym: "stimulation of fat cell differentiation" NARROW [] +synonym: "up regulation of fat cell differentiation" EXACT [] +synonym: "up-regulation of fat cell differentiation" EXACT [] +synonym: "upregulation of fat cell differentiation" EXACT [] +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0045598 ! regulation of fat cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0045444 ! fat cell differentiation +relationship: positively_regulates GO:0045444 ! fat cell differentiation + +[Term] +id: GO:0045601 +name: regulation of endothelial cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of endothelial cell differentiation." [GOC:go_curators] +is_a: GO:0030856 ! regulation of epithelial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045446 ! endothelial cell differentiation +relationship: regulates GO:0045446 ! endothelial cell differentiation + +[Term] +id: GO:0045603 +name: positive regulation of endothelial cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation." [GOC:go_curators] +synonym: "activation of endothelial cell differentiation" NARROW [] +synonym: "stimulation of endothelial cell differentiation" NARROW [] +synonym: "up regulation of endothelial cell differentiation" EXACT [] +synonym: "up-regulation of endothelial cell differentiation" EXACT [] +synonym: "upregulation of endothelial cell differentiation" EXACT [] +is_a: GO:0030858 ! positive regulation of epithelial cell differentiation +is_a: GO:0045601 ! regulation of endothelial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0045446 ! endothelial cell differentiation +relationship: positively_regulates GO:0045446 ! endothelial cell differentiation + +[Term] +id: GO:0045619 +name: regulation of lymphocyte differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of lymphocyte differentiation." [GOC:go_curators] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "regulation of lymphocyte development" RELATED [GOC:add] +is_a: GO:0051249 ! regulation of lymphocyte activation +is_a: GO:1902105 ! regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030098 ! lymphocyte differentiation +relationship: regulates GO:0030098 ! lymphocyte differentiation + +[Term] +id: GO:0045620 +name: negative regulation of lymphocyte differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte differentiation." [GOC:go_curators] +comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. +synonym: "down regulation of lymphocyte differentiation" EXACT [] +synonym: "down-regulation of lymphocyte differentiation" EXACT [] +synonym: "downregulation of lymphocyte differentiation" EXACT [] +synonym: "inhibition of lymphocyte differentiation" NARROW [] +synonym: "negative regulation of lymphocyte development" RELATED [GOC:add] +is_a: GO:0045619 ! regulation of lymphocyte differentiation +is_a: GO:0051250 ! negative regulation of lymphocyte activation +is_a: GO:1902106 ! negative regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030098 ! lymphocyte differentiation +relationship: negatively_regulates GO:0030098 ! lymphocyte differentiation + +[Term] +id: GO:0045637 +name: regulation of myeloid cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of myeloid cell differentiation." [GOC:go_curators] +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030099 ! myeloid cell differentiation +relationship: regulates GO:0030099 ! myeloid cell differentiation + +[Term] +id: GO:0045638 +name: negative regulation of myeloid cell differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation." [GOC:go_curators] +synonym: "down regulation of myeloid cell differentiation" EXACT [] +synonym: "down-regulation of myeloid cell differentiation" EXACT [] +synonym: "downregulation of myeloid cell differentiation" EXACT [] +synonym: "inhibition of myeloid cell differentiation" NARROW [] +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0045637 ! regulation of myeloid cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030099 ! myeloid cell differentiation +relationship: negatively_regulates GO:0030099 ! myeloid cell differentiation + +[Term] +id: GO:0045639 +name: positive regulation of myeloid cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation." [GOC:go_curators] +synonym: "activation of myeloid cell differentiation" NARROW [] +synonym: "stimulation of myeloid cell differentiation" NARROW [] +synonym: "up regulation of myeloid cell differentiation" EXACT [] +synonym: "up-regulation of myeloid cell differentiation" EXACT [] +synonym: "upregulation of myeloid cell differentiation" EXACT [] +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0045637 ! regulation of myeloid cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030099 ! myeloid cell differentiation +relationship: positively_regulates GO:0030099 ! myeloid cell differentiation + +[Term] +id: GO:0045655 +name: regulation of monocyte differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of monocyte differentiation." [GOC:go_curators] +is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030224 ! monocyte differentiation +relationship: regulates GO:0030224 ! monocyte differentiation + +[Term] +id: GO:0045657 +name: positive regulation of monocyte differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of monocyte differentiation." [GOC:go_curators] +synonym: "activation of monocyte differentiation" NARROW [] +synonym: "stimulation of monocyte differentiation" NARROW [] +synonym: "up regulation of monocyte differentiation" EXACT [] +synonym: "up-regulation of monocyte differentiation" EXACT [] +synonym: "upregulation of monocyte differentiation" EXACT [] +is_a: GO:0002763 ! positive regulation of myeloid leukocyte differentiation +is_a: GO:0045655 ! regulation of monocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030224 ! monocyte differentiation +relationship: positively_regulates GO:0030224 ! monocyte differentiation + +[Term] +id: GO:0045664 +name: regulation of neuron differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of neuron differentiation." [GOC:go_curators] +is_a: GO:0050767 ! regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030182 ! neuron differentiation +relationship: regulates GO:0030182 ! neuron differentiation + +[Term] +id: GO:0045665 +name: negative regulation of neuron differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation." [GOC:go_curators] +synonym: "down regulation of neuron differentiation" EXACT [] +synonym: "down-regulation of neuron differentiation" EXACT [] +synonym: "downregulation of neuron differentiation" EXACT [] +synonym: "inhibition of neuron differentiation" NARROW [] +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0045664 ! regulation of neuron differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030182 ! neuron differentiation +relationship: negatively_regulates GO:0030182 ! neuron differentiation + +[Term] +id: GO:0045666 +name: positive regulation of neuron differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of neuron differentiation." [GOC:go_curators] +synonym: "activation of neuron differentiation" NARROW [] +synonym: "stimulation of neuron differentiation" NARROW [] +synonym: "up regulation of neuron differentiation" EXACT [] +synonym: "up-regulation of neuron differentiation" EXACT [] +synonym: "upregulation of neuron differentiation" EXACT [] +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0045664 ! regulation of neuron differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030182 ! neuron differentiation +relationship: positively_regulates GO:0030182 ! neuron differentiation + +[Term] +id: GO:0045667 +name: regulation of osteoblast differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of osteoblast differentiation." [GOC:go_curators] +is_a: GO:0030278 ! regulation of ossification +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001649 ! osteoblast differentiation +relationship: regulates GO:0001649 ! osteoblast differentiation + +[Term] +id: GO:0045668 +name: negative regulation of osteoblast differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation." [GOC:go_curators] +synonym: "down regulation of osteoblast differentiation" EXACT [] +synonym: "down-regulation of osteoblast differentiation" EXACT [] +synonym: "downregulation of osteoblast differentiation" EXACT [] +synonym: "inhibition of osteoblast differentiation" NARROW [] +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:0045667 ! regulation of osteoblast differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001649 ! osteoblast differentiation +relationship: negatively_regulates GO:0001649 ! osteoblast differentiation + +[Term] +id: GO:0045669 +name: positive regulation of osteoblast differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of osteoblast differentiation." [GOC:go_curators] +synonym: "activation of osteoblast differentiation" NARROW [] +synonym: "stimulation of osteoblast differentiation" NARROW [] +synonym: "up regulation of osteoblast differentiation" EXACT [] +synonym: "up-regulation of osteoblast differentiation" EXACT [] +synonym: "upregulation of osteoblast differentiation" EXACT [] +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0045667 ! regulation of osteoblast differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001649 ! osteoblast differentiation +relationship: positively_regulates GO:0001649 ! osteoblast differentiation + +[Term] +id: GO:0045670 +name: regulation of osteoclast differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of osteoclast differentiation." [GOC:go_curators] +is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030316 ! osteoclast differentiation +relationship: regulates GO:0030316 ! osteoclast differentiation + +[Term] +id: GO:0045671 +name: negative regulation of osteoclast differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation." [GOC:go_curators] +synonym: "down regulation of osteoclast differentiation" EXACT [] +synonym: "down-regulation of osteoclast differentiation" EXACT [] +synonym: "downregulation of osteoclast differentiation" EXACT [] +synonym: "inhibition of osteoclast differentiation" NARROW [] +is_a: GO:0002762 ! negative regulation of myeloid leukocyte differentiation +is_a: GO:0045670 ! regulation of osteoclast differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030316 ! osteoclast differentiation +relationship: negatively_regulates GO:0030316 ! osteoclast differentiation + +[Term] +id: GO:0045685 +name: regulation of glial cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of glia cell differentiation." [GOC:go_curators] +synonym: "regulation of glia cell differentiation" EXACT [] +synonym: "regulation of neuroglia differentiation" EXACT [] +is_a: GO:0014013 ! regulation of gliogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010001 ! glial cell differentiation +relationship: regulates GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0045686 +name: negative regulation of glial cell differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation." [GOC:go_curators] +synonym: "down regulation of glial cell differentiation" EXACT [] +synonym: "down-regulation of glial cell differentiation" EXACT [] +synonym: "downregulation of glial cell differentiation" EXACT [] +synonym: "inhibition of glial cell differentiation" NARROW [] +synonym: "negative regulation of glia cell differentiation" EXACT [] +synonym: "negative regulation of neuroglia differentiation" EXACT [] +is_a: GO:0014014 ! negative regulation of gliogenesis +is_a: GO:0045685 ! regulation of glial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010001 ! glial cell differentiation +relationship: negatively_regulates GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0045732 +name: positive regulation of protein catabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of protein catabolic process" NARROW [] +synonym: "positive regulation of protein breakdown" EXACT [] +synonym: "positive regulation of protein catabolism" EXACT [] +synonym: "positive regulation of protein degradation" EXACT [] +synonym: "stimulation of protein catabolic process" NARROW [] +synonym: "up regulation of protein catabolic process" EXACT [] +synonym: "up-regulation of protein catabolic process" EXACT [] +synonym: "upregulation of protein catabolic process" EXACT [] +is_a: GO:0009896 ! positive regulation of catabolic process +is_a: GO:0042176 ! regulation of protein catabolic process +is_a: GO:0051247 ! positive regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0030163 ! protein catabolic process +relationship: positively_regulates GO:0030163 ! protein catabolic process + +[Term] +id: GO:0045743 +name: positive regulation of fibroblast growth factor receptor signaling pathway +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:go_curators] +synonym: "activation of fibroblast growth factor receptor signaling pathway" NARROW [] +synonym: "positive regulation of FGF receptor signaling pathway" EXACT [] +synonym: "positive regulation of FGF receptor signalling pathway" EXACT [] +synonym: "positive regulation of FGFR signaling pathway" EXACT [] +synonym: "stimulation of fibroblast growth factor receptor signaling pathway" NARROW [] +synonym: "up regulation of fibroblast growth factor receptor signaling pathway" EXACT [] +synonym: "up-regulation of fibroblast growth factor receptor signaling pathway" EXACT [] +synonym: "upregulation of fibroblast growth factor receptor signaling pathway" EXACT [] +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0040036 ! regulation of fibroblast growth factor receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway +relationship: positively_regulates GO:0008543 ! fibroblast growth factor receptor signaling pathway + +[Term] +id: GO:0045747 +name: positive regulation of Notch signaling pathway +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the Notch signaling pathway." [GOC:go_curators] +synonym: "activation of Notch signaling pathway" NARROW [] +synonym: "positive regulation of N signaling pathway" EXACT [] +synonym: "positive regulation of N signalling pathway" EXACT [] +synonym: "positive regulation of Notch signalling pathway" EXACT [] +synonym: "stimulation of Notch signaling pathway" NARROW [] +synonym: "up regulation of Notch signaling pathway" EXACT [] +synonym: "up-regulation of Notch signaling pathway" EXACT [] +synonym: "upregulation of Notch signaling pathway" EXACT [] +is_a: GO:0008593 ! regulation of Notch signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007219 ! Notch signaling pathway +relationship: positively_regulates GO:0007219 ! Notch signaling pathway + +[Term] +id: GO:0045765 +name: regulation of angiogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of angiogenesis." [GOC:go_curators] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:1901342 ! regulation of vasculature development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001525 ! angiogenesis +relationship: regulates GO:0001525 ! angiogenesis + +[Term] +id: GO:0045766 +name: positive regulation of angiogenesis +namespace: biological_process +def: "Any process that activates or increases angiogenesis." [GOC:go_curators] +synonym: "activation of angiogenesis" NARROW [] +synonym: "stimulation of angiogenesis" NARROW [] +synonym: "up regulation of angiogenesis" EXACT [] +synonym: "up-regulation of angiogenesis" EXACT [] +synonym: "upregulation of angiogenesis" EXACT [] +is_a: GO:0045765 ! regulation of angiogenesis +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001525 ! angiogenesis +relationship: positively_regulates GO:0001525 ! angiogenesis + +[Term] +id: GO:0045778 +name: positive regulation of ossification +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of bone formation." [GOC:go_curators] +synonym: "activation of ossification" NARROW [] +synonym: "positive regulation of bone biosynthesis" EXACT [] +synonym: "positive regulation of bone formation" EXACT [] +synonym: "stimulation of ossification" NARROW [] +synonym: "up regulation of ossification" EXACT [] +synonym: "up-regulation of ossification" EXACT [] +synonym: "upregulation of ossification" EXACT [] +is_a: GO:0030278 ! regulation of ossification +is_a: GO:0051240 ! positive regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001503 ! ossification +relationship: positively_regulates GO:0001503 ! ossification + +[Term] +id: GO:0045780 +name: positive regulation of bone resorption +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of bone resorption." [GOC:go_curators] +synonym: "activation of bone resorption" NARROW [] +synonym: "stimulation of bone resorption" NARROW [] +synonym: "up regulation of bone resorption" EXACT [] +synonym: "up-regulation of bone resorption" EXACT [] +synonym: "upregulation of bone resorption" EXACT [] +is_a: GO:0032846 ! positive regulation of homeostatic process +is_a: GO:0045124 ! regulation of bone resorption +is_a: GO:0046852 ! positive regulation of bone remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0045453 ! bone resorption +relationship: positively_regulates GO:0045453 ! bone resorption + +[Term] +id: GO:0045785 +name: positive regulation of cell adhesion +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell adhesion." [GOC:go_curators] +synonym: "activation of cell adhesion" NARROW [] +synonym: "stimulation of cell adhesion" NARROW [] +synonym: "up regulation of cell adhesion" EXACT [] +synonym: "up-regulation of cell adhesion" EXACT [] +synonym: "upregulation of cell adhesion" EXACT [] +is_a: GO:0030155 ! regulation of cell adhesion +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007155 ! cell adhesion +relationship: positively_regulates GO:0007155 ! cell adhesion + +[Term] +id: GO:0045786 +name: negative regulation of cell cycle +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle." [GOC:dph, GOC:go_curators, GOC:tb] +synonym: "down regulation of progression through cell cycle" EXACT [] +synonym: "down-regulation of progression through cell cycle" EXACT [] +synonym: "downregulation of progression through cell cycle" EXACT [] +synonym: "inhibition of progression through cell cycle" NARROW [] +synonym: "negative regulation of cell cycle progression" EXACT [] +synonym: "negative regulation of progression through cell cycle" EXACT [] +xref: Reactome:REACT_102454 "p75NTR negatively regulates cell cycle via SC1, Taeniopygia guttata" +xref: Reactome:REACT_102880 "p75NTR negatively regulates cell cycle via SC1, Xenopus tropicalis" +xref: Reactome:REACT_112803 "p75NTR negatively regulates cell cycle via SC1, Drosophila melanogaster" +xref: Reactome:REACT_13695 "p75NTR negatively regulates cell cycle via SC1, Homo sapiens" +xref: Reactome:REACT_31060 "p75NTR negatively regulates cell cycle via SC1, Rattus norvegicus" +xref: Reactome:REACT_32970 "p75NTR negatively regulates cell cycle via SC1, Sus scrofa" +xref: Reactome:REACT_78219 "p75NTR negatively regulates cell cycle via SC1, Gallus gallus" +xref: Reactome:REACT_83256 "p75NTR negatively regulates cell cycle via SC1, Bos taurus" +xref: Reactome:REACT_88108 "p75NTR negatively regulates cell cycle via SC1, Canis familiaris" +xref: Reactome:REACT_93253 "p75NTR negatively regulates cell cycle via SC1, Danio rerio" +xref: Reactome:REACT_99982 "p75NTR negatively regulates cell cycle via SC1, Mus musculus" +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051726 ! regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007049 ! cell cycle +relationship: negatively_regulates GO:0007049 ! cell cycle + +[Term] +id: GO:0045787 +name: positive regulation of cell cycle +namespace: biological_process +def: "Any process that activates or increases the rate or extent of progression through the cell cycle." [GOC:go_curators] +synonym: "activation of progression through cell cycle" NARROW [] +synonym: "positive regulation of cell cycle progression" EXACT [] +synonym: "positive regulation of progression through cell cycle" EXACT [GOC:dph, GOC:tb] +synonym: "stimulation of progression through cell cycle" NARROW [] +synonym: "up regulation of progression through cell cycle" EXACT [] +synonym: "up-regulation of progression through cell cycle" EXACT [] +synonym: "upregulation of progression through cell cycle" EXACT [] +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051726 ! regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007049 ! cell cycle +relationship: positively_regulates GO:0007049 ! cell cycle + +[Term] +id: GO:0045807 +name: positive regulation of endocytosis +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of endocytosis." [GOC:go_curators] +synonym: "activation of endocytosis" NARROW [] +synonym: "stimulation of endocytosis" NARROW [] +synonym: "up regulation of endocytosis" EXACT [] +synonym: "up-regulation of endocytosis" EXACT [] +synonym: "upregulation of endocytosis" EXACT [] +is_a: GO:0030100 ! regulation of endocytosis +is_a: GO:0051050 ! positive regulation of transport +is_a: GO:0051130 ! positive regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006897 ! endocytosis +relationship: positively_regulates GO:0006897 ! endocytosis + +[Term] +id: GO:0045833 +name: negative regulation of lipid metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of lipid metabolic process" EXACT [] +synonym: "down-regulation of lipid metabolic process" EXACT [] +synonym: "downregulation of lipid metabolic process" EXACT [] +synonym: "inhibition of lipid metabolic process" NARROW [] +synonym: "negative regulation of lipid metabolism" EXACT [] +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0019216 ! regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006629 ! lipid metabolic process +relationship: negatively_regulates GO:0006629 ! lipid metabolic process + +[Term] +id: GO:0045834 +name: positive regulation of lipid metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of lipid metabolic process" NARROW [] +synonym: "positive regulation of lipid metabolism" EXACT [] +synonym: "stimulation of lipid metabolic process" NARROW [] +synonym: "up regulation of lipid metabolic process" EXACT [] +synonym: "up-regulation of lipid metabolic process" EXACT [] +synonym: "upregulation of lipid metabolic process" EXACT [] +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0019216 ! regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006629 ! lipid metabolic process +relationship: positively_regulates GO:0006629 ! lipid metabolic process + +[Term] +id: GO:0045836 +name: positive regulation of meiosis +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of meiosis." [GOC:go_curators] +synonym: "activation of meiosis" NARROW [] +synonym: "stimulation of meiosis" NARROW [] +synonym: "up regulation of meiosis" EXACT [] +synonym: "up-regulation of meiosis" EXACT [] +synonym: "upregulation of meiosis" EXACT [] +is_a: GO:0040020 ! regulation of meiosis +is_a: GO:0090068 ! positive regulation of cell cycle process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007126 ! meiosis +relationship: positively_regulates GO:0007126 ! meiosis + +[Term] +id: GO:0045840 +name: positive regulation of mitosis +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of mitosis." [GOC:go_curators] +synonym: "activation of mitosis" NARROW [] +synonym: "mitogenic activity" NARROW [] +synonym: "stimulation of mitosis" NARROW [] +synonym: "up regulation of mitosis" EXACT [] +synonym: "up-regulation of mitosis" EXACT [] +synonym: "upregulation of mitosis" EXACT [] +is_a: GO:0007088 ! regulation of mitosis +is_a: GO:0045787 ! positive regulation of cell cycle +is_a: GO:0051785 ! positive regulation of nuclear division +is_a: GO:0090068 ! positive regulation of cell cycle process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007067 ! mitosis +relationship: positively_regulates GO:0007067 ! mitosis + +[Term] +id: GO:0045859 +name: regulation of protein kinase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of protein kinase activity." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0001932 ! regulation of protein phosphorylation +is_a: GO:0043549 ! regulation of kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004672 ! protein kinase activity +relationship: regulates GO:0004672 ! protein kinase activity + +[Term] +id: GO:0045860 +name: positive regulation of protein kinase activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of protein kinase activity." [GOC:go_curators] +subset: gosubset_prok +synonym: "stimulation of protein kinase activity" NARROW [] +synonym: "up regulation of protein kinase activity" EXACT [] +synonym: "up-regulation of protein kinase activity" EXACT [] +synonym: "upregulation of protein kinase activity" EXACT [] +is_a: GO:0001934 ! positive regulation of protein phosphorylation +is_a: GO:0033674 ! positive regulation of kinase activity +is_a: GO:0045859 ! regulation of protein kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004672 ! protein kinase activity +relationship: positively_regulates GO:0004672 ! protein kinase activity + +[Term] +id: GO:0045879 +name: negative regulation of smoothened signaling pathway +namespace: biological_process +alt_id: GO:0045877 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of smoothened signaling." [GOC:go_curators] +synonym: "down regulation of smoothened signaling pathway" EXACT [] +synonym: "down-regulation of smoothened signaling pathway" EXACT [] +synonym: "downregulation of smoothened signaling pathway" EXACT [] +synonym: "inhibition of smoothened signaling pathway" NARROW [] +synonym: "negative regulation of hedgehog signaling pathway" EXACT [GOC:bf, GOC:ecd] +synonym: "negative regulation of hh signaling pathway" EXACT [GOC:bf, GOC:ecd] +synonym: "negative regulation of smoothened activity" RELATED [] +synonym: "negative regulation of smoothened by patched" NARROW [] +synonym: "negative regulation of smoothened receptor activity by patched" RELATED [] +synonym: "negative regulation of smoothened signalling pathway" EXACT [] +is_a: GO:0008589 ! regulation of smoothened signaling pathway +is_a: GO:0009968 ! negative regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007224 ! smoothened signaling pathway +relationship: negatively_regulates GO:0007224 ! smoothened signaling pathway + +[Term] +id: GO:0045880 +name: positive regulation of smoothened signaling pathway +namespace: biological_process +alt_id: GO:0045878 +def: "Any process that activates or increases the frequency, rate or extent of smoothened signaling." [GOC:go_curators] +synonym: "activation of smoothened signaling pathway" NARROW [] +synonym: "positive regulation of hedgehog signaling pathway" EXACT [GOC:bf, GOC:ecd] +synonym: "positive regulation of hh signaling pathway" EXACT [GOC:bf, GOC:ecd] +synonym: "positive regulation of smoothened by patched" RELATED [] +synonym: "positive regulation of smoothened receptor activity by patched" RELATED [] +synonym: "positive regulation of smoothened signalling pathway" EXACT [] +synonym: "stimulation of smoothened signaling pathway" NARROW [] +synonym: "up regulation of smoothened signaling pathway" EXACT [] +synonym: "up-regulation of smoothened signaling pathway" EXACT [] +synonym: "upregulation of smoothened signaling pathway" EXACT [] +is_a: GO:0008589 ! regulation of smoothened signaling pathway +is_a: GO:0009967 ! positive regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007224 ! smoothened signaling pathway +relationship: positively_regulates GO:0007224 ! smoothened signaling pathway + +[Term] +id: GO:0045892 +name: negative regulation of transcription, DNA-templated +namespace: biological_process +alt_id: GO:0016481 +alt_id: GO:0032582 +alt_id: GO:0061021 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] +subset: gosubset_prok +synonym: "down regulation of gene-specific transcription" RELATED [] +synonym: "down regulation of transcription, DNA-dependent" EXACT [] +synonym: "down-regulation of gene-specific transcription" RELATED [] +synonym: "down-regulation of transcription, DNA-dependent" EXACT [] +synonym: "downregulation of gene-specific transcription" RELATED [] +synonym: "downregulation of transcription, DNA-dependent" EXACT [] +synonym: "inhibition of gene-specific transcription" RELATED [] +synonym: "inhibition of transcription, DNA-dependent" NARROW [] +synonym: "negative regulation of cellular transcription, DNA-dependent" EXACT [] +synonym: "negative regulation of gene-specific transcription" RELATED [] +synonym: "negative regulation of transcription, DNA-dependent" EXACT [GOC:txnOH] +synonym: "transcription repressor activity" RELATED [] +is_a: GO:0006355 ! regulation of transcription, DNA-templated +is_a: GO:0010629 ! negative regulation of gene expression +is_a: GO:1902679 ! negative regulation of RNA biosynthetic process +is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006351 ! transcription, DNA-templated +relationship: negatively_regulates GO:0006351 ! transcription, DNA-templated + +[Term] +id: GO:0045893 +name: positive regulation of transcription, DNA-templated +namespace: biological_process +alt_id: GO:0043193 +alt_id: GO:0045941 +alt_id: GO:0061020 +def: "Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] +subset: gosubset_prok +synonym: "activation of gene-specific transcription" RELATED [] +synonym: "activation of transcription, DNA-dependent" NARROW [] +synonym: "positive regulation of cellular transcription, DNA-dependent" EXACT [] +synonym: "positive regulation of gene-specific transcription" RELATED [] +synonym: "positive regulation of transcription, DNA-dependent" EXACT [GOC:txnOH] +synonym: "stimulation of gene-specific transcription" NARROW [] +synonym: "stimulation of transcription, DNA-dependent" NARROW [] +synonym: "transcription activator activity" RELATED [] +synonym: "up regulation of gene-specific transcription" RELATED [] +synonym: "up regulation of transcription, DNA-dependent" EXACT [] +synonym: "up-regulation of gene-specific transcription" RELATED [] +synonym: "up-regulation of transcription, DNA-dependent" EXACT [] +synonym: "upregulation of gene-specific transcription" RELATED [] +synonym: "upregulation of transcription, DNA-dependent" EXACT [] +is_a: GO:0006355 ! regulation of transcription, DNA-templated +is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process +is_a: GO:0010628 ! positive regulation of gene expression +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0051254 ! positive regulation of RNA metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006351 ! transcription, DNA-templated +relationship: positively_regulates GO:0006351 ! transcription, DNA-templated + +[Term] +id: GO:0045926 +name: negative regulation of growth +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of growth" EXACT [] +synonym: "down-regulation of growth" EXACT [] +synonym: "downregulation of growth" EXACT [] +synonym: "inhibition of growth" NARROW [] +is_a: GO:0040008 ! regulation of growth +is_a: GO:0048519 ! negative regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0040007 ! growth +relationship: negatively_regulates GO:0040007 ! growth + +[Term] +id: GO:0045927 +name: positive regulation of growth +namespace: biological_process +def: "Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of growth" NARROW [] +synonym: "stimulation of growth" NARROW [] +synonym: "up regulation of growth" EXACT [] +synonym: "up-regulation of growth" EXACT [] +synonym: "upregulation of growth" EXACT [] +is_a: GO:0040008 ! regulation of growth +is_a: GO:0048518 ! positive regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0040007 ! growth +relationship: positively_regulates GO:0040007 ! growth + +[Term] +id: GO:0045930 +name: negative regulation of mitotic cell cycle +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb] +synonym: "down regulation of progression through mitotic cell cycle" EXACT [] +synonym: "down-regulation of progression through mitotic cell cycle" EXACT [] +synonym: "downregulation of progression through mitotic cell cycle" EXACT [] +synonym: "inhibition of progression through mitotic cell cycle" NARROW [] +synonym: "negative regulation of mitotic cell cycle progression" EXACT [] +synonym: "negative regulation of progression through mitotic cell cycle" EXACT [GOC:dph, GOC:tb] +is_a: GO:0007346 ! regulation of mitotic cell cycle +is_a: GO:0045786 ! negative regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0000278 ! mitotic cell cycle +relationship: negatively_regulates GO:0000278 ! mitotic cell cycle + +[Term] +id: GO:0045934 +name: negative regulation of nucleobase-containing compound metabolic process +namespace: biological_process +def: "Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] +synonym: "down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] +synonym: "downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] +synonym: "inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] +synonym: "negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] +synonym: "negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process +relationship: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process + +[Term] +id: GO:0045935 +name: positive regulation of nucleobase-containing compound metabolic process +namespace: biological_process +def: "Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] +synonym: "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] +synonym: "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] +synonym: "stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] +synonym: "up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] +synonym: "up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] +synonym: "upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006139 ! nucleobase-containing compound metabolic process +relationship: positively_regulates GO:0006139 ! nucleobase-containing compound metabolic process + +[Term] +id: GO:0045936 +name: negative regulation of phosphate metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of phosphate metabolic process" EXACT [] +synonym: "down-regulation of phosphate metabolic process" EXACT [] +synonym: "downregulation of phosphate metabolic process" EXACT [] +synonym: "inhibition of phosphate metabolic process" NARROW [] +synonym: "negative regulation of phosphate metabolism" EXACT [] +is_a: GO:0010563 ! negative regulation of phosphorus metabolic process +is_a: GO:0019220 ! regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006796 ! phosphate-containing compound metabolic process +relationship: negatively_regulates GO:0006796 ! phosphate-containing compound metabolic process + +[Term] +id: GO:0045937 +name: positive regulation of phosphate metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of phosphate metabolic process" NARROW [] +synonym: "positive regulation of phosphate metabolism" EXACT [] +synonym: "stimulation of phosphate metabolic process" NARROW [] +synonym: "up regulation of phosphate metabolic process" EXACT [] +synonym: "up-regulation of phosphate metabolic process" EXACT [] +synonym: "upregulation of phosphate metabolic process" EXACT [] +is_a: GO:0010562 ! positive regulation of phosphorus metabolic process +is_a: GO:0019220 ! regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006796 ! phosphate-containing compound metabolic process +relationship: positively_regulates GO:0006796 ! phosphate-containing compound metabolic process + +[Term] +id: GO:0045939 +name: negative regulation of steroid metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC:go_curators] +subset: gosubset_prok +synonym: "down regulation of steroid metabolic process" EXACT [] +synonym: "down-regulation of steroid metabolic process" EXACT [] +synonym: "downregulation of steroid metabolic process" EXACT [] +synonym: "inhibition of steroid metabolic process" NARROW [] +synonym: "negative regulation of steroid metabolism" EXACT [] +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0045833 ! negative regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008202 ! steroid metabolic process +relationship: negatively_regulates GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0045940 +name: positive regulation of steroid metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of steroid metabolic process" NARROW [] +synonym: "positive regulation of steroid metabolism" EXACT [] +synonym: "stimulation of steroid metabolic process" NARROW [] +synonym: "up regulation of steroid metabolic process" EXACT [] +synonym: "up-regulation of steroid metabolic process" EXACT [] +synonym: "upregulation of steroid metabolic process" EXACT [] +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0045834 ! positive regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008202 ! steroid metabolic process +relationship: positively_regulates GO:0008202 ! steroid metabolic process + +[Term] +id: GO:0045944 +name: positive regulation of transcription from RNA polymerase II promoter +namespace: biological_process +alt_id: GO:0010552 +alt_id: GO:0045817 +def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] +synonym: "activation of global transcription from RNA polymerase II promoter" RELATED [] +synonym: "activation of transcription from RNA polymerase II promoter" EXACT [] +synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] +synonym: "positive regulation of global transcription from Pol II promoter" RELATED [] +synonym: "positive regulation of transcription from Pol II promoter" EXACT [] +synonym: "positive regulation of transcription from RNA polymerase II promoter, global" RELATED [] +synonym: "stimulation of global transcription from RNA polymerase II promoter" NARROW [] +synonym: "stimulation of transcription from RNA polymerase II promoter" EXACT [] +synonym: "up regulation of global transcription from RNA polymerase II promoter" RELATED [] +synonym: "up regulation of transcription from RNA polymerase II promoter" EXACT [] +synonym: "up-regulation of global transcription from RNA polymerase II promoter" RELATED [] +synonym: "up-regulation of transcription from RNA polymerase II promoter" EXACT [] +synonym: "upregulation of global transcription from RNA polymerase II promoter" RELATED [] +synonym: "upregulation of transcription from RNA polymerase II promoter" EXACT [] +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0045893 ! positive regulation of transcription, DNA-templated +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter +relationship: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter + +[Term] +id: GO:0045945 +name: positive regulation of transcription from RNA polymerase III promoter +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III promoter." [GOC:go_curators, GOC:txnOH] +synonym: "activation of transcription from RNA polymerase III promoter" NARROW [] +synonym: "positive regulation of transcription from Pol III promoter" EXACT [] +synonym: "stimulation of transcription from RNA polymerase III promoter" NARROW [] +synonym: "up regulation of transcription from RNA polymerase III promoter" EXACT [] +synonym: "up-regulation of transcription from RNA polymerase III promoter" EXACT [] +synonym: "upregulation of transcription from RNA polymerase III promoter" EXACT [] +is_a: GO:0006359 ! regulation of transcription from RNA polymerase III promoter +is_a: GO:0045893 ! positive regulation of transcription, DNA-templated +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006383 ! transcription from RNA polymerase III promoter +relationship: positively_regulates GO:0006383 ! transcription from RNA polymerase III promoter + +[Term] +id: GO:0045981 +name: positive regulation of nucleotide metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleotides." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of nucleotide metabolic process" NARROW [] +synonym: "positive regulation of nucleotide metabolism" EXACT [] +synonym: "stimulation of nucleotide metabolic process" NARROW [] +synonym: "up regulation of nucleotide metabolic process" EXACT [] +synonym: "up-regulation of nucleotide metabolic process" EXACT [] +synonym: "upregulation of nucleotide metabolic process" EXACT [] +is_a: GO:0006140 ! regulation of nucleotide metabolic process +is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process +is_a: GO:0045937 ! positive regulation of phosphate metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009117 ! nucleotide metabolic process +relationship: positively_regulates GO:0009117 ! nucleotide metabolic process + +[Term] +id: GO:0045990 +name: carbon catabolite regulation of transcription +namespace: biological_process +def: "A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources." [GOC:go_curators, GOC:mah, PMID:18359269, PMID:9618445] +subset: gosubset_prok +synonym: "regulation of transcription by carbon catabolites" EXACT [GOC:mah] +is_a: GO:0006355 ! regulation of transcription, DNA-templated +is_a: GO:0031670 ! cellular response to nutrient + +[Term] +id: GO:0045991 +name: carbon catabolite activation of transcription +namespace: biological_process +def: "A transcription regulation process in which the presence of one carbon source leads to an increase in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources." [GOC:mah, PMID:10559153] +subset: gosubset_prok +synonym: "positive regulation of transcription by carbon catabolites" EXACT [GOC:mah] +is_a: GO:0045893 ! positive regulation of transcription, DNA-templated +is_a: GO:0045990 ! carbon catabolite regulation of transcription + +[Term] +id: GO:0045992 +name: negative regulation of embryonic development +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development." [GOC:go_curators] +synonym: "down regulation of embryonic development" EXACT [] +synonym: "down-regulation of embryonic development" EXACT [] +synonym: "downregulation of embryonic development" EXACT [] +synonym: "inhibition of embryonic development" NARROW [] +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051093 ! negative regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009790 ! embryo development +relationship: negatively_regulates GO:0009790 ! embryo development + +[Term] +id: GO:0045995 +name: regulation of embryonic development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of embryonic development." [GOC:go_curators] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009790 ! embryo development +relationship: regulates GO:0009790 ! embryo development + +[Term] +id: GO:0046015 +name: regulation of transcription by glucose +namespace: biological_process +def: "Any process involving glucose that modulates the frequency, rate or extent or transcription." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0045990 ! carbon catabolite regulation of transcription + +[Term] +id: GO:0046016 +name: positive regulation of transcription by glucose +namespace: biological_process +def: "Any process involving glucose that activates or increases the rate of transcription." [GOC:go_curators] +subset: gosubset_prok +synonym: "activation of transcription by glucose" NARROW [] +synonym: "stimulation of transcription by glucose" NARROW [] +synonym: "up regulation of transcription by glucose" EXACT [] +synonym: "up-regulation of transcription by glucose" EXACT [] +synonym: "upregulation of transcription by glucose" EXACT [] +is_a: GO:0045991 ! carbon catabolite activation of transcription +is_a: GO:0046015 ! regulation of transcription by glucose + +[Term] +id: GO:0046039 +name: GTP metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving GTP, guanosine triphosphate." [GOC:go_curators] +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "GTP metabolism" EXACT [] +is_a: GO:0009150 ! purine ribonucleotide metabolic process +is_a: GO:0009205 ! purine ribonucleoside triphosphate metabolic process +is_a: GO:1901068 ! guanosine-containing compound metabolic process + +[Term] +id: GO:0046068 +name: cGMP metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate." [GOC:go_curators] +subset: gosubset_prok +synonym: "cGMP metabolism" EXACT [] +is_a: GO:0009150 ! purine ribonucleotide metabolic process +is_a: GO:0009187 ! cyclic nucleotide metabolic process + +[Term] +id: GO:0046128 +name: purine ribonucleoside metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving any ribonucleoside, a nucleoside in which purine base is linked to a ribose (beta-D-ribofuranose) molecule." [GOC:ai] +subset: gosubset_prok +synonym: "purine ribonucleoside metabolism" EXACT [] +is_a: GO:0009119 ! ribonucleoside metabolic process +is_a: GO:0042278 ! purine nucleoside metabolic process + +[Term] +id: GO:0046130 +name: purine ribonucleoside catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of any purine ribonucleoside, a nucleoside in which purine base is linked to a ribose (beta-D-ribofuranose) molecule." [GOC:ai] +subset: gosubset_prok +synonym: "purine ribonucleoside breakdown" EXACT [] +synonym: "purine ribonucleoside catabolism" EXACT [] +synonym: "purine ribonucleoside degradation" EXACT [] +is_a: GO:0006152 ! purine nucleoside catabolic process +is_a: GO:0042454 ! ribonucleoside catabolic process +is_a: GO:0046128 ! purine ribonucleoside metabolic process + +[Term] +id: GO:0046165 +name: alcohol biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [CHEBI:30879, GOC:ai] +subset: gosubset_prok +synonym: "alcohol anabolism" EXACT [] +synonym: "alcohol biosynthesis" EXACT [] +synonym: "alcohol formation" EXACT [] +synonym: "alcohol synthesis" EXACT [] +is_a: GO:0006066 ! alcohol metabolic process +is_a: GO:0044283 ! small molecule biosynthetic process +is_a: GO:1901617 ! organic hydroxy compound biosynthetic process + +[Term] +id: GO:0046328 +name: regulation of JNK cascade +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of signal transduction mediated by the JNK cascade." [GOC:bf] +synonym: "regulation of SAPK cascade" BROAD [] +is_a: GO:0032872 ! regulation of stress-activated MAPK cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007254 ! JNK cascade +relationship: regulates GO:0007254 ! JNK cascade + +[Term] +id: GO:0046330 +name: positive regulation of JNK cascade +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade." [GOC:bf] +synonym: "activation of JNK cascade" NARROW [] +synonym: "stimulation of JNK cascade" NARROW [] +synonym: "up regulation of JNK cascade" EXACT [] +synonym: "up-regulation of JNK cascade" EXACT [] +synonym: "upregulation of JNK cascade" EXACT [] +is_a: GO:0032874 ! positive regulation of stress-activated MAPK cascade +is_a: GO:0046328 ! regulation of JNK cascade +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007254 ! JNK cascade +relationship: positively_regulates GO:0007254 ! JNK cascade + +[Term] +id: GO:0046332 +name: SMAD binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a SMAD signaling protein." [GOC:ai] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0046365 +name: monosaccharide catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms." [ISBN:0198506732] +subset: gosubset_prok +synonym: "monosaccharide breakdown" EXACT [] +synonym: "monosaccharide catabolism" EXACT [] +synonym: "monosaccharide degradation" EXACT [] +is_a: GO:0005996 ! monosaccharide metabolic process +is_a: GO:0044724 ! single-organism carbohydrate catabolic process + +[Term] +id: GO:0046434 +name: organophosphate catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of organophosphates, any phosphate-containing organic compound." [GOC:ai] +subset: gosubset_prok +synonym: "organophosphate breakdown" EXACT [] +synonym: "organophosphate catabolism" EXACT [] +synonym: "organophosphate degradation" EXACT [] +is_a: GO:0019637 ! organophosphate metabolic process +is_a: GO:1901575 ! organic substance catabolic process + +[Term] +id: GO:0046483 +name: heterocycle metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [CHEBI:5686, ISBN:0198506732] +subset: goslim_pir +subset: gosubset_prok +synonym: "heterocycle metabolism" EXACT [] +is_a: GO:0044237 ! cellular metabolic process + +[Term] +id: GO:0046543 +name: development of secondary female sexual characteristics +namespace: biological_process +def: "The process whose specific outcome is the progression of the secondary female sexual characteristics over time, from their formation to the mature structures. In female humans, these include growth of axillary and pubic hair, breast development and menstrual periods. Their development occurs in response to sex hormone secretion." [GOC:ai] +is_a: GO:0045136 ! development of secondary sexual characteristics +relationship: part_of GO:0046660 ! female sex differentiation + +[Term] +id: GO:0046545 +name: development of primary female sexual characteristics +namespace: biological_process +def: "The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion." [GOC:ai] +is_a: GO:0045137 ! development of primary sexual characteristics +relationship: part_of GO:0046660 ! female sex differentiation + +[Term] +id: GO:0046546 +name: development of primary male sexual characteristics +namespace: biological_process +def: "The process whose specific outcome is the progression of the primary male sexual characteristics over time, from their formation to the mature structures. The primary male sexual characteristics are the testes, and they develop in response to sex hormone secretion." [GOC:ai] +is_a: GO:0045137 ! development of primary sexual characteristics +relationship: part_of GO:0046661 ! male sex differentiation + +[Term] +id: GO:0046578 +name: regulation of Ras protein signal transduction +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of Ras protein signal transduction." [GOC:bf] +is_a: GO:0051056 ! regulation of small GTPase mediated signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007265 ! Ras protein signal transduction +relationship: regulates GO:0007265 ! Ras protein signal transduction + +[Term] +id: GO:0046620 +name: regulation of organ growth +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of growth of an organ of an organism." [GOC:bf, GOC:tb] +is_a: GO:0040008 ! regulation of growth +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035265 ! organ growth +relationship: regulates GO:0035265 ! organ growth + +[Term] +id: GO:0046649 +name: lymphocyte activation +namespace: biological_process +def: "A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735140] +is_a: GO:0045321 ! leukocyte activation + +[Term] +id: GO:0046651 +name: lymphocyte proliferation +namespace: biological_process +def: "The expansion of a lymphocyte population by cell division." [GOC:ai] +is_a: GO:0032943 ! mononuclear cell proliferation +is_a: GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0046660 +name: female sex differentiation +namespace: biological_process +def: "The establishment of the sex of a female organism by physical differentiation." [GOC:bf] +is_a: GO:0007548 ! sex differentiation +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0046661 +name: male sex differentiation +namespace: biological_process +def: "The establishment of the sex of a male organism by physical differentiation." [GOC:bf] +is_a: GO:0007548 ! sex differentiation +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0046676 +name: negative regulation of insulin secretion +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin." [GOC:ai] +synonym: "down regulation of insulin secretion" EXACT [] +synonym: "down-regulation of insulin secretion" EXACT [] +synonym: "downregulation of insulin secretion" EXACT [] +synonym: "inhibition of insulin secretion" NARROW [] +is_a: GO:0050796 ! regulation of insulin secretion +is_a: GO:0090278 ! negative regulation of peptide hormone secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030073 ! insulin secretion +relationship: negatively_regulates GO:0030073 ! insulin secretion + +[Term] +id: GO:0046700 +name: heterocycle catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [GOC:ai] +subset: gosubset_prok +synonym: "heterocycle breakdown" EXACT [] +synonym: "heterocycle catabolism" EXACT [] +synonym: "heterocycle degradation" EXACT [] +is_a: GO:0044248 ! cellular catabolic process +is_a: GO:0046483 ! heterocycle metabolic process + +[Term] +id: GO:0046822 +name: regulation of nucleocytoplasmic transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm." [GOC:bf] +is_a: GO:0032386 ! regulation of intracellular transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006913 ! nucleocytoplasmic transport +relationship: regulates GO:0006913 ! nucleocytoplasmic transport + +[Term] +id: GO:0046823 +name: negative regulation of nucleocytoplasmic transport +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus." [GOC:bf] +synonym: "down regulation of nucleocytoplasmic transport" EXACT [] +synonym: "down-regulation of nucleocytoplasmic transport" EXACT [] +synonym: "downregulation of nucleocytoplasmic transport" EXACT [] +synonym: "inhibition of nucleocytoplasmic transport" NARROW [] +is_a: GO:0032387 ! negative regulation of intracellular transport +is_a: GO:0046822 ! regulation of nucleocytoplasmic transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006913 ! nucleocytoplasmic transport +relationship: negatively_regulates GO:0006913 ! nucleocytoplasmic transport + +[Term] +id: GO:0046824 +name: positive regulation of nucleocytoplasmic transport +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm." [GOC:bf] +synonym: "activation of nucleocytoplasmic transport" NARROW [] +synonym: "stimulation of nucleocytoplasmic transport" NARROW [] +synonym: "up regulation of nucleocytoplasmic transport" EXACT [] +synonym: "up-regulation of nucleocytoplasmic transport" EXACT [] +synonym: "upregulation of nucleocytoplasmic transport" EXACT [] +is_a: GO:0032388 ! positive regulation of intracellular transport +is_a: GO:0046822 ! regulation of nucleocytoplasmic transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006913 ! nucleocytoplasmic transport +relationship: positively_regulates GO:0006913 ! nucleocytoplasmic transport + +[Term] +id: GO:0046835 +name: carbohydrate phosphorylation +namespace: biological_process +def: "The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y." [ISBN:0198506732] +subset: gosubset_prok +is_a: GO:0016310 ! phosphorylation +is_a: GO:0044262 ! cellular carbohydrate metabolic process + +[Term] +id: GO:0046849 +name: bone remodeling +namespace: biological_process +def: "The continuous turnover of bone matrix and mineral that involves first, an increase in resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). The process of bone remodeling takes place in the adult skeleton at discrete foci. The process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of bone resorption and bone formation results in many of the metabolic bone diseases, such as osteoporosis." [GOC:curators] +synonym: "bone remodelling" EXACT [] +xref: Wikipedia:Bone_remodeling +is_a: GO:0048771 ! tissue remodeling + +[Term] +id: GO:0046850 +name: regulation of bone remodeling +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of bone remodeling, the processes of bone formation and resorption that combine to maintain skeletal integrity." [GOC:ai] +is_a: GO:0034103 ! regulation of tissue remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046849 ! bone remodeling +relationship: regulates GO:0046849 ! bone remodeling + +[Term] +id: GO:0046851 +name: negative regulation of bone remodeling +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of bone remodeling." [GOC:ai] +synonym: "down regulation of bone remodeling" EXACT [] +synonym: "down-regulation of bone remodeling" EXACT [] +synonym: "downregulation of bone remodeling" EXACT [] +synonym: "inhibition of bone remodeling" NARROW [] +is_a: GO:0034104 ! negative regulation of tissue remodeling +is_a: GO:0046850 ! regulation of bone remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046849 ! bone remodeling +relationship: negatively_regulates GO:0046849 ! bone remodeling + +[Term] +id: GO:0046852 +name: positive regulation of bone remodeling +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of bone remodeling." [GOC:ai] +synonym: "activation of bone remodeling" NARROW [] +synonym: "stimulation of bone remodeling" NARROW [] +synonym: "up regulation of bone remodeling" EXACT [] +synonym: "up-regulation of bone remodeling" EXACT [] +synonym: "upregulation of bone remodeling" EXACT [] +is_a: GO:0034105 ! positive regulation of tissue remodeling +is_a: GO:0046850 ! regulation of bone remodeling +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046849 ! bone remodeling +relationship: positively_regulates GO:0046849 ! bone remodeling + +[Term] +id: GO:0046872 +name: metal ion binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any metal ion." [GOC:ai] +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "heavy metal binding" NARROW [] +synonym: "metal binding" EXACT [] +is_a: GO:0043169 ! cation binding + +[Term] +id: GO:0046879 +name: hormone secretion +namespace: biological_process +def: "The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells." [ISBN:0198506732] +is_a: GO:0009914 ! hormone transport +is_a: GO:0023061 ! signal release + +[Term] +id: GO:0046883 +name: regulation of hormone secretion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell." [GOC:ai] +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0023051 ! regulation of signaling +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046879 ! hormone secretion +relationship: regulates GO:0046879 ! hormone secretion + +[Term] +id: GO:0046885 +name: regulation of hormone biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones." [GOC:ai] +synonym: "regulation of hormone anabolism" EXACT [] +synonym: "regulation of hormone biosynthesis" EXACT [] +synonym: "regulation of hormone formation" EXACT [] +synonym: "regulation of hormone synthesis" EXACT [] +is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0032350 ! regulation of hormone metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042446 ! hormone biosynthetic process +relationship: regulates GO:0042446 ! hormone biosynthetic process + +[Term] +id: GO:0046886 +name: positive regulation of hormone biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones." [GOC:ai] +synonym: "activation of hormone biosynthetic process" NARROW [] +synonym: "positive regulation of hormone anabolism" EXACT [] +synonym: "positive regulation of hormone biosynthesis" EXACT [] +synonym: "positive regulation of hormone formation" EXACT [] +synonym: "positive regulation of hormone synthesis" EXACT [] +synonym: "stimulation of hormone biosynthetic process" NARROW [] +synonym: "up regulation of hormone biosynthetic process" EXACT [] +synonym: "up-regulation of hormone biosynthetic process" EXACT [] +synonym: "upregulation of hormone biosynthetic process" EXACT [] +is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0032352 ! positive regulation of hormone metabolic process +is_a: GO:0046885 ! regulation of hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042446 ! hormone biosynthetic process +relationship: positively_regulates GO:0042446 ! hormone biosynthetic process + +[Term] +id: GO:0046888 +name: negative regulation of hormone secretion +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell." [GOC:ai] +synonym: "down regulation of hormone secretion" EXACT [] +synonym: "down-regulation of hormone secretion" EXACT [] +synonym: "downregulation of hormone secretion" EXACT [] +synonym: "inhibition of hormone secretion" NARROW [] +is_a: GO:0046883 ! regulation of hormone secretion +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051048 ! negative regulation of secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046879 ! hormone secretion +relationship: negatively_regulates GO:0046879 ! hormone secretion + +[Term] +id: GO:0046889 +name: positive regulation of lipid biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." [GOC:ai] +subset: gosubset_prok +synonym: "activation of lipid biosynthetic process" NARROW [] +synonym: "positive regulation of lipid anabolism" EXACT [] +synonym: "positive regulation of lipid biosynthesis" EXACT [] +synonym: "positive regulation of lipid formation" EXACT [] +synonym: "positive regulation of lipid synthesis" EXACT [] +synonym: "positive regulation of lipogenesis" EXACT [GOC:sl] +synonym: "stimulation of lipid biosynthetic process" NARROW [] +synonym: "up regulation of lipid biosynthetic process" EXACT [] +synonym: "up-regulation of lipid biosynthetic process" EXACT [] +synonym: "upregulation of lipid biosynthetic process" EXACT [] +is_a: GO:0009891 ! positive regulation of biosynthetic process +is_a: GO:0045834 ! positive regulation of lipid metabolic process +is_a: GO:0046890 ! regulation of lipid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008610 ! lipid biosynthetic process +relationship: positively_regulates GO:0008610 ! lipid biosynthetic process + +[Term] +id: GO:0046890 +name: regulation of lipid biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." [GOC:ai] +subset: gosubset_prok +synonym: "regulation of lipid anabolism" EXACT [] +synonym: "regulation of lipid biosynthesis" EXACT [] +synonym: "regulation of lipid formation" EXACT [] +synonym: "regulation of lipid synthesis" EXACT [] +synonym: "regulation of lipogenesis" EXACT [GOC:sl] +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0019216 ! regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008610 ! lipid biosynthetic process +relationship: regulates GO:0008610 ! lipid biosynthetic process + +[Term] +id: GO:0046903 +name: secretion +namespace: biological_process +def: "The controlled release of a substance by a cell or a tissue." [GOC:ai] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0046907 +name: intracellular transport +namespace: biological_process +def: "The directed movement of substances within a cell." [GOC:ai] +subset: gosubset_prok +is_a: GO:0006810 ! transport +is_a: GO:0051649 ! establishment of localization in cell +intersection_of: GO:0006810 ! transport +intersection_of: occurs_in GO:0005622 ! intracellular + +[Term] +id: GO:0046982 +name: protein heterodimerization activity +namespace: molecular_function +def: "Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer." [GOC:ai] +is_a: GO:0046983 ! protein dimerization activity + +[Term] +id: GO:0046983 +name: protein dimerization activity +namespace: molecular_function +def: "The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits." [ISBN:0198506732] +subset: gosubset_prok +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0048009 +name: insulin-like growth factor receptor signaling pathway +namespace: biological_process +def: "The series of molecular signals generated as a consequence of the insulin-like growth factor receptor binding to one of its physiological ligands." [GOC:ceb] +synonym: "IGF receptor signaling pathway" EXACT [] +synonym: "IGF receptor signalling pathway" EXACT [] +is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway + +[Term] +id: GO:0048010 +name: vascular endothelial growth factor receptor signaling pathway +namespace: biological_process +def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling, PR:000001971] +comment: In GO, a gene product with 'vascular endothelial growth factor-activated receptor activity ; GO:0005021' necessarily binds VEGF to transduce a signal. In contrast, the VEGFR refers to PR:000001971. To represent cross-talk between ligands and receptors, signaling pathways in GO are starting to be named after the receptor and/or the signal. GO:0048010 is for annotation of any pathway in which a ligand (VEGF or an alternative growth factor) binds and activates a VEGFR (PR:000001971). For annotation of signaling pathways where a VEGF binds to a cell surface receptor (VEGFR, PDGFR etc.), consider 'vascular endothelial growth factor signaling pathway ; GO:0038084'. +synonym: "VEGF receptor signaling pathway" EXACT [] +synonym: "VEGF receptor signalling pathway" EXACT [] +synonym: "VEGFR signaling pathway" EXACT [] +xref: Reactome:REACT_100751 "Signaling by VEGF, Xenopus tropicalis" +xref: Reactome:REACT_102305 "Signaling by VEGF, Gallus gallus" +xref: Reactome:REACT_105684 "Signaling by VEGF, Taeniopygia guttata" +xref: Reactome:REACT_106374 "Signaling by VEGF, Sus scrofa" +xref: Reactome:REACT_108554 "VEGF ligand-receptor interactions, Mus musculus" +xref: Reactome:REACT_110014 "Signaling by VEGF, Canis familiaris" +xref: Reactome:REACT_12380 "VEGF ligand-receptor interactions, Homo sapiens" +xref: Reactome:REACT_12529 "Signaling by VEGF, Homo sapiens" +xref: Reactome:REACT_28600 "VEGF ligand-receptor interactions, Rattus norvegicus" +xref: Reactome:REACT_29612 "VEGF ligand-receptor interactions, Danio rerio" +xref: Reactome:REACT_79122 "VEGF ligand-receptor interactions, Bos taurus" +xref: Reactome:REACT_82633 "VEGF ligand-receptor interactions, Taeniopygia guttata" +xref: Reactome:REACT_82784 "Signaling by VEGF, Danio rerio" +xref: Reactome:REACT_82920 "Signaling by VEGF, Bos taurus" +xref: Reactome:REACT_85693 "Signaling by VEGF, Rattus norvegicus" +xref: Reactome:REACT_86899 "VEGF ligand-receptor interactions, Sus scrofa" +xref: Reactome:REACT_90528 "Signaling by VEGF, Mus musculus" +xref: Reactome:REACT_94269 "VEGF ligand-receptor interactions, Canis familiaris" +xref: Reactome:REACT_98511 "VEGF ligand-receptor interactions, Gallus gallus" +xref: Reactome:REACT_99958 "VEGF ligand-receptor interactions, Xenopus tropicalis" +is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway + +[Term] +id: GO:0048018 +name: receptor agonist activity +namespace: molecular_function +def: "Interacts with receptors such that the proportion of receptors in the active form is increased." [GOC:ceb, ISBN:0198506732] +synonym: "receptor ligand activity" BROAD [GOC:mtg_signaling] +is_a: GO:0005102 ! receptor binding +is_a: GO:0030546 ! receptor activator activity +relationship: part_of GO:0007165 ! signal transduction + +[Term] +id: GO:0048019 +name: receptor antagonist activity +namespace: molecular_function +def: "Interacts with receptors to reduce the action of another ligand, the agonist." [GOC:ceb, ISBN:0198506732] +synonym: "receptor ligand activity" BROAD [GOC:mtg_signaling] +is_a: GO:0005102 ! receptor binding +is_a: GO:0030547 ! receptor inhibitor activity +relationship: part_of GO:1900116 ! extracellular negative regulation of signal transduction + +[Term] +id: GO:0048041 +name: focal adhesion assembly +namespace: biological_process +def: "The aggregation and bonding together of a set of components to form a focal adhesion, a complex of intracellular signaling and structural proteins that provides a structural link between the internal actin cytoskeleton and the ECM, and also function as a locus of signal transduction activity." [GOC:jid, GOC:mah] +synonym: "focal adhesion formation" RELATED [GOC:mah] +is_a: GO:0007045 ! cell-substrate adherens junction assembly +relationship: part_of GO:0007160 ! cell-matrix adhesion + +[Term] +id: GO:0048048 +name: embryonic eye morphogenesis +namespace: biological_process +def: "The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized." [GOC:jid] +is_a: GO:0048562 ! embryonic organ morphogenesis +is_a: GO:0048592 ! eye morphogenesis + +[Term] +id: GO:0048066 +name: developmental pigmentation +namespace: biological_process +def: "The developmental process that results in the deposition of coloring matter in an organism, tissue or cell." [ISBN:0582227089] +subset: gosubset_prok +synonym: "pigmentation during development" RELATED [] +is_a: GO:0043473 ! pigmentation +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0048103 +name: somatic stem cell division +namespace: biological_process +def: "The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line." [GOC:jid, ISBN:0582227089] +synonym: "somatic stem cell renewal" EXACT [] +is_a: GO:0017145 ! stem cell division + +[Term] +id: GO:0048144 +name: fibroblast proliferation +namespace: biological_process +def: "The multiplication or reproduction of fibroblast cells, resulting in the expansion of the fibroblast population." [GOC:jid] +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0048145 +name: regulation of fibroblast proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of multiplication or reproduction of fibroblast cells." [GOC:jid] +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048144 ! fibroblast proliferation +relationship: regulates GO:0048144 ! fibroblast proliferation + +[Term] +id: GO:0048146 +name: positive regulation of fibroblast proliferation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells." [GOC:jid] +synonym: "activation of fibroblast proliferation" NARROW [] +synonym: "stimulation of fibroblast proliferation" NARROW [] +synonym: "up regulation of fibroblast proliferation" EXACT [] +synonym: "up-regulation of fibroblast proliferation" EXACT [] +synonym: "upregulation of fibroblast proliferation" EXACT [] +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0048145 ! regulation of fibroblast proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048144 ! fibroblast proliferation +relationship: positively_regulates GO:0048144 ! fibroblast proliferation + +[Term] +id: GO:0048147 +name: negative regulation of fibroblast proliferation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells." [GOC:jid] +synonym: "down regulation of fibroblast proliferation" EXACT [] +synonym: "down-regulation of fibroblast proliferation" EXACT [] +synonym: "downregulation of fibroblast proliferation" EXACT [] +synonym: "inhibition of fibroblast proliferation" NARROW [] +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0048145 ! regulation of fibroblast proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048144 ! fibroblast proliferation +relationship: negatively_regulates GO:0048144 ! fibroblast proliferation + +[Term] +id: GO:0048237 +name: rough endoplasmic reticulum lumen +namespace: cellular_component +def: "The volume enclosed by the membranes of the rough endoplasmic reticulum." [GOC:jid] +synonym: "RER lumen" EXACT [] +synonym: "rough ER lumen" EXACT [] +xref: NIF_Subcellular:sao1819509473 +is_a: GO:0005788 ! endoplasmic reticulum lumen +relationship: part_of GO:0005791 ! rough endoplasmic reticulum + +[Term] +id: GO:0048247 +name: lymphocyte chemotaxis +namespace: biological_process +def: "The directed movement of a lymphocyte in response to an external stimulus." [GOC:hjd, GOC:jid, PMID:12391252] +is_a: GO:0030595 ! leukocyte chemotaxis +is_a: GO:0072676 ! lymphocyte migration + +[Term] +id: GO:0048259 +name: regulation of receptor-mediated endocytosis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport." [GOC:go_curators, GOC:tb] +synonym: "regulation of receptor mediated endocytosis" EXACT [GOC:tb] +is_a: GO:0030100 ! regulation of endocytosis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006898 ! receptor-mediated endocytosis +relationship: regulates GO:0006898 ! receptor-mediated endocytosis + +[Term] +id: GO:0048260 +name: positive regulation of receptor-mediated endocytosis +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport." [GOC:go_curators, GOC:tb] +synonym: "activation of receptor mediated endocytosis" NARROW [] +synonym: "positive regulation of receptor mediated endocytosis" EXACT [GOC:tb] +synonym: "stimulation of receptor mediated endocytosis" NARROW [] +synonym: "up regulation of receptor mediated endocytosis" EXACT [] +synonym: "up-regulation of receptor mediated endocytosis" EXACT [] +synonym: "upregulation of receptor mediated endocytosis" EXACT [] +is_a: GO:0045807 ! positive regulation of endocytosis +is_a: GO:0048259 ! regulation of receptor-mediated endocytosis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006898 ! receptor-mediated endocytosis +relationship: positively_regulates GO:0006898 ! receptor-mediated endocytosis + +[Term] +id: GO:0048262 +name: determination of dorsal/ventral asymmetry +namespace: biological_process +def: "Determination of asymmetry from the dorsal to the ventral side; as, the dorsoventral axis." [GOC:jid] +synonym: "determination of adaxial/abaxial asymmetry" RELATED [GOC:dph, GOC:tb] +synonym: "determination of dorsal-ventral asymmetry" EXACT [GOC:mah] +synonym: "determination of dorsoventral asymmetry" EXACT [GOC:mah] +is_a: GO:0009855 ! determination of bilateral symmetry +relationship: part_of GO:0009953 ! dorsal/ventral pattern formation + +[Term] +id: GO:0048263 +name: determination of dorsal identity +namespace: biological_process +def: "Determination of the identity of part of an organism or organ where those parts are of the type that occur in the dorsal region. Identity is considered to be the aggregate of characteristics by which a structure is recognized." [GOC:jid] +synonym: "determination of adaxial identity" RELATED [GOC:dph, GOC:tb] +is_a: GO:0009953 ! dorsal/ventral pattern formation +relationship: part_of GO:0048262 ! determination of dorsal/ventral asymmetry + +[Term] +id: GO:0048285 +name: organelle fission +namespace: biological_process +def: "The creation of two or more organelles by division of one organelle." [GOC:jid] +subset: goslim_pir +subset: goslim_yeast +is_a: GO:0006996 ! organelle organization + +[Term] +id: GO:0048286 +name: lung alveolus development +namespace: biological_process +def: "The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways." [GOC:mtg_lung, PMID:9751757] +synonym: "alveolarization" EXACT [PMID:17911382] +synonym: "alveologenesis" EXACT [GOC:17911382] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0048306 +name: calcium-dependent protein binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium." [GOC:jid, PMID:10485905] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0048318 +name: axial mesoderm development +namespace: biological_process +def: "The process whose specific outcome is the progression of the axial mesoderm over time, from its formation to the mature structure. The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." [GOC:dgh] +is_a: GO:0007498 ! mesoderm development + +[Term] +id: GO:0048332 +name: mesoderm morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the mesoderm are generated and organized." [GOC:go_curators] +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0007498 ! mesoderm development + +[Term] +id: GO:0048333 +name: mesodermal cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell." [GOC:dgh] +synonym: "mesoderm cell differentiation" EXACT [] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0001707 ! mesoderm formation + +[Term] +id: GO:0048337 +name: positive regulation of mesodermal cell fate specification +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of mesoderm cell fate specification." [GOC:dgh] +synonym: "activation of mesodermal cell fate specification" NARROW [] +synonym: "stimulation of mesodermal cell fate specification" NARROW [] +synonym: "up regulation of mesodermal cell fate specification" EXACT [] +synonym: "up-regulation of mesodermal cell fate specification" EXACT [] +synonym: "upregulation of mesodermal cell fate specification" EXACT [] +is_a: GO:0042660 ! positive regulation of cell fate specification +is_a: GO:0042661 ! regulation of mesodermal cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007501 ! mesodermal cell fate specification +relationship: positively_regulates GO:0007501 ! mesodermal cell fate specification + +[Term] +id: GO:0048339 +name: paraxial mesoderm development +namespace: biological_process +def: "The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube." [GOC:dgh] +is_a: GO:0007498 ! mesoderm development + +[Term] +id: GO:0048340 +name: paraxial mesoderm morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the paraxial mesoderm are generated and organized." [GOC:go_curators] +is_a: GO:0048332 ! mesoderm morphogenesis +relationship: part_of GO:0048339 ! paraxial mesoderm development + +[Term] +id: GO:0048341 +name: paraxial mesoderm formation +namespace: biological_process +def: "The process that gives rise to the paraxial mesoderm. This process pertains to the initial formation of the structure from unspecified parts." [GOC:dgh] +is_a: GO:0001707 ! mesoderm formation +relationship: part_of GO:0048340 ! paraxial mesoderm morphogenesis + +[Term] +id: GO:0048342 +name: paraxial mesodermal cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires the specialized features of a paraxial mesoderm cell." [GOC:dgh] +is_a: GO:0048333 ! mesodermal cell differentiation +relationship: part_of GO:0048341 ! paraxial mesoderm formation + +[Term] +id: GO:0048343 +name: paraxial mesodermal cell fate commitment +namespace: biological_process +def: "The process in which a cell becomes committed to become a paraxial mesoderm cell." [GOC:dgh] +is_a: GO:0001710 ! mesodermal cell fate commitment +relationship: part_of GO:0048342 ! paraxial mesodermal cell differentiation + +[Term] +id: GO:0048468 +name: cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:go_curators] +subset: goslim_candida +subset: gosubset_prok +synonym: "terminal differentiation" RELATED [GOC:dph, GOC:tb] +is_a: GO:0048856 ! anatomical structure development +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0030154 ! cell differentiation + +[Term] +id: GO:0048469 +name: cell maturation +namespace: biological_process +def: "A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state." [GOC:go_curators] +subset: goslim_pir +subset: gosubset_prok +synonym: "functional differentiation" RELATED [GOC:dph] +is_a: GO:0021700 ! developmental maturation +is_a: GO:0048869 ! cellular developmental process +relationship: part_of GO:0048468 ! cell development + +[Term] +id: GO:0048471 +name: perinuclear region of cytoplasm +namespace: cellular_component +def: "Cytoplasm situated near, or occurring around, the nucleus." [GOC:jid] +comment: Note that this term should not be confused with the cellular component term 'nuclear membrane lumen ; GO:0005641', which has the synonym 'perinuclear space'. +is_a: GO:0044444 ! cytoplasmic part + +[Term] +id: GO:0048477 +name: oogenesis +namespace: biological_process +alt_id: GO:0009993 +alt_id: GO:0048157 +def: "The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster." [GOC:kmv, GOC:mtg_sensu] +synonym: "ovum development" EXACT systematic_synonym [] +xref: Wikipedia:Oogenesis +is_a: GO:0007292 ! female gamete generation + +[Term] +id: GO:0048483 +name: autonomic nervous system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the autonomic nervous system over time, from its formation to the mature structure. The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands." [FMA:9905, GOC:jid, GOC:sr] +is_a: GO:0048731 ! system development +relationship: part_of GO:0007399 ! nervous system development + +[Term] +id: GO:0048484 +name: enteric nervous system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the enteric nervous system over time, from its formation to the mature structure. The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation." [FMA:66070, GOC:jid, GOC:sr] +is_a: GO:0048731 ! system development +relationship: part_of GO:0048483 ! autonomic nervous system development + +[Term] +id: GO:0048485 +name: sympathetic nervous system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the sympathetic nervous system over time, from its formation to the mature structure. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter." [FMA:9906, GOC:jid, GOC:sr] +is_a: GO:0048731 ! system development +relationship: part_of GO:0048483 ! autonomic nervous system development + +[Term] +id: GO:0048489 +name: synaptic vesicle transport +namespace: biological_process +alt_id: GO:0016181 +def: "The directed movement of substances in synaptic membrane-bounded vesicles within the neuron along the cytoskeleton either toward or away from the neuronal cell body." [GOC:jid, GOC:lmg, GOC:pr] +subset: gosubset_prok +synonym: "synaptic vesicle fission" RELATED [] +synonym: "synaptic vesicle fusion" RELATED [] +is_a: GO:0016192 ! vesicle-mediated transport +is_a: GO:0044765 ! single-organism transport +is_a: GO:0097480 ! establishment of synaptic vesicle localization +relationship: part_of GO:0007268 ! synaptic transmission + +[Term] +id: GO:0048511 +name: rhythmic process +namespace: biological_process +def: "Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism." [GOC:jid] +subset: goslim_pir +subset: gosubset_prok +synonym: "rhythm" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0048513 +name: organ development +namespace: biological_process +def: "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:dph, GOC:jid] +synonym: "development of an organ" EXACT [] +synonym: "organogenesis" EXACT [] +xref: Wikipedia:Organogenesis +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0048731 ! system development + +[Term] +id: GO:0048514 +name: blood vessel morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood." [GOC:jid] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0001568 ! blood vessel development + +[Term] +id: GO:0048518 +name: positive regulation of biological process +namespace: biological_process +alt_id: GO:0043119 +def: "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] +subset: gosubset_prok +synonym: "activation of biological process" NARROW [] +synonym: "positive regulation of physiological process" EXACT [] +synonym: "stimulation of biological process" NARROW [] +synonym: "up regulation of biological process" EXACT [] +synonym: "up-regulation of biological process" EXACT [] +synonym: "upregulation of biological process" EXACT [] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008150 ! biological_process +relationship: positively_regulates GO:0008150 ! biological_process + +[Term] +id: GO:0048519 +name: negative regulation of biological process +namespace: biological_process +alt_id: GO:0043118 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] +subset: gosubset_prok +synonym: "down regulation of biological process" EXACT [] +synonym: "down-regulation of biological process" EXACT [] +synonym: "downregulation of biological process" EXACT [] +synonym: "inhibition of biological process" NARROW [] +synonym: "negative regulation of physiological process" EXACT [] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008150 ! biological_process +relationship: negatively_regulates GO:0008150 ! biological_process + +[Term] +id: GO:0048520 +name: positive regulation of behavior +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [GOC:jid, GOC:pr] +synonym: "activation of behavior" NARROW [] +synonym: "stimulation of behavior" NARROW [] +synonym: "up regulation of behavior" EXACT [] +synonym: "up-regulation of behavior" EXACT [] +synonym: "upregulation of behavior" EXACT [] +is_a: GO:0048584 ! positive regulation of response to stimulus +is_a: GO:0050795 ! regulation of behavior +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007610 ! behavior +relationship: positively_regulates GO:0007610 ! behavior + +[Term] +id: GO:0048521 +name: negative regulation of behavior +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [GOC:jid, GOC:pr] +synonym: "down regulation of behavior" EXACT [] +synonym: "down-regulation of behavior" EXACT [] +synonym: "downregulation of behavior" EXACT [] +synonym: "inhibition of behavior" NARROW [] +is_a: GO:0048585 ! negative regulation of response to stimulus +is_a: GO:0050795 ! regulation of behavior +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007610 ! behavior +relationship: negatively_regulates GO:0007610 ! behavior + +[Term] +id: GO:0048522 +name: positive regulation of cellular process +namespace: biological_process +alt_id: GO:0051242 +def: "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] +subset: gosubset_prok +synonym: "activation of cellular process" NARROW [] +synonym: "positive regulation of cellular physiological process" EXACT [] +synonym: "stimulation of cellular process" NARROW [] +synonym: "up regulation of cellular process" EXACT [] +synonym: "up-regulation of cellular process" EXACT [] +synonym: "upregulation of cellular process" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009987 ! cellular process +relationship: positively_regulates GO:0009987 ! cellular process + +[Term] +id: GO:0048523 +name: negative regulation of cellular process +namespace: biological_process +alt_id: GO:0051243 +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] +subset: gosubset_prok +synonym: "down regulation of cellular process" EXACT [] +synonym: "down-regulation of cellular process" EXACT [] +synonym: "downregulation of cellular process" EXACT [] +synonym: "inhibition of cellular process" NARROW [] +synonym: "negative regulation of cellular physiological process" EXACT [] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0009987 ! cellular process +relationship: negatively_regulates GO:0009987 ! cellular process + +[Term] +id: GO:0048534 +name: hematopoietic or lymphoid organ development +namespace: biological_process +def: "The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation." [GOC:add, GOC:rl, ISBN:0781735149] +synonym: "haematopoietic or lymphoid organ development" EXACT [] +synonym: "haemopoietic or lymphoid organ development" EXACT [] +synonym: "hemopoietic or lymphoid organ development" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0002520 ! immune system development + +[Term] +id: GO:0048538 +name: thymus development +namespace: biological_process +def: "The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components." [GOC:add, ISBN:0781735149] +comment: Note that this term is reserved for annotation of gene products involved in the formation of the thymus itself, not for gene products involved in T cell differentiation in the thymus or elsewhere. +is_a: GO:0048534 ! hematopoietic or lymphoid organ development + +[Term] +id: GO:0048539 +name: bone marrow development +namespace: biological_process +def: "The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure." [GOC:add, ISBN:0781735149] +is_a: GO:0048534 ! hematopoietic or lymphoid organ development +relationship: part_of GO:0060348 ! bone development + +[Term] +id: GO:0048545 +name: response to steroid hormone +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus." [GOC:go_curators] +synonym: "response to steroid hormone stimulus" EXACT [GOC:dos] +is_a: GO:0009725 ! response to hormone +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0033993 ! response to lipid + +[Term] +id: GO:0048546 +name: digestive tract morphogenesis +namespace: biological_process +alt_id: GO:0048547 +def: "The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:dph, GOC:go_curators, PMID:12618131] +synonym: "alimentary canal morphogenesis" EXACT [] +synonym: "digestive tube morphogenesis" EXACT [] +synonym: "gastrointestinal tract morphogenesis" EXACT [] +synonym: "gut morphogenesis" BROAD [GOC:dph] +synonym: "intestinal morphogenesis" NARROW [] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048565 ! digestive tract development + +[Term] +id: GO:0048562 +name: embryonic organ morphogenesis +namespace: biological_process +def: "Morphogenesis, during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:jid] +is_a: GO:0009887 ! organ morphogenesis +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0048568 ! embryonic organ development + +[Term] +id: GO:0048565 +name: digestive tract development +namespace: biological_process +def: "The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:go_curators] +synonym: "gut development" BROAD [GOC:dph] +synonym: "intestinal development" NARROW [] +synonym: "intestine development" NARROW [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0055123 ! digestive system development + +[Term] +id: GO:0048568 +name: embryonic organ development +namespace: biological_process +def: "Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:jid] +synonym: "embryonic organogenesis" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0009790 ! embryo development + +[Term] +id: GO:0048583 +name: regulation of response to stimulus +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: gosubset_prok +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050896 ! response to stimulus +relationship: regulates GO:0050896 ! response to stimulus + +[Term] +id: GO:0048584 +name: positive regulation of response to stimulus +namespace: biological_process +def: "Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +synonym: "activation of response to stimulus" NARROW [] +synonym: "stimulation of response to stimulus" NARROW [] +synonym: "up regulation of response to stimulus" EXACT [] +synonym: "up-regulation of response to stimulus" EXACT [] +synonym: "upregulation of response to stimulus" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050896 ! response to stimulus +relationship: positively_regulates GO:0050896 ! response to stimulus + +[Term] +id: GO:0048585 +name: negative regulation of response to stimulus +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +synonym: "down regulation of response to stimulus" EXACT [] +synonym: "down-regulation of response to stimulus" EXACT [] +synonym: "downregulation of response to stimulus" EXACT [] +synonym: "inhibition of response to stimulus" NARROW [] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0050896 ! response to stimulus +relationship: negatively_regulates GO:0050896 ! response to stimulus + +[Term] +id: GO:0048588 +name: developmental cell growth +namespace: biological_process +def: "The growth of a cell, where growth contributes to the progression of the cell over time from one condition to another." [GOC:go_curators, GOC:isa_complete] +synonym: "developmental growth of a unicellular organism" EXACT [] +is_a: GO:0016049 ! cell growth +is_a: GO:0048589 ! developmental growth +relationship: part_of GO:0048468 ! cell development + +[Term] +id: GO:0048589 +name: developmental growth +namespace: biological_process +def: "The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another." [GOC:go_curators] +is_a: GO:0040007 ! growth +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0048592 +name: eye morphogenesis +namespace: biological_process +alt_id: GO:0048748 +def: "The process in which the anatomical structures of the eye are generated and organized." [GOC:jid, GOC:mtg_sensu] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0001654 ! eye development + +[Term] +id: GO:0048593 +name: camera-type eye morphogenesis +namespace: biological_process +alt_id: GO:0048594 +alt_id: GO:0048595 +def: "The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field." [GOC:jid, GOC:mtg_sensu] +synonym: "camera-style eye morphogenesis" EXACT [GOC:dph] +is_a: GO:0048592 ! eye morphogenesis +relationship: part_of GO:0043010 ! camera-type eye development + +[Term] +id: GO:0048596 +name: embryonic camera-type eye morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the eye are generated and organized during embryonic development." [GOC:jid, GOC:mtg_sensu] +synonym: "embryonic eye morphogenesis" BROAD [] +is_a: GO:0048048 ! embryonic eye morphogenesis +relationship: part_of GO:0031076 ! embryonic camera-type eye development +relationship: part_of GO:0048593 ! camera-type eye morphogenesis + +[Term] +id: GO:0048598 +name: embryonic morphogenesis +namespace: biological_process +alt_id: GO:0048828 +def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] +synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0009790 ! embryo development + +[Term] +id: GO:0048599 +name: oocyte development +namespace: biological_process +def: "The process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." [GOC:go_curators] +is_a: GO:0007281 ! germ cell development +relationship: part_of GO:0009994 ! oocyte differentiation + +[Term] +id: GO:0048608 +name: reproductive structure development +namespace: biological_process +def: "The reproductive developmental process whose specific outcome is the progression of structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures." [GOC:dph, GOC:isa_complete, GOC:jid] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061458 ! reproductive system development + +[Term] +id: GO:0048609 +name: multicellular organismal reproductive process +namespace: biological_process +def: "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs." [GOC:dph, GOC:jid, GOC:tb] +synonym: "organismal reproductive process" BROAD [GOC:curators] +synonym: "reproductive process in a multicellular organism" EXACT [GOC:curators] +is_a: GO:0022414 ! reproductive process +relationship: part_of GO:0032504 ! multicellular organism reproduction + +[Term] +id: GO:0048610 +name: cellular process involved in reproduction +namespace: biological_process +def: "A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular or single-celled organism." [GOC:dph, GOC:jid] +subset: gosubset_prok +synonym: "reproductive cellular process" RELATED [GOC:dph, GOC:tb] +is_a: GO:0009987 ! cellular process +intersection_of: GO:0009987 ! cellular process +intersection_of: part_of GO:0000003 ! reproduction +relationship: part_of GO:0000003 ! reproduction + +[Term] +id: GO:0048617 +name: embryonic foregut morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the foregut are generated and organized, during the embryonic phase." [GOC:jid, GOC:rc] +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0007440 ! foregut morphogenesis + +[Term] +id: GO:0048634 +name: regulation of muscle organ development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of muscle development." [GOC:go_curators] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007517 ! muscle organ development +relationship: regulates GO:0007517 ! muscle organ development + +[Term] +id: GO:0048638 +name: regulation of developmental growth +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of developmental growth." [GOC:go_curators] +is_a: GO:0040008 ! regulation of growth +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048589 ! developmental growth +relationship: regulates GO:0048589 ! developmental growth + +[Term] +id: GO:0048639 +name: positive regulation of developmental growth +namespace: biological_process +def: "Any process that activates, maintains or increases the rate of developmental growth." [GOC:go_curators] +synonym: "activation of developmental growth" NARROW [] +synonym: "stimulation of developmental growth" NARROW [] +synonym: "up regulation of developmental growth" EXACT [] +synonym: "up-regulation of developmental growth" EXACT [] +synonym: "upregulation of developmental growth" EXACT [] +is_a: GO:0045927 ! positive regulation of growth +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048589 ! developmental growth +relationship: positively_regulates GO:0048589 ! developmental growth + +[Term] +id: GO:0048640 +name: negative regulation of developmental growth +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth." [GOC:go_curators] +synonym: "down regulation of developmental growth" EXACT [] +synonym: "down-regulation of developmental growth" EXACT [] +synonym: "downregulation of developmental growth" EXACT [] +synonym: "inhibition of developmental growth" NARROW [] +is_a: GO:0045926 ! negative regulation of growth +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:0051093 ! negative regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048589 ! developmental growth +relationship: negatively_regulates GO:0048589 ! developmental growth + +[Term] +id: GO:0048644 +name: muscle organ morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of muscle are generated and organized." [GOC:jid] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0007517 ! muscle organ development + +[Term] +id: GO:0048645 +name: organ formation +namespace: biological_process +def: "The process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. Organs are a natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole. The heart and lungs are organs of animals, and the petal and leaf are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ." [GOC:dph, GOC:jid] +synonym: "initiation of an organ primordium" NARROW [] +synonym: "organ primordium initiation" NARROW [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0009887 ! organ morphogenesis + +[Term] +id: GO:0048646 +name: anatomical structure formation involved in morphogenesis +namespace: biological_process +def: "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph, GOC:jid, GOC:tb] +comment: Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. +subset: goslim_generic +synonym: "formation of an anatomical structure involved in morphogenesis" EXACT [GOC:dph, GOC:tb] +is_a: GO:0032502 ! developmental process +relationship: part_of GO:0009653 ! anatomical structure morphogenesis + +[Term] +id: GO:0048659 +name: smooth muscle cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of smooth muscle cells, resulting in the expansion of a cell population." [CL:0000192, GOC:ebc, PMID:1840698] +synonym: "SMC proliferation" EXACT [] +is_a: GO:0033002 ! muscle cell proliferation + +[Term] +id: GO:0048660 +name: regulation of smooth muscle cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of smooth muscle cell proliferation." [CL:0000192, GOC:ebc] +synonym: "regulation of SMC proliferation" EXACT [] +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048659 ! smooth muscle cell proliferation +relationship: regulates GO:0048659 ! smooth muscle cell proliferation + +[Term] +id: GO:0048662 +name: negative regulation of smooth muscle cell proliferation +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation." [CL:0000192, GOC:ebc] +synonym: "down regulation of smooth muscle cell proliferation" EXACT [] +synonym: "down-regulation of smooth muscle cell proliferation" EXACT [] +synonym: "downregulation of smooth muscle cell proliferation" EXACT [] +synonym: "inhibition of smooth muscle cell proliferation" NARROW [] +synonym: "negative regulation of SMC proliferation" EXACT [] +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0048660 ! regulation of smooth muscle cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048659 ! smooth muscle cell proliferation +relationship: negatively_regulates GO:0048659 ! smooth muscle cell proliferation + +[Term] +id: GO:0048663 +name: neuron fate commitment +namespace: biological_process +alt_id: GO:0042055 +def: "The process in which the developmental fate of a cell becomes restricted such that it will develop into a neuron." [GOC:dph] +synonym: "neuron lineage restriction" EXACT [] +synonym: "neuronal lineage restriction" EXACT [] +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0030182 ! neuron differentiation + +[Term] +id: GO:0048664 +name: neuron fate determination +namespace: biological_process +def: "The process in which a cell becomes capable of differentiating autonomously into a neuron regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:dph] +is_a: GO:0001709 ! cell fate determination +relationship: part_of GO:0048663 ! neuron fate commitment + +[Term] +id: GO:0048665 +name: neuron fate specification +namespace: biological_process +def: "The process in which a cell becomes capable of differentiating autonomously into a neuron in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed." [GOC:dph] +is_a: GO:0001708 ! cell fate specification +relationship: part_of GO:0048663 ! neuron fate commitment + +[Term] +id: GO:0048666 +name: neuron development +namespace: biological_process +def: "The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." [GOC:dph] +is_a: GO:0048468 ! cell development +relationship: part_of GO:0030182 ! neuron differentiation + +[Term] +id: GO:0048667 +name: cell morphogenesis involved in neuron differentiation +namespace: biological_process +def: "The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron." [GOC:dph, GOC:tb] +synonym: "neuron morphogenesis involved in differentiation" EXACT [GOC:dph, GOC:tb] +is_a: GO:0000904 ! cell morphogenesis involved in differentiation +intersection_of: GO:0000902 ! cell morphogenesis +intersection_of: part_of GO:0030182 ! neuron differentiation +relationship: part_of GO:0048666 ! neuron development + +[Term] +id: GO:0048668 +name: collateral sprouting +namespace: biological_process +def: "The process in which outgrowths develop from the shafts of existing axons." [GOC:dgh, GOC:dph, GOC:jid, GOC:lm] +synonym: "axon branching" BROAD [GOC:BHF, PMID:21463686] +is_a: GO:0048588 ! developmental cell growth +is_a: GO:0060560 ! developmental growth involved in morphogenesis +relationship: part_of GO:0007409 ! axonogenesis + +[Term] +id: GO:0048669 +name: collateral sprouting in absence of injury +namespace: biological_process +def: "The process in which outgrowths develop from the axons of intact undamaged neurons." [GOC:dgh, GOC:dph, GOC:jid, GOC:lm] +is_a: GO:0048668 ! collateral sprouting + +[Term] +id: GO:0048670 +name: regulation of collateral sprouting +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of collateral sprouting." [GOC:dgh, GOC:dph, GOC:jid, GOC:lm] +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:0050770 ! regulation of axonogenesis +is_a: GO:0061387 ! regulation of extent of cell growth +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048668 ! collateral sprouting +relationship: regulates GO:0048668 ! collateral sprouting + +[Term] +id: GO:0048672 +name: positive regulation of collateral sprouting +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of collateral sprouting." [GOC:dgh, GOC:dph, GOC:jid, GOC:lm] +synonym: "activation of collateral sprouting" NARROW [] +synonym: "stimulation of collateral sprouting" NARROW [] +synonym: "up regulation of collateral sprouting" EXACT [] +synonym: "up-regulation of collateral sprouting" EXACT [] +synonym: "upregulation of collateral sprouting" EXACT [] +is_a: GO:0030307 ! positive regulation of cell growth +is_a: GO:0048639 ! positive regulation of developmental growth +is_a: GO:0048670 ! regulation of collateral sprouting +is_a: GO:0050772 ! positive regulation of axonogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048668 ! collateral sprouting +relationship: positively_regulates GO:0048668 ! collateral sprouting + +[Term] +id: GO:0048675 +name: axon extension +namespace: biological_process +alt_id: GO:0048676 +def: "Long distance growth of a single axon process involved in cellular development." [GOC:BHF, GOC:dgh, GOC:dph, GOC:jid, GOC:lm, GOC:rl] +synonym: "axon extension involved in development" EXACT [] +is_a: GO:1990138 ! neuron projection extension +relationship: part_of GO:0007409 ! axonogenesis + +[Term] +id: GO:0048696 +name: regulation of collateral sprouting in absence of injury +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of collateral sprouting in the absence of injury." [GOC:dgh, GOC:dph, GOC:jid, GOC:lm] +is_a: GO:0048670 ! regulation of collateral sprouting +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048669 ! collateral sprouting in absence of injury +relationship: regulates GO:0048669 ! collateral sprouting in absence of injury + +[Term] +id: GO:0048697 +name: positive regulation of collateral sprouting in absence of injury +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of collateral sprouting in the absence of injury." [GOC:dgh, GOC:dph, GOC:jid, GOC:lm] +synonym: "activation of collateral sprouting in the absence of injury" NARROW [] +synonym: "stimulation of collateral sprouting in the absence of injury" NARROW [] +synonym: "up regulation of collateral sprouting in the absence of injury" EXACT [] +synonym: "up-regulation of collateral sprouting in the absence of injury" EXACT [] +synonym: "upregulation of collateral sprouting in the absence of injury" EXACT [] +is_a: GO:0048672 ! positive regulation of collateral sprouting +is_a: GO:0048696 ! regulation of collateral sprouting in absence of injury +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048669 ! collateral sprouting in absence of injury +relationship: positively_regulates GO:0048669 ! collateral sprouting in absence of injury + +[Term] +id: GO:0048699 +name: generation of neurons +namespace: biological_process +def: "The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons." [GOC:nln] +synonym: "neuron generation" EXACT [GOC:curators] +is_a: GO:0022008 ! neurogenesis + +[Term] +id: GO:0048701 +name: embryonic cranial skeleton morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the cranial skeleton are generated and organized during the embryonic phase." [GOC:dsf, GOC:jid, PMID:16049113] +synonym: "embryonic cranium morphogenesis" EXACT [] +is_a: GO:0048704 ! embryonic skeletal system morphogenesis + +[Term] +id: GO:0048703 +name: embryonic viscerocranium morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the viscerocranium are generated and organized during the embryonic phase. The viscerocranium is the part of the skull comprising the facial bones." [GOC:dsf, GOC:jid, PMID:16049113] +synonym: "embryonic pharyngeal skeleton morphogenesis" EXACT [] +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0048701 ! embryonic cranial skeleton morphogenesis + +[Term] +id: GO:0048704 +name: embryonic skeletal system morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase." [GOC:dph, GOC:dsf, GOC:jid, GOC:tb, PMID:16049113] +synonym: "embryonic skeletal morphogenesis" EXACT [GOC:dph, GOC:tb] +is_a: GO:0048562 ! embryonic organ morphogenesis +is_a: GO:0048705 ! skeletal system morphogenesis +relationship: part_of GO:0048706 ! embryonic skeletal system development + +[Term] +id: GO:0048705 +name: skeletal system morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the skeleton are generated and organized." [GOC:dph, GOC:dsf, GOC:jid, GOC:tb] +synonym: "skeletal morphogenesis" EXACT [GOC:dph, GOC:tb] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0001501 ! skeletal system development + +[Term] +id: GO:0048706 +name: embryonic skeletal system development +namespace: biological_process +def: "The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure." [GOC:dph, GOC:dsf, GOC:jid, GOC:tb, PMID:16049113] +synonym: "embryonic skeletal development" EXACT [GOC:dph, GOC:tb] +is_a: GO:0001501 ! skeletal system development +relationship: part_of GO:0043009 ! chordate embryonic development + +[Term] +id: GO:0048709 +name: oligodendrocyte differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system." [GOC:vp, PMID:15139015] +is_a: GO:0010001 ! glial cell differentiation +relationship: part_of GO:0007417 ! central nervous system development + +[Term] +id: GO:0048713 +name: regulation of oligodendrocyte differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of oligodendrocyte differentiation." [GOC:vp, PMID:15139015] +is_a: GO:0045685 ! regulation of glial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048709 ! oligodendrocyte differentiation +relationship: regulates GO:0048709 ! oligodendrocyte differentiation + +[Term] +id: GO:0048715 +name: negative regulation of oligodendrocyte differentiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of oligodendrocyte differentiation." [GOC:vp, PMID:15139015] +synonym: "down regulation of oligodendrocyte differentiation" EXACT [] +synonym: "down-regulation of oligodendrocyte differentiation" EXACT [] +synonym: "downregulation of oligodendrocyte differentiation" EXACT [] +synonym: "inhibition of oligodendrocyte differentiation" NARROW [] +is_a: GO:0045686 ! negative regulation of glial cell differentiation +is_a: GO:0048713 ! regulation of oligodendrocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048709 ! oligodendrocyte differentiation +relationship: negatively_regulates GO:0048709 ! oligodendrocyte differentiation + +[Term] +id: GO:0048729 +name: tissue morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a tissue are generated and organized." [GOC:dph, GOC:jid] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0009888 ! tissue development + +[Term] +id: GO:0048730 +name: epidermis morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the epidermis are generated and organized. The epidermis is the outer epithelial layer of a plant or animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." [GOC:jid, UBERON:0001003] +synonym: "hypodermis morphogenesis" RELATED [GOC:kmv, GOC:rk] +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0008544 ! epidermis development +relationship: part_of GO:0043589 ! skin morphogenesis + +[Term] +id: GO:0048731 +name: system development +namespace: biological_process +def: "The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." [GOC:dph, GOC:jid] +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0048732 +name: gland development +namespace: biological_process +def: "The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion." [GOC:jid] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development + +[Term] +id: GO:0048736 +name: appendage development +namespace: biological_process +def: "The process whose specific outcome is the progression of an appendage over time, from its formation to the mature structure. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch." [GOC:jid, GOC:rc] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0007275 ! multicellular organismal development + +[Term] +id: GO:0048738 +name: cardiac muscle tissue development +namespace: biological_process +def: "The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure." [GOC:dph, GOC:jid, GOC:lm] +synonym: "heart muscle development" EXACT [] +is_a: GO:0014706 ! striated muscle tissue development +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0048745 +name: smooth muscle tissue development +namespace: biological_process +def: "The process whose specific outcome is the progression of smooth muscle over time, from its formation to the mature structure." [GOC:dph, GOC:jid, GOC:lm] +is_a: GO:0060537 ! muscle tissue development + +[Term] +id: GO:0048754 +name: branching morphogenesis of an epithelial tube +namespace: biological_process +def: "The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder." [GOC:dgh, GOC:dph, GOC:jid] +synonym: "tubulogenesis" RELATED [GOC:dph, GOC:tb] +is_a: GO:0061138 ! morphogenesis of a branching epithelium +relationship: part_of GO:0060562 ! epithelial tube morphogenesis + +[Term] +id: GO:0048762 +name: mesenchymal cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types." [GOC:dph, GOC:jid] +is_a: GO:0048863 ! stem cell differentiation +relationship: part_of GO:0060485 ! mesenchyme development + +[Term] +id: GO:0048771 +name: tissue remodeling +namespace: biological_process +def: "The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling." [GOC:ebc] +subset: goslim_pir +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0048806 +name: genitalia development +namespace: biological_process +def: "The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure." [GOC:jid] +synonym: "genital development" EXACT [] +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +is_a: GO:0048608 ! reproductive structure development +relationship: part_of GO:0007548 ! sex differentiation + +[Term] +id: GO:0048812 +name: neuron projection morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites." [GOC:mah] +synonym: "neurite biosynthesis" NARROW [] +synonym: "neurite formation" NARROW [] +synonym: "neurite growth" NARROW [] +synonym: "neurite morphogenesis" RELATED [GOC:dph, GOC:tb] +is_a: GO:0048858 ! cell projection morphogenesis +relationship: part_of GO:0031175 ! neuron projection development + +[Term] +id: GO:0048813 +name: dendrite morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell." [GOC:jl, ISBN:0198506732] +is_a: GO:0048812 ! neuron projection morphogenesis +relationship: part_of GO:0016358 ! dendrite development +relationship: part_of GO:0048667 ! cell morphogenesis involved in neuron differentiation + +[Term] +id: GO:0048814 +name: regulation of dendrite morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of dendrite morphogenesis." [GOC:ai] +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:0050773 ! regulation of dendrite development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048813 ! dendrite morphogenesis +relationship: regulates GO:0048813 ! dendrite morphogenesis + +[Term] +id: GO:0048839 +name: inner ear development +namespace: biological_process +def: "The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure." [GOC:sr] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0043583 ! ear development + +[Term] +id: GO:0048841 +name: regulation of axon extension involved in axon guidance +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of axon extension involved in axon guidance." [GOC:devbiol] +is_a: GO:0030516 ! regulation of axon extension +is_a: GO:1902667 ! regulation of axon guidance +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048846 ! axon extension involved in axon guidance +relationship: regulates GO:0048846 ! axon extension involved in axon guidance + +[Term] +id: GO:0048843 +name: negative regulation of axon extension involved in axon guidance +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of axon extension involved in axon guidance." [GOC:devbiol] +synonym: "down regulation of axon extension involved in axon guidance" EXACT [] +synonym: "down-regulation of axon extension involved in axon guidance" EXACT [] +synonym: "downregulation of axon extension involved in axon guidance" EXACT [] +synonym: "inhibition of axon extension involved in axon guidance" NARROW [] +is_a: GO:0030517 ! negative regulation of axon extension +is_a: GO:0048841 ! regulation of axon extension involved in axon guidance +is_a: GO:0050922 ! negative regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048846 ! axon extension involved in axon guidance +relationship: negatively_regulates GO:0048846 ! axon extension involved in axon guidance + +[Term] +id: GO:0048844 +name: artery morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs." [GOC:dsf, PMID:16740480] +synonym: "arterial morphogenesis" EXACT [] +synonym: "arteriogenesis" EXACT [GOC:mtg_heart] +is_a: GO:0048514 ! blood vessel morphogenesis +relationship: part_of GO:0060840 ! artery development + +[Term] +id: GO:0048846 +name: axon extension involved in axon guidance +namespace: biological_process +def: "The long distance growth of a single cell process, that is involved in the migration of an axon growth cone, where the migration is directed to a specific target site by a combination of attractive and repulsive cues." [GOC:ef, GOC:jid] +is_a: GO:0048675 ! axon extension +is_a: GO:1902284 ! neuron projection extension involved in neuron projection guidance +intersection_of: GO:0048675 ! axon extension +intersection_of: part_of GO:0007411 ! axon guidance +relationship: part_of GO:0007411 ! axon guidance + +[Term] +id: GO:0048850 +name: hypophysis morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the hypophysis are generated and organized. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands." [GOC:cls, GOC:dgh, GOC:dph, GOC:jid] +synonym: "pituitary gland morphogenesis" EXACT [] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021983 ! pituitary gland development +relationship: part_of GO:0022612 ! gland morphogenesis +relationship: part_of GO:0048852 ! diencephalon morphogenesis + +[Term] +id: GO:0048852 +name: diencephalon morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the diencephalon are generated and organized. The diencephalon is the paired caudal parts of the prosencephalon from which the thalamus, hypothalamus, epithalamus and subthalamus are derived; these regions regulate autonomic, visceral and endocrine function, and process information directed to the cerebral cortex." [GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0021536 ! diencephalon development +relationship: part_of GO:0048853 ! forebrain morphogenesis + +[Term] +id: GO:0048853 +name: forebrain morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the forebrain are generated and organized. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions)." [GOC:cvs, GOC:dgh, GOC:dph, GOC:jid] +synonym: "prosencephalon morphogenesis" EXACT [] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0030900 ! forebrain development +relationship: part_of GO:0048854 ! brain morphogenesis + +[Term] +id: GO:0048854 +name: brain morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.)." [GOC:dgh, GOC:jid] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0007420 ! brain development + +[Term] +id: GO:0048856 +name: anatomical structure development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GO_REF:0000021, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +subset: goslim_generic +synonym: "development of an anatomical structure" EXACT [] +is_a: GO:0032502 ! developmental process + +[Term] +id: GO:0048857 +name: neural nucleus development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a neural nucleus from its initial condition to its mature state. A neural nucleus is an anatomical structure consisting of a discrete aggregate of neuronal soma." [GO_REF:0000021, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0048858 +name: cell projection morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a cell projection are generated and organized." [GO_REF:0000021, GOC:mtg_15jun06] +comment: This term was added by GO_REF:0000021. +is_a: GO:0030030 ! cell projection organization +is_a: GO:0032990 ! cell part morphogenesis +relationship: part_of GO:0000902 ! cell morphogenesis + +[Term] +id: GO:0048863 +name: stem cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [CL:0000034, GOC:isa_complete] +xref: Wikipedia:Stem_cell_differentiation +is_a: GO:0030154 ! cell differentiation + +[Term] +id: GO:0048864 +name: stem cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of the stem cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to its specific fate." [CL:0000034, GOC:isa_complete] +is_a: GO:0048468 ! cell development +relationship: part_of GO:0048863 ! stem cell differentiation + +[Term] +id: GO:0048869 +name: cellular developmental process +namespace: biological_process +def: "A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition." [GOC:isa_complete] +subset: gosubset_prok +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0044767 ! single-organism developmental process + +[Term] +id: GO:0048870 +name: cell motility +namespace: biological_process +def: "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another." [GOC:dgh, GOC:dph, GOC:isa_complete, GOC:mlg] +subset: goslim_generic +subset: goslim_metagenomics +subset: gosubset_prok +synonym: "cell locomotion" EXACT [] +synonym: "cell movement" RELATED [] +synonym: "movement of a cell" EXACT [] +is_a: GO:0006928 ! cellular component movement +is_a: GO:0040011 ! locomotion +relationship: part_of GO:0051674 ! localization of cell + +[Term] +id: GO:0048871 +name: multicellular organismal homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state at the level of the multicellular organism." [GOC:isa_complete] +is_a: GO:0042592 ! homeostatic process +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0048878 +name: chemical homeostasis +namespace: biological_process +def: "Any biological process involved in the maintenance of an internal steady state of a chemical." [GOC:isa_complete] +subset: gosubset_prok +is_a: GO:0042592 ! homeostatic process + +[Term] +id: GO:0048880 +name: sensory system development +namespace: biological_process +def: "The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure." [GOC:dgh] +is_a: GO:0048731 ! system development + +[Term] +id: GO:0048892 +name: lateral line nerve development +namespace: biological_process +def: "The process whose specific outcome is the progression of the lateral line nerve over time, form its formation to the mature structure. Lateral line nerves project primarily to an octavolateralis column in the hindbrain that consists of the medial octavolateralis nucleus (MON), the caudal octavolateralis nucleus, and the magnocellular nucleus." [ISBN:0125296509] +synonym: "nLL development" EXACT [] +is_a: GO:0021545 ! cranial nerve development +relationship: part_of GO:0048925 ! lateral line system development + +[Term] +id: GO:0048895 +name: lateral line nerve glial cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a glial cell in a lateral line nerve." [PMID:12062041] +is_a: GO:0010001 ! glial cell differentiation +relationship: part_of GO:0048892 ! lateral line nerve development + +[Term] +id: GO:0048925 +name: lateral line system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the lateral line system over time, from its formation to the mature structure. The lateral line system is a network of sensory organs (neuromasts) and lateral line nerves located superficially on the skin or just under the skin in fluid-filled canals on the head and body of all fishes and most amphibians. The lateral line system develops from cranial ectodermal placodes situated between the eye and ear." [GOC:dgh, ISBN:0125296509] +is_a: GO:0048880 ! sensory system development + +[Term] +id: GO:0048937 +name: lateral line nerve glial cell development +namespace: biological_process +def: "The process aimed at the progression of a lateral line glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." [GOC:dgh] +is_a: GO:0021782 ! glial cell development +relationship: part_of GO:0048895 ! lateral line nerve glial cell differentiation + +[Term] +id: GO:0050663 +name: cytokine secretion +namespace: biological_process +def: "The regulated release of cytokines from a cell. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity." [GOC:ai, GOC:bf, ISBN:0198599471] +synonym: "interferon secretion" NARROW [GOC:add, GOC:mah] +synonym: "interleukin secretion" NARROW [GOC:add, GOC:mah] +is_a: GO:0009306 ! protein secretion +relationship: part_of GO:0001816 ! cytokine production + +[Term] +id: GO:0050670 +name: regulation of lymphocyte proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of lymphocyte proliferation." [GOC:ai] +is_a: GO:0032944 ! regulation of mononuclear cell proliferation +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046651 ! lymphocyte proliferation +relationship: regulates GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0050671 +name: positive regulation of lymphocyte proliferation +namespace: biological_process +def: "Any process that activates or increases the rate or extent of lymphocyte proliferation." [GOC:ai] +synonym: "activation of lymphocyte proliferation" NARROW [] +synonym: "stimulation of lymphocyte proliferation" NARROW [] +synonym: "up regulation of lymphocyte proliferation" EXACT [] +synonym: "up-regulation of lymphocyte proliferation" EXACT [] +synonym: "upregulation of lymphocyte proliferation" EXACT [] +is_a: GO:0032946 ! positive regulation of mononuclear cell proliferation +is_a: GO:0050670 ! regulation of lymphocyte proliferation +is_a: GO:0051251 ! positive regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046651 ! lymphocyte proliferation +relationship: positively_regulates GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0050672 +name: negative regulation of lymphocyte proliferation +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of lymphocyte proliferation." [GOC:ai] +synonym: "down regulation of lymphocyte proliferation" EXACT [] +synonym: "down-regulation of lymphocyte proliferation" EXACT [] +synonym: "downregulation of lymphocyte proliferation" EXACT [] +synonym: "inhibition of lymphocyte proliferation" NARROW [] +is_a: GO:0032945 ! negative regulation of mononuclear cell proliferation +is_a: GO:0050670 ! regulation of lymphocyte proliferation +is_a: GO:0051250 ! negative regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046651 ! lymphocyte proliferation +relationship: negatively_regulates GO:0046651 ! lymphocyte proliferation + +[Term] +id: GO:0050673 +name: epithelial cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances." [ISBN:0721662544] +is_a: GO:0008283 ! cell proliferation + +[Term] +id: GO:0050678 +name: regulation of epithelial cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of epithelial cell proliferation." [GOC:ai] +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050673 ! epithelial cell proliferation +relationship: regulates GO:0050673 ! epithelial cell proliferation + +[Term] +id: GO:0050679 +name: positive regulation of epithelial cell proliferation +namespace: biological_process +def: "Any process that activates or increases the rate or extent of epithelial cell proliferation." [GOC:ai] +synonym: "activation of epithelial cell proliferation" NARROW [] +synonym: "stimulation of epithelial cell proliferation" NARROW [] +synonym: "up regulation of epithelial cell proliferation" EXACT [] +synonym: "up-regulation of epithelial cell proliferation" EXACT [] +synonym: "upregulation of epithelial cell proliferation" EXACT [] +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0050678 ! regulation of epithelial cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050673 ! epithelial cell proliferation +relationship: positively_regulates GO:0050673 ! epithelial cell proliferation + +[Term] +id: GO:0050680 +name: negative regulation of epithelial cell proliferation +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation." [GOC:ai] +synonym: "down regulation of epithelial cell proliferation" EXACT [] +synonym: "down-regulation of epithelial cell proliferation" EXACT [] +synonym: "downregulation of epithelial cell proliferation" EXACT [] +synonym: "inhibition of epithelial cell proliferation" NARROW [] +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0050678 ! regulation of epithelial cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0050673 ! epithelial cell proliferation +relationship: negatively_regulates GO:0050673 ! epithelial cell proliferation + +[Term] +id: GO:0050681 +name: androgen receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an androgen receptor." [GOC:ai] +synonym: "AR binding" EXACT [] +is_a: GO:0035258 ! steroid hormone receptor binding + +[Term] +id: GO:0050701 +name: interleukin-1 secretion +namespace: biological_process +def: "The regulated release of interleukin-1 from a cell. Interleukin 1 is produced mainly by activated macrophages; it stimulates thymocyte proliferation by inducing interleukin 2 release and it is involved in the inflammatory response." [GOC:ai, ISBN:0198506732] +synonym: "IL-1 secretion" EXACT [] +is_a: GO:0050663 ! cytokine secretion +relationship: part_of GO:0032612 ! interleukin-1 production + +[Term] +id: GO:0050702 +name: interleukin-1 beta secretion +namespace: biological_process +def: "The regulated release of interleukin 1 beta from a cell." [GOC:ai] +synonym: "IL-1b secretion" EXACT [] +is_a: GO:0050701 ! interleukin-1 secretion +relationship: part_of GO:0032611 ! interleukin-1 beta production + +[Term] +id: GO:0050704 +name: regulation of interleukin-1 secretion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the regulated release of interleukin-1 from a cell." [GOC:ai] +is_a: GO:0032652 ! regulation of interleukin-1 production +is_a: GO:0050707 ! regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050701 ! interleukin-1 secretion +relationship: regulates GO:0050701 ! interleukin-1 secretion + +[Term] +id: GO:0050706 +name: regulation of interleukin-1 beta secretion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell." [GOC:ai] +is_a: GO:0032651 ! regulation of interleukin-1 beta production +is_a: GO:0050704 ! regulation of interleukin-1 secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050702 ! interleukin-1 beta secretion +relationship: regulates GO:0050702 ! interleukin-1 beta secretion + +[Term] +id: GO:0050707 +name: regulation of cytokine secretion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the regulated release of cytokines from a cell." [GOC:ai] +is_a: GO:0001817 ! regulation of cytokine production +is_a: GO:0050708 ! regulation of protein secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050663 ! cytokine secretion +relationship: regulates GO:0050663 ! cytokine secretion + +[Term] +id: GO:0050708 +name: regulation of protein secretion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell." [GOC:ai] +subset: gosubset_prok +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0051223 ! regulation of protein transport +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009306 ! protein secretion +relationship: regulates GO:0009306 ! protein secretion + +[Term] +id: GO:0050714 +name: positive regulation of protein secretion +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell." [GOC:ai] +synonym: "activation of protein secretion" NARROW [] +synonym: "stimulation of protein secretion" NARROW [] +synonym: "up regulation of protein secretion" EXACT [] +synonym: "up-regulation of protein secretion" EXACT [] +synonym: "upregulation of protein secretion" EXACT [] +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0050708 ! regulation of protein secretion +is_a: GO:0051047 ! positive regulation of secretion +is_a: GO:0051222 ! positive regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0009306 ! protein secretion +relationship: positively_regulates GO:0009306 ! protein secretion + +[Term] +id: GO:0050715 +name: positive regulation of cytokine secretion +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell." [GOC:ai] +synonym: "activation of cytokine secretion" NARROW [] +synonym: "stimulation of cytokine secretion" NARROW [] +synonym: "up regulation of cytokine secretion" EXACT [] +synonym: "up-regulation of cytokine secretion" EXACT [] +synonym: "upregulation of cytokine secretion" EXACT [] +is_a: GO:0050707 ! regulation of cytokine secretion +is_a: GO:0050714 ! positive regulation of protein secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050663 ! cytokine secretion +relationship: positively_regulates GO:0050663 ! cytokine secretion + +[Term] +id: GO:0050716 +name: positive regulation of interleukin-1 secretion +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 from a cell." [GOC:ai] +synonym: "activation of interleukin-1 secretion" NARROW [] +synonym: "stimulation of interleukin-1 secretion" NARROW [] +synonym: "up regulation of interleukin-1 secretion" EXACT [] +synonym: "up-regulation of interleukin-1 secretion" EXACT [] +synonym: "upregulation of interleukin-1 secretion" EXACT [] +is_a: GO:0032732 ! positive regulation of interleukin-1 production +is_a: GO:0050704 ! regulation of interleukin-1 secretion +is_a: GO:0050715 ! positive regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050701 ! interleukin-1 secretion +relationship: positively_regulates GO:0050701 ! interleukin-1 secretion + +[Term] +id: GO:0050718 +name: positive regulation of interleukin-1 beta secretion +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell." [GOC:ai] +synonym: "activation of interleukin-1 beta secretion" NARROW [] +synonym: "stimulation of interleukin-1 beta secretion" NARROW [] +synonym: "up regulation of interleukin-1 beta secretion" EXACT [] +synonym: "up-regulation of interleukin-1 beta secretion" EXACT [] +synonym: "upregulation of interleukin-1 beta secretion" EXACT [] +is_a: GO:0032731 ! positive regulation of interleukin-1 beta production +is_a: GO:0050706 ! regulation of interleukin-1 beta secretion +is_a: GO:0050716 ! positive regulation of interleukin-1 secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0050702 ! interleukin-1 beta secretion +relationship: positively_regulates GO:0050702 ! interleukin-1 beta secretion + +[Term] +id: GO:0050727 +name: regulation of inflammatory response +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents." [GOC:ai] +is_a: GO:0031347 ! regulation of defense response +is_a: GO:0032101 ! regulation of response to external stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006954 ! inflammatory response +relationship: regulates GO:0006954 ! inflammatory response + +[Term] +id: GO:0050729 +name: positive regulation of inflammatory response +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the inflammatory response." [GOC:ai] +synonym: "activation of inflammatory response" NARROW [] +synonym: "stimulation of inflammatory response" NARROW [] +synonym: "up regulation of inflammatory response" EXACT [] +synonym: "up-regulation of inflammatory response" EXACT [] +synonym: "upregulation of inflammatory response" EXACT [] +is_a: GO:0031349 ! positive regulation of defense response +is_a: GO:0032103 ! positive regulation of response to external stimulus +is_a: GO:0050727 ! regulation of inflammatory response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006954 ! inflammatory response +relationship: positively_regulates GO:0006954 ! inflammatory response + +[Term] +id: GO:0050730 +name: regulation of peptidyl-tyrosine phosphorylation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine." [GOC:ai] +subset: gosubset_prok +is_a: GO:0001932 ! regulation of protein phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0018108 ! peptidyl-tyrosine phosphorylation +relationship: regulates GO:0018108 ! peptidyl-tyrosine phosphorylation + +[Term] +id: GO:0050731 +name: positive regulation of peptidyl-tyrosine phosphorylation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine." [GOC:ai] +subset: gosubset_prok +synonym: "activation of peptidyl-tyrosine phosphorylation" NARROW [] +synonym: "stimulation of peptidyl-tyrosine phosphorylation" NARROW [] +synonym: "up regulation of peptidyl-tyrosine phosphorylation" EXACT [] +synonym: "up-regulation of peptidyl-tyrosine phosphorylation" EXACT [] +synonym: "upregulation of peptidyl-tyrosine phosphorylation" EXACT [] +is_a: GO:0001934 ! positive regulation of protein phosphorylation +is_a: GO:0050730 ! regulation of peptidyl-tyrosine phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation +relationship: positively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation + +[Term] +id: GO:0050732 +name: negative regulation of peptidyl-tyrosine phosphorylation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of peptidyl-tyrosine phosphorylation" EXACT [] +synonym: "down-regulation of peptidyl-tyrosine phosphorylation" EXACT [] +synonym: "downregulation of peptidyl-tyrosine phosphorylation" EXACT [] +synonym: "inhibition of peptidyl-tyrosine phosphorylation" NARROW [] +is_a: GO:0001933 ! negative regulation of protein phosphorylation +is_a: GO:0050730 ! regulation of peptidyl-tyrosine phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation +relationship: negatively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation + +[Term] +id: GO:0050750 +name: low-density lipoprotein particle receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a low-density lipoprotein receptor." [GOC:ai] +synonym: "LDL receptor binding" EXACT [] +synonym: "low-density lipoprotein receptor binding" EXACT [GOC:dph] +is_a: GO:0070325 ! lipoprotein particle receptor binding + +[Term] +id: GO:0050755 +name: chemokine metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving chemokines, any member of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria." [GOC:BHF, GOC:rl, http://en.wikipedia.org/wiki/Chemokine, ISBN:0198506732, PMID:12183377] +synonym: "chemokine metabolism" EXACT [] +is_a: GO:0042107 ! cytokine metabolic process + +[Term] +id: GO:0050767 +name: regulation of neurogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons." [GOC:ai] +is_a: GO:0051960 ! regulation of nervous system development +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0022008 ! neurogenesis +relationship: part_of GO:0048699 ! generation of neurons +relationship: regulates GO:0022008 ! neurogenesis + +[Term] +id: GO:0050768 +name: negative regulation of neurogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the origin and formation of neurons." [GOC:ai] +synonym: "down regulation of neurogenesis" EXACT [] +synonym: "down-regulation of neurogenesis" EXACT [] +synonym: "downregulation of neurogenesis" EXACT [] +synonym: "inhibition of neurogenesis" NARROW [] +is_a: GO:0010721 ! negative regulation of cell development +is_a: GO:0050767 ! regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0022008 ! neurogenesis +relationship: negatively_regulates GO:0022008 ! neurogenesis + +[Term] +id: GO:0050769 +name: positive regulation of neurogenesis +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of neurogenesis, the origin and formation of neurons." [GOC:ai] +synonym: "activation of neurogenesis" NARROW [] +synonym: "stimulation of neurogenesis" NARROW [] +synonym: "up regulation of neurogenesis" EXACT [] +synonym: "up-regulation of neurogenesis" EXACT [] +synonym: "upregulation of neurogenesis" EXACT [] +is_a: GO:0010720 ! positive regulation of cell development +is_a: GO:0050767 ! regulation of neurogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0022008 ! neurogenesis +relationship: positively_regulates GO:0022008 ! neurogenesis + +[Term] +id: GO:0050770 +name: regulation of axonogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron." [GOC:ai] +xref: Reactome:REACT_100877 "p75NTR regulates axonogenesis, Taeniopygia guttata" +xref: Reactome:REACT_103034 "p75NTR regulates axonogenesis, Sus scrofa" +xref: Reactome:REACT_105471 "p75NTR regulates axonogenesis, Xenopus tropicalis" +xref: Reactome:REACT_109191 "p75NTR regulates axonogenesis, Gallus gallus" +xref: Reactome:REACT_13620 "p75NTR regulates axonogenesis, Homo sapiens" +xref: Reactome:REACT_28624 "p75NTR regulates axonogenesis, Rattus norvegicus" +xref: Reactome:REACT_31549 "p75NTR regulates axonogenesis, Danio rerio" +xref: Reactome:REACT_78884 "p75NTR regulates axonogenesis, Caenorhabditis elegans" +xref: Reactome:REACT_89480 "p75NTR regulates axonogenesis, Canis familiaris" +xref: Reactome:REACT_89995 "p75NTR regulates axonogenesis, Mus musculus" +xref: Reactome:REACT_93864 "p75NTR regulates axonogenesis, Bos taurus" +xref: Reactome:REACT_96905 "p75NTR regulates axonogenesis, Drosophila melanogaster" +is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation +is_a: GO:0010975 ! regulation of neuron projection development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007409 ! axonogenesis +relationship: regulates GO:0007409 ! axonogenesis + +[Term] +id: GO:0050771 +name: negative regulation of axonogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis." [GOC:ai] +synonym: "down regulation of axonogenesis" EXACT [] +synonym: "down-regulation of axonogenesis" EXACT [] +synonym: "downregulation of axonogenesis" EXACT [] +synonym: "inhibition of axonogenesis" NARROW [] +xref: Reactome:REACT_103974 "Axonal growth inhibition (RHOA activation), Danio rerio" +xref: Reactome:REACT_105638 "Axonal growth inhibition (RHOA activation), Mus musculus" +xref: Reactome:REACT_13815 "Axonal growth inhibition (RHOA activation), Homo sapiens" +xref: Reactome:REACT_29558 "Axonal growth inhibition (RHOA activation), Caenorhabditis elegans" +xref: Reactome:REACT_32480 "Axonal growth inhibition (RHOA activation), Rattus norvegicus" +xref: Reactome:REACT_79935 "Axonal growth inhibition (RHOA activation), Drosophila melanogaster" +xref: Reactome:REACT_84319 "Axonal growth inhibition (RHOA activation), Xenopus tropicalis" +xref: Reactome:REACT_89521 "Axonal growth inhibition (RHOA activation), Bos taurus" +xref: Reactome:REACT_95704 "Axonal growth inhibition (RHOA activation), Canis familiaris" +xref: Reactome:REACT_97524 "Axonal growth inhibition (RHOA activation), Sus scrofa" +xref: Reactome:REACT_97819 "Axonal growth inhibition (RHOA activation), Gallus gallus" +xref: Reactome:REACT_99775 "Axonal growth inhibition (RHOA activation), Taeniopygia guttata" +is_a: GO:0031345 ! negative regulation of cell projection organization +is_a: GO:0050768 ! negative regulation of neurogenesis +is_a: GO:0050770 ! regulation of axonogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007409 ! axonogenesis +relationship: negatively_regulates GO:0007409 ! axonogenesis + +[Term] +id: GO:0050772 +name: positive regulation of axonogenesis +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of axonogenesis." [GOC:ai] +synonym: "activation of axonogenesis" NARROW [] +synonym: "stimulation of axonogenesis" NARROW [] +synonym: "up regulation of axonogenesis" EXACT [] +synonym: "up-regulation of axonogenesis" EXACT [] +synonym: "upregulation of axonogenesis" EXACT [] +xref: Reactome:REACT_104800 "Axonal growth stimulation, Bos taurus" +xref: Reactome:REACT_108274 "Axonal growth stimulation, Canis familiaris" +xref: Reactome:REACT_112731 "Axonal growth stimulation, Danio rerio" +xref: Reactome:REACT_113936 "Axonal growth stimulation, Rattus norvegicus" +xref: Reactome:REACT_13779 "Axonal growth stimulation, Homo sapiens" +xref: Reactome:REACT_29835 "Axonal growth stimulation, Xenopus tropicalis" +xref: Reactome:REACT_80113 "Axonal growth stimulation, Mus musculus" +xref: Reactome:REACT_84675 "Axonal growth stimulation, Gallus gallus" +is_a: GO:0031346 ! positive regulation of cell projection organization +is_a: GO:0050769 ! positive regulation of neurogenesis +is_a: GO:0050770 ! regulation of axonogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007409 ! axonogenesis +relationship: positively_regulates GO:0007409 ! axonogenesis + +[Term] +id: GO:0050773 +name: regulation of dendrite development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of dendrite development." [GOC:ai] +is_a: GO:0010975 ! regulation of neuron projection development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016358 ! dendrite development +relationship: regulates GO:0016358 ! dendrite development + +[Term] +id: GO:0050776 +name: regulation of immune response +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." [GOC:ai] +xref: Reactome:REACT_101484 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Gallus gallus" +xref: Reactome:REACT_106667 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Rattus norvegicus" +xref: Reactome:REACT_107426 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Mus musculus" +xref: Reactome:REACT_11152 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Homo sapiens" +xref: Reactome:REACT_81657 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Danio rerio" +xref: Reactome:REACT_82803 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Canis familiaris" +xref: Reactome:REACT_87475 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Bos taurus" +xref: Reactome:REACT_94152 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Sus scrofa" +xref: Reactome:REACT_95389 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Taeniopygia guttata" +xref: Reactome:REACT_97860 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Xenopus tropicalis" +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006955 ! immune response +relationship: regulates GO:0006955 ! immune response + +[Term] +id: GO:0050777 +name: negative regulation of immune response +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." [GOC:ai] +synonym: "down regulation of immune response" EXACT [] +synonym: "down-regulation of immune response" EXACT [] +synonym: "downregulation of immune response" EXACT [] +synonym: "inhibition of immune response" NARROW [] +is_a: GO:0002683 ! negative regulation of immune system process +is_a: GO:0048585 ! negative regulation of response to stimulus +is_a: GO:0050776 ! regulation of immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006955 ! immune response +relationship: negatively_regulates GO:0006955 ! immune response + +[Term] +id: GO:0050789 +name: regulation of biological process +namespace: biological_process +alt_id: GO:0050791 +def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] +subset: goslim_aspergillus +subset: goslim_candida +subset: gosubset_prok +synonym: "regulation of physiological process" EXACT [] +is_a: GO:0065007 ! biological regulation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008150 ! biological_process +relationship: regulates GO:0008150 ! biological_process + +[Term] +id: GO:0050790 +name: regulation of catalytic activity +namespace: biological_process +def: "Any process that modulates the activity of an enzyme." [GOC:ai] +subset: gosubset_prok +synonym: "regulation of enzyme activity" EXACT [] +is_a: GO:0019222 ! regulation of metabolic process +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003824 ! catalytic activity +relationship: regulates GO:0003824 ! catalytic activity + +[Term] +id: GO:0050793 +name: regulation of developmental process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032502 ! developmental process +relationship: regulates GO:0032502 ! developmental process + +[Term] +id: GO:0050794 +name: regulation of cellular process +namespace: biological_process +alt_id: GO:0051244 +def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] +subset: gosubset_prok +synonym: "regulation of cellular physiological process" EXACT [] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009987 ! cellular process +relationship: regulates GO:0009987 ! cellular process + +[Term] +id: GO:0050795 +name: regulation of behavior +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [GOC:go_curators, GOC:pr] +subset: gosubset_prok +synonym: "regulation of behaviour" EXACT [] +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007610 ! behavior +relationship: regulates GO:0007610 ! behavior + +[Term] +id: GO:0050796 +name: regulation of insulin secretion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the regulated release of insulin." [GOC:ai] +xref: Reactome:REACT_101597 "Regulation of Insulin Secretion, Xenopus tropicalis" +xref: Reactome:REACT_104758 "Incretin Synthesis, Secretion, and Inactivation, Mus musculus" +xref: Reactome:REACT_105869 "Regulation of Insulin Secretion, Taeniopygia guttata" +xref: Reactome:REACT_107553 "Incretin Synthesis, Secretion, and Inactivation, Sus scrofa" +xref: Reactome:REACT_108613 "Regulation of Insulin Secretion, Gallus gallus" +xref: Reactome:REACT_114254 "Regulation of Insulin Secretion, Oryza sativa" +xref: Reactome:REACT_114277 "Regulation of Insulin Secretion, Saccharomyces cerevisiae" +xref: Reactome:REACT_114911 "Regulation of Insulin Secretion, Arabidopsis thaliana" +xref: Reactome:REACT_115218 "Regulation of Insulin Secretion, Schizosaccharomyces pombe" +xref: Reactome:REACT_18325 "Regulation of Insulin Secretion, Homo sapiens" +xref: Reactome:REACT_23974 "Incretin Synthesis, Secretion, and Inactivation, Homo sapiens" +xref: Reactome:REACT_28774 "Regulation of Insulin Secretion, Canis familiaris" +xref: Reactome:REACT_30526 "Incretin Synthesis, Secretion, and Inactivation, Canis familiaris" +xref: Reactome:REACT_35721 "Regulation of Insulin Secretion, Dictyostelium discoideum" +xref: Reactome:REACT_82381 "Regulation of Insulin Secretion, Rattus norvegicus" +xref: Reactome:REACT_82648 "Incretin Synthesis, Secretion, and Inactivation, Bos taurus" +xref: Reactome:REACT_84459 "Regulation of Insulin Secretion, Bos taurus" +xref: Reactome:REACT_87602 "Regulation of Insulin Secretion, Drosophila melanogaster" +xref: Reactome:REACT_88056 "Regulation of Insulin Secretion, Mus musculus" +xref: Reactome:REACT_88814 "Regulation of Insulin Secretion, Caenorhabditis elegans" +xref: Reactome:REACT_89023 "Incretin Synthesis, Secretion, and Inactivation, Danio rerio" +xref: Reactome:REACT_90639 "Incretin Synthesis, Secretion, and Inactivation, Taeniopygia guttata" +xref: Reactome:REACT_92637 "Regulation of Insulin Secretion, Danio rerio" +xref: Reactome:REACT_94670 "Incretin Synthesis, Secretion, and Inactivation, Rattus norvegicus" +xref: Reactome:REACT_95188 "Regulation of Insulin Secretion, Sus scrofa" +xref: Reactome:REACT_96232 "Incretin Synthesis, Secretion, and Inactivation, Gallus gallus" +xref: Reactome:REACT_99834 "Incretin Synthesis, Secretion, and Inactivation, Xenopus tropicalis" +is_a: GO:0090276 ! regulation of peptide hormone secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030073 ! insulin secretion +relationship: regulates GO:0030073 ! insulin secretion + +[Term] +id: GO:0050801 +name: ion homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of ions within an organism or cell." [GOC:ai] +subset: gosubset_prok +synonym: "electrolyte homeostasis" RELATED [] +synonym: "negative regulation of crystal biosynthesis" RELATED [] +synonym: "negative regulation of crystal formation" RELATED [] +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0050803 +name: regulation of synapse structure and activity +namespace: biological_process +def: "Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell)." [GOC:ai] +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0007268 ! synaptic transmission + +[Term] +id: GO:0050804 +name: regulation of synaptic transmission +namespace: biological_process +def: "Any process that modulates the frequency or rate of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse." [GOC:ai] +is_a: GO:0065007 ! biological regulation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007268 ! synaptic transmission +relationship: regulates GO:0007268 ! synaptic transmission + +[Term] +id: GO:0050807 +name: regulation of synapse organization +namespace: biological_process +def: "Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell)." [GOC:ai, GOC:dph, GOC:tb] +synonym: "regulation of synapse organisation" EXACT [GOC:mah] +synonym: "regulation of synapse organization and biogenesis" RELATED [GOC:mah] +synonym: "regulation of synapse structure" EXACT [] +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050808 ! synapse organization +relationship: part_of GO:0050803 ! regulation of synapse structure and activity +relationship: regulates GO:0050808 ! synapse organization + +[Term] +id: GO:0050808 +name: synapse organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell)." [GOC:ai, GOC:pr] +synonym: "synapse development" EXACT [] +synonym: "synapse morphogenesis" RELATED [GOC:BHF] +synonym: "synapse organisation" EXACT [GOC:curators] +synonym: "synapse organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0050810 +name: regulation of steroid biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." [GOC:ai] +subset: gosubset_prok +synonym: "regulation of steroid anabolism" EXACT [] +synonym: "regulation of steroid biosynthesis" EXACT [] +synonym: "regulation of steroid formation" EXACT [] +synonym: "regulation of steroid synthesis" EXACT [] +synonym: "regulation of steroidogenesis" EXACT [] +is_a: GO:0019218 ! regulation of steroid metabolic process +is_a: GO:0046890 ! regulation of lipid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006694 ! steroid biosynthetic process +relationship: regulates GO:0006694 ! steroid biosynthetic process + +[Term] +id: GO:0050817 +name: coagulation +namespace: biological_process +def: "The process in which a fluid solution, or part of it, changes into a solid or semisolid mass." [ISBN:0198506732] +subset: goslim_pir +synonym: "clotting" EXACT [] +is_a: GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0050818 +name: regulation of coagulation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of coagulation, the process in which a fluid solution, or part of it, changes into a solid or semisolid mass." [GOC:ai] +synonym: "regulation of clotting" EXACT [] +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0050817 ! coagulation +relationship: regulates GO:0050817 ! coagulation + +[Term] +id: GO:0050839 +name: cell adhesion molecule binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a cell adhesion molecule." [GOC:ai] +synonym: "adhesive extracellular matrix constituent" RELATED [] +synonym: "CAM binding" EXACT [] +synonym: "cell adhesion molecule activity" RELATED [] +synonym: "cell adhesion receptor activity" RELATED [] +is_a: GO:0005515 ! protein binding + +[Term] +id: GO:0050863 +name: regulation of T cell activation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of T cell activation." [GOC:ai] +synonym: "regulation of T lymphocyte activation" EXACT [] +synonym: "regulation of T-cell activation" EXACT [] +synonym: "regulation of T-lymphocyte activation" EXACT [] +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042110 ! T cell activation +relationship: regulates GO:0042110 ! T cell activation + +[Term] +id: GO:0050864 +name: regulation of B cell activation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of B cell activation." [GOC:ai] +synonym: "regulation of B lymphocyte activation" EXACT [] +synonym: "regulation of B-cell activation" EXACT [] +synonym: "regulation of B-lymphocyte activation" EXACT [] +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042113 ! B cell activation +relationship: regulates GO:0042113 ! B cell activation + +[Term] +id: GO:0050865 +name: regulation of cell activation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:ai] +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001775 ! cell activation +relationship: regulates GO:0001775 ! cell activation + +[Term] +id: GO:0050866 +name: negative regulation of cell activation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell activation." [GOC:ai] +synonym: "down regulation of cell activation" EXACT [] +synonym: "down-regulation of cell activation" EXACT [] +synonym: "downregulation of cell activation" EXACT [] +synonym: "inhibition of cell activation" NARROW [] +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0050865 ! regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0001775 ! cell activation +relationship: negatively_regulates GO:0001775 ! cell activation + +[Term] +id: GO:0050867 +name: positive regulation of cell activation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of activation." [GOC:ai] +synonym: "activation of cell activation" NARROW [] +synonym: "stimulation of cell activation" NARROW [] +synonym: "up regulation of cell activation" EXACT [] +synonym: "up-regulation of cell activation" EXACT [] +synonym: "upregulation of cell activation" EXACT [] +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0050865 ! regulation of cell activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001775 ! cell activation +relationship: positively_regulates GO:0001775 ! cell activation + +[Term] +id: GO:0050868 +name: negative regulation of T cell activation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation." [GOC:ai] +synonym: "down regulation of T cell activation" EXACT [] +synonym: "down-regulation of T cell activation" EXACT [] +synonym: "downregulation of T cell activation" EXACT [] +synonym: "inhibition of T cell activation" NARROW [] +synonym: "negative regulation of T lymphocyte activation" EXACT [] +synonym: "negative regulation of T-cell activation" EXACT [] +synonym: "negative regulation of T-lymphocyte activation" EXACT [] +is_a: GO:0050863 ! regulation of T cell activation +is_a: GO:0051250 ! negative regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042110 ! T cell activation +relationship: negatively_regulates GO:0042110 ! T cell activation + +[Term] +id: GO:0050869 +name: negative regulation of B cell activation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of B cell activation." [GOC:ai] +synonym: "down regulation of B cell activation" EXACT [] +synonym: "down-regulation of B cell activation" EXACT [] +synonym: "downregulation of B cell activation" EXACT [] +synonym: "inhibition of B cell activation" NARROW [] +synonym: "negative regulation of B lymphocyte activation" EXACT [] +synonym: "negative regulation of B-cell activation" EXACT [] +synonym: "negative regulation of B-lymphocyte activation" EXACT [] +is_a: GO:0050864 ! regulation of B cell activation +is_a: GO:0051250 ! negative regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042113 ! B cell activation +relationship: negatively_regulates GO:0042113 ! B cell activation + +[Term] +id: GO:0050871 +name: positive regulation of B cell activation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of B cell activation." [GOC:ai] +synonym: "activation of B cell activation" NARROW [] +synonym: "positive regulation of B lymphocyte activation" EXACT [] +synonym: "positive regulation of B-cell activation" EXACT [] +synonym: "positive regulation of B-lymphocyte activation" EXACT [] +synonym: "stimulation of B cell activation" NARROW [] +synonym: "up regulation of B cell activation" EXACT [] +synonym: "up-regulation of B cell activation" EXACT [] +synonym: "upregulation of B cell activation" EXACT [] +is_a: GO:0050864 ! regulation of B cell activation +is_a: GO:0051251 ! positive regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042113 ! B cell activation +relationship: positively_regulates GO:0042113 ! B cell activation + +[Term] +id: GO:0050877 +name: neurological system process +namespace: biological_process +def: "A organ system process carried out by any of the organs or tissues of neurological system." [GOC:ai, GOC:mtg_cardio] +subset: goslim_generic +subset: goslim_pir +synonym: "neurophysiological process" EXACT [] +synonym: "pan-neural process" RELATED [] +is_a: GO:0003008 ! system process + +[Term] +id: GO:0050878 +name: regulation of body fluid levels +namespace: biological_process +def: "Any process that modulates the levels of body fluids." [GOC:ai, GOC:dph, GOC:tb] +subset: goslim_pir +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0065008 ! regulation of biological quality + +[Term] +id: GO:0050880 +name: regulation of blood vessel size +namespace: biological_process +def: "Any process that modulates the size of blood vessels." [GOC:ai] +is_a: GO:0003018 ! vascular process in circulatory system +is_a: GO:0035150 ! regulation of tube size +relationship: part_of GO:0008015 ! blood circulation + +[Term] +id: GO:0050890 +name: cognition +namespace: biological_process +def: "The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory." [http://www.onelook.com/, ISBN:0721619908] +xref: Wikipedia:Cognition +is_a: GO:0050877 ! neurological system process + +[Term] +id: GO:0050896 +name: response to stimulus +namespace: biological_process +alt_id: GO:0051869 +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_pir +subset: gosubset_prok +synonym: "physiological response to stimulus" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0050900 +name: leukocyte migration +namespace: biological_process +def: "The movement of a leukocyte within or between different tissues and organs of the body." [GOC:add, ISBN:0781735149, PMID:14680625, PMID:14708592, PMID:7507411, PMID:8600538] +synonym: "immune cell migration" EXACT [] +synonym: "immune cell trafficking" EXACT [] +synonym: "leucocyte migration" EXACT [] +synonym: "leucocyte trafficking" EXACT [] +synonym: "leukocyte trafficking" EXACT [] +xref: Reactome:REACT_100059 "Cell surface interactions at the vascular wall, Sus scrofa" +xref: Reactome:REACT_12051 "Cell surface interactions at the vascular wall, Homo sapiens" +xref: Reactome:REACT_28425 "Cell surface interactions at the vascular wall, Bos taurus" +xref: Reactome:REACT_34071 "Cell surface interactions at the vascular wall, Xenopus tropicalis" +xref: Reactome:REACT_77198 "Cell surface interactions at the vascular wall, Taeniopygia guttata" +xref: Reactome:REACT_83057 "Cell surface interactions at the vascular wall, Danio rerio" +xref: Reactome:REACT_86476 "Cell surface interactions at the vascular wall, Canis familiaris" +xref: Reactome:REACT_86886 "Cell surface interactions at the vascular wall, Mus musculus" +xref: Reactome:REACT_89386 "Cell surface interactions at the vascular wall, Gallus gallus" +xref: Reactome:REACT_93252 "Cell surface interactions at the vascular wall, Rattus norvegicus" +xref: Reactome:REACT_98799 "Cell surface interactions at the vascular wall, Drosophila melanogaster" +is_a: GO:0002376 ! immune system process +is_a: GO:0016477 ! cell migration + +[Term] +id: GO:0050919 +name: negative chemotaxis +namespace: biological_process +def: "The directed movement of a motile cell or organism towards a lower concentration of a chemical." [GOC:ai, GOC:bf, GOC:isa_complete] +synonym: "chemoaversion" EXACT [] +synonym: "chemorepulsion" EXACT [] +is_a: GO:0006935 ! chemotaxis + +[Term] +id: GO:0050920 +name: regulation of chemotaxis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." [GOC:ai] +subset: gosubset_prok +is_a: GO:0032101 ! regulation of response to external stimulus +is_a: GO:0040012 ! regulation of locomotion +is_a: GO:0050795 ! regulation of behavior +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006935 ! chemotaxis +relationship: regulates GO:0006935 ! chemotaxis + +[Term] +id: GO:0050921 +name: positive regulation of chemotaxis +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." [GOC:ai] +subset: gosubset_prok +synonym: "activation of chemotaxis" NARROW [] +synonym: "stimulation of chemotaxis" NARROW [] +synonym: "up regulation of chemotaxis" EXACT [] +synonym: "up-regulation of chemotaxis" EXACT [] +synonym: "upregulation of chemotaxis" EXACT [] +is_a: GO:0032103 ! positive regulation of response to external stimulus +is_a: GO:0040017 ! positive regulation of locomotion +is_a: GO:0048520 ! positive regulation of behavior +is_a: GO:0050920 ! regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006935 ! chemotaxis +relationship: positively_regulates GO:0006935 ! chemotaxis + +[Term] +id: GO:0050922 +name: negative regulation of chemotaxis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." [GOC:ai] +synonym: "down regulation of chemotaxis" EXACT [] +synonym: "down-regulation of chemotaxis" EXACT [] +synonym: "downregulation of chemotaxis" EXACT [] +synonym: "inhibition of chemotaxis" NARROW [] +is_a: GO:0032102 ! negative regulation of response to external stimulus +is_a: GO:0040013 ! negative regulation of locomotion +is_a: GO:0048521 ! negative regulation of behavior +is_a: GO:0050920 ! regulation of chemotaxis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006935 ! chemotaxis +relationship: negatively_regulates GO:0006935 ! chemotaxis + +[Term] +id: GO:0050931 +name: pigment cell differentiation +namespace: biological_process +alt_id: GO:0043357 +alt_id: GO:0043358 +def: "The process in which a relatively unspecialized cell acquires the specialized features of a pigmented cell, such as a melanocyte." [GOC:dgh] +comment: Note that the chromatophore mentioned here is distinct from the pigment bearing structure found in certain photosynthetic bacteria and cyanobacteria. It is also different from the plant chromoplast, which is also sometimes called a chromatophore. +synonym: "chromatophore differentiation" EXACT [] +synonym: "pigmented cell differentiation" EXACT [] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0048066 ! developmental pigmentation + +[Term] +id: GO:0050935 +name: iridophore differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires the specialized features of an iridophore. Iridophores are pigment cells derived from the neural crest. They contain guanidine or other purine crystals deposited in stacks called reflecting platets or iridisomes. This gives them a silver, gold, or iridescent appearance." [GOC:jid, GOC:mh, PMID:11858836] +synonym: "iridophore cell differentiation" EXACT [] +is_a: GO:0050931 ! pigment cell differentiation + +[Term] +id: GO:0051017 +name: actin filament bundle assembly +namespace: biological_process +alt_id: GO:0045011 +def: "The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness." [GOC:ai] +synonym: "actin bundling activity" RELATED [] +synonym: "actin cable assembly" RELATED [GOC:mah] +synonym: "actin cable formation" RELATED [GOC:mah] +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0061572 ! actin filament bundle organization + +[Term] +id: GO:0051046 +name: regulation of secretion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." [GOC:ai] +subset: gosubset_prok +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046903 ! secretion +relationship: regulates GO:0046903 ! secretion + +[Term] +id: GO:0051047 +name: positive regulation of secretion +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." [GOC:ai] +synonym: "activation of secretion" NARROW [] +synonym: "stimulation of secretion" NARROW [] +synonym: "up regulation of secretion" EXACT [] +synonym: "up-regulation of secretion" EXACT [] +synonym: "upregulation of secretion" EXACT [] +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0051050 ! positive regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046903 ! secretion +relationship: positively_regulates GO:0046903 ! secretion + +[Term] +id: GO:0051048 +name: negative regulation of secretion +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." [GOC:ai] +synonym: "down regulation of secretion" EXACT [] +synonym: "down-regulation of secretion" EXACT [] +synonym: "downregulation of secretion" EXACT [] +synonym: "inhibition of secretion" NARROW [] +is_a: GO:0051046 ! regulation of secretion +is_a: GO:0051051 ! negative regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046903 ! secretion +relationship: negatively_regulates GO:0046903 ! secretion + +[Term] +id: GO:0051049 +name: regulation of transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0032879 ! regulation of localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006810 ! transport +relationship: regulates GO:0006810 ! transport + +[Term] +id: GO:0051050 +name: positive regulation of transport +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +subset: gosubset_prok +synonym: "activation of transport" NARROW [] +synonym: "stimulation of transport" NARROW [] +synonym: "up regulation of transport" EXACT [] +synonym: "up-regulation of transport" EXACT [] +synonym: "upregulation of transport" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006810 ! transport +relationship: positively_regulates GO:0006810 ! transport + +[Term] +id: GO:0051051 +name: negative regulation of transport +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of transport" EXACT [] +synonym: "down-regulation of transport" EXACT [] +synonym: "downregulation of transport" EXACT [] +synonym: "inhibition of transport" NARROW [] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006810 ! transport +relationship: negatively_regulates GO:0006810 ! transport + +[Term] +id: GO:0051055 +name: negative regulation of lipid biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of lipid biosynthetic process" EXACT [] +synonym: "down-regulation of lipid biosynthetic process" EXACT [] +synonym: "downregulation of lipid biosynthetic process" EXACT [] +synonym: "inhibition of lipid biosynthetic process" NARROW [] +synonym: "negative regulation of lipid anabolism" EXACT [] +synonym: "negative regulation of lipid biosynthesis" EXACT [] +synonym: "negative regulation of lipid formation" EXACT [] +synonym: "negative regulation of lipid synthesis" EXACT [] +synonym: "negative regulation of lipogenesis" EXACT [GOC:sl] +is_a: GO:0009890 ! negative regulation of biosynthetic process +is_a: GO:0045833 ! negative regulation of lipid metabolic process +is_a: GO:0046890 ! regulation of lipid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008610 ! lipid biosynthetic process +relationship: negatively_regulates GO:0008610 ! lipid biosynthetic process + +[Term] +id: GO:0051056 +name: regulation of small GTPase mediated signal transduction +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction." [GOC:go_curators] +synonym: "regulation of small GTPase-mediated signal transduction" EXACT [] +xref: Reactome:REACT_101392 "Rho GTPase cycle, Canis familiaris" +xref: Reactome:REACT_105151 "Rho GTPase cycle, Xenopus tropicalis" +xref: Reactome:REACT_110059 "Rho GTPase cycle, Bos taurus" +xref: Reactome:REACT_11051 "Rho GTPase cycle, Homo sapiens" +xref: Reactome:REACT_28304 "Rho GTPase cycle, Taeniopygia guttata" +xref: Reactome:REACT_30809 "Rho GTPase cycle, Saccharomyces cerevisiae" +xref: Reactome:REACT_32940 "Rho GTPase cycle, Gallus gallus" +xref: Reactome:REACT_77671 "Rho GTPase cycle, Caenorhabditis elegans" +xref: Reactome:REACT_77929 "Rho GTPase cycle, Mus musculus" +xref: Reactome:REACT_78559 "Rho GTPase cycle, Arabidopsis thaliana" +xref: Reactome:REACT_82220 "Rho GTPase cycle, Drosophila melanogaster" +xref: Reactome:REACT_88001 "Rho GTPase cycle, Oryza sativa" +xref: Reactome:REACT_88549 "Rho GTPase cycle, Dictyostelium discoideum" +xref: Reactome:REACT_90249 "Rho GTPase cycle, Sus scrofa" +xref: Reactome:REACT_91095 "Rho GTPase cycle, Danio rerio" +xref: Reactome:REACT_92646 "Rho GTPase cycle, Rattus norvegicus" +xref: Reactome:REACT_99648 "Rho GTPase cycle, Schizosaccharomyces pombe" +is_a: GO:1902531 ! regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007264 ! small GTPase mediated signal transduction +relationship: regulates GO:0007264 ! small GTPase mediated signal transduction + +[Term] +id: GO:0051090 +name: regulation of sequence-specific DNA binding transcription factor activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] +subset: gosubset_prok +synonym: "regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb] +xref: Reactome:REACT_104536 "Activation of the AP-1 family of transcription factors, Bos taurus" +xref: Reactome:REACT_107559 "Activation of the AP-1 family of transcription factors, Danio rerio" +xref: Reactome:REACT_109535 "Activation of the AP-1 family of transcription factors, Schizosaccharomyces pombe" +xref: Reactome:REACT_110257 "Activation of the AP-1 family of transcription factors, Drosophila melanogaster" +xref: Reactome:REACT_110693 "Activation of the AP-1 family of transcription factors, Gallus gallus" +xref: Reactome:REACT_21326 "Activation of the AP-1 family of transcription factors, Homo sapiens" +xref: Reactome:REACT_82719 "Activation of the AP-1 family of transcription factors, Xenopus tropicalis" +xref: Reactome:REACT_83365 "Activation of the AP-1 family of transcription factors, Sus scrofa" +xref: Reactome:REACT_90659 "Activation of the AP-1 family of transcription factors, Taeniopygia guttata" +xref: Reactome:REACT_92725 "Activation of the AP-1 family of transcription factors, Canis familiaris" +xref: Reactome:REACT_96476 "Activation of the AP-1 family of transcription factors, Rattus norvegicus" +xref: Reactome:REACT_99415 "Activation of the AP-1 family of transcription factors, Mus musculus" +is_a: GO:0006355 ! regulation of transcription, DNA-templated +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity +relationship: regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0051091 +name: positive regulation of sequence-specific DNA binding transcription factor activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] +subset: gosubset_prok +synonym: "activation of transcription factor activity" NARROW [] +synonym: "positive regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb] +synonym: "stimulation of transcription factor activity" NARROW [] +synonym: "up regulation of transcription factor activity" EXACT [] +synonym: "up-regulation of transcription factor activity" EXACT [] +synonym: "upregulation of transcription factor activity" EXACT [] +is_a: GO:0044093 ! positive regulation of molecular function +is_a: GO:0051090 ! regulation of sequence-specific DNA binding transcription factor activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity +relationship: positively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0051092 +name: positive regulation of NF-kappaB transcription factor activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB." [GOC:dph, GOC:tb, PMID:15087454, PMID:15170030] +synonym: "activation of NF-kappaB" EXACT [] +synonym: "activation of NF-kappaB transcription factor" EXACT [GOC:dph, GOC:tb] +synonym: "NF-kappaB activation" EXACT [] +xref: Reactome:REACT_107873 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Rattus norvegicus" +xref: Reactome:REACT_113398 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Taeniopygia guttata" +xref: Reactome:REACT_113766 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Drosophila melanogaster" +xref: Reactome:REACT_21281 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Homo sapiens" +xref: Reactome:REACT_31084 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Canis familiaris" +xref: Reactome:REACT_33907 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Danio rerio" +xref: Reactome:REACT_34168 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Sus scrofa" +xref: Reactome:REACT_34256 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Bos taurus" +xref: Reactome:REACT_87914 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Xenopus tropicalis" +xref: Reactome:REACT_95400 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Mus musculus" +is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity + +[Term] +id: GO:0051093 +name: negative regulation of developmental process +namespace: biological_process +def: "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of developmental process" EXACT [] +synonym: "down-regulation of developmental process" EXACT [] +synonym: "downregulation of developmental process" EXACT [] +synonym: "inhibition of developmental process" NARROW [] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032502 ! developmental process +relationship: negatively_regulates GO:0032502 ! developmental process + +[Term] +id: GO:0051094 +name: positive regulation of developmental process +namespace: biological_process +def: "Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] +subset: gosubset_prok +synonym: "activation of developmental process" NARROW [] +synonym: "stimulation of developmental process" NARROW [] +synonym: "up regulation of developmental process" EXACT [] +synonym: "up-regulation of developmental process" EXACT [] +synonym: "upregulation of developmental process" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032502 ! developmental process +relationship: positively_regulates GO:0032502 ! developmental process + +[Term] +id: GO:0051098 +name: regulation of binding +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule." [GOC:ai] +subset: gosubset_prok +is_a: GO:0065009 ! regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0005488 ! binding +relationship: regulates GO:0005488 ! binding + +[Term] +id: GO:0051099 +name: positive regulation of binding +namespace: biological_process +def: "Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule." [GOC:ai] +subset: gosubset_prok +synonym: "activation of binding" NARROW [] +synonym: "stimulation of binding" NARROW [] +synonym: "up regulation of binding" EXACT [] +synonym: "up-regulation of binding" EXACT [] +synonym: "upregulation of binding" EXACT [] +is_a: GO:0044093 ! positive regulation of molecular function +is_a: GO:0051098 ! regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0005488 ! binding +relationship: positively_regulates GO:0005488 ! binding + +[Term] +id: GO:0051100 +name: negative regulation of binding +namespace: biological_process +def: "Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of binding" EXACT [] +synonym: "down-regulation of binding" EXACT [] +synonym: "downregulation of binding" EXACT [] +synonym: "inhibition of binding" NARROW [] +is_a: GO:0044092 ! negative regulation of molecular function +is_a: GO:0051098 ! regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0005488 ! binding +relationship: negatively_regulates GO:0005488 ! binding + +[Term] +id: GO:0051101 +name: regulation of DNA binding +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC:ai, GOC:dph, GOC:tb] +subset: gosubset_prok +is_a: GO:0051098 ! regulation of binding +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003677 ! DNA binding +relationship: regulates GO:0003677 ! DNA binding + +[Term] +id: GO:0051124 +name: synaptic growth at neuromuscular junction +namespace: biological_process +def: "The growth of a synapse at a neuromuscular junction, the site of apposition of a motor end plate and the subneural cleft of the skeletal muscle fiber that it innervates." [ISBN:0721662544] +synonym: "cholinergic synaptogenesis" RELATED [] +is_a: GO:0007416 ! synapse assembly +is_a: GO:0007528 ! neuromuscular junction development +is_a: GO:0048589 ! developmental growth + +[Term] +id: GO:0051128 +name: regulation of cellular component organization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai] +subset: gosubset_prok +synonym: "regulation of cell organisation" RELATED [GOC:mah] +synonym: "regulation of cell organization" RELATED [GOC:mah] +synonym: "regulation of cellular component organisation" EXACT [GOC:curators] +synonym: "regulation of cellular component organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016043 ! cellular component organization +relationship: regulates GO:0016043 ! cellular component organization + +[Term] +id: GO:0051129 +name: negative regulation of cellular component organization +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of cell organization" EXACT [] +synonym: "down-regulation of cell organization" EXACT [] +synonym: "downregulation of cell organization" EXACT [] +synonym: "inhibition of cell organization" NARROW [] +synonym: "negative regulation of cell organisation" RELATED [GOC:mah] +synonym: "negative regulation of cellular component organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016043 ! cellular component organization +relationship: negatively_regulates GO:0016043 ! cellular component organization + +[Term] +id: GO:0051130 +name: positive regulation of cellular component organization +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai] +synonym: "activation of cell organization" NARROW [] +synonym: "positive regulation of cell organisation" EXACT [] +synonym: "positive regulation of cellular component organization and biogenesis" RELATED [GOC:mah] +synonym: "stimulation of cell organization" NARROW [] +synonym: "up regulation of cell organization" EXACT [] +synonym: "up-regulation of cell organization" EXACT [] +synonym: "upregulation of cell organization" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016043 ! cellular component organization +relationship: positively_regulates GO:0016043 ! cellular component organization + +[Term] +id: GO:0051145 +name: smooth muscle cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell; smooth muscle lacks transverse striations in its constituent fibers and are almost always involuntary." [CL:0000192, GOC:ai] +synonym: "nonstriated muscle cell differentiation" EXACT [] +is_a: GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0051146 +name: striated muscle cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle." [CL:0000737, GOC:ai] +synonym: "voluntary muscle cell differentiation" NARROW [] +is_a: GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0051147 +name: regulation of muscle cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of muscle cell differentiation." [CL:0000187, GOC:ai] +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042692 ! muscle cell differentiation +relationship: regulates GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0051149 +name: positive regulation of muscle cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of muscle cell differentiation." [CL:0000187, GOC:ai] +synonym: "activation of muscle cell differentiation" NARROW [] +synonym: "stimulation of muscle cell differentiation" NARROW [] +synonym: "up regulation of muscle cell differentiation" EXACT [] +synonym: "up-regulation of muscle cell differentiation" EXACT [] +synonym: "upregulation of muscle cell differentiation" EXACT [] +xref: Reactome:REACT_106354 "CDO in myogenesis, Gallus gallus" +xref: Reactome:REACT_113620 "CDO in myogenesis, Caenorhabditis elegans" +xref: Reactome:REACT_21402 "CDO in myogenesis, Homo sapiens" +xref: Reactome:REACT_33069 "CDO in myogenesis, Xenopus tropicalis" +xref: Reactome:REACT_77777 "CDO in myogenesis, Sus scrofa" +xref: Reactome:REACT_78092 "CDO in myogenesis, Drosophila melanogaster" +xref: Reactome:REACT_85123 "CDO in myogenesis, Danio rerio" +xref: Reactome:REACT_85269 "CDO in myogenesis, Taeniopygia guttata" +xref: Reactome:REACT_86878 "CDO in myogenesis, Bos taurus" +xref: Reactome:REACT_94854 "CDO in myogenesis, Rattus norvegicus" +xref: Reactome:REACT_96248 "CDO in myogenesis, Mus musculus" +xref: Reactome:REACT_97269 "CDO in myogenesis, Canis familiaris" +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:0051147 ! regulation of muscle cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042692 ! muscle cell differentiation +relationship: positively_regulates GO:0042692 ! muscle cell differentiation + +[Term] +id: GO:0051153 +name: regulation of striated muscle cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of striated muscle cell differentiation." [CL:0000737, GOC:ai] +is_a: GO:0051147 ! regulation of muscle cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051146 ! striated muscle cell differentiation +relationship: regulates GO:0051146 ! striated muscle cell differentiation + +[Term] +id: GO:0051155 +name: positive regulation of striated muscle cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of striated muscle cell differentiation." [CL:0000737, GOC:ai] +synonym: "activation of striated muscle cell differentiation" NARROW [] +synonym: "stimulation of striated muscle cell differentiation" NARROW [] +synonym: "up regulation of striated muscle cell differentiation" EXACT [] +synonym: "up-regulation of striated muscle cell differentiation" EXACT [] +synonym: "upregulation of striated muscle cell differentiation" EXACT [] +is_a: GO:0051149 ! positive regulation of muscle cell differentiation +is_a: GO:0051153 ! regulation of striated muscle cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0051146 ! striated muscle cell differentiation +relationship: positively_regulates GO:0051146 ! striated muscle cell differentiation + +[Term] +id: GO:0051156 +name: glucose 6-phosphate metabolic process +namespace: biological_process +alt_id: GO:0006010 +def: "The chemical reactions and pathways involving glucose 6-phosphate, a monophosphorylated derivative of glucose with the phosphate group attached to C-6." [GOC:ai] +subset: gosubset_prok +synonym: "glucose 6-phosphate metabolism" EXACT [] +synonym: "glucose 6-phosphate utilization" RELATED [GOC:mah] +is_a: GO:0006796 ! phosphate-containing compound metabolic process +is_a: GO:0019637 ! organophosphate metabolic process +is_a: GO:1901135 ! carbohydrate derivative metabolic process + +[Term] +id: GO:0051169 +name: nuclear transport +namespace: biological_process +def: "The directed movement of substances into, out of, or within the nucleus." [GOC:ai] +subset: goslim_yeast +synonym: "nucleus transport" EXACT [] +xref: Reactome:REACT_9004 "Import of PIC to the Host Nucleus, Homo sapiens" +xref: Wikipedia:Nuclear_transport +is_a: GO:0046907 ! intracellular transport + +[Term] +id: GO:0051170 +name: nuclear import +namespace: biological_process +def: "The directed movement of substances into the nucleus." [GOC:ai] +synonym: "import into nucleus" EXACT [] +synonym: "nucleus import" EXACT [] +synonym: "substance nuclear import" EXACT [] +xref: Reactome:REACT_10010 "snRNP nuclear import and release, Homo sapiens" +xref: Reactome:REACT_32050 "snRNP nuclear import and release, Xenopus tropicalis" +xref: Reactome:REACT_91459 "snRNP nuclear import and release, Mus musculus" +xref: Reactome:REACT_97007 "snRNP nuclear import and release, Danio rerio" +is_a: GO:0006913 ! nucleocytoplasmic transport + +[Term] +id: GO:0051171 +name: regulation of nitrogen compound metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] +subset: gosubset_prok +synonym: "regulation of nitrogen metabolic process" EXACT [GOC:tb] +synonym: "regulation of nitrogen metabolism" EXACT [] +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006807 ! nitrogen compound metabolic process +relationship: regulates GO:0006807 ! nitrogen compound metabolic process + +[Term] +id: GO:0051172 +name: negative regulation of nitrogen compound metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] +synonym: "down regulation of nitrogen metabolic process" EXACT [] +synonym: "down-regulation of nitrogen metabolic process" EXACT [] +synonym: "downregulation of nitrogen metabolic process" EXACT [] +synonym: "inhibition of nitrogen metabolic process" NARROW [] +synonym: "negative regulation of nitrogen metabolic process" EXACT [GOC:tb] +synonym: "negative regulation of nitrogen metabolism" EXACT [] +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0051171 ! regulation of nitrogen compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006807 ! nitrogen compound metabolic process +relationship: negatively_regulates GO:0006807 ! nitrogen compound metabolic process + +[Term] +id: GO:0051173 +name: positive regulation of nitrogen compound metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] +synonym: "activation of nitrogen metabolic process" NARROW [] +synonym: "positive regulation of nitrogen metabolic process" EXACT [GOC:tb] +synonym: "positive regulation of nitrogen metabolism" EXACT [] +synonym: "stimulation of nitrogen metabolic process" NARROW [] +synonym: "up regulation of nitrogen metabolic process" EXACT [] +synonym: "up-regulation of nitrogen metabolic process" EXACT [] +synonym: "upregulation of nitrogen metabolic process" EXACT [] +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0051171 ! regulation of nitrogen compound metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006807 ! nitrogen compound metabolic process +relationship: positively_regulates GO:0006807 ! nitrogen compound metabolic process + +[Term] +id: GO:0051174 +name: regulation of phosphorus metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus." [GOC:ai] +subset: gosubset_prok +synonym: "regulation of phosphorus metabolism" EXACT [] +is_a: GO:0031323 ! regulation of cellular metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006793 ! phosphorus metabolic process +relationship: regulates GO:0006793 ! phosphorus metabolic process + +[Term] +id: GO:0051176 +name: positive regulation of sulfur metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur." [GOC:ai] +subset: gosubset_prok +synonym: "activation of sulfur metabolic process" NARROW [] +synonym: "positive regulation of sulfur metabolism" EXACT [] +synonym: "positive regulation of sulphur metabolic process" EXACT [] +synonym: "positive regulation of sulphur metabolism" EXACT [] +synonym: "stimulation of sulfur metabolic process" NARROW [] +synonym: "up regulation of sulfur metabolic process" EXACT [] +synonym: "up-regulation of sulfur metabolic process" EXACT [] +synonym: "upregulation of sulfur metabolic process" EXACT [] +is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0042762 ! regulation of sulfur metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006790 ! sulfur compound metabolic process +relationship: positively_regulates GO:0006790 ! sulfur compound metabolic process + +[Term] +id: GO:0051179 +name: localization +namespace: biological_process +def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location." [GOC:ai] +subset: goslim_pir +subset: gosubset_prok +synonym: "establishment and maintenance of cellular component location" NARROW [] +synonym: "establishment and maintenance of localization" EXACT [] +synonym: "establishment and maintenance of position" EXACT [] +synonym: "establishment and maintenance of substance location" NARROW [] +synonym: "establishment and maintenance of substrate location" NARROW [] +synonym: "localisation" EXACT [GOC:mah] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0051216 +name: cartilage development +namespace: biological_process +def: "The process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." [http://www.onelook.com] +synonym: "cartilage biogenesis" EXACT [] +synonym: "cartilage biosynthesis" EXACT [] +synonym: "cartilage formation" EXACT [] +synonym: "chondrogenesis" EXACT [] +xref: Wikipedia:Chondrogenesis +is_a: GO:0061448 ! connective tissue development +relationship: part_of GO:0001501 ! skeletal system development +relationship: part_of GO:0048513 ! organ development + +[Term] +id: GO:0051222 +name: positive regulation of protein transport +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +synonym: "activation of protein transport" NARROW [] +synonym: "stimulation of protein transport" NARROW [] +synonym: "up regulation of protein transport" EXACT [] +synonym: "up-regulation of protein transport" EXACT [] +synonym: "upregulation of protein transport" EXACT [] +is_a: GO:0051050 ! positive regulation of transport +is_a: GO:0051223 ! regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0015031 ! protein transport +relationship: positively_regulates GO:0015031 ! protein transport + +[Term] +id: GO:0051223 +name: regulation of protein transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +is_a: GO:0051049 ! regulation of transport +is_a: GO:0070201 ! regulation of establishment of protein localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0015031 ! protein transport +relationship: regulates GO:0015031 ! protein transport + +[Term] +id: GO:0051224 +name: negative regulation of protein transport +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +synonym: "down regulation of protein transport" EXACT [] +synonym: "down-regulation of protein transport" EXACT [] +synonym: "downregulation of protein transport" EXACT [] +synonym: "inhibition of protein transport" NARROW [] +is_a: GO:0051051 ! negative regulation of transport +is_a: GO:0051223 ! regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0015031 ! protein transport +relationship: negatively_regulates GO:0015031 ! protein transport + +[Term] +id: GO:0051234 +name: establishment of localization +namespace: biological_process +def: "The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location." [GOC:ai] +subset: goslim_pir +subset: gosubset_prok +synonym: "establishment of localisation" EXACT [GOC:mah] +is_a: GO:0008150 ! biological_process +relationship: part_of GO:0051179 ! localization + +[Term] +id: GO:0051235 +name: maintenance of location +namespace: biological_process +def: "Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere." [GOC:ai, GOC:dph, GOC:tb] +subset: gosubset_prok +synonym: "retention" NARROW [] +synonym: "sequestering" NARROW [] +synonym: "storage" NARROW [] +is_a: GO:0065008 ! regulation of biological quality +relationship: part_of GO:0051179 ! localization + +[Term] +id: GO:0051239 +name: regulation of multicellular organismal process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai, GOC:dph, GOC:tb] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0051240 +name: positive regulation of multicellular organismal process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] +synonym: "activation of multicellular organismal process" NARROW [] +synonym: "stimulation of multicellular organismal process" NARROW [] +synonym: "up regulation of multicellular organismal process" EXACT [] +synonym: "up-regulation of multicellular organismal process" EXACT [] +synonym: "upregulation of multicellular organismal process" EXACT [] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0032501 ! multicellular organismal process +relationship: positively_regulates GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0051241 +name: negative regulation of multicellular organismal process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] +synonym: "down regulation of multicellular organismal process" EXACT [] +synonym: "down-regulation of multicellular organismal process" EXACT [] +synonym: "downregulation of multicellular organismal process" EXACT [] +synonym: "inhibition of multicellular organismal process" NARROW [] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032501 ! multicellular organismal process +relationship: negatively_regulates GO:0044707 ! single-multicellular organism process + +[Term] +id: GO:0051246 +name: regulation of protein metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai] +subset: gosubset_prok +synonym: "regulation of protein metabolism" EXACT [] +is_a: GO:0060255 ! regulation of macromolecule metabolic process +is_a: GO:0080090 ! regulation of primary metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0019538 ! protein metabolic process +relationship: regulates GO:0019538 ! protein metabolic process + +[Term] +id: GO:0051247 +name: positive regulation of protein metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai] +subset: gosubset_prok +synonym: "activation of protein metabolic process" NARROW [] +synonym: "positive regulation of protein metabolism" EXACT [] +synonym: "stimulation of protein metabolic process" NARROW [] +synonym: "up regulation of protein metabolic process" EXACT [] +synonym: "up-regulation of protein metabolic process" EXACT [] +synonym: "upregulation of protein metabolic process" EXACT [] +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0019538 ! protein metabolic process +relationship: positively_regulates GO:0019538 ! protein metabolic process + +[Term] +id: GO:0051248 +name: negative regulation of protein metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of protein metabolic process" EXACT [] +synonym: "down-regulation of protein metabolic process" EXACT [] +synonym: "downregulation of protein metabolic process" EXACT [] +synonym: "inhibition of protein metabolic process" NARROW [] +synonym: "negative regulation of protein metabolism" EXACT [] +is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +is_a: GO:0051246 ! regulation of protein metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0019538 ! protein metabolic process +relationship: negatively_regulates GO:0019538 ! protein metabolic process + +[Term] +id: GO:0051249 +name: regulation of lymphocyte activation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of lymphocyte activation." [GOC:ai] +is_a: GO:0002694 ! regulation of leukocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046649 ! lymphocyte activation +relationship: regulates GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0051250 +name: negative regulation of lymphocyte activation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte activation." [GOC:ai] +synonym: "down regulation of lymphocyte activation" EXACT [] +synonym: "down-regulation of lymphocyte activation" EXACT [] +synonym: "downregulation of lymphocyte activation" EXACT [] +synonym: "inhibition of lymphocyte activation" NARROW [] +is_a: GO:0002695 ! negative regulation of leukocyte activation +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046649 ! lymphocyte activation +relationship: negatively_regulates GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0051251 +name: positive regulation of lymphocyte activation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of lymphocyte activation." [GOC:ai] +synonym: "activation of lymphocyte activation" NARROW [] +synonym: "stimulation of lymphocyte activation" NARROW [] +synonym: "up regulation of lymphocyte activation" EXACT [] +synonym: "up-regulation of lymphocyte activation" EXACT [] +synonym: "upregulation of lymphocyte activation" EXACT [] +is_a: GO:0002696 ! positive regulation of leukocyte activation +is_a: GO:0051249 ! regulation of lymphocyte activation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046649 ! lymphocyte activation +relationship: positively_regulates GO:0046649 ! lymphocyte activation + +[Term] +id: GO:0051252 +name: regulation of RNA metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA." [GOC:ai] +subset: gosubset_prok +synonym: "regulation of RNA metabolism" EXACT [] +is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process +is_a: GO:0060255 ! regulation of macromolecule metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016070 ! RNA metabolic process +relationship: regulates GO:0016070 ! RNA metabolic process + +[Term] +id: GO:0051253 +name: negative regulation of RNA metabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of RNA metabolic process" EXACT [] +synonym: "down-regulation of RNA metabolic process" EXACT [] +synonym: "downregulation of RNA metabolic process" EXACT [] +synonym: "inhibition of RNA metabolic process" NARROW [] +synonym: "negative regulation of RNA metabolism" EXACT [] +is_a: GO:0010605 ! negative regulation of macromolecule metabolic process +is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process +is_a: GO:0051252 ! regulation of RNA metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016070 ! RNA metabolic process +relationship: negatively_regulates GO:0016070 ! RNA metabolic process + +[Term] +id: GO:0051254 +name: positive regulation of RNA metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA." [GOC:ai] +subset: gosubset_prok +synonym: "activation of RNA metabolic process" NARROW [] +synonym: "positive regulation of RNA metabolism" EXACT [] +synonym: "stimulation of RNA metabolic process" NARROW [] +synonym: "up regulation of RNA metabolic process" EXACT [] +synonym: "up-regulation of RNA metabolic process" EXACT [] +synonym: "upregulation of RNA metabolic process" EXACT [] +is_a: GO:0010604 ! positive regulation of macromolecule metabolic process +is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process +is_a: GO:0051252 ! regulation of RNA metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016070 ! RNA metabolic process +relationship: positively_regulates GO:0016070 ! RNA metabolic process + +[Term] +id: GO:0051259 +name: protein oligomerization +namespace: biological_process +def: "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC:ai] +subset: gosubset_prok +synonym: "protein oligomer assembly" EXACT [] +synonym: "protein oligomer biosynthesis" EXACT [] +synonym: "protein oligomer biosynthetic process" EXACT [] +synonym: "protein oligomer formation" EXACT [] +is_a: GO:0006461 ! protein complex assembly + +[Term] +id: GO:0051270 +name: regulation of cellular component movement +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl] +subset: gosubset_prok +synonym: "regulation of cell movement" RELATED [] +synonym: "regulation of cellular component motion" EXACT [GOC:mah] +is_a: GO:0032879 ! regulation of localization +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006928 ! cellular component movement +relationship: regulates GO:0006928 ! cellular component movement + +[Term] +id: GO:0051271 +name: negative regulation of cellular component movement +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl] +subset: gosubset_prok +synonym: "down regulation of cell motility" EXACT [] +synonym: "down-regulation of cell motility" EXACT [] +synonym: "downregulation of cell motility" EXACT [] +synonym: "inhibition of cell motility" NARROW [] +synonym: "negative regulation of cell movement" RELATED [] +synonym: "negative regulation of cellular component motion" EXACT [GOC:mah] +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051270 ! regulation of cellular component movement +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006928 ! cellular component movement +relationship: negatively_regulates GO:0006928 ! cellular component movement + +[Term] +id: GO:0051272 +name: positive regulation of cellular component movement +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl] +subset: gosubset_prok +synonym: "activation of cell motility" NARROW [] +synonym: "positive regulation of cell movement" RELATED [] +synonym: "positive regulation of cellular component motion" EXACT [GOC:mah] +synonym: "stimulation of cell motility" NARROW [] +synonym: "up regulation of cell motility" EXACT [] +synonym: "up-regulation of cell motility" EXACT [] +synonym: "upregulation of cell motility" EXACT [] +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051270 ! regulation of cellular component movement +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006928 ! cellular component movement +relationship: positively_regulates GO:0006928 ! cellular component movement + +[Term] +id: GO:0051276 +name: chromosome organization +namespace: biological_process +alt_id: GO:0007001 +alt_id: GO:0051277 +def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] +subset: goslim_generic +subset: goslim_pir +subset: goslim_pombe +subset: gosubset_prok +synonym: "chromosome organisation" EXACT [] +synonym: "chromosome organization and biogenesis" RELATED [GOC:mah] +synonym: "maintenance of genome integrity" RELATED [] +synonym: "nuclear genome maintenance" RELATED [] +is_a: GO:0006996 ! organelle organization + +[Term] +id: GO:0051291 +name: protein heterooligomerization +namespace: biological_process +def: "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC:ai] +subset: gosubset_prok +synonym: "protein heterooligomer assembly" EXACT [] +synonym: "protein heterooligomer biosynthesis" EXACT [] +synonym: "protein heterooligomer biosynthetic process" EXACT [] +synonym: "protein heterooligomer formation" EXACT [] +is_a: GO:0051259 ! protein oligomerization + +[Term] +id: GO:0051297 +name: centrosome organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] +synonym: "centrosome organisation" EXACT [GOC:curators] +synonym: "centrosome organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0031023 ! microtubule organizing center organization + +[Term] +id: GO:0051301 +name: cell division +namespace: biological_process +def: "The process resulting in the physical partitioning and separation of a cell into daughter cells." [GOC:go_curators] +comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: gosubset_prok +xref: Wikipedia:Cell_division +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0051302 +name: regulation of cell division +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells." [GOC:go_curators] +subset: gosubset_prok +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051301 ! cell division +relationship: regulates GO:0051301 ! cell division + +[Term] +id: GO:0051321 +name: meiotic cell cycle +namespace: biological_process +def: "Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell." [GOC:ai] +subset: goslim_yeast +is_a: GO:0007049 ! cell cycle +relationship: part_of GO:0000003 ! reproduction + +[Term] +id: GO:0051336 +name: regulation of hydrolase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [EC:3.-.-.-, GOC:ai] +subset: gosubset_prok +synonym: "hydrolase regulator" EXACT [] +is_a: GO:0050790 ! regulation of catalytic activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016787 ! hydrolase activity +relationship: regulates GO:0016787 ! hydrolase activity + +[Term] +id: GO:0051338 +name: regulation of transferase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [EC:2.-.-.-, GOC:ai] +subset: gosubset_prok +synonym: "transferase regulator" EXACT [] +is_a: GO:0050790 ! regulation of catalytic activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016740 ! transferase activity +relationship: regulates GO:0016740 ! transferase activity + +[Term] +id: GO:0051345 +name: positive regulation of hydrolase activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds." [GOC:ai] +subset: gosubset_prok +synonym: "activation of hydrolase activity" NARROW [] +synonym: "hydrolase activator" EXACT [] +synonym: "stimulation of hydrolase activity" NARROW [] +synonym: "up regulation of hydrolase activity" EXACT [] +synonym: "up-regulation of hydrolase activity" EXACT [] +synonym: "upregulation of hydrolase activity" EXACT [] +is_a: GO:0043085 ! positive regulation of catalytic activity +is_a: GO:0051336 ! regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016787 ! hydrolase activity +relationship: positively_regulates GO:0016787 ! hydrolase activity + +[Term] +id: GO:0051346 +name: negative regulation of hydrolase activity +namespace: biological_process +def: "Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of hydrolase activity" EXACT [] +synonym: "down-regulation of hydrolase activity" EXACT [] +synonym: "downregulation of hydrolase activity" EXACT [] +synonym: "hydrolase inhibitor" EXACT [] +synonym: "inhibition of hydrolase activity" NARROW [] +is_a: GO:0043086 ! negative regulation of catalytic activity +is_a: GO:0051336 ! regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016787 ! hydrolase activity +relationship: negatively_regulates GO:0016787 ! hydrolase activity + +[Term] +id: GO:0051347 +name: positive regulation of transferase activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai] +subset: gosubset_prok +synonym: "activation of transferase activity" NARROW [] +synonym: "stimulation of transferase activity" NARROW [] +synonym: "transferase activator" EXACT [] +synonym: "up regulation of transferase activity" EXACT [] +synonym: "up-regulation of transferase activity" EXACT [] +synonym: "upregulation of transferase activity" EXACT [] +is_a: GO:0043085 ! positive regulation of catalytic activity +is_a: GO:0051338 ! regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016740 ! transferase activity +relationship: positively_regulates GO:0016740 ! transferase activity + +[Term] +id: GO:0051348 +name: negative regulation of transferase activity +namespace: biological_process +def: "Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai] +subset: gosubset_prok +synonym: "down regulation of transferase activity" EXACT [] +synonym: "down-regulation of transferase activity" EXACT [] +synonym: "downregulation of transferase activity" EXACT [] +synonym: "inhibition of transferase activity" NARROW [] +synonym: "transferase inhibitor" EXACT [] +is_a: GO:0043086 ! negative regulation of catalytic activity +is_a: GO:0051338 ! regulation of transferase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0016740 ! transferase activity +relationship: negatively_regulates GO:0016740 ! transferase activity + +[Term] +id: GO:0051402 +name: neuron apoptotic process +namespace: biological_process +def: "Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [CL:0000540, GOC:mtg_apoptosis, MeSH:A.08.663] +synonym: "apoptosis of neuronal cells" EXACT [] +synonym: "apoptosis of neurons" EXACT [] +synonym: "neuron apoptosis" NARROW [] +synonym: "neuron programmed cell death by apoptosis" EXACT [] +synonym: "neuronal cell apoptosis" EXACT [] +synonym: "neuronal cell programmed cell death by apoptosis" EXACT [] +synonym: "programmed cell death of neuronal cells by apoptosis" EXACT [] +synonym: "programmed cell death of neurons by apoptosis" EXACT [] +synonym: "programmed cell death, neuronal cells" EXACT [] +synonym: "programmed cell death, neurons" EXACT [] +is_a: GO:0070997 ! neuron death +is_a: GO:0097285 ! cell-type specific apoptotic process + +[Term] +id: GO:0051403 +name: stress-activated MAPK cascade +namespace: biological_process +def: "A series of molecular signals in which a stress-activated MAP kinase cascade relays one or more of the signals; MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase." [GOC:ai, PMID:15936270] +synonym: "MAPK11 cascade" NARROW [GOC:add] +synonym: "MAPK12 cascade" NARROW [GOC:add] +synonym: "MAPK13 cascade" NARROW [GOC:add] +synonym: "MAPK14 cascade" NARROW [GOC:add] +synonym: "p38 cascade" NARROW [GOC:add] +synonym: "p38 MAPK signaling" NARROW [] +synonym: "p38 MAPK signalling" NARROW [] +synonym: "SAPK cascade" BROAD [GOC:add] +synonym: "stress-activated MAPK signaling pathway" EXACT [] +synonym: "stress-activated MAPK signalling pathway" EXACT [] +synonym: "stress-activated MAPKKK cascade" EXACT [] +synonym: "stress-activated MAPKKK signaling pathway" EXACT [] +synonym: "stress-activated MAPKKK signalling pathway" EXACT [] +xref: Reactome:REACT_103389 "MAP kinase activation in TLR cascade, Dictyostelium discoideum" +xref: Reactome:REACT_104595 "MAP kinase activation in TLR cascade, Taeniopygia guttata" +xref: Reactome:REACT_104796 "MAP kinase activation in TLR cascade, Mus musculus" +xref: Reactome:REACT_105109 "MAP kinase activation in TLR cascade, Danio rerio" +xref: Reactome:REACT_109896 "MAP kinase activation in TLR cascade, Canis familiaris" +xref: Reactome:REACT_21308 "MAP kinase activation in TLR cascade, Homo sapiens" +xref: Reactome:REACT_30115 "MAP kinase activation in TLR cascade, Rattus norvegicus" +xref: Reactome:REACT_32136 "MAP kinase activation in TLR cascade, Caenorhabditis elegans" +xref: Reactome:REACT_34622 "MAP kinase activation in TLR cascade, Oryza sativa" +xref: Reactome:REACT_79433 "MAP kinase activation in TLR cascade, Xenopus tropicalis" +xref: Reactome:REACT_82500 "MAP kinase activation in TLR cascade, Drosophila melanogaster" +xref: Reactome:REACT_85645 "MAP kinase activation in TLR cascade, Saccharomyces cerevisiae" +xref: Reactome:REACT_85847 "MAP kinase activation in TLR cascade, Bos taurus" +xref: Reactome:REACT_89123 "MAP kinase activation in TLR cascade, Sus scrofa" +xref: Reactome:REACT_95758 "MAP kinase activation in TLR cascade, Gallus gallus" +xref: Reactome:REACT_95991 "MAP kinase activation in TLR cascade, Schizosaccharomyces pombe" +xref: Reactome:REACT_98311 "MAP kinase activation in TLR cascade, Arabidopsis thaliana" +is_a: GO:0000165 ! MAPK cascade +is_a: GO:0031098 ! stress-activated protein kinase signaling cascade + +[Term] +id: GO:0051427 +name: hormone receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a receptor for hormones." [GOC:ai] +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0051445 +name: regulation of meiotic cell cycle +namespace: biological_process +def: "Any process that modulates the rate or extent of progression through the meiotic cell cycle." [GOC:ai, GOC:dph, GOC:tb] +synonym: "control of meiotic cell cycle progression" EXACT [] +synonym: "meiotic cell cycle control" EXACT [] +synonym: "meiotic cell cycle modulation" EXACT [] +synonym: "meiotic cell cycle regulation" EXACT [] +synonym: "meiotic cell cycle regulator" RELATED [] +synonym: "modulation of meiotic cell cycle progression" EXACT [] +synonym: "regulation of meiotic cell cycle progression" EXACT [] +synonym: "regulation of progression through meiotic cell cycle" EXACT [GOC:dph, GOC:tb] +is_a: GO:0051726 ! regulation of cell cycle +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051321 ! meiotic cell cycle +relationship: regulates GO:0051321 ! meiotic cell cycle + +[Term] +id: GO:0051480 +name: cytosolic calcium ion homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings." [GOC:ai, GOC:mah, GOC:rph] +synonym: "calcium ion homeostasis in cytoplasm" BROAD [] +synonym: "calcium ion homeostasis in cytosol" EXACT [] +synonym: "cytoplasmic calcium ion concentration regulation" BROAD [] +synonym: "cytoplasmic calcium ion homeostasis" BROAD [] +synonym: "cytosolic calcium ion concentration regulation" EXACT [] +synonym: "regulation of calcium ion concentration in cytoplasm" BROAD [] +synonym: "regulation of calcium ion concentration in cytosol" EXACT [] +synonym: "regulation of cytoplasmic calcium ion concentration" BROAD [] +synonym: "regulation of cytosolic calcium ion concentration" EXACT [] +is_a: GO:0006874 ! cellular calcium ion homeostasis + +[Term] +id: GO:0051492 +name: regulation of stress fiber assembly +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts." [GOC:ai] +synonym: "regulation of stress fibre biosynthesis" RELATED [] +synonym: "regulation of stress fibre formation" EXACT [] +is_a: GO:0032231 ! regulation of actin filament bundle assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043149 ! stress fiber assembly +relationship: regulates GO:0043149 ! stress fiber assembly + +[Term] +id: GO:0051493 +name: regulation of cytoskeleton organization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:ai] +synonym: "regulation of cytoskeleton organisation" EXACT [GOC:mah] +synonym: "regulation of cytoskeleton organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0033043 ! regulation of organelle organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007010 ! cytoskeleton organization +relationship: regulates GO:0007010 ! cytoskeleton organization + +[Term] +id: GO:0051495 +name: positive regulation of cytoskeleton organization +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:ai] +synonym: "activation of cytoskeleton organization" NARROW [] +synonym: "positive regulation of cytoskeleton organisation" EXACT [GOC:mah] +synonym: "positive regulation of cytoskeleton organization and biogenesis" RELATED [GOC:mah] +synonym: "stimulation of cytoskeleton organization" NARROW [] +synonym: "up regulation of cytoskeleton organization" EXACT [] +synonym: "up-regulation of cytoskeleton organization" EXACT [] +synonym: "upregulation of cytoskeleton organization" EXACT [] +is_a: GO:0010638 ! positive regulation of organelle organization +is_a: GO:0051493 ! regulation of cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007010 ! cytoskeleton organization +relationship: positively_regulates GO:0007010 ! cytoskeleton organization + +[Term] +id: GO:0051496 +name: positive regulation of stress fiber assembly +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts." [GOC:ai] +synonym: "activation of stress fiber formation" NARROW [] +synonym: "positive regulation of stress fibre biosynthesis" RELATED [] +synonym: "positive regulation of stress fibre formation" RELATED [] +synonym: "stimulation of stress fiber formation" NARROW [] +synonym: "up regulation of stress fiber formation" RELATED [] +synonym: "up-regulation of stress fiber formation" EXACT [] +synonym: "upregulation of stress fiber formation" RELATED [] +is_a: GO:0032233 ! positive regulation of actin filament bundle assembly +is_a: GO:0051492 ! regulation of stress fiber assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0043149 ! stress fiber assembly +relationship: positively_regulates GO:0043149 ! stress fiber assembly + +[Term] +id: GO:0051593 +name: response to folic acid +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a folic acid stimulus." [GOC:ai] +synonym: "cellular response to folate" EXACT [GOC:mah] +synonym: "cellular response to vitamin B9" EXACT [GOC:mah] +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0033273 ! response to vitamin +is_a: GO:0043200 ! response to amino acid + +[Term] +id: GO:0051594 +name: detection of glucose +namespace: biological_process +def: "The series of events in which a glucose stimulus is received by a cell and converted into a molecular signal." [GOC:ai] +synonym: "glucose detection" EXACT [] +synonym: "glucose perception" RELATED [] +synonym: "glucose sensing" RELATED [] +is_a: GO:0009732 ! detection of hexose stimulus +is_a: GO:0009749 ! response to glucose + +[Term] +id: GO:0051603 +name: proteolysis involved in cellular protein catabolic process +namespace: biological_process +def: "The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells." [GOC:ai, GOC:dph, GOC:tb] +subset: goslim_yeast +subset: gosubset_prok +synonym: "peptidolysis during cellular protein catabolic process" RELATED [] +synonym: "peptidolysis during cellular protein catabolism" RELATED [] +synonym: "peptidolysis involved in cellular protein catabolic process" EXACT [] +synonym: "peptidolysis involved in cellular protein catabolism" EXACT [] +synonym: "proteolysis during cellular protein catabolic process" RELATED [] +synonym: "proteolysis during cellular protein catabolism" RELATED [] +is_a: GO:0006508 ! proteolysis +intersection_of: GO:0006508 ! proteolysis +intersection_of: part_of GO:0044257 ! cellular protein catabolic process +relationship: part_of GO:0044257 ! cellular protein catabolic process + +[Term] +id: GO:0051606 +name: detection of stimulus +namespace: biological_process +def: "The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal." [GOC:add, GOC:ai, GOC:dph, GOC:mah] +subset: goslim_pir +subset: gosubset_prok +synonym: "perception of stimulus" RELATED [] +synonym: "stimulus detection" EXACT [] +synonym: "stimulus sensing" RELATED [] +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0051640 +name: organelle localization +namespace: biological_process +def: "Any process in which an organelle is transported to, and/or maintained in, a specific location." [GOC:ai] +subset: goslim_pir +synonym: "establishment and maintenance of organelle localization" EXACT [] +synonym: "organelle localisation" EXACT [GOC:mah] +is_a: GO:0051641 ! cellular localization + +[Term] +id: GO:0051641 +name: cellular localization +namespace: biological_process +def: "A localization process that takes place at the cellular level; as a result of a cellular localization process, a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within or in the membrane of a cell." [GOC:ai, GOC:mah] +subset: goslim_pir +subset: gosubset_prok +synonym: "cellular localisation" EXACT [GOC:mah] +synonym: "establishment and maintenance of cellular localization" EXACT [] +synonym: "establishment and maintenance of localization in cell or cell membrane" EXACT [] +synonym: "intracellular localization" NARROW [] +synonym: "localization within cell" NARROW [] +is_a: GO:0051179 ! localization + +[Term] +id: GO:0051648 +name: vesicle localization +namespace: biological_process +def: "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location." [GOC:ai] +synonym: "cytoplasmic vesicle localization" EXACT [] +synonym: "establishment and maintenance of vesicle localization" EXACT [] +synonym: "vesicle localisation" EXACT [GOC:mah] +is_a: GO:0051640 ! organelle localization + +[Term] +id: GO:0051649 +name: establishment of localization in cell +namespace: biological_process +def: "The directed movement of a substance or cellular entity, such as a protein complex or organelle, to a specific location within, or in the membrane of, a cell." [GOC:ai, GOC:dph, GOC:tb] +subset: gosubset_prok +synonym: "establishment of cellular localization" RELATED [GOC:dph, GOC:tb] +synonym: "establishment of intracellular localization" NARROW [] +synonym: "establishment of localisation in cell" EXACT [GOC:mah] +synonym: "establishment of localization within cell" NARROW [] +synonym: "positioning within cell" NARROW [] +is_a: GO:0051234 ! establishment of localization +intersection_of: GO:0051234 ! establishment of localization +intersection_of: occurs_in GO:0005623 ! cell +relationship: part_of GO:0051641 ! cellular localization + +[Term] +id: GO:0051650 +name: establishment of vesicle localization +namespace: biological_process +def: "The directed movement of a vesicle to a specific location." [GOC:ai] +subset: goslim_aspergillus +synonym: "establishment of vesicle localisation" EXACT [GOC:mah] +is_a: GO:0051649 ! establishment of localization in cell +is_a: GO:0051656 ! establishment of organelle localization +relationship: part_of GO:0051648 ! vesicle localization + +[Term] +id: GO:0051651 +name: maintenance of location in cell +namespace: biological_process +def: "Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere." [GOC:ai] +subset: gosubset_prok +synonym: "cellular retention" NARROW [] +synonym: "cellular sequestering" NARROW [] +synonym: "cellular storage" NARROW [] +synonym: "intracellular retention" NARROW [] +synonym: "intracellular sequestering" NARROW [] +synonym: "intracellular storage" NARROW [] +synonym: "maintenance of cellular localization" RELATED [GOC:dph, GOC:tb] +synonym: "maintenance of intracellular localization" NARROW [] +synonym: "maintenance of localization in cell" RELATED [GOC:dph, GOC:tb] +synonym: "maintenance of localization within cell" NARROW [] +synonym: "retention within cell" NARROW [] +synonym: "sequestering within cell" NARROW [] +synonym: "storage within cell" NARROW [] +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0051235 ! maintenance of location +relationship: part_of GO:0051641 ! cellular localization + +[Term] +id: GO:0051656 +name: establishment of organelle localization +namespace: biological_process +def: "The directed movement of an organelle to a specific location." [GOC:ai] +synonym: "establishment of organelle localisation" EXACT [GOC:mah] +is_a: GO:0051234 ! establishment of localization +relationship: part_of GO:0051640 ! organelle localization + +[Term] +id: GO:0051674 +name: localization of cell +namespace: biological_process +def: "Any process in which a cell is transported to, and/or maintained in, a specific location." [GOC:ai] +subset: gosubset_prok +synonym: "cell localization" EXACT [] +synonym: "establishment and maintenance of cell localization" EXACT [] +synonym: "establishment and maintenance of localization of cell" EXACT [] +synonym: "localisation of cell" EXACT [GOC:mah] +is_a: GO:0051179 ! localization + +[Term] +id: GO:0051704 +name: multi-organism process +namespace: biological_process +alt_id: GO:0051706 +def: "A biological process which involves another organism of the same or different species." [GOC:jl] +subset: goslim_pir +subset: gosubset_prok +synonym: "interaction between organisms" EXACT [] +synonym: "physiological interaction between organisms" EXACT [] +synonym: "physiological interaction with other organism" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0051707 +name: response to other organism +namespace: biological_process +alt_id: GO:0009613 +alt_id: GO:0042828 +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism." [GOC:ai] +subset: gosubset_prok +is_a: GO:0043207 ! response to external biotic stimulus +is_a: GO:0051704 ! multi-organism process + +[Term] +id: GO:0051716 +name: cellular response to stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell." [GOC:bf, GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: gosubset_prok +is_a: GO:0009987 ! cellular process +is_a: GO:0050896 ! response to stimulus + +[Term] +id: GO:0051726 +name: regulation of cell cycle +namespace: biological_process +alt_id: GO:0000074 +def: "Any process that modulates the rate or extent of progression through the cell cycle." [GOC:ai, GOC:dph, GOC:tb] +subset: goslim_yeast +subset: gosubset_prok +synonym: "cell cycle control" EXACT [] +synonym: "cell cycle modulation" EXACT [] +synonym: "cell cycle regulation" EXACT [] +synonym: "cell cycle regulator" RELATED [] +synonym: "control of cell cycle progression" EXACT [] +synonym: "modulation of cell cycle progression" EXACT [] +synonym: "regulation of cell cycle progression" EXACT [] +synonym: "regulation of progression through cell cycle" EXACT [] +synonym: "tumor suppressor" RELATED [] +xref: Reactome:REACT_100159 "Inactivation of Myt1 kinase, Mus musculus" +xref: Reactome:REACT_1006 "Polo-like kinase mediated events, Homo sapiens" +xref: Reactome:REACT_102418 "Polo-like kinase mediated events, Schizosaccharomyces pombe" +xref: Reactome:REACT_102475 "Inactivation of Myt1 kinase, Rattus norvegicus" +xref: Reactome:REACT_103468 "Activation of Cdc25C, Drosophila melanogaster" +xref: Reactome:REACT_104523 "Inactivation of Wee1 kinase, Bos taurus" +xref: Reactome:REACT_105454 "Polo-like kinase mediated events, Dictyostelium discoideum" +xref: Reactome:REACT_106237 "Polo-like kinase mediated events, Caenorhabditis elegans" +xref: Reactome:REACT_106324 "Activation of Cdc25C, Mus musculus" +xref: Reactome:REACT_107424 "Inactivation of Myt1 kinase, Canis familiaris" +xref: Reactome:REACT_108578 "Inactivation of Myt1 kinase, Xenopus tropicalis" +xref: Reactome:REACT_109244 "Inactivation of Myt1 kinase, Schizosaccharomyces pombe" +xref: Reactome:REACT_109507 "Polo-like kinase mediated events, Taeniopygia guttata" +xref: Reactome:REACT_109584 "Polo-like kinase mediated events, Saccharomyces cerevisiae" +xref: Reactome:REACT_110774 "Inactivation of Myt1 kinase, Drosophila melanogaster" +xref: Reactome:REACT_112480 "Inactivation of Wee1 kinase, Dictyostelium discoideum" +xref: Reactome:REACT_113569 "Activation of Cdc25C, Saccharomyces cerevisiae" +xref: Reactome:REACT_113990 "Activation of Cdc25C, Schizosaccharomyces pombe" +xref: Reactome:REACT_114323 "Activation of Cdc25C, Caenorhabditis elegans" +xref: Reactome:REACT_1944 "Inactivation of Wee1 kinase, Homo sapiens" +xref: Reactome:REACT_2119 "Activation of Cdc25C, Homo sapiens" +xref: Reactome:REACT_28091 "Inactivation of Wee1 kinase, Canis familiaris" +xref: Reactome:REACT_29213 "Activation of Cdc25C, Rattus norvegicus" +xref: Reactome:REACT_30490 "Inactivation of Myt1 kinase, Danio rerio" +xref: Reactome:REACT_30836 "Inactivation of Myt1 kinase, Bos taurus" +xref: Reactome:REACT_30859 "Polo-like kinase mediated events, Gallus gallus" +xref: Reactome:REACT_32077 "Inactivation of Myt1 kinase, Dictyostelium discoideum" +xref: Reactome:REACT_34285 "Activation of Cdc25C, Bos taurus" +xref: Reactome:REACT_414 "Inactivation of Myt1 kinase, Homo sapiens" +xref: Reactome:REACT_80617 "Inactivation of Wee1 kinase, Xenopus tropicalis" +xref: Reactome:REACT_81789 "Polo-like kinase mediated events, Drosophila melanogaster" +xref: Reactome:REACT_82824 "Inactivation of Wee1 kinase, Rattus norvegicus" +xref: Reactome:REACT_83089 "Inactivation of Myt1 kinase, Saccharomyces cerevisiae" +xref: Reactome:REACT_83883 "Polo-like kinase mediated events, Canis familiaris" +xref: Reactome:REACT_87352 "Polo-like kinase mediated events, Danio rerio" +xref: Reactome:REACT_88486 "Inactivation of Wee1 kinase, Taeniopygia guttata" +xref: Reactome:REACT_89122 "Activation of Cdc25C, Canis familiaris" +xref: Reactome:REACT_91085 "Inactivation of Wee1 kinase, Danio rerio" +xref: Reactome:REACT_92033 "Inactivation of Myt1 kinase, Caenorhabditis elegans" +xref: Reactome:REACT_93521 "Polo-like kinase mediated events, Mus musculus" +xref: Reactome:REACT_93702 "Polo-like kinase mediated events, Rattus norvegicus" +xref: Reactome:REACT_95088 "Inactivation of Wee1 kinase, Mus musculus" +xref: Reactome:REACT_96524 "Activation of Cdc25C, Xenopus tropicalis" +xref: Reactome:REACT_97306 "Polo-like kinase mediated events, Bos taurus" +xref: Reactome:REACT_97384 "Polo-like kinase mediated events, Xenopus tropicalis" +xref: Reactome:REACT_98443 "Inactivation of Wee1 kinase, Gallus gallus" +xref: Reactome:REACT_99158 "Inactivation of Wee1 kinase, Drosophila melanogaster" +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007049 ! cell cycle +relationship: regulates GO:0007049 ! cell cycle + +[Term] +id: GO:0051783 +name: regulation of nuclear division +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information." [GOC:ai] +is_a: GO:0033043 ! regulation of organelle organization +is_a: GO:0051302 ! regulation of cell division +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000280 ! nuclear division +relationship: regulates GO:0000280 ! nuclear division + +[Term] +id: GO:0051785 +name: positive regulation of nuclear division +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information." [GOC:ai] +synonym: "activation of nuclear division" NARROW [] +synonym: "stimulation of nuclear division" NARROW [] +synonym: "up regulation of nuclear division" EXACT [] +synonym: "up-regulation of nuclear division" EXACT [] +synonym: "upregulation of nuclear division" EXACT [] +is_a: GO:0010638 ! positive regulation of organelle organization +is_a: GO:0051783 ! regulation of nuclear division +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0000280 ! nuclear division +relationship: positively_regulates GO:0000280 ! nuclear division + +[Term] +id: GO:0051890 +name: regulation of cardioblast differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:ai] +is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:2000736 ! regulation of stem cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0010002 ! cardioblast differentiation +relationship: regulates GO:0010002 ! cardioblast differentiation + +[Term] +id: GO:0051893 +name: regulation of focal adhesion assembly +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of focal adhesion formation, the establishment and maturation of focal adhesions." [GOC:ai] +is_a: GO:0001952 ! regulation of cell-matrix adhesion +is_a: GO:0090109 ! regulation of cell-substrate junction assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048041 ! focal adhesion assembly +relationship: regulates GO:0048041 ! focal adhesion assembly + +[Term] +id: GO:0051894 +name: positive regulation of focal adhesion assembly +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions." [GOC:ai] +synonym: "activation of focal adhesion formation" NARROW [] +synonym: "stimulation of focal adhesion formation" NARROW [] +synonym: "up regulation of focal adhesion formation" EXACT [] +synonym: "up-regulation of focal adhesion formation" EXACT [] +synonym: "upregulation of focal adhesion formation" EXACT [] +is_a: GO:0001954 ! positive regulation of cell-matrix adhesion +is_a: GO:0051893 ! regulation of focal adhesion assembly +is_a: GO:1901890 ! positive regulation of cell junction assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048041 ! focal adhesion assembly +relationship: positively_regulates GO:0048041 ! focal adhesion assembly + +[Term] +id: GO:0051896 +name: regulation of protein kinase B signaling +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B." [GOC:ai] +synonym: "regulation of AKT signaling cascade" RELATED [] +synonym: "regulation of AKT signalling cascade" RELATED [] +synonym: "regulation of PKB signaling cascade" RELATED [] +synonym: "regulation of PKB signalling cascade" RELATED [] +synonym: "regulation of protein kinase B signaling cascade" RELATED [GOC:signaling] +synonym: "regulation of protein kinase B signalling cascade" RELATED [] +is_a: GO:1902531 ! regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043491 ! protein kinase B signaling +relationship: regulates GO:0043491 ! protein kinase B signaling + +[Term] +id: GO:0051898 +name: negative regulation of protein kinase B signaling +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B." [GOC:ai] +synonym: "down regulation of protein kinase B signaling cascade" RELATED [] +synonym: "down-regulation of protein kinase B signaling cascade" RELATED [] +synonym: "downregulation of protein kinase B signaling cascade" RELATED [] +synonym: "inhibition of protein kinase B signaling cascade" NARROW [] +synonym: "negative regulation of AKT signaling cascade" RELATED [] +synonym: "negative regulation of AKT signalling cascade" EXACT [] +synonym: "negative regulation of PKB signaling cascade" EXACT [] +synonym: "negative regulation of PKB signalling cascade" RELATED [] +synonym: "negative regulation of protein kinase B signaling cascade" RELATED [GOC:signaling] +synonym: "negative regulation of protein kinase B signalling cascade" RELATED [] +is_a: GO:0051896 ! regulation of protein kinase B signaling +is_a: GO:1902532 ! negative regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0043491 ! protein kinase B signaling +relationship: negatively_regulates GO:0043491 ! protein kinase B signaling + +[Term] +id: GO:0051924 +name: regulation of calcium ion transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of calcium ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +synonym: "regulation of calcium transport" EXACT [] +is_a: GO:0010959 ! regulation of metal ion transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006816 ! calcium ion transport +relationship: regulates GO:0006816 ! calcium ion transport + +[Term] +id: GO:0051960 +name: regulation of nervous system development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue." [GOC:ai] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007399 ! nervous system development +relationship: regulates GO:0007399 ! nervous system development + +[Term] +id: GO:0051961 +name: negative regulation of nervous system development +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue." [GOC:ai] +synonym: "down regulation of nervous system development" EXACT [] +synonym: "down-regulation of nervous system development" EXACT [] +synonym: "downregulation of nervous system development" EXACT [] +synonym: "inhibition of nervous system development" NARROW [] +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0051960 ! regulation of nervous system development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007399 ! nervous system development +relationship: negatively_regulates GO:0007399 ! nervous system development + +[Term] +id: GO:0051962 +name: positive regulation of nervous system development +namespace: biological_process +def: "Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue." [GOC:ai] +synonym: "activation of nervous system development" NARROW [] +synonym: "stimulation of nervous system development" NARROW [] +synonym: "up regulation of nervous system development" EXACT [] +synonym: "up-regulation of nervous system development" EXACT [] +synonym: "upregulation of nervous system development" EXACT [] +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051960 ! regulation of nervous system development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007399 ! nervous system development +relationship: positively_regulates GO:0007399 ! nervous system development + +[Term] +id: GO:0051963 +name: regulation of synapse assembly +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse." [GOC:ai, GOC:pr] +synonym: "regulation of synapse biogenesis" EXACT [] +synonym: "regulation of synaptogenesis" EXACT [] +is_a: GO:0044087 ! regulation of cellular component biogenesis +is_a: GO:0050807 ! regulation of synapse organization +is_a: GO:0051960 ! regulation of nervous system development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007416 ! synapse assembly +relationship: regulates GO:0007416 ! synapse assembly + +[Term] +id: GO:0051964 +name: negative regulation of synapse assembly +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse." [GOC:ai, GOC:pr] +synonym: "down regulation of synapse assembly" EXACT [] +synonym: "down-regulation of synapse assembly" EXACT [] +synonym: "downregulation of synapse assembly" EXACT [] +synonym: "inhibition of synapse assembly" NARROW [] +synonym: "negative regulation of synapse biogenesis" EXACT [] +synonym: "negative regulation of synaptogenesis" EXACT [] +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051129 ! negative regulation of cellular component organization +is_a: GO:0051961 ! negative regulation of nervous system development +is_a: GO:0051963 ! regulation of synapse assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007416 ! synapse assembly +relationship: negatively_regulates GO:0007416 ! synapse assembly + +[Term] +id: GO:0051965 +name: positive regulation of synapse assembly +namespace: biological_process +def: "Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse." [GOC:ai, GOC:pr] +synonym: "activation of synapse assembly" NARROW [] +synonym: "positive regulation of synapse biogenesis" EXACT [] +synonym: "positive regulation of synaptogenesis" EXACT [] +synonym: "stimulation of synapse assembly" NARROW [] +synonym: "up regulation of synapse assembly" EXACT [] +synonym: "up-regulation of synapse assembly" EXACT [] +synonym: "upregulation of synapse assembly" EXACT [] +is_a: GO:0044089 ! positive regulation of cellular component biogenesis +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051130 ! positive regulation of cellular component organization +is_a: GO:0051962 ! positive regulation of nervous system development +is_a: GO:0051963 ! regulation of synapse assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007416 ! synapse assembly +relationship: positively_regulates GO:0007416 ! synapse assembly + +[Term] +id: GO:0051983 +name: regulation of chromosome segregation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets." [GOC:ai] +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007059 ! chromosome segregation +relationship: regulates GO:0007059 ! chromosome segregation + +[Term] +id: GO:0052547 +name: regulation of peptidase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins." [EC:3.4, GOC:ai] +synonym: "peptidase regulator activity" RELATED [] +is_a: GO:0051336 ! regulation of hydrolase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008233 ! peptidase activity +relationship: regulates GO:0008233 ! peptidase activity + +[Term] +id: GO:0052548 +name: regulation of endopeptidase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins." [GOC:ai, GOC:hjd] +synonym: "protease regulator activity" RELATED [] +is_a: GO:0052547 ! regulation of peptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004175 ! endopeptidase activity +relationship: regulates GO:0004175 ! endopeptidase activity + +[Term] +id: GO:0055007 +name: cardiac muscle cell differentiation +namespace: biological_process +def: "The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction." [GOC:devbiol, GOC:mtg_heart] +synonym: "cardiomyocyte differentiation" EXACT [] +synonym: "heart muscle cell differentiation" RELATED [] +is_a: GO:0035051 ! cardiocyte differentiation +is_a: GO:0051146 ! striated muscle cell differentiation +relationship: part_of GO:0048738 ! cardiac muscle tissue development + +[Term] +id: GO:0055008 +name: cardiac muscle tissue morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of cardiac muscle tissue are generated and organized." [GOC:devbiol] +synonym: "heart muscle morphogenesis" EXACT [] +synonym: "myocardium morphogenesis" BROAD [GOC:mtg_heart] +is_a: GO:0060415 ! muscle tissue morphogenesis +relationship: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0048738 ! cardiac muscle tissue development + +[Term] +id: GO:0055010 +name: ventricular cardiac muscle tissue morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of cardiac ventricle muscle is generated and organized." [GOC:devbiol] +synonym: "cardiac ventricle muscle morphogenesis" EXACT [] +synonym: "ventricular heart muscle morphogenesis" EXACT [] +is_a: GO:0055008 ! cardiac muscle tissue morphogenesis +relationship: part_of GO:0003208 ! cardiac ventricle morphogenesis +relationship: part_of GO:0003229 ! ventricular cardiac muscle tissue development + +[Term] +id: GO:0055017 +name: cardiac muscle tissue growth +namespace: biological_process +def: "The increase in size or mass of a cardiac muscle, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another." [GOC:devbiol] +synonym: "heart muscle growth" EXACT [] +is_a: GO:0040007 ! growth +relationship: part_of GO:0048738 ! cardiac muscle tissue development +relationship: part_of GO:0060419 ! heart growth + +[Term] +id: GO:0055024 +name: regulation of cardiac muscle tissue development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cardiac muscle tissue development." [GOC:vk] +synonym: "regulation of heart muscle development" EXACT [] +is_a: GO:0016202 ! regulation of striated muscle tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048738 ! cardiac muscle tissue development +relationship: regulates GO:0048738 ! cardiac muscle tissue development + +[Term] +id: GO:0055057 +name: neuroblast division +namespace: biological_process +def: "The process resulting in the physical partitioning and separation of a neuroblast into daughter cells. A neuroblast is any cell that will divide and give rise to a neuron." [PMID:11163136, PMID:11250167] +synonym: "neuroblast cell division" EXACT [] +is_a: GO:0036445 ! neuronal stem cell division +relationship: part_of GO:0007405 ! neuroblast proliferation + +[Term] +id: GO:0055065 +name: metal ion homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of metal ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah] +subset: gosubset_prok +is_a: GO:0055080 ! cation homeostasis + +[Term] +id: GO:0055074 +name: calcium ion homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell." [GOC:ceb, GOC:jid, GOC:mah] +synonym: "regulation of calcium ion concentration" EXACT [] +is_a: GO:0055065 ! metal ion homeostasis +is_a: GO:0072507 ! divalent inorganic cation homeostasis + +[Term] +id: GO:0055080 +name: cation homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of cations within an organism or cell." [GOC:ceb, GOC:jid, GOC:mah] +subset: gosubset_prok +is_a: GO:0050801 ! ion homeostasis + +[Term] +id: GO:0055082 +name: cellular chemical homeostasis +namespace: biological_process +def: "Any biological process involved in the maintenance of an internal steady state of a chemical at the level of the cell." [GOC:isa_complete, GOC:jid] +subset: gosubset_prok +is_a: GO:0019725 ! cellular homeostasis +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0055085 +name: transmembrane transport +namespace: biological_process +def: "The process in which a solute is transported from one side of a membrane to the other." [GOC:dph, GOC:jid] +comment: Transmembrane transport requires transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. +subset: goslim_generic +subset: goslim_pombe +subset: goslim_yeast +synonym: "membrane transport" EXACT [] +xref: Reactome:REACT_100480 "SLC-mediated transmembrane transport, Taeniopygia guttata" +xref: Reactome:REACT_101577 "SLC-mediated transmembrane transport, Caenorhabditis elegans" +xref: Reactome:REACT_101877 "SLC-mediated transmembrane transport, Escherichia coli" +xref: Reactome:REACT_101975 "SLC-mediated transmembrane transport, Sus scrofa" +xref: Reactome:REACT_102348 "Transmembrane transport of small molecules, Staphylococcus aureus N315" +xref: Reactome:REACT_102897 "Transmembrane transport of small molecules, Caenorhabditis elegans" +xref: Reactome:REACT_102974 "SLC-mediated transmembrane transport, Canis familiaris" +xref: Reactome:REACT_104555 "SLC-mediated transmembrane transport, Xenopus tropicalis" +xref: Reactome:REACT_108243 "SLC-mediated transmembrane transport, Staphylococcus aureus N315" +xref: Reactome:REACT_109832 "Transmembrane transport of small molecules, Plasmodium falciparum" +xref: Reactome:REACT_110770 "ABC-family proteins mediated transport, Mus musculus" +xref: Reactome:REACT_114546 "ABC-family proteins mediated transport, Staphylococcus aureus N315" +xref: Reactome:REACT_114763 "ABC-family proteins mediated transport, Escherichia coli" +xref: Reactome:REACT_114890 "ABC-family proteins mediated transport, Plasmodium falciparum" +xref: Reactome:REACT_115378 "ABC-family proteins mediated transport, Mycobacterium tuberculosis" +xref: Reactome:REACT_15480 "ABC-family proteins mediated transport, Homo sapiens" +xref: Reactome:REACT_15518 "Transmembrane transport of small molecules, Homo sapiens" +xref: Reactome:REACT_19118 "SLC-mediated transmembrane transport, Homo sapiens" +xref: Reactome:REACT_29093 "ABC-family proteins mediated transport, Taeniopygia guttata" +xref: Reactome:REACT_29184 "SLC-mediated transmembrane transport, Gallus gallus" +xref: Reactome:REACT_29635 "Transmembrane transport of small molecules, Canis familiaris" +xref: Reactome:REACT_30969 "ABC-family proteins mediated transport, Canis familiaris" +xref: Reactome:REACT_32055 "Transmembrane transport of small molecules, Saccharomyces cerevisiae" +xref: Reactome:REACT_32223 "Transmembrane transport of small molecules, Rattus norvegicus" +xref: Reactome:REACT_32423 "SLC-mediated transmembrane transport, Bos taurus" +xref: Reactome:REACT_32713 "ABC-family proteins mediated transport, Sus scrofa" +xref: Reactome:REACT_33571 "SLC-mediated transmembrane transport, Danio rerio" +xref: Reactome:REACT_61245 "Transmembrane transport of small molecules, Bos taurus" +xref: Reactome:REACT_79086 "SLC-mediated transmembrane transport, Plasmodium falciparum" +xref: Reactome:REACT_79921 "SLC-mediated transmembrane transport, Saccharomyces cerevisiae" +xref: Reactome:REACT_80022 "ABC-family proteins mediated transport, Bos taurus" +xref: Reactome:REACT_80510 "ABC-family proteins mediated transport, Rattus norvegicus" +xref: Reactome:REACT_80848 "ABC-family proteins mediated transport, Schizosaccharomyces pombe" +xref: Reactome:REACT_80977 "ABC-family proteins mediated transport, Caenorhabditis elegans" +xref: Reactome:REACT_81024 "Transmembrane transport of small molecules, Oryza sativa" +xref: Reactome:REACT_81153 "SLC-mediated transmembrane transport, Mus musculus" +xref: Reactome:REACT_82725 "SLC-mediated transmembrane transport, Rattus norvegicus" +xref: Reactome:REACT_83770 "Transmembrane transport of small molecules, Escherichia coli" +xref: Reactome:REACT_86135 "ABC-family proteins mediated transport, Oryza sativa" +xref: Reactome:REACT_86409 "Transmembrane transport of small molecules, Drosophila melanogaster" +xref: Reactome:REACT_86576 "Transmembrane transport of small molecules, Schizosaccharomyces pombe" +xref: Reactome:REACT_87124 "SLC-mediated transmembrane transport, Oryza sativa" +xref: Reactome:REACT_88059 "ABC-family proteins mediated transport, Xenopus tropicalis" +xref: Reactome:REACT_88521 "Transmembrane transport of small molecules, Taeniopygia guttata" +xref: Reactome:REACT_88894 "Transmembrane transport of small molecules, Gallus gallus" +xref: Reactome:REACT_89376 "SLC-mediated transmembrane transport, Schizosaccharomyces pombe" +xref: Reactome:REACT_91272 "ABC-family proteins mediated transport, Arabidopsis thaliana" +xref: Reactome:REACT_91803 "SLC-mediated transmembrane transport, Mycobacterium tuberculosis" +xref: Reactome:REACT_92006 "Transmembrane transport of small molecules, Mycobacterium tuberculosis" +xref: Reactome:REACT_92624 "ABC-family proteins mediated transport, Gallus gallus" +xref: Reactome:REACT_93747 "Transmembrane transport of small molecules, Dictyostelium discoideum" +xref: Reactome:REACT_94160 "Transmembrane transport of small molecules, Mus musculus" +xref: Reactome:REACT_94393 "ABC-family proteins mediated transport, Drosophila melanogaster" +xref: Reactome:REACT_94944 "ABC-family proteins mediated transport, Danio rerio" +xref: Reactome:REACT_94972 "SLC-mediated transmembrane transport, Dictyostelium discoideum" +xref: Reactome:REACT_96633 "Transmembrane transport of small molecules, Sus scrofa" +xref: Reactome:REACT_96636 "SLC-mediated transmembrane transport, Arabidopsis thaliana" +xref: Reactome:REACT_97365 "Transmembrane transport of small molecules, Arabidopsis thaliana" +xref: Reactome:REACT_97867 "ABC-family proteins mediated transport, Saccharomyces cerevisiae" +xref: Reactome:REACT_98509 "Transmembrane transport of small molecules, Xenopus tropicalis" +xref: Reactome:REACT_98716 "SLC-mediated transmembrane transport, Drosophila melanogaster" +xref: Reactome:REACT_99579 "Transmembrane transport of small molecules, Danio rerio" +xref: Reactome:REACT_99829 "ABC-family proteins mediated transport, Dictyostelium discoideum" +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0044765 ! single-organism transport + +[Term] +id: GO:0055086 +name: nucleobase-containing small molecule metabolic process +namespace: biological_process +def: "The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide." [GOC:vw] +subset: goslim_pombe +subset: goslim_yeast +subset: gosubset_prok +synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] +synonym: "nucleobase, nucleoside and nucleotide metabolism" EXACT [] +xref: Reactome:REACT_100770 "Metabolism of nucleotides, Plasmodium falciparum" +xref: Reactome:REACT_105851 "Metabolism of nucleotides, Schizosaccharomyces pombe" +xref: Reactome:REACT_107755 "Metabolism of nucleotides, Mycobacterium tuberculosis" +xref: Reactome:REACT_107894 "Metabolism of nucleotides, Rattus norvegicus" +xref: Reactome:REACT_116039 "Nucleotide metabolism, Gallus gallus" +xref: Reactome:REACT_1698 "Metabolism of nucleotides, Homo sapiens" +xref: Reactome:REACT_28046 "Metabolism of nucleotides, Drosophila melanogaster" +xref: Reactome:REACT_29205 "Metabolism of nucleotides, Dictyostelium discoideum" +xref: Reactome:REACT_29767 "Metabolism of nucleotides, Saccharomyces cerevisiae" +xref: Reactome:REACT_31512 "Metabolism of nucleotides, Sus scrofa" +xref: Reactome:REACT_33967 "Metabolism of nucleotides, Mus musculus" +xref: Reactome:REACT_77113 "Metabolism of nucleotides, Taeniopygia guttata" +xref: Reactome:REACT_78257 "Metabolism of nucleotides, Staphylococcus aureus N315" +xref: Reactome:REACT_82673 "Metabolism of nucleotides, Caenorhabditis elegans" +xref: Reactome:REACT_82902 "Metabolism of nucleotides, Canis familiaris" +xref: Reactome:REACT_82978 "Metabolism of nucleotides, Escherichia coli" +xref: Reactome:REACT_83845 "Metabolism of nucleotides, Bos taurus" +xref: Reactome:REACT_86759 "Metabolism of nucleotides, Oryza sativa" +xref: Reactome:REACT_90903 "Metabolism of nucleotides, Gallus gallus" +xref: Reactome:REACT_96600 "Metabolism of nucleotides, Danio rerio" +xref: Reactome:REACT_97332 "Metabolism of nucleotides, Arabidopsis thaliana" +xref: Reactome:REACT_99343 "Metabolism of nucleotides, Xenopus tropicalis" +is_a: GO:0006139 ! nucleobase-containing compound metabolic process +is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:0044763 ! single-organism cellular process + +[Term] +id: GO:0055088 +name: lipid homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of lipid within an organism or cell." [GOC:BHF, GOC:rl] +is_a: GO:0048878 ! chemical homeostasis + +[Term] +id: GO:0055092 +name: sterol homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of sterol within an organism or cell." [GOC:BHF, GOC:rl] +is_a: GO:0055088 ! lipid homeostasis + +[Term] +id: GO:0055123 +name: digestive system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the digestive system over time, from its formation to the mature structure. The digestive system is the entire structure in which digestion takes place. Digestion is all of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:jid] +is_a: GO:0048731 ! system development + +[Term] +id: GO:0060004 +name: reflex +namespace: biological_process +def: "An automatic response to a stimulus beginning with a nerve impulse from a receptor and ending with the action of an effector such as a gland or a muscle. Signaling never reaches a level of consciousness." [GOC:dph, ISBN:087797099] +xref: Wikipedia:Reflex +is_a: GO:0009605 ! response to external stimulus + +[Term] +id: GO:0060013 +name: righting reflex +namespace: biological_process +def: "A reflex process in which an animal immediately tries to turn over after being placed in a supine position." [GOC:dph, PMID:8635460] +synonym: "righting response" EXACT [GOC:dph] +is_a: GO:0060004 ! reflex + +[Term] +id: GO:0060019 +name: radial glial cell differentiation +namespace: biological_process +def: "The process in which neuroepithelial cells of the neural tube give rise to radial glial cells, specialized bipotential progenitors cells of the brain. Differentiation includes the processes involved in commitment of a cell to a specific fate." [GOC:dph] +is_a: GO:0010001 ! glial cell differentiation + +[Term] +id: GO:0060021 +name: palate development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities." [GOC:dph, ISBN:0721662544] +synonym: "palatum development" EXACT [ISBN:0721662544] +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0060026 +name: convergent extension +namespace: biological_process +def: "The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis." [GOC:dgf, GOC:dph, PMID:12062082] +xref: Wikipedia:Convergent_extension +is_a: GO:0002009 ! morphogenesis of an epithelium + +[Term] +id: GO:0060028 +name: convergent extension involved in axis elongation +namespace: biological_process +def: "The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis contributing to the lengthening of the axis of an organism." [GOC:dph, PMID:12062082] +is_a: GO:0060026 ! convergent extension +intersection_of: GO:0060026 ! convergent extension +intersection_of: part_of GO:0003401 ! axis elongation +relationship: part_of GO:0003401 ! axis elongation + +[Term] +id: GO:0060029 +name: convergent extension involved in organogenesis +namespace: biological_process +def: "The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis contribution to the shaping of an organ." [GOC:dph, PMID:12062082] +is_a: GO:0060026 ! convergent extension +intersection_of: GO:0060026 ! convergent extension +intersection_of: part_of GO:0048513 ! organ development + +[Term] +id: GO:0060033 +name: anatomical structure regression +namespace: biological_process +def: "The developmental process in which an anatomical stucture is destroyed as a part of its normal progression." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0009653 ! anatomical structure morphogenesis + +[Term] +id: GO:0060038 +name: cardiac muscle cell proliferation +namespace: biological_process +def: "The expansion of a cardiac muscle cell population by cell division." [GOC:dph, GOC:rph, PMID:11161571] +synonym: "cardiac myocyte proliferation" EXACT [] +synonym: "cardiomyocyte proliferation" RELATED [GOC:dph, PMID:10074473] +synonym: "heart muscle cell proliferation" EXACT [] +is_a: GO:0014855 ! striated muscle cell proliferation +relationship: part_of GO:0055017 ! cardiac muscle tissue growth + +[Term] +id: GO:0060039 +name: pericardium development +namespace: biological_process +def: "The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery." [GOC:dph, GOC:rph, PMID:15138308, PMID:16376438] +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0060041 +name: retina development in camera-type eye +namespace: biological_process +alt_id: GO:0002073 +def: "The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC:bf, GOC:dph, ISBN:0815340729] +synonym: "retina development in camera-style eye" EXACT [] +synonym: "retinal development" RELATED [GOC:dph, GOC:tb] +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0043010 ! camera-type eye development + +[Term] +id: GO:0060042 +name: retina morphogenesis in camera-type eye +namespace: biological_process +def: "The process in which the anatomical structure of the retina is generated and organized." [GOC:bf, GOC:dph, GOC:mtg_sensu] +synonym: "retina morphogenesis in camera-style eye" EXACT [] +synonym: "retinogenesis" EXACT [] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048593 ! camera-type eye morphogenesis +relationship: part_of GO:0060041 ! retina development in camera-type eye + +[Term] +id: GO:0060047 +name: heart contraction +namespace: biological_process +def: "The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body." [GOC:dph] +synonym: "cardiac contraction" RELATED [] +synonym: "heart beating" EXACT [] +synonym: "hemolymph circulation" RELATED [] +is_a: GO:0003015 ! heart process +relationship: part_of GO:0008015 ! blood circulation + +[Term] +id: GO:0060054 +name: positive regulation of epithelial cell proliferation involved in wound healing +namespace: biological_process +def: "Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury." [GOC:dph] +is_a: GO:0050679 ! positive regulation of epithelial cell proliferation +intersection_of: GO:0050679 ! positive regulation of epithelial cell proliferation +intersection_of: part_of GO:0042060 ! wound healing +relationship: part_of GO:0042060 ! wound healing + +[Term] +id: GO:0060055 +name: angiogenesis involved in wound healing +namespace: biological_process +def: "Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to a damaged tissue, following an injury." [GOC:dph, PMID:15039218] +is_a: GO:0001525 ! angiogenesis +intersection_of: GO:0001525 ! angiogenesis +intersection_of: part_of GO:0042060 ! wound healing +relationship: part_of GO:0042060 ! wound healing + +[Term] +id: GO:0060059 +name: embryonic retina morphogenesis in camera-type eye +namespace: biological_process +def: "The process in which the anatomical structure of the retina is generated and organized in a camera-type eye during the embryonic life stage." [GOC:dgh, GOC:dph] +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0060042 ! retina morphogenesis in camera-type eye + +[Term] +id: GO:0060061 +name: Spemann organizer formation +namespace: biological_process +def: "Formation of the specialized region on the dorsalmost side of the embryo that acts as the main signaling center establishing the vertebrate body plan." [GOC:bf, GOC:dph] +synonym: "Spemann's organizer formation" EXACT [] +synonym: "Spemann-Mangold organizer formation" EXACT [] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0031128 ! developmental induction + +[Term] +id: GO:0060065 +name: uterus development +namespace: biological_process +def: "The reproductive developmental process whose specific outcome is the progression of the uterus over time, from its formation to the mature structure." [GOC:dph, GOC:ebc] +synonym: "Mullerian tract development" RELATED [] +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +is_a: GO:0048608 ! reproductive structure development + +[Term] +id: GO:0060066 +name: oviduct development +namespace: biological_process +def: "The reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism." [GOC:dph, GOC:ebc, http://www.thefreedictionary.com/oviduct] +synonym: "fallopian tube development" NARROW [GOC:bf] +synonym: "Mullerian tract development" RELATED [] +is_a: GO:0035295 ! tube development +is_a: GO:0048608 ! reproductive structure development + +[Term] +id: GO:0060067 +name: cervix development +namespace: biological_process +def: "The reproductive developmental process whose specific outcome is the progression of the cervix over time, from its formation to the mature structure." [GOC:dph, GOC:ebc] +synonym: "Mullerian tract development" RELATED [] +is_a: GO:0048608 ! reproductive structure development + +[Term] +id: GO:0060068 +name: vagina development +namespace: biological_process +def: "The reproductive developmental process whose specific outcome is the progression of the vagina over time, from its formation to the mature structure." [GOC:dph, GOC:ebc] +is_a: GO:0030540 ! female genitalia development + +[Term] +id: GO:0060070 +name: canonical Wnt signaling pathway +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes." [GOC:bf, GOC:dph, PMID:11532397, PMID:19619488] +synonym: "canonical Wnt receptor signaling pathway" EXACT [GOC:signaling] +synonym: "canonical Wnt-activated signaling pathway" EXACT [GOC:signaling] +synonym: "frizzled-1 receptor signaling pathway" NARROW [] +synonym: "Wnt receptor signaling pathway through beta-catenin" EXACT [GOC:mtg_signal] +synonym: "Wnt receptor signaling pathway via beta-catenin" EXACT [] +synonym: "Wnt receptor signalling pathway through beta-catenin" EXACT [] +is_a: GO:0016055 ! Wnt signaling pathway + +[Term] +id: GO:0060071 +name: Wnt signaling pathway, planar cell polarity pathway +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity." [GOC:bf, GOC:dph, PMID:11532397] +synonym: "non-canonical Wnt signaling pathway" RELATED [GOC:bf] +synonym: "PCP pathway" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb] +synonym: "planar cell polarity pathway" EXACT [GOC:cjm] +synonym: "Wnt receptor signaling pathway, planar cell polarity pathway" EXACT [] +synonym: "Wnt receptor signalling pathway, planar cell polarity pathway" EXACT [] +synonym: "Wnt-activated signaling pathway, planar cell polarity pathway" EXACT [GOC:signaling] +synonym: "Wnt-JNK signaling pathway" RELATED [GOC:bf] +synonym: "Wnt-PCP signaling pathway" RELATED [GOC:rph] +is_a: GO:0035567 ! non-canonical Wnt signaling pathway +is_a: GO:0090175 ! regulation of establishment of planar polarity + +[Term] +id: GO:0060089 +name: molecular transducer activity +namespace: molecular_function +def: "The molecular function that accepts an input of one form and creates an output of a different form." [GOC:mtg_MIT_16mar07] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0060126 +name: somatotropin secreting cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a somatotropin secreting cell. A somatotropin secreting cell is an acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin." [GOC:dph] +synonym: "growth hormone secreting cell differentiation" EXACT [] +synonym: "somatotrope differentiation" RELATED [] +synonym: "somatotroph differentiation" RELATED [] +synonym: "somatotrophin secreting cell differentiation" EXACT [] +synonym: "somatotropic cell differentiation" RELATED [] +synonym: "somatrophic cell differentiation" RELATED [] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0021984 ! adenohypophysis development + +[Term] +id: GO:0060129 +name: thyroid-stimulating hormone-secreting cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a thyroid-stimulating hormone-secreting cell. A thyroid-stimulating hormone-secreting cell is a basophil cell of the anterior pituitary that produces thyroid-stimulating hormone, thyrotrophin." [GOC:dph] +synonym: "beta-basophil differentiation" EXACT [] +synonym: "thyroid stimulating hormone secreting cell differentiation" EXACT [] +synonym: "thyrotrope differentiation" EXACT [] +synonym: "thyrotroph differentiation" EXACT [] +synonym: "TSH-secreting cell differentiation" EXACT [] +is_a: GO:0002067 ! glandular epithelial cell differentiation +is_a: GO:0061101 ! neuroendocrine cell differentiation +relationship: part_of GO:0021984 ! adenohypophysis development + +[Term] +id: GO:0060135 +name: maternal process involved in female pregnancy +namespace: biological_process +def: "A reproductive process occurring in the mother that allows an embryo or fetus to develop within it." [GOC:dph] +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048609 ! multicellular organismal reproductive process +relationship: part_of GO:0007565 ! female pregnancy + +[Term] +id: GO:0060157 +name: urinary bladder development +namespace: biological_process +def: "The process whose specific outcome is the progression of the urinary bladder over time, from its formation to the mature structure. The urinary bladder is an elastic, muscular sac situated in the anterior part of the pelvic cavity in which urine collects before excretion." [GOC:dph, GOC:ln] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0072001 ! renal system development + +[Term] +id: GO:0060173 +name: limb development +namespace: biological_process +def: "The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin." [GOC:dgh, GOC:dph, PMID:11487378] +synonym: "limb bud development" NARROW [GOC:dph] +xref: Wikipedia:Limb_development +is_a: GO:0048736 ! appendage development + +[Term] +id: GO:0060218 +name: hematopoietic stem cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a hematopoietic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC:bf, GOC:dph, GOC:rl, PMID:15378083] +synonym: "haematopoietic stem cell differentiation" EXACT [] +synonym: "haemopoietic stem cell differentiation" EXACT [] +synonym: "hemopoietic stem cell differentiation" EXACT [] +is_a: GO:0002244 ! hematopoietic progenitor cell differentiation +is_a: GO:0048863 ! stem cell differentiation +relationship: part_of GO:0030097 ! hemopoiesis + +[Term] +id: GO:0060231 +name: mesenchymal to epithelial transition +namespace: biological_process +def: "A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell." [GOC:ascb_2009, GOC:dph, GOC:tb] +synonym: "mesenchymal-epithelial transition" EXACT [GOC:dph] +is_a: GO:0003382 ! epithelial cell morphogenesis + +[Term] +id: GO:0060249 +name: anatomical structure homeostasis +namespace: biological_process +def: "A homeostatic process involved in the maintenance of an internal steady state within a defined anatomical structure of an organism, including control of cellular proliferation and death and control of metabolic function. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph] +synonym: "anatomical structure maintenance" EXACT [GOC:dph] +is_a: GO:0042592 ! homeostatic process + +[Term] +id: GO:0060255 +name: regulation of macromolecule metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] +subset: gosubset_prok +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0043170 ! macromolecule metabolic process +relationship: regulates GO:0043170 ! macromolecule metabolic process + +[Term] +id: GO:0060260 +name: regulation of transcription initiation from RNA polymerase II promoter +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH] +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:2000142 ! regulation of DNA-templated transcription, initiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter +relationship: regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter + +[Term] +id: GO:0060271 +name: cilium morphogenesis +namespace: biological_process +def: "A process that is carried out at the cellular level and in which the structure of a cilium is organized." [GOC:BHF, GOC:dph] +comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. +synonym: "cilium organization" RELATED [GOC:dph] +is_a: GO:0048858 ! cell projection morphogenesis + +[Term] +id: GO:0060272 +name: embryonic skeletal joint morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of skeletal joints are generated and organized during the embryonic phase. A skeletal joint is the connecting structure between the bones of the skeleton." [GOC:bf, GOC:BHF, GOC:dph, UBERON:0000982] +is_a: GO:0048704 ! embryonic skeletal system morphogenesis +relationship: part_of GO:0072498 ! embryonic skeletal joint development + +[Term] +id: GO:0060284 +name: regulation of cell development +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:dph, GOC:tb] +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048468 ! cell development +relationship: regulates GO:0048468 ! cell development + +[Term] +id: GO:0060322 +name: head development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development + +[Term] +id: GO:0060323 +name: head morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the head are generated and organized. The head is the anterior-most division of the body." [GOC:dph] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0010171 ! body morphogenesis +relationship: part_of GO:0060322 ! head development + +[Term] +id: GO:0060324 +name: face development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0060322 ! head development + +[Term] +id: GO:0060325 +name: face morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head." [GOC:dph] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0060323 ! head morphogenesis +relationship: part_of GO:0060324 ! face development + +[Term] +id: GO:0060326 +name: cell chemotaxis +namespace: biological_process +def: "The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." [GOC:dph] +is_a: GO:0006935 ! chemotaxis +is_a: GO:0016477 ! cell migration +is_a: GO:0070887 ! cellular response to chemical stimulus + +[Term] +id: GO:0060337 +name: type I interferon signaling pathway +namespace: biological_process +def: "A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, GOC:dph, GOC:signaling, PR:000025848] +synonym: "type I interferon-activated signaling pathway" EXACT [GOC:signaling] +synonym: "type I interferon-mediated signaling pathway" RELATED [GOC:signaling] +synonym: "type I interferon-mediated signalling pathway" EXACT [GOC:mah] +xref: Reactome:REACT_25162 "Interferon alpha/beta signaling, Homo sapiens" +is_a: GO:0019221 ! cytokine-mediated signaling pathway +is_a: GO:0071357 ! cellular response to type I interferon + +[Term] +id: GO:0060338 +name: regulation of type I interferon-mediated signaling pathway +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor." [GOC:dph] +synonym: "regulation of type I interferon-mediated signalling pathway" EXACT [GOC:mah] +xref: Reactome:REACT_25216 "Regulation of IFNA signaling, Homo sapiens" +is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway +is_a: GO:0045088 ! regulation of innate immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060337 ! type I interferon signaling pathway +relationship: regulates GO:0060337 ! type I interferon signaling pathway + +[Term] +id: GO:0060340 +name: positive regulation of type I interferon-mediated signaling pathway +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor." [GOC:dph] +synonym: "positive regulation of type I interferon-mediated signalling pathway" EXACT [GOC:mah] +is_a: GO:0001961 ! positive regulation of cytokine-mediated signaling pathway +is_a: GO:0060338 ! regulation of type I interferon-mediated signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060337 ! type I interferon signaling pathway +relationship: positively_regulates GO:0060337 ! type I interferon signaling pathway + +[Term] +id: GO:0060341 +name: regulation of cellular localization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell." [GOC:dph, GOC:tb] +synonym: "regulation of cellular localisation" EXACT [GOC:mah] +is_a: GO:0032879 ! regulation of localization +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051641 ! cellular localization +relationship: regulates GO:0051641 ! cellular localization + +[Term] +id: GO:0060343 +name: trabecula formation +namespace: biological_process +def: "The process of creating a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue." [GOC:dph] +synonym: "trabecula biogenesis" RELATED [GOC:dph] +synonym: "trabeculation" EXACT [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0009887 ! organ morphogenesis +relationship: part_of GO:0061383 ! trabecula morphogenesis + +[Term] +id: GO:0060346 +name: bone trabecula formation +namespace: biological_process +def: "The process of creating a trabecula in the bone. A trabecula is a tissue element in the form of a small beam, strut or rod." [GOC:dph] +synonym: "bone trabecula biogenesis" RELATED [GOC:dph] +synonym: "bone trabeculation" EXACT [GOC:dph] +synonym: "skeletal trabecula biogenesis" RELATED [GOC:dph] +synonym: "skeletal trabecula formation" EXACT [GOC:dph] +synonym: "skeletal trabeculation" EXACT [GOC:dph] +is_a: GO:0060343 ! trabecula formation +relationship: part_of GO:0048705 ! skeletal system morphogenesis +relationship: part_of GO:0061430 ! bone trabecula morphogenesis + +[Term] +id: GO:0060348 +name: bone development +namespace: biological_process +def: "The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001501 ! skeletal system development + +[Term] +id: GO:0060349 +name: bone morphogenesis +namespace: biological_process +def: "The process in which bones are generated and organized." [GOC:dph] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0048705 ! skeletal system morphogenesis +relationship: part_of GO:0060348 ! bone development + +[Term] +id: GO:0060411 +name: cardiac septum morphogenesis +namespace: biological_process +alt_id: GO:0003280 +def: "The process in which the anatomical structure of a cardiac septum is generated and organized. A cardiac septum is a partition that separates parts of the heart." [GOC:dph, GOC:mtg_heart] +synonym: "heart septum morphogenesis" EXACT [] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0003206 ! cardiac chamber morphogenesis +relationship: part_of GO:0003279 ! cardiac septum development + +[Term] +id: GO:0060412 +name: ventricular septum morphogenesis +namespace: biological_process +def: "The developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another." [GOC:dph] +synonym: "interventricular septum morphogenesis" EXACT [GOC:dph] +is_a: GO:0060411 ! cardiac septum morphogenesis +relationship: part_of GO:0003281 ! ventricular septum development + +[Term] +id: GO:0060415 +name: muscle tissue morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of muscle tissue are generated and organized. Muscle tissue consists of a set of cells that are part of an organ and carry out a contractive function." [GOC:dph] +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0048644 ! muscle organ morphogenesis + +[Term] +id: GO:0060419 +name: heart growth +namespace: biological_process +def: "The increase in size or mass of the heart." [GOC:dph, GOC:tb] +is_a: GO:0035265 ! organ growth +relationship: part_of GO:0007507 ! heart development + +[Term] +id: GO:0060423 +name: foregut regionalization +namespace: biological_process +def: "The pattern specification process that results in the spatial subdivision of an axis or axes along the foregut to define an area or volume in which specific patterns of cell differentiation will take place." [GOC:dph, GOC:mtg_lung] +is_a: GO:0009952 ! anterior/posterior pattern specification + +[Term] +id: GO:0060424 +name: lung field specification +namespace: biological_process +def: "The process that results in the delineation of a specific region of the foregut into the area in which the lung will develop." [GOC:dph, GOC:mtg_lung] +synonym: "lung specification" EXACT [GOC:dph, GOC:mtg_lung] +is_a: GO:0010092 ! specification of organ identity +is_a: GO:0060423 ! foregut regionalization +relationship: part_of GO:0060431 ! primary lung bud formation + +[Term] +id: GO:0060425 +name: lung morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the lung are generated and organized." [GOC:dph] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0060428 +name: lung epithelium development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of the lung epithelium from an initial condition to its mature state. This process begins with the formation of lung epithelium and ends with the mature structure. The lung epithelium is the specialized epithelium that lines the inside of the lung." [GOC:dph, GOC:mtg_lung] +synonym: "pulmonary epithelium development" EXACT [GOC:dph, GOC:mtg_lung] +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0060429 +name: epithelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." [GOC:dph, GOC:mtg_lung] +is_a: GO:0009888 ! tissue development + +[Term] +id: GO:0060431 +name: primary lung bud formation +namespace: biological_process +def: "The morphogenetic process in which the foregut region specified to become the lung forms the initial left and right buds." [GOC:dph, GOC:mtg_lung] +synonym: "lung formation" EXACT [GOC:dph] +is_a: GO:0016331 ! morphogenesis of embryonic epithelium +is_a: GO:0048645 ! organ formation +is_a: GO:0060441 ! epithelial tube branching involved in lung morphogenesis +is_a: GO:0060572 ! morphogenesis of an epithelial bud + +[Term] +id: GO:0060433 +name: bronchus development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a bronchus from an initial condition to its mature state. This process begins with the formation of the bronchus and ends with the mature structure. The bronchus is the portion of the airway that connects to the lungs." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0060541 ! respiratory system development + +[Term] +id: GO:0060438 +name: trachea development +namespace: biological_process +def: "The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048513 ! organ development +relationship: part_of GO:0060541 ! respiratory system development + +[Term] +id: GO:0060439 +name: trachea morphogenesis +namespace: biological_process +def: "The process in which a trachea is generated and organized. The trachea is the portion of the airway that attaches to the bronchi as it branches." [GOC:dph] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0060438 ! trachea development + +[Term] +id: GO:0060440 +name: trachea formation +namespace: biological_process +def: "The process pertaining to the initial formation of a trachea from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the trachea is recognizable. The trachea is the portion of the airway that attaches to the bronchi as it branches." [GOC:dph] +is_a: GO:0048645 ! organ formation +relationship: part_of GO:0060439 ! trachea morphogenesis + +[Term] +id: GO:0060441 +name: epithelial tube branching involved in lung morphogenesis +namespace: biological_process +def: "The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units." [GOC:dph, GOC:mtg_lung] +synonym: "lung branching morphogenesis" EXACT [GOC:dph] +is_a: GO:0048754 ! branching morphogenesis of an epithelial tube +intersection_of: GO:0048754 ! branching morphogenesis of an epithelial tube +intersection_of: part_of GO:0060425 ! lung morphogenesis +relationship: part_of GO:0060425 ! lung morphogenesis + +[Term] +id: GO:0060442 +name: branching involved in prostate gland morphogenesis +namespace: biological_process +def: "The process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem." [GOC:dph] +synonym: "prostate branching" RELATED [GOC:dph] +synonym: "prostate gland branching morphogenesis" EXACT [GOC:dph] +is_a: GO:0060740 ! prostate gland epithelium morphogenesis +is_a: GO:0061138 ! morphogenesis of a branching epithelium +intersection_of: GO:0061138 ! morphogenesis of a branching epithelium +intersection_of: part_of GO:0060512 ! prostate gland morphogenesis + +[Term] +id: GO:0060443 +name: mammary gland morphogenesis +namespace: biological_process +def: "The process in which anatomical structures of the mammary gland are generated and organized. Morphogenesis refers to the creation of shape. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." [GOC:dph] +is_a: GO:0022612 ! gland morphogenesis +relationship: part_of GO:0030879 ! mammary gland development + +[Term] +id: GO:0060444 +name: branching involved in mammary gland duct morphogenesis +namespace: biological_process +def: "The process in which the branching structure of the mammary gland duct is generated and organized. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." [GOC:dph] +synonym: "mammary gland branching morphogenesis" EXACT [GOC:dph] +is_a: GO:0048754 ! branching morphogenesis of an epithelial tube +intersection_of: GO:0061138 ! morphogenesis of a branching epithelium +intersection_of: part_of GO:0060603 ! mammary gland duct morphogenesis +relationship: part_of GO:0060603 ! mammary gland duct morphogenesis + +[Term] +id: GO:0060479 +name: lung cell differentiation +namespace: biological_process +def: "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features of a mature cell found in the lung. Differentiation includes the processes involved in commitment of a cell to a specific fate." [GOC:dph, GOC:mtg_lung] +synonym: "pulmonary cell differentiation" EXACT [GOC:dph] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0060482 +name: lobar bronchus development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a lobar bronchus from an initial condition to its mature state. This process begins with the formation of the lobar bronchus and ends with the mature structure. The lobar bronchus is the major airway within the respiratory tree that starts by division of the principal bronchi on both sides and ends at the point of its own subdivision into tertiary or segmental bronchi." [GOC:dph, GOC:mtg_lung] +is_a: GO:0060433 ! bronchus development + +[Term] +id: GO:0060484 +name: lung-associated mesenchyme development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a lung-associated mesenchyme from an initial condition to its mature state. This process begins with the formation of lung-associated mesenchyme and ends with the mature structure. Lung-associated mesenchyme is the tissue made up of loosely connected mesenchymal cells in the lung." [GOC:dph, GOC:mtg_lung] +synonym: "lung mesenchyme development" EXACT [GOC:dph] +synonym: "pulmonary mesenchyme development" EXACT [GOC:dph] +is_a: GO:0060485 ! mesenchyme development +relationship: part_of GO:0030324 ! lung development + +[Term] +id: GO:0060485 +name: mesenchyme development +namespace: biological_process +def: "The process whose specific outcome is the progression of a mesenchymal tissue over time, from its formation to the mature structure. A mesenchymal tissue is made up of loosely packed stellate cells." [GOC:dph] +synonym: "mesenchymal development" EXACT [GOC:dph] +is_a: GO:0009888 ! tissue development +relationship: part_of GO:0048513 ! organ development + +[Term] +id: GO:0060487 +name: lung epithelial cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell that contributes to the epithelium of the lung." [GOC:dph] +synonym: "pulmonary epithelial cell differentiation" RELATED [GOC:dph] +is_a: GO:0030855 ! epithelial cell differentiation +is_a: GO:0060479 ! lung cell differentiation +relationship: part_of GO:0060428 ! lung epithelium development + +[Term] +id: GO:0060491 +name: regulation of cell projection assembly +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of cell projection assembly." [GOC:dph, GOC:tb] +synonym: "regulation of cell projection formation" RELATED [GOC:dph, GOC:tb] +is_a: GO:0031344 ! regulation of cell projection organization +is_a: GO:0044087 ! regulation of cellular component biogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030031 ! cell projection assembly +relationship: regulates GO:0030031 ! cell projection assembly + +[Term] +id: GO:0060492 +name: lung induction +namespace: biological_process +def: "The close range interaction of two or more cells or tissues that causes the cells of the foregut to change their fates and specify the development of the lung." [GOC:dph] +is_a: GO:0001759 ! organ induction +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0061046 ! regulation of branching involved in lung morphogenesis +relationship: positively_regulates GO:0060424 ! lung field specification + +[Term] +id: GO:0060501 +name: positive regulation of epithelial cell proliferation involved in lung morphogenesis +namespace: biological_process +def: "Any process that increases the rate or frequency of epithelial cell proliferation that results in the lung attaining its shape." [GOC:dph] +is_a: GO:0050679 ! positive regulation of epithelial cell proliferation +is_a: GO:2000794 ! regulation of epithelial cell proliferation involved in lung morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis +relationship: positively_regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis + +[Term] +id: GO:0060502 +name: epithelial cell proliferation involved in lung morphogenesis +namespace: biological_process +def: "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the lung." [GOC:dph] +is_a: GO:0050673 ! epithelial cell proliferation +intersection_of: GO:0050673 ! epithelial cell proliferation +intersection_of: part_of GO:0060425 ! lung morphogenesis +relationship: part_of GO:0060425 ! lung morphogenesis +relationship: part_of GO:0060428 ! lung epithelium development + +[Term] +id: GO:0060512 +name: prostate gland morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a prostate gland are generated and organized." [GOC:dph, PMID:18977204] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0009887 ! organ morphogenesis +is_a: GO:0022612 ! gland morphogenesis +is_a: GO:0044702 ! single organism reproductive process +relationship: part_of GO:0030850 ! prostate gland development + +[Term] +id: GO:0060513 +name: prostatic bud formation +namespace: biological_process +def: "The morphogenetic process in which a region of the fetal urogenital sinus epithelium is specified to become the prostate, resulting in prostate bud outgrowth." [GOC:dph, PMID:18977204] +synonym: "primary prostate bud formation" EXACT [GOC:dph] +synonym: "prostate ductal budding" EXACT [GOC:dph, PMID:11401393] +synonym: "prostate gland formation" EXACT [GOC:dph] +is_a: GO:0016331 ! morphogenesis of embryonic epithelium +is_a: GO:0048645 ! organ formation +is_a: GO:0060572 ! morphogenesis of an epithelial bud +is_a: GO:0060601 ! lateral sprouting from an epithelium +is_a: GO:0060740 ! prostate gland epithelium morphogenesis + +[Term] +id: GO:0060525 +name: prostate glandular acinus development +namespace: biological_process +def: "The progression of a glandular acinus of the prostate gland over time, from its initial formation to the mature structure. The glandular acini are the saclike structures of the gland." [GOC:dph, PMID:18977204] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030850 ! prostate gland development + +[Term] +id: GO:0060526 +name: prostate glandular acinus morphogenesis +namespace: biological_process +def: "The process in which the prostate glandular acini are generated and organized. The glandular acini are the saclike structures of the gland." [GOC:dph] +is_a: GO:0060740 ! prostate gland epithelium morphogenesis +relationship: part_of GO:0060525 ! prostate glandular acinus development + +[Term] +id: GO:0060527 +name: prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis +namespace: biological_process +def: "The branching morphogenesis process in which the prostate epithelial cords branch freely to create the structure of the prostate acini." [GOC:dph, PMID:18977204] +is_a: GO:0060442 ! branching involved in prostate gland morphogenesis +relationship: part_of GO:0060526 ! prostate glandular acinus morphogenesis + +[Term] +id: GO:0060534 +name: trachea cartilage development +namespace: biological_process +def: "The process whose specific outcome is the progression of the tracheal cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." [GOC:dph] +is_a: GO:0051216 ! cartilage development +relationship: part_of GO:0060438 ! trachea development +created_by: dph +creation_date: 2009-04-10T09:00:18Z + +[Term] +id: GO:0060535 +name: trachea cartilage morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of cartilage in the trachea are generated and organized." [GOC:dph] +is_a: GO:0060536 ! cartilage morphogenesis +relationship: part_of GO:0060439 ! trachea morphogenesis +relationship: part_of GO:0060534 ! trachea cartilage development +created_by: dph +creation_date: 2009-04-10T09:07:48Z + +[Term] +id: GO:0060536 +name: cartilage morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of cartilage are generated and organized." [GOC:dph] +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0009887 ! organ morphogenesis +relationship: part_of GO:0051216 ! cartilage development +created_by: dph +creation_date: 2009-04-10T09:13:27Z + +[Term] +id: GO:0060537 +name: muscle tissue development +namespace: biological_process +def: "The progression of muscle tissue over time, from its initial formation to its mature state. Muscle tissue is a contractile tissue made up of actin and myosin fibers." [GOC:dph] +is_a: GO:0009888 ! tissue development +created_by: dph +creation_date: 2009-04-10T08:05:37Z + +[Term] +id: GO:0060538 +name: skeletal muscle organ development +namespace: biological_process +def: "The progression of a skeletal muscle organ over time from its initial formation to its mature state. A skeletal muscle organ includes the skeletal muscle tissue and its associated connective tissue." [GOC:dph] +is_a: GO:0007517 ! muscle organ development +created_by: dph +creation_date: 2009-04-10T08:25:12Z + +[Term] +id: GO:0060541 +name: respiratory system development +namespace: biological_process +def: "The progression of the respiratory system over time from its formation to its mature structure. The respiratory system carries out respiratory gaseous exchange." [GOC:dph] +is_a: GO:0048731 ! system development +created_by: dph +creation_date: 2009-04-10T08:55:42Z + +[Term] +id: GO:0060548 +name: negative regulation of cell death +namespace: biological_process +def: "Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0010941 ! regulation of cell death +is_a: GO:0048523 ! negative regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008219 ! cell death +relationship: negatively_regulates GO:0008219 ! cell death +created_by: dph +creation_date: 2009-04-13T01:56:10Z + +[Term] +id: GO:0060560 +name: developmental growth involved in morphogenesis +namespace: biological_process +def: "The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape." [GOC:dph] +synonym: "differential growth" EXACT [GOC:dph] +is_a: GO:0048589 ! developmental growth +intersection_of: GO:0048589 ! developmental growth +intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis +relationship: part_of GO:0009653 ! anatomical structure morphogenesis +created_by: dph +creation_date: 2009-04-28T08:42:53Z + +[Term] +id: GO:0060561 +name: apoptotic process involved in morphogenesis +namespace: biological_process +def: "Any apoptotic process that contributes to the shaping of an anatomical structure." [GOC:dph, GOC:mtg_apoptosis] +synonym: "apoptosis involved in development" RELATED [] +synonym: "apoptosis involved in morphogenesis" NARROW [] +synonym: "morphogenetic apoptosis" RELATED [GOC:dph] +is_a: GO:0006915 ! apoptotic process +is_a: GO:0010623 ! developmental programmed cell death +intersection_of: GO:0006915 ! apoptotic process +intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis +relationship: part_of GO:0009653 ! anatomical structure morphogenesis +created_by: dph +creation_date: 2009-04-28T09:17:27Z + +[Term] +id: GO:0060562 +name: epithelial tube morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [GOC:dph] +is_a: GO:0002009 ! morphogenesis of an epithelium +is_a: GO:0035239 ! tube morphogenesis +created_by: dph +creation_date: 2009-04-28T09:33:36Z + +[Term] +id: GO:0060563 +name: neuroepithelial cell differentiation +namespace: biological_process +def: "The process in which epiblast cells acquire specialized features of neuroepithelial cells." [GOC:dph, GOC:tb] +is_a: GO:0002065 ! columnar/cuboidal epithelial cell differentiation +created_by: dph +creation_date: 2009-04-29T01:50:05Z + +[Term] +id: GO:0060571 +name: morphogenesis of an epithelial fold +namespace: biological_process +def: "The morphogenetic process in which an epithelial sheet bends along a linear axis." [GOC:dph] +synonym: "epithelial folding" EXACT [GOC:dph] +synonym: "folding of an epithelial sheet" RELATED [GOC:dph] +is_a: GO:0002009 ! morphogenesis of an epithelium +created_by: dph +creation_date: 2009-04-30T09:27:17Z + +[Term] +id: GO:0060572 +name: morphogenesis of an epithelial bud +namespace: biological_process +def: "The morphogenetic process in which a bud forms from an epithelial sheet. A bud is a protrusion that forms form the sheet by localized folding." [GOC:dph] +is_a: GO:0060571 ! morphogenesis of an epithelial fold +created_by: dph +creation_date: 2009-04-30T09:38:35Z + +[Term] +id: GO:0060592 +name: mammary gland formation +namespace: biological_process +def: "The process pertaining to the initial formation of the mammary gland from unspecified parts. The process begins with formation of the mammary line and ends when the solid mammary bud invades the primary mammary mesenchyme." [GOC:dph, PMID:16168142, PMID:17120154] +synonym: "mammary bud formation" RELATED [GOC:dph] +synonym: "mammary line formation" NARROW [GOC:dph] +synonym: "mammary placode formation" NARROW [GOC:dph] +synonym: "mammary sprout formation" RELATED [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0060443 ! mammary gland morphogenesis +created_by: dph +creation_date: 2009-05-13T08:47:52Z + +[Term] +id: GO:0060596 +name: mammary placode formation +namespace: biological_process +def: "The developmental process in which the mammary placode forms. The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper." [GOC:dph, PMID:16168142] +is_a: GO:0060788 ! ectodermal placode formation +relationship: part_of GO:0060592 ! mammary gland formation +created_by: dph +creation_date: 2009-05-13T11:55:20Z + +[Term] +id: GO:0060599 +name: lateral sprouting involved in mammary gland duct morphogenesis +namespace: biological_process +def: "The process in which a branch forms along the side of a mammary duct." [GOC:dph, PMID:17120154] +synonym: "mammary gland duct secondary branching" EXACT [GOC:dph] +is_a: GO:0060601 ! lateral sprouting from an epithelium +intersection_of: GO:0060601 ! lateral sprouting from an epithelium +intersection_of: part_of GO:0060444 ! branching involved in mammary gland duct morphogenesis +relationship: part_of GO:0060444 ! branching involved in mammary gland duct morphogenesis +created_by: dph +creation_date: 2009-05-13T12:38:06Z + +[Term] +id: GO:0060600 +name: dichotomous subdivision of an epithelial terminal unit +namespace: biological_process +def: "The process in which an epithelial cord, rod or tube bifurcates at its end." [GOC:dph] +synonym: "primary branching of an epithelium" RELATED [GOC:dph] +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0061138 ! morphogenesis of a branching epithelium +created_by: dph +creation_date: 2009-05-14T02:14:50Z + +[Term] +id: GO:0060601 +name: lateral sprouting from an epithelium +namespace: biological_process +def: "The process in which a branch forms along the side of an epithelium." [GOC:dph] +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0061138 ! morphogenesis of a branching epithelium +created_by: dph +creation_date: 2009-05-14T02:33:01Z + +[Term] +id: GO:0060602 +name: branch elongation of an epithelium +namespace: biological_process +def: "The growth process in which a branch increases in length from its base to its tip." [GOC:dph] +is_a: GO:0003401 ! axis elongation +relationship: part_of GO:0061138 ! morphogenesis of a branching epithelium +created_by: dph +creation_date: 2009-05-14T02:45:44Z + +[Term] +id: GO:0060603 +name: mammary gland duct morphogenesis +namespace: biological_process +def: "The process in which anatomical structures of the mammary ducts are generated and organized. Mammary ducts are epithelial tubes that transport milk." [GOC:dph, PMID:17120154] +is_a: GO:0060562 ! epithelial tube morphogenesis +relationship: part_of GO:0060443 ! mammary gland morphogenesis +relationship: part_of GO:0061180 ! mammary gland epithelium development +created_by: dph +creation_date: 2009-05-15T09:22:25Z + +[Term] +id: GO:0060606 +name: tube closure +namespace: biological_process +def: "Creation of the central hole of a tube in an anatomical structure by sealing the edges of an epithelial fold." [GOC:dph] +is_a: GO:0035148 ! tube formation +created_by: dph +creation_date: 2009-05-15T09:44:07Z + +[Term] +id: GO:0060612 +name: adipose tissue development +namespace: biological_process +def: "The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat." [GOC:dph] +synonym: "adipogenesis" RELATED [GOC:mah, GOC:sl] +is_a: GO:0061448 ! connective tissue development +relationship: part_of GO:0048513 ! organ development +created_by: dph +creation_date: 2009-05-15T12:36:28Z + +[Term] +id: GO:0060627 +name: regulation of vesicle-mediated transport +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell." [GOC:dph, GOC:tb] +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0016192 ! vesicle-mediated transport +relationship: regulates GO:0016192 ! vesicle-mediated transport +created_by: dph +creation_date: 2009-05-18T02:29:43Z + +[Term] +id: GO:0060633 +name: negative regulation of transcription initiation from RNA polymerase II promoter +namespace: biological_process +def: "Any process that decreases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH] +is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter +is_a: GO:2000143 ! negative regulation of DNA-templated transcription, initiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter +relationship: negatively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter +created_by: dph +creation_date: 2009-05-18T03:11:26Z + +[Term] +id: GO:0060638 +name: mesenchymal-epithelial cell signaling +namespace: biological_process +def: "Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted." [GOC:dph] +synonym: "mesenchymal-epithelial cell signalling" EXACT [GOC:mah] +is_a: GO:0007267 ! cell-cell signaling +created_by: dph +creation_date: 2009-05-19T03:59:05Z + +[Term] +id: GO:0060644 +name: mammary gland epithelial cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland." [GOC:dph] +is_a: GO:0030855 ! epithelial cell differentiation +relationship: part_of GO:0061180 ! mammary gland epithelium development +created_by: dph +creation_date: 2009-05-29T08:03:07Z + +[Term] +id: GO:0060669 +name: embryonic placenta morphogenesis +namespace: biological_process +def: "The process in which the embryonic placenta is generated and organized." [GOC:dph] +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0001892 ! embryonic placenta development +created_by: dph +creation_date: 2009-06-02T09:33:37Z + +[Term] +id: GO:0060675 +name: ureteric bud morphogenesis +namespace: biological_process +def: "The process in which the ureteric bud is generated and organized." [GOC:dph, GOC:mtg_kidney_jan10] +is_a: GO:0060562 ! epithelial tube morphogenesis +relationship: part_of GO:0001657 ! ureteric bud development +created_by: dph +creation_date: 2009-06-02T01:31:41Z + +[Term] +id: GO:0060678 +name: dichotomous subdivision of terminal units involved in ureteric bud branching +namespace: biological_process +def: "The process in which a ureteric bud bifurcates at its end." [GOC:dph, PMID:16916378] +synonym: "bifid subdivision of terminal units involved in ureteric bud branching" EXACT [GOC:dph, PMID:16916378] +is_a: GO:0060600 ! dichotomous subdivision of an epithelial terminal unit +intersection_of: GO:0060600 ! dichotomous subdivision of an epithelial terminal unit +intersection_of: part_of GO:0001658 ! branching involved in ureteric bud morphogenesis +relationship: part_of GO:0001658 ! branching involved in ureteric bud morphogenesis +created_by: dph +creation_date: 2009-06-02T02:18:17Z + +[Term] +id: GO:0060685 +name: regulation of prostatic bud formation +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of prostatic bud formation, the morphogenetic process in which a region of the fetal urogenital sinus epithelium is specified to become the prostate, resulting in prostate bud outgrowth." [GOC:dph] +is_a: GO:0003156 ! regulation of organ formation +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0060688 ! regulation of morphogenesis of a branching structure +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060513 ! prostatic bud formation +relationship: regulates GO:0060513 ! prostatic bud formation +created_by: dph +creation_date: 2009-06-05T12:29:26Z + +[Term] +id: GO:0060686 +name: negative regulation of prostatic bud formation +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of prostatic bud formation, the morphogenetic process in which a region of the fetal urogenital sinus epithelium is specified to become the prostate, resulting in prostate bud outgrowth." [GOC:dph] +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0060685 ! regulation of prostatic bud formation +is_a: GO:2000242 ! negative regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0060513 ! prostatic bud formation +relationship: negatively_regulates GO:0060513 ! prostatic bud formation +created_by: dph +creation_date: 2009-06-05T12:35:25Z + +[Term] +id: GO:0060687 +name: regulation of branching involved in prostate gland morphogenesis +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of prostate gland branching, the process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem." [GOC:dph] +is_a: GO:0060688 ! regulation of morphogenesis of a branching structure +is_a: GO:2000027 ! regulation of organ morphogenesis +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060442 ! branching involved in prostate gland morphogenesis +relationship: regulates GO:0060442 ! branching involved in prostate gland morphogenesis +created_by: dph +creation_date: 2009-06-05T12:37:14Z + +[Term] +id: GO:0060688 +name: regulation of morphogenesis of a branching structure +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized." [GOC:dph] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001763 ! morphogenesis of a branching structure +relationship: regulates GO:0001763 ! morphogenesis of a branching structure +created_by: dph +creation_date: 2009-06-05T12:41:44Z + +[Term] +id: GO:0060710 +name: chorio-allantoic fusion +namespace: biological_process +def: "The cell-cell adhesion process in which the cells of the chorion fuse to the cells of the allantois." [GOC:dph] +is_a: GO:0016337 ! cell-cell adhesion +relationship: part_of GO:0060713 ! labyrinthine layer morphogenesis +created_by: dph +creation_date: 2009-06-09T03:24:27Z + +[Term] +id: GO:0060711 +name: labyrinthine layer development +namespace: biological_process +def: "The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001892 ! embryonic placenta development +created_by: dph +creation_date: 2009-06-09T03:27:43Z + +[Term] +id: GO:0060713 +name: labyrinthine layer morphogenesis +namespace: biological_process +def: "The process in which the labyrinthine layer of the placenta is generated and organized." [GOC:dph] +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0060669 ! embryonic placenta morphogenesis +relationship: part_of GO:0060711 ! labyrinthine layer development +created_by: dph +creation_date: 2009-06-10T08:10:19Z + +[Term] +id: GO:0060740 +name: prostate gland epithelium morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of epithelia of the prostate gland are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube." [GOC:dph] +is_a: GO:0002009 ! morphogenesis of an epithelium +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0044702 ! single organism reproductive process +relationship: part_of GO:0060512 ! prostate gland morphogenesis +created_by: dph +creation_date: 2009-06-16T09:23:22Z + +[Term] +id: GO:0060742 +name: epithelial cell differentiation involved in prostate gland development +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell of the prostate gland." [GOC:dph] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0030855 ! epithelial cell differentiation +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0048610 ! cellular process involved in reproduction +intersection_of: GO:0030855 ! epithelial cell differentiation +intersection_of: part_of GO:0030850 ! prostate gland development +relationship: part_of GO:0030850 ! prostate gland development +created_by: dph +creation_date: 2009-06-16T09:32:34Z + +[Term] +id: GO:0060744 +name: mammary gland branching involved in thelarche +namespace: biological_process +def: "The process in which the branching structure of the mammary gland duct is generated and organized during the period of sexual maturity in mammals. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." [GOC:dph, PMID:19261859] +synonym: "mammary gland branching involved in puberty" RELATED [GOC:dph] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0060444 ! branching involved in mammary gland duct morphogenesis +intersection_of: GO:0060444 ! branching involved in mammary gland duct morphogenesis +intersection_of: part_of GO:0042695 ! thelarche +relationship: part_of GO:0042695 ! thelarche +created_by: dph +creation_date: 2009-06-22T08:12:17Z + +[Term] +id: GO:0060745 +name: mammary gland branching involved in pregnancy +namespace: biological_process +def: "The process in which the branching structure of the mammary gland duct is generated and organized as a part of pregnancy." [GOC:dph, PMID:19261859] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0060135 ! maternal process involved in female pregnancy +is_a: GO:0060444 ! branching involved in mammary gland duct morphogenesis +created_by: dph +creation_date: 2009-06-22T08:25:19Z + +[Term] +id: GO:0060748 +name: tertiary branching involved in mammary gland duct morphogenesis +namespace: biological_process +def: "The branching process in which the mammary gland ducts form tertiary branches off of the secondary branches as part of diestrus and pregnancy." [GOC:dph, PMID:18614704] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0044702 ! single organism reproductive process +is_a: GO:0060444 ! branching involved in mammary gland duct morphogenesis +relationship: part_of GO:0060745 ! mammary gland branching involved in pregnancy +created_by: dph +creation_date: 2009-06-22T10:44:51Z + +[Term] +id: GO:0060749 +name: mammary gland alveolus development +namespace: biological_process +def: "The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061377 ! mammary gland lobule development +created_by: dph +creation_date: 2009-06-22T10:52:12Z + +[Term] +id: GO:0060750 +name: epithelial cell proliferation involved in mammary gland duct elongation +namespace: biological_process +def: "The multiplication or reproduction of mammary gland branch epithelial cells, resulting in the elongation of the branch. The mammary gland branch differs from the bud in that it is not the initial curved portion of the outgrowth." [GOC:dph] +is_a: GO:0033598 ! mammary gland epithelial cell proliferation +intersection_of: GO:0033598 ! mammary gland epithelial cell proliferation +intersection_of: part_of GO:0060751 ! branch elongation involved in mammary gland duct branching +relationship: part_of GO:0060751 ! branch elongation involved in mammary gland duct branching +created_by: dph +creation_date: 2009-06-22T10:58:12Z + +[Term] +id: GO:0060751 +name: branch elongation involved in mammary gland duct branching +namespace: biological_process +def: "The developmental growth process in which a branch of a mammary gland duct elongates." [GOC:dph] +synonym: "mammary gland duct branch elongation" EXACT [GOC:dph] +is_a: GO:0060602 ! branch elongation of an epithelium +intersection_of: GO:0060602 ! branch elongation of an epithelium +intersection_of: part_of GO:0060603 ! mammary gland duct morphogenesis +relationship: part_of GO:0060444 ! branching involved in mammary gland duct morphogenesis +created_by: dph +creation_date: 2009-06-22T11:02:44Z + +[Term] +id: GO:0060759 +name: regulation of response to cytokine stimulus +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of a response to cytokine stimulus." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034097 ! response to cytokine +relationship: regulates GO:0034097 ! response to cytokine +created_by: dph +creation_date: 2009-06-22T02:56:12Z + +[Term] +id: GO:0060760 +name: positive regulation of response to cytokine stimulus +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of a response to cytokine stimulus." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0048584 ! positive regulation of response to stimulus +is_a: GO:0060759 ! regulation of response to cytokine stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0034097 ! response to cytokine +relationship: positively_regulates GO:0034097 ! response to cytokine +created_by: dph +creation_date: 2009-06-22T02:58:04Z + +[Term] +id: GO:0060762 +name: regulation of branching involved in mammary gland duct morphogenesis +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of branching involved in mammary gland duct morphogenesis." [GOC:dph] +is_a: GO:0060688 ! regulation of morphogenesis of a branching structure +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060444 ! branching involved in mammary gland duct morphogenesis +relationship: regulates GO:0060444 ! branching involved in mammary gland duct morphogenesis +created_by: dph +creation_date: 2009-06-22T05:20:33Z + +[Term] +id: GO:0060764 +name: cell-cell signaling involved in mammary gland development +namespace: biological_process +def: "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the mammary gland, from its initial state to the mature structure." [GOC:dph] +synonym: "cell-cell signalling involved in mammary gland development" EXACT [GOC:mah] +is_a: GO:0007267 ! cell-cell signaling +intersection_of: GO:0007267 ! cell-cell signaling +intersection_of: part_of GO:0030879 ! mammary gland development +relationship: part_of GO:0030879 ! mammary gland development +created_by: dph +creation_date: 2009-07-06T09:24:53Z + +[Term] +id: GO:0060765 +name: regulation of androgen receptor signaling pathway +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the androgen receptor signaling pathway." [GOC:dph] +synonym: "regulation of androgen receptor signalling pathway" EXACT [GOC:mah] +is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030521 ! androgen receptor signaling pathway +relationship: regulates GO:0030521 ! androgen receptor signaling pathway +created_by: dph +creation_date: 2009-07-06T11:07:38Z + +[Term] +id: GO:0060766 +name: negative regulation of androgen receptor signaling pathway +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of the androgen receptor signaling pathway." [GOC:dph] +synonym: "negative regulation of androgen receptor signalling pathway" EXACT [GOC:mah] +is_a: GO:0033144 ! negative regulation of intracellular steroid hormone receptor signaling pathway +is_a: GO:0060765 ! regulation of androgen receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030521 ! androgen receptor signaling pathway +relationship: negatively_regulates GO:0030521 ! androgen receptor signaling pathway +created_by: dph +creation_date: 2009-07-06T11:09:36Z + +[Term] +id: GO:0060767 +name: epithelial cell proliferation involved in prostate gland development +namespace: biological_process +def: "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the progression of the prostate gland over time." [GOC:dph] +is_a: GO:0044763 ! single-organism cellular process +is_a: GO:0048610 ! cellular process involved in reproduction +is_a: GO:0050673 ! epithelial cell proliferation +intersection_of: GO:0050673 ! epithelial cell proliferation +intersection_of: part_of GO:0030850 ! prostate gland development +relationship: part_of GO:0030850 ! prostate gland development +created_by: dph +creation_date: 2009-07-08T07:32:34Z + +[Term] +id: GO:0060768 +name: regulation of epithelial cell proliferation involved in prostate gland development +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time." [GOC:dph] +is_a: GO:0050678 ! regulation of epithelial cell proliferation +is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development +relationship: regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development +created_by: dph +creation_date: 2009-07-08T07:34:56Z + +[Term] +id: GO:0060769 +name: positive regulation of epithelial cell proliferation involved in prostate gland development +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time." [GOC:dph] +is_a: GO:0050679 ! positive regulation of epithelial cell proliferation +is_a: GO:0060768 ! regulation of epithelial cell proliferation involved in prostate gland development +is_a: GO:2000243 ! positive regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development +relationship: positively_regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development +created_by: dph +creation_date: 2009-07-08T07:38:02Z + +[Term] +id: GO:0060788 +name: ectodermal placode formation +namespace: biological_process +def: "The developmental process in which an ectodermal placode forms. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm." [GOC:dph, GOC:sdb_2009, GOC:tb] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0071697 ! ectodermal placode morphogenesis +created_by: dph +creation_date: 2009-08-04T12:15:57Z + +[Term] +id: GO:0060789 +name: hair follicle placode formation +namespace: biological_process +def: "The developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud." [GOC:dph, GOC:sdb_2009, GOC:tb] +is_a: GO:0060788 ! ectodermal placode formation +relationship: part_of GO:0001942 ! hair follicle development +created_by: dph +creation_date: 2009-08-04T12:18:26Z + +[Term] +id: GO:0060795 +name: cell fate commitment involved in formation of primary germ layer +namespace: biological_process +def: "The commitment of cells to specific cell fates of the endoderm, ectoderm, or mesoderm as a part of gastrulation." [GOC:dph, GOC:sdb_2009, GOC:tb] +is_a: GO:0045165 ! cell fate commitment +intersection_of: GO:0045165 ! cell fate commitment +intersection_of: part_of GO:0001704 ! formation of primary germ layer +relationship: part_of GO:0001704 ! formation of primary germ layer +created_by: dph +creation_date: 2009-08-04T03:11:22Z + +[Term] +id: GO:0060828 +name: regulation of canonical Wnt signaling pathway +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes." [GOC:dph, GOC:sdb_2009, GOC:tb] +synonym: "regulation of canonical Wnt receptor signaling pathway" EXACT [] +synonym: "regulation of canonical Wnt receptor signalling pathway" EXACT [GOC:mah] +synonym: "regulation of canonical Wnt-activated signaling pathway" EXACT [GOC:signaling] +synonym: "regulation of Wnt receptor signaling pathway through beta-catenin" EXACT [GOC:mtg_signal] +is_a: GO:0030111 ! regulation of Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060070 ! canonical Wnt signaling pathway +relationship: regulates GO:0060070 ! canonical Wnt signaling pathway +created_by: dph +creation_date: 2009-08-11T01:54:47Z + +[Term] +id: GO:0060840 +name: artery development +namespace: biological_process +def: "The progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed." [GOC:dph, GOC:sdb_2009, GOC:tb] +is_a: GO:0001568 ! blood vessel development +created_by: dph +creation_date: 2009-08-12T10:10:51Z + +[Term] +id: GO:0060856 +name: establishment of blood-brain barrier +namespace: biological_process +def: "Establishment of the barrier between the blood and the brain. The cells in the brain are packed tightly together preventing the passage of most molecules from the blood into the brain. Only lipid soluble molecules or those that are actively transported can pass through the blood-brain barrier." [GOC:dph, GOC:sart] +synonym: "establishment of BBB" EXACT [PMID:20080302] +is_a: GO:0048468 ! cell development +created_by: dph +creation_date: 2009-08-12T12:12:59Z + +[Term] +id: GO:0060907 +name: positive regulation of macrophage cytokine production +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:dph, GOC:tb] +is_a: GO:0010935 ! regulation of macrophage cytokine production +is_a: GO:0061081 ! positive regulation of myeloid leukocyte cytokine production involved in immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0010934 ! macrophage cytokine production +relationship: positively_regulates GO:0010934 ! macrophage cytokine production +created_by: dph +creation_date: 2009-09-04T02:32:18Z + +[Term] +id: GO:0060911 +name: cardiac cell fate commitment +namespace: biological_process +def: "The commitment of cells to specific cardiac cell fates and their capacity to differentiate into cardiac cells. Cardiac cells are cells that comprise the organ which pumps blood through the circulatory system." [GOC:mtg_heart] +is_a: GO:0045165 ! cell fate commitment +relationship: part_of GO:0035051 ! cardiocyte differentiation +created_by: dph +creation_date: 2009-09-17T08:47:00Z + +[Term] +id: GO:0060912 +name: cardiac cell fate specification +namespace: biological_process +def: "The process involved in the specification of cardiac cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment." [GOC:mtg_heart] +is_a: GO:0001708 ! cell fate specification +relationship: part_of GO:0060911 ! cardiac cell fate commitment +created_by: dph +creation_date: 2009-09-17T08:53:21Z + +[Term] +id: GO:0060914 +name: heart formation +namespace: biological_process +def: "The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable." [GOC:mtg_heart] +synonym: "cardiogenesis" RELATED [GOC:mtg_heart] +is_a: GO:0048645 ! organ formation +relationship: part_of GO:0003007 ! heart morphogenesis +created_by: dph +creation_date: 2009-09-17T09:02:13Z + +[Term] +id: GO:0060916 +name: mesenchymal cell proliferation involved in lung development +namespace: biological_process +def: "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population that contributes to the progression of the lung over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." [GOC:dph] +is_a: GO:0010463 ! mesenchymal cell proliferation +intersection_of: GO:0010463 ! mesenchymal cell proliferation +intersection_of: part_of GO:0030324 ! lung development +relationship: part_of GO:0030324 ! lung development +created_by: dph +creation_date: 2009-09-18T11:50:17Z + +[Term] +id: GO:0060923 +name: cardiac muscle cell fate commitment +namespace: biological_process +def: "The commitment of cells to specific cardiac muscle cell fates and their capacity to differentiate into cardiac muscle cells. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction." [GOC:mtg_heart] +synonym: "cardiomyocyte cell fate commitment" EXACT [GOC:mtg_heart] +synonym: "heart muscle cell fate commitment" EXACT [GOC:mtg_heart] +is_a: GO:0042693 ! muscle cell fate commitment +is_a: GO:0060911 ! cardiac cell fate commitment +relationship: part_of GO:0055007 ! cardiac muscle cell differentiation +created_by: dph +creation_date: 2009-09-29T11:13:32Z + +[Term] +id: GO:0060947 +name: cardiac vascular smooth muscle cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a cardiac vascular smooth muscle cell. A cardiac vascular smooth muscle cell covers the heart vasculature and lacks transverse striations in its constituent fibers." [GOC:mtg_heart] +synonym: "heart vascular smooth muscle cell differentiation" EXACT [GOC:mtg_heart] +is_a: GO:0035051 ! cardiocyte differentiation +is_a: GO:0035886 ! vascular smooth muscle cell differentiation +relationship: part_of GO:0060976 ! coronary vasculature development +created_by: dph +creation_date: 2009-09-29T02:56:08Z + +[Term] +id: GO:0060972 +name: left/right pattern formation +namespace: biological_process +def: "The pattern specification process that results in the subdivision of the left/right axis in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment." [GOC:mtg_heart] +is_a: GO:0003002 ! regionalization +created_by: dph +creation_date: 2009-10-06T10:25:58Z + +[Term] +id: GO:0060976 +name: coronary vasculature development +namespace: biological_process +def: "The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure." [GOC:mtg_heart] +synonym: "cardiac blood vessel development" EXACT [GOC:mtg_heart] +synonym: "cardiac vasculature development" EXACT [GOC:mtg_heart] +synonym: "coronary blood vessel development" EXACT [GOC:mtg_heart] +synonym: "heart blood vessel development" EXACT [GOC:mtg_heart] +synonym: "heart vasculature development" EXACT [GOC:mtg_heart] +is_a: GO:0001568 ! blood vessel development +relationship: part_of GO:0007507 ! heart development +created_by: dph +creation_date: 2009-10-06T12:15:23Z + +[Term] +id: GO:0060977 +name: coronary vasculature morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of blood vessels of the heart are generated and organized. The blood vessel is the vasculature carrying blood." [GOC:mtg_heart] +synonym: "cardiac blood vessel morphogenesis" EXACT [GOC:mtg_heart] +synonym: "cardiac vasculature morphogenesis" EXACT [GOC:mtg_heart] +synonym: "coronary blood vessel morphogenesis" EXACT [GOC:mtg_heart] +synonym: "heart blood vessel morphogenesis" EXACT [GOC:mtg_heart] +synonym: "heart vasculature morphogenesis" EXACT [GOC:mtg_heart] +is_a: GO:0048514 ! blood vessel morphogenesis +relationship: part_of GO:0060976 ! coronary vasculature development +created_by: dph +creation_date: 2009-10-06T12:28:23Z + +[Term] +id: GO:0060982 +name: coronary artery morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of coronary arteries are generated and organized. Coronary arteries are blood vessels that transport blood to the heart muscle." [GOC:mtg_heart] +is_a: GO:0048844 ! artery morphogenesis +is_a: GO:0060977 ! coronary vasculature morphogenesis +created_by: dph +creation_date: 2009-10-06T02:58:52Z + +[Term] +id: GO:0060983 +name: epicardium-derived cardiac vascular smooth muscle cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell derived from the epicardium acquires specialized features of a cardiac vascular smooth muscle cell. A cardiac vascular smooth muscle cell covers the heart vasculature and lacks transverse striations in its constituent fibers." [GOC:mtg_heart] +is_a: GO:0060947 ! cardiac vascular smooth muscle cell differentiation +created_by: dph +creation_date: 2009-10-06T03:05:33Z + +[Term] +id: GO:0060993 +name: kidney morphogenesis +namespace: biological_process +def: "Morphogenesis of a kidney. A kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." [GOC:dph, GOC:mtg_kidney_jan10] +is_a: GO:0009887 ! organ morphogenesis +relationship: part_of GO:0001822 ! kidney development +created_by: dph +creation_date: 2010-01-19T08:16:55Z + +[Term] +id: GO:0060996 +name: dendritic spine development +namespace: biological_process +def: "The process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0016358 ! dendrite development +created_by: dph +creation_date: 2010-01-20T09:06:33Z + +[Term] +id: GO:0060997 +name: dendritic spine morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission." [GOC:dph] +is_a: GO:0048812 ! neuron projection morphogenesis +is_a: GO:0097061 ! dendritic spine organization +relationship: part_of GO:0048813 ! dendrite morphogenesis +relationship: part_of GO:0060996 ! dendritic spine development +created_by: dph +creation_date: 2010-01-20T09:09:57Z + +[Term] +id: GO:0060998 +name: regulation of dendritic spine development +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure." [GOC:dph] +is_a: GO:0050773 ! regulation of dendrite development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060996 ! dendritic spine development +relationship: regulates GO:0060996 ! dendritic spine development +created_by: dph +creation_date: 2010-01-20T09:17:06Z + +[Term] +id: GO:0060999 +name: positive regulation of dendritic spine development +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure." [GOC:dph] +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0060998 ! regulation of dendritic spine development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060996 ! dendritic spine development +relationship: positively_regulates GO:0060996 ! dendritic spine development +created_by: dph +creation_date: 2010-01-20T09:27:21Z + +[Term] +id: GO:0061001 +name: regulation of dendritic spine morphogenesis +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission." [GOC:dph] +is_a: GO:0048814 ! regulation of dendrite morphogenesis +is_a: GO:0060998 ! regulation of dendritic spine development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060997 ! dendritic spine morphogenesis +relationship: regulates GO:0060997 ! dendritic spine morphogenesis +created_by: dph +creation_date: 2010-01-20T09:31:52Z + +[Term] +id: GO:0061003 +name: positive regulation of dendritic spine morphogenesis +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission." [GOC:dph] +is_a: GO:0031346 ! positive regulation of cell projection organization +is_a: GO:0060999 ! positive regulation of dendritic spine development +is_a: GO:0061001 ! regulation of dendritic spine morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060997 ! dendritic spine morphogenesis +relationship: positively_regulates GO:0060997 ! dendritic spine morphogenesis +created_by: dph +creation_date: 2010-01-20T09:36:54Z + +[Term] +id: GO:0061004 +name: pattern specification involved in kidney development +namespace: biological_process +def: "Any developmental process that results in the creation of defined areas or spaces within the kidney to which cells respond and eventually are instructed to differentiate." [GOC:dph, GOC:mtg_kidney_jan10] +synonym: "kidney pattern formation" RELATED [GOC:mtg_kidney_jan10] +synonym: "kidney pattern specification" EXACT [GOC:mtg_kidney_jan10] +synonym: "pattern formation involved in kidney development" RELATED [GOC:mtg_kidney_jan10] +is_a: GO:0007389 ! pattern specification process +intersection_of: GO:0007389 ! pattern specification process +intersection_of: part_of GO:0001822 ! kidney development +relationship: part_of GO:0001822 ! kidney development +relationship: part_of GO:0072048 ! renal system pattern specification +created_by: dph +creation_date: 2010-01-21T09:05:54Z + +[Term] +id: GO:0061005 +name: cell differentiation involved in kidney development +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the kidney as it progresses from its formation to the mature state." [GOC:mtg_kidney_jan10] +is_a: GO:0030154 ! cell differentiation +intersection_of: GO:0030154 ! cell differentiation +intersection_of: part_of GO:0001822 ! kidney development +relationship: part_of GO:0001822 ! kidney development +created_by: dph +creation_date: 2010-01-21T09:13:55Z + +[Term] +id: GO:0061008 +name: hepaticobiliary system development +namespace: biological_process +def: "The progression of the hepaticobiliary system over time, from its formation to the mature structure. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins." [GOC:dph] +synonym: "hepatobiliary system development" EXACT [GOC:dph] +is_a: GO:0048731 ! system development +created_by: dph +creation_date: 2010-01-22T09:11:59Z + +[Term] +id: GO:0061024 +name: membrane organization +namespace: biological_process +alt_id: GO:0016044 +def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] +subset: goslim_generic +synonym: "cellular membrane organisation" EXACT [GOC:curators] +synonym: "cellular membrane organization" EXACT [] +synonym: "membrane organisation" EXACT [GOC:mah] +synonym: "membrane organization and biogenesis" RELATED [GOC:mah] +xref: Reactome:REACT_101524 "Membrane Trafficking, Dictyostelium discoideum" +xref: Reactome:REACT_103082 "Membrane Trafficking, Schizosaccharomyces pombe" +xref: Reactome:REACT_11123 "Membrane Trafficking, Homo sapiens" +xref: Reactome:REACT_29278 "Membrane Trafficking, Sus scrofa" +xref: Reactome:REACT_32337 "Membrane Trafficking, Taeniopygia guttata" +xref: Reactome:REACT_33741 "Membrane Trafficking, Bos taurus" +xref: Reactome:REACT_34084 "Membrane Trafficking, Caenorhabditis elegans" +xref: Reactome:REACT_78213 "Membrane Trafficking, Plasmodium falciparum" +xref: Reactome:REACT_78288 "Membrane Trafficking, Xenopus tropicalis" +xref: Reactome:REACT_83546 "Membrane Trafficking, Oryza sativa" +xref: Reactome:REACT_86557 "Membrane Trafficking, Arabidopsis thaliana" +xref: Reactome:REACT_87431 "Membrane Trafficking, Drosophila melanogaster" +xref: Reactome:REACT_88307 "Membrane Trafficking, Mus musculus" +xref: Reactome:REACT_91154 "Membrane Trafficking, Saccharomyces cerevisiae" +xref: Reactome:REACT_93714 "Membrane Trafficking, Danio rerio" +xref: Reactome:REACT_95586 "Membrane Trafficking, Gallus gallus" +xref: Reactome:REACT_96516 "Membrane Trafficking, Canis familiaris" +xref: Reactome:REACT_97881 "Membrane Trafficking, Rattus norvegicus" +is_a: GO:0016043 ! cellular component organization +created_by: dph +creation_date: 2010-02-08T02:43:11Z + +[Term] +id: GO:0061025 +name: membrane fusion +namespace: biological_process +alt_id: GO:0006944 +def: "The membrane organization process that joins two lipid bilayers to form a single membrane." [GOC:dph, GOC:tb] +subset: goslim_yeast +synonym: "cellular membrane fusion" EXACT [] +xref: Wikipedia:Lipid_bilayer_fusion +is_a: GO:0061024 ! membrane organization +created_by: dph +creation_date: 2010-02-08T02:48:06Z + +[Term] +id: GO:0061028 +name: establishment of endothelial barrier +namespace: biological_process +def: "The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition." [GOC:dph] +is_a: GO:0001885 ! endothelial cell development +created_by: dph +creation_date: 2010-02-09T09:26:59Z + +[Term] +id: GO:0061030 +name: epithelial cell differentiation involved in mammary gland alveolus development +namespace: biological_process +def: "The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland alveolus." [GOC:dph, GOC:yaf] +is_a: GO:0060644 ! mammary gland epithelial cell differentiation +intersection_of: GO:0030855 ! epithelial cell differentiation +intersection_of: part_of GO:0060749 ! mammary gland alveolus development +relationship: part_of GO:0060749 ! mammary gland alveolus development +created_by: dph +creation_date: 2010-02-09T09:43:00Z + +[Term] +id: GO:0061035 +name: regulation of cartilage development +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." [GOC:dph] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051216 ! cartilage development +relationship: regulates GO:0051216 ! cartilage development +created_by: dph +creation_date: 2010-02-09T03:41:35Z + +[Term] +id: GO:0061036 +name: positive regulation of cartilage development +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." [GOC:dph] +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0061035 ! regulation of cartilage development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0051216 ! cartilage development +relationship: positively_regulates GO:0051216 ! cartilage development +created_by: dph +creation_date: 2010-02-09T03:41:35Z + +[Term] +id: GO:0061038 +name: uterus morphogenesis +namespace: biological_process +def: "The process in which anatomical structures of the uterus are generated and organized." [GOC:BHF, GOC:dph] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0009887 ! organ morphogenesis +is_a: GO:0044702 ! single organism reproductive process +relationship: part_of GO:0060065 ! uterus development +created_by: dph +creation_date: 2010-02-22T11:12:35Z + +[Term] +id: GO:0061041 +name: regulation of wound healing +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." [GOC:BHF, GOC:dph] +is_a: GO:0080134 ! regulation of response to stress +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042060 ! wound healing +relationship: regulates GO:0042060 ! wound healing +created_by: dph +creation_date: 2010-02-25T10:14:37Z + +[Term] +id: GO:0061042 +name: vascular wound healing +namespace: biological_process +def: "Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature." [GOC:BHF, GOC:dph] +is_a: GO:0060055 ! angiogenesis involved in wound healing +created_by: dph +creation_date: 2010-02-25T10:18:26Z + +[Term] +id: GO:0061043 +name: regulation of vascular wound healing +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature." [GOC:dph] +is_a: GO:0045765 ! regulation of angiogenesis +is_a: GO:0061041 ! regulation of wound healing +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061042 ! vascular wound healing +relationship: regulates GO:0061042 ! vascular wound healing +created_by: dph +creation_date: 2010-02-25T10:21:59Z + +[Term] +id: GO:0061045 +name: negative regulation of wound healing +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." [GOC:dph] +is_a: GO:0032102 ! negative regulation of response to external stimulus +is_a: GO:0061041 ! regulation of wound healing +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042060 ! wound healing +relationship: negatively_regulates GO:0042060 ! wound healing +created_by: dph +creation_date: 2010-02-25T10:33:30Z + +[Term] +id: GO:0061046 +name: regulation of branching involved in lung morphogenesis +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units." [GOC:dph, GOC:yaf] +is_a: GO:0060688 ! regulation of morphogenesis of a branching structure +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis +relationship: regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis +created_by: dph +creation_date: 2010-02-25T10:41:38Z + +[Term] +id: GO:0061047 +name: positive regulation of branching involved in lung morphogenesis +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units." [GOC:dph, GOC:yaf] +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +is_a: GO:0061046 ! regulation of branching involved in lung morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis +relationship: positively_regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis +created_by: dph +creation_date: 2010-02-25T10:50:01Z + +[Term] +id: GO:0061053 +name: somite development +namespace: biological_process +def: "The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo." [GOC:dph] +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0009790 ! embryo development +created_by: dph +creation_date: 2010-03-02T12:05:13Z + +[Term] +id: GO:0061054 +name: dermatome development +namespace: biological_process +def: "The progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061053 ! somite development +created_by: dph +creation_date: 2010-03-02T12:07:37Z + +[Term] +id: GO:0061061 +name: muscle structure development +namespace: biological_process +def: "The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +created_by: dph +creation_date: 2010-03-09T08:55:14Z + +[Term] +id: GO:0061081 +name: positive regulation of myeloid leukocyte cytokine production involved in immune response +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the production of a cytokine that contributes to the immune response." [GOC:BHF, GOC:dph] +synonym: "positive regulation of myeloid cell cytokine production involved in immune response" RELATED [GOC:dph] +is_a: GO:0002720 ! positive regulation of cytokine production involved in immune response +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061082 ! myeloid leukocyte cytokine production +relationship: positively_regulates GO:0061082 ! myeloid leukocyte cytokine production +created_by: dph +creation_date: 2010-04-13T11:26:41Z + +[Term] +id: GO:0061082 +name: myeloid leukocyte cytokine production +namespace: biological_process +def: "Any process that contributes to cytokine production by a myeloid cell." [GOC:dph] +is_a: GO:0002367 ! cytokine production involved in immune response +created_by: dph +creation_date: 2010-04-13T11:29:42Z + +[Term] +id: GO:0061097 +name: regulation of protein tyrosine kinase activity +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of protein tyrosine kinase activity." [GOC:dph, GOC:tb] +is_a: GO:0045859 ! regulation of protein kinase activity +is_a: GO:0050730 ! regulation of peptidyl-tyrosine phosphorylation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004713 ! protein tyrosine kinase activity +relationship: regulates GO:0004713 ! protein tyrosine kinase activity +created_by: dph +creation_date: 2010-04-26T02:34:53Z + +[Term] +id: GO:0061098 +name: positive regulation of protein tyrosine kinase activity +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity." [GOC:dph, GOC:tb] +is_a: GO:0045860 ! positive regulation of protein kinase activity +is_a: GO:0050731 ! positive regulation of peptidyl-tyrosine phosphorylation +is_a: GO:0061097 ! regulation of protein tyrosine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004713 ! protein tyrosine kinase activity +relationship: positively_regulates GO:0004713 ! protein tyrosine kinase activity +created_by: dph +creation_date: 2010-04-26T02:34:53Z + +[Term] +id: GO:0061101 +name: neuroendocrine cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a neuroendocrine cell. A neuroendocrine cell is a cell that receives input form a neuron which controls the secretion of an endocrine substance." [GOC:dph] +is_a: GO:0060563 ! neuroepithelial cell differentiation +created_by: dph +creation_date: 2010-04-28T09:42:20Z + +[Term] +id: GO:0061133 +name: endopeptidase activator activity +namespace: molecular_function +def: "Increases the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides." [GOC:dph, GOC:tb] +is_a: GO:0016504 ! peptidase activator activity +is_a: GO:0061135 ! endopeptidase regulator activity +relationship: part_of GO:0010950 ! positive regulation of endopeptidase activity +relationship: positively_regulates GO:0004175 ! endopeptidase activity +created_by: dph +creation_date: 2010-05-17T01:08:29Z + +[Term] +id: GO:0061134 +name: peptidase regulator activity +namespace: molecular_function +def: "Modulates the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds." [GOC:dph, GOC:tb] +is_a: GO:0030234 ! enzyme regulator activity +relationship: has_part GO:0002020 ! protease binding +relationship: part_of GO:0052547 ! regulation of peptidase activity +relationship: regulates GO:0008233 ! peptidase activity +created_by: dph +creation_date: 2010-05-17T01:15:24Z + +[Term] +id: GO:0061135 +name: endopeptidase regulator activity +namespace: molecular_function +def: "Modulates the activity of a peptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides." [GOC:dph, GOC:tb] +is_a: GO:0061134 ! peptidase regulator activity +relationship: part_of GO:0052548 ! regulation of endopeptidase activity +relationship: regulates GO:0004175 ! endopeptidase activity +created_by: dph +creation_date: 2010-05-17T01:19:36Z + +[Term] +id: GO:0061138 +name: morphogenesis of a branching epithelium +namespace: biological_process +def: "The process in which the anatomical structures of a branched epithelium are generated and organized." [GOC:dph] +is_a: GO:0001763 ! morphogenesis of a branching structure +is_a: GO:0002009 ! morphogenesis of an epithelium +created_by: dph +creation_date: 2010-05-25T09:05:34Z + +[Term] +id: GO:0061141 +name: lung ciliated cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a lung ciliated cell. A lung ciliated cell is a specialized lung epithelial cell that contains a motile cilium for moving substances released from lung secretory cells." [GOC:dph] +is_a: GO:0060487 ! lung epithelial cell differentiation +created_by: dph +creation_date: 2010-05-25T09:31:14Z + +[Term] +id: GO:0061154 +name: endothelial tube morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells." [GOC:dph, GOC:yaf] +is_a: GO:0003159 ! morphogenesis of an endothelium +is_a: GO:0060562 ! epithelial tube morphogenesis +created_by: dph +creation_date: 2010-06-15T09:05:00Z + +[Term] +id: GO:0061162 +name: establishment of monopolar cell polarity +namespace: biological_process +def: "The specification and formation of monopolar intracellular organization or cell growth patterns. Monopolar cell organization is directional organization along an axis." [GOC:dph, GOC:vw] +is_a: GO:0030010 ! establishment of cell polarity +is_a: GO:0061339 ! establishment or maintenance of monopolar cell polarity +created_by: dph +creation_date: 2010-06-23T09:30:59Z + +[Term] +id: GO:0061178 +name: regulation of insulin secretion involved in cellular response to glucose stimulus +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose." [GOC:BHF, GOC:dph] +synonym: "regulation of insulin secretion in response to glucose" EXACT [GOC:dph] +is_a: GO:0032844 ! regulation of homeostatic process +is_a: GO:0048583 ! regulation of response to stimulus +is_a: GO:0050796 ! regulation of insulin secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus +relationship: regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus +created_by: dph +creation_date: 2010-07-13T09:38:42Z + +[Term] +id: GO:0061180 +name: mammary gland epithelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of the mammary gland epithelium over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." [GOC:dph, GOC:yaf] +synonym: "breast epithelium development" EXACT [GOC:dph] +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0030879 ! mammary gland development +created_by: dph +creation_date: 2010-07-14T08:18:24Z + +[Term] +id: GO:0061183 +name: regulation of dermatome development +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin." [GOC:BHF, GOC:dph] +is_a: GO:0045995 ! regulation of embryonic development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061054 ! dermatome development +relationship: regulates GO:0061054 ! dermatome development +created_by: dph +creation_date: 2010-07-14T08:40:26Z + +[Term] +id: GO:0061184 +name: positive regulation of dermatome development +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin." [GOC:BHF, GOC:dph] +is_a: GO:0040019 ! positive regulation of embryonic development +is_a: GO:0061183 ! regulation of dermatome development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061054 ! dermatome development +relationship: positively_regulates GO:0061054 ! dermatome development +created_by: dph +creation_date: 2010-07-14T08:42:03Z + +[Term] +id: GO:0061185 +name: negative regulation of dermatome development +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin." [GOC:BHF, GOC:dph] +is_a: GO:0045992 ! negative regulation of embryonic development +is_a: GO:0061183 ! regulation of dermatome development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061054 ! dermatome development +relationship: negatively_regulates GO:0061054 ! dermatome development +created_by: dph +creation_date: 2010-07-14T08:43:08Z + +[Term] +id: GO:0061196 +name: fungiform papilla development +namespace: biological_process +def: "The progression of the fungiform papilla over time, from its formation to the mature structure. The fungiform papilla is a mushroom-shaped papilla of the tongue." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0043586 ! tongue development +created_by: dph +creation_date: 2010-07-27T12:23:48Z + +[Term] +id: GO:0061197 +name: fungiform papilla morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the fungiform papilla are generated and organized. The fungiform papilla is a mushroom-shaped papilla of the tongue." [GOC:dph] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0043587 ! tongue morphogenesis +relationship: part_of GO:0061196 ! fungiform papilla development +created_by: dph +creation_date: 2010-07-27T12:26:40Z + +[Term] +id: GO:0061198 +name: fungiform papilla formation +namespace: biological_process +def: "The developmental process pertaining to the initial formation of a spongiform papilla from unspecified parts. The fungiform papilla is a mushroom-shaped papilla of the tongue." [GOC:dph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0061197 ! fungiform papilla morphogenesis +created_by: dph +creation_date: 2010-07-27T12:29:03Z + +[Term] +id: GO:0061205 +name: paramesonephric duct development +namespace: biological_process +def: "The process whose specific outcome is the progression of the paramesonephric duct over time, from its formation to the mature structure. Mullerian ducts (or paramesonephric ducts) are paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, cervix, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin." [GOC:dph, GOC:yaf] +synonym: "Mullerian duct development" EXACT [GOC:dph] +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0048856 ! anatomical structure development +created_by: dph +creation_date: 2010-07-30T10:54:47Z + +[Term] +id: GO:0061245 +name: establishment or maintenance of bipolar cell polarity +namespace: biological_process +def: "Any cellular process that results in the specification, formation or maintenance of a bipolar intracellular organization or cell growth patterns." [GOC:dph, GOC:vw] +is_a: GO:0007163 ! establishment or maintenance of cell polarity +created_by: dph +creation_date: 2010-08-23T09:42:05Z + +[Term] +id: GO:0061298 +name: retina vasculature development in camera-type eye +namespace: biological_process +def: "The process whose specific outcome is the progression of the vasculature of the retina over time, from its formation to the mature structure." [GOC:BHF, GOC:dph] +synonym: "retinal vasculature development" EXACT [GOC:dph] +is_a: GO:0001944 ! vasculature development +relationship: part_of GO:0060041 ! retina development in camera-type eye +created_by: dph +creation_date: 2010-09-06T03:27:06Z + +[Term] +id: GO:0061299 +name: retina vasculature morphogenesis in camera-type eye +namespace: biological_process +def: "The process in which the vasculature of the retina is generated and organized." [GOC:BHF, GOC:dph] +synonym: "retinal vasculature morphogenesis" EXACT [GOC:dph] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0061298 ! retina vasculature development in camera-type eye +created_by: dph +creation_date: 2010-09-06T03:28:25Z + +[Term] +id: GO:0061304 +name: retinal blood vessel morphogenesis +namespace: biological_process +def: "The process whose specific outcome is the progression of a blood vessel of the retina over time, from its formation to the mature structure." [GOC:BHF, GOC:dph] +is_a: GO:0048514 ! blood vessel morphogenesis +is_a: GO:0061299 ! retina vasculature morphogenesis in camera-type eye +created_by: dph +creation_date: 2010-09-16T09:02:59Z + +[Term] +id: GO:0061307 +name: cardiac neural crest cell differentiation involved in heart development +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a cardiac neural crest cell that will migrate to the heart and contribute to its development. Cardiac neural crest cells are specialized cells that migrate toward the heart from the third, fourth and sixth pharyngeal arches." [GOC:dph, GOC:mtg_heart, PMID:19705442] +is_a: GO:0014033 ! neural crest cell differentiation +is_a: GO:0035051 ! cardiocyte differentiation +intersection_of: GO:0014033 ! neural crest cell differentiation +intersection_of: part_of GO:0007507 ! heart development +created_by: dph +creation_date: 2010-09-23T08:50:56Z + +[Term] +id: GO:0061310 +name: canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in cardiac neural crest cell differentiation." [GOC:dph, GOC:mtg_heart] +synonym: "canonical Wnt receptor signaling pathway involved in cardiac neural crest cell differentiation involved in heart development" EXACT [GOC:signaling] +synonym: "canonical Wnt receptor signalling pathway involved in cardiac neural crest cell differentiation involved in heart development" EXACT [GOC:mah] +synonym: "canonical Wnt-activated signaling pathway involved in cardiac neural crest cell differentiation involved in heart development" EXACT [GOC:signaling] +is_a: GO:0044335 ! canonical Wnt signaling pathway involved in neural crest cell differentiation +is_a: GO:0061316 ! canonical Wnt signaling pathway involved in heart development +intersection_of: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: part_of GO:0061307 ! cardiac neural crest cell differentiation involved in heart development +relationship: part_of GO:0061307 ! cardiac neural crest cell differentiation involved in heart development +created_by: dph +creation_date: 2010-09-23T09:12:36Z + +[Term] +id: GO:0061311 +name: cell surface receptor signaling pathway involved in heart development +namespace: biological_process +def: "Any series of molecular signals initiated by the binding of a receptor on the surface of a cell to a physiological ligand, which contributes to the progression of the heart over time." [GOC:dph, GOC:mtg_heart, GOC:signaling] +synonym: "cell surface receptor linked signaling pathway involved in heart development" EXACT [GOC:bf] +synonym: "cell surface receptor linked signalling pathway involved in heart development" EXACT [GOC:mah] +is_a: GO:0007166 ! cell surface receptor signaling pathway +intersection_of: GO:0007166 ! cell surface receptor signaling pathway +intersection_of: part_of GO:0007507 ! heart development +relationship: part_of GO:0007507 ! heart development +created_by: dph +creation_date: 2010-09-23T09:18:32Z + +[Term] +id: GO:0061316 +name: canonical Wnt signaling pathway involved in heart development +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contributes to the progression of the heart over time. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes." [GOC:mtg_heart] +synonym: "canonical Wnt receptor signaling pathway involved in heart development" EXACT [GOC:signaling] +synonym: "canonical Wnt receptor signalling pathway involved in heart development" EXACT [GOC:mah] +synonym: "canonical Wnt-activated signaling pathway involved in heart development" EXACT [GOC:signaling] +is_a: GO:0003306 ! Wnt signaling pathway involved in heart development +is_a: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: part_of GO:0007507 ! heart development +created_by: dph +creation_date: 2010-09-24T09:25:03Z + +[Term] +id: GO:0061317 +name: canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin and contributing to cardiac muscle cell fate commitment. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes." [GOC:mtg_heart, PMID:17576928] +synonym: "canonical Wnt receptor signaling pathway involved in cardiac muscle cell fate commitment" EXACT [GOC:signaling] +synonym: "canonical Wnt receptor signalling pathway involved in cardiac muscle cell fate commitment" EXACT [GOC:mah] +synonym: "canonical Wnt-activated signaling pathway involved in cardiac muscle cell fate commitment" EXACT [GOC:signaling] +is_a: GO:0061316 ! canonical Wnt signaling pathway involved in heart development +intersection_of: GO:0060070 ! canonical Wnt signaling pathway +intersection_of: part_of GO:0060923 ! cardiac muscle cell fate commitment +relationship: part_of GO:0060923 ! cardiac muscle cell fate commitment +created_by: dph +creation_date: 2010-09-24T09:29:21Z + +[Term] +id: GO:0061318 +name: renal filtration cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a renal filtration cell. Renal filtration cells are specialized cells of the renal system that filter fluids by charge, size or both. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [GOC:dph, GOC:mtg_kidney_jan10] +is_a: GO:0030154 ! cell differentiation +relationship: part_of GO:0072001 ! renal system development +created_by: dph +creation_date: 2010-09-24T12:18:35Z + +[Term] +id: GO:0061323 +name: cell proliferation involved in heart morphogenesis +namespace: biological_process +def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the heart." [GOC:dph, GOC:mtg_heart] +is_a: GO:0008283 ! cell proliferation +intersection_of: GO:0008283 ! cell proliferation +intersection_of: part_of GO:0003007 ! heart morphogenesis +relationship: part_of GO:0003007 ! heart morphogenesis +created_by: dph +creation_date: 2010-09-28T09:05:26Z + +[Term] +id: GO:0061324 +name: canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation +namespace: biological_process +def: "The canonical Wnt signaling pathway that contributes to the modulation of the expansion of a population of cardiac outflow tract cells." [GOC:dph, GOC:mtg_heart] +synonym: "canonical Wnt receptor signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation" EXACT [] +synonym: "canonical Wnt receptor signalling pathway involved in positive regulation of cardiac outflow tract cell proliferation" EXACT [GOC:mah] +synonym: "canonical Wnt-activated signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation" EXACT [GOC:signaling] +is_a: GO:0044340 ! canonical Wnt signaling pathway involved in regulation of cell proliferation +is_a: GO:0061316 ! canonical Wnt signaling pathway involved in heart development +is_a: GO:1901963 ! regulation of cell proliferation involved in outflow tract morphogenesis +relationship: regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis +created_by: dph +creation_date: 2010-09-28T09:19:37Z + +[Term] +id: GO:0061325 +name: cell proliferation involved in outflow tract morphogenesis +namespace: biological_process +def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the outflow tract." [GOC:dph, GOC:mtg_heart] +is_a: GO:0061323 ! cell proliferation involved in heart morphogenesis +intersection_of: GO:0008283 ! cell proliferation +intersection_of: part_of GO:0003151 ! outflow tract morphogenesis +relationship: part_of GO:0003151 ! outflow tract morphogenesis +created_by: dph +creation_date: 2010-09-28T09:29:30Z + +[Term] +id: GO:0061326 +name: renal tubule development +namespace: biological_process +def: "The progression of the renal tubule over time from its formation to the mature form. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis." [GOC:dph, GOC:mtg_kidney_jan10] +is_a: GO:0035295 ! tube development +relationship: part_of GO:0072001 ! renal system development +created_by: dph +creation_date: 2010-09-28T12:50:43Z + +[Term] +id: GO:0061333 +name: renal tubule morphogenesis +namespace: biological_process +def: "The process in which the renal tubule is generated by specification of cell fate, through the maintenance of cell polarity, regulated cell proliferation and morphogenetic cell rearrangements, shape changes and growth. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis." [GOC:dph, GOC:mtg_kidney_jan10] +is_a: GO:0060562 ! epithelial tube morphogenesis +relationship: part_of GO:0061326 ! renal tubule development +created_by: dph +creation_date: 2010-09-28T01:43:04Z + +[Term] +id: GO:0061339 +name: establishment or maintenance of monopolar cell polarity +namespace: biological_process +def: "Any cellular process that results in the specification, formation or maintenance of monopolar intracellular organization or cell growth patterns. Monopolar cell organization is directional organization along an axis." [GOC:dph, GOC:vw] +is_a: GO:0007163 ! establishment or maintenance of cell polarity +created_by: dph +creation_date: 2010-09-29T09:10:05Z + +[Term] +id: GO:0061341 +name: non-canonical Wnt signaling pathway involved in heart development +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via effectors other than beta-catenin and contributing to the progression of the heart over time." [GOC:dph, GOC:mtg_heart, PMID:16860783] +synonym: "non-canonical Wnt receptor signaling pathway involved in heart development" EXACT [] +synonym: "non-canonical Wnt receptor signalling pathway involved in heart development" EXACT [GOC:mah] +synonym: "non-canonical Wnt-activated signaling pathway involved in heart development" EXACT [GOC:signaling] +is_a: GO:0003306 ! Wnt signaling pathway involved in heart development +is_a: GO:0035567 ! non-canonical Wnt signaling pathway +intersection_of: GO:0035567 ! non-canonical Wnt signaling pathway +intersection_of: part_of GO:0007507 ! heart development +created_by: dph +creation_date: 2010-09-29T11:27:34Z + +[Term] +id: GO:0061346 +name: planar cell polarity pathway involved in heart morphogenesis +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity that contributes to the shaping of the heart." [GOC:dph, GOC:mtg_heart, PMID:16860783] +is_a: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway +is_a: GO:0061341 ! non-canonical Wnt signaling pathway involved in heart development +relationship: part_of GO:0003007 ! heart morphogenesis +created_by: dph +creation_date: 2010-09-30T12:47:24Z + +[Term] +id: GO:0061347 +name: planar cell polarity pathway involved in outflow tract morphogenesis +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity that contributes to the shaping of the outflow tract." [GOC:dph, GOC:mtg_heart, PMID:19056682] +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway +intersection_of: part_of GO:0003151 ! outflow tract morphogenesis +relationship: part_of GO:0003151 ! outflow tract morphogenesis +created_by: dph +creation_date: 2010-10-01T10:38:56Z + +[Term] +id: GO:0061348 +name: planar cell polarity pathway involved in ventricular septum morphogenesis +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity that contributes to the shaping of the ventricular septum." [GOC:dph, GOC:mtg_heart, PMID:19056682] +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: part_of GO:0060412 ! ventricular septum morphogenesis +created_by: dph +creation_date: 2010-10-01T10:47:49Z + +[Term] +id: GO:0061349 +name: planar cell polarity pathway involved in cardiac right atrium morphogenesis +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity that contributes to the shaping of the cardiac right atrium." [GOC:dph, GOC:mtg_heart, PMID:19056682] +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: part_of GO:0003213 ! cardiac right atrium morphogenesis +created_by: dph +creation_date: 2010-10-01T10:52:01Z + +[Term] +id: GO:0061350 +name: planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity that contributes to the shaping of the cardiac muscle tissue." [GOC:dph, GOC:mtg_heart, PMID:19056682] +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: part_of GO:0055008 ! cardiac muscle tissue morphogenesis +created_by: dph +creation_date: 2010-10-01T10:57:33Z + +[Term] +id: GO:0061351 +name: neural precursor cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of neural precursor cells, resulting in the expansion of a cell population. A neural precursor cell is either a nervous system stem cell or a nervous system progenitor cell." [GOC:dph, GOC:yaf] +is_a: GO:0008283 ! cell proliferation +created_by: dph +creation_date: 2010-10-01T11:06:04Z + +[Term] +id: GO:0061354 +name: planar cell polarity pathway involved in pericardium morphogenesis +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity that contributes to the shaping of the pericardium." [GOC:dph, GOC:mtg_heart, PMID:19056682] +is_a: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: part_of GO:0003344 ! pericardium morphogenesis +created_by: dph +creation_date: 2010-10-01T03:12:53Z + +[Term] +id: GO:0061369 +name: negative regulation of testicular blood vessel morphogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis in the testicle." [GOC:BHF, GOC:dph] +synonym: "negative regulation of testicular vasculature morphogenesis" BROAD [GOC:BHF, GOC:dph] +is_a: GO:2000181 ! negative regulation of blood vessel morphogenesis +created_by: dph +creation_date: 2010-10-27T02:47:14Z + +[Term] +id: GO:0061370 +name: testosterone biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of testosterone, an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4 C-5." [GOC:dph, GOC:yaf] +is_a: GO:0006702 ! androgen biosynthetic process +is_a: GO:0042181 ! ketone biosynthetic process +is_a: GO:0046165 ! alcohol biosynthetic process +created_by: dph +creation_date: 2010-10-27T02:50:48Z + +[Term] +id: GO:0061371 +name: determination of heart left/right asymmetry +namespace: biological_process +def: "Determination of the asymmetric location of the heart with respect to the left and right halves of the organism." [GOC:dph, GOC:mtg_heart] +synonym: "determination of cardiac left/right asymmetry" EXACT [GOC:dph] +is_a: GO:0007368 ! determination of left/right symmetry +relationship: part_of GO:0007507 ! heart development +created_by: dph +creation_date: 2010-11-03T02:13:58Z + +[Term] +id: GO:0061373 +name: mammillary axonal complex development +namespace: biological_process +def: "The progression of the mammillary axonal complex over time, from its formation to the mature structure. The mammillary axonal complex is formed by the axons from the lateral, medial mammillary and the dorsal premammillary nuclei which share a branching pattern. Every neuron gives off one axonal stem that bifurcates into 2 branches. One of the branches is directed dorsally to the thalamus and another caudally to the midbrain." [GOC:dph, GOC:yaf, PMID:10662642] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0021767 ! mammillary body development +created_by: dph +creation_date: 2010-11-09T08:49:59Z + +[Term] +id: GO:0061374 +name: mammillothalamic axonal tract development +namespace: biological_process +def: "The progression of the mammillothalamic axonal tract, from its formation to the mature structure. The mammillothalamic tract is the collection of axons that connects the two major subdivisions of the diencephalon (hypothalamus and thalamus) and closes the diencephalic circuit." [GOC:dph, GOC:yaf, PMID:10662642] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061373 ! mammillary axonal complex development +created_by: dph +creation_date: 2010-11-09T08:54:43Z + +[Term] +id: GO:0061377 +name: mammary gland lobule development +namespace: biological_process +def: "The progression of the mammary gland lobule over time, from its formation to the mature structure. A mammary gland lobule is a small rounded projection of the mammary gland." [GOC:dph, GOC:yaf] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030879 ! mammary gland development +created_by: dph +creation_date: 2010-11-09T09:36:29Z + +[Term] +id: GO:0061378 +name: corpora quadrigemina development +namespace: biological_process +def: "The progression of the corpora quadrigemina over time, from its formation to the mature structure. The corpora quadrigemina is a part of the midbrain that is made up of the superior and inferior colliculi." [GOC:dph, GOC:yaf] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0030901 ! midbrain development +created_by: dph +creation_date: 2010-11-09T09:45:36Z + +[Term] +id: GO:0061379 +name: inferior colliculus development +namespace: biological_process +def: "The process whose specific outcome is the progression of the inferior colliculus over time, from its formation to the mature structure. The inferior colliculus (IC) (Latin, lower hill) is the principal midbrain nucleus of the auditory pathway and receives input from several more peripheral brainstem nuclei in the auditory pathway, as well as inputs from the auditory cortex. The inferior colliculus has three subdivisions: the central nucleus (CIC), a dorsal cortex (DCIC) by which it is surrounded, and an external cortex (ICX) which is located laterally." [GOC:dph, GOC:yaf] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0061378 ! corpora quadrigemina development +created_by: dph +creation_date: 2010-11-09T09:49:24Z + +[Term] +id: GO:0061381 +name: cell migration in diencephalon +namespace: biological_process +def: "The orderly movement of a cell that will reside in the diencephalon." [GOC:dph] +is_a: GO:0021885 ! forebrain cell migration +relationship: part_of GO:0021536 ! diencephalon development +created_by: dph +creation_date: 2010-11-09T09:54:27Z + +[Term] +id: GO:0061383 +name: trabecula morphogenesis +namespace: biological_process +def: "The process of shaping a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue." [GOC:dph] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +created_by: dph +creation_date: 2010-12-02T08:51:45Z + +[Term] +id: GO:0061384 +name: heart trabecula morphogenesis +namespace: biological_process +def: "The process of shaping a trabecula in the heart. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue." [GOC:dph] +is_a: GO:0061383 ! trabecula morphogenesis +created_by: dph +creation_date: 2010-12-02T08:54:20Z + +[Term] +id: GO:0061387 +name: regulation of extent of cell growth +namespace: biological_process +def: "Any process that modulates the extent of cell growth." [GOC:mah, GOC:vw] +is_a: GO:0001558 ! regulation of cell growth +relationship: part_of GO:0008361 ! regulation of cell size +created_by: dph +creation_date: 2011-07-14T10:15:42Z + +[Term] +id: GO:0061430 +name: bone trabecula morphogenesis +namespace: biological_process +def: "The process of shaping a trabecula in bone. A trabecula is a tissue element in the form of a small beam, strut or rod." [GOC:BHF, GOC:dph, GOC:vk] +is_a: GO:0061383 ! trabecula morphogenesis +created_by: dph +creation_date: 2012-02-07T10:15:36Z + +[Term] +id: GO:0061437 +name: renal system vasculature development +namespace: biological_process +def: "The process whose specific outcome is the progression of vasculature of the renal system over time, from its formation to the mature structure." [GOC:dph, GOC:mtg_kidney_jan10, PMID:11891195] +is_a: GO:0001944 ! vasculature development +relationship: part_of GO:0072001 ! renal system development +created_by: dph +creation_date: 2012-03-08T12:16:24Z + +[Term] +id: GO:0061440 +name: kidney vasculature development +namespace: biological_process +def: "The process whose specific outcome is the progression of the vasculature of the kidney over time, from its formation to the mature structure." [GOC:dph, GOC:mtg_kidney_jan10, PMID:11891195] +is_a: GO:0061437 ! renal system vasculature development +relationship: part_of GO:0001822 ! kidney development +created_by: dph +creation_date: 2012-03-08T12:39:09Z + +[Term] +id: GO:0061448 +name: connective tissue development +namespace: biological_process +def: "The progression of a connective tissue over time, from its formation to the mature structure." [GOC:BHF] +is_a: GO:0009888 ! tissue development +created_by: dph +creation_date: 2012-03-22T12:53:41Z + +[Term] +id: GO:0061458 +name: reproductive system development +namespace: biological_process +def: "The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction." [GOC:dph] +is_a: GO:0048731 ! system development +created_by: dph +creation_date: 2012-08-22T17:47:53Z + +[Term] +id: GO:0061469 +name: regulation of type B pancreatic cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of type B pancreatic cell proliferation." [GOC:dph] +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044342 ! type B pancreatic cell proliferation +relationship: regulates GO:0044342 ! type B pancreatic cell proliferation +created_by: dph +creation_date: 2012-11-01T13:16:23Z + +[Term] +id: GO:0061525 +name: hindgut development +namespace: biological_process +def: "The process whose specific outcome is the progression of the hindgut over time, from its formation to the mature structure. The hindgut is part of the alimentary canal that lies posterior to the midgut." [GOC:dph] +is_a: GO:0048565 ! digestive tract development +created_by: dph +creation_date: 2013-06-14T11:22:21Z + +[Term] +id: GO:0061564 +name: axon development +namespace: biological_process +def: "The progession of an axon over time, from its initial formation to the mature structure." [GOC:dph] +is_a: GO:0031175 ! neuron projection development +created_by: dph +creation_date: 2013-07-18T14:43:01Z + +[Term] +id: GO:0061572 +name: actin filament bundle organization +namespace: biological_process +def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of an actin filament bundle." [GOC:dph] +synonym: "actin filament cable organization" RELATED [GOC:dph] +is_a: GO:0007015 ! actin filament organization +created_by: dph +creation_date: 2013-08-02T11:24:11Z + +[Term] +id: GO:0065003 +name: macromolecular complex assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex." [GOC:jl] +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +synonym: "macromolecule complex assembly" EXACT [] +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0043933 ! macromolecular complex subunit organization + +[Term] +id: GO:0065007 +name: biological regulation +namespace: biological_process +def: "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] +subset: goslim_pir +subset: gosubset_prok +synonym: "regulation" BROAD [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0065008 +name: regulation of biological quality +namespace: biological_process +def: "Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] +subset: gosubset_prok +synonym: "regulation of biological attribute" EXACT [] +synonym: "regulation of biological characteristic" EXACT [] +is_a: GO:0065007 ! biological regulation + +[Term] +id: GO:0065009 +name: regulation of molecular function +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GOC:isa_complete] +subset: gosubset_prok +synonym: "regulation of a molecular function" EXACT [] +is_a: GO:0065007 ! biological regulation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003674 ! molecular_function +relationship: regulates GO:0003674 ! molecular_function + +[Term] +id: GO:0070011 +name: peptidase activity, acting on L-amino acid peptides +namespace: molecular_function +def: "Catalysis of the hydrolysis of peptide bonds formed between L-amino acids." [GOC:mah] +subset: gosubset_prok +is_a: GO:0008233 ! peptidase activity + +[Term] +id: GO:0070013 +name: intracellular organelle lumen +namespace: cellular_component +def: "An organelle lumen that is part of an intracellular organelle." [GOC:mah] +is_a: GO:0043233 ! organelle lumen +is_a: GO:0044446 ! intracellular organelle part + +[Term] +id: GO:0070016 +name: armadillo repeat domain binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with the armadillo repeat domain of a protein, an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity protein armadillo. Arm-repeat proteins are involved in various processes, including intracellular signalling and cytoskeletal regulation." [GOC:BHF, GOC:mah, GOC:vk, InterPro:IPR000225] +synonym: "Arm repeat domain binding" EXACT [] +synonym: "armadillo domain binding" EXACT [] +synonym: "armadillo repeat binding" EXACT [] +is_a: GO:0019904 ! protein domain specific binding + +[Term] +id: GO:0070161 +name: anchoring junction +namespace: cellular_component +def: "A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix." [ISBN:0815332181] +synonym: "anchoring cell junction" EXACT [GOC:mah] +is_a: GO:0030054 ! cell junction + +[Term] +id: GO:0070167 +name: regulation of biomineral tissue development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of biomineral tissue development, the formation of hard tissues that consist mainly of inorganic compounds." [GOC:mah] +synonym: "regulation of biomineral formation" EXACT [GOC:dph, GOC:tb] +synonym: "regulation of biomineralization" EXACT [GOC:mah] +synonym: "regulation of mineralization" EXACT [GOC:mah] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031214 ! biomineral tissue development +relationship: regulates GO:0031214 ! biomineral tissue development + +[Term] +id: GO:0070169 +name: positive regulation of biomineral tissue development +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of biomineral tissue development, the formation of hard tissues that consist mainly of inorganic compounds." [GOC:mah] +synonym: "positive regulation of biomineral formation" EXACT [GOC:dph, GOC:tb] +synonym: "positive regulation of biomineralization" EXACT [GOC:mah] +synonym: "positive regulation of mineralization" EXACT [GOC:mah] +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +is_a: GO:0070167 ! regulation of biomineral tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031214 ! biomineral tissue development +relationship: positively_regulates GO:0031214 ! biomineral tissue development + +[Term] +id: GO:0070201 +name: regulation of establishment of protein localization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location." [GOC:BHF, GOC:mah] +synonym: "regulation of establishment of protein localisation" EXACT [GOC:mah] +is_a: GO:0032880 ! regulation of protein localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0045184 ! establishment of protein localization +relationship: regulates GO:0045184 ! establishment of protein localization + +[Term] +id: GO:0070227 +name: lymphocyte apoptotic process +namespace: biological_process +def: "Any apoptotic process in a lymphocyte, a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] +comment: Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). +synonym: "lymphocyte apoptosis" NARROW [] +is_a: GO:0071887 ! leukocyte apoptotic process + +[Term] +id: GO:0070228 +name: regulation of lymphocyte apoptotic process +namespace: biological_process +def: "Any process that modulates the occurrence or rate of lymphocyte death by apoptotic process." [GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] +comment: Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). +synonym: "regulation of lymphocyte apoptosis" NARROW [] +is_a: GO:2000106 ! regulation of leukocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070227 ! lymphocyte apoptotic process +relationship: regulates GO:0070227 ! lymphocyte apoptotic process + +[Term] +id: GO:0070230 +name: positive regulation of lymphocyte apoptotic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of lymphocyte death by apoptotic process." [GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] +comment: Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). +synonym: "activation of lymphocyte apoptosis" NARROW [GOC:add] +synonym: "positive regulation of lymphocyte apoptosis" NARROW [] +synonym: "stimulation of lymphocyte apoptosis" NARROW [GOC:add] +synonym: "up regulation of lymphocyte apoptosis" EXACT [GOC:add] +synonym: "up-regulation of lymphocyte apoptosis" EXACT [GOC:add] +synonym: "upregulation of lymphocyte apoptosis" EXACT [GOC:add] +is_a: GO:0070228 ! regulation of lymphocyte apoptotic process +is_a: GO:2000108 ! positive regulation of leukocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070227 ! lymphocyte apoptotic process +relationship: positively_regulates GO:0070227 ! lymphocyte apoptotic process + +[Term] +id: GO:0070231 +name: T cell apoptotic process +namespace: biological_process +def: "Any apoptotic process in a T cell, a type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." [CL:0000084, GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] +synonym: "programmed cell death of T cells by apoptosis" EXACT [GOC:add] +synonym: "T cell apoptosis" NARROW [] +synonym: "T lymphocyte apoptosis" EXACT [GOC:add] +synonym: "T-cell apoptosis" EXACT [GOC:add] +synonym: "T-lymphocyte apoptosis" EXACT [GOC:add] +is_a: GO:0070227 ! lymphocyte apoptotic process + +[Term] +id: GO:0070232 +name: regulation of T cell apoptotic process +namespace: biological_process +def: "Any process that modulates the occurrence or rate of T cell death by apoptotic process." [GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] +synonym: "regulation of programmed cell death of T cells by apoptosis" EXACT [GOC:add] +synonym: "regulation of T cell apoptosis" NARROW [] +synonym: "regulation of T lymphocyte apoptosis" EXACT [GOC:add] +synonym: "regulation of T-cell apoptosis" EXACT [GOC:add] +synonym: "regulation of T-lymphocyte apoptosis" EXACT [GOC:add] +is_a: GO:0070228 ! regulation of lymphocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070231 ! T cell apoptotic process +relationship: regulates GO:0070231 ! T cell apoptotic process + +[Term] +id: GO:0070234 +name: positive regulation of T cell apoptotic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of T cell death by apoptotic process." [GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] +synonym: "activation of T cell apoptosis" NARROW [GOC:add] +synonym: "positive regulation of programmed cell death of T cells by apoptosis" EXACT [GOC:add] +synonym: "positive regulation of T cell apoptosis" NARROW [] +synonym: "positive regulation of T lymphocyte apoptosis" EXACT [GOC:add] +synonym: "positive regulation of T-cell apoptosis" EXACT [GOC:add] +synonym: "positive regulation of T-lymphocyte apoptosis" EXACT [GOC:add] +synonym: "stimulation of T cell apoptosis" NARROW [GOC:add] +synonym: "up regulation of T cell apoptosis" EXACT [GOC:add] +synonym: "up-regulation of T cell apoptosis" EXACT [GOC:add] +synonym: "upregulation of T cell apoptosis" EXACT [GOC:add] +is_a: GO:0070230 ! positive regulation of lymphocyte apoptotic process +is_a: GO:0070232 ! regulation of T cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070231 ! T cell apoptotic process +relationship: positively_regulates GO:0070231 ! T cell apoptotic process + +[Term] +id: GO:0070242 +name: thymocyte apoptotic process +namespace: biological_process +def: "Any apoptotic process in a thymocyte, an immature T cell located in the thymus." [CL:0000893, GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] +comment: Note that a thymocyte is an immature T cell located in the thymus (CL:0000893). +synonym: "immature T cell apoptosis" RELATED [GOC:add] +synonym: "thymocyte apoptosis" NARROW [] +is_a: GO:0070231 ! T cell apoptotic process + +[Term] +id: GO:0070243 +name: regulation of thymocyte apoptotic process +namespace: biological_process +def: "Any process that modulates the occurrence or rate of thymocyte death by apoptotic process." [GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] +comment: Note that a thymocyte is an immature T cell located in the thymus (CL:0000893). +synonym: "regulation of immature T cell apoptosis" RELATED [GOC:add] +synonym: "regulation of thymocyte apoptosis" NARROW [] +is_a: GO:0070232 ! regulation of T cell apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070242 ! thymocyte apoptotic process +relationship: regulates GO:0070242 ! thymocyte apoptotic process + +[Term] +id: GO:0070245 +name: positive regulation of thymocyte apoptotic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of thymocyte death by apoptotic process." [GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] +comment: Note that a thymocyte is an immature T cell located in the thymus (CL:0000893). +synonym: "activation of thymocyte apoptosis" NARROW [GOC:add] +synonym: "positive regulation of immature T cell apoptosis" RELATED [GOC:add] +synonym: "positive regulation of thymocyte apoptosis" NARROW [] +synonym: "stimulation of thymocyte apoptosis" NARROW [GOC:add] +synonym: "up regulation of thymocyte apoptosis" EXACT [GOC:add] +synonym: "up-regulation of thymocyte apoptosis" EXACT [GOC:add] +synonym: "upregulation of thymocyte apoptosis" EXACT [GOC:add] +is_a: GO:0070234 ! positive regulation of T cell apoptotic process +is_a: GO:0070243 ! regulation of thymocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070242 ! thymocyte apoptotic process +relationship: positively_regulates GO:0070242 ! thymocyte apoptotic process + +[Term] +id: GO:0070271 +name: protein complex biogenesis +namespace: biological_process +def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a protein complex. Includes the synthesis of the constituent protein molecules, and those protein modifications that are involved in synthesis or assembly of the complex." [GOC:mah] +subset: goslim_yeast +subset: gosubset_prok +synonym: "protein complex biogenesis and assembly" EXACT [GOC:mah] +is_a: GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0070302 +name: regulation of stress-activated protein kinase signaling cascade +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of signaling via a stress-activated protein kinase signaling cascade." [GOC:mah] +synonym: "regulation of SAPK signaling pathway" EXACT [GOC:mah] +synonym: "regulation of stress-activated protein kinase signaling pathway" EXACT [] +synonym: "regulation of stress-activated protein kinase signalling pathway" EXACT [GOC:mah] +is_a: GO:0080135 ! regulation of cellular response to stress +is_a: GO:1902531 ! regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0031098 ! stress-activated protein kinase signaling cascade +relationship: regulates GO:0031098 ! stress-activated protein kinase signaling cascade + +[Term] +id: GO:0070304 +name: positive regulation of stress-activated protein kinase signaling cascade +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of signaling via the stress-activated protein kinase signaling cascade." [GOC:mah] +synonym: "activation of stress-activated protein kinase signaling pathway" NARROW [GOC:mah] +synonym: "positive regulation of SAPK signaling pathway" EXACT [GOC:mah] +synonym: "positive regulation of stress-activated protein kinase signaling pathway" EXACT [] +synonym: "positive regulation of stress-activated protein kinase signalling pathway" EXACT [GOC:mah] +synonym: "stimulation of stress-activated protein kinase signaling pathway" NARROW [GOC:mah] +synonym: "up regulation of stress-activated protein kinase signaling pathway" EXACT [GOC:mah] +synonym: "up-regulation of stress-activated protein kinase signaling pathway" EXACT [GOC:mah] +synonym: "upregulation of stress-activated protein kinase signaling pathway" EXACT [GOC:mah] +is_a: GO:0070302 ! regulation of stress-activated protein kinase signaling cascade +is_a: GO:1902533 ! positive regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0031098 ! stress-activated protein kinase signaling cascade +relationship: positively_regulates GO:0031098 ! stress-activated protein kinase signaling cascade + +[Term] +id: GO:0070325 +name: lipoprotein particle receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a lipoprotein particle receptor." [GOC:BHF, GOC:rl] +is_a: GO:0005102 ! receptor binding + +[Term] +id: GO:0070326 +name: very-low-density lipoprotein particle receptor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a very-low-density lipoprotein receptor." [GOC:BHF, GOC:mah] +synonym: "apolipoprotein E receptor binding" RELATED [GOC:rl] +synonym: "very-low-density lipoprotein receptor binding" EXACT [GOC:bf, GOC:dph] +synonym: "VLDL receptor binding" EXACT [GOC:mah] +synonym: "VLDLR binding" EXACT [GOC:mah] +is_a: GO:0070325 ! lipoprotein particle receptor binding + +[Term] +id: GO:0070365 +name: hepatocyte differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires the specialized features of a hepatocyte. A hepatocyte is specialized epithelial cell that is organized into interconnected plates called lobules, and is the main structural component of the liver." [CL:0000182, PMID:7588884] +synonym: "liver cell differentiation" EXACT [GOC:mah] +is_a: GO:0030855 ! epithelial cell differentiation +relationship: part_of GO:0001889 ! liver development + +[Term] +id: GO:0070369 +name: beta-catenin-TCF7L2 complex +namespace: cellular_component +def: "A protein complex that contains beta-catenin and TCF7L2 (TCF4), binds to the TCF DNA motif within a promoter element, and is involved in the regulation of WNT target gene transcription." [GOC:BHF, GOC:rl, PMID:9065401, PMID:9065402] +subset: gosubset_prok +synonym: "beta-catenin-TCF4 complex" EXACT [PMID:9065401, PMID:9065402] +is_a: GO:0071664 ! catenin-TCF7L2 complex + +[Term] +id: GO:0070410 +name: co-SMAD binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a common mediator SMAD signaling protein." [GOC:BHF, GOC:vk, PMID:19114992] +is_a: GO:0046332 ! SMAD binding + +[Term] +id: GO:0070411 +name: I-SMAD binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an inhibitory SMAD signaling protein." [GOC:BHF, GOC:vk, PMID:19114992] +is_a: GO:0046332 ! SMAD binding + +[Term] +id: GO:0070412 +name: R-SMAD binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a receptor-regulated SMAD signaling protein." [GOC:BHF, GOC:vk, PMID:19114992] +is_a: GO:0046332 ! SMAD binding + +[Term] +id: GO:0070491 +name: repressing transcription factor binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription." [GOC:mah, GOC:txnOH] +is_a: GO:0008134 ! transcription factor binding + +[Term] +id: GO:0070507 +name: regulation of microtubule cytoskeleton organization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GOC:mah] +synonym: "regulation of microtubule cytoskeleton organisation" EXACT [GOC:mah] +synonym: "regulation of microtubule dynamics" EXACT [GOC:dph, GOC:tb] +is_a: GO:0032886 ! regulation of microtubule-based process +is_a: GO:0051493 ! regulation of cytoskeleton organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000226 ! microtubule cytoskeleton organization +relationship: regulates GO:0000226 ! microtubule cytoskeleton organization + +[Term] +id: GO:0070509 +name: calcium ion import +namespace: biological_process +def: "The directed movement of calcium ions into a cell or organelle." [GOC:mah] +synonym: "calcium ion uptake" EXACT [GOC:mah] +synonym: "transmembrane calcium influx" RELATED [GOC:tb] +is_a: GO:0070588 ! calcium ion transmembrane transport + +[Term] +id: GO:0070527 +name: platelet aggregation +namespace: biological_process +def: "The adhesion of one platelet to one or more other platelets via adhesion molecules." [GOC:BHF, GOC:vk] +synonym: "blood platelet aggregation" EXACT [CL:0000233] +synonym: "thrombocyte aggregation" RELATED [CL:0000233] +is_a: GO:0034109 ! homotypic cell-cell adhesion +relationship: part_of GO:0030168 ! platelet activation + +[Term] +id: GO:0070528 +name: protein kinase C signaling +namespace: biological_process +def: "A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound." [GOC:BHF, GOC:mah] +synonym: "PKC signal transduction" EXACT [GOC:signaling] +synonym: "PKC signaling cascade" RELATED [GOC:mah] +synonym: "protein kinase C signal transduction" EXACT [GOC:signaling] +synonym: "protein kinase C signaling cascade" RELATED [GOC:signaling] +synonym: "protein kinase C signalling cascade" RELATED [GOC:mah] +is_a: GO:0035556 ! intracellular signal transduction + +[Term] +id: GO:0070588 +name: calcium ion transmembrane transport +namespace: biological_process +def: "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC:mah] +comment: Note that this term is not intended for use in annotating lateral movement within membranes. +subset: gosubset_prok +synonym: "calcium ion membrane transport" EXACT [] +synonym: "transmembrane calcium transport" EXACT [GOC:mah] +is_a: GO:0006816 ! calcium ion transport +is_a: GO:0034220 ! ion transmembrane transport +created_by: midori +creation_date: 2009-04-28T10:44:09Z + +[Term] +id: GO:0070601 +name: centromeric sister chromatid cohesion +namespace: biological_process +def: "The cell cycle process in which the sister chromatids of a replicated chromosome are joined along the length of the centromeric region of the chromosome." [GOC:mah] +synonym: "sister chromatid cohesion at centromere" EXACT [GOC:mah] +is_a: GO:0007062 ! sister chromatid cohesion +created_by: midori +creation_date: 2009-04-28T04:31:00Z + +[Term] +id: GO:0070602 +name: regulation of centromeric sister chromatid cohesion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of sister chromatid cohesion in the centromeric region of a chromosome." [GOC:mah] +synonym: "regulation of sister chromatid cohesion at centromere" EXACT [GOC:mah] +is_a: GO:0007063 ! regulation of sister chromatid cohesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070601 ! centromeric sister chromatid cohesion +relationship: regulates GO:0070601 ! centromeric sister chromatid cohesion +created_by: midori +creation_date: 2009-04-28T04:32:53Z + +[Term] +id: GO:0070647 +name: protein modification by small protein conjugation or removal +namespace: biological_process +def: "A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to or removed from a target protein." [GOC:mah] +subset: goslim_pombe +subset: goslim_yeast +is_a: GO:0006464 ! cellular protein modification process +created_by: midori +creation_date: 2009-05-11T02:54:03Z + +[Term] +id: GO:0070661 +name: leukocyte proliferation +namespace: biological_process +def: "The expansion of a leukocyte population by cell division." [GOC:add] +is_a: GO:0008283 ! cell proliferation +created_by: midori +creation_date: 2009-05-28T05:25:28Z + +[Term] +id: GO:0070663 +name: regulation of leukocyte proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of leukocyte proliferation." [GOC:add, GOC:mah] +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070661 ! leukocyte proliferation +relationship: regulates GO:0070661 ! leukocyte proliferation +created_by: midori +creation_date: 2009-05-28T05:30:39Z + +[Term] +id: GO:0070664 +name: negative regulation of leukocyte proliferation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation." [GOC:add, GOC:mah] +synonym: "down regulation of leukocyte proliferation" EXACT [GOC:mah] +synonym: "down-regulation of leukocyte proliferation" EXACT [GOC:mah] +synonym: "downregulation of leukocyte proliferation" EXACT [GOC:mah] +synonym: "inhibition of leukocyte proliferation" NARROW [GOC:mah] +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0070663 ! regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0070661 ! leukocyte proliferation +relationship: negatively_regulates GO:0070661 ! leukocyte proliferation +created_by: midori +creation_date: 2009-05-28T05:34:50Z + +[Term] +id: GO:0070665 +name: positive regulation of leukocyte proliferation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of leukocyte proliferation." [GOC:add, GOC:mah] +synonym: "activation of leukocyte proliferation" NARROW [GOC:mah] +synonym: "stimulation of leukocyte proliferation" NARROW [GOC:mah] +synonym: "up regulation of leukocyte proliferation" EXACT [GOC:mah] +synonym: "up-regulation of leukocyte proliferation" EXACT [GOC:mah] +synonym: "upregulation of leukocyte proliferation" EXACT [GOC:mah] +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0070663 ! regulation of leukocyte proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070661 ! leukocyte proliferation +relationship: positively_regulates GO:0070661 ! leukocyte proliferation +created_by: midori +creation_date: 2009-05-28T05:36:46Z + +[Term] +id: GO:0070723 +name: response to cholesterol +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cholesterol stimulus." [GOC:BHF, GOC:vk] +is_a: GO:0036314 ! response to sterol +created_by: midori +creation_date: 2009-06-15T02:28:27Z + +[Term] +id: GO:0070727 +name: cellular macromolecule localization +namespace: biological_process +def: "Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah] +synonym: "cellular macromolecule localisation" EXACT [GOC:mah] +is_a: GO:0033036 ! macromolecule localization +is_a: GO:0051641 ! cellular localization +created_by: midori +creation_date: 2009-06-16T04:08:29Z + +[Term] +id: GO:0070741 +name: response to interleukin-6 +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-6 stimulus." [GOC:mah] +synonym: "response to IL-6" EXACT [GOC:mah] +is_a: GO:0034097 ! response to cytokine +created_by: midori +creation_date: 2009-06-19T03:39:12Z + +[Term] +id: GO:0070838 +name: divalent metal ion transport +namespace: biological_process +def: "The directed movement of divalent metal cations, any metal ion with a +2 electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] +subset: gosubset_prok +is_a: GO:0030001 ! metal ion transport +is_a: GO:0072511 ! divalent inorganic cation transport +created_by: midori +creation_date: 2009-07-31T01:02:39Z + +[Term] +id: GO:0070848 +name: response to growth factor +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:BHF, GOC:mah] +synonym: "response to growth factor stimulus" EXACT [GOC:dos] +is_a: GO:0010033 ! response to organic substance +created_by: midori +creation_date: 2009-08-04T04:24:18Z + +[Term] +id: GO:0070887 +name: cellular response to chemical stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +is_a: GO:0042221 ! response to chemical +is_a: GO:0051716 ! cellular response to stimulus +created_by: midori +creation_date: 2009-08-27T04:41:45Z + +[Term] +id: GO:0070925 +name: organelle assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] +subset: goslim_yeast +is_a: GO:0022607 ! cellular component assembly +relationship: part_of GO:0006996 ! organelle organization +created_by: midori +creation_date: 2009-09-15T03:00:51Z + +[Term] +id: GO:0070997 +name: neuron death +namespace: biological_process +def: "The process of cell death in a neuron." [GOC:BHF, GOC:mah] +synonym: "neuron cell death" EXACT [GOC:mah, GOC:rl] +synonym: "neuronal cell death" EXACT [GOC:mah] +is_a: GO:0008219 ! cell death +created_by: midori +creation_date: 2009-11-03T02:37:17Z + +[Term] +id: GO:0071214 +name: cellular response to abiotic stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: gosubset_prok +synonym: "cellular response to abiotic stress" NARROW [GOC:mah] +is_a: GO:0009628 ! response to abiotic stimulus +is_a: GO:0051716 ! cellular response to stimulus +created_by: midori +creation_date: 2009-12-03T01:02:11Z + +[Term] +id: GO:0071216 +name: cellular response to biotic stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +synonym: "cellular response to biotic stress" NARROW [GOC:mah] +is_a: GO:0009607 ! response to biotic stimulus +is_a: GO:0051716 ! cellular response to stimulus +created_by: midori +creation_date: 2009-12-03T01:09:08Z + +[Term] +id: GO:0071219 +name: cellular response to molecule of bacterial origin +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin." [GOC:mah] +synonym: "cellular response to bacteria associated molecule" EXACT [GOC:mah] +synonym: "cellular response to bacterial associated molecule" EXACT [GOC:mah] +synonym: "cellular response to bacterium associated molecule" EXACT [GOC:mah] +is_a: GO:0002237 ! response to molecule of bacterial origin +is_a: GO:0071216 ! cellular response to biotic stimulus +created_by: midori +creation_date: 2009-12-03T01:22:00Z + +[Term] +id: GO:0071260 +name: cellular response to mechanical stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus." [GOC:mah] +synonym: "cellular mechanical stimulus response" EXACT [GOC:mah] +is_a: GO:0009612 ! response to mechanical stimulus +is_a: GO:0071214 ! cellular response to abiotic stimulus +is_a: GO:0071496 ! cellular response to external stimulus +created_by: midori +creation_date: 2009-12-04T03:55:44Z + +[Term] +id: GO:0071310 +name: cellular response to organic substance +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus." [GOC:mah] +subset: gosubset_prok +is_a: GO:0010033 ! response to organic substance +is_a: GO:0070887 ! cellular response to chemical stimulus +created_by: midori +creation_date: 2009-12-10T04:46:04Z + +[Term] +id: GO:0071322 +name: cellular response to carbohydrate stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus." [GOC:mah] +is_a: GO:0009743 ! response to carbohydrate +is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:1901701 ! cellular response to oxygen-containing compound +created_by: midori +creation_date: 2009-12-10T05:13:33Z + +[Term] +id: GO:0071326 +name: cellular response to monosaccharide stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus." [GOC:mah] +is_a: GO:0034284 ! response to monosaccharide +is_a: GO:0071322 ! cellular response to carbohydrate stimulus +created_by: midori +creation_date: 2009-12-10T05:27:18Z + +[Term] +id: GO:0071331 +name: cellular response to hexose stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus." [GOC:mah] +is_a: GO:0009746 ! response to hexose +is_a: GO:0071326 ! cellular response to monosaccharide stimulus +created_by: midori +creation_date: 2009-12-10T05:37:00Z + +[Term] +id: GO:0071333 +name: cellular response to glucose stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus." [GOC:mah] +is_a: GO:0001678 ! cellular glucose homeostasis +is_a: GO:0009749 ! response to glucose +is_a: GO:0071331 ! cellular response to hexose stimulus +created_by: midori +creation_date: 2009-12-10T05:38:03Z + +[Term] +id: GO:0071345 +name: cellular response to cytokine stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus." [GOC:mah] +is_a: GO:0034097 ! response to cytokine +is_a: GO:0071310 ! cellular response to organic substance +created_by: midori +creation_date: 2009-12-11T02:41:12Z + +[Term] +id: GO:0071356 +name: cellular response to tumor necrosis factor +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus." [GOC:mah] +synonym: "cellular response to TNF" EXACT [GOC:mah] +is_a: GO:0034612 ! response to tumor necrosis factor +is_a: GO:0071345 ! cellular response to cytokine stimulus +created_by: midori +creation_date: 2009-12-11T02:51:37Z + +[Term] +id: GO:0071357 +name: cellular response to type I interferon +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a type I interferon stimulus. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:mah, PR:000025848] +synonym: "cellular response to type I IFN" EXACT [GOC:mah] +is_a: GO:0034340 ! response to type I interferon +is_a: GO:0071345 ! cellular response to cytokine stimulus +created_by: midori +creation_date: 2009-12-11T02:51:47Z + +[Term] +id: GO:0071363 +name: cellular response to growth factor stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:mah] +is_a: GO:0070848 ! response to growth factor +is_a: GO:0071310 ! cellular response to organic substance +created_by: midori +creation_date: 2009-12-11T03:05:07Z + +[Term] +id: GO:0071375 +name: cellular response to peptide hormone stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals." [GOC:mah] +synonym: "cellular response to polypeptide hormone stimulus" EXACT [GOC:mah] +is_a: GO:0032870 ! cellular response to hormone stimulus +is_a: GO:0043434 ! response to peptide hormone +is_a: GO:1901653 ! cellular response to peptide +created_by: midori +creation_date: 2009-12-11T03:24:18Z + +[Term] +id: GO:0071383 +name: cellular response to steroid hormone stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus." [GOC:mah] +is_a: GO:0032870 ! cellular response to hormone stimulus +is_a: GO:0048545 ! response to steroid hormone +is_a: GO:0071396 ! cellular response to lipid +is_a: GO:0071407 ! cellular response to organic cyclic compound +created_by: midori +creation_date: 2009-12-11T03:49:02Z + +[Term] +id: GO:0071391 +name: cellular response to estrogen stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics." [GOC:mah] +synonym: "cellular response to oestrogen stimulus" EXACT [GOC:mah] +is_a: GO:0043627 ! response to estrogen +is_a: GO:0071383 ! cellular response to steroid hormone stimulus +created_by: midori +creation_date: 2009-12-11T04:09:56Z + +[Term] +id: GO:0071396 +name: cellular response to lipid +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus." [GOC:mah] +is_a: GO:0033993 ! response to lipid +is_a: GO:0071310 ! cellular response to organic substance +created_by: midori +creation_date: 2009-12-11T04:37:10Z + +[Term] +id: GO:0071397 +name: cellular response to cholesterol +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cholesterol stimulus." [GOC:mah] +is_a: GO:0036315 ! cellular response to sterol +is_a: GO:0070723 ! response to cholesterol +created_by: midori +creation_date: 2009-12-11T04:39:31Z + +[Term] +id: GO:0071407 +name: cellular response to organic cyclic compound +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus." [GOC:mah] +synonym: "cellular response to organic cyclic substance" EXACT [GOC:mah] +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0071310 ! cellular response to organic substance +created_by: midori +creation_date: 2009-12-14T02:55:58Z + +[Term] +id: GO:0071417 +name: cellular response to organonitrogen compound +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond." [CHEBI:35352, GOC:mah] +synonym: "cellular response to organic nitrogen" EXACT [GOC:mah] +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:0071495 ! cellular response to endogenous stimulus +is_a: GO:1901699 ! cellular response to nitrogen compound +created_by: midori +creation_date: 2009-12-14T04:07:27Z + +[Term] +id: GO:0071425 +name: hematopoietic stem cell proliferation +namespace: biological_process +def: "The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop." [CL:0000037, GOC:add, GOC:mah, GOC:rl] +synonym: "hemopoietic stem cell proliferation" EXACT [] +is_a: GO:0072089 ! stem cell proliferation +relationship: part_of GO:0030097 ! hemopoiesis +created_by: midori +creation_date: 2009-12-16T10:22:52Z + +[Term] +id: GO:0071478 +name: cellular response to radiation +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation." [GOC:mah] +comment: Note that 'radiation' refers to electromagnetic radiation of any wavelength. +subset: gosubset_prok +synonym: "cellular response to electromagnetic radiation stimulus" EXACT [GOC:mah] +synonym: "cellular response to radiation stimulus" EXACT [GOC:mah] +is_a: GO:0009314 ! response to radiation +is_a: GO:0071214 ! cellular response to abiotic stimulus +created_by: midori +creation_date: 2009-12-18T01:59:37Z + +[Term] +id: GO:0071479 +name: cellular response to ionizing radiation +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [GOC:mah] +synonym: "cellular response to ionising radiation" EXACT [GOC:mah] +synonym: "cellular response to ionizing radiation stimulus" EXACT [GOC:mah] +is_a: GO:0010212 ! response to ionizing radiation +is_a: GO:0071478 ! cellular response to radiation +created_by: midori +creation_date: 2009-12-18T02:00:31Z + +[Term] +id: GO:0071481 +name: cellular response to X-ray +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz)." [GOC:mah] +synonym: "cellular response to X-ray radiation stimulus" EXACT [GOC:mah] +is_a: GO:0010165 ! response to X-ray +is_a: GO:0071479 ! cellular response to ionizing radiation +created_by: midori +creation_date: 2009-12-18T02:00:59Z + +[Term] +id: GO:0071495 +name: cellular response to endogenous stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: gosubset_prok +is_a: GO:0009719 ! response to endogenous stimulus +created_by: midori +creation_date: 2009-12-18T02:25:40Z + +[Term] +id: GO:0071496 +name: cellular response to external stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." [GOC:mah] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: gosubset_prok +synonym: "cellular response to environmental stimulus" EXACT [GOC:mah] +is_a: GO:0009605 ! response to external stimulus +created_by: midori +creation_date: 2009-12-18T02:36:52Z + +[Term] +id: GO:0071503 +name: response to heparin +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heparin stimulus." [GOC:mah, GOC:yaf] +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:1901700 ! response to oxygen-containing compound +created_by: midori +creation_date: 2009-12-18T03:33:49Z + +[Term] +id: GO:0071504 +name: cellular response to heparin +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heparin stimulus." [GOC:mah, GOC:yaf] +is_a: GO:0071417 ! cellular response to organonitrogen compound +is_a: GO:0071503 ! response to heparin +is_a: GO:1901701 ! cellular response to oxygen-containing compound +created_by: midori +creation_date: 2009-12-18T03:34:38Z + +[Term] +id: GO:0071542 +name: dopaminergic neuron differentiation +namespace: biological_process +def: "The process in which a neuroblast acquires the specialized structural and functional features of a dopaminergic neuron, a neuron that secretes dopamine." [GOC:rph] +is_a: GO:0030182 ! neuron differentiation +created_by: midori +creation_date: 2010-01-12T02:28:44Z + +[Term] +id: GO:0071559 +name: response to transforming growth factor beta +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus." [GOC:mah] +synonym: "response to TGF-beta stimulus" EXACT [GOC:mah] +synonym: "response to TGFbeta stimulus" EXACT [GOC:mah] +synonym: "response to transforming growth factor beta stimulus" EXACT [GOC:dos] +is_a: GO:0009719 ! response to endogenous stimulus +is_a: GO:0070848 ! response to growth factor +created_by: midori +creation_date: 2010-01-20T11:49:59Z + +[Term] +id: GO:0071560 +name: cellular response to transforming growth factor beta stimulus +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus." [GOC:ecd, PMID:15451575] +synonym: "cellular response to TGF-beta stimulus" EXACT [GOC:mah] +synonym: "cellular response to TGFbeta stimulus" EXACT [GOC:mah] +is_a: GO:0071363 ! cellular response to growth factor stimulus +is_a: GO:0071495 ! cellular response to endogenous stimulus +is_a: GO:0071559 ! response to transforming growth factor beta +created_by: midori +creation_date: 2010-01-20T11:51:18Z + +[Term] +id: GO:0071599 +name: otic vesicle development +namespace: biological_process +def: "The process whose specific outcome is the progression of the otic vesicle over time, from its formation to the mature structure. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear." [GOC:mah] +is_a: GO:0007423 ! sensory organ development +is_a: GO:0048839 ! inner ear development +created_by: midori +creation_date: 2010-02-04T04:07:17Z + +[Term] +id: GO:0071600 +name: otic vesicle morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the otic vesicle are generated and organized. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear." [GOC:mah] +is_a: GO:0042472 ! inner ear morphogenesis +is_a: GO:0048562 ! embryonic organ morphogenesis +relationship: part_of GO:0071599 ! otic vesicle development +created_by: midori +creation_date: 2010-02-04T04:07:27Z + +[Term] +id: GO:0071664 +name: catenin-TCF7L2 complex +namespace: cellular_component +def: "A protein complex that contains a catenin and TCF7L2 (TCF4), binds to the TCF DNA motif within a promoter element, and is involved in the regulation of WNT target gene transcription." [GOC:BHF, GOC:rl, GOC:vk, PMID:14661054] +subset: gosubset_prok +synonym: "catenin-TCF4 complex" EXACT [GOC:mah] +is_a: GO:0043234 ! protein complex +is_a: GO:0044428 ! nuclear part +created_by: midori +creation_date: 2010-02-12T03:19:16Z + +[Term] +id: GO:0071680 +name: response to indole-3-methanol +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an indole-3-methanol stimulus." [CHEBI:24814, GOC:mah, GOC:yaf] +synonym: "response to indole-3-carbinol" EXACT [CHEBI:24814] +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:0014070 ! response to organic cyclic compound +is_a: GO:0097305 ! response to alcohol +created_by: midori +creation_date: 2010-02-18T04:05:09Z + +[Term] +id: GO:0071681 +name: cellular response to indole-3-methanol +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an indole-3-methanol stimulus." [CHEBI:24814, GOC:mah, GOC:yaf] +synonym: "cellular response to indole-3-carbinol" EXACT [CHEBI:24814] +is_a: GO:0071407 ! cellular response to organic cyclic compound +is_a: GO:0071417 ! cellular response to organonitrogen compound +is_a: GO:0071680 ! response to indole-3-methanol +is_a: GO:0097306 ! cellular response to alcohol +created_by: midori +creation_date: 2010-02-18T04:05:29Z + +[Term] +id: GO:0071695 +name: anatomical structure maturation +namespace: biological_process +def: "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state." [GOC:mah] +is_a: GO:0021700 ! developmental maturation +relationship: part_of GO:0048856 ! anatomical structure development +created_by: midori +creation_date: 2010-03-02T11:43:38Z + +[Term] +id: GO:0071696 +name: ectodermal placode development +namespace: biological_process +def: "The progression of an ectodermal placode over time from its initial formation until its mature state. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm." [GOC:mah] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +created_by: midori +creation_date: 2010-03-02T11:48:01Z + +[Term] +id: GO:0071697 +name: ectodermal placode morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of an ectodermal placode are generated and organized. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm." [GOC:mah] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0071696 ! ectodermal placode development +created_by: midori +creation_date: 2010-03-02T11:49:51Z + +[Term] +id: GO:0071702 +name: organic substance transport +namespace: biological_process +def: "The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon." [CHEBI:50860, GOC:mah] +is_a: GO:0006810 ! transport +created_by: midori +creation_date: 2010-03-08T02:15:14Z + +[Term] +id: GO:0071704 +name: organic substance metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [CHEBI:50860, GOC:mah] +synonym: "organic molecular entity metabolic process" EXACT [] +synonym: "organic molecular entity metabolism" EXACT [] +synonym: "organic substance metabolism" EXACT [] +is_a: GO:0008152 ! metabolic process +created_by: midori +creation_date: 2010-03-08T03:32:18Z + +[Term] +id: GO:0071705 +name: nitrogen compound transport +namespace: biological_process +def: "The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [CHEBI:51143, GOC:mah] +is_a: GO:0006810 ! transport +created_by: midori +creation_date: 2010-03-08T03:56:28Z + +[Term] +id: GO:0071774 +name: response to fibroblast growth factor +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fibroblast growth factor stimulus." [GOC:mah] +synonym: "response to FGF stimulus" EXACT [GOC:mah] +synonym: "response to fibroblast growth factor stimulus" EXACT [GOC:dos] +is_a: GO:0009719 ! response to endogenous stimulus +is_a: GO:0070848 ! response to growth factor +created_by: midori +creation_date: 2010-08-31T11:06:32Z + +[Term] +id: GO:0071813 +name: lipoprotein particle binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a lipoprotein particle. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids." [CHEBI:6495, GOC:BHF, GOC:mah] +synonym: "lipoprotein binding" RELATED [GOC:mah] +synonym: "plasma lipoprotein binding" RELATED [GOC:mah] +synonym: "plasma lipoprotein particle binding" EXACT [GOC:mah] +is_a: GO:0071814 ! protein-lipid complex binding +created_by: midori +creation_date: 2010-09-06T03:16:01Z + +[Term] +id: GO:0071814 +name: protein-lipid complex binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a protein-lipid complex, any macromolecular complex that contains both protein and lipid molecules." [GOC:BHF, GOC:mah] +is_a: GO:0005488 ! binding +created_by: midori +creation_date: 2010-09-06T04:26:27Z + +[Term] +id: GO:0071822 +name: protein complex subunit organization +namespace: biological_process +def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] +synonym: "protein complex subunit organisation" EXACT [GOC:mah] +is_a: GO:0043933 ! macromolecular complex subunit organization +created_by: midori +creation_date: 2010-09-08T10:01:42Z + +[Term] +id: GO:0071825 +name: protein-lipid complex subunit organization +namespace: biological_process +def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-lipid complex." [GOC:mah] +synonym: "protein-lipid complex subunit organisation" EXACT [GOC:mah] +is_a: GO:0043933 ! macromolecular complex subunit organization +created_by: midori +creation_date: 2010-09-08T10:04:36Z + +[Term] +id: GO:0071827 +name: plasma lipoprotein particle organization +namespace: biological_process +def: "A protein-lipid complex subunit organization process that results in the formation, disassembly, or alteration of a plasma lipoprotein particle. A plasma lipoprotein particle is a spherical particle with a hydrophobic core of triglycerides and/or cholesterol esters, surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins." [GOC:BHF, GOC:mah] +synonym: "plasma lipoprotein particle organisation" EXACT [GOC:mah] +is_a: GO:0044707 ! single-multicellular organism process +is_a: GO:0071825 ! protein-lipid complex subunit organization +created_by: midori +creation_date: 2010-09-08T10:32:26Z + +[Term] +id: GO:0071829 +name: plasma lipoprotein particle disassembly +namespace: biological_process +def: "The disaggregation of a plasma lipoprotein particle into its constituent components." [GOC:mah] +is_a: GO:0032987 ! protein-lipid complex disassembly +is_a: GO:0071827 ! plasma lipoprotein particle organization +relationship: part_of GO:0097006 ! regulation of plasma lipoprotein particle levels +created_by: midori +creation_date: 2010-09-08T11:14:21Z + +[Term] +id: GO:0071840 +name: cellular component organization or biogenesis +namespace: biological_process +alt_id: GO:0071841 +def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] +synonym: "cellular component organisation or biogenesis" EXACT [GOC:mah] +synonym: "cellular component organisation or biogenesis at cellular level" EXACT [GOC:mah] +synonym: "cellular component organization or biogenesis at cellular level" EXACT [] +is_a: GO:0008150 ! biological_process +created_by: midori +creation_date: 2010-09-10T01:39:16Z + +[Term] +id: GO:0071887 +name: leukocyte apoptotic process +namespace: biological_process +def: "Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [CL:0000738, GOC:BHF, GOC:mah, GOC:mtg_apoptosis] +comment: Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). +synonym: "leukocyte apoptosis" NARROW [] +is_a: GO:0097285 ! cell-type specific apoptotic process +created_by: midori +creation_date: 2010-09-14T12:44:09Z + +[Term] +id: GO:0071900 +name: regulation of protein serine/threonine kinase activity +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of protein serine/threonine kinase activity." [GOC:mah] +is_a: GO:0045859 ! regulation of protein kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004674 ! protein serine/threonine kinase activity +relationship: regulates GO:0004674 ! protein serine/threonine kinase activity +created_by: midori +creation_date: 2010-09-15T03:08:35Z + +[Term] +id: GO:0071901 +name: negative regulation of protein serine/threonine kinase activity +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity." [GOC:BHF, GOC:mah] +is_a: GO:0006469 ! negative regulation of protein kinase activity +is_a: GO:0071900 ! regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004674 ! protein serine/threonine kinase activity +relationship: negatively_regulates GO:0004674 ! protein serine/threonine kinase activity +created_by: midori +creation_date: 2010-09-15T03:09:43Z + +[Term] +id: GO:0071902 +name: positive regulation of protein serine/threonine kinase activity +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity." [GOC:mah] +is_a: GO:0045860 ! positive regulation of protein kinase activity +is_a: GO:0071900 ! regulation of protein serine/threonine kinase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004674 ! protein serine/threonine kinase activity +relationship: positively_regulates GO:0004674 ! protein serine/threonine kinase activity +created_by: midori +creation_date: 2010-09-15T03:09:57Z + +[Term] +id: GO:0071936 +name: coreceptor activity involved in Wnt signaling pathway +namespace: molecular_function +def: "In cooperation with a primary Wnt receptor, initiating a change in cell activity through the Wnt signaling pathway." [GOC:BHF, GOC:mah] +synonym: "coreceptor activity involved in Wnt receptor signaling pathway" EXACT [] +synonym: "coreceptor activity involved in Wnt receptor signalling pathway" EXACT [GOC:mah] +synonym: "coreceptor activity involved in Wnt-activated signaling pathway" EXACT [GOC:signaling] +is_a: GO:0015026 ! coreceptor activity +intersection_of: GO:0015026 ! coreceptor activity +intersection_of: part_of GO:0016055 ! Wnt signaling pathway +relationship: part_of GO:0016055 ! Wnt signaling pathway +created_by: midori +creation_date: 2010-09-30T03:54:34Z + +[Term] +id: GO:0071944 +name: cell periphery +namespace: cellular_component +def: "The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures." [GOC:mah] +is_a: GO:0044464 ! cell part +created_by: midori +creation_date: 2010-10-04T01:51:47Z + +[Term] +id: GO:0072001 +name: renal system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels." [GOC:mtg_kidney_jan10, GOC:yaf, http://en.wikibooks.org/wiki/Human_Physiology/The_Urinary_System] +synonym: "urinary system development" BROAD [GOC:yaf] +synonym: "urinary tract development" BROAD [GOC:yaf, PMID:17881463] +is_a: GO:0048731 ! system development +relationship: part_of GO:0001655 ! urogenital system development +created_by: midori +creation_date: 2010-01-25T10:31:00Z + +[Term] +id: GO:0072006 +name: nephron development +namespace: biological_process +def: "The process whose specific outcome is the progression of the nephron over time, from its formation to the mature structure. A nephron is the functional unit of the kidney." [GOC:mtg_kidney_jan10] +synonym: "nephrogenesis" RELATED [GOC:rph] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001822 ! kidney development +created_by: midori +creation_date: 2010-01-25T01:37:16Z + +[Term] +id: GO:0072007 +name: mesangial cell differentiation +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesangial cells of the kidney as it progresses from its formation to the mature state." [GOC:mtg_kidney_jan10] +is_a: GO:0061005 ! cell differentiation involved in kidney development +created_by: midori +creation_date: 2010-01-25T01:59:09Z + +[Term] +id: GO:0072008 +name: glomerular mesangial cell differentiation +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the glomerular mesangial cells of the kidney as it progresses from its formation to the mature state." [GOC:mtg_kidney_jan10] +is_a: GO:0035850 ! epithelial cell differentiation involved in kidney development +is_a: GO:0072007 ! mesangial cell differentiation +is_a: GO:0072071 ! renal interstitial cell differentiation +relationship: part_of GO:0072109 ! glomerular mesangium development +created_by: midori +creation_date: 2010-01-25T01:59:33Z + +[Term] +id: GO:0072009 +name: nephron epithelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of the nephron epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The nephron epithelium is a tissue that covers the surface of a nephron." [GOC:mtg_kidney_jan10] +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0072006 ! nephron development +created_by: midori +creation_date: 2010-01-25T02:01:39Z + +[Term] +id: GO:0072010 +name: glomerular epithelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of the glomerular epithelium over time, from its formation to the mature structure. The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the metanephros." [GOC:mtg_kidney_jan10] +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0032835 ! glomerulus development +created_by: midori +creation_date: 2010-01-25T02:02:14Z + +[Term] +id: GO:0072011 +name: glomerular endothelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of the glomerular endothelium over time, from its formation to the mature structure. The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus." [GOC:mtg_kidney_jan10] +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0072012 ! glomerulus vasculature development +created_by: midori +creation_date: 2010-01-25T02:02:57Z + +[Term] +id: GO:0072012 +name: glomerulus vasculature development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a glomerulus vasculature from an initial condition to its mature state. This process begins with the formation of the glomerulus vasculature and ends with the mature structure. The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus." [GOC:mtg_kidney_jan10] +synonym: "glomerulus capillary development" RELATED [GOC:mtg_kidney_jan10] +is_a: GO:0001568 ! blood vessel development +relationship: part_of GO:0032835 ! glomerulus development +relationship: part_of GO:0061440 ! kidney vasculature development +created_by: midori +creation_date: 2010-01-25T02:05:04Z + +[Term] +id: GO:0072028 +name: nephron morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the nephron are generated and organized. A nephron is the functional unit of the kidney." [GOC:mtg_kidney_jan10] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0060993 ! kidney morphogenesis +relationship: part_of GO:0072006 ! nephron development +created_by: midori +creation_date: 2010-01-25T02:45:52Z + +[Term] +id: GO:0072033 +name: renal vesicle formation +namespace: biological_process +def: "The developmental process pertaining to the initial formation of the renal vesicle from condensed mesenchymal cells. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." [GOC:mtg_kidney_jan10] +synonym: "nephron epithelium formation" RELATED [GOC:mtg_kidney_jan10] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0072077 ! renal vesicle morphogenesis +created_by: midori +creation_date: 2010-01-25T02:57:03Z + +[Term] +id: GO:0072034 +name: renal vesicle induction +namespace: biological_process +def: "Signaling at short range between cells of the ureteric bud terminus and the kidney mesenchyme that positively regulates the formation of the renal vesicle." [GOC:mtg_kidney_jan10] +synonym: "nephron induction" EXACT [GOC:mtg_kidney_jan10] +synonym: "positive regulation of nephron formation" EXACT [GOC:mtg_kidney_jan10] +is_a: GO:0031128 ! developmental induction +is_a: GO:0090184 ! positive regulation of kidney development +is_a: GO:2000027 ! regulation of organ morphogenesis +relationship: positively_regulates GO:0072033 ! renal vesicle formation +created_by: midori +creation_date: 2010-01-25T02:58:18Z + +[Term] +id: GO:0072044 +name: collecting duct development +namespace: biological_process +def: "The process whose specific outcome is the progression of a collecting duct over time, from its formation to the mature structure. The collecting duct responds to vasopressin and aldosterone to regulate water, electrolyte and acid-base balance. It is the final common path through which urine flows before entering the ureter and then emptying into the bladder." [GOC:mtg_kidney_jan10] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001822 ! kidney development +created_by: midori +creation_date: 2010-01-25T03:18:06Z + +[Term] +id: GO:0072048 +name: renal system pattern specification +namespace: biological_process +def: "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate into the anatomical structures of the renal system." [GOC:mtg_kidney_jan10] +synonym: "renal system pattern formation" RELATED [GOC:mtg_kidney_jan10] +is_a: GO:0007389 ! pattern specification process +relationship: part_of GO:0072001 ! renal system development +created_by: midori +creation_date: 2010-01-25T03:31:51Z + +[Term] +id: GO:0072053 +name: renal inner medulla development +namespace: biological_process +def: "The process whose specific outcome is the progression of the renal inner medulla over time, from its formation to the mature structure. The renal inner medulla is unique to mammalian kidneys and is the innermost region of the mammalian kidney." [GOC:mtg_kidney_jan10] +synonym: "inner renal medulla development" EXACT [GOC:mtg_kidney_jan10] +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001822 ! kidney development +created_by: midori +creation_date: 2010-01-25T03:59:37Z + +[Term] +id: GO:0072054 +name: renal outer medulla development +namespace: biological_process +def: "The process whose specific outcome is the progression of the renal outer medulla over time, from its formation to the mature structure. The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla." [GOC:mtg_kidney_jan10] +synonym: "outer renal medulla development" EXACT [GOC:mtg_kidney_jan10] +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0001822 ! kidney development +created_by: midori +creation_date: 2010-01-25T04:00:42Z + +[Term] +id: GO:0072060 +name: outer medullary collecting duct development +namespace: biological_process +def: "The process whose specific outcome is the progression of the outer medullary collecting duct over time, from its formation to the mature structure. The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla." [GOC:mtg_kidney_jan10] +is_a: GO:0072044 ! collecting duct development +created_by: midori +creation_date: 2010-01-25T04:08:18Z + +[Term] +id: GO:0072061 +name: inner medullary collecting duct development +namespace: biological_process +def: "The process whose specific outcome is the progression of the inner medullary collecting duct over time, from its formation to the mature structure. The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla." [GOC:mtg_kidney_jan10] +is_a: GO:0072044 ! collecting duct development +created_by: midori +creation_date: 2010-01-25T04:08:45Z + +[Term] +id: GO:0072070 +name: loop of Henle development +namespace: biological_process +alt_id: GO:0072018 +def: "The process whose specific outcome is the progression of the loop of Henle over time, from its formation to the mature structure. The loop of Henle is a nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule." [GOC:mtg_kidney_jan10] +synonym: "intermediate tubule development" EXACT [] +is_a: GO:0072080 ! nephron tubule development +created_by: midori +creation_date: 2010-01-25T04:20:27Z + +[Term] +id: GO:0072071 +name: renal interstitial cell differentiation +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the interstitial cells of the kidney as it progresses from its formation to the mature state." [GOC:mtg_kidney_jan10] +synonym: "kidney interstitial cell differentiation" EXACT [GOC:mtg_kidney_jan10] +is_a: GO:0061005 ! cell differentiation involved in kidney development +created_by: midori +creation_date: 2010-01-25T04:34:31Z + +[Term] +id: GO:0072073 +name: kidney epithelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of an epithelium in the kidney over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." [GOC:mtg_kidney_jan10] +is_a: GO:0060429 ! epithelium development +relationship: part_of GO:0001822 ! kidney development +created_by: midori +creation_date: 2010-01-25T04:37:42Z + +[Term] +id: GO:0072074 +name: kidney mesenchyme development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a kidney mesenchyme from an initial condition to its mature state. This process begins with the formation of kidney mesenchyme and ends with the mature structure. Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney." [GOC:mtg_kidney_jan10] +is_a: GO:0060485 ! mesenchyme development +relationship: part_of GO:0001822 ! kidney development +created_by: midori +creation_date: 2010-01-25T04:39:04Z + +[Term] +id: GO:0072075 +name: metanephric mesenchyme development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a metanephric mesenchyme from an initial condition to its mature state. This process begins with the formation of metanephric mesenchyme and ends with the mature structure. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros." [GOC:mtg_kidney_jan10] +is_a: GO:0072074 ! kidney mesenchyme development +relationship: part_of GO:0001656 ! metanephros development +created_by: midori +creation_date: 2010-01-25T04:40:11Z + +[Term] +id: GO:0072076 +name: nephrogenic mesenchyme development +namespace: biological_process +def: "The biological process whose specific outcome is the progression of a nephrogenic mesenchyme from an initial condition to its mature state. This process begins with the formation of nephrogenic mesenchyme and ends with the mature structure. Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron." [GOC:mtg_kidney_jan10] +is_a: GO:0072074 ! kidney mesenchyme development +relationship: part_of GO:0072006 ! nephron development +created_by: midori +creation_date: 2010-01-25T04:40:44Z + +[Term] +id: GO:0072077 +name: renal vesicle morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the renal vesicle are generated and organized. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." [GOC:mtg_kidney_jan10] +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0072028 ! nephron morphogenesis +relationship: part_of GO:0072087 ! renal vesicle development +relationship: part_of GO:0072088 ! nephron epithelium morphogenesis +created_by: midori +creation_date: 2010-02-01T02:21:06Z + +[Term] +id: GO:0072078 +name: nephron tubule morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a nephron tubule are generated and organized. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney." [GOC:mtg_kidney_jan10] +is_a: GO:0061333 ! renal tubule morphogenesis +is_a: GO:0072088 ! nephron epithelium morphogenesis +relationship: part_of GO:0072080 ! nephron tubule development +created_by: midori +creation_date: 2010-02-01T02:25:14Z + +[Term] +id: GO:0072079 +name: nephron tubule formation +namespace: biological_process +def: "The developmental process pertaining to the initial formation of a nephron tubule from unspecified parts. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney." [GOC:mtg_kidney_jan10] +is_a: GO:0001838 ! embryonic epithelial tube formation +relationship: part_of GO:0072078 ! nephron tubule morphogenesis +created_by: midori +creation_date: 2010-02-01T02:29:26Z + +[Term] +id: GO:0072080 +name: nephron tubule development +namespace: biological_process +def: "The progression of a nephron tubule over time, from its initial formation to the mature structure. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney." [GOC:mtg_kidney_jan10] +is_a: GO:0061326 ! renal tubule development +is_a: GO:0072009 ! nephron epithelium development +created_by: midori +creation_date: 2010-02-01T02:32:12Z + +[Term] +id: GO:0072087 +name: renal vesicle development +namespace: biological_process +def: "The process whose specific outcome is the progression of the renal vesicle over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." [GOC:mtg_kidney_jan10] +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0072009 ! nephron epithelium development +created_by: midori +creation_date: 2010-02-08T01:18:31Z + +[Term] +id: GO:0072088 +name: nephron epithelium morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the nephron epithelium are generated and organized. The nephron epithelium is a tissue that covers the surface of a nephron." [GOC:mtg_kidney_jan10] +is_a: GO:0002009 ! morphogenesis of an epithelium +relationship: part_of GO:0072009 ! nephron epithelium development +relationship: part_of GO:0072028 ! nephron morphogenesis +created_by: midori +creation_date: 2010-02-08T01:19:06Z + +[Term] +id: GO:0072089 +name: stem cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC:mtg_kidney_jan10] +is_a: GO:0008283 ! cell proliferation +created_by: midori +creation_date: 2010-02-08T02:03:36Z + +[Term] +id: GO:0072091 +name: regulation of stem cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC:mtg_kidney_jan10] +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072089 ! stem cell proliferation +relationship: regulates GO:0072089 ! stem cell proliferation +created_by: midori +creation_date: 2010-02-08T02:09:03Z + +[Term] +id: GO:0072109 +name: glomerular mesangium development +namespace: biological_process +def: "The process whose specific outcome is the progression of the glomerular mesangium over time, from its formation to the mature structure. The glomerular mesangium is the thin membrane connective tissue composed of mesangial cells, which helps to support the capillary loops in a renal glomerulus." [GOC:mtg_kidney_jan10] +is_a: GO:0061448 ! connective tissue development +relationship: part_of GO:0072012 ! glomerulus vasculature development +created_by: midori +creation_date: 2010-02-22T10:35:24Z + +[Term] +id: GO:0072112 +name: glomerular visceral epithelial cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a glomerular visceral epithelial cell. A glomerular visceral epithelial cell is a specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells." [GOC:mtg_kidney_jan10] +synonym: "podocyte differentiation" RELATED [GOC:mtg_kidney_jan10] +is_a: GO:0061318 ! renal filtration cell differentiation +is_a: GO:0072311 ! glomerular epithelial cell differentiation +created_by: midori +creation_date: 2010-02-22T10:52:11Z + +[Term] +id: GO:0072127 +name: renal capsule development +namespace: biological_process +def: "The process whose specific outcome is the progression of the renal capsule over time, from its formation to the mature structure. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands." [GOC:mtg_kidney_jan10] +is_a: GO:0061448 ! connective tissue development +relationship: part_of GO:0001822 ! kidney development +created_by: midori +creation_date: 2010-02-22T02:02:55Z + +[Term] +id: GO:0072128 +name: renal capsule morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the renal capsule are generated and organized. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands." [GOC:mtg_kidney_jan10] +is_a: GO:0009653 ! anatomical structure morphogenesis +is_a: GO:0044767 ! single-organism developmental process +relationship: part_of GO:0072127 ! renal capsule development +created_by: midori +creation_date: 2010-02-22T02:06:19Z + +[Term] +id: GO:0072129 +name: renal capsule formation +namespace: biological_process +def: "The developmental process pertaining to the initial formation of a renal capsule from unspecified parts. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands." [GOC:mtg_kidney_jan10] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0072128 ! renal capsule morphogenesis +created_by: midori +creation_date: 2010-02-22T02:08:14Z + +[Term] +id: GO:0072130 +name: renal capsule specification +namespace: biological_process +def: "The regionalization process in which the identity of the renal capsule is specified. Identity is considered to be the aggregate of characteristics by which a structure is recognized." [GOC:mtg_kidney_jan10] +is_a: GO:0003002 ! regionalization +is_a: GO:0061004 ! pattern specification involved in kidney development +relationship: part_of GO:0072129 ! renal capsule formation +created_by: midori +creation_date: 2010-02-22T02:12:34Z + +[Term] +id: GO:0072132 +name: mesenchyme morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of a mesenchymal tissue are generated and organized. A mesenchymal tissue is made up of loosely packed stellate cells." [GOC:mtg_kidney_jan10] +is_a: GO:0048729 ! tissue morphogenesis +relationship: part_of GO:0009887 ! organ morphogenesis +relationship: part_of GO:0060485 ! mesenchyme development +created_by: midori +creation_date: 2010-02-22T02:17:15Z + +[Term] +id: GO:0072141 +name: renal interstitial cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of a renal interstitial cell over time, from its formation to the mature structure." [GOC:mtg_kidney_jan10] +synonym: "kidney interstitial cell development" EXACT [GOC:mtg_kidney_jan10] +is_a: GO:0048468 ! cell development +relationship: part_of GO:0072071 ! renal interstitial cell differentiation +created_by: midori +creation_date: 2010-02-24T01:39:05Z + +[Term] +id: GO:0072143 +name: mesangial cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of a mesangial cell in the kidney over time, from its formation to the mature structure." [GOC:mtg_kidney_jan10] +is_a: GO:0048468 ! cell development +relationship: part_of GO:0072007 ! mesangial cell differentiation +created_by: midori +creation_date: 2010-02-24T01:44:28Z + +[Term] +id: GO:0072144 +name: glomerular mesangial cell development +namespace: biological_process +def: "The process whose specific outcome is the progression of a glomerular mesangial cell in the kidney over time, from its formation to the mature structure." [GOC:mtg_kidney_jan10] +is_a: GO:0002064 ! epithelial cell development +is_a: GO:0072141 ! renal interstitial cell development +is_a: GO:0072143 ! mesangial cell development +relationship: part_of GO:0072008 ! glomerular mesangial cell differentiation +created_by: midori +creation_date: 2010-02-24T01:53:13Z + +[Term] +id: GO:0072160 +name: nephron tubule epithelial cell differentiation +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the nephron tubule as it progresses from its formation to the mature state." [GOC:mtg_kidney_jan10] +is_a: GO:0035850 ! epithelial cell differentiation involved in kidney development +relationship: part_of GO:0072080 ! nephron tubule development +created_by: midori +creation_date: 2010-02-24T02:40:11Z + +[Term] +id: GO:0072161 +name: mesenchymal cell differentiation involved in kidney development +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the kidney as it progresses from its formation to the mature state." [GOC:mtg_kidney_jan10] +is_a: GO:0061005 ! cell differentiation involved in kidney development +is_a: GO:2001012 ! mesenchymal cell differentiation involved in renal system development +intersection_of: GO:0048762 ! mesenchymal cell differentiation +intersection_of: part_of GO:0001822 ! kidney development +relationship: part_of GO:0072074 ! kidney mesenchyme development +created_by: midori +creation_date: 2010-02-26T01:31:49Z + +[Term] +id: GO:0072162 +name: metanephric mesenchymal cell differentiation +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the metanephros as it progresses from its formation to the mature state." [GOC:mtg_kidney_jan10] +is_a: GO:0072161 ! mesenchymal cell differentiation involved in kidney development +is_a: GO:0072202 ! cell differentiation involved in metanephros development +relationship: part_of GO:0072075 ! metanephric mesenchyme development +created_by: midori +creation_date: 2010-02-26T01:35:00Z + +[Term] +id: GO:0072163 +name: mesonephric epithelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of an epithelium in the mesonephros over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." [GOC:mtg_kidney_jan10] +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0001823 ! mesonephros development +created_by: midori +creation_date: 2010-02-26T01:40:43Z + +[Term] +id: GO:0072164 +name: mesonephric tubule development +namespace: biological_process +def: "The progression of a mesonephric tubule over time, from its initial formation to the mature structure. A mesonephric tubule is an epithelial tube that is part of the mesonephros." [GOC:mtg_kidney_jan10] +is_a: GO:0035295 ! tube development +is_a: GO:0072163 ! mesonephric epithelium development +created_by: midori +creation_date: 2010-02-26T01:45:58Z + +[Term] +id: GO:0072170 +name: metanephric tubule development +namespace: biological_process +def: "The progression of a metanephric tubule over time, from its initial formation to the mature structure. A metanephric tubule is an epithelial tube that is part of the metanephros." [GOC:mtg_kidney_jan10] +is_a: GO:0035295 ! tube development +relationship: part_of GO:0001656 ! metanephros development +created_by: midori +creation_date: 2010-02-26T01:58:18Z + +[Term] +id: GO:0072175 +name: epithelial tube formation +namespace: biological_process +def: "The developmental process pertaining to the initial formation of an epithelial tube." [GOC:mtg_kidney_jan10] +is_a: GO:0035148 ! tube formation +relationship: part_of GO:0060562 ! epithelial tube morphogenesis +created_by: midori +creation_date: 2010-02-26T02:15:40Z + +[Term] +id: GO:0072182 +name: regulation of nephron tubule epithelial cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of nephron tubule epithelial cell differentiation." [GOC:mtg_kidney_jan10] +is_a: GO:2000696 ! regulation of epithelial cell differentiation involved in kidney development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072160 ! nephron tubule epithelial cell differentiation +relationship: regulates GO:0072160 ! nephron tubule epithelial cell differentiation +created_by: midori +creation_date: 2010-02-26T02:45:09Z + +[Term] +id: GO:0072201 +name: negative regulation of mesenchymal cell proliferation +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." [GOC:mtg_kidney_jan10] +is_a: GO:0010464 ! regulation of mesenchymal cell proliferation +is_a: GO:2000647 ! negative regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0010463 ! mesenchymal cell proliferation +relationship: negatively_regulates GO:0010463 ! mesenchymal cell proliferation +created_by: midori +creation_date: 2010-03-01T03:43:29Z + +[Term] +id: GO:0072202 +name: cell differentiation involved in metanephros development +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the metanephros as it progresses from its formation to the mature state." [GOC:mah, GOC:mtg_kidney_jan10] +is_a: GO:0061005 ! cell differentiation involved in kidney development +intersection_of: GO:0030154 ! cell differentiation +intersection_of: part_of GO:0001656 ! metanephros development +relationship: part_of GO:0001656 ! metanephros development +created_by: midori +creation_date: 2010-03-18T10:40:14Z + +[Term] +id: GO:0072205 +name: metanephric collecting duct development +namespace: biological_process +def: "The process whose specific outcome is the progression of a collecting duct in the metanephros over time, from its formation to the mature structure. The collecting duct responds to vasopressin and aldosterone to regulate water, electrolyte and acid-base balance. The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder." [GOC:mtg_kidney_jan10] +is_a: GO:0072044 ! collecting duct development +relationship: part_of GO:0001656 ! metanephros development +created_by: midori +creation_date: 2010-03-18T11:15:37Z + +[Term] +id: GO:0072207 +name: metanephric epithelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of an epithelium in the metanephros over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." [GOC:mtg_kidney_jan10] +is_a: GO:0072073 ! kidney epithelium development +relationship: part_of GO:0001656 ! metanephros development +created_by: midori +creation_date: 2010-03-18T11:50:37Z + +[Term] +id: GO:0072210 +name: metanephric nephron development +namespace: biological_process +def: "The process whose specific outcome is the progression of a nephron in the metanephros over time, from its formation to the mature structure. A nephron is the functional unit of the kidney." [GOC:mtg_kidney_jan10] +is_a: GO:0072006 ! nephron development +relationship: part_of GO:0001656 ! metanephros development +created_by: midori +creation_date: 2010-03-18T12:52:57Z + +[Term] +id: GO:0072213 +name: metanephric capsule development +namespace: biological_process +def: "The process whose specific outcome is the progression of the metanephric capsule over time, from its formation to the mature structure. The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage." [GOC:mtg_kidney_jan10] +is_a: GO:0072127 ! renal capsule development +relationship: part_of GO:0001656 ! metanephros development +created_by: midori +creation_date: 2010-03-18T01:25:19Z + +[Term] +id: GO:0072234 +name: metanephric nephron tubule development +namespace: biological_process +def: "The progression of a metanephric nephron tubule over time, from its initial formation to the mature structure. A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros." [GOC:mtg_kidney_jan10] +is_a: GO:0072080 ! nephron tubule development +is_a: GO:0072170 ! metanephric tubule development +is_a: GO:0072243 ! metanephric nephron epithelium development +created_by: midori +creation_date: 2010-03-18T03:41:23Z + +[Term] +id: GO:0072236 +name: metanephric loop of Henle development +namespace: biological_process +def: "The process whose specific outcome is the progression of the metanephric loop of Henle over time, from its formation to the mature structure. The metanephric loop of Henle is a metanephric nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule in the metanephros." [GOC:mtg_kidney_jan10] +synonym: "metanephric intermediate tubule development" EXACT [] +is_a: GO:0072070 ! loop of Henle development +relationship: part_of GO:0072234 ! metanephric nephron tubule development +created_by: midori +creation_date: 2010-03-18T03:46:18Z + +[Term] +id: GO:0072243 +name: metanephric nephron epithelium development +namespace: biological_process +def: "The process whose specific outcome is the progression of the metanephric nephron epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros." [GOC:mtg_kidney_jan10] +is_a: GO:0072009 ! nephron epithelium development +is_a: GO:0072207 ! metanephric epithelium development +created_by: midori +creation_date: 2010-03-19T03:29:49Z + +[Term] +id: GO:0072265 +name: metanephric capsule morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the metanephric capsule are generated and organized. The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage." [GOC:mtg_kidney_jan10] +is_a: GO:0072128 ! renal capsule morphogenesis +relationship: part_of GO:0072213 ! metanephric capsule development +created_by: midori +creation_date: 2010-03-30T02:54:49Z + +[Term] +id: GO:0072266 +name: metanephric capsule formation +namespace: biological_process +def: "The developmental process pertaining to the initial formation of a metanephric capsule from unspecified parts. The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage." [GOC:mtg_kidney_jan10] +is_a: GO:0072129 ! renal capsule formation +relationship: part_of GO:0072265 ! metanephric capsule morphogenesis +created_by: midori +creation_date: 2010-03-30T02:56:35Z + +[Term] +id: GO:0072267 +name: metanephric capsule specification +namespace: biological_process +def: "The regionalization process in which the identity of the metanephric capsule is specified. Identity is considered to be the aggregate of characteristics by which a structure is recognized." [GOC:mtg_kidney_jan10] +is_a: GO:0072130 ! renal capsule specification +is_a: GO:0072268 ! pattern specification involved in metanephros development +relationship: part_of GO:0072266 ! metanephric capsule formation +created_by: midori +creation_date: 2010-03-30T02:57:36Z + +[Term] +id: GO:0072268 +name: pattern specification involved in metanephros development +namespace: biological_process +def: "Any developmental process that results in the creation of defined areas or spaces within the metanephros to which cells respond and eventually are instructed to differentiate." [GOC:mtg_kidney_jan10] +synonym: "metanephros pattern formation" RELATED [GOC:mtg_kidney_jan10] +synonym: "metanephros pattern specification" EXACT [GOC:mtg_kidney_jan10] +synonym: "pattern formation involved in metanephros development" RELATED [GOC:mtg_kidney_jan10] +is_a: GO:0061004 ! pattern specification involved in kidney development +intersection_of: GO:0007389 ! pattern specification process +intersection_of: part_of GO:0001656 ! metanephros development +relationship: part_of GO:0001656 ! metanephros development +created_by: midori +creation_date: 2010-03-30T03:06:30Z + +[Term] +id: GO:0072273 +name: metanephric nephron morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the metanephric nephron are generated and organized. A metanephric nephron is the functional unit of the metanephros." [GOC:mtg_kidney_jan10] +is_a: GO:0072028 ! nephron morphogenesis +relationship: part_of GO:0003338 ! metanephros morphogenesis +relationship: part_of GO:0072210 ! metanephric nephron development +created_by: midori +creation_date: 2010-03-30T03:33:19Z + +[Term] +id: GO:0072283 +name: metanephric renal vesicle morphogenesis +namespace: biological_process +def: "The process in which the anatomical structures of the metanephric renal vesicle are generated and organized. The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells." [GOC:mtg_kidney_jan10] +is_a: GO:0072077 ! renal vesicle morphogenesis +relationship: part_of GO:0072273 ! metanephric nephron morphogenesis +created_by: midori +creation_date: 2010-04-01T03:28:00Z + +[Term] +id: GO:0072311 +name: glomerular epithelial cell differentiation +namespace: biological_process +def: "The process in which a relatively unspecialized cell acquires specialized features of a glomerular epithelial cell. Glomerular epithelial cells are specialized epithelial cells that form part of the glomerulus; there are two types, glomerular parietal epithelial cells and glomerular visceral epithelial cells." [GOC:mtg_kidney_jan10] +is_a: GO:0035850 ! epithelial cell differentiation involved in kidney development +relationship: part_of GO:0072010 ! glomerular epithelium development +created_by: midori +creation_date: 2010-04-09T06:49:21Z + +[Term] +id: GO:0072358 +name: cardiovascular system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the cardiovascular system over time, from its formation to the mature structure. The cardiovascular system is the anatomical system that has as its parts the heart and blood vessels." [GOC:mah, UBERON:0004535] +is_a: GO:0048731 ! system development +relationship: part_of GO:0072359 ! circulatory system development +created_by: midori +creation_date: 2010-11-16T11:25:49Z + +[Term] +id: GO:0072359 +name: circulatory system development +namespace: biological_process +def: "The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis." [GOC:mah, UBERON:0001009] +is_a: GO:0048731 ! system development +created_by: midori +creation_date: 2010-11-16T11:27:39Z + +[Term] +id: GO:0072498 +name: embryonic skeletal joint development +namespace: biological_process +def: "The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeletal joints over time, from formation to mature structure." [GOC:BHF, GOC:vk] +is_a: GO:0048706 ! embryonic skeletal system development +created_by: midori +creation_date: 2010-12-15T04:14:42Z + +[Term] +id: GO:0072503 +name: cellular divalent inorganic cation homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of divalent cations at the level of a cell." [GOC:mah] +comment: Note that this term was split from 'cellular di-, tri-valent inorganic cation homeostasis ; GO:0030005' (sibling term 'cellular trivalent inorganic cation homeostasis' ; GO:0072504'). +subset: gosubset_prok +is_a: GO:0030003 ! cellular cation homeostasis +is_a: GO:0072507 ! divalent inorganic cation homeostasis +created_by: midori +creation_date: 2010-12-16T01:25:40Z + +[Term] +id: GO:0072507 +name: divalent inorganic cation homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of divalent cations within an organism or cell." [GOC:mah] +comment: Note that this term was split from 'di-, tri-valent inorganic cation homeostasis ; GO:0055066' (sibling term 'trivalent inorganic cation homeostasis' ; GO:0072508'). +subset: gosubset_prok +is_a: GO:0055080 ! cation homeostasis +created_by: midori +creation_date: 2010-12-16T03:22:48Z + +[Term] +id: GO:0072511 +name: divalent inorganic cation transport +namespace: biological_process +def: "The directed movement of inorganic cations with a valency of two into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic cations are atoms or small molecules with a positive charge which do not contain carbon in covalent linkage." [GOC:mah] +subset: gosubset_prok +is_a: GO:0006812 ! cation transport +created_by: midori +creation_date: 2010-12-16T04:11:02Z + +[Term] +id: GO:0072521 +name: purine-containing compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof." [CHEBI:26401, GOC:mah] +synonym: "purine and derivative metabolic process" EXACT [GOC:curators] +synonym: "purine-containing compound metabolism" EXACT [GOC:mah] +is_a: GO:0006725 ! cellular aromatic compound metabolic process +is_a: GO:0034641 ! cellular nitrogen compound metabolic process +is_a: GO:0046483 ! heterocycle metabolic process +is_a: GO:1901360 ! organic cyclic compound metabolic process +is_a: GO:1901564 ! organonitrogen compound metabolic process +created_by: midori +creation_date: 2011-01-04T03:03:59Z + +[Term] +id: GO:0072523 +name: purine-containing compound catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof." [CHEBI:26401, GOC:mah] +synonym: "purine and derivative catabolic process" EXACT [GOC:curators] +synonym: "purine-containing compound breakdown" EXACT [GOC:mah] +synonym: "purine-containing compound catabolism" EXACT [GOC:mah] +synonym: "purine-containing compound degradation" EXACT [GOC:mah] +is_a: GO:0019439 ! aromatic compound catabolic process +is_a: GO:0044270 ! cellular nitrogen compound catabolic process +is_a: GO:0046700 ! heterocycle catabolic process +is_a: GO:0072521 ! purine-containing compound metabolic process +is_a: GO:1901361 ! organic cyclic compound catabolic process +is_a: GO:1901565 ! organonitrogen compound catabolic process +created_by: midori +creation_date: 2011-01-04T03:17:20Z + +[Term] +id: GO:0072594 +name: establishment of protein localization to organelle +namespace: biological_process +def: "The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle." [GOC:mah] +synonym: "establishment of protein localisation to organelle" EXACT [GOC:mah] +is_a: GO:0045184 ! establishment of protein localization +relationship: part_of GO:0033365 ! protein localization to organelle +created_by: midori +creation_date: 2011-02-14T01:56:51Z + +[Term] +id: GO:0072606 +name: interleukin-8 secretion +namespace: biological_process +def: "The regulated release of interleukin-8 from a cell." [GOC:BHF, GOC:mah, http://www.copewithcytokines.de/cope.cgi?key=interleukins] +synonym: "IL-8 secretion" EXACT [GOC:BHF] +is_a: GO:0050663 ! cytokine secretion +relationship: part_of GO:0032637 ! interleukin-8 production + +[Term] +id: GO:0072657 +name: protein localization to membrane +namespace: biological_process +def: "A process in which a protein is transported to, or maintained in, a specific location in a membrane." [GOC:mah] +synonym: "protein localisation in membrane" EXACT [GOC:mah] +synonym: "protein localization in membrane" EXACT [GOC:curators] +is_a: GO:0034613 ! cellular protein localization +is_a: GO:0044802 ! single-organism membrane organization +is_a: GO:1902580 ! single-organism cellular localization +created_by: midori +creation_date: 2011-02-14T02:35:18Z + +[Term] +id: GO:0072659 +name: protein localization to plasma membrane +namespace: biological_process +def: "A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane." [GOC:mah] +synonym: "protein localisation in plasma membrane" EXACT [GOC:mah] +synonym: "protein localization in plasma membrane" EXACT [GOC:curators] +is_a: GO:0007009 ! plasma membrane organization +is_a: GO:0072657 ! protein localization to membrane +created_by: midori +creation_date: 2011-02-14T02:43:05Z + +[Term] +id: GO:0072676 +name: lymphocyte migration +namespace: biological_process +def: "The movement of a lymphocyte within or between different tissues and organs of the body." [CL:0000542, GOC:BHF, GOC:mah] +is_a: GO:0050900 ! leukocyte migration +created_by: midori +creation_date: 2011-02-22T03:38:12Z + +[Term] +id: GO:0072678 +name: T cell migration +namespace: biological_process +def: "The movement of a T cell within or between different tissues and organs of the body." [CL:0000084, GOC:BHF, GOC:mah] +synonym: "T lymphocyte migration" EXACT [CL:0000084] +synonym: "T-cell migration" EXACT [CL:0000084] +synonym: "T-lymphocyte migration" EXACT [CL:0000084] +is_a: GO:0072676 ! lymphocyte migration +created_by: midori +creation_date: 2011-02-22T03:40:40Z + +[Term] +id: GO:0080090 +name: regulation of primary metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [PMID:19211694] +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044238 ! primary metabolic process +relationship: regulates GO:0044238 ! primary metabolic process +created_by: donghui +creation_date: 2009-04-22T04:30:52Z + +[Term] +id: GO:0080134 +name: regulation of response to stress +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:dhl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006950 ! response to stress +relationship: regulates GO:0006950 ! response to stress +created_by: donghui +creation_date: 2009-05-06T04:51:28Z + +[Term] +id: GO:0080135 +name: regulation of cellular response to stress +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of a cellular response to stress. Cellular response to stress is a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:dhl] +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0080134 ! regulation of response to stress +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0033554 ! cellular response to stress +relationship: regulates GO:0033554 ! cellular response to stress +created_by: donghui +creation_date: 2009-05-06T05:02:52Z + +[Term] +id: GO:0090002 +name: establishment of protein localization to plasma membrane +namespace: biological_process +def: "The directed movement of a protein to a specific location in the plasma membrane." [GOC:dph, GOC:tb] +synonym: "establishment of protein localisation in plasma membrane" EXACT [GOC:mah] +synonym: "establishment of protein localization in plasma membrane" EXACT [GOC:curators] +is_a: GO:0090150 ! establishment of protein localization to membrane +relationship: part_of GO:0072659 ! protein localization to plasma membrane +created_by: tanyaberardini +creation_date: 2009-07-10T10:29:23Z + +[Term] +id: GO:0090009 +name: primitive streak formation +namespace: biological_process +def: "The developmental process pertaining to the initial formation of the primitive streak from unspecified parts. The primitive streak is a ridge of cells running along the midline of the embryo where the mesoderm ingresses. It defines the anterior-posterior axis." [GOC:dph, GOC:sdb_2009, GOC:tb] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +relationship: part_of GO:0001702 ! gastrulation with mouth forming second +relationship: part_of GO:0009948 ! anterior/posterior axis specification +created_by: tanyaberardini +creation_date: 2009-07-29T10:31:31Z + +[Term] +id: GO:0090030 +name: regulation of steroid hormone biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones." [GOC:dph, GOC:tb] +is_a: GO:0046885 ! regulation of hormone biosynthetic process +is_a: GO:0050810 ! regulation of steroid biosynthetic process +created_by: tanyaberardini +creation_date: 2009-08-03T10:38:27Z + +[Term] +id: GO:0090031 +name: positive regulation of steroid hormone biosynthetic process +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones." [GOC:dph, GOC:tb] +is_a: GO:0010893 ! positive regulation of steroid biosynthetic process +is_a: GO:0046886 ! positive regulation of hormone biosynthetic process +is_a: GO:0090030 ! regulation of steroid hormone biosynthetic process +created_by: tanyaberardini +creation_date: 2009-08-03T10:40:32Z + +[Term] +id: GO:0090036 +name: regulation of protein kinase C signaling +namespace: biological_process +def: "Any process that modulates the frequency, rate, or extent of a series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound." [GOC:dph, GOC:tb] +synonym: "regulation of protein kinase C signaling cascade" RELATED [GOC:signaling] +synonym: "regulation of protein kinase C signalling cascade" RELATED [GOC:mah] +is_a: GO:1902531 ! regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070528 ! protein kinase C signaling +relationship: regulates GO:0070528 ! protein kinase C signaling +created_by: tanyaberardini +creation_date: 2009-08-03T11:27:26Z + +[Term] +id: GO:0090037 +name: positive regulation of protein kinase C signaling +namespace: biological_process +def: "Any process that increases the frequency, rate, or extent of a series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound." [GOC:dph, GOC:tb] +synonym: "positive regulation of protein kinase C signaling cascade" RELATED [GOC:signaling] +synonym: "positive regulation of protein kinase C signalling cascade" EXACT [GOC:mah] +is_a: GO:0090036 ! regulation of protein kinase C signaling +is_a: GO:1902533 ! positive regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0070528 ! protein kinase C signaling +relationship: positively_regulates GO:0070528 ! protein kinase C signaling +created_by: tanyaberardini +creation_date: 2009-08-03T11:28:44Z + +[Term] +id: GO:0090049 +name: regulation of cell migration involved in sprouting angiogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell migration involved in sprouting angiogenesis. Cell migration involved in sprouting angiogenesis is the orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels contributing to the process of sprouting angiogenesis." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb] +is_a: GO:0043535 ! regulation of blood vessel endothelial cell migration +is_a: GO:0045765 ! regulation of angiogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002042 ! cell migration involved in sprouting angiogenesis +relationship: regulates GO:0002042 ! cell migration involved in sprouting angiogenesis +created_by: tanyaberardini +creation_date: 2009-08-07T10:37:16Z + +[Term] +id: GO:0090050 +name: positive regulation of cell migration involved in sprouting angiogenesis +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of cell migration involved in sprouting angiogenesis. Cell migration involved in sprouting angiogenesis is the orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels contributing to the process of sprouting angiogenesis." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb] +is_a: GO:0043536 ! positive regulation of blood vessel endothelial cell migration +is_a: GO:0045766 ! positive regulation of angiogenesis +is_a: GO:0090049 ! regulation of cell migration involved in sprouting angiogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002042 ! cell migration involved in sprouting angiogenesis +relationship: positively_regulates GO:0002042 ! cell migration involved in sprouting angiogenesis +created_by: tanyaberardini +creation_date: 2009-08-07T10:41:09Z + +[Term] +id: GO:0090066 +name: regulation of anatomical structure size +namespace: biological_process +def: "Any process that modulates the size of an anatomical structure." [GOC:dph, GOC:tb] +subset: gosubset_prok +is_a: GO:0065008 ! regulation of biological quality +created_by: tanyaberardini +creation_date: 2009-09-02T11:00:08Z + +[Term] +id: GO:0090068 +name: positive regulation of cell cycle process +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events." [GOC:dph, GOC:tb] +is_a: GO:0010564 ! regulation of cell cycle process +is_a: GO:0048522 ! positive regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0022402 ! cell cycle process +relationship: positively_regulates GO:0022402 ! cell cycle process +created_by: tanyaberardini +creation_date: 2009-09-09T11:39:52Z + +[Term] +id: GO:0090087 +name: regulation of peptide transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb] +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0015833 ! peptide transport +relationship: regulates GO:0015833 ! peptide transport +created_by: tanyaberardini +creation_date: 2009-10-23T11:21:38Z + +[Term] +id: GO:0090090 +name: negative regulation of canonical Wnt signaling pathway +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes." [GOC:dph, GOC:tb] +synonym: "negative regulation of canonical Wnt receptor signaling pathway" EXACT [] +synonym: "negative regulation of canonical Wnt receptor signalling pathway" EXACT [GOC:mah] +synonym: "negative regulation of canonical Wnt-activated signaling pathway" EXACT [GOC:signaling] +synonym: "negative regulation of Wnt receptor signaling pathway through beta-catenin" EXACT [GOC:mtg_signal] +is_a: GO:0030178 ! negative regulation of Wnt signaling pathway +is_a: GO:0060828 ! regulation of canonical Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0060070 ! canonical Wnt signaling pathway +relationship: negatively_regulates GO:0060070 ! canonical Wnt signaling pathway +created_by: tanyaberardini +creation_date: 2009-10-30T11:27:17Z + +[Term] +id: GO:0090092 +name: regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the series of molecular signals generated as a consequence of a transmembrane receptor serine/threonine kinase binding to its physiological ligand." [GOC:dph, GOC:tb] +synonym: "regulation of transmembrane receptor protein serine/threonine kinase signalling pathway" EXACT [GOC:mah] +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +relationship: regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +created_by: tanyaberardini +creation_date: 2009-11-04T11:46:40Z + +[Term] +id: GO:0090100 +name: positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of the series of molecular signals generated as a consequence of a transmembrane receptor serine/threonine kinase binding to its physiological ligand." [GOC:dph, GOC:tb] +synonym: "positive regulation of transmembrane receptor protein serine/threonine kinase signalling pathway" EXACT [GOC:mah] +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:0090092 ! regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +relationship: positively_regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +created_by: tanyaberardini +creation_date: 2009-11-13T10:55:53Z + +[Term] +id: GO:0090101 +name: negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of the series of molecular signals generated as a consequence of a transmembrane receptor serine/threonine kinase binding to its physiological ligand." [GOC:dph, GOC:tb] +synonym: "negative regulation of transmembrane receptor protein serine/threonine kinase signalling pathway" EXACT [GOC:mah] +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:0090092 ! regulation of transmembrane receptor protein serine/threonine kinase signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +relationship: negatively_regulates GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway +created_by: tanyaberardini +creation_date: 2009-11-13T10:56:52Z + +[Term] +id: GO:0090102 +name: cochlea development +namespace: biological_process +def: "The progression of the cochlea over time from its formation to the mature structure. The cochlea is the snail-shaped portion of the inner ear that is responsible for the detection of sound." [GOC:dph, GOC:tb] +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development +relationship: part_of GO:0048839 ! inner ear development +created_by: tanyaberardini +creation_date: 2009-11-18T11:42:15Z + +[Term] +id: GO:0090103 +name: cochlea morphogenesis +namespace: biological_process +def: "The process in which the cochlea is generated and organized." [GOC:dph, GOC:tb] +is_a: GO:0048598 ! embryonic morphogenesis +relationship: part_of GO:0042472 ! inner ear morphogenesis +relationship: part_of GO:0090102 ! cochlea development +created_by: tanyaberardini +creation_date: 2009-11-18T11:45:11Z + +[Term] +id: GO:0090109 +name: regulation of cell-substrate junction assembly +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of cell-substrate junction assembly. Cell-substrate junction assembly is the aggregation, arrangement and bonding together of a set of components to form a junction between a cell and its substrate." [GOC:dph, GOC:tb] +is_a: GO:1901888 ! regulation of cell junction assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007044 ! cell-substrate junction assembly +relationship: regulates GO:0007044 ! cell-substrate junction assembly +created_by: tanyaberardini +creation_date: 2009-11-25T11:00:58Z + +[Term] +id: GO:0090118 +name: receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport +namespace: biological_process +def: "A receptor-mediated endocytosis process that results in the uptake of low-density lipoprotein by cells." [GOC:ascb_2009, GOC:dph, GOC:tb] +synonym: "receptor-mediated endocytosis of LDL" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb] +synonym: "receptor-mediated endocytosis of low-density lipoprotein involved in cholesterol transport" RELATED [GOC:dph] +is_a: GO:0006898 ! receptor-mediated endocytosis +is_a: GO:0044765 ! single-organism transport +relationship: part_of GO:0032367 ! intracellular cholesterol transport +relationship: part_of GO:0034383 ! low-density lipoprotein particle clearance +created_by: tanyaberardini +creation_date: 2009-12-07T12:06:05Z + +[Term] +id: GO:0090130 +name: tissue migration +namespace: biological_process +def: "The process in which the population of cells that make up a tissue undergo directed movement." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0044707 ! single-multicellular organism process +created_by: tanyaberardini +creation_date: 2009-12-07T03:13:55Z + +[Term] +id: GO:0090132 +name: epithelium migration +namespace: biological_process +def: "The process in which the population of cells that make up an epithelium undergo directed movement." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0090130 ! tissue migration +created_by: tanyaberardini +creation_date: 2009-12-07T03:19:34Z + +[Term] +id: GO:0090150 +name: establishment of protein localization to membrane +namespace: biological_process +def: "The directed movement of a protein to a specific location in a membrane." [GOC:ascb_2009, GOC:dph, GOC:tb] +synonym: "establishment of protein localisation in membrane" EXACT [GOC:mah] +synonym: "establishment of protein localization in membrane" EXACT [GOC:curators] +is_a: GO:0045184 ! establishment of protein localization +relationship: part_of GO:0072657 ! protein localization to membrane +created_by: tanyaberardini +creation_date: 2009-12-08T03:18:51Z + +[Term] +id: GO:0090175 +name: regulation of establishment of planar polarity +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of the establishment of planar polarity, the coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001736 ! establishment of planar polarity +relationship: regulates GO:0001736 ! establishment of planar polarity +created_by: tanyaberardini +creation_date: 2009-12-14T10:29:41Z + +[Term] +id: GO:0090177 +name: establishment of planar polarity involved in neural tube closure +namespace: biological_process +def: "Coordinated organization of groups of cells in the plane of an epithelium that contributes to the closure of the neural tube." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0042249 ! establishment of planar polarity of embryonic epithelium +is_a: GO:0048598 ! embryonic morphogenesis +intersection_of: GO:0001736 ! establishment of planar polarity +intersection_of: part_of GO:0001843 ! neural tube closure +relationship: part_of GO:0001843 ! neural tube closure +created_by: tanyaberardini +creation_date: 2009-12-14T10:38:46Z + +[Term] +id: GO:0090178 +name: regulation of establishment of planar polarity involved in neural tube closure +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the establishment of planar polarity involved in neural tube closure, the coordinated organization of groups of cells in the plane of an epithelium that contributes to the closure of the neural tube." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051960 ! regulation of nervous system development +is_a: GO:0090175 ! regulation of establishment of planar polarity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0090177 ! establishment of planar polarity involved in neural tube closure +relationship: regulates GO:0090177 ! establishment of planar polarity involved in neural tube closure +created_by: tanyaberardini +creation_date: 2009-12-14T11:14:27Z + +[Term] +id: GO:0090179 +name: planar cell polarity pathway involved in neural tube closure +namespace: biological_process +def: "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors that modulates the establishment of planar polarity contributing to neural tube closure." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway +is_a: GO:0090178 ! regulation of establishment of planar polarity involved in neural tube closure +created_by: tanyaberardini +creation_date: 2009-12-14T11:20:27Z + +[Term] +id: GO:0090183 +name: regulation of kidney development +namespace: biological_process +def: "Any process that modulates the rate, frequency or extent of kidney development. Kidney development is the process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." [GOC:dph, GOC:tb, GOC:yaf] +synonym: "regulation of nephrogenesis" RELATED [GOC:dph, GOC:tb] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001822 ! kidney development +relationship: regulates GO:0001822 ! kidney development +created_by: tanyaberardini +creation_date: 2009-12-18T10:50:56Z + +[Term] +id: GO:0090184 +name: positive regulation of kidney development +namespace: biological_process +def: "Any process that increases the rate, frequency or extent of kidney development. Kidney development is the process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." [GOC:dph, GOC:tb, GOC:yaf] +synonym: "positive regulation of nephrogenesis" RELATED [GOC:dph, GOC:tb] +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +is_a: GO:0090183 ! regulation of kidney development +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0001822 ! kidney development +relationship: positively_regulates GO:0001822 ! kidney development +created_by: tanyaberardini +creation_date: 2009-12-18T10:52:01Z + +[Term] +id: GO:0090244 +name: Wnt signaling pathway involved in somitogenesis +namespace: biological_process +def: "The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state that contributes to somitogenesis." [GOC:ascb_2009, GOC:dph, GOC:tb] +synonym: "Wnt receptor signaling pathway involved in somitogenesis" EXACT [] +synonym: "Wnt receptor signalling" EXACT [GOC:mah] +synonym: "Wnt-activated signaling pathway involved in somitogenesis" EXACT [GOC:signaling] +is_a: GO:0016055 ! Wnt signaling pathway +intersection_of: GO:0016055 ! Wnt signaling pathway +intersection_of: part_of GO:0001756 ! somitogenesis +relationship: part_of GO:0001756 ! somitogenesis +created_by: tanyaberardini +creation_date: 2010-01-22T10:47:59Z + +[Term] +id: GO:0090245 +name: axis elongation involved in somitogenesis +namespace: biological_process +def: "The developmental growth that results in the elongation of the rostral-caudal axis that contributes to somitogenesis." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0003401 ! axis elongation +intersection_of: GO:0003401 ! axis elongation +intersection_of: part_of GO:0001756 ! somitogenesis +relationship: part_of GO:0001756 ! somitogenesis +created_by: tanyaberardini +creation_date: 2010-01-22T10:54:29Z + +[Term] +id: GO:0090246 +name: convergent extension involved in somitogenesis +namespace: biological_process +def: "The morphogenetic process in which a presomitic mesoderm narrows along the left-right axis and lengthens in the rostral-caudal axis contributing to somitogenesis." [GOC:ascb_2009, GOC:dph, GOC:tb] +is_a: GO:0048598 ! embryonic morphogenesis +is_a: GO:0060028 ! convergent extension involved in axis elongation +intersection_of: GO:0060026 ! convergent extension +intersection_of: part_of GO:0001756 ! somitogenesis +relationship: part_of GO:0090245 ! axis elongation involved in somitogenesis +created_by: tanyaberardini +creation_date: 2010-01-22T10:59:06Z + +[Term] +id: GO:0090263 +name: positive regulation of canonical Wnt signaling pathway +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes." [GOC:tb] +synonym: "positive regulation of canonical Wnt receptor signaling pathway" EXACT [] +synonym: "positive regulation of canonical Wnt receptor signalling pathway" EXACT [GOC:mah] +synonym: "positive regulation of canonical Wnt-activated signaling pathway" EXACT [GOC:signaling] +synonym: "positive regulation of Wnt receptor signaling pathway through beta-catenin" EXACT [GOC:mtg_signal] +is_a: GO:0030177 ! positive regulation of Wnt signaling pathway +is_a: GO:0060828 ! regulation of canonical Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0060070 ! canonical Wnt signaling pathway +relationship: positively_regulates GO:0060070 ! canonical Wnt signaling pathway +created_by: tanyaberardini +creation_date: 2010-02-03T04:32:16Z + +[Term] +id: GO:0090276 +name: regulation of peptide hormone secretion +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules." [GOC:tb] +is_a: GO:0002791 ! regulation of peptide secretion +is_a: GO:0046883 ! regulation of hormone secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0030072 ! peptide hormone secretion +relationship: regulates GO:0030072 ! peptide hormone secretion +created_by: tanyaberardini +creation_date: 2010-02-05T02:56:39Z + +[Term] +id: GO:0090278 +name: negative regulation of peptide hormone secretion +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules." [GOC:tb] +is_a: GO:0002792 ! negative regulation of peptide secretion +is_a: GO:0046888 ! negative regulation of hormone secretion +is_a: GO:0090276 ! regulation of peptide hormone secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0030072 ! peptide hormone secretion +relationship: negatively_regulates GO:0030072 ! peptide hormone secretion +created_by: tanyaberardini +creation_date: 2010-02-05T02:56:39Z + +[Term] +id: GO:0090279 +name: regulation of calcium ion import +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle." [GOC:BHF] +synonym: "regulation of transmembrane calcium influx" RELATED [GOC:tb] +is_a: GO:0034765 ! regulation of ion transmembrane transport +is_a: GO:0051924 ! regulation of calcium ion transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070509 ! calcium ion import +relationship: regulates GO:0070509 ! calcium ion import +created_by: tanyaberardini +creation_date: 2010-02-08T05:11:20Z + +[Term] +id: GO:0090287 +name: regulation of cellular response to growth factor stimulus +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:tb] +is_a: GO:0048583 ! regulation of response to stimulus +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0071363 ! cellular response to growth factor stimulus +relationship: regulates GO:0071363 ! cellular response to growth factor stimulus +created_by: tanyaberardini +creation_date: 2010-02-18T03:01:25Z + +[Term] +id: GO:0090288 +name: negative regulation of cellular response to growth factor stimulus +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:BHF] +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0048585 ! negative regulation of response to stimulus +is_a: GO:0090287 ! regulation of cellular response to growth factor stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0071363 ! cellular response to growth factor stimulus +relationship: negatively_regulates GO:0071363 ! cellular response to growth factor stimulus +created_by: tanyaberardini +creation_date: 2010-02-18T03:01:25Z + +[Term] +id: GO:0090303 +name: positive regulation of wound healing +namespace: biological_process +def: "Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." [GOC:BHF] +is_a: GO:0048584 ! positive regulation of response to stimulus +is_a: GO:0061041 ! regulation of wound healing +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0042060 ! wound healing +relationship: positively_regulates GO:0042060 ! wound healing +created_by: tanyaberardini +creation_date: 2010-03-22T02:12:03Z + +[Term] +id: GO:0090304 +name: nucleic acid metabolic process +namespace: biological_process +def: "Any cellular metabolic process involving nucleic acids." [GOC:dph, GOC:tb] +is_a: GO:0006139 ! nucleobase-containing compound metabolic process +is_a: GO:0043170 ! macromolecule metabolic process +created_by: tanyaberardini +creation_date: 2010-04-07T10:18:47Z + +[Term] +id: GO:0090305 +name: nucleic acid phosphodiester bond hydrolysis +namespace: biological_process +def: "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC:dph, GOC:tb] +synonym: "nucleic acid cleavage" EXACT [GOC:dph, GOC:tb] +is_a: GO:0090304 ! nucleic acid metabolic process +created_by: tanyaberardini +creation_date: 2010-04-07T10:26:30Z + +[Term] +id: GO:0090316 +name: positive regulation of intracellular protein transport +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells." [GOC:tb] +is_a: GO:0032388 ! positive regulation of intracellular transport +is_a: GO:0033157 ! regulation of intracellular protein transport +is_a: GO:0051222 ! positive regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006886 ! intracellular protein transport +relationship: positively_regulates GO:0006886 ! intracellular protein transport +created_by: tanyaberardini +creation_date: 2010-04-16T03:45:07Z + +[Term] +id: GO:0090317 +name: negative regulation of intracellular protein transport +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells." [GOC:tb] +is_a: GO:0032387 ! negative regulation of intracellular transport +is_a: GO:0033157 ! regulation of intracellular protein transport +is_a: GO:0051224 ! negative regulation of protein transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006886 ! intracellular protein transport +relationship: negatively_regulates GO:0006886 ! intracellular protein transport +created_by: tanyaberardini +creation_date: 2010-04-16T03:45:07Z + +[Term] +id: GO:0090342 +name: regulation of cell aging +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0050794 ! regulation of cellular process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007569 ! cell aging +relationship: regulates GO:0007569 ! cell aging +created_by: tanyaberardini +creation_date: 2010-06-02T10:12:37Z + +[Term] +id: GO:0090344 +name: negative regulation of cell aging +namespace: biological_process +def: "Any process that decreases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb] +is_a: GO:0048523 ! negative regulation of cellular process +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:0090342 ! regulation of cell aging +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0007569 ! cell aging +relationship: negatively_regulates GO:0007569 ! cell aging +created_by: tanyaberardini +creation_date: 2010-06-02T10:12:37Z + +[Term] +id: GO:0090381 +name: regulation of heart induction +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of heart induction. Heart induction is the close range interaction between mesoderm and endoderm or ectoderm that causes cells to change their fates and specify the development of the heart." [GOC:dph, GOC:tb] +is_a: GO:0010453 ! regulation of cell fate commitment +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0023051 ! regulation of signaling +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003129 ! heart induction +relationship: regulates GO:0003129 ! heart induction +created_by: tanyaberardini +creation_date: 2010-10-04T10:23:43Z + +[Term] +id: GO:0090495 +name: low-density lipoprotein particle disassembly +namespace: biological_process +def: "The disaggregation of a low-density lipoprotein particle into its constituent components." [GOC:dph, GOC:tb] +is_a: GO:0071829 ! plasma lipoprotein particle disassembly +created_by: tanyaberardini +creation_date: 2012-10-17T11:48:56Z + +[Term] +id: GO:0090504 +name: epiboly +namespace: biological_process +def: "The expansion of one cell sheet over other cells or yolk." [GOC:dph, GOC:tb] +is_a: GO:0002011 ! morphogenesis of an epithelial sheet +created_by: tanyaberardini +creation_date: 2012-10-22T12:29:52Z + +[Term] +id: GO:0090505 +name: epiboly involved in wound healing +namespace: biological_process +def: "The expansion of one cell sheet over other cells involved in wound healing." [GOC:dph, GOC:tb] +is_a: GO:0090504 ! epiboly +intersection_of: GO:0090504 ! epiboly +intersection_of: part_of GO:0042060 ! wound healing +relationship: part_of GO:0042060 ! wound healing +created_by: tanyaberardini +creation_date: 2012-10-22T12:38:51Z + +[Term] +id: GO:0097006 +name: regulation of plasma lipoprotein particle levels +namespace: biological_process +def: "Any process involved in the maintenance of internal levels of plasma lipoprotein particles within an organism." [GOC:BHF] +synonym: "plasma lipoprotein particle homeostasis" NARROW [] +is_a: GO:0050789 ! regulation of biological process +created_by: paola +creation_date: 2011-03-15T09:52:53Z + +[Term] +id: GO:0097061 +name: dendritic spine organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a dendritic spine. A dendritic spine is a specialized protrusion from a neuronal dendrite and is involved in synaptic transmission." [GOC:BHF, PMID:20410104] +synonym: "dendritic spine organisation" EXACT [] +is_a: GO:0016043 ! cellular component organization +is_a: GO:0044763 ! single-organism cellular process +created_by: paola +creation_date: 2011-06-07T11:26:53Z + +[Term] +id: GO:0097153 +name: cysteine-type endopeptidase activity involved in apoptotic process +namespace: molecular_function +def: "Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile, and contributing to the apoptotic process." [GOC:mtg_apoptosis] +synonym: "caspase activity" BROAD [] +synonym: "metacaspase activity" NARROW [GOC:mtg_apoptosis] +is_a: GO:0004197 ! cysteine-type endopeptidase activity +intersection_of: GO:0004197 ! cysteine-type endopeptidase activity +intersection_of: part_of GO:0006915 ! apoptotic process +relationship: part_of GO:0006915 ! apoptotic process +created_by: paola +creation_date: 2011-09-09T10:21:56Z + +[Term] +id: GO:0097159 +name: organic cyclic compound binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." [CHEBI:33832, GOC:sjw, PMID:7583672] +is_a: GO:0005488 ! binding +created_by: paola +creation_date: 2011-09-23T02:31:01Z + +[Term] +id: GO:0097190 +name: apoptotic signaling pathway +namespace: biological_process +alt_id: GO:0008624 +def: "A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis] +comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. +synonym: "apoptotic signalling pathway" EXACT [GOC:mah] +synonym: "induction of apoptosis by extracellular signals" EXACT [] +xref: Reactome:REACT_101039 "Ceramide signalling, Canis familiaris" +xref: Reactome:REACT_101287 "Death Receptor Signalling, Xenopus tropicalis" +xref: Reactome:REACT_101722 "FasL/ CD95L signaling, Rattus norvegicus" +xref: Reactome:REACT_102105 "FASL binds FAS Receptor, Taeniopygia guttata" +xref: Reactome:REACT_102682 "Ceramide signalling, Bos taurus" +xref: Reactome:REACT_103565 "Death Receptor Signalling, Danio rerio" +xref: Reactome:REACT_104430 "Ceramide signalling, Gallus gallus" +xref: Reactome:REACT_104446 "Death Receptor Signalling, Bos taurus" +xref: Reactome:REACT_104880 "Cell death signalling via NRAGE, NRIF and NADE, Drosophila melanogaster" +xref: Reactome:REACT_105789 "Cell death signalling via NRAGE, NRIF and NADE, Canis familiaris" +xref: Reactome:REACT_1059 "Extrinsic Pathway for Apoptosis, Homo sapiens" +xref: Reactome:REACT_106019 "Ceramide signalling, Caenorhabditis elegans" +xref: Reactome:REACT_106417 "Cell death signalling via NRAGE, NRIF and NADE, Oryza sativa" +xref: Reactome:REACT_107145 "FASL binds FAS Receptor, Rattus norvegicus" +xref: Reactome:REACT_107277 "Cell death signalling via NRAGE, NRIF and NADE, Rattus norvegicus" +xref: Reactome:REACT_108226 "Ceramide signalling, Rattus norvegicus" +xref: Reactome:REACT_108738 "FASL binds FAS Receptor, Canis familiaris" +xref: Reactome:REACT_108954 "Cell death signalling via NRAGE, NRIF and NADE, Sus scrofa" +xref: Reactome:REACT_110327 "FASL binds FAS Receptor, Gallus gallus" +xref: Reactome:REACT_110777 "Extrinsic Pathway for Apoptosis, Canis familiaris" +xref: Reactome:REACT_113012 "Extrinsic Pathway for Apoptosis, Caenorhabditis elegans" +xref: Reactome:REACT_113720 "FasL/ CD95L signaling, Xenopus tropicalis" +xref: Reactome:REACT_114928 "Cell death signalling via NRAGE, NRIF and NADE, Dictyostelium discoideum" +xref: Reactome:REACT_115331 "FASL binds FAS Receptor, Xenopus tropicalis" +xref: Reactome:REACT_13720 "Cell death signalling via NRAGE, NRIF and NADE, Homo sapiens" +xref: Reactome:REACT_13806 "Ceramide signalling, Homo sapiens" +xref: Reactome:REACT_1426 "FASL binds FAS Receptor, Homo sapiens" +xref: Reactome:REACT_1619 "Death Receptor Signalling, Homo sapiens" +xref: Reactome:REACT_28136 "Death Receptor Signalling, Taeniopygia guttata" +xref: Reactome:REACT_30777 "Death Receptor Signalling, Sus scrofa" +xref: Reactome:REACT_32035 "FasL/ CD95L signaling, Danio rerio" +xref: Reactome:REACT_33023 "Ceramide signalling, Xenopus tropicalis" +xref: Reactome:REACT_33363 "Death Receptor Signalling, Gallus gallus" +xref: Reactome:REACT_47012 "Death Receptor Signalling, Mus musculus" +xref: Reactome:REACT_78512 "Ceramide signalling, Taeniopygia guttata" +xref: Reactome:REACT_78709 "Ceramide signalling, Drosophila melanogaster" +xref: Reactome:REACT_79738 "Extrinsic Pathway for Apoptosis, Xenopus tropicalis" +xref: Reactome:REACT_81353 "Ceramide signalling, Mus musculus" +xref: Reactome:REACT_81381 "FasL/ CD95L signaling, Gallus gallus" +xref: Reactome:REACT_82611 "Cell death signalling via NRAGE, NRIF and NADE, Taeniopygia guttata" +xref: Reactome:REACT_83750 "Extrinsic Pathway for Apoptosis, Gallus gallus" +xref: Reactome:REACT_84151 "Extrinsic Pathway for Apoptosis, Bos taurus" +xref: Reactome:REACT_85830 "Cell death signalling via NRAGE, NRIF and NADE, Danio rerio" +xref: Reactome:REACT_86320 "Cell death signalling via NRAGE, NRIF and NADE, Gallus gallus" +xref: Reactome:REACT_86807 "Death Receptor Signalling, Canis familiaris" +xref: Reactome:REACT_88410 "Cell death signalling via NRAGE, NRIF and NADE, Schizosaccharomyces pombe" +xref: Reactome:REACT_88562 "Ceramide signalling, Danio rerio" +xref: Reactome:REACT_89305 "FASL binds FAS Receptor, Bos taurus" +xref: Reactome:REACT_89421 "Cell death signalling via NRAGE, NRIF and NADE, Xenopus tropicalis" +xref: Reactome:REACT_900 "FasL/ CD95L signaling, Homo sapiens" +xref: Reactome:REACT_90409 "Ceramide signalling, Schizosaccharomyces pombe" +xref: Reactome:REACT_90414 "Cell death signalling via NRAGE, NRIF and NADE, Arabidopsis thaliana" +xref: Reactome:REACT_90980 "FasL/ CD95L signaling, Canis familiaris" +xref: Reactome:REACT_91488 "Cell death signalling via NRAGE, NRIF and NADE, Bos taurus" +xref: Reactome:REACT_92659 "Extrinsic Pathway for Apoptosis, Sus scrofa" +xref: Reactome:REACT_92947 "Extrinsic Pathway for Apoptosis, Danio rerio" +xref: Reactome:REACT_93354 "Ceramide signalling, Sus scrofa" +xref: Reactome:REACT_93927 "Cell death signalling via NRAGE, NRIF and NADE, Caenorhabditis elegans" +xref: Reactome:REACT_94832 "Ceramide signalling, Saccharomyces cerevisiae" +xref: Reactome:REACT_94837 "Extrinsic Pathway for Apoptosis, Taeniopygia guttata" +xref: Reactome:REACT_95750 "FASL binds FAS Receptor, Danio rerio" +xref: Reactome:REACT_95777 "FasL/ CD95L signaling, Taeniopygia guttata" +xref: Reactome:REACT_96066 "Death Receptor Signalling, Rattus norvegicus" +xref: Reactome:REACT_96229 "Extrinsic Pathway for Apoptosis, Rattus norvegicus" +xref: Reactome:REACT_96867 "Cell death signalling via NRAGE, NRIF and NADE, Saccharomyces cerevisiae" +xref: Reactome:REACT_97301 "Extrinsic Pathway for Apoptosis, Mus musculus" +xref: Reactome:REACT_98119 "Cell death signalling via NRAGE, NRIF and NADE, Mus musculus" +xref: Reactome:REACT_98804 "FasL/ CD95L signaling, Bos taurus" +xref: Reactome:REACT_99367 "FASL binds FAS Receptor, Mus musculus" +xref: Reactome:REACT_99865 "FasL/ CD95L signaling, Mus musculus" +is_a: GO:0007165 ! signal transduction +relationship: part_of GO:0006915 ! apoptotic process +created_by: paola +creation_date: 2011-11-23T09:30:23Z + +[Term] +id: GO:0097191 +name: extrinsic apoptotic signaling pathway +namespace: biological_process +def: "A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis, GOC:yaf, PMID:17340152] +comment: Fas acts as a death receptor with a role in apoptosis, but can also act as a non-apoptotic signal transducer. +synonym: "death receptor-mediated apoptosis" NARROW [] +synonym: "extrinsic apoptosis" NARROW [] +synonym: "extrinsic apoptotic pathway" EXACT [] +synonym: "extrinsic apoptotic signaling pathway in presence of ligand" NARROW [] +synonym: "extrinsic apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:0007166 ! cell surface receptor signaling pathway +is_a: GO:0097190 ! apoptotic signaling pathway +created_by: paola +creation_date: 2011-11-23T09:34:28Z + +[Term] +id: GO:0097194 +name: execution phase of apoptosis +namespace: biological_process +def: "A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. The execution phase ends when the cell has died." [GOC:mtg_apoptosis] +synonym: "apoptosis" NARROW [] +synonym: "execution phase of apoptotic process" EXACT [] +is_a: GO:0044763 ! single-organism cellular process +relationship: part_of GO:0006915 ! apoptotic process +created_by: paola +creation_date: 2011-11-23T09:45:24Z + +[Term] +id: GO:0097242 +name: beta-amyloid clearance +namespace: biological_process +def: "The process in which beta-amyloid is removed from the brain via receptors." [GOC:BHF, PMID:19098903] +is_a: GO:0044707 ! single-multicellular organism process +created_by: paola +creation_date: 2012-02-16T05:32:29Z + +[Term] +id: GO:0097285 +name: cell-type specific apoptotic process +namespace: biological_process +def: "Any apoptotic process in a specific cell type." [GOC:mtg_apoptosis] +comment: This term was created as a generic parent to group terms indicating occurrences of apoptotic process in specific cell types. The process of apoptosis may not vary, but the cell type does. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. Alternatively, you may annotate to the parent term GO:0006915 apoptotic process. +subset: gocheck_do_not_manually_annotate +synonym: "cell-type specific apoptosis" NARROW [] +is_a: GO:0006915 ! apoptotic process +created_by: paola +creation_date: 2012-03-29T04:00:25Z + +[Term] +id: GO:0097305 +name: response to alcohol +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an alcohol stimulus." [CHEBI:30879, GOC:pr] +is_a: GO:0010033 ! response to organic substance +is_a: GO:1901700 ! response to oxygen-containing compound +created_by: paola +creation_date: 2012-05-15T03:48:45Z + +[Term] +id: GO:0097306 +name: cellular response to alcohol +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an alcohol stimulus." [CHEBI:30879, GOC:pr] +is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:0097305 ! response to alcohol +is_a: GO:1901701 ! cellular response to oxygen-containing compound +created_by: paola +creation_date: 2012-05-15T03:49:51Z + +[Term] +id: GO:0097367 +name: carbohydrate derivative binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a carbohydrate derivative." [GOC:pr] +is_a: GO:0005488 ! binding +created_by: paola +creation_date: 2012-08-02T13:03:39Z + +[Term] +id: GO:0097458 +name: neuron part +namespace: cellular_component +def: "Any constituent part of a neuron, the basic cellular unit of nervous tissue. A typical neuron consists of a cell body (often called the soma), an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [GOC:pr, http://en.wikipedia.org/wiki/Neuron] +subset: gocheck_do_not_annotate +is_a: GO:0044464 ! cell part +created_by: paola +creation_date: 2012-12-19T16:53:50Z + +[Term] +id: GO:0097478 +name: leaflet of membrane bilayer +namespace: cellular_component +def: "Any of the two layers of lipid molecules that constitute a membrane." [GOC:cjm] +synonym: "membrane leaflet" EXACT [] +is_a: GO:0044425 ! membrane part +created_by: paola +creation_date: 2013-05-07T14:24:37Z + +[Term] +id: GO:0097479 +name: synaptic vesicle localization +namespace: biological_process +def: "Any process in which a synaptic vesicle or vesicles are transported to, and/or maintained in, a specific location." [GOC:pr] +synonym: "establishment and maintenance of synaptic vesicle localization" EXACT [] +synonym: "establishment and maintenance of synaptic vesicle position" EXACT [] +synonym: "synaptic vesicle localisation" EXACT [] +is_a: GO:0051648 ! vesicle localization +created_by: paola +creation_date: 2013-05-22T14:29:55Z + +[Term] +id: GO:0097480 +name: establishment of synaptic vesicle localization +namespace: biological_process +def: "The directed movement of a synaptic vesicle or vesicles to a specific location." [GOC:pr] +synonym: "establishment of synaptic vesicle localisation" EXACT [] +is_a: GO:0051650 ! establishment of vesicle localization +relationship: part_of GO:0097479 ! synaptic vesicle localization +created_by: paola +creation_date: 2013-05-22T14:32:12Z + +[Term] +id: GO:0097485 +name: neuron projection guidance +namespace: biological_process +def: "The process in which the migration of a neuron projection is directed to a specific target site in response to a combination of attractive and repulsive cues." [GOC:BHF, GOC:rl, PMID:22790009] +synonym: "neurite guidance" NARROW [] +synonym: "neuron process guidance" EXACT [] +synonym: "neuron protrusion guidance" EXACT [] +synonym: "neuronal cell projection guidance" EXACT [] +is_a: GO:0006928 ! cellular component movement +relationship: part_of GO:0006935 ! chemotaxis +relationship: part_of GO:0048812 ! neuron projection morphogenesis +created_by: paola +creation_date: 2013-07-08T13:32:37Z + +[Term] +id: GO:0098531 +name: direct ligand regulated sequence-specific DNA binding transcription factor activity +namespace: molecular_function +def: "A DNA binding transcription factor activity that is directly regulated by binding of a ligand to the protein with this activity. Examples include the lac and trp repressors in E.coli and many steroid hormone receptors." [GOC:dos, http://www.ecocyc.org/ECOLI/NEW-IMAGE?object=BC-3.1.2.3] +is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity +created_by: davidos +creation_date: 2013-10-17T15:51:30Z + +[Term] +id: GO:0098552 +name: side of membrane +namespace: cellular_component +def: "A cellular component consisting of one leaflet of a membrane bilayer and any proteins embedded or anchored in it or attached to its surface." [GOC:dos] +is_a: GO:0044425 ! membrane part +relationship: has_part GO:0097478 ! leaflet of membrane bilayer +relationship: part_of GO:0016020 ! membrane +created_by: davidos +creation_date: 2013-12-03T11:28:04Z + +[Term] +id: GO:0098562 +name: cytoplasmic side of membrane +namespace: cellular_component +def: "The side of a membrane that faces the cytoplasm." [GOC:dos] +is_a: GO:0098552 ! side of membrane +created_by: davidos +creation_date: 2013-12-12T11:21:30Z + +[Term] +id: GO:1900006 +name: positive regulation of dendrite development +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of dendrite development." [GOC:TermGenie] +synonym: "up regulation of dendrite development" RELATED [GOC:TermGenie] +is_a: GO:0010976 ! positive regulation of neuron projection development +is_a: GO:0050773 ! regulation of dendrite development +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0016358 ! dendrite development +relationship: positively_regulates GO:0016358 ! dendrite development +created_by: hjd +creation_date: 2012-01-09T10:41:31Z + +[Term] +id: GO:1900046 +name: regulation of hemostasis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of hemostasis." [GOC:TermGenie] +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007599 ! hemostasis +relationship: regulates GO:0007599 ! hemostasis +created_by: jl +creation_date: 2012-01-19T03:23:38Z + +[Term] +id: GO:1900115 +name: extracellular regulation of signal transduction +namespace: biological_process +def: "Any regulation of signal transduction that takes place in the extracellular region." [GOC:signaling, GOC:TermGenie] +synonym: "regulation of signaling pathway in extracellular region" EXACT [GOC:TermGenie] +synonym: "regulation of signalling pathway in extracellular region" EXACT [GOC:TermGenie] +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0009966 ! regulation of signal transduction +intersection_of: occurs_in GO:0005576 ! extracellular region +relationship: occurs_in GO:0005576 ! extracellular region +created_by: bf +creation_date: 2012-02-22T10:21:48Z + +[Term] +id: GO:1900116 +name: extracellular negative regulation of signal transduction +namespace: biological_process +def: "Any negative regulation of signal transduction that takes place in extracellular region." [GOC:signaling, GOC:TermGenie] +synonym: "down regulation of signal transduction in extracellular region" EXACT [GOC:TermGenie] +synonym: "down-regulation of signal transduction in extracellular region" EXACT [GOC:TermGenie] +synonym: "downregulation of signal transduction in extracellular region" EXACT [GOC:TermGenie] +synonym: "extracellular inhibition of signaling pathway" NARROW [GOC:bf] +synonym: "inhibition of signal transduction in extracellular region" NARROW [GOC:TermGenie] +synonym: "negative regulation of signaling pathway in extracellular region" EXACT [GOC:TermGenie] +synonym: "negative regulation of signalling pathway in extracellular region" EXACT [GOC:TermGenie] +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:1900115 ! extracellular regulation of signal transduction +intersection_of: GO:0009968 ! negative regulation of signal transduction +intersection_of: occurs_in GO:0005576 ! extracellular region +relationship: occurs_in GO:0005576 ! extracellular region +created_by: bf +creation_date: 2012-02-22T10:27:56Z + +[Term] +id: GO:1900180 +name: regulation of protein localization to nucleus +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of protein localization to nucleus." [GOC:TermGenie] +synonym: "regulation of protein localisation to nucleus" EXACT [GOC:TermGenie] +synonym: "regulation of protein localization in cell nucleus" EXACT [GOC:TermGenie] +synonym: "regulation of protein localization in nucleus" EXACT [GOC:TermGenie] +is_a: GO:0032880 ! regulation of protein localization +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034504 ! protein localization to nucleus +relationship: regulates GO:0034504 ! protein localization to nucleus +created_by: bf +creation_date: 2012-03-12T01:23:44Z + +[Term] +id: GO:1900221 +name: regulation of beta-amyloid clearance +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of beta-amyloid clearance." [GOC:BHF, GOC:TermGenie] +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097242 ! beta-amyloid clearance +relationship: regulates GO:0097242 ! beta-amyloid clearance +created_by: vk +creation_date: 2012-03-22T01:29:32Z + +[Term] +id: GO:1900222 +name: negative regulation of beta-amyloid clearance +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of beta-amyloid clearance." [GOC:BHF, GOC:TermGenie] +synonym: "down regulation of beta-amyloid clearance" EXACT [GOC:TermGenie] +synonym: "down-regulation of beta-amyloid clearance" EXACT [GOC:TermGenie] +synonym: "downregulation of beta-amyloid clearance" EXACT [GOC:TermGenie] +synonym: "inhibition of beta-amyloid clearance" NARROW [GOC:TermGenie] +is_a: GO:0051241 ! negative regulation of multicellular organismal process +is_a: GO:1900221 ! regulation of beta-amyloid clearance +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097242 ! beta-amyloid clearance +relationship: negatively_regulates GO:0097242 ! beta-amyloid clearance +created_by: vk +creation_date: 2012-03-22T01:29:41Z + +[Term] +id: GO:1900542 +name: regulation of purine nucleotide metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of purine nucleotide metabolic process." [GOC:TermGenie] +synonym: "regulation of purine metabolic process" NARROW [GOC:TermGenie] +synonym: "regulation of purine metabolism" NARROW [GOC:TermGenie] +synonym: "regulation of purine nucleotide metabolism" EXACT [GOC:TermGenie] +is_a: GO:0006140 ! regulation of nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006163 ! purine nucleotide metabolic process +relationship: regulates GO:0006163 ! purine nucleotide metabolic process +created_by: krc +creation_date: 2012-05-11T05:43:15Z + +[Term] +id: GO:1900544 +name: positive regulation of purine nucleotide metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of purine nucleotide metabolic process." [GOC:TermGenie] +synonym: "activation of purine metabolic process" NARROW [GOC:TermGenie] +synonym: "activation of purine metabolism" NARROW [GOC:TermGenie] +synonym: "activation of purine nucleotide metabolic process" NARROW [GOC:TermGenie] +synonym: "activation of purine nucleotide metabolism" NARROW [GOC:TermGenie] +synonym: "positive regulation of purine metabolic process" NARROW [GOC:TermGenie] +synonym: "positive regulation of purine metabolism" NARROW [GOC:TermGenie] +synonym: "positive regulation of purine nucleotide metabolism" EXACT [GOC:TermGenie] +synonym: "up regulation of purine metabolic process" NARROW [GOC:TermGenie] +synonym: "up regulation of purine metabolism" NARROW [GOC:TermGenie] +synonym: "up regulation of purine nucleotide metabolic process" EXACT [GOC:TermGenie] +synonym: "up regulation of purine nucleotide metabolism" EXACT [GOC:TermGenie] +synonym: "up-regulation of purine metabolic process" NARROW [GOC:TermGenie] +synonym: "up-regulation of purine metabolism" NARROW [GOC:TermGenie] +synonym: "up-regulation of purine nucleotide metabolic process" EXACT [GOC:TermGenie] +synonym: "up-regulation of purine nucleotide metabolism" EXACT [GOC:TermGenie] +synonym: "upregulation of purine metabolic process" NARROW [GOC:TermGenie] +synonym: "upregulation of purine metabolism" NARROW [GOC:TermGenie] +synonym: "upregulation of purine nucleotide metabolic process" EXACT [GOC:TermGenie] +synonym: "upregulation of purine nucleotide metabolism" EXACT [GOC:TermGenie] +is_a: GO:0045981 ! positive regulation of nucleotide metabolic process +is_a: GO:1900542 ! regulation of purine nucleotide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006163 ! purine nucleotide metabolic process +relationship: positively_regulates GO:0006163 ! purine nucleotide metabolic process +created_by: krc +creation_date: 2012-05-11T05:44:43Z + +[Term] +id: GO:1901068 +name: guanosine-containing compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving guanosine-containing compounds (guanosines)." [GOC:TermGenie] +synonym: "guanosine-containing compound metabolism" EXACT [GOC:bf] +synonym: "guanosines metabolic process" EXACT [CHEBI:24458] +synonym: "guanosines metabolism" EXACT [GOC:TermGenie] +is_a: GO:0046128 ! purine ribonucleoside metabolic process +created_by: bf +creation_date: 2012-07-02T01:51:37Z + +[Term] +id: GO:1901069 +name: guanosine-containing compound catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of guanosine-containing compounds (guanosines)." [GOC:TermGenie] +synonym: "guanosine-containing compound breakdown" EXACT [GOC:bf] +synonym: "guanosine-containing compound catabolism" EXACT [GOC:bf] +synonym: "guanosine-containing compound degradation" EXACT [GOC:bf] +synonym: "guanosines breakdown" EXACT [GOC:TermGenie] +synonym: "guanosines catabolic process" EXACT [CHEBI:24458] +synonym: "guanosines catabolism" EXACT [GOC:TermGenie] +synonym: "guanosines degradation" EXACT [GOC:TermGenie] +is_a: GO:0046130 ! purine ribonucleoside catabolic process +is_a: GO:1901068 ! guanosine-containing compound metabolic process +created_by: bf +creation_date: 2012-07-02T01:52:00Z + +[Term] +id: GO:1901135 +name: carbohydrate derivative metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving carbohydrate derivative." [GOC:TermGenie] +synonym: "carbohydrate derivative metabolism" EXACT [GOC:TermGenie] +is_a: GO:0071704 ! organic substance metabolic process +created_by: bf +creation_date: 2012-07-12T04:05:09Z + +[Term] +id: GO:1901136 +name: carbohydrate derivative catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative." [GOC:TermGenie] +synonym: "carbohydrate derivative breakdown" EXACT [GOC:TermGenie] +synonym: "carbohydrate derivative catabolism" EXACT [GOC:TermGenie] +synonym: "carbohydrate derivative degradation" EXACT [GOC:TermGenie] +is_a: GO:1901135 ! carbohydrate derivative metabolic process +is_a: GO:1901575 ! organic substance catabolic process +created_by: bf +creation_date: 2012-07-12T04:05:31Z + +[Term] +id: GO:1901137 +name: carbohydrate derivative biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of carbohydrate derivative." [GOC:TermGenie] +synonym: "carbohydrate derivative anabolism" EXACT [GOC:TermGenie] +synonym: "carbohydrate derivative biosynthesis" EXACT [GOC:TermGenie] +synonym: "carbohydrate derivative formation" EXACT [GOC:TermGenie] +synonym: "carbohydrate derivative synthesis" EXACT [GOC:TermGenie] +is_a: GO:1901135 ! carbohydrate derivative metabolic process +is_a: GO:1901576 ! organic substance biosynthetic process +created_by: bf +creation_date: 2012-07-12T04:05:39Z + +[Term] +id: GO:1901214 +name: regulation of neuron death +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of neuron death." [GOC:rph, GOC:TermGenie] +synonym: "regulation of neuron cell death" EXACT [GOC:TermGenie] +synonym: "regulation of neuronal cell death" EXACT [GOC:TermGenie] +is_a: GO:0010941 ! regulation of cell death +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0070997 ! neuron death +relationship: regulates GO:0070997 ! neuron death +created_by: rph +creation_date: 2012-08-02T09:57:41Z + +[Term] +id: GO:1901215 +name: negative regulation of neuron death +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of neuron death." [GOC:rph, GOC:TermGenie] +synonym: "down regulation of neuron cell death" EXACT [GOC:TermGenie] +synonym: "down regulation of neuron death" EXACT [GOC:TermGenie] +synonym: "down regulation of neuronal cell death" EXACT [GOC:TermGenie] +synonym: "down-regulation of neuron cell death" EXACT [GOC:TermGenie] +synonym: "down-regulation of neuron death" EXACT [GOC:TermGenie] +synonym: "down-regulation of neuronal cell death" EXACT [GOC:TermGenie] +synonym: "downregulation of neuron cell death" EXACT [GOC:TermGenie] +synonym: "downregulation of neuron death" EXACT [GOC:TermGenie] +synonym: "downregulation of neuronal cell death" EXACT [GOC:TermGenie] +synonym: "inhibition of neuron cell death" NARROW [GOC:TermGenie] +synonym: "inhibition of neuron death" NARROW [GOC:TermGenie] +synonym: "inhibition of neuronal cell death" NARROW [GOC:TermGenie] +synonym: "negative regulation of neuron cell death" EXACT [GOC:TermGenie] +synonym: "negative regulation of neuronal cell death" EXACT [GOC:TermGenie] +is_a: GO:0060548 ! negative regulation of cell death +is_a: GO:1901214 ! regulation of neuron death +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0070997 ! neuron death +relationship: negatively_regulates GO:0070997 ! neuron death +created_by: rph +creation_date: 2012-08-02T09:58:07Z + +[Term] +id: GO:1901219 +name: regulation of cardiac chamber morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cardiac chamber morphogenesis." [GOC:BHF, GOC:TermGenie] +synonym: "regulation of heart chamber morphogenesis" EXACT [GOC:TermGenie] +is_a: GO:2000826 ! regulation of heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003206 ! cardiac chamber morphogenesis +relationship: regulates GO:0003206 ! cardiac chamber morphogenesis +created_by: rl +creation_date: 2012-08-06T17:59:11Z + +[Term] +id: GO:1901246 +name: regulation of lung ciliated cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of lung ciliated cell differentiation." [GOC:BHF, GOC:TermGenie] +is_a: GO:0030856 ! regulation of epithelial cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061141 ! lung ciliated cell differentiation +relationship: regulates GO:0061141 ! lung ciliated cell differentiation +created_by: vk +creation_date: 2012-08-08T08:58:34Z + +[Term] +id: GO:1901248 +name: positive regulation of lung ciliated cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of lung ciliated cell differentiation." [GOC:BHF, GOC:TermGenie] +synonym: "activation of lung ciliated cell differentiation" NARROW [GOC:TermGenie] +synonym: "up regulation of lung ciliated cell differentiation" EXACT [GOC:TermGenie] +synonym: "up-regulation of lung ciliated cell differentiation" EXACT [GOC:TermGenie] +synonym: "upregulation of lung ciliated cell differentiation" EXACT [GOC:TermGenie] +is_a: GO:0030858 ! positive regulation of epithelial cell differentiation +is_a: GO:1901246 ! regulation of lung ciliated cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061141 ! lung ciliated cell differentiation +relationship: positively_regulates GO:0061141 ! lung ciliated cell differentiation +created_by: vk +creation_date: 2012-08-08T08:59:05Z + +[Term] +id: GO:1901292 +name: nucleoside phosphate catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a nucleoside phosphate." [GOC:TermGenie] +synonym: "nucleoside phosphate breakdown" EXACT [GOC:TermGenie] +synonym: "nucleoside phosphate catabolism" EXACT [GOC:TermGenie] +synonym: "nucleoside phosphate degradation" EXACT [GOC:TermGenie] +is_a: GO:0006753 ! nucleoside phosphate metabolic process +is_a: GO:0034655 ! nucleobase-containing compound catabolic process +is_a: GO:0044712 ! single-organism catabolic process +is_a: GO:0046434 ! organophosphate catabolic process +created_by: bf +creation_date: 2012-08-20T12:33:25Z + +[Term] +id: GO:1901320 +name: negative regulation of heart induction +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of heart induction." [GOC:TermGenie] +synonym: "down regulation of heart induction" EXACT [GOC:TermGenie] +synonym: "down-regulation of heart induction" EXACT [GOC:TermGenie] +synonym: "downregulation of heart induction" EXACT [GOC:TermGenie] +synonym: "inhibition of heart induction" NARROW [GOC:TermGenie] +is_a: GO:0010648 ! negative regulation of cell communication +is_a: GO:0023057 ! negative regulation of signaling +is_a: GO:0090381 ! regulation of heart induction +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003129 ! heart induction +relationship: negatively_regulates GO:0003129 ! heart induction +created_by: bf +creation_date: 2012-08-28T15:48:38Z + +[Term] +id: GO:1901342 +name: regulation of vasculature development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of vasculature development." [GOC:TermGenie] +synonym: "regulation of vascular system development" RELATED [GOC:TermGenie] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0001944 ! vasculature development +relationship: regulates GO:0001944 ! vasculature development +created_by: bf +creation_date: 2012-09-06T09:16:15Z + +[Term] +id: GO:1901360 +name: organic cyclic compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving organic cyclic compound." [GOC:TermGenie] +synonym: "organic cyclic compound metabolism" EXACT [GOC:TermGenie] +is_a: GO:0071704 ! organic substance metabolic process +created_by: bf +creation_date: 2012-09-14T09:03:51Z + +[Term] +id: GO:1901361 +name: organic cyclic compound catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound." [GOC:TermGenie] +synonym: "organic cyclic compound breakdown" EXACT [GOC:TermGenie] +synonym: "organic cyclic compound catabolism" EXACT [GOC:TermGenie] +synonym: "organic cyclic compound degradation" EXACT [GOC:TermGenie] +is_a: GO:1901360 ! organic cyclic compound metabolic process +is_a: GO:1901575 ! organic substance catabolic process +created_by: bf +creation_date: 2012-09-14T09:05:04Z + +[Term] +id: GO:1901362 +name: organic cyclic compound biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of organic cyclic compound." [GOC:TermGenie] +synonym: "organic cyclic compound anabolism" EXACT [GOC:TermGenie] +synonym: "organic cyclic compound biosynthesis" EXACT [GOC:TermGenie] +synonym: "organic cyclic compound formation" EXACT [GOC:TermGenie] +synonym: "organic cyclic compound synthesis" EXACT [GOC:TermGenie] +is_a: GO:1901360 ! organic cyclic compound metabolic process +is_a: GO:1901576 ! organic substance biosynthetic process +created_by: bf +creation_date: 2012-09-14T09:05:22Z + +[Term] +id: GO:1901363 +name: heterocyclic compound binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with heterocyclic compound." [GOC:TermGenie] +is_a: GO:0005488 ! binding +created_by: bf +creation_date: 2012-09-14T13:53:50Z + +[Term] +id: GO:1901564 +name: organonitrogen compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving organonitrogen compound." [GOC:pr, GOC:TermGenie] +synonym: "organonitrogen compound metabolism" EXACT [GOC:TermGenie] +is_a: GO:0006807 ! nitrogen compound metabolic process +is_a: GO:0071704 ! organic substance metabolic process +created_by: pr +creation_date: 2012-11-04T15:17:52Z + +[Term] +id: GO:1901565 +name: organonitrogen compound catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound." [GOC:pr, GOC:TermGenie] +synonym: "organonitrogen compound breakdown" EXACT [GOC:TermGenie] +synonym: "organonitrogen compound catabolism" EXACT [GOC:TermGenie] +synonym: "organonitrogen compound degradation" EXACT [GOC:TermGenie] +is_a: GO:1901564 ! organonitrogen compound metabolic process +is_a: GO:1901575 ! organic substance catabolic process +created_by: pr +creation_date: 2012-11-04T15:17:56Z + +[Term] +id: GO:1901575 +name: organic substance catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] +synonym: "organic molecular entity breakdown" EXACT [GOC:TermGenie] +synonym: "organic molecular entity catabolic process" EXACT [] +synonym: "organic molecular entity catabolism" EXACT [GOC:TermGenie] +synonym: "organic molecular entity degradation" EXACT [GOC:TermGenie] +synonym: "organic substance breakdown" EXACT [] +synonym: "organic substance catabolism" EXACT [] +synonym: "organic substance degradation" EXACT [] +is_a: GO:0009056 ! catabolic process +is_a: GO:0071704 ! organic substance metabolic process +created_by: pr +creation_date: 2012-11-05T11:04:36Z + +[Term] +id: GO:1901576 +name: organic substance biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] +synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] +synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] +synonym: "organic molecular entity biosynthetic process" EXACT [] +synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] +synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] +synonym: "organic substance anabolism" EXACT [] +synonym: "organic substance biosynthesis" EXACT [] +synonym: "organic substance formation" EXACT [] +synonym: "organic substance synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0071704 ! organic substance metabolic process +created_by: pr +creation_date: 2012-11-05T11:04:40Z + +[Term] +id: GO:1901615 +name: organic hydroxy compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving organic hydroxy compound." [GOC:pr, GOC:TermGenie] +synonym: "organic hydroxy compound metabolism" EXACT [GOC:TermGenie] +is_a: GO:0071704 ! organic substance metabolic process +created_by: pr +creation_date: 2012-11-13T12:54:27Z + +[Term] +id: GO:1901617 +name: organic hydroxy compound biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of organic hydroxy compound." [GOC:pr, GOC:TermGenie] +synonym: "organic hydroxy compound anabolism" EXACT [GOC:TermGenie] +synonym: "organic hydroxy compound biosynthesis" EXACT [GOC:TermGenie] +synonym: "organic hydroxy compound formation" EXACT [GOC:TermGenie] +synonym: "organic hydroxy compound synthesis" EXACT [GOC:TermGenie] +is_a: GO:1901576 ! organic substance biosynthetic process +is_a: GO:1901615 ! organic hydroxy compound metabolic process +created_by: pr +creation_date: 2012-11-13T12:54:36Z + +[Term] +id: GO:1901623 +name: regulation of lymphocyte chemotaxis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of lymphocyte chemotaxis." [GOC:TermGenie] +is_a: GO:0002688 ! regulation of leukocyte chemotaxis +is_a: GO:2000401 ! regulation of lymphocyte migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048247 ! lymphocyte chemotaxis +relationship: regulates GO:0048247 ! lymphocyte chemotaxis +created_by: tb +creation_date: 2012-11-13T23:03:23Z + +[Term] +id: GO:1901652 +name: response to peptide +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus." [GOC:pr, GOC:TermGenie] +is_a: GO:0010243 ! response to organonitrogen compound +is_a: GO:1901700 ! response to oxygen-containing compound +created_by: pr +creation_date: 2012-11-20T09:45:15Z + +[Term] +id: GO:1901653 +name: cellular response to peptide +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus." [GOC:pr, GOC:TermGenie] +is_a: GO:0071417 ! cellular response to organonitrogen compound +is_a: GO:1901652 ! response to peptide +is_a: GO:1901701 ! cellular response to oxygen-containing compound +created_by: pr +creation_date: 2012-11-20T09:45:19Z + +[Term] +id: GO:1901657 +name: glycosyl compound metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving glycosyl compound." [GOC:pr, GOC:TermGenie] +synonym: "glycosyl compound metabolism" EXACT [GOC:TermGenie] +is_a: GO:0044710 ! single-organism metabolic process +is_a: GO:0071704 ! organic substance metabolic process +created_by: pr +creation_date: 2012-11-20T14:24:07Z + +[Term] +id: GO:1901658 +name: glycosyl compound catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of glycosyl compound." [GOC:pr, GOC:TermGenie] +synonym: "glycosyl compound breakdown" EXACT [GOC:TermGenie] +synonym: "glycosyl compound catabolism" EXACT [GOC:TermGenie] +synonym: "glycosyl compound degradation" EXACT [GOC:TermGenie] +is_a: GO:0044712 ! single-organism catabolic process +is_a: GO:1901575 ! organic substance catabolic process +is_a: GO:1901657 ! glycosyl compound metabolic process +created_by: pr +creation_date: 2012-11-20T14:24:11Z + +[Term] +id: GO:1901681 +name: sulfur compound binding +namespace: molecular_function +def: "Interacting selectively and non-covalently with a sulfur compound." [GOC:pr, GOC:TermGenie] +synonym: "sulfur molecular entity binding" EXACT [] +is_a: GO:0005488 ! binding +created_by: pr +creation_date: 2012-11-26T20:45:23Z + +[Term] +id: GO:1901698 +name: response to nitrogen compound +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus." [GOC:pr, GOC:TermGenie] +synonym: "response to nitrogen molecular entity" EXACT [] +is_a: GO:0042221 ! response to chemical +created_by: pr +creation_date: 2012-12-13T15:06:08Z + +[Term] +id: GO:1901699 +name: cellular response to nitrogen compound +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus." [GOC:pr, GOC:TermGenie] +synonym: "cellular response to nitrogen molecular entity" EXACT [] +is_a: GO:0070887 ! cellular response to chemical stimulus +is_a: GO:1901698 ! response to nitrogen compound +created_by: pr +creation_date: 2012-12-13T15:06:13Z + +[Term] +id: GO:1901700 +name: response to oxygen-containing compound +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus." [GOC:pr, GOC:TermGenie] +synonym: "response to oxygen molecular entity" EXACT [] +is_a: GO:0042221 ! response to chemical +created_by: pr +creation_date: 2012-12-13T15:11:37Z + +[Term] +id: GO:1901701 +name: cellular response to oxygen-containing compound +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus." [GOC:pr, GOC:TermGenie] +synonym: "cellular response to oxygen molecular entity" EXACT [] +is_a: GO:0070887 ! cellular response to chemical stimulus +is_a: GO:1901700 ! response to oxygen-containing compound +created_by: pr +creation_date: 2012-12-13T15:11:42Z + +[Term] +id: GO:1901861 +name: regulation of muscle tissue development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of muscle tissue development." [GOC:TermGenie, GOC:yaf, PMID:23150719] +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060537 ! muscle tissue development +relationship: regulates GO:0060537 ! muscle tissue development +created_by: yaf +creation_date: 2013-02-01T10:30:47Z + +[Term] +id: GO:1901888 +name: regulation of cell junction assembly +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell junction assembly." [GOC:TermGenie] +is_a: GO:0044087 ! regulation of cellular component biogenesis +is_a: GO:0050794 ! regulation of cellular process +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034329 ! cell junction assembly +relationship: regulates GO:0034329 ! cell junction assembly +created_by: tb +creation_date: 2013-02-06T19:40:32Z + +[Term] +id: GO:1901890 +name: positive regulation of cell junction assembly +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell junction assembly." [GOC:TermGenie] +synonym: "activation of cell junction assembly" NARROW [GOC:TermGenie] +synonym: "up regulation of cell junction assembly" EXACT [GOC:TermGenie] +synonym: "up-regulation of cell junction assembly" EXACT [GOC:TermGenie] +synonym: "upregulation of cell junction assembly" EXACT [GOC:TermGenie] +is_a: GO:0048522 ! positive regulation of cellular process +is_a: GO:0051130 ! positive regulation of cellular component organization +is_a: GO:1901888 ! regulation of cell junction assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0034329 ! cell junction assembly +relationship: positively_regulates GO:0034329 ! cell junction assembly +created_by: tb +creation_date: 2013-02-06T19:40:46Z + +[Term] +id: GO:1901963 +name: regulation of cell proliferation involved in outflow tract morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis." [GOC:dph, GOC:mtg_heart, GOC:TermGenie, PMID:21419760] +is_a: GO:2000136 ! regulation of cell proliferation involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis +relationship: regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis +created_by: dph +creation_date: 2013-02-20T20:30:26Z + +[Term] +id: GO:1901998 +name: toxin transport +namespace: biological_process +def: "The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:TermGenie, PMID:17118486] +is_a: GO:0006810 ! transport +created_by: dph +creation_date: 2013-03-19T19:24:55Z + +[Term] +id: GO:1902041 +name: regulation of extrinsic apoptotic signaling pathway via death domain receptors +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors." [GOC:TermGenie, PMID:17245429] +synonym: "regulation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +is_a: GO:2001236 ! regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors +relationship: regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors +created_by: lb +creation_date: 2013-04-03T07:16:59Z + +[Term] +id: GO:1902042 +name: negative regulation of extrinsic apoptotic signaling pathway via death domain receptors +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors." [GOC:TermGenie, PMID:17245429] +synonym: "down regulation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +synonym: "down regulation of extrinsic apoptotic signaling pathway via death domain receptors" EXACT [GOC:TermGenie] +synonym: "down-regulation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +synonym: "down-regulation of extrinsic apoptotic signaling pathway via death domain receptors" EXACT [GOC:TermGenie] +synonym: "downregulation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +synonym: "downregulation of extrinsic apoptotic signaling pathway via death domain receptors" EXACT [GOC:TermGenie] +synonym: "inhibition of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +synonym: "inhibition of extrinsic apoptotic signaling pathway via death domain receptors" NARROW [GOC:TermGenie] +synonym: "negative regulation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +is_a: GO:1902041 ! regulation of extrinsic apoptotic signaling pathway via death domain receptors +is_a: GO:2001237 ! negative regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors +relationship: negatively_regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors +created_by: lb +creation_date: 2013-04-03T07:17:04Z + +[Term] +id: GO:1902043 +name: positive regulation of extrinsic apoptotic signaling pathway via death domain receptors +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors." [GOC:TermGenie, PMID:17245429] +synonym: "activation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +synonym: "activation of extrinsic apoptotic signaling pathway via death domain receptors" NARROW [GOC:TermGenie] +synonym: "positive regulation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +synonym: "up regulation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +synonym: "up regulation of extrinsic apoptotic signaling pathway via death domain receptors" EXACT [GOC:TermGenie] +synonym: "up-regulation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +synonym: "up-regulation of extrinsic apoptotic signaling pathway via death domain receptors" EXACT [GOC:TermGenie] +synonym: "upregulation of death receptor-mediated apoptosis" NARROW [GOC:TermGenie] +synonym: "upregulation of extrinsic apoptotic signaling pathway via death domain receptors" EXACT [GOC:TermGenie] +is_a: GO:1902041 ! regulation of extrinsic apoptotic signaling pathway via death domain receptors +is_a: GO:2001238 ! positive regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors +relationship: positively_regulates GO:0008625 ! extrinsic apoptotic signaling pathway via death domain receptors +created_by: lb +creation_date: 2013-04-03T07:17:11Z + +[Term] +id: GO:1902105 +name: regulation of leukocyte differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of leukocyte differentiation." [GOC:add, GOC:TermGenie] +synonym: "regulation of immune cell differentiation" EXACT [GOC:TermGenie] +synonym: "regulation of leucocyte differentiation" EXACT [GOC:TermGenie] +is_a: GO:0002682 ! regulation of immune system process +is_a: GO:0045595 ! regulation of cell differentiation +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0002521 ! leukocyte differentiation +relationship: regulates GO:0002521 ! leukocyte differentiation +created_by: pr +creation_date: 2013-05-02T17:32:42Z + +[Term] +id: GO:1902106 +name: negative regulation of leukocyte differentiation +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation." [GOC:add, GOC:TermGenie] +synonym: "down regulation of immune cell differentiation" EXACT [GOC:TermGenie] +synonym: "down regulation of leucocyte differentiation" EXACT [GOC:TermGenie] +synonym: "down regulation of leukocyte differentiation" EXACT [GOC:TermGenie] +synonym: "down-regulation of immune cell differentiation" EXACT [GOC:TermGenie] +synonym: "down-regulation of leucocyte differentiation" EXACT [GOC:TermGenie] +synonym: "down-regulation of leukocyte differentiation" EXACT [GOC:TermGenie] +synonym: "downregulation of immune cell differentiation" EXACT [GOC:TermGenie] +synonym: "downregulation of leucocyte differentiation" EXACT [GOC:TermGenie] +synonym: "downregulation of leukocyte differentiation" EXACT [GOC:TermGenie] +synonym: "inhibition of immune cell differentiation" NARROW [GOC:TermGenie] +synonym: "inhibition of leucocyte differentiation" NARROW [GOC:TermGenie] +synonym: "inhibition of leukocyte differentiation" NARROW [GOC:TermGenie] +synonym: "negative regulation of immune cell differentiation" EXACT [GOC:TermGenie] +synonym: "negative regulation of leucocyte differentiation" EXACT [GOC:TermGenie] +is_a: GO:0045596 ! negative regulation of cell differentiation +is_a: GO:1902105 ! regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0002521 ! leukocyte differentiation +relationship: negatively_regulates GO:0002521 ! leukocyte differentiation +created_by: pr +creation_date: 2013-05-02T17:32:47Z + +[Term] +id: GO:1902107 +name: positive regulation of leukocyte differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of leukocyte differentiation." [GOC:add, GOC:TermGenie] +synonym: "activation of immune cell differentiation" NARROW [GOC:TermGenie] +synonym: "activation of leucocyte differentiation" NARROW [GOC:TermGenie] +synonym: "activation of leukocyte differentiation" NARROW [GOC:TermGenie] +synonym: "positive regulation of immune cell differentiation" EXACT [GOC:TermGenie] +synonym: "positive regulation of leucocyte differentiation" EXACT [GOC:TermGenie] +synonym: "up regulation of immune cell differentiation" EXACT [GOC:TermGenie] +synonym: "up regulation of leucocyte differentiation" EXACT [GOC:TermGenie] +synonym: "up regulation of leukocyte differentiation" EXACT [GOC:TermGenie] +synonym: "up-regulation of immune cell differentiation" EXACT [GOC:TermGenie] +synonym: "up-regulation of leucocyte differentiation" EXACT [GOC:TermGenie] +synonym: "up-regulation of leukocyte differentiation" EXACT [GOC:TermGenie] +synonym: "upregulation of immune cell differentiation" EXACT [GOC:TermGenie] +synonym: "upregulation of leucocyte differentiation" EXACT [GOC:TermGenie] +synonym: "upregulation of leukocyte differentiation" EXACT [GOC:TermGenie] +is_a: GO:0045597 ! positive regulation of cell differentiation +is_a: GO:1902105 ! regulation of leukocyte differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0002521 ! leukocyte differentiation +relationship: positively_regulates GO:0002521 ! leukocyte differentiation +created_by: pr +creation_date: 2013-05-02T17:32:52Z + +[Term] +id: GO:1902256 +name: regulation of apoptotic process involved in outflow tract morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis." [GOC:dph, GOC:mtg_apoptosis, GOC:TermGenie, PMID:16839542] +synonym: "regulation of apoptosis involved in outflow tract morphogenesis" NARROW [GOC:TermGenie] +is_a: GO:1902337 ! regulation of apoptotic process involved in morphogenesis +is_a: GO:2000826 ! regulation of heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis +relationship: regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis +created_by: dph +creation_date: 2013-06-24T19:12:24Z + +[Term] +id: GO:1902257 +name: negative regulation of apoptotic process involved in outflow tract morphogenesis +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis." [GOC:dph, GOC:mtg_apoptosis, GOC:TermGenie, PMID:16839542] +synonym: "down regulation of apoptosis involved in outflow tract morphogenesis" NARROW [GOC:TermGenie] +synonym: "down regulation of apoptotic process involved in outflow tract morphogenesis" EXACT [GOC:TermGenie] +synonym: "down-regulation of apoptosis involved in outflow tract morphogenesis" NARROW [GOC:TermGenie] +synonym: "down-regulation of apoptotic process involved in outflow tract morphogenesis" EXACT [GOC:TermGenie] +synonym: "downregulation of apoptosis involved in outflow tract morphogenesis" NARROW [GOC:TermGenie] +synonym: "downregulation of apoptotic process involved in outflow tract morphogenesis" EXACT [GOC:TermGenie] +synonym: "inhibition of apoptosis involved in outflow tract morphogenesis" NARROW [GOC:TermGenie] +synonym: "inhibition of apoptotic process involved in outflow tract morphogenesis" NARROW [GOC:TermGenie] +synonym: "negative regulation of apoptosis involved in outflow tract morphogenesis" NARROW [GOC:TermGenie] +is_a: GO:1902256 ! regulation of apoptotic process involved in outflow tract morphogenesis +is_a: GO:1902338 ! negative regulation of apoptotic process involved in morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis +relationship: negatively_regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis +created_by: dph +creation_date: 2013-06-24T19:12:30Z + +[Term] +id: GO:1902262 +name: apoptotic process involved in patterning of blood vessels +namespace: biological_process +def: "Any apoptotic process that is involved in patterning of blood vessels." [GOC:dph, GOC:mtg_apoptosis, GOC:TermGenie, PMID:16163358] +synonym: "apoptosis involved in patterning of blood vessels" NARROW [GOC:TermGenie] +synonym: "apoptotic cell death involved in patterning of blood vessels" EXACT [GOC:TermGenie] +synonym: "apoptotic program involved in patterning of blood vessels" NARROW [GOC:TermGenie] +synonym: "apoptotic programmed cell death involved in patterning of blood vessels" EXACT [GOC:TermGenie] +synonym: "programmed cell death by apoptosis involved in patterning of blood vessels" EXACT [GOC:TermGenie] +synonym: "signaling (initiator) caspase activity involved in patterning of blood vessels" RELATED [GOC:TermGenie] +synonym: "type I programmed cell death involved in patterning of blood vessels" NARROW [GOC:TermGenie] +is_a: GO:0060561 ! apoptotic process involved in morphogenesis +intersection_of: GO:0006915 ! apoptotic process +intersection_of: part_of GO:0001569 ! patterning of blood vessels +relationship: part_of GO:0001569 ! patterning of blood vessels +created_by: dph +creation_date: 2013-06-25T16:16:00Z + +[Term] +id: GO:1902284 +name: neuron projection extension involved in neuron projection guidance +namespace: biological_process +def: "Any neuron projection extension that is involved in neuron projection guidance." [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:22790009] +synonym: "neurite extension involved in neurite guidance" NARROW [GOC:TermGenie] +synonym: "neurite extension involved in neuron process guidance" NARROW [GOC:TermGenie] +synonym: "neurite extension involved in neuron projection guidance" NARROW [GOC:TermGenie] +synonym: "neurite extension involved in neuron protrusion guidance" NARROW [GOC:TermGenie] +synonym: "neurite extension involved in neuronal cell projection guidance" NARROW [GOC:TermGenie] +synonym: "neuron process extension involved in neurite guidance" NARROW [GOC:TermGenie] +synonym: "neuron process extension involved in neuron process guidance" EXACT [GOC:TermGenie] +synonym: "neuron process extension involved in neuron projection guidance" EXACT [GOC:TermGenie] +synonym: "neuron process extension involved in neuron protrusion guidance" EXACT [GOC:TermGenie] +synonym: "neuron process extension involved in neuronal cell projection guidance" EXACT [GOC:TermGenie] +synonym: "neuron projection extension involved in neurite guidance" NARROW [GOC:TermGenie] +synonym: "neuron projection extension involved in neuron process guidance" EXACT [GOC:TermGenie] +synonym: "neuron projection extension involved in neuron protrusion guidance" EXACT [GOC:TermGenie] +synonym: "neuron projection extension involved in neuronal cell projection guidance" EXACT [GOC:TermGenie] +synonym: "neuron protrusion extension involved in neurite guidance" NARROW [GOC:TermGenie] +synonym: "neuron protrusion extension involved in neuron process guidance" EXACT [GOC:TermGenie] +synonym: "neuron protrusion extension involved in neuron projection guidance" EXACT [GOC:TermGenie] +synonym: "neuron protrusion extension involved in neuron protrusion guidance" EXACT [GOC:TermGenie] +synonym: "neuron protrusion extension involved in neuronal cell projection guidance" EXACT [GOC:TermGenie] +synonym: "neuronal cell projection extension involved in neurite guidance" NARROW [GOC:TermGenie] +synonym: "neuronal cell projection extension involved in neuron process guidance" EXACT [GOC:TermGenie] +synonym: "neuronal cell projection extension involved in neuron projection guidance" EXACT [GOC:TermGenie] +synonym: "neuronal cell projection extension involved in neuron protrusion guidance" EXACT [GOC:TermGenie] +synonym: "neuronal cell projection extension involved in neuronal cell projection guidance" EXACT [GOC:TermGenie] +is_a: GO:1990138 ! neuron projection extension +intersection_of: GO:1990138 ! neuron projection extension +intersection_of: part_of GO:0097485 ! neuron projection guidance +relationship: part_of GO:0097485 ! neuron projection guidance +created_by: pr +creation_date: 2013-07-08T15:55:17Z + +[Term] +id: GO:1902337 +name: regulation of apoptotic process involved in morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis." [GOC:sart, GOC:TermGenie, PMID:12202035] +synonym: "regulation of apoptosis involved in development" RELATED [GOC:TermGenie] +synonym: "regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] +synonym: "regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0042981 ! regulation of apoptotic process +is_a: GO:0060284 ! regulation of cell development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060561 ! apoptotic process involved in morphogenesis +relationship: regulates GO:0060561 ! apoptotic process involved in morphogenesis +created_by: sart +creation_date: 2013-07-29T15:03:16Z + +[Term] +id: GO:1902338 +name: negative regulation of apoptotic process involved in morphogenesis +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis." [GOC:sart, GOC:TermGenie, PMID:12202035] +synonym: "down regulation of apoptosis involved in development" RELATED [GOC:TermGenie] +synonym: "down regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] +synonym: "down regulation of apoptotic process involved in morphogenesis" EXACT [GOC:TermGenie] +synonym: "down regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] +synonym: "down-regulation of apoptosis involved in development" RELATED [GOC:TermGenie] +synonym: "down-regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] +synonym: "down-regulation of apoptotic process involved in morphogenesis" EXACT [GOC:TermGenie] +synonym: "down-regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] +synonym: "downregulation of apoptosis involved in development" RELATED [GOC:TermGenie] +synonym: "downregulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] +synonym: "downregulation of apoptotic process involved in morphogenesis" EXACT [GOC:TermGenie] +synonym: "downregulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] +synonym: "inhibition of apoptosis involved in development" RELATED [GOC:TermGenie] +synonym: "inhibition of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] +synonym: "inhibition of apoptotic process involved in morphogenesis" NARROW [GOC:TermGenie] +synonym: "inhibition of morphogenetic apoptosis" RELATED [GOC:TermGenie] +synonym: "negative regulation of apoptosis involved in development" RELATED [GOC:TermGenie] +synonym: "negative regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] +synonym: "negative regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] +is_a: GO:0043066 ! negative regulation of apoptotic process +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:1902337 ! regulation of apoptotic process involved in morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0060561 ! apoptotic process involved in morphogenesis +relationship: negatively_regulates GO:0060561 ! apoptotic process involved in morphogenesis +created_by: sart +creation_date: 2013-07-29T15:03:25Z + +[Term] +id: GO:1902531 +name: regulation of intracellular signal transduction +namespace: biological_process +alt_id: GO:0010627 +def: "Any process that modulates the frequency, rate or extent of intracellular signal transduction." [GOC:dph, GOC:signaling, GOC:tb, GOC:TermGenie] +synonym: "regulation of intracellular protein kinase cascade" NARROW [] +synonym: "regulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "regulation of intracellular signaling cascade" EXACT [GOC:TermGenie] +synonym: "regulation of intracellular signaling chain" EXACT [GOC:TermGenie] +synonym: "regulation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "regulation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "regulation of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +is_a: GO:0009966 ! regulation of signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035556 ! intracellular signal transduction +relationship: regulates GO:0035556 ! intracellular signal transduction +created_by: bf +creation_date: 2013-12-02T11:32:52Z + +[Term] +id: GO:1902532 +name: negative regulation of intracellular signal transduction +namespace: biological_process +alt_id: GO:0010741 +def: "Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction." [GOC:dph, GOC:signaling, GOC:tb, GOC:TermGenie] +synonym: "down regulation of intracellular signal transduction" EXACT [GOC:TermGenie] +synonym: "down regulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "down regulation of intracellular signaling cascade" NARROW [GOC:TermGenie] +synonym: "down regulation of intracellular signaling chain" EXACT [GOC:TermGenie] +synonym: "down regulation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "down regulation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "down regulation of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +synonym: "down-regulation of intracellular signal transduction" EXACT [GOC:TermGenie] +synonym: "down-regulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "down-regulation of intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "down-regulation of intracellular signaling chain" EXACT [GOC:TermGenie] +synonym: "down-regulation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "down-regulation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "down-regulation of signal transmission via intracellular cascade" RELATED [GOC:TermGenie] +synonym: "downregulation of intracellular signal transduction" EXACT [GOC:TermGenie] +synonym: "downregulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "downregulation of intracellular signaling cascade" NARROW [GOC:TermGenie] +synonym: "downregulation of intracellular signaling chain" EXACT [GOC:TermGenie] +synonym: "downregulation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "downregulation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "downregulation of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +synonym: "inhibition of intracellular signal transduction" NARROW [GOC:TermGenie] +synonym: "inhibition of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "inhibition of intracellular signaling cascade" NARROW [GOC:TermGenie] +synonym: "inhibition of intracellular signaling chain" NARROW [GOC:TermGenie] +synonym: "inhibition of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "inhibition of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "inhibition of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +synonym: "negative regulation of intracellular protein kinase cascade" EXACT [] +synonym: "negative regulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "negative regulation of intracellular signaling cascade" EXACT [GOC:TermGenie] +synonym: "negative regulation of intracellular signaling chain" EXACT [GOC:TermGenie] +synonym: "negative regulation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "negative regulation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "negative regulation of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:1902531 ! regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0035556 ! intracellular signal transduction +relationship: negatively_regulates GO:0035556 ! intracellular signal transduction +created_by: bf +creation_date: 2013-12-02T11:33:01Z + +[Term] +id: GO:1902533 +name: positive regulation of intracellular signal transduction +namespace: biological_process +alt_id: GO:0010740 +def: "Any process that activates or increases the frequency, rate or extent of intracellular signal transduction." [GOC:BHF, GOC:dph, GOC:signaling, GOC:tb, GOC:TermGenie] +synonym: "activation of intracellular signal transduction" NARROW [GOC:TermGenie] +synonym: "activation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "activation of intracellular signaling cascade" NARROW [GOC:TermGenie] +synonym: "activation of intracellular signaling chain" NARROW [GOC:TermGenie] +synonym: "activation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "activation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "activation of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +synonym: "positive regulation of intracellular protein kinase cascade" NARROW [] +synonym: "positive regulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "positive regulation of intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "positive regulation of intracellular signaling chain" EXACT [GOC:TermGenie] +synonym: "positive regulation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "positive regulation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "positive regulation of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +synonym: "up regulation of intracellular signal transduction" EXACT [GOC:TermGenie] +synonym: "up regulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "up regulation of intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "up regulation of intracellular signaling chain" EXACT [GOC:TermGenie] +synonym: "up regulation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "up regulation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "up regulation of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +synonym: "up-regulation of intracellular signal transduction" EXACT [GOC:TermGenie] +synonym: "up-regulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "up-regulation of intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "up-regulation of intracellular signaling chain" EXACT [GOC:TermGenie] +synonym: "up-regulation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "up-regulation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "up-regulation of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +synonym: "upregulation of intracellular signal transduction" EXACT [GOC:TermGenie] +synonym: "upregulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] +synonym: "upregulation of intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "upregulation of intracellular signaling chain" EXACT [GOC:TermGenie] +synonym: "upregulation of intracellular signaling pathway" RELATED [GOC:TermGenie] +synonym: "upregulation of signal transduction via intracellular signaling cascade" RELATED [GOC:TermGenie] +synonym: "upregulation of signal transmission via intracellular cascade" NARROW [GOC:TermGenie] +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:1902531 ! regulation of intracellular signal transduction +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0035556 ! intracellular signal transduction +relationship: positively_regulates GO:0035556 ! intracellular signal transduction +created_by: bf +creation_date: 2013-12-02T11:33:10Z + +[Term] +id: GO:1902578 +name: single-organism localization +namespace: biological_process +def: "A localization which involves only one organism." [GO_REF:0000089, GOC:jl, PMID:1234] +synonym: "single organism localization" EXACT [GOC:TermGenie] +is_a: GO:0044699 ! single-organism process +is_a: GO:0051179 ! localization +created_by: jl +creation_date: 2013-12-18T13:51:04Z + +[Term] +id: GO:1902580 +name: single-organism cellular localization +namespace: biological_process +def: "A cellular localization which involves only one organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie] +synonym: "single organism cellular localization" EXACT [GOC:TermGenie] +is_a: GO:0051641 ! cellular localization +is_a: GO:1902578 ! single-organism localization +created_by: jl +creation_date: 2013-12-18T14:04:32Z + +[Term] +id: GO:1902582 +name: single-organism intracellular transport +namespace: biological_process +def: "An intracellular transport which involves only one organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie] +synonym: "single organism intracellular transport" EXACT [GOC:TermGenie] +is_a: GO:0044765 ! single-organism transport +is_a: GO:0046907 ! intracellular transport +created_by: jl +creation_date: 2013-12-18T14:04:50Z + +[Term] +id: GO:1902589 +name: single-organism organelle organization +namespace: biological_process +def: "An organelle organization which involves only one organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie] +synonym: "single organism organelle organization" EXACT [GOC:TermGenie] +is_a: GO:0006996 ! organelle organization +is_a: GO:0044763 ! single-organism cellular process +created_by: jl +creation_date: 2013-12-19T15:25:51Z + +[Term] +id: GO:1902593 +name: single-organism nuclear import +namespace: biological_process +def: "A nuclear import which involves only one organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie] +synonym: "single organism nuclear import" EXACT [GOC:TermGenie] +is_a: GO:0051170 ! nuclear import +is_a: GO:1902582 ! single-organism intracellular transport +created_by: jl +creation_date: 2013-12-19T15:26:34Z + +[Term] +id: GO:1902667 +name: regulation of axon guidance +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of axon guidance." [GO_REF:0000058, GOC:hjd, GOC:TermGenie, PMID:23006775] +synonym: "regulation of axon chemotaxis" RELATED [GOC:TermGenie] +synonym: "regulation of axon growth cone guidance" NARROW [GOC:TermGenie] +synonym: "regulation of axon pathfinding" EXACT [GOC:TermGenie] +is_a: GO:0050770 ! regulation of axonogenesis +is_a: GO:0050920 ! regulation of chemotaxis +is_a: GO:0051270 ! regulation of cellular component movement +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007411 ! axon guidance +relationship: regulates GO:0007411 ! axon guidance +created_by: hjd +creation_date: 2014-01-31T18:50:10Z + +[Term] +id: GO:1902679 +name: negative regulation of RNA biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process." [GO:jl, GO_REF:0000058, GOC:TermGenie] +synonym: "down regulation of RNA anabolism" EXACT [GOC:TermGenie] +synonym: "down regulation of RNA biosynthesis" EXACT [GOC:TermGenie] +synonym: "down regulation of RNA biosynthetic process" EXACT [GOC:TermGenie] +synonym: "down regulation of RNA formation" EXACT [GOC:TermGenie] +synonym: "down regulation of RNA synthesis" EXACT [GOC:TermGenie] +synonym: "down-regulation of RNA anabolism" EXACT [GOC:TermGenie] +synonym: "down-regulation of RNA biosynthesis" EXACT [GOC:TermGenie] +synonym: "down-regulation of RNA biosynthetic process" EXACT [GOC:TermGenie] +synonym: "down-regulation of RNA formation" EXACT [GOC:TermGenie] +synonym: "down-regulation of RNA synthesis" EXACT [GOC:TermGenie] +synonym: "downregulation of RNA anabolism" EXACT [GOC:TermGenie] +synonym: "downregulation of RNA biosynthesis" EXACT [GOC:TermGenie] +synonym: "downregulation of RNA biosynthetic process" EXACT [GOC:TermGenie] +synonym: "downregulation of RNA formation" EXACT [GOC:TermGenie] +synonym: "downregulation of RNA synthesis" EXACT [GOC:TermGenie] +synonym: "inhibition of RNA anabolism" NARROW [GOC:TermGenie] +synonym: "inhibition of RNA biosynthesis" NARROW [GOC:TermGenie] +synonym: "inhibition of RNA biosynthetic process" NARROW [GOC:TermGenie] +synonym: "inhibition of RNA formation" NARROW [GOC:TermGenie] +synonym: "inhibition of RNA synthesis" NARROW [GOC:TermGenie] +synonym: "negative regulation of RNA anabolism" EXACT [GOC:TermGenie] +synonym: "negative regulation of RNA biosynthesis" EXACT [GOC:TermGenie] +synonym: "negative regulation of RNA formation" EXACT [GOC:TermGenie] +synonym: "negative regulation of RNA synthesis" EXACT [GOC:TermGenie] +is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process +is_a: GO:0031327 ! negative regulation of cellular biosynthetic process +is_a: GO:0051253 ! negative regulation of RNA metabolic process +is_a: GO:2001141 ! regulation of RNA biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0032774 ! RNA biosynthetic process +relationship: negatively_regulates GO:0032774 ! RNA biosynthetic process +created_by: jl +creation_date: 2014-02-05T16:32:01Z + +[Term] +id: GO:1990138 +name: neuron projection extension +namespace: biological_process +def: "Long distance growth of a single neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:BHF, GOC:rl, PMID:22790009] +synonym: "neurite extension" NARROW [] +synonym: "neuron process extension" EXACT [] +synonym: "neuron protrusion extension" EXACT [] +synonym: "neuronal cell projection extension" EXACT [] +is_a: GO:0048588 ! developmental cell growth +is_a: GO:0060560 ! developmental growth involved in morphogenesis +relationship: part_of GO:0048812 ! neuron projection morphogenesis +created_by: pr +creation_date: 2013-07-08T08:40:45Z + +[Term] +id: GO:2000008 +name: regulation of protein localization to cell surface +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of protein localization to the cell surface." [GOC:obol] +synonym: "regulation of protein localisation at cell surface" EXACT [GOC:mah] +synonym: "regulation of protein localization at cell surface" EXACT [GOC:curators] +is_a: GO:0032880 ! regulation of protein localization +is_a: GO:0060341 ! regulation of cellular localization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034394 ! protein localization to cell surface +relationship: regulates GO:0034394 ! protein localization to cell surface +created_by: jane +creation_date: 2010-08-04T01:43:48Z + +[Term] +id: GO:2000015 +name: regulation of determination of dorsal identity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of determination of dorsal identity." [GOC:obol] +synonym: "regulation of determination of adaxial identity" RELATED [GOC:obol] +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048263 ! determination of dorsal identity +relationship: regulates GO:0048263 ! determination of dorsal identity +created_by: janelomax +creation_date: 2010-07-15T03:27:49Z + +[Term] +id: GO:2000017 +name: positive regulation of determination of dorsal identity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of determination of dorsal identity." [GOC:obol] +synonym: "positive regulation of determination of adaxial identity" RELATED [GOC:obol] +is_a: GO:0051094 ! positive regulation of developmental process +is_a: GO:0051240 ! positive regulation of multicellular organismal process +is_a: GO:2000015 ! regulation of determination of dorsal identity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048263 ! determination of dorsal identity +relationship: positively_regulates GO:0048263 ! determination of dorsal identity +created_by: janelomax +creation_date: 2010-07-15T03:27:59Z + +[Term] +id: GO:2000018 +name: regulation of male gonad development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of male gonad development." [GOC:obol, GOC:yaf] +synonym: "regulation of testicular development" EXACT [GOC:obol] +synonym: "regulation of testis development" EXACT [GOC:obol] +is_a: GO:2000026 ! regulation of multicellular organismal development +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0008584 ! male gonad development +relationship: regulates GO:0008584 ! male gonad development +created_by: janelomax +creation_date: 2010-07-15T03:29:05Z + +[Term] +id: GO:2000019 +name: negative regulation of male gonad development +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of male gonad development." [GOC:obol, GOC:yaf] +synonym: "negative regulation of testicular development" EXACT [GOC:obol] +synonym: "negative regulation of testis development" EXACT [GOC:obol] +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:2000018 ! regulation of male gonad development +is_a: GO:2000242 ! negative regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0008584 ! male gonad development +relationship: negatively_regulates GO:0008584 ! male gonad development +created_by: janelomax +creation_date: 2010-07-15T03:29:10Z + +[Term] +id: GO:2000026 +name: regulation of multicellular organismal development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of multicellular organismal development." [GOC:obol] +is_a: GO:0050793 ! regulation of developmental process +is_a: GO:0051239 ! regulation of multicellular organismal process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007275 ! multicellular organismal development +relationship: regulates GO:0007275 ! multicellular organismal development +created_by: tanyaberardini +creation_date: 2010-08-05T11:25:59Z + +[Term] +id: GO:2000027 +name: regulation of organ morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of organ morphogenesis." [GOC:obol] +synonym: "regulation of histogenesis and organogenesis" RELATED [GOC:obol] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0009887 ! organ morphogenesis +relationship: regulates GO:0009887 ! organ morphogenesis +created_by: tanyaberardini +creation_date: 2010-08-05T11:26:27Z + +[Term] +id: GO:2000035 +name: regulation of stem cell division +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of stem cell division." [GOC:obol] +synonym: "regulation of stem cell renewal" EXACT [GOC:obol] +is_a: GO:0051302 ! regulation of cell division +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0017145 ! stem cell division +relationship: regulates GO:0017145 ! stem cell division +created_by: tanyaberardini +creation_date: 2010-08-05T11:34:53Z + +[Term] +id: GO:2000040 +name: regulation of planar cell polarity pathway involved in axis elongation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of planar cell polarity pathway involved in axis elongation." [GOC:dph] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0048638 ! regulation of developmental growth +is_a: GO:2000095 ! regulation of Wnt signaling pathway, planar cell polarity pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003402 ! planar cell polarity pathway involved in axis elongation +relationship: regulates GO:0003402 ! planar cell polarity pathway involved in axis elongation +created_by: dph +creation_date: 2010-08-18T02:47:49Z + +[Term] +id: GO:2000041 +name: negative regulation of planar cell polarity pathway involved in axis elongation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of planar cell polarity pathway involved in axis elongation." [GOC:dph] +is_a: GO:2000040 ! regulation of planar cell polarity pathway involved in axis elongation +is_a: GO:2000051 ! negative regulation of non-canonical Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0003402 ! planar cell polarity pathway involved in axis elongation +relationship: negatively_regulates GO:0003402 ! planar cell polarity pathway involved in axis elongation +created_by: dph +creation_date: 2010-08-18T02:47:54Z + +[Term] +id: GO:2000043 +name: regulation of cardiac cell fate specification +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cardiac cell fate specification." [GOC:BHF] +is_a: GO:0042659 ! regulation of cell fate specification +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060912 ! cardiac cell fate specification +relationship: regulates GO:0060912 ! cardiac cell fate specification +created_by: tanyaberardini +creation_date: 2010-08-19T09:01:04Z + +[Term] +id: GO:2000044 +name: negative regulation of cardiac cell fate specification +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac cell fate specification." [GOC:BHF] +is_a: GO:0009996 ! negative regulation of cell fate specification +is_a: GO:2000043 ! regulation of cardiac cell fate specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0060912 ! cardiac cell fate specification +relationship: negatively_regulates GO:0060912 ! cardiac cell fate specification +created_by: tanyaberardini +creation_date: 2010-08-19T09:01:10Z + +[Term] +id: GO:2000047 +name: regulation of cell-cell adhesion mediated by cadherin +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell-cell adhesion mediated by cadherin." [GOC:obol] +is_a: GO:0022407 ! regulation of cell-cell adhesion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044331 ! cell-cell adhesion mediated by cadherin +relationship: regulates GO:0044331 ! cell-cell adhesion mediated by cadherin +created_by: jane +creation_date: 2010-08-20T12:56:44Z + +[Term] +id: GO:2000049 +name: positive regulation of cell-cell adhesion mediated by cadherin +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell-cell adhesion mediated by cadherin." [GOC:obol] +is_a: GO:2000047 ! regulation of cell-cell adhesion mediated by cadherin +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044331 ! cell-cell adhesion mediated by cadherin +relationship: positively_regulates GO:0044331 ! cell-cell adhesion mediated by cadherin +created_by: jane +creation_date: 2010-08-20T12:56:57Z + +[Term] +id: GO:2000050 +name: regulation of non-canonical Wnt signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of non-canonical Wnt signaling pathway." [GOC:obol, GOC:yaf] +synonym: "regulation of beta-catenin-independent Wnt receptor signaling pathway" EXACT [GOC:obol] +synonym: "regulation of non-canonical Wnt receptor signaling pathway" EXACT [] +synonym: "regulation of non-canonical Wnt receptor signalling pathway" EXACT [GOC:mah] +synonym: "regulation of non-canonical Wnt-activated signaling pathway" EXACT [GOC:signaling] +is_a: GO:0030111 ! regulation of Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035567 ! non-canonical Wnt signaling pathway +relationship: regulates GO:0035567 ! non-canonical Wnt signaling pathway +created_by: jane +creation_date: 2010-08-20T01:04:12Z + +[Term] +id: GO:2000051 +name: negative regulation of non-canonical Wnt signaling pathway +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of non-canonical Wnt signaling pathway." [GOC:obol, GOC:yaf] +synonym: "negative regulation of beta-catenin-independent Wnt receptor signaling pathway" EXACT [GOC:obol] +synonym: "negative regulation of non-canonical Wnt receptor signaling pathway" EXACT [] +synonym: "negative regulation of non-canonical Wnt receptor signalling pathway" EXACT [GOC:mah] +synonym: "negative regulation of non-canonical Wnt-activated signaling pathway" EXACT [GOC:signaling] +is_a: GO:0030178 ! negative regulation of Wnt signaling pathway +is_a: GO:2000050 ! regulation of non-canonical Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0035567 ! non-canonical Wnt signaling pathway +relationship: negatively_regulates GO:0035567 ! non-canonical Wnt signaling pathway +created_by: jane +creation_date: 2010-08-20T01:04:20Z + +[Term] +id: GO:2000052 +name: positive regulation of non-canonical Wnt signaling pathway +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of non-canonical Wnt-activated signaling pathway." [GOC:obol, GOC:yaf] +synonym: "positive regulation of beta-catenin-independent Wnt receptor signaling pathway" EXACT [GOC:obol] +synonym: "positive regulation of non-canonical Wnt receptor signaling pathway" EXACT [] +synonym: "positive regulation of non-canonical Wnt receptor signalling pathway" EXACT [GOC:mah] +synonym: "positive regulation of non-canonical Wnt-activated signaling pathway" EXACT [GOC:signaling] +is_a: GO:0030177 ! positive regulation of Wnt signaling pathway +is_a: GO:2000050 ! regulation of non-canonical Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0035567 ! non-canonical Wnt signaling pathway +relationship: positively_regulates GO:0035567 ! non-canonical Wnt signaling pathway +created_by: jane +creation_date: 2010-08-20T01:04:25Z + +[Term] +id: GO:2000053 +name: regulation of Wnt signaling pathway involved in dorsal/ventral axis specification +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of Wnt signaling pathway involved in dorsal/ventral axis specification." [GOC:obol, GOC:yaf] +synonym: "regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification" EXACT [] +synonym: "regulation of Wnt receptor signalling pathway involved in dorsal/ventral axis specification" EXACT [GOC:mah] +synonym: "regulation of Wnt-activated signaling pathway involved in dorsal/ventral axis specification" EXACT [GOC:signaling] +is_a: GO:0030111 ! regulation of Wnt signaling pathway +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044332 ! Wnt signaling pathway involved in dorsal/ventral axis specification +relationship: regulates GO:0044332 ! Wnt signaling pathway involved in dorsal/ventral axis specification +created_by: jane +creation_date: 2010-08-20T01:13:28Z + +[Term] +id: GO:2000054 +name: negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of Wnt signaling pathway involved in dorsal/ventral axis specification." [GOC:obol, GOC:yaf] +synonym: "negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification" EXACT [] +synonym: "negative regulation of Wnt receptor signalling pathway involved in dorsal/ventral axis specification" EXACT [GOC:mah] +synonym: "negative regulation of Wnt-activated signaling pathway involved in dorsal/ventral axis specification" EXACT [GOC:signaling] +is_a: GO:0030178 ! negative regulation of Wnt signaling pathway +is_a: GO:2000053 ! regulation of Wnt signaling pathway involved in dorsal/ventral axis specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044332 ! Wnt signaling pathway involved in dorsal/ventral axis specification +relationship: negatively_regulates GO:0044332 ! Wnt signaling pathway involved in dorsal/ventral axis specification +created_by: jane +creation_date: 2010-08-20T01:13:35Z + +[Term] +id: GO:2000055 +name: positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of Wnt signaling pathway involved in dorsal/ventral axis specification." [GOC:obol] +synonym: "positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification" EXACT [] +synonym: "positive regulation of Wnt receptor signalling pathway involved in dorsal/ventral axis specification" EXACT [GOC:mah] +synonym: "positive regulation of Wnt-activated signaling pathway involved in dorsal/ventral axis specification" EXACT [GOC:signaling] +is_a: GO:0030177 ! positive regulation of Wnt signaling pathway +is_a: GO:2000053 ! regulation of Wnt signaling pathway involved in dorsal/ventral axis specification +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044332 ! Wnt signaling pathway involved in dorsal/ventral axis specification +relationship: positively_regulates GO:0044332 ! Wnt signaling pathway involved in dorsal/ventral axis specification +created_by: jane +creation_date: 2010-08-20T01:13:40Z + +[Term] +id: GO:2000056 +name: regulation of Wnt signaling pathway involved in digestive tract morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of Wnt signaling pathway involved in digestive tract morphogenesis." [GOC:obol] +synonym: "regulation of Wnt receptor signaling pathway involved in digestive tract morphogenesis" EXACT [] +synonym: "regulation of Wnt receptor signalling pathway involved in digestive tract morphogenesis" EXACT [GOC:mah] +synonym: "regulation of Wnt-activated signaling pathway involved in digestive tract morphogenesis" RELATED [GOC:signaling] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0030111 ! regulation of Wnt signaling pathway +is_a: GO:2000026 ! regulation of multicellular organismal development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044333 ! Wnt signaling pathway involved in digestive tract morphogenesis +relationship: regulates GO:0044333 ! Wnt signaling pathway involved in digestive tract morphogenesis +created_by: jane +creation_date: 2010-08-20T01:17:27Z + +[Term] +id: GO:2000057 +name: negative regulation of Wnt signaling pathway involved in digestive tract morphogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of Wnt signaling pathway involved in digestive tract morphogenesis." [GOC:obol] +synonym: "negative regulation of Wnt receptor signaling pathway involved in digestive tract morphogenesis" EXACT [] +synonym: "negative regulation of Wnt receptor signalling pathway involved in digestive tract morphogenesis" EXACT [GOC:mah] +synonym: "negative regulation of Wnt-activated signaling pathway involved in digestive tract morphogenesis" EXACT [GOC:signaling] +is_a: GO:0030178 ! negative regulation of Wnt signaling pathway +is_a: GO:2000056 ! regulation of Wnt signaling pathway involved in digestive tract morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044333 ! Wnt signaling pathway involved in digestive tract morphogenesis +relationship: negatively_regulates GO:0044333 ! Wnt signaling pathway involved in digestive tract morphogenesis +created_by: jane +creation_date: 2010-08-20T01:17:35Z + +[Term] +id: GO:2000058 +name: regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of protein ubiquitination involved in ubiquitin-dependent protein catabolic process." [GOC:BHF] +synonym: "regulation of myofibrillar protein ubiquitination during ubiquitin-dependent protein breakdown" RELATED [GOC:obol] +synonym: "regulation of myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolic process" RELATED [GOC:obol] +synonym: "regulation of myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolism" RELATED [GOC:obol] +synonym: "regulation of myofibrillar protein ubiquitination during ubiquitin-dependent protein degradation" RELATED [GOC:obol] +synonym: "regulation of protein degradation tagging activity" RELATED [GOC:obol] +synonym: "regulation of protein ubiquitination during ubiquitin-dependent protein breakdown" EXACT [GOC:obol] +synonym: "regulation of protein ubiquitination during ubiquitin-dependent protein catabolic process" RELATED [GOC:obol] +synonym: "regulation of protein ubiquitination during ubiquitin-dependent protein catabolism" EXACT [GOC:obol] +synonym: "regulation of protein ubiquitination during ubiquitin-dependent protein degradation" EXACT [GOC:obol] +synonym: "regulation of protein ubiquitinylation during ubiquitin-dependent protein catabolic process" EXACT [GOC:obol] +synonym: "regulation of protein ubiquitinylation during ubiquitin-dependent protein catabolism" EXACT [GOC:obol] +synonym: "regulation of protein ubiquitylation during ubiquitin-dependent protein catabolic process" EXACT [GOC:obol] +synonym: "regulation of protein ubiquitylation during ubiquitin-dependent protein catabolism" EXACT [GOC:obol] +is_a: GO:0030162 ! regulation of proteolysis +is_a: GO:0031329 ! regulation of cellular catabolic process +is_a: GO:0031396 ! regulation of protein ubiquitination +is_a: GO:0042176 ! regulation of protein catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0042787 ! protein ubiquitination involved in ubiquitin-dependent protein catabolic process +relationship: regulates GO:0042787 ! protein ubiquitination involved in ubiquitin-dependent protein catabolic process +created_by: jane +creation_date: 2010-08-20T01:23:46Z + +[Term] +id: GO:2000059 +name: negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein ubiquitination involved in ubiquitin-dependent protein catabolic process." [GOC:BHF] +synonym: "negative regulation of myofibrillar protein ubiquitination during ubiquitin-dependent protein breakdown" RELATED [GOC:obol] +synonym: "negative regulation of myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolic process" RELATED [GOC:obol] +synonym: "negative regulation of myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolism" RELATED [GOC:obol] +synonym: "negative regulation of myofibrillar protein ubiquitination during ubiquitin-dependent protein degradation" RELATED [GOC:obol] +synonym: "negative regulation of protein degradation tagging activity" RELATED [GOC:obol] +synonym: "negative regulation of protein ubiquitination during ubiquitin-dependent protein breakdown" EXACT [GOC:obol] +synonym: "negative regulation of protein ubiquitination during ubiquitin-dependent protein catabolic process" RELATED [GOC:obol] +synonym: "negative regulation of protein ubiquitination during ubiquitin-dependent protein catabolism" EXACT [GOC:obol] +synonym: "negative regulation of protein ubiquitination during ubiquitin-dependent protein degradation" EXACT [GOC:obol] +synonym: "negative regulation of protein ubiquitinylation during ubiquitin-dependent protein catabolic process" EXACT [GOC:obol] +synonym: "negative regulation of protein ubiquitinylation during ubiquitin-dependent protein catabolism" EXACT [GOC:obol] +synonym: "negative regulation of protein ubiquitylation during ubiquitin-dependent protein catabolic process" EXACT [GOC:obol] +synonym: "negative regulation of protein ubiquitylation during ubiquitin-dependent protein catabolism" EXACT [GOC:obol] +is_a: GO:0031397 ! negative regulation of protein ubiquitination +is_a: GO:2000058 ! regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0042787 ! protein ubiquitination involved in ubiquitin-dependent protein catabolic process +relationship: negatively_regulates GO:0042787 ! protein ubiquitination involved in ubiquitin-dependent protein catabolic process +created_by: jane +creation_date: 2010-08-20T01:23:56Z + +[Term] +id: GO:2000064 +name: regulation of cortisol biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cortisol biosynthetic process." [GOC:obol, GOC:yaf] +synonym: "regulation of cortisol anabolism" RELATED [GOC:obol] +synonym: "regulation of cortisol biosynthesis" EXACT [GOC:obol] +synonym: "regulation of cortisol formation" EXACT [GOC:obol] +synonym: "regulation of cortisol synthesis" EXACT [GOC:obol] +is_a: GO:0010566 ! regulation of ketone biosynthetic process +is_a: GO:0031946 ! regulation of glucocorticoid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034651 ! cortisol biosynthetic process +relationship: regulates GO:0034651 ! cortisol biosynthetic process +created_by: jane +creation_date: 2010-08-20T01:51:15Z + +[Term] +id: GO:2000066 +name: positive regulation of cortisol biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cortisol biosynthetic process." [GOC:obol, GOC:yaf] +synonym: "positive regulation of cortisol anabolism" RELATED [GOC:obol] +synonym: "positive regulation of cortisol biosynthesis" EXACT [GOC:obol] +synonym: "positive regulation of cortisol formation" EXACT [GOC:obol] +synonym: "positive regulation of cortisol synthesis" EXACT [GOC:obol] +is_a: GO:0031948 ! positive regulation of glucocorticoid biosynthetic process +is_a: GO:2000064 ! regulation of cortisol biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0034651 ! cortisol biosynthetic process +relationship: positively_regulates GO:0034651 ! cortisol biosynthetic process +created_by: jane +creation_date: 2010-08-20T01:51:32Z + +[Term] +id: GO:2000079 +name: regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of canonical Wnt signaling pathway modulating the rate or frequency of pancreatic B cell proliferation." [GOC:obol, GOC:yaf] +synonym: "regulation of canonical Wnt receptor signaling pathway involved in controlling pancreatic B cell proliferation" EXACT [GOC:mah] +synonym: "regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation" EXACT [] +synonym: "regulation of canonical Wnt receptor signaling pathway involved in pancreatic beta cell proliferation" EXACT [GOC:obol] +synonym: "regulation of canonical Wnt receptor signalling pathway involved in controlling pancreatic B cell proliferation" EXACT [GOC:mah] +synonym: "regulation of canonical Wnt receptor signalling pathway involved in controlling type B pancreatic cell proliferation" EXACT [GOC:mah] +synonym: "regulation of canonical Wnt-activated signaling pathway involved in controlling type B pancreatic cell proliferation" EXACT [GOC:signaling] +is_a: GO:0042127 ! regulation of cell proliferation +is_a: GO:0060828 ! regulation of canonical Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044343 ! canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation +relationship: regulates GO:0044343 ! canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation +created_by: tanyaberardini +creation_date: 2010-08-27T11:22:56Z + +[Term] +id: GO:2000080 +name: negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of canonical Wnt signaling pathway modulating the rate or frequency of pancreatic B cell proliferation." [GOC:obol, GOC:yaf] +synonym: "negative regulation of canonical Wnt receptor signaling pathway involved in controlling pancreatic B cell proliferation" EXACT [GOC:mah] +synonym: "negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation" EXACT [] +synonym: "negative regulation of canonical Wnt receptor signaling pathway involved in pancreatic beta cell proliferation" EXACT [GOC:obol] +synonym: "negative regulation of canonical Wnt receptor signalling pathway involved in controlling pancreatic B cell proliferation" EXACT [GOC:mah] +synonym: "negative regulation of canonical Wnt receptor signalling pathway involved in controlling type B pancreatic cell proliferation" EXACT [GOC:mah] +synonym: "negative regulation of canonical Wnt-activated signaling pathway involved in controlling type B pancreatic cell proliferation" EXACT [GOC:signaling] +is_a: GO:0090090 ! negative regulation of canonical Wnt signaling pathway +is_a: GO:2000079 ! regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044343 ! canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation +relationship: negatively_regulates GO:0044343 ! canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation +created_by: tanyaberardini +creation_date: 2010-08-27T11:22:58Z + +[Term] +id: GO:2000081 +name: positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of canonical Wnt signaling pathway modulating the rate or frequency of pancreatic B cell proliferation." [GOC:obol, GOC:yaf] +synonym: "positive regulation of canonical Wnt receptor signaling pathway involved in controlling pancreatic B cell proliferation" EXACT [GOC:mah] +synonym: "positive regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation" EXACT [] +synonym: "positive regulation of canonical Wnt receptor signaling pathway involved in pancreatic beta cell proliferation" EXACT [GOC:obol] +synonym: "positive regulation of canonical Wnt receptor signalling pathway involved in controlling pancreatic B cell proliferation" EXACT [GOC:mah] +synonym: "positive regulation of canonical Wnt receptor signalling pathway involved in controlling type B pancreatic cell proliferation" EXACT [GOC:mah] +synonym: "positive regulation of canonical Wnt-activated signaling pathway involved in controlling type B pancreatic cell proliferation" EXACT [GOC:signaling] +is_a: GO:0090263 ! positive regulation of canonical Wnt signaling pathway +is_a: GO:2000079 ! regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044343 ! canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation +relationship: positively_regulates GO:0044343 ! canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation +created_by: tanyaberardini +creation_date: 2010-08-27T11:23:00Z + +[Term] +id: GO:2000095 +name: regulation of Wnt signaling pathway, planar cell polarity pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of Wnt signaling pathway, planar cell polarity pathway." [GOC:BHF] +synonym: "regulation of non-canonical Wnt signaling pathway" RELATED [GOC:obol] +synonym: "regulation of PCP pathway" EXACT [GOC:obol] +synonym: "regulation of Wnt receptor signaling pathway, planar cell polarity pathway" EXACT [] +synonym: "regulation of Wnt receptor signalling pathway, planar cell polarity pathway" EXACT [GOC:obol] +synonym: "regulation of Wnt-activated signaling pathway, planar cell polarity pathway" EXACT [GOC:signaling] +synonym: "regulation of Wnt-JNK signaling pathway" RELATED [GOC:obol] +synonym: "regulation of Wnt-PCP signaling pathway" RELATED [GOC:obol] +is_a: GO:2000050 ! regulation of non-canonical Wnt signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway +relationship: regulates GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway +created_by: jane +creation_date: 2010-09-08T01:07:39Z + +[Term] +id: GO:2000106 +name: regulation of leukocyte apoptotic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of leukocyte apoptotic process." [GOC:BHF, GOC:mtg_apoptosis] +synonym: "regulation of leukocyte apoptosis" NARROW [] +is_a: GO:0042981 ! regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0071887 ! leukocyte apoptotic process +relationship: regulates GO:0071887 ! leukocyte apoptotic process +created_by: midori +creation_date: 2010-09-15T01:42:05Z + +[Term] +id: GO:2000108 +name: positive regulation of leukocyte apoptotic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of leukocyte apoptotic process." [GOC:BHF, GOC:mtg_apoptosis] +synonym: "positive regulation of leukocyte apoptosis" NARROW [] +is_a: GO:0043065 ! positive regulation of apoptotic process +is_a: GO:2000106 ! regulation of leukocyte apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0071887 ! leukocyte apoptotic process +relationship: positively_regulates GO:0071887 ! leukocyte apoptotic process +created_by: midori +creation_date: 2010-09-15T01:42:12Z + +[Term] +id: GO:2000112 +name: regulation of cellular macromolecule biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol] +synonym: "regulation of cellular biopolymer biosynthetic process" EXACT [GOC:obol] +synonym: "regulation of cellular macromolecule anabolism" EXACT [GOC:obol] +synonym: "regulation of cellular macromolecule biosynthesis" EXACT [GOC:obol] +synonym: "regulation of cellular macromolecule formation" EXACT [GOC:obol] +synonym: "regulation of cellular macromolecule synthesis" EXACT [GOC:obol] +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0034645 ! cellular macromolecule biosynthetic process +relationship: regulates GO:0034645 ! cellular macromolecule biosynthetic process +created_by: tanyaberardini +creation_date: 2010-09-15T08:55:45Z + +[Term] +id: GO:2000113 +name: negative regulation of cellular macromolecule biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol] +synonym: "negative regulation of cellular biopolymer biosynthetic process" EXACT [GOC:obol] +synonym: "negative regulation of cellular macromolecule anabolism" EXACT [GOC:obol] +synonym: "negative regulation of cellular macromolecule biosynthesis" EXACT [GOC:obol] +synonym: "negative regulation of cellular macromolecule formation" EXACT [GOC:obol] +synonym: "negative regulation of cellular macromolecule synthesis" EXACT [GOC:obol] +is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process +is_a: GO:0031327 ! negative regulation of cellular biosynthetic process +is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0034645 ! cellular macromolecule biosynthetic process +relationship: negatively_regulates GO:0034645 ! cellular macromolecule biosynthetic process +created_by: tanyaberardini +creation_date: 2010-09-15T08:55:48Z + +[Term] +id: GO:2000116 +name: regulation of cysteine-type endopeptidase activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cysteine-type endopeptidase activity." [GOC:obol, GOC:yaf] +synonym: "regulation of lysosomal cysteine-type endopeptidase" RELATED [GOC:obol] +synonym: "regulation of thiol endopeptidase activity" EXACT [GOC:obol] +is_a: GO:0052548 ! regulation of endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004197 ! cysteine-type endopeptidase activity +relationship: regulates GO:0004197 ! cysteine-type endopeptidase activity +created_by: jane +creation_date: 2010-09-23T10:24:33Z + +[Term] +id: GO:2000117 +name: negative regulation of cysteine-type endopeptidase activity +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cysteine-type endopeptidase activity." [GOC:obol, GOC:yaf] +synonym: "negative regulation of lysosomal cysteine-type endopeptidase" RELATED [GOC:obol] +synonym: "negative regulation of thiol endopeptidase activity" EXACT [GOC:obol] +is_a: GO:0010951 ! negative regulation of endopeptidase activity +is_a: GO:2000116 ! regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004197 ! cysteine-type endopeptidase activity +relationship: negatively_regulates GO:0004197 ! cysteine-type endopeptidase activity +created_by: jane +creation_date: 2010-09-23T10:24:35Z + +[Term] +id: GO:2000136 +name: regulation of cell proliferation involved in heart morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell proliferation involved in heart morphogenesis." [GOC:dph] +is_a: GO:0042127 ! regulation of cell proliferation +is_a: GO:2000826 ! regulation of heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061323 ! cell proliferation involved in heart morphogenesis +relationship: regulates GO:0061323 ! cell proliferation involved in heart morphogenesis +created_by: dph +creation_date: 2010-09-29T12:43:53Z + +[Term] +id: GO:2000142 +name: regulation of DNA-templated transcription, initiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of DNA-templated transcription initiation." [GOC:mah, GOC:txnOH] +synonym: "regulation of DNA-dependent RNA polymerase complex assembly at promoter" EXACT [GOC:obol] +synonym: "regulation of DNA-dependent transcription, initiation" EXACT [GOC:txnOH] +synonym: "regulation of initiation of DNA-dependent transcription" EXACT [GOC:jh2] +synonym: "regulation of transcription initiation, DNA-dependent" EXACT [GOC:jh2] +is_a: GO:0006355 ! regulation of transcription, DNA-templated +is_a: GO:0043254 ! regulation of protein complex assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006352 ! DNA-templated transcription, initiation +relationship: regulates GO:0006352 ! DNA-templated transcription, initiation +created_by: midori +creation_date: 2010-10-01T09:11:35Z + +[Term] +id: GO:2000143 +name: negative regulation of DNA-templated transcription, initiation +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-templated transcription initiation." [GOC:mah, GOC:txnOH] +synonym: "negative regulation of DNA-dependent RNA polymerase complex assembly at promoter" EXACT [GOC:obol] +synonym: "negative regulation of DNA-dependent transcription, initiation" EXACT [GOC:txnOH] +synonym: "negative regulation of initiation of DNA-dependent transcription" EXACT [GOC:jh2] +synonym: "negative regulation of transcription initiation, DNA-dependent" EXACT [GOC:jh2] +is_a: GO:0031333 ! negative regulation of protein complex assembly +is_a: GO:0045892 ! negative regulation of transcription, DNA-templated +is_a: GO:2000142 ! regulation of DNA-templated transcription, initiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006352 ! DNA-templated transcription, initiation +relationship: negatively_regulates GO:0006352 ! DNA-templated transcription, initiation +created_by: midori +creation_date: 2010-10-01T09:11:40Z + +[Term] +id: GO:2000145 +name: regulation of cell motility +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell motility." [GOC:mah] +synonym: "regulation of cell locomotion" EXACT [GOC:obol] +synonym: "regulation of cell movement" RELATED [GOC:obol] +synonym: "regulation of movement of a cell" EXACT [GOC:obol] +is_a: GO:0040012 ! regulation of locomotion +is_a: GO:0051270 ! regulation of cellular component movement +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048870 ! cell motility +relationship: regulates GO:0048870 ! cell motility +created_by: midori +creation_date: 2010-10-01T09:41:21Z + +[Term] +id: GO:2000146 +name: negative regulation of cell motility +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility." [GOC:mah] +synonym: "negative regulation of cell locomotion" EXACT [GOC:obol] +synonym: "negative regulation of cell movement" RELATED [GOC:obol] +synonym: "negative regulation of movement of a cell" EXACT [GOC:obol] +is_a: GO:0040013 ! negative regulation of locomotion +is_a: GO:0051271 ! negative regulation of cellular component movement +is_a: GO:2000145 ! regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048870 ! cell motility +relationship: negatively_regulates GO:0048870 ! cell motility +created_by: midori +creation_date: 2010-10-01T09:41:26Z + +[Term] +id: GO:2000147 +name: positive regulation of cell motility +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell motility." [GOC:mah] +synonym: "positive regulation of cell locomotion" EXACT [GOC:obol] +synonym: "positive regulation of cell movement" RELATED [GOC:obol] +synonym: "positive regulation of movement of a cell" EXACT [GOC:obol] +is_a: GO:0040017 ! positive regulation of locomotion +is_a: GO:0051272 ! positive regulation of cellular component movement +is_a: GO:2000145 ! regulation of cell motility +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0048870 ! cell motility +relationship: positively_regulates GO:0048870 ! cell motility +created_by: midori +creation_date: 2010-10-01T09:41:30Z + +[Term] +id: GO:2000148 +name: regulation of planar cell polarity pathway involved in ventricular septum morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of planar cell polarity pathway involved in ventricular septum morphogenesis." [GOC:dph] +is_a: GO:1901219 ! regulation of cardiac chamber morphogenesis +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061348 ! planar cell polarity pathway involved in ventricular septum morphogenesis +relationship: regulates GO:0061348 ! planar cell polarity pathway involved in ventricular septum morphogenesis +created_by: dph +creation_date: 2010-10-01T07:09:49Z + +[Term] +id: GO:2000149 +name: negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of planar cell polarity pathway involved in ventricular septum morphogenesis." [GOC:dph] +is_a: GO:2000148 ! regulation of planar cell polarity pathway involved in ventricular septum morphogenesis +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061348 ! planar cell polarity pathway involved in ventricular septum morphogenesis +relationship: negatively_regulates GO:0061348 ! planar cell polarity pathway involved in ventricular septum morphogenesis +created_by: dph +creation_date: 2010-10-01T07:09:53Z + +[Term] +id: GO:2000150 +name: regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis." [GOC:dph] +is_a: GO:0055024 ! regulation of cardiac muscle tissue development +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061350 ! planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +relationship: regulates GO:0061350 ! planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +created_by: dph +creation_date: 2010-10-01T07:11:11Z + +[Term] +id: GO:2000151 +name: negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis." [GOC:dph] +is_a: GO:2000150 ! regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061350 ! planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +relationship: negatively_regulates GO:0061350 ! planar cell polarity pathway involved in cardiac muscle tissue morphogenesis +created_by: dph +creation_date: 2010-10-01T07:11:15Z + +[Term] +id: GO:2000159 +name: regulation of planar cell polarity pathway involved in heart morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of planar cell polarity pathway involved in heart morphogenesis." [GOC:dph] +is_a: GO:0003307 ! regulation of Wnt signaling pathway involved in heart development +is_a: GO:2000095 ! regulation of Wnt signaling pathway, planar cell polarity pathway +is_a: GO:2000826 ! regulation of heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: regulates GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +created_by: dph +creation_date: 2010-10-05T01:03:22Z + +[Term] +id: GO:2000160 +name: negative regulation of planar cell polarity pathway involved in heart morphogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of planar cell polarity pathway involved in heart morphogenesis." [GOC:dph] +is_a: GO:0003308 ! negative regulation of Wnt signaling pathway involved in heart development +is_a: GO:2000051 ! negative regulation of non-canonical Wnt signaling pathway +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +relationship: negatively_regulates GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis +created_by: dph +creation_date: 2010-10-05T01:03:25Z + +[Term] +id: GO:2000161 +name: regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of planar cell polarity pathway involved in cardiac right atrium morphogenesis." [GOC:dph] +is_a: GO:1901219 ! regulation of cardiac chamber morphogenesis +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061349 ! planar cell polarity pathway involved in cardiac right atrium morphogenesis +relationship: regulates GO:0061349 ! planar cell polarity pathway involved in cardiac right atrium morphogenesis +created_by: dph +creation_date: 2010-10-05T01:05:21Z + +[Term] +id: GO:2000162 +name: negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of planar cell polarity pathway involved in cardiac right atrium morphogenesis." [GOC:dph] +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +is_a: GO:2000161 ! regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061349 ! planar cell polarity pathway involved in cardiac right atrium morphogenesis +relationship: negatively_regulates GO:0061349 ! planar cell polarity pathway involved in cardiac right atrium morphogenesis +created_by: dph +creation_date: 2010-10-05T01:05:24Z + +[Term] +id: GO:2000163 +name: regulation of planar cell polarity pathway involved in outflow tract morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of planar cell polarity pathway involved in outflow tract morphogenesis." [GOC:dph] +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061347 ! planar cell polarity pathway involved in outflow tract morphogenesis +relationship: regulates GO:0061347 ! planar cell polarity pathway involved in outflow tract morphogenesis +created_by: dph +creation_date: 2010-10-05T01:06:13Z + +[Term] +id: GO:2000164 +name: negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of planar cell polarity pathway involved in outflow tract morphogenesis." [GOC:dph] +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +is_a: GO:2000163 ! regulation of planar cell polarity pathway involved in outflow tract morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061347 ! planar cell polarity pathway involved in outflow tract morphogenesis +relationship: negatively_regulates GO:0061347 ! planar cell polarity pathway involved in outflow tract morphogenesis +created_by: dph +creation_date: 2010-10-05T01:06:15Z + +[Term] +id: GO:2000165 +name: regulation of planar cell polarity pathway involved in pericardium morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of planar cell polarity pathway involved in pericardium morphogenesis." [GOC:dph] +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:2000159 ! regulation of planar cell polarity pathway involved in heart morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061354 ! planar cell polarity pathway involved in pericardium morphogenesis +relationship: regulates GO:0061354 ! planar cell polarity pathway involved in pericardium morphogenesis +created_by: dph +creation_date: 2010-10-05T01:07:36Z + +[Term] +id: GO:2000166 +name: negative regulation of planar cell polarity pathway involved in pericardium morphogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of planar cell polarity pathway involved in pericardium morphogenesis." [GOC:dph] +is_a: GO:2000160 ! negative regulation of planar cell polarity pathway involved in heart morphogenesis +is_a: GO:2000165 ! regulation of planar cell polarity pathway involved in pericardium morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061354 ! planar cell polarity pathway involved in pericardium morphogenesis +relationship: negatively_regulates GO:0061354 ! planar cell polarity pathway involved in pericardium morphogenesis +created_by: dph +creation_date: 2010-10-05T01:07:39Z + +[Term] +id: GO:2000167 +name: regulation of planar cell polarity pathway involved in neural tube closure +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of planar cell polarity pathway involved in neural tube closure." [GOC:dph] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0045995 ! regulation of embryonic development +is_a: GO:0051960 ! regulation of nervous system development +is_a: GO:2000095 ! regulation of Wnt signaling pathway, planar cell polarity pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0090179 ! planar cell polarity pathway involved in neural tube closure +relationship: regulates GO:0090179 ! planar cell polarity pathway involved in neural tube closure +created_by: dph +creation_date: 2010-10-05T01:08:53Z + +[Term] +id: GO:2000168 +name: negative regulation of planar cell polarity pathway involved in neural tube closure +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of planar cell polarity pathway involved in neural tube closure." [GOC:dph] +is_a: GO:2000051 ! negative regulation of non-canonical Wnt signaling pathway +is_a: GO:2000167 ! regulation of planar cell polarity pathway involved in neural tube closure +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0090179 ! planar cell polarity pathway involved in neural tube closure +relationship: negatively_regulates GO:0090179 ! planar cell polarity pathway involved in neural tube closure +created_by: dph +creation_date: 2010-10-05T01:08:56Z + +[Term] +id: GO:2000177 +name: regulation of neural precursor cell proliferation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of neural precursor cell proliferation." [GOC:dph, GOC:yaf] +is_a: GO:0042127 ! regulation of cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061351 ! neural precursor cell proliferation +relationship: regulates GO:0061351 ! neural precursor cell proliferation +created_by: dph +creation_date: 2010-10-13T12:40:41Z + +[Term] +id: GO:2000179 +name: positive regulation of neural precursor cell proliferation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation." [GOC:dph, GOC:yaf] +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:2000177 ! regulation of neural precursor cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0061351 ! neural precursor cell proliferation +relationship: positively_regulates GO:0061351 ! neural precursor cell proliferation +created_by: dph +creation_date: 2010-10-13T12:40:45Z + +[Term] +id: GO:2000180 +name: negative regulation of androgen biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of androgen biosynthetic process." [GOC:dph, GOC:yaf] +synonym: "negative regulation of androgen anabolism" EXACT [GOC:obol] +synonym: "negative regulation of androgen biosynthesis" EXACT [GOC:obol] +synonym: "negative regulation of androgen formation" EXACT [GOC:obol] +synonym: "negative regulation of androgen synthesis" EXACT [GOC:obol] +is_a: GO:0010894 ! negative regulation of steroid biosynthetic process +is_a: GO:0032353 ! negative regulation of hormone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006702 ! androgen biosynthetic process +relationship: negatively_regulates GO:0006702 ! androgen biosynthetic process +created_by: dph +creation_date: 2010-10-13T12:43:17Z + +[Term] +id: GO:2000181 +name: negative regulation of blood vessel morphogenesis +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis." [GOC:dph, GOC:yaf] +is_a: GO:0022603 ! regulation of anatomical structure morphogenesis +is_a: GO:0051093 ! negative regulation of developmental process +is_a: GO:1901342 ! regulation of vasculature development +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0048514 ! blood vessel morphogenesis +relationship: negatively_regulates GO:0048514 ! blood vessel morphogenesis +created_by: dph +creation_date: 2010-10-13T12:46:31Z + +[Term] +id: GO:2000224 +name: regulation of testosterone biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of testosterone biosynthetic process." [GOC:obol, GOC:yaf] +is_a: GO:0010566 ! regulation of ketone biosynthetic process +is_a: GO:0046885 ! regulation of hormone biosynthetic process +is_a: GO:0050810 ! regulation of steroid biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0061370 ! testosterone biosynthetic process +relationship: regulates GO:0061370 ! testosterone biosynthetic process +created_by: yaf +creation_date: 2010-11-09T10:38:33Z + +[Term] +id: GO:2000225 +name: negative regulation of testosterone biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of testosterone biosynthetic process." [GOC:obol, GOC:yaf] +is_a: GO:2000180 ! negative regulation of androgen biosynthetic process +is_a: GO:2000224 ! regulation of testosterone biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0061370 ! testosterone biosynthetic process +relationship: negatively_regulates GO:0061370 ! testosterone biosynthetic process +created_by: yaf +creation_date: 2010-11-09T10:38:37Z + +[Term] +id: GO:2000241 +name: regulation of reproductive process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of reproductive process." [GOC:mah] +is_a: GO:0050789 ! regulation of biological process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0022414 ! reproductive process +relationship: regulates GO:0022414 ! reproductive process +created_by: midori +creation_date: 2010-11-10T02:44:02Z + +[Term] +id: GO:2000242 +name: negative regulation of reproductive process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process." [GOC:mah] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0022414 ! reproductive process +relationship: negatively_regulates GO:0022414 ! reproductive process +created_by: midori +creation_date: 2010-11-10T02:44:05Z + +[Term] +id: GO:2000243 +name: positive regulation of reproductive process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of reproductive process." [GOC:mah] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:2000241 ! regulation of reproductive process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0022414 ! reproductive process +relationship: positively_regulates GO:0022414 ! reproductive process +created_by: midori +creation_date: 2010-11-10T02:44:08Z + +[Term] +id: GO:2000269 +name: regulation of fibroblast apoptotic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of fibroblast apoptotic process." [GOC:mtg_apoptosis, GOC:obol, GOC:yaf] +synonym: "regulation of fibroblast apoptosis" NARROW [] +is_a: GO:0042981 ! regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0044346 ! fibroblast apoptotic process +relationship: regulates GO:0044346 ! fibroblast apoptotic process +created_by: jane +creation_date: 2010-11-23T01:07:23Z + +[Term] +id: GO:2000270 +name: negative regulation of fibroblast apoptotic process +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast apoptotic process." [GOC:mtg_apoptosis, GOC:obol, GOC:yaf] +synonym: "negative regulation of fibroblast apoptosis" NARROW [] +is_a: GO:0043066 ! negative regulation of apoptotic process +is_a: GO:2000269 ! regulation of fibroblast apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0044346 ! fibroblast apoptotic process +relationship: negatively_regulates GO:0044346 ! fibroblast apoptotic process +created_by: jane +creation_date: 2010-11-23T01:07:27Z + +[Term] +id: GO:2000271 +name: positive regulation of fibroblast apoptotic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of fibroblast apoptotic process." [GOC:mtg_apoptosis, GOC:obol, GOC:yaf] +synonym: "positive regulation of fibroblast apoptosis" NARROW [] +is_a: GO:0043065 ! positive regulation of apoptotic process +is_a: GO:2000269 ! regulation of fibroblast apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0044346 ! fibroblast apoptotic process +relationship: positively_regulates GO:0044346 ! fibroblast apoptotic process +created_by: jane +creation_date: 2010-11-23T01:07:29Z + +[Term] +id: GO:2000272 +name: negative regulation of receptor activity +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of receptor activity." [GOC:obol] +is_a: GO:0010469 ! regulation of receptor activity +is_a: GO:0044092 ! negative regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004872 ! receptor activity +relationship: negatively_regulates GO:0004872 ! receptor activity +created_by: rfoulger +creation_date: 2010-12-02T09:28:47Z + +[Term] +id: GO:2000273 +name: positive regulation of receptor activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of receptor activity." [GOC:obol] +is_a: GO:0010469 ! regulation of receptor activity +is_a: GO:0044093 ! positive regulation of molecular function +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004872 ! receptor activity +relationship: positively_regulates GO:0004872 ! receptor activity +created_by: rfoulger +creation_date: 2010-12-02T09:28:50Z + +[Term] +id: GO:2000380 +name: regulation of mesoderm development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of mesoderm development." [GOC:BHF] +is_a: GO:0050793 ! regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007498 ! mesoderm development +relationship: regulates GO:0007498 ! mesoderm development +created_by: vk +creation_date: 2011-02-15T03:09:46Z + +[Term] +id: GO:2000401 +name: regulation of lymphocyte migration +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of lymphocyte migration." [GOC:mah] +is_a: GO:0002685 ! regulation of leukocyte migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072676 ! lymphocyte migration +relationship: regulates GO:0072676 ! lymphocyte migration +created_by: midori +creation_date: 2011-02-23T10:45:19Z + +[Term] +id: GO:2000403 +name: positive regulation of lymphocyte migration +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of lymphocyte migration." [GOC:mah] +is_a: GO:0002687 ! positive regulation of leukocyte migration +is_a: GO:2000401 ! regulation of lymphocyte migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0072676 ! lymphocyte migration +relationship: positively_regulates GO:0072676 ! lymphocyte migration +created_by: midori +creation_date: 2011-02-23T10:46:06Z + +[Term] +id: GO:2000404 +name: regulation of T cell migration +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of T cell migration." [GOC:mah] +synonym: "regulation of T lymphocyte migration" EXACT [GOC:obol] +synonym: "regulation of T-cell migration" EXACT [GOC:obol] +synonym: "regulation of T-lymphocyte migration" EXACT [GOC:obol] +is_a: GO:2000401 ! regulation of lymphocyte migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072678 ! T cell migration +relationship: regulates GO:0072678 ! T cell migration +created_by: midori +creation_date: 2011-02-23T10:48:24Z + +[Term] +id: GO:2000406 +name: positive regulation of T cell migration +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of T cell migration." [GOC:mah] +synonym: "positive regulation of T lymphocyte migration" EXACT [GOC:obol] +synonym: "positive regulation of T-cell migration" EXACT [GOC:obol] +synonym: "positive regulation of T-lymphocyte migration" EXACT [GOC:obol] +is_a: GO:2000403 ! positive regulation of lymphocyte migration +is_a: GO:2000404 ! regulation of T cell migration +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0072678 ! T cell migration +relationship: positively_regulates GO:0072678 ! T cell migration +created_by: midori +creation_date: 2011-02-23T10:49:12Z + +[Term] +id: GO:2000482 +name: regulation of interleukin-8 secretion +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of interleukin-8 secretion." [GOC:obol] +synonym: "regulation of IL-8 secretion" EXACT [GOC:obol] +is_a: GO:0032677 ! regulation of interleukin-8 production +is_a: GO:0050707 ! regulation of cytokine secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0072606 ! interleukin-8 secretion +relationship: regulates GO:0072606 ! interleukin-8 secretion +created_by: yaf +creation_date: 2011-03-10T02:37:11Z + +[Term] +id: GO:2000484 +name: positive regulation of interleukin-8 secretion +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of interleukin-8 secretion." [GOC:obol] +synonym: "positive regulation of IL-8 secretion" EXACT [GOC:obol] +is_a: GO:0050715 ! positive regulation of cytokine secretion +is_a: GO:2000482 ! regulation of interleukin-8 secretion +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0072606 ! interleukin-8 secretion +relationship: positively_regulates GO:0072606 ! interleukin-8 secretion +created_by: yaf +creation_date: 2011-03-10T02:38:20Z + +[Term] +id: GO:2000543 +name: positive regulation of gastrulation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of gastrulation." [GOC:obol] +is_a: GO:0010470 ! regulation of gastrulation +is_a: GO:0051094 ! positive regulation of developmental process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0007369 ! gastrulation +relationship: positively_regulates GO:0007369 ! gastrulation +created_by: yaf +creation_date: 2011-04-01T04:10:15Z + +[Term] +id: GO:2000647 +name: negative regulation of stem cell proliferation +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of stem cell proliferation." [GOC:dph] +is_a: GO:0008285 ! negative regulation of cell proliferation +is_a: GO:0072091 ! regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0072089 ! stem cell proliferation +relationship: negatively_regulates GO:0072089 ! stem cell proliferation +created_by: dph +creation_date: 2011-04-27T01:04:22Z + +[Term] +id: GO:2000648 +name: positive regulation of stem cell proliferation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of stem cell proliferation." [GOC:dph] +is_a: GO:0008284 ! positive regulation of cell proliferation +is_a: GO:0072091 ! regulation of stem cell proliferation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0072089 ! stem cell proliferation +relationship: positively_regulates GO:0072089 ! stem cell proliferation +created_by: dph +creation_date: 2011-04-27T01:04:25Z + +[Term] +id: GO:2000696 +name: regulation of epithelial cell differentiation involved in kidney development +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of epithelial cell differentiation involved in kidney development." [GOC:mtg_kidney_jan10, GOC:yaf] +is_a: GO:0030856 ! regulation of epithelial cell differentiation +is_a: GO:0090183 ! regulation of kidney development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035850 ! epithelial cell differentiation involved in kidney development +relationship: regulates GO:0035850 ! epithelial cell differentiation involved in kidney development +created_by: rfoulger +creation_date: 2011-05-16T04:23:52Z + +[Term] +id: GO:2000725 +name: regulation of cardiac muscle cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cardiac muscle cell differentiation." [GOC:BHF] +synonym: "regulation of cardiomyocyte differentiation" EXACT [GOC:obol] +synonym: "regulation of heart muscle cell differentiation" RELATED [GOC:obol] +is_a: GO:0051153 ! regulation of striated muscle cell differentiation +is_a: GO:0055024 ! regulation of cardiac muscle tissue development +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0055007 ! cardiac muscle cell differentiation +relationship: regulates GO:0055007 ! cardiac muscle cell differentiation +created_by: vk +creation_date: 2011-06-08T10:51:06Z + +[Term] +id: GO:2000727 +name: positive regulation of cardiac muscle cell differentiation +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cardiac muscle cell differentiation." [GOC:BHF] +synonym: "positive regulation of cardiomyocyte differentiation" EXACT [GOC:obol] +synonym: "positive regulation of heart muscle cell differentiation" RELATED [GOC:obol] +is_a: GO:0051155 ! positive regulation of striated muscle cell differentiation +is_a: GO:2000725 ! regulation of cardiac muscle cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0055007 ! cardiac muscle cell differentiation +relationship: positively_regulates GO:0055007 ! cardiac muscle cell differentiation +created_by: vk +creation_date: 2011-06-08T10:51:15Z + +[Term] +id: GO:2000736 +name: regulation of stem cell differentiation +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of stem cell differentiation." [GOC:obol] +is_a: GO:0045595 ! regulation of cell differentiation +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0048863 ! stem cell differentiation +relationship: regulates GO:0048863 ! stem cell differentiation +created_by: yaf +creation_date: 2011-06-14T02:05:16Z + +[Term] +id: GO:2000794 +name: regulation of epithelial cell proliferation involved in lung morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis." [PMID:21513708] +is_a: GO:0050678 ! regulation of epithelial cell proliferation +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis +relationship: regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis +created_by: pr +creation_date: 2011-06-25T07:22:38Z + +[Term] +id: GO:2000823 +name: regulation of androgen receptor activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of androgen receptor activity." [GOC:obol] +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +is_a: GO:0010469 ! regulation of receptor activity +is_a: GO:0051090 ! regulation of sequence-specific DNA binding transcription factor activity +is_a: GO:0060765 ! regulation of androgen receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0004882 ! androgen receptor activity +relationship: regulates GO:0004882 ! androgen receptor activity +created_by: yaf +creation_date: 2011-07-15T10:56:08Z + +[Term] +id: GO:2000824 +name: negative regulation of androgen receptor activity +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of androgen receptor activity." [GOC:obol] +is_a: GO:0043433 ! negative regulation of sequence-specific DNA binding transcription factor activity +is_a: GO:2000272 ! negative regulation of receptor activity +is_a: GO:2000823 ! regulation of androgen receptor activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0004882 ! androgen receptor activity +relationship: negatively_regulates GO:0004882 ! androgen receptor activity +created_by: yaf +creation_date: 2011-07-15T10:56:12Z + +[Term] +id: GO:2000826 +name: regulation of heart morphogenesis +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of heart morphogenesis." [GOC:BHF] +synonym: "regulation of cardiac morphogenesis" RELATED [GOC:obol] +is_a: GO:2000027 ! regulation of organ morphogenesis +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0003007 ! heart morphogenesis +relationship: regulates GO:0003007 ! heart morphogenesis +created_by: vk +creation_date: 2011-07-19T10:08:58Z + +[Term] +id: GO:2000970 +name: regulation of detection of glucose +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of detection of glucose." [GOC:BHF] +synonym: "regulation of glucose detection" EXACT [GOC:obol] +synonym: "regulation of glucose perception" RELATED [GOC:obol] +synonym: "regulation of glucose sensing" RELATED [GOC:obol] +is_a: GO:0048583 ! regulation of response to stimulus +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0051594 ! detection of glucose +relationship: regulates GO:0051594 ! detection of glucose +created_by: vk +creation_date: 2011-08-02T10:18:52Z + +[Term] +id: GO:2000971 +name: negative regulation of detection of glucose +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of detection of glucose." [GOC:BHF] +synonym: "negative regulation of glucose detection" EXACT [GOC:obol] +synonym: "negative regulation of glucose perception" RELATED [GOC:obol] +synonym: "negative regulation of glucose sensing" RELATED [GOC:obol] +is_a: GO:0048585 ! negative regulation of response to stimulus +is_a: GO:2000970 ! regulation of detection of glucose +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0051594 ! detection of glucose +relationship: negatively_regulates GO:0051594 ! detection of glucose +created_by: vk +creation_date: 2011-08-02T10:18:54Z + +[Term] +id: GO:2000976 +name: regulation of transcription from RNA polymerase II promoter involved in detection of glucose +namespace: biological_process +def: "Any regulation of transcription from RNA polymerase II promoter that is involved in detection of glucose." [GOC:BHF] +synonym: "global transcription regulation from Pol II promoter involved in detection of glucose" RELATED [GOC:obol] +synonym: "global transcription regulation from Pol II promoter involved in glucose detection" RELATED [GOC:obol] +synonym: "global transcription regulation from Pol II promoter involved in glucose perception" RELATED [GOC:obol] +synonym: "global transcription regulation from Pol II promoter involved in glucose sensing" RELATED [GOC:obol] +synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in detection of glucose" RELATED [GOC:obol] +synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in glucose detection" RELATED [GOC:obol] +synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in glucose perception" RELATED [GOC:obol] +synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in glucose sensing" RELATED [GOC:obol] +synonym: "regulation of global transcription from Pol II promoter involved in detection of glucose" RELATED [GOC:obol] +synonym: "regulation of global transcription from Pol II promoter involved in glucose detection" RELATED [GOC:obol] +synonym: "regulation of global transcription from Pol II promoter involved in glucose perception" RELATED [GOC:obol] +synonym: "regulation of global transcription from Pol II promoter involved in glucose sensing" RELATED [GOC:obol] +synonym: "regulation of transcription from Pol II promoter involved in detection of glucose" EXACT [GOC:obol] +synonym: "regulation of transcription from Pol II promoter involved in glucose detection" EXACT [GOC:obol] +synonym: "regulation of transcription from Pol II promoter involved in glucose perception" RELATED [GOC:obol] +synonym: "regulation of transcription from Pol II promoter involved in glucose sensing" RELATED [GOC:obol] +synonym: "regulation of transcription from RNA polymerase II promoter involved in glucose detection" EXACT [GOC:obol] +synonym: "regulation of transcription from RNA polymerase II promoter involved in glucose perception" RELATED [GOC:obol] +synonym: "regulation of transcription from RNA polymerase II promoter involved in glucose sensing" RELATED [GOC:obol] +synonym: "regulation of transcription from RNA polymerase II promoter, global involved in detection of glucose" RELATED [GOC:obol] +synonym: "regulation of transcription from RNA polymerase II promoter, global involved in glucose detection" RELATED [GOC:obol] +synonym: "regulation of transcription from RNA polymerase II promoter, global involved in glucose perception" RELATED [GOC:obol] +synonym: "regulation of transcription from RNA polymerase II promoter, global involved in glucose sensing" RELATED [GOC:obol] +is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter +intersection_of: part_of GO:0051594 ! detection of glucose +relationship: part_of GO:0051594 ! detection of glucose +created_by: vk +creation_date: 2011-08-02T05:06:52Z + +[Term] +id: GO:2001012 +name: mesenchymal cell differentiation involved in renal system development +namespace: biological_process +def: "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the renal system as it progresses from its formation to the mature state." [GOC:mtg_kidney_jan10, GOC:obol, GOC:yaf] +synonym: "mesenchymal cell differentiation involved in urinary system development" RELATED [GOC:obol] +synonym: "mesenchymal cell differentiation involved in urinary tract development" RELATED [GOC:obol] +is_a: GO:0048762 ! mesenchymal cell differentiation +intersection_of: GO:0048762 ! mesenchymal cell differentiation +intersection_of: part_of GO:0072001 ! renal system development +relationship: part_of GO:0072001 ! renal system development +created_by: yaf +creation_date: 2011-08-09T04:05:14Z + +[Term] +id: GO:2001056 +name: positive regulation of cysteine-type endopeptidase activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cysteine-type endopeptidase activity." [GOC:obol] +synonym: "positive regulation of lysosomal cysteine-type endopeptidase" RELATED [GOC:obol] +synonym: "positive regulation of thiol endopeptidase activity" EXACT [GOC:obol] +is_a: GO:0010950 ! positive regulation of endopeptidase activity +is_a: GO:2000116 ! regulation of cysteine-type endopeptidase activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004197 ! cysteine-type endopeptidase activity +relationship: positively_regulates GO:0004197 ! cysteine-type endopeptidase activity +created_by: pr +creation_date: 2011-09-09T08:53:43Z + +[Term] +id: GO:2001141 +name: regulation of RNA biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of RNA biosynthetic process." [GOC:dph] +synonym: "regulation of RNA anabolism" EXACT [GOC:obol] +synonym: "regulation of RNA biosynthesis" EXACT [GOC:obol] +synonym: "regulation of RNA formation" EXACT [GOC:obol] +synonym: "regulation of RNA synthesis" EXACT [GOC:obol] +is_a: GO:0010556 ! regulation of macromolecule biosynthetic process +is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0051252 ! regulation of RNA metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0032774 ! RNA biosynthetic process +relationship: regulates GO:0032774 ! RNA biosynthetic process +created_by: dph +creation_date: 2011-10-17T11:36:25Z + +[Term] +id: GO:2001233 +name: regulation of apoptotic signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of apoptotic signaling pathway." [GOC:mtg_apoptosis] +synonym: "regulation of apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:0042981 ! regulation of apoptotic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097190 ! apoptotic signaling pathway +relationship: regulates GO:0097190 ! apoptotic signaling pathway +created_by: pr +creation_date: 2011-11-24T01:20:49Z + +[Term] +id: GO:2001234 +name: negative regulation of apoptotic signaling pathway +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway." [GOC:mtg_apoptosis] +synonym: "negative regulation of apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:0009968 ! negative regulation of signal transduction +is_a: GO:2001233 ! regulation of apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097190 ! apoptotic signaling pathway +relationship: negatively_regulates GO:0097190 ! apoptotic signaling pathway +created_by: pr +creation_date: 2011-11-24T01:20:54Z + +[Term] +id: GO:2001235 +name: positive regulation of apoptotic signaling pathway +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway." [GOC:mtg_apoptosis] +synonym: "positive regulation of apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:0009967 ! positive regulation of signal transduction +is_a: GO:2001233 ! regulation of apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0097190 ! apoptotic signaling pathway +relationship: positively_regulates GO:0097190 ! apoptotic signaling pathway +created_by: pr +creation_date: 2011-11-24T01:20:58Z + +[Term] +id: GO:2001236 +name: regulation of extrinsic apoptotic signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway." [GOC:mtg_apoptosis] +synonym: "regulation of extrinsic apoptosis" NARROW [] +synonym: "regulation of extrinsic apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:2001233 ! regulation of apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: regulates GO:0097191 ! extrinsic apoptotic signaling pathway +created_by: pr +creation_date: 2011-11-24T01:30:05Z + +[Term] +id: GO:2001237 +name: negative regulation of extrinsic apoptotic signaling pathway +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway." [GOC:mtg_apoptosis] +synonym: "negative regulation of extrinsic apoptosis" NARROW [] +synonym: "negative regulation of extrinsic apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:2001234 ! negative regulation of apoptotic signaling pathway +is_a: GO:2001236 ! regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: negatively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +created_by: pr +creation_date: 2011-11-24T01:30:11Z + +[Term] +id: GO:2001238 +name: positive regulation of extrinsic apoptotic signaling pathway +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway." [GOC:mtg_apoptosis] +synonym: "positive regulation of extrinsic apoptosis" NARROW [] +synonym: "positive regulation of extrinsic apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:2001235 ! positive regulation of apoptotic signaling pathway +is_a: GO:2001236 ! regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: positively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +created_by: pr +creation_date: 2011-11-24T01:30:16Z + +[Typedef] +id: ends_during +name: ends_during +namespace: gene_ontology +comment: This relation will be used after 2013-05-21. +xref: RO:0002093 + +[Typedef] +id: happens_during +name: happens_during +namespace: gene_ontology +comment: This relation will be used after 2013-05-21. +xref: RO:0002092 +is_transitive: true +is_a: ends_during ! ends_during + +[Typedef] +id: has_part +name: has_part +namespace: gene_ontology +xref: BFO:0000051 +xref: OBO_REL:has_part +is_transitive: true +inverse_of: part_of ! part_of + +[Typedef] +id: negatively_regulates +name: negatively_regulates +namespace: gene_ontology +xref: RO:0002212 +holds_over_chain: results_in negatively_regulates +is_a: regulates ! regulates + +[Typedef] +id: occurs_in +name: occurs in +namespace: gene_ontology +xref: BFO:0000066 +transitive_over: part_of ! part_of + +[Typedef] +id: part_of +name: part_of +namespace: gene_ontology +xref: BFO:0000050 +xref: OBO_REL:part_of +is_transitive: true + +[Typedef] +id: positively_regulates +name: positively_regulates +namespace: gene_ontology +xref: RO:0002213 +holds_over_chain: results_in positively_regulates +is_a: regulates ! regulates + +[Typedef] +id: regulates +name: regulates +namespace: gene_ontology +xref: RO:0002211 +holds_over_chain: results_in regulates +transitive_over: part_of ! part_of + +[Typedef] +id: results_in +name: results_in +namespace: gene_ontology +comment: This relation is currently used to connect two regulation processes p1 and p2, such that if r1 regulates p1 and r2 regulates p2, and r1 results_in r2 then the regulation of p1 is required for the regulation of p2. For an example of use, see GO:0035958 'regulation of glyoxylate cycle by regulation of transcription from RNA polymerase II promoter'. Note that a precise definition of this relation is under discussion. After it has been formalized it will be added to RO, where it will have a RO ID. Note that the existing identifier and label are subject to change. +created_by: cjm +creation_date: 2012-03-14T10:35:44Z + +[Typedef] +id: starts_during +name: starts_during +namespace: gene_ontology +comment: This relations will be used after 2013-05-21. +xref: RO:0002091 + diff --git a/minerva-core/src/test/resources/mmg/anonClassAssertions.owl b/minerva-core/src/test/resources/mmg/anonClassAssertions.owl new file mode 100644 index 00000000..f4859799 --- /dev/null +++ b/minerva-core/src/test/resources/mmg/anonClassAssertions.owl @@ -0,0 +1,600 @@ + + + + + + + + + + + + + + + + part_of + + + + + + + + phenotype_in + + + + + + + + + + + + + brain + + + + + + + + liver + + + + + + + + region1 + + + + + + + + + + + + + + region10 + + + + + + + + + + + + + + region2 + + + + + + + + + + + + + + region3 + + + + + + + + + + + + + + region4 + + + + + + + + + + + + + + region5 + + + + + + + + + + + + + + region6 + + + + + + + + + + + + + + region7 + + + + + + + + + + + + + + region8 + + + + + + + + + + + + + + region9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + i1 + + + + + + + + + + + + + + + + + + + i10 + + + + + + + + + + + + + + + + + + + i2 + + + + + + + + + + + + + + + + + + + i3 + + + + + + + + + + + + + + + + + + + i4 + + + + + + + + + + + + + + + + + + + i5 + + + + + + + + + + + + + + + + + + + i6 + + + + + + + + + + + + + + + + + + + i7 + + + + + + + + + + + + + + + + + + + i8 + + + + + + + + + + + + + + + + + + + i9 + + + + + + + + + + + + + + + + + + + j1 + + + + + + + + + + + + + + + + + + + j10 + + + + + + + + + + + + + + + + + + + j2 + + + + + + + + + + + + + + + + + + + j3 + + + + + + + + + + + + + + + + + + + j4 + + + + + + + + + + + + + + + + + + + j5 + + + + + + + + + + + + + + + + + + + j6 + + + + + + + + + + + + + + + + + + + j7 + + + + + + + + + + + + + + + + + + + j8 + + + + + + + + + + + + + + + + + + + j9 + + + + + + + diff --git a/minerva-core/src/test/resources/mmg/basic-tbox-importer.omn b/minerva-core/src/test/resources/mmg/basic-tbox-importer.omn new file mode 100644 index 00000000..0e44479f --- /dev/null +++ b/minerva-core/src/test/resources/mmg/basic-tbox-importer.omn @@ -0,0 +1,2 @@ +Ontology: +Import: \ No newline at end of file diff --git a/minerva-core/src/test/resources/mmg/basic-tbox.omn b/minerva-core/src/test/resources/mmg/basic-tbox.omn new file mode 100644 index 00000000..d8d2c11a --- /dev/null +++ b/minerva-core/src/test/resources/mmg/basic-tbox.omn @@ -0,0 +1,75 @@ +Ontology: +Prefix: obo: +Prefix: occurs_in: +Prefix: enabled_by: +Prefix: rdfs: +Prefix: : + +ObjectProperty: part_of InverseOf: has_part Characteristics: transitive +ObjectProperty: has_part + +ObjectProperty: starts_with SubPropertyOf: has_part +ObjectProperty: ends_with SubPropertyOf: has_part +ObjectProperty: activates +ObjectProperty: activated_by InverseOf: activates +ObjectProperty: regulates +ObjectProperty: enabled_by: +ObjectProperty: occurs_in: Annotations: rdfs:label "occurs in" SubPropertyChain: occurs_in: o part_of SubPropertyChain: part_of o occurs_in: +ObjectProperty: directly_activates SubPropertyOf: activates +ObjectProperty: indirectly_activates SubPropertyOf: activates Characteristics: transitive ### SubPropertyChain: activates o activates + +## LIMB ONTOLOGY +Class: limb SubClassOf: part_of some organism +Class: forelimb SubClassOf: limb +Class: hindlimb SubClassOf: limb +Class: autopod SubClassOf: part_of some limb, has_part some digit +Class: hand EquivalentTo: autopod and part_of some forelimb +Class: foot EquivalentTo: autopod and part_of some hindlimb +Class: digit +Class: finger EquivalentTo: digit and part_of some hand +Class: toe EquivalentTo: digit and part_of some foot +Class: human SubClassOf: organism, has_part some forelimb, has_part some hindlimb +Class: organism + +## wish we could do GCIs in manchester... +Class: _human_limb EquivalentTo: limb and part_of some human SubClassOf: has_part some autopod +Class: _human_autopod EquivalentTo: autopod and part_of some human + + +## PATHWAY ONTOLOGY +Class: obo:GO_0008150 +Class: phosphorylation SubClassOf: cellular_process +Class: regulation SubClassOf: obo:GO_0008150 +### Class: cellular_process SubClassOf: obo:GO_0008150, has_part some activity +Class: cellular_process SubClassOf: obo:GO_0008150 +Class: regulation_of_cellular_process EquivalentTo: regulation and regulates some cellular_process +Class: signal_transduction SubClassOf: cellular_process, ends_with some regulation_of_cellular_process +Class: foo_pathway EquivalentTo: signal_transduction and starts_with some (foo_receptor_activity and occurs_in: some plasma_membrane) and has_part some (mapk_cascade and occurs_in: some cytosol) +Class: bar_response_pathway SubClassOf: foo_pathway and starts_with some (receptor_activity and activated_by some detection_of_misfolded_proteins) and ends_with some regulation_of_transcription + +Class: receptor_activity SubClassOf: activity +Class: foo_receptor_activity EquivalentTo: receptor_activity and has_part some foo_receptor_binding +Class: foo_receptor_binding EquivalentTo: binding and activates some receptor_activity + +Class: detection_of_misfolded_proteins SubClassOf: cellular_process +Class: transcription SubClassOf: cellular_process, occurs_in: some nucleus +Class: regulation_of_transcription EquivalentTo: regulation and regulates some transcription + +Class: obo:GO_0003674 +Class: activity SubClassOf: obo:GO_0003674, enabled_by: some molecular_entity +Class: binding SubClassOf: activity +Class: catalytic_activity SubClassOf: activity +Class: kinase_activity SubClassOf: catalytic_activity, part_of some phosphorylation +Class: mapk_cascade SubClassOf: cellular_process, starts_with some mapkkk_activity, has_part some mapkk_activity, has_part some mapk_activity +Class: mapkkk_activity EquivalentTo: kinase_activity and directly_activates some mapkk_activity +Class: mapkk_activity EquivalentTo: kinase_activity and directly_activates some mapk_activity +Class: mapk_activity SubClassOf: kinase_activity + +Class: obo:GO_0005575 +Class: cell SubClassOf: obo:GO_0005575 +Class: membrane SubClassOf: obo:GO_0005575 +Class: nucleus SubClassOf: obo:GO_0005575 +Class: cytosol SubClassOf: obo:GO_0005575 +Class: plasma_membrane SubClassOf: membrane, part_of some cell + +Class: molecular_entity diff --git a/minerva-core/src/test/resources/mmg/catalog-v001.xml b/minerva-core/src/test/resources/mmg/catalog-v001.xml new file mode 100644 index 00000000..9f20a5ab --- /dev/null +++ b/minerva-core/src/test/resources/mmg/catalog-v001.xml @@ -0,0 +1,4 @@ + + + + diff --git a/minerva-core/src/test/resources/mmg/cycle.omn b/minerva-core/src/test/resources/mmg/cycle.omn new file mode 100644 index 00000000..1a6a147c --- /dev/null +++ b/minerva-core/src/test/resources/mmg/cycle.omn @@ -0,0 +1,27 @@ +Ontology: +Prefix: obo: +Prefix: occurs_in: +Prefix: enabled_by: +Prefix: rdfs: +Prefix: : + +ObjectProperty: part_of InverseOf: has_part Characteristics: transitive +ObjectProperty: has_part + +ObjectProperty: connected_to Characteristics: transitive + +Class: molecule + +Class: c +Class: cyclic_molecule + SubClassOf: molecule, has_part some (c and connected_to some (c and connected_to some (c and connected_to some (c and connected_to some (c and connected_to some c))))) + +Class: c1 SubClassOf: c +Class: c2 SubClassOf: c +Class: c3 SubClassOf: c +Class: c4 SubClassOf: c +Class: c5 SubClassOf: c +Class: c6 SubClassOf: c + +Class: cyclic_molecule2 + SubClassOf: molecule, has_part some (c1 and connected_to some (c2 and connected_to some (c3 and connected_to some (c4 and connected_to some (c5 and connected_to some (c6 and connected_to some c1)))))) diff --git a/minerva-core/src/test/resources/mmg/dna-replication-tbox.owl b/minerva-core/src/test/resources/mmg/dna-replication-tbox.owl new file mode 100644 index 00000000..9ffb0a3f --- /dev/null +++ b/minerva-core/src/test/resources/mmg/dna-replication-tbox.owl @@ -0,0 +1,1959 @@ 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it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion( "endurant"@en) +AnnotationAssertion(rdfs:label "continuant"@en) +AnnotationAssertion( "a symphony orchestra"@en) +AnnotationAssertion( "the disposition of blood to coagulate"@en) +AnnotationAssertion( "the lawn and atmosphere in front of our building"@en) +AnnotationAssertion( "a person"@en) +AnnotationAssertion( "continuant"@en) +SubClassOf( ) +AnnotationAssertion( "the spatiotemporal region occupied by the development of a cancer tumor"@en) +AnnotationAssertion( "the most interesting part of Van Gogh's life"@en) +AnnotationAssertion( "perdurant"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion( "a surgical operation as processual context for a nosocomical infection"@en) +AnnotationAssertion( "the spatiotemporal context occupied by a process of cellular meiosis"@en) +AnnotationAssertion(rdfs:label "occurrent"@en) +AnnotationAssertion( "occurrent"@en) +SubClassOf( ) +AnnotationAssertion( "a symphony orchestra"@en) +AnnotationAssertion( "independent continuant"@en) +AnnotationAssertion( "a heart"@en) +AnnotationAssertion(rdfs:label "independent continuant"@en) +AnnotationAssertion( "a person"@en) +AnnotationAssertion( "the bottom right portion of a human torso"@en) +AnnotationAssertion( "a leg"@en) +AnnotationAssertion( "the lawn and atmosphere in front of our building"@en) +AnnotationAssertion( "substantial entity"@en) +AnnotationAssertion( "an organism"@en) +AnnotationAssertion( "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion( "a chair"@en) +SubClassOf( ) +AnnotationAssertion( "A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities."@en) +AnnotationAssertion( "the process of cell-division"@en) +AnnotationAssertion(rdfs:label "processual entity"@en) +AnnotationAssertion( "the process of sleeping"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "process"@en) +SubClassOf( ) +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion( "collection of random bacteria"@en) +AnnotationAssertion( "Material entity subsumes object, fiat object part, and object aggregate, which assume a three level theory of granularity, which is inadequate for some domains, such as biology."@en) +AnnotationAssertion(rdfs:label "material entity"@en) +AnnotationAssertion( "a chair"@en) +AnnotationAssertion( "material entity"@en) +AnnotationAssertion( "dorsal surface of the body"@en) +SubClassOf( ) +AnnotationAssertion(rdfs:label 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+SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "biomacromolecule"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "information biomacromolecule"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleic acid"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "ribonucleic acid"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "canonical nucleoside residue"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "canonical ribonucleoside residue"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "canonical deoxyribonucleoside residue"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "organic cyclic compound"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "heteroarene"^^xsd:string) +SubClassOf( ) 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residue"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleotide residue"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleoside residue"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "organic molecular entity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "nitrogen molecular entity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "heterocyclic compound"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleobase-containing molecular entity"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "organic molecule"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "mitochondrial genome maintenance"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nuclear chromosome"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cytoplasmic chromosome"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "mitochondrial chromosome"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "plastid-encoded plastid RNA polymerase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "DNA-directed RNA polymerase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "telomere maintenance"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "origin recognition complex"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cytoplasmic origin of replication recognition complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "GINS complex"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "mitochondrial RNA catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "mitochondrial RNA metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "regulation of mitochondrial RNA catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "reverse transcription"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "transcription, RNA-templated"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "progressive alteration of chromatin involved in cell aging"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "replicative cell aging"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "progressive alteration of chromatin involved in replicative cell aging"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "extrachromosomal circular DNA accumulation involved in replicative cell aging"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "extrachromosomal rDNA circle accumulation involved in replicative cell aging"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "replication of extrachromosomal rDNA circles involved in replicative cell aging"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "replication of extrachromosomal circular DNA involved in replicative cell aging"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "replication of extrachromosomal circular DNA"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "molecular_function"^^xsd:string) +DisjointClasses( ) +DisjointClasses( ) +AnnotationAssertion(rdfs:label "DNA helicase activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "telomerase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "catalytic activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA-directed DNA polymerase activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA primase activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA-directed RNA polymerase activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA ligase activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "RNA-directed DNA polymerase activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "RNA-directed RNA polymerase activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "helicase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nuclease activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "endonuclease activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "endoribonuclease activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "RNA-DNA hybrid ribonuclease activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "exonuclease activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "exoribonuclease activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "exoribonuclease H activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "ribonuclease activity"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cellular_component"^^xsd:string) +DisjointClasses( ) +AnnotationAssertion(rdfs:label "intracellular"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cell"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleus"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleoplasm"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "nuclear pre-replicative complex"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "replication fork"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "chromosome"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cytoplasm"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "mitochondrion"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "mitochondrial matrix"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleobase-containing compound metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "DNA metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ))) +AnnotationAssertion(rdfs:label "DNA replication"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA-dependent DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "mitochondrial DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "DNA ligation"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "pre-replicative complex assembly involved in nuclear cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA unwinding involved in DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication, synthesis of RNA primer"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication initiation"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA strand elongation involved in DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "leading strand elongation"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "lagging strand elongation"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication termination"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "RNA-dependent DNA replication"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "DNA catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "chromatin organization"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "transcription, DNA-templated"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of transcription, DNA-templated"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "transcription from mitochondrial promoter"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "RNA catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "protein complex assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cellular aromatic compound metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nitrogen compound metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "organelle organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleus organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "telomere maintenance via telomerase"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "mitochondrion organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "cytoplasm organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cell cycle"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "aging"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cell aging"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "extrachromosomal circular DNA accumulation involved in cell aging"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "biological_process"^^xsd:string) +AnnotationAssertion(rdfs:label "metabolic process"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "catabolic process"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "macromolecule catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "biosynthetic process"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "macromolecule biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "nucleoid"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "DNA polymerase III complex"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "plastid chromosome"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "plastid stroma"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "plastid"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "plastid organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "regulation of biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cellular process"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "gene expression"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of gene expression"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of transposition, RNA-mediated"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of transposition"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of macromolecule biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of cell cycle process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of mitochondrion organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "telomere maintenance via telomere lengthening"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "viral process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular component organization"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "RNA metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "pyrophosphatase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "chromatin modification"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "transferase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleotidyltransferase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "hydrolase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "hydrolase activity, acting on ester bonds"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "hydrolase activity, acting on acid anhydrides"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "ligase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "ligase activity, forming phosphoric ester bonds"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "endoribonuclease activity, producing 5'-phosphomonoesters"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "exoribonuclease activity, producing 5'-phosphomonoesters"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleoside-triphosphatase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "heterocycle biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "viral life cycle"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "viral genome replication"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "viral gene expression"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "viral transcription"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of nucleobase-containing compound metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "aromatic compound biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "aromatic compound catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cell cycle process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cellular component disassembly"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular component assembly"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA strand elongation"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of DNA-dependent DNA replication initiation"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "RNA polymerase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "replisome"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication preinitiation complex"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of cellular metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of cellular biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of cellular catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "RNA-directed RNA polymerase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nuclear RNA-directed RNA polymerase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "membrane-enclosed lumen"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nuclear lumen"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "mitochondrial DNA metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "mitochondrial DNA catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "regulation of nuclease activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "transposition"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "transposition, RNA-mediated"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "reverse transcription involved in RNA-mediated transposition"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "telomere organization"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of telomere maintenance"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of telomere maintenance via telomerase"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA geometric change"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "developmental process"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "DNA duplex unwinding"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "RNA biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "regulation of homeostatic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of DNA endoreduplication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "macromolecular complex disassembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "protein-DNA complex disassembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "macromolecular complex"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "protein-DNA complex"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of organelle organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of chromosome organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA helicase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "plastid DNA metabolic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "plastid DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nuclear cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of nuclear cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication, Okazaki fragment processing"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA polymerase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "RNA polymerase activity"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "mitochondrial DNA-directed RNA polymerase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "regulation of transcription by chromatin organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular macromolecular complex assembly"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular nitrogen compound metabolic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular macromolecule biosynthetic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleobase-containing compound biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "nucleobase-containing compound catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "pre-replicative complex"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "pre-replicative complex assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "rolling circle viral DNA replication"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "rolling circle double-stranded viral DNA replication"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "rolling circle single-stranded viral DNA replication"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "rolling hairpin viral DNA replication"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "bidirectional double-stranded viral DNA replication"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "viral DNA strand displacement replication"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "viral double stranded DNA replication via reverse transcription"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "viral DNA genome replication"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "DNA-templated viral transcription"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "DNA endoreduplication"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "MCM complex"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA polymerase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "homeostatic process"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "mitochondrial nucleoid"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "plastid nucleoid"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication, removal of RNA primer"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "macromolecule metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "organelle"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "membrane-bounded organelle"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "non-membrane-bounded organelle"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "intracellular organelle"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "intracellular membrane-bounded organelle"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "intracellular non-membrane-bounded organelle"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "organelle lumen"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "protein complex"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "protein complex disassembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of protein complex disassembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of protein complex assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "nuclear replication fork"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cytoplasmic replication fork"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cytoplasmic replisome"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "nuclear replisome"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cellular protein complex assembly"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of multi-organism process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of symbiosis, encompassing mutualism through parasitism"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "macromolecular complex subunit organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "multi-organism metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "multi-organism biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "multi-organism catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular component biogenesis"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of cellular component biogenesis"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "development involved in symbiotic interaction"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cellular metabolic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "primary metabolic process"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular catabolic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular biosynthetic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular macromolecule metabolic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular macromolecule catabolic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular nitrogen compound catabolic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "cellular nitrogen compound biosynthetic process"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "symbiosis, encompassing mutualism through parasitism"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "interspecies interaction between organisms"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "organelle part"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "intracellular part"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "chromosomal part"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "nuclear part"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "mitochondrial part"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "plastid part"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cytoplasmic part"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "intracellular organelle part"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "nucleoplasm part"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "nuclear chromosome part"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cell part"^^xsd:string) +AnnotationAssertion(rdfs:label "cell part"@en) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "single-organism process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "single-organism metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "single-organism biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "single-organism catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "single-organism cellular process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "multi-organism cellular process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "single-organism developmental process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "single-stranded DNA-binding protein complex"^^xsd:string) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "bacterial-type DNA replication"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of viral genome replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "heterocycle metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "heterocycle catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of viral transcription"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of biological process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of catalytic activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of viral process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of developmental process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of cellular process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of DNA metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of helicase activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA ligation involved in DNA-dependent DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of DNA ligation"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of cellular component organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of nitrogen compound metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of RNA metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "chromosome organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "regulation of hydrolase activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of transferase activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of ligase activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "multi-organism process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of cell cycle"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of telomerase activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "nuclear DNA-directed RNA polymerase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "anatomical structure homeostasis"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of macromolecule metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of DNA strand elongation"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of endoribonuclease activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of ribonuclease activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "macromolecular complex assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "protein-DNA complex assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "biological regulation"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of biological quality"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of molecular function"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "intracellular organelle lumen"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "protein complex biogenesis"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "rolling circle DNA replication"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "theta DNA replication"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "organelle assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA conformation change"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "CMG complex"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication preinitiation complex assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "GINS complex assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "organic substance metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "protein complex subunit organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "protein-DNA complex subunit organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "cellular component organization or biogenesis"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "DNA biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "MCM complex assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of primary metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of mitochondrial DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "nucleic acid metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "nucleic acid phosphodiester bond hydrolysis"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of DNA-dependent DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of cell aging"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "RNA phosphodiester bond hydrolysis"^^xsd:string) +SubClassOf( ) +SubClassOf( ) +AnnotationAssertion(rdfs:label "RNA phosphodiester bond hydrolysis, endonucleolytic"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "RNA phosphodiester bond hydrolysis, exonucleolytic"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "MCM core complex"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "regulation of extrachromosomal rDNA circle accumulation involved in replicative cell aging"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of replicative cell aging"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of RNA-directed RNA polymerase activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of DNA-directed DNA polymerase activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of reverse transcription"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "organic cyclic compound metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "organic cyclic compound catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "organic cyclic compound biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "organic substance catabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "organic substance biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "regulation of mitochondrial DNA metabolic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of exoribonuclease activity"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of organelle assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of chromatin organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA ligation involved in cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication initiation involved in cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication termination involved in cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "synthesis of RNA primer involved in cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA strand elongation involved in cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA unwinding involved in cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "pre-replicative complex assembly involved in cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication initiation involved in nuclear cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication termination involved in nuclear cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication, synthesis of RNA primer involved in nuclear cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA strand elongation involved in nuclear cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA duplex unwinding involved in nuclear cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA ligation involved in bacterial-type DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication initiation involved in bacterial-type DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication termination involved in bacterial-type DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA replication, synthesis of RNA primer involved in bacterial-type DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA strand elongation involved in bacterial-type DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA duplex unwinding involved in bacterial-type DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "DNA ligation involved in nuclear cell cycle DNA replication"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf(Annotation( "true"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "catalytic complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "endoribonuclease complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "origin recognition complex assembly"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "single-organism organelle organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "multi-organism organelle organization"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "transferase complex"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +AnnotationAssertion(rdfs:label "regulation of cellular macromolecule biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of DNA biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of DNA replication termination"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "regulation of RNA biosynthetic process"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) )) +SubClassOf( ObjectSomeValuesFrom( )) +AnnotationAssertion(rdfs:label "quality"^^xsd:string) +AnnotationAssertion(rdfs:label "process quality"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "multi-organismal process"^^xsd:string) +SubClassOf( ) +AnnotationAssertion(rdfs:label "single organismal"^^xsd:string) +SubClassOf( ) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:part_of") +AnnotationAssertion( "BFO:0000050"^^xsd:string) +AnnotationAssertion(rdfs:label "part_of"^^xsd:string) +AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion( ) +AnnotationAssertion( "part_of"^^xsd:string) +AnnotationAssertion( "Intended meaning: +Ambiguous between continuant-parthood and occurrent-parthood. + +domain: continuant +range: continuant +time: at some time + +domain: occurrent +range: occurrent +time: atemporal"@en) +AnnotationAssertion( "part of"@en) +AnnotationAssertion( "Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell."@en) +AnnotationAssertion( "part_of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +AnnotationAssertion( "has_part"^^xsd:string) +AnnotationAssertion( "BFO:0000051"^^xsd:string) +AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "Intended meaning: +Ambiguous between continuant-parthood and occurrent-parthood. + +domain: continuant +range: continuant +time: at some time + +domain: occurrent +range: occurrent +time: atemporal"@en) +AnnotationAssertion( "has_part"^^xsd:string) +AnnotationAssertion(rdfs:label "has_part"^^xsd:string) +AnnotationAssertion(rdfs:label "has part"^^xsd:string) +AnnotationAssertion( "has_part"@en) +AnnotationAssertion( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +AnnotationAssertion(rdfs:label "occurs in"@en) +AnnotationAssertion(rdfs:label "occurs in"^^xsd:string) +AnnotationAssertion( "unfolds in"@en) +AnnotationAssertion( "Intended meaning: +domain: occurrent +range: independent continuant +time: atemporal"@en) +AnnotationAssertion( "occurs_in"@en) +AnnotationAssertion( "unfolds_in"@en) +AnnotationAssertion( "occurs in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) +AnnotationAssertion( "site of"@en) +AnnotationAssertion(rdfs:label "contains process"@en) +AnnotationAssertion(rdfs:label "results_in_assembly_of"^^xsd:string) +AnnotationAssertion( "GOREL:0002001"^^xsd:string) +AnnotationAssertion( "results_in_assembly_of"^^xsd:string) +AnnotationAssertion( "results_in_assembly_of"^^xsd:string) +AnnotationAssertion(rdfs:label "results_in_disassembly_of"^^xsd:string) +AnnotationAssertion( "results_in_disassembly_of"^^xsd:string) +AnnotationAssertion( "GOREL:0002002"^^xsd:string) +AnnotationAssertion( "results_in_disassembly_of"^^xsd:string) +AnnotationAssertion( "results_in_organization_of"^^xsd:string) +AnnotationAssertion(rdfs:label "results_in_organization_of"^^xsd:string) +AnnotationAssertion( "GOREL:0002006"^^xsd:string) +AnnotationAssertion( "results_in_organization_of"^^xsd:string) +AnnotationAssertion(rdfs:label "inheres in"@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "Intended meaning: +domain: specifically dependent continuant +range: independent continuant +time: at all times + +A specifically dependent continuant A inheres in its independent continuant B at all times during which A exists."@en) +AnnotationAssertion( ) +InverseObjectProperties( ) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Intended meaning: +domain: independent continuant +range: specifically dependent continuant +time: at some time"@en) +AnnotationAssertion(rdfs:label "bearer of"@en) +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "participates in"@en) +AnnotationAssertion( "participates_in"@en) +AnnotationAssertion(rdfs:label "participates in"@en) +AnnotationAssertion( "Intended meaning: +domain: continuant and (not spatial region) +range: processual entity +time: at some time"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) +AnnotationAssertion( "has_participant"^^xsd:string) +AnnotationAssertion( "has_participant"@en) +AnnotationAssertion( "has participant"@en) +AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion( "has_participant"^^xsd:string) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion( "RO:0000057"^^xsd:string) +AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) +AnnotationAssertion( "Intended meaning: +domain: processual entity +range: continuant and (not spatial region) +time: at some time"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) +AnnotationAssertion(rdfs:label "overlaps"^^xsd:string) +AnnotationAssertion(rdfs:label "overlaps"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") +AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") +SubObjectPropertyOf( ) +AnnotationAssertion(rdfs:label "regulates"@en) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Tanya Berardini") +AnnotationAssertion( "David Hill") +AnnotationAssertion(rdfs:label "regulates"^^xsd:string) +AnnotationAssertion( "x regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect on the frequency, rate or exteny of y") +AnnotationAssertion( ) +AnnotationAssertion( "GO") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +AnnotationAssertion( "RO_0000053 some (RO_0000054 only ?Y)") +AnnotationAssertion( "PMID:21208450") +AnnotationAssertion( "has function realized in") +AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") +AnnotationAssertion(rdfs:label "capable_of"^^xsd:string) +AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") +AnnotationAssertion( "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") +AnnotationAssertion(rdfs:label "capable of"@en) +AnnotationAssertion( "PMID:20123131") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) +AnnotationAssertion(rdfs:label "capable of part of"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))") +AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") +AnnotationAssertion( "has function in") +SubObjectPropertyOf( ) +AnnotationAssertion(rdfs:label "temporally related to"@en) +AnnotationAssertion( "Allen") +AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") +AnnotationAssertion( ) +AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "inverse of starts with") +AnnotationAssertion( ) +AnnotationAssertion( "Allen") +AnnotationAssertion(rdfs:label "starts"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +AnnotationAssertion( "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") +AnnotationAssertion( "started by") +AnnotationAssertion(rdfs:label "starts with"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor") +SubObjectPropertyOf( ) +TransitiveObjectProperty() +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ends"@en) +AnnotationAssertion( "inverse of ends with") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +AnnotationAssertion( "finished by") +AnnotationAssertion(rdfs:label "ends with"@en) +AnnotationAssertion( ) +AnnotationAssertion( "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") +SubObjectPropertyOf( ) +TransitiveObjectProperty() +AnnotationAssertion( "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has start location"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has end location"@en) +AnnotationAssertion( "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has input"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +AnnotationAssertion(rdfs:label "has output"@en) +AnnotationAssertion( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +AnnotationAssertion(rdfs:label "inheres in part of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mereotopologically related to"@en) +AnnotationAssertion( "A mereological relationship or a topological relationship") +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "functionally related to"@en) +AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) +AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") +SubObjectPropertyOf( ) +AnnotationAssertion(rdfs:label "regulated by"@en) +SubObjectPropertyOf( ) +AnnotationAssertion(rdfs:label "input of"@en) +SubObjectPropertyOf( ) +AnnotationAssertion(rdfs:label "output of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +) \ No newline at end of file diff --git a/minerva-core/src/test/resources/mmg/glycolysis-abox.omn b/minerva-core/src/test/resources/mmg/glycolysis-abox.omn new file mode 100644 index 00000000..89dfcb35 --- /dev/null +++ b/minerva-core/src/test/resources/mmg/glycolysis-abox.omn @@ -0,0 +1,927 @@ +Prefix: owl: +Prefix: rdf: +Prefix: xml: +Prefix: xsd: +Prefix: rdfs: + + + +Ontology: + + +AnnotationProperty: + + +AnnotationProperty: + + +AnnotationProperty: rdfs:label + + +Datatype: rdf:PlainLiteral + + +Datatype: xsd:string + + +ObjectProperty: + + +ObjectProperty: + + Annotations: + rdfs:label "negatively_regulates"^^xsd:string + + SubPropertyChain: + o + + SubPropertyChain: + o + +ObjectProperty: + + Annotations: + rdfs:label "has_part"^^xsd:string + + InverseOf: + + +ObjectProperty: + + Annotations: + rdfs:label "part_of"^^xsd:string, + "OBO_REL:part_of"^^xsd:string, + "BFO:0000050"^^xsd:string, + "part_of"^^xsd:string + + Characteristics: + Transitive + + +Class: + + Annotations: + rdfs:label "hexokinase activity"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "transferase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "small molecule binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "hexose catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "heterocyclic compound binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "carbohydrate metabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "organic cyclic compound binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "cellular metabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "purine nucleotide binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "hydro-lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "primary metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "ion binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "anion binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "organic substance catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "oxidoreductase activity"^^xsd:string + + SubClassOf: + , + some + + +Class: + + Annotations: + rdfs:label "transferase activity, transferring phosphorus-containing groups"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "phosphorus metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "monosaccharide catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "phosphopyruvate hydratase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "phosphate-containing compound metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "carbon-carbon lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "single-organism metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "kinase activity"^^xsd:string + + SubClassOf: + , + some + + +Class: + + Annotations: + rdfs:label "carbon-oxygen lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "generation of precursor metabolites and energy"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "molecular_function"^^xsd:string + + +Class: + + Annotations: + rdfs:label "phosphotransferase activity, alcohol group as acceptor"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "phosphotransferase activity, carboxyl group as acceptor"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "aldehyde-lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "glycolysis"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "phosphorylation"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "biological_process"^^xsd:string + + +Class: + + Annotations: + rdfs:label "oxidation-reduction process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "pyruvate kinase activity"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "carbohydrate kinase activity"^^xsd:string + + SubClassOf: + some , + + + +Class: + + Annotations: + rdfs:label "intramolecular oxidoreductase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "fructose-bisphosphate aldolase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "cellular carbohydrate metabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "monosaccharide metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "ATP binding"^^xsd:string + + SubClassOf: + , + , + + + +Class: + + Annotations: + rdfs:label "intramolecular transferase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "adenyl ribonucleotide binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "intramolecular transferase activity, phosphotransferases"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "nucleoside binding"^^xsd:string + + SubClassOf: + , + , + + + +Class: + + Annotations: + rdfs:label "purine nucleoside binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "intramolecular oxidoreductase activity, interconverting aldoses and ketoses"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "purine ribonucleotide binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "organic substance metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "nucleotide binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "triose-phosphate isomerase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "catalytic activity"^^xsd:string + + SubClassOf: + , + some + + +Class: + + Annotations: + rdfs:label "single-organism carbohydrate metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "single-organism carbohydrate catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "catabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "adenyl nucleotide binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "carbohydrate catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "phosphoglycerate mutase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "phosphoglycerate kinase activity"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "phosphofructokinase activity"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "glucose-6-phosphate isomerase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "purine ribonucleoside triphosphate binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "hexose metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "ribonucleoside binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "glucose catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "glucose metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "isomerase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "oxidoreductase activity, acting on the aldehyde or oxo group of donors"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "cellular process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "nucleoside phosphate binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "ribonucleotide binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "purine ribonucleoside binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "carbohydrate phosphorylation"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor"^^xsd:string + + SubClassOf: + + + +Individual: + + Annotations: + rdfs:label "phosphoglycerate mutase activity involved in glycolysis"@en + + Types: + + + Facts: + , + + + +Individual: + + Annotations: + rdfs:label "glyceraldehyde-3-phosphate dehydrogenase activity involved in glycolysis"@en + + Types: + + + Facts: + , + + + +Individual: + + Annotations: + rdfs:label "phosphoglycerate kinase activity involved in glycolysis"@en + + Types: + + + Facts: + , + + + +Individual: + + Annotations: + rdfs:label "enolase activity involved in glycolysis"@en + + Types: + + + Facts: + , + + + +Individual: + + Annotations: + rdfs:label "aldolase activity involved in glycolysis"@en + + Types: + + + Facts: + , + , + + + +Individual: + + Annotations: + rdfs:label "triose phosphate isomerse activity involved in glycolysis"@en + + Types: + + + Facts: + , + + + +Individual: + + Annotations: + rdfs:label "pyruvate kinase activity involved in glycolysis"@en + + Types: + + + Facts: + + + +Individual: + + Annotations: + rdfs:label "phosphofructokinase:ATP binding"@en + + Types: + + + Facts: + + + +Individual: + + Annotations: + rdfs:label "phosphoglucose isomerase activity involved in glycolysis"@en + + Types: + + + Facts: + , + + + +Individual: + + Annotations: + rdfs:label "phosphofructokinase activity involved in glycolysis"@en + + Types: + + + Facts: + , + + + +Individual: + + Annotations: + rdfs:label "canonical glycolysis"@en + + Types: + + + +Individual: + + Annotations: + rdfs:label "hexokinase activity involved in glycolysis"@en + + Types: + + + Facts: + , + + + diff --git a/minerva-core/src/test/resources/mmg/glycolysis-tbox.omn b/minerva-core/src/test/resources/mmg/glycolysis-tbox.omn new file mode 100644 index 00000000..e79802f9 --- /dev/null +++ b/minerva-core/src/test/resources/mmg/glycolysis-tbox.omn @@ -0,0 +1,804 @@ +Prefix: owl: +Prefix: rdf: +Prefix: xml: +Prefix: xsd: +Prefix: rdfs: + + + +Ontology: + + +AnnotationProperty: + + +AnnotationProperty: + + +AnnotationProperty: rdfs:label + + +Datatype: rdf:PlainLiteral + + +Datatype: xsd:string + + +ObjectProperty: + + +ObjectProperty: + + Annotations: + rdfs:label "negatively_regulates"^^xsd:string + + SubPropertyChain: + o + + SubPropertyChain: + o + + +ObjectProperty: + + Annotations: + rdfs:label "part_of"^^xsd:string, + "OBO_REL:part_of"^^xsd:string, + "BFO:0000050"^^xsd:string, + "part_of"^^xsd:string + + Characteristics: + Transitive + + InverseOf: + + + +ObjectProperty: + + Annotations: + rdfs:label "has_part"^^xsd:string + + InverseOf: + + + +Class: + + Annotations: + rdfs:label "hexokinase activity"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "transferase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "small molecule binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "heterocyclic compound binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "carbohydrate metabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "hexose catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "organic cyclic compound binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "cellular metabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "hydro-lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "purine nucleotide binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "primary metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "ion binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "anion binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "organic substance catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "oxidoreductase activity"^^xsd:string + + SubClassOf: + , + some + + +Class: + + Annotations: + rdfs:label "transferase activity, transferring phosphorus-containing groups"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "phosphorus metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "phosphopyruvate hydratase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "monosaccharide catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "carbon-carbon lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "phosphate-containing compound metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "single-organism metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "carbon-oxygen lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "generation of precursor metabolites and energy"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "kinase activity"^^xsd:string + + SubClassOf: + , + some + + +Class: + + Annotations: + rdfs:label "molecular_function"^^xsd:string + + +Class: + + Annotations: + rdfs:label "phosphotransferase activity, alcohol group as acceptor"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "phosphotransferase activity, carboxyl group as acceptor"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "aldehyde-lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "glycolysis"^^xsd:string + + EquivalentTo: + + and ( some + ( + and ( some + ()))) + and ( some + ( + and ( some + ()))) + and ( some + ( + and ( some + ()))) + and ( some + ()) + and ( some + ( + and ( some + ( + and ( some + ()))))) + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "phosphorylation"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "lyase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "biological_process"^^xsd:string + + +Class: + + Annotations: + rdfs:label "oxidation-reduction process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "pyruvate kinase activity"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "carbohydrate kinase activity"^^xsd:string + + SubClassOf: + some , + + + +Class: + + Annotations: + rdfs:label "intramolecular oxidoreductase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "fructose-bisphosphate aldolase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "monosaccharide metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "cellular carbohydrate metabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "ATP binding"^^xsd:string + + SubClassOf: + , + , + + + +Class: + + Annotations: + rdfs:label "intramolecular transferase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "adenyl ribonucleotide binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "intramolecular transferase activity, phosphotransferases"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "nucleoside binding"^^xsd:string + + SubClassOf: + , + , + + + +Class: + + Annotations: + rdfs:label "purine nucleoside binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "intramolecular oxidoreductase activity, interconverting aldoses and ketoses"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "purine ribonucleotide binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "organic substance metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "triose-phosphate isomerase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "nucleotide binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "catalytic activity"^^xsd:string + + SubClassOf: + , + some + + +Class: + + Annotations: + rdfs:label "single-organism carbohydrate metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "single-organism carbohydrate catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "catabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "adenyl nucleotide binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "carbohydrate catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "phosphoglycerate mutase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "phosphoglycerate kinase activity"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "phosphofructokinase activity"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "glucose-6-phosphate isomerase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "purine ribonucleoside triphosphate binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "hexose metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "ribonucleoside binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "glucose catabolic process"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "glucose metabolic process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "isomerase activity"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "oxidoreductase activity, acting on the aldehyde or oxo group of donors"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "cellular process"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "nucleoside phosphate binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "ribonucleotide binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "binding"^^xsd:string + + SubClassOf: + + + +Class: + + Annotations: + rdfs:label "purine ribonucleoside binding"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "carbohydrate phosphorylation"^^xsd:string + + SubClassOf: + , + + + +Class: + + Annotations: + rdfs:label "oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor"^^xsd:string + + SubClassOf: + + + diff --git a/minerva-core/src/test/resources/mmg/pathway-abox.omn b/minerva-core/src/test/resources/mmg/pathway-abox.omn new file mode 100644 index 00000000..f37b7a58 --- /dev/null +++ b/minerva-core/src/test/resources/mmg/pathway-abox.omn @@ -0,0 +1,41 @@ +Ontology: +Prefix: : + +ObjectProperty: part_of InverseOf: has_part Characteristics: transitive +ObjectProperty: has_part +ObjectProperty: activates + +Class: Process +Class: FooPathway SubClassOf: Process +Class: Apoptosis SubClassOf: Process +Class: Activity +Class: Binding SubClassOf: Activity +Class: Transport SubClassOf: Activity + +Individual: pathway1 + Types: FooPathway + Facts: has_part step1 + +Individual: step1 + Types: Binding + Facts: activates step2 + +Individual: step2 + Types: Transport + Facts: activates step3 + +Individual: external + Types: Binding + Facts: activates step3 + +Individual: step3 + Types: Binding + Facts: activates step4 + +Individual: step4 + Types: Binding + Facts: part_of ap1 + +Individual: ap1 + Types: Apoptosis + diff --git a/minerva-json/.classpath b/minerva-json/.classpath new file mode 100644 index 00000000..f5f81df6 --- /dev/null +++ b/minerva-json/.classpath @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/minerva-json/.gitignore b/minerva-json/.gitignore new file mode 100644 index 00000000..2f7896d1 --- /dev/null +++ b/minerva-json/.gitignore @@ -0,0 +1 @@ +target/ diff --git a/minerva-json/.project b/minerva-json/.project new file mode 100644 index 00000000..e6ad8324 --- /dev/null +++ b/minerva-json/.project @@ -0,0 +1,23 @@ + + + minerva-json + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/minerva-json/.settings/org.eclipse.core.resources.prefs b/minerva-json/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 00000000..e9441bb1 --- /dev/null +++ b/minerva-json/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,3 @@ +eclipse.preferences.version=1 +encoding//src/main/java=UTF-8 +encoding/=UTF-8 diff --git a/minerva-json/.settings/org.eclipse.jdt.core.prefs b/minerva-json/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 00000000..ec4300d5 --- /dev/null +++ b/minerva-json/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7 +org.eclipse.jdt.core.compiler.compliance=1.7 +org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning +org.eclipse.jdt.core.compiler.source=1.7 diff --git a/minerva-json/.settings/org.eclipse.m2e.core.prefs b/minerva-json/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/minerva-json/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/minerva-json/pom.xml b/minerva-json/pom.xml new file mode 100644 index 00000000..9152217e --- /dev/null +++ b/minerva-json/pom.xml @@ -0,0 +1,18 @@ + + 4.0.0 + + minerva + org.geneontology + 0.2.2-SNAPSHOT + + minerva-json + Minerva-JSON-Model + + + + com.google.code.gson + gson + + + diff --git a/minerva-json/src/main/java/org/geneontology/minerva/json/JsonAnnotatedObject.java b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonAnnotatedObject.java new file mode 100644 index 00000000..a2b1050d --- /dev/null +++ b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonAnnotatedObject.java @@ -0,0 +1,41 @@ +package org.geneontology.minerva.json; + +import java.util.Arrays; + + +abstract class JsonAnnotatedObject { + public JsonAnnotation[] annotations; + + /* (non-Javadoc) + * @see java.lang.Object#hashCode() + */ + @Override + public int hashCode() { + final int prime = 31; + int result = 1; + result = prime * result + Arrays.hashCode(annotations); + return result; + } + + /* (non-Javadoc) + * @see java.lang.Object#equals(java.lang.Object) + */ + @Override + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + if (obj == null) { + return false; + } + if (getClass() != obj.getClass()) { + return false; + } + JsonAnnotatedObject other = (JsonAnnotatedObject) obj; + if (!Arrays.equals(annotations, other.annotations)) { + return false; + } + return true; + } + +} \ No newline at end of file diff --git a/minerva-json/src/main/java/org/geneontology/minerva/json/JsonAnnotation.java b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonAnnotation.java new file mode 100644 index 00000000..9a859d73 --- /dev/null +++ b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonAnnotation.java @@ -0,0 +1,66 @@ +package org.geneontology.minerva.json; + +import com.google.gson.annotations.SerializedName; + +public class JsonAnnotation { + + public String key; + public String value; + @SerializedName("value-type") + public String valueType; // optional, defaults to OWL string literal for null + + static JsonAnnotation create(String key, String value, String type) { + JsonAnnotation a = new JsonAnnotation(); + a.key = key; + a.value = value; + a.valueType = type; + return a; + } + + @Override + public int hashCode() { + final int prime = 31; + int result = 1; + result = prime * result + ((key == null) ? 0 : key.hashCode()); + result = prime * result + ((value == null) ? 0 : value.hashCode()); + result = prime * result + ((valueType == null) ? 0 : valueType.hashCode()); + return result; + } + + @Override + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + if (obj == null) { + return false; + } + if (getClass() != obj.getClass()) { + return false; + } + JsonAnnotation other = (JsonAnnotation) obj; + if (key == null) { + if (other.key != null) { + return false; + } + } else if (!key.equals(other.key)) { + return false; + } + if (value == null) { + if (other.value != null) { + return false; + } + } else if (!value.equals(other.value)) { + return false; + } + if (valueType == null) { + if (other.valueType != null) { + return false; + } + } else if (!valueType.equals(other.valueType)) { + return false; + } + return true; + } + +} \ No newline at end of file diff --git a/minerva-json/src/main/java/org/geneontology/minerva/json/JsonEvidenceInfo.java b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonEvidenceInfo.java new file mode 100644 index 00000000..2ad94d83 --- /dev/null +++ b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonEvidenceInfo.java @@ -0,0 +1,7 @@ +package org.geneontology.minerva.json; + +public class JsonEvidenceInfo { + public String id; + public String label; + public String code; +} \ No newline at end of file diff --git a/minerva-json/src/main/java/org/geneontology/minerva/json/JsonModel.java b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonModel.java new file mode 100644 index 00000000..c5c56814 --- /dev/null +++ b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonModel.java @@ -0,0 +1,43 @@ +package org.geneontology.minerva.json; + +import java.util.Arrays; + +public class JsonModel extends JsonAnnotatedObject { + public JsonOwlIndividual[] individuals; + public JsonOwlFact[] facts; + public JsonOwlObject[] properties; + + @Override + public int hashCode() { + final int prime = 31; + int result = super.hashCode(); + result = prime * result + Arrays.hashCode(facts); + result = prime * result + Arrays.hashCode(individuals); + result = prime * result + Arrays.hashCode(properties); + return result; + } + + @Override + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + if (!super.equals(obj)) { + return false; + } + if (getClass() != obj.getClass()) { + return false; + } + JsonModel other = (JsonModel) obj; + if (!Arrays.equals(facts, other.facts)) { + return false; + } + if (!Arrays.equals(individuals, other.individuals)) { + return false; + } + if (!Arrays.equals(properties, other.properties)) { + return false; + } + return true; + } +} \ No newline at end of file diff --git a/minerva-json/src/main/java/org/geneontology/minerva/json/JsonOwlFact.java b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonOwlFact.java new file mode 100644 index 00000000..c43cd049 --- /dev/null +++ b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonOwlFact.java @@ -0,0 +1,55 @@ +package org.geneontology.minerva.json; + +public class JsonOwlFact extends JsonAnnotatedObject { + public String subject; + public String property; + public String object; + + @Override + public int hashCode() { + final int prime = 31; + int result = super.hashCode(); + result = prime * result + ((object == null) ? 0 : object.hashCode()); + result = prime * result + + ((property == null) ? 0 : property.hashCode()); + result = prime * result + ((subject == null) ? 0 : subject.hashCode()); + return result; + } + + @Override + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + if (!super.equals(obj)) { + return false; + } + if (getClass() != obj.getClass()) { + return false; + } + JsonOwlFact other = (JsonOwlFact) obj; + if (object == null) { + if (other.object != null) { + return false; + } + } else if (!object.equals(other.object)) { + return false; + } + if (property == null) { + if (other.property != null) { + return false; + } + } else if (!property.equals(other.property)) { + return false; + } + if (subject == null) { + if (other.subject != null) { + return false; + } + } else if (!subject.equals(other.subject)) { + return false; + } + return true; + } + +} \ No newline at end of file diff --git a/minerva-json/src/main/java/org/geneontology/minerva/json/JsonOwlIndividual.java b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonOwlIndividual.java new file mode 100644 index 00000000..4d5c4fe9 --- /dev/null +++ b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonOwlIndividual.java @@ -0,0 +1,52 @@ +package org.geneontology.minerva.json; + +import java.util.Arrays; + + +public class JsonOwlIndividual extends JsonAnnotatedObject { + public String id; + public String label; // TODO why do we have this? an individual should never have a label, right? + public JsonOwlObject[] type; + + @Override + public int hashCode() { + final int prime = 31; + int result = super.hashCode(); + result = prime * result + ((id == null) ? 0 : id.hashCode()); + result = prime * result + ((label == null) ? 0 : label.hashCode()); + result = prime * result + Arrays.hashCode(type); + return result; + } + + @Override + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + if (!super.equals(obj)) { + return false; + } + if (getClass() != obj.getClass()) { + return false; + } + JsonOwlIndividual other = (JsonOwlIndividual) obj; + if (id == null) { + if (other.id != null) { + return false; + } + } else if (!id.equals(other.id)) { + return false; + } + if (label == null) { + if (other.label != null) { + return false; + } + } else if (!label.equals(other.label)) { + return false; + } + if (!Arrays.equals(type, other.type)) { + return false; + } + return true; + } +} \ No newline at end of file diff --git a/minerva-json/src/main/java/org/geneontology/minerva/json/JsonOwlObject.java b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonOwlObject.java new file mode 100644 index 00000000..a51eae88 --- /dev/null +++ b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonOwlObject.java @@ -0,0 +1,139 @@ +package org.geneontology.minerva.json; + +import java.util.Arrays; +import java.util.List; + +import com.google.gson.annotations.SerializedName; + +public final class JsonOwlObject extends JsonAnnotatedObject { + + public static enum JsonOwlObjectType { + @SerializedName("svf") + SomeValueFrom, + + @SerializedName("property") + ObjectProperty, + + @SerializedName("class") + Class, + + @SerializedName("intersection") + IntersectionOf, + + @SerializedName("union") + UnionOf + + } + + public JsonOwlObject.JsonOwlObjectType type; + public String id; + public String label; + public JsonOwlObject[] expressions; // union, intersection + public JsonOwlObject property; + public JsonOwlObject filler; + + static JsonOwlObject createCls(String id, String label) { + JsonOwlObject json = new JsonOwlObject(); + json.type = JsonOwlObjectType.Class; + json.id = id; + json.label = label; + return json; + } + + static JsonOwlObject createProperty(String id, String label) { + JsonOwlObject json = new JsonOwlObject(); + json.type = JsonOwlObjectType.ObjectProperty; + json.id = id; + json.label = label; + return json; + } + + public static JsonOwlObject createIntersection(List expressions) { + JsonOwlObject json = new JsonOwlObject(); + json.type = JsonOwlObjectType.IntersectionOf; + if (expressions != null && !expressions.isEmpty()) { + json.expressions = expressions.toArray(new JsonOwlObject[expressions.size()]); + } + return json; + } + + public static JsonOwlObject createUnion(List expressions) { + JsonOwlObject json = new JsonOwlObject(); + json.type = JsonOwlObjectType.UnionOf; + if (expressions != null && !expressions.isEmpty()) { + json.expressions = expressions.toArray(new JsonOwlObject[expressions.size()]); + } + return json; + } + + public static JsonOwlObject createSvf(JsonOwlObject prop, JsonOwlObject filler) { + JsonOwlObject json = new JsonOwlObject(); + json.type = JsonOwlObjectType.SomeValueFrom; + json.property = prop; + json.filler = filler; + return json; + } + + @Override + public int hashCode() { + final int prime = 31; + int result = super.hashCode(); + result = prime * result + Arrays.hashCode(expressions); + result = prime * result + ((filler == null) ? 0 : filler.hashCode()); + result = prime * result + ((id == null) ? 0 : id.hashCode()); + result = prime * result + ((label == null) ? 0 : label.hashCode()); + result = prime * result + + ((property == null) ? 0 : property.hashCode()); + result = prime * result + ((type == null) ? 0 : type.hashCode()); + return result; + } + + @Override + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + if (!super.equals(obj)) { + return false; + } + if (getClass() != obj.getClass()) { + return false; + } + JsonOwlObject other = (JsonOwlObject) obj; + if (!Arrays.equals(expressions, other.expressions)) { + return false; + } + if (filler == null) { + if (other.filler != null) { + return false; + } + } else if (!filler.equals(other.filler)) { + return false; + } + if (id == null) { + if (other.id != null) { + return false; + } + } else if (!id.equals(other.id)) { + return false; + } + if (label == null) { + if (other.label != null) { + return false; + } + } else if (!label.equals(other.label)) { + return false; + } + if (property == null) { + if (other.property != null) { + return false; + } + } else if (!property.equals(other.property)) { + return false; + } + if (type != other.type) { + return false; + } + return true; + } +} \ No newline at end of file diff --git a/minerva-json/src/main/java/org/geneontology/minerva/json/JsonRelationInfo.java b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonRelationInfo.java new file mode 100644 index 00000000..dc1ac42b --- /dev/null +++ b/minerva-json/src/main/java/org/geneontology/minerva/json/JsonRelationInfo.java @@ -0,0 +1,7 @@ +package org.geneontology.minerva.json; + +public class JsonRelationInfo { + public String id; + public String label; + public boolean relevant; +} \ No newline at end of file diff --git a/minerva-server/.classpath b/minerva-server/.classpath new file mode 100644 index 00000000..e43402fa --- /dev/null +++ b/minerva-server/.classpath @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/minerva-server/.gitignore b/minerva-server/.gitignore new file mode 100644 index 00000000..2f7896d1 --- /dev/null +++ b/minerva-server/.gitignore @@ -0,0 +1 @@ +target/ diff --git a/minerva-server/.project b/minerva-server/.project new file mode 100644 index 00000000..36f96961 --- /dev/null +++ b/minerva-server/.project @@ -0,0 +1,23 @@ + + + Minerva-Server + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.m2e.core.maven2Nature + org.eclipse.jdt.core.javanature + + diff --git a/minerva-server/.settings/org.eclipse.core.resources.prefs b/minerva-server/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 00000000..29abf999 --- /dev/null +++ b/minerva-server/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,6 @@ +eclipse.preferences.version=1 +encoding//src/main/java=UTF-8 +encoding//src/main/resources=UTF-8 +encoding//src/test/java=UTF-8 +encoding//src/test/resources=UTF-8 +encoding/=UTF-8 diff --git a/minerva-server/.settings/org.eclipse.jdt.core.prefs b/minerva-server/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 00000000..ec4300d5 --- /dev/null +++ b/minerva-server/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7 +org.eclipse.jdt.core.compiler.compliance=1.7 +org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning +org.eclipse.jdt.core.compiler.source=1.7 diff --git a/minerva-server/.settings/org.eclipse.m2e.core.prefs b/minerva-server/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/minerva-server/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/bin/.gitignore b/minerva-server/bin/.gitignore similarity index 100% rename from bin/.gitignore rename to minerva-server/bin/.gitignore diff --git a/bin/start-go-minerva.sh b/minerva-server/bin/start-go-minerva.sh similarity index 100% rename from bin/start-go-minerva.sh rename to minerva-server/bin/start-go-minerva.sh diff --git a/bin/start-m3-server.sh b/minerva-server/bin/start-m3-server.sh similarity index 100% rename from bin/start-m3-server.sh rename to minerva-server/bin/start-m3-server.sh diff --git a/minerva-server/pom.xml b/minerva-server/pom.xml new file mode 100644 index 00000000..3dfa35c2 --- /dev/null +++ b/minerva-server/pom.xml @@ -0,0 +1,95 @@ + + 4.0.0 + + minerva + org.geneontology + 0.2.2-SNAPSHOT + + minerva-server + Minerva-Server + + + + + org.apache.maven.plugins + maven-surefire-plugin + + + + **/GolrExternalLookupServiceTest.java + **/SeedHandlerTest.java + + + + + org.apache.maven.plugins + maven-assembly-plugin + + minerva-server + false + false + ${project.basedir}/bin + + src/main/assembly/minerva-server.xml + + + + true + owltools.gaf.lego.server.StartUpTool + + + + + + make-assembly + package + + single + + + + + + + + + + org.geneontology + minerva-core + ${project.parent.version} + + + org.geneontology + minerva-json + ${project.parent.version} + + + org.geneontology + minerva-converter + ${project.parent.version} + + + org.bbop + golr-client + + + org.eclipse.jetty + jetty-server + + + org.eclipse.jetty + jetty-servlet + + + org.glassfish.jersey.containers + jersey-container-servlet-core + + + org.apache.httpcomponents + httpclient + test + + + + diff --git a/src/main/assembly/minerva-server.xml b/minerva-server/src/main/assembly/minerva-server.xml similarity index 100% rename from src/main/assembly/minerva-server.xml rename to minerva-server/src/main/assembly/minerva-server.xml diff --git a/src/main/java/owltools/annotation/lego/generate/GolrSeedingDataProvider.java b/minerva-server/src/main/java/org/geneontology/minerva/generate/GolrSeedingDataProvider.java similarity index 99% rename from src/main/java/owltools/annotation/lego/generate/GolrSeedingDataProvider.java rename to minerva-server/src/main/java/org/geneontology/minerva/generate/GolrSeedingDataProvider.java index 060142f0..3aaa69ac 100644 --- a/src/main/java/owltools/annotation/lego/generate/GolrSeedingDataProvider.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/generate/GolrSeedingDataProvider.java @@ -1,4 +1,4 @@ -package owltools.annotation.lego.generate; +package org.geneontology.minerva.generate; import java.io.IOException; import java.net.URI; diff --git a/src/main/java/owltools/annotation/lego/generate/ModelSeeding.java b/minerva-server/src/main/java/org/geneontology/minerva/generate/ModelSeeding.java similarity index 97% rename from src/main/java/owltools/annotation/lego/generate/ModelSeeding.java rename to minerva-server/src/main/java/org/geneontology/minerva/generate/ModelSeeding.java index fa0ec476..808e8cc1 100644 --- a/src/main/java/owltools/annotation/lego/generate/ModelSeeding.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/generate/ModelSeeding.java @@ -1,4 +1,4 @@ -package owltools.annotation.lego.generate; +package org.geneontology.minerva.generate; import java.util.ArrayList; import java.util.HashMap; @@ -9,6 +9,10 @@ import java.util.Set; import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.MolecularModelManager; +import org.geneontology.minerva.util.IdStringManager; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; import org.geneontology.reasoner.ExpressionMaterializingReasoner; import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLAnnotation; @@ -23,11 +27,7 @@ import owltools.gaf.Bioentity; import owltools.gaf.GeneAnnotation; -import owltools.gaf.lego.IdStringManager; -import owltools.gaf.lego.IdStringManager.AnnotationShorthand; -import owltools.gaf.lego.MolecularModelManager; import owltools.graph.OWLGraphWrapper; -import owltools.util.ModelContainer; import com.google.common.collect.Sets; diff --git a/src/main/java/owltools/annotation/lego/generate/SeedingDataProvider.java b/minerva-server/src/main/java/org/geneontology/minerva/generate/SeedingDataProvider.java similarity index 92% rename from src/main/java/owltools/annotation/lego/generate/SeedingDataProvider.java rename to minerva-server/src/main/java/org/geneontology/minerva/generate/SeedingDataProvider.java index 48ff172c..bc552687 100644 --- a/src/main/java/owltools/annotation/lego/generate/SeedingDataProvider.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/generate/SeedingDataProvider.java @@ -1,4 +1,4 @@ -package owltools.annotation.lego.generate; +package org.geneontology.minerva.generate; import java.io.IOException; import java.util.List; diff --git a/src/main/java/owltools/gaf/lego/server/AuthorizationRequestFilter.java b/minerva-server/src/main/java/org/geneontology/minerva/server/AuthorizationRequestFilter.java similarity index 97% rename from src/main/java/owltools/gaf/lego/server/AuthorizationRequestFilter.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/AuthorizationRequestFilter.java index b031bb0e..37274f2f 100644 --- a/src/main/java/owltools/gaf/lego/server/AuthorizationRequestFilter.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/AuthorizationRequestFilter.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server; +package org.geneontology.minerva.server; import java.io.IOException; import java.util.Collections; diff --git a/src/main/java/owltools/gaf/lego/server/GenerateProteinOntologies.java b/minerva-server/src/main/java/org/geneontology/minerva/server/GenerateProteinOntologies.java similarity index 96% rename from src/main/java/owltools/gaf/lego/server/GenerateProteinOntologies.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/GenerateProteinOntologies.java index 4723355f..b5716ed6 100644 --- a/src/main/java/owltools/gaf/lego/server/GenerateProteinOntologies.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/GenerateProteinOntologies.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server; +package org.geneontology.minerva.server; import java.util.HashSet; import java.util.Set; diff --git a/src/main/java/owltools/gaf/lego/server/GsonMessageBodyHandler.java b/minerva-server/src/main/java/org/geneontology/minerva/server/GsonMessageBodyHandler.java similarity index 98% rename from src/main/java/owltools/gaf/lego/server/GsonMessageBodyHandler.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/GsonMessageBodyHandler.java index 2d5d516a..c91d5fee 100644 --- a/src/main/java/owltools/gaf/lego/server/GsonMessageBodyHandler.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/GsonMessageBodyHandler.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server; +package org.geneontology.minerva.server; import java.io.IOException; import java.io.InputStream; diff --git a/src/main/java/owltools/gaf/lego/server/RequireJsonpFilter.java b/minerva-server/src/main/java/org/geneontology/minerva/server/RequireJsonpFilter.java similarity index 90% rename from src/main/java/owltools/gaf/lego/server/RequireJsonpFilter.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/RequireJsonpFilter.java index 5cdc004e..7136bd4b 100644 --- a/src/main/java/owltools/gaf/lego/server/RequireJsonpFilter.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/RequireJsonpFilter.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server; +package org.geneontology.minerva.server; import java.io.IOException; @@ -8,7 +8,7 @@ import javax.ws.rs.core.MultivaluedMap; import javax.ws.rs.core.UriInfo; -import owltools.gaf.lego.server.handler.JsonOrJsonpBatchHandler; +import org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler; /** * Replace the accepted request type, if there is a 'json.wrf' query parameter.
    diff --git a/src/main/java/owltools/gaf/lego/server/StartUpTool.java b/minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java similarity index 94% rename from src/main/java/owltools/gaf/lego/server/StartUpTool.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java index eec75df2..1d561b4d 100644 --- a/src/main/java/owltools/gaf/lego/server/StartUpTool.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server; +package org.geneontology.minerva.server; import java.util.ArrayList; import java.util.Arrays; @@ -11,6 +11,13 @@ import org.eclipse.jetty.server.Server; import org.eclipse.jetty.servlet.ServletContextHandler; import org.eclipse.jetty.servlet.ServletHolder; +import org.geneontology.minerva.UndoAwareMolecularModelManager; +import org.geneontology.minerva.server.external.CachingExternalLookupService; +import org.geneontology.minerva.server.external.CombinedExternalLookupService; +import org.geneontology.minerva.server.external.ExternalLookupService; +import org.geneontology.minerva.server.external.GolrExternalLookupService; +import org.geneontology.minerva.server.external.ProteinToolService; +import org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler; import org.glassfish.jersey.server.ResourceConfig; import org.glassfish.jersey.servlet.ServletContainer; import org.semanticweb.owlapi.model.IRI; @@ -21,13 +28,6 @@ import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom; import owltools.cli.Opts; -import owltools.gaf.lego.UndoAwareMolecularModelManager; -import owltools.gaf.lego.server.external.CachingExternalLookupService; -import owltools.gaf.lego.server.external.CombinedExternalLookupService; -import owltools.gaf.lego.server.external.ExternalLookupService; -import owltools.gaf.lego.server.external.GolrExternalLookupService; -import owltools.gaf.lego.server.external.ProteinToolService; -import owltools.gaf.lego.server.handler.JsonOrJsonpBatchHandler; import owltools.graph.OWLGraphWrapper; import owltools.io.CatalogXmlIRIMapper; import owltools.io.ParserWrapper; diff --git a/src/main/java/owltools/gaf/lego/server/external/CachingExternalLookupService.java b/minerva-server/src/main/java/org/geneontology/minerva/server/external/CachingExternalLookupService.java similarity index 97% rename from src/main/java/owltools/gaf/lego/server/external/CachingExternalLookupService.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/external/CachingExternalLookupService.java index c893f5da..b6244502 100644 --- a/src/main/java/owltools/gaf/lego/server/external/CachingExternalLookupService.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/external/CachingExternalLookupService.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.external; +package org.geneontology.minerva.server.external; import java.util.Arrays; import java.util.List; diff --git a/src/main/java/owltools/gaf/lego/server/external/CombinedExternalLookupService.java b/minerva-server/src/main/java/org/geneontology/minerva/server/external/CombinedExternalLookupService.java similarity index 95% rename from src/main/java/owltools/gaf/lego/server/external/CombinedExternalLookupService.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/external/CombinedExternalLookupService.java index 9f45bfab..40433fa1 100644 --- a/src/main/java/owltools/gaf/lego/server/external/CombinedExternalLookupService.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/external/CombinedExternalLookupService.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.external; +package org.geneontology.minerva.server.external; import java.util.ArrayList; import java.util.Arrays; diff --git a/src/main/java/owltools/gaf/lego/server/external/ExternalLookupService.java b/minerva-server/src/main/java/org/geneontology/minerva/server/external/ExternalLookupService.java similarity index 95% rename from src/main/java/owltools/gaf/lego/server/external/ExternalLookupService.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/external/ExternalLookupService.java index 97e54294..f60f88bf 100644 --- a/src/main/java/owltools/gaf/lego/server/external/ExternalLookupService.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/external/ExternalLookupService.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.external; +package org.geneontology.minerva.server.external; import java.util.List; diff --git a/src/main/java/owltools/gaf/lego/server/external/GolrExternalLookupService.java b/minerva-server/src/main/java/org/geneontology/minerva/server/external/GolrExternalLookupService.java similarity index 96% rename from src/main/java/owltools/gaf/lego/server/external/GolrExternalLookupService.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/external/GolrExternalLookupService.java index 20631411..bd467c4b 100644 --- a/src/main/java/owltools/gaf/lego/server/external/GolrExternalLookupService.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/external/GolrExternalLookupService.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.external; +package org.geneontology.minerva.server.external; import java.io.IOException; import java.util.ArrayList; diff --git a/src/main/java/owltools/gaf/lego/server/external/ProteinToolService.java b/minerva-server/src/main/java/org/geneontology/minerva/server/external/ProteinToolService.java similarity index 98% rename from src/main/java/owltools/gaf/lego/server/external/ProteinToolService.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/external/ProteinToolService.java index 4a61bec9..895e83e1 100644 --- a/src/main/java/owltools/gaf/lego/server/external/ProteinToolService.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/external/ProteinToolService.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.external; +package org.geneontology.minerva.server.external; import java.io.File; import java.io.IOException; diff --git a/src/main/java/owltools/gaf/lego/server/external/TableLookupService.java b/minerva-server/src/main/java/org/geneontology/minerva/server/external/TableLookupService.java similarity index 95% rename from src/main/java/owltools/gaf/lego/server/external/TableLookupService.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/external/TableLookupService.java index 076da76a..bc549421 100644 --- a/src/main/java/owltools/gaf/lego/server/external/TableLookupService.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/external/TableLookupService.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.external; +package org.geneontology.minerva.server.external; import java.util.ArrayList; import java.util.Collections; diff --git a/src/main/java/owltools/gaf/lego/server/handler/JsonOrJsonpBatchHandler.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpBatchHandler.java similarity index 92% rename from src/main/java/owltools/gaf/lego/server/handler/JsonOrJsonpBatchHandler.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpBatchHandler.java index 77f10cd4..8ff61f94 100644 --- a/src/main/java/owltools/gaf/lego/server/handler/JsonOrJsonpBatchHandler.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpBatchHandler.java @@ -1,6 +1,6 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; -import static owltools.gaf.lego.server.handler.OperationsTools.*; +import static org.geneontology.minerva.server.handler.OperationsTools.*; import java.io.PrintWriter; import java.io.StringWriter; @@ -9,22 +9,21 @@ import org.apache.commons.lang3.tuple.Pair; import org.apache.log4j.Logger; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.UndoAwareMolecularModelManager; +import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; +import org.geneontology.minerva.UndoAwareMolecularModelManager.UndoMetadata; +import org.geneontology.minerva.json.JsonAnnotation; +import org.geneontology.minerva.json.JsonModel; +import org.geneontology.minerva.json.JsonOwlFact; +import org.geneontology.minerva.json.JsonOwlIndividual; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.geneontology.minerva.server.external.ExternalLookupService; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse.ResponseData; import org.glassfish.jersey.server.JSONP; import org.semanticweb.owlapi.model.OWLObjectProperty; import org.semanticweb.owlapi.reasoner.OWLReasoner; -import owltools.gaf.lego.MolecularModelManager.UnknownIdentifierException; -import owltools.gaf.lego.UndoAwareMolecularModelManager; -import owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata; -import owltools.gaf.lego.json.JsonAnnotation; -import owltools.gaf.lego.json.JsonModel; -import owltools.gaf.lego.json.JsonOwlFact; -import owltools.gaf.lego.json.JsonOwlIndividual; -import owltools.gaf.lego.json.MolecularModelJsonRenderer; -import owltools.gaf.lego.server.external.ExternalLookupService; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3BatchResponse.ResponseData; -import owltools.util.ModelContainer; - import com.google.common.reflect.TypeToken; public class JsonOrJsonpBatchHandler extends OperationsImpl implements M3BatchHandler { diff --git a/src/main/java/owltools/gaf/lego/server/handler/JsonOrJsonpSeedHandler.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpSeedHandler.java similarity index 89% rename from src/main/java/owltools/gaf/lego/server/handler/JsonOrJsonpSeedHandler.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpSeedHandler.java index e9ef828b..1cfb6016 100644 --- a/src/main/java/owltools/gaf/lego/server/handler/JsonOrJsonpSeedHandler.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpSeedHandler.java @@ -1,6 +1,6 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; -import static owltools.gaf.lego.server.handler.OperationsTools.*; +import static org.geneontology.minerva.server.handler.OperationsTools.*; import java.io.PrintWriter; import java.io.StringWriter; @@ -10,6 +10,16 @@ import java.util.Set; import org.apache.log4j.Logger; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.UndoAwareMolecularModelManager; +import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; +import org.geneontology.minerva.UndoAwareMolecularModelManager.UndoMetadata; +import org.geneontology.minerva.generate.GolrSeedingDataProvider; +import org.geneontology.minerva.generate.ModelSeeding; +import org.geneontology.minerva.json.JsonModel; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.geneontology.minerva.server.external.ExternalLookupService; +import org.geneontology.minerva.server.handler.M3SeedHandler.SeedResponse.SeedResponseData; import org.geneontology.reasoner.ExpressionMaterializingReasoner; import org.geneontology.reasoner.ExpressionMaterializingReasonerFactory; import org.geneontology.reasoner.OWLExtendedReasonerFactory; @@ -17,17 +27,7 @@ import org.semanticweb.elk.owlapi.ElkReasonerFactory; import org.semanticweb.owlapi.model.OWLClass; -import owltools.annotation.lego.generate.GolrSeedingDataProvider; -import owltools.annotation.lego.generate.ModelSeeding; -import owltools.gaf.lego.MolecularModelManager.UnknownIdentifierException; -import owltools.gaf.lego.UndoAwareMolecularModelManager; -import owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata; -import owltools.gaf.lego.json.JsonModel; -import owltools.gaf.lego.json.MolecularModelJsonRenderer; -import owltools.gaf.lego.server.external.ExternalLookupService; -import owltools.gaf.lego.server.handler.M3SeedHandler.SeedResponse.SeedResponseData; import owltools.graph.OWLGraphWrapper; -import owltools.util.ModelContainer; public class JsonOrJsonpSeedHandler implements M3SeedHandler { diff --git a/src/main/java/owltools/gaf/lego/server/handler/M3BatchHandler.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java similarity index 94% rename from src/main/java/owltools/gaf/lego/server/handler/M3BatchHandler.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java index 1209af63..ce807a3d 100644 --- a/src/main/java/owltools/gaf/lego/server/handler/M3BatchHandler.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; import javax.ws.rs.Consumes; import javax.ws.rs.FormParam; @@ -7,14 +7,14 @@ import javax.ws.rs.Path; import javax.ws.rs.QueryParam; -import com.google.gson.annotations.SerializedName; +import org.geneontology.minerva.json.JsonAnnotation; +import org.geneontology.minerva.json.JsonEvidenceInfo; +import org.geneontology.minerva.json.JsonOwlFact; +import org.geneontology.minerva.json.JsonOwlIndividual; +import org.geneontology.minerva.json.JsonOwlObject; +import org.geneontology.minerva.json.JsonRelationInfo; -import owltools.gaf.lego.json.JsonAnnotation; -import owltools.gaf.lego.json.JsonEvidenceInfo; -import owltools.gaf.lego.json.JsonOwlFact; -import owltools.gaf.lego.json.JsonOwlIndividual; -import owltools.gaf.lego.json.JsonOwlObject; -import owltools.gaf.lego.json.JsonRelationInfo; +import com.google.gson.annotations.SerializedName; @Path("/") public interface M3BatchHandler { diff --git a/src/main/java/owltools/gaf/lego/server/handler/M3ExpressionParser.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3ExpressionParser.java similarity index 91% rename from src/main/java/owltools/gaf/lego/server/handler/M3ExpressionParser.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3ExpressionParser.java index b872e35a..5b73473f 100644 --- a/src/main/java/owltools/gaf/lego/server/handler/M3ExpressionParser.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3ExpressionParser.java @@ -1,25 +1,25 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; import java.util.HashSet; import java.util.List; import java.util.Set; import org.apache.commons.lang3.StringUtils; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.MolecularModelManager; +import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; +import org.geneontology.minerva.json.JsonOwlObject; +import org.geneontology.minerva.json.JsonOwlObject.JsonOwlObjectType; +import org.geneontology.minerva.server.external.ExternalLookupService; +import org.geneontology.minerva.server.external.ExternalLookupService.LookupEntry; +import org.geneontology.minerva.server.handler.OperationsTools.MissingParameterException; import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLClass; import org.semanticweb.owlapi.model.OWLClassExpression; import org.semanticweb.owlapi.model.OWLException; import org.semanticweb.owlapi.model.OWLObjectProperty; -import owltools.gaf.lego.MolecularModelManager; -import owltools.gaf.lego.MolecularModelManager.UnknownIdentifierException; -import owltools.gaf.lego.json.JsonOwlObject; -import owltools.gaf.lego.json.JsonOwlObject.JsonOwlObjectType; -import owltools.gaf.lego.server.external.ExternalLookupService; -import owltools.gaf.lego.server.external.ExternalLookupService.LookupEntry; -import owltools.gaf.lego.server.handler.OperationsTools.MissingParameterException; import owltools.graph.OWLGraphWrapper; -import owltools.util.ModelContainer; public class M3ExpressionParser { diff --git a/src/main/java/owltools/gaf/lego/server/handler/M3SeedHandler.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3SeedHandler.java similarity index 94% rename from src/main/java/owltools/gaf/lego/server/handler/M3SeedHandler.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3SeedHandler.java index 42593013..8880d1dc 100644 --- a/src/main/java/owltools/gaf/lego/server/handler/M3SeedHandler.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3SeedHandler.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; import javax.ws.rs.Consumes; import javax.ws.rs.FormParam; @@ -7,10 +7,10 @@ import javax.ws.rs.Path; import javax.ws.rs.QueryParam; -import owltools.gaf.lego.json.JsonAnnotation; -import owltools.gaf.lego.json.JsonOwlFact; -import owltools.gaf.lego.json.JsonOwlIndividual; -import owltools.gaf.lego.json.JsonOwlObject; +import org.geneontology.minerva.json.JsonAnnotation; +import org.geneontology.minerva.json.JsonOwlFact; +import org.geneontology.minerva.json.JsonOwlIndividual; +import org.geneontology.minerva.json.JsonOwlObject; import com.google.gson.annotations.SerializedName; diff --git a/src/main/java/owltools/gaf/lego/server/handler/OperationsImpl.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsImpl.java similarity index 93% rename from src/main/java/owltools/gaf/lego/server/handler/OperationsImpl.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsImpl.java index f001b80c..4bf2c899 100644 --- a/src/main/java/owltools/gaf/lego/server/handler/OperationsImpl.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsImpl.java @@ -1,6 +1,6 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; -import static owltools.gaf.lego.server.handler.OperationsTools.*; +import static org.geneontology.minerva.server.handler.OperationsTools.*; import java.io.IOException; import java.util.ArrayList; @@ -14,6 +14,30 @@ import java.util.Set; import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.MolecularModelManager; +import org.geneontology.minerva.UndoAwareMolecularModelManager; +import org.geneontology.minerva.CoreMolecularModelManager.DeleteInformation; +import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; +import org.geneontology.minerva.UndoAwareMolecularModelManager.ChangeEvent; +import org.geneontology.minerva.UndoAwareMolecularModelManager.UndoMetadata; +import org.geneontology.minerva.json.JsonAnnotation; +import org.geneontology.minerva.json.JsonEvidenceInfo; +import org.geneontology.minerva.json.JsonOwlObject; +import org.geneontology.minerva.json.JsonRelationInfo; +import org.geneontology.minerva.json.JsonTools; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.geneontology.minerva.legacy.GafExportTool; +import org.geneontology.minerva.server.external.ExternalLookupService; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3Request; +import org.geneontology.minerva.server.handler.M3BatchHandler.Operation; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse.MetaResponse; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse.ResponseData; +import org.geneontology.minerva.server.handler.OperationsTools.MissingParameterException; +import org.geneontology.minerva.server.validation.BeforeSaveModelValidator; +import org.geneontology.minerva.util.IdStringManager; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLAnnotation; import org.semanticweb.owlapi.model.OWLAnnotationProperty; @@ -30,28 +54,6 @@ import org.semanticweb.owlapi.model.OWLOntologyCreationException; import org.semanticweb.owlapi.model.OWLOntologyStorageException; -import owltools.gaf.lego.CoreMolecularModelManager.DeleteInformation; -import owltools.gaf.lego.IdStringManager; -import owltools.gaf.lego.IdStringManager.AnnotationShorthand; -import owltools.gaf.lego.MolecularModelManager; -import owltools.gaf.lego.MolecularModelManager.UnknownIdentifierException; -import owltools.gaf.lego.UndoAwareMolecularModelManager; -import owltools.gaf.lego.UndoAwareMolecularModelManager.ChangeEvent; -import owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata; -import owltools.gaf.lego.json.JsonAnnotation; -import owltools.gaf.lego.json.JsonEvidenceInfo; -import owltools.gaf.lego.json.JsonOwlObject; -import owltools.gaf.lego.json.JsonRelationInfo; -import owltools.gaf.lego.json.MolecularModelJsonRenderer; -import owltools.gaf.lego.server.external.ExternalLookupService; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3BatchResponse; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3BatchResponse.MetaResponse; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3BatchResponse.ResponseData; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3Request; -import owltools.gaf.lego.server.handler.M3BatchHandler.Operation; -import owltools.gaf.lego.server.handler.OperationsTools.MissingParameterException; -import owltools.gaf.lego.server.validation.BeforeSaveModelValidator; - /** * Separate the actual calls to the {@link UndoAwareMolecularModelManager} from the * request, error and response handling. @@ -65,7 +67,7 @@ abstract class OperationsImpl { final BeforeSaveModelValidator beforeSaveValidator; final ExternalLookupService externalLookupService; final Set dataPropertyIRIs; - + OperationsImpl(UndoAwareMolecularModelManager models, Set importantRelations, ExternalLookupService externalLookupService) { @@ -642,7 +644,7 @@ void getMeta(M3BatchResponse response, String userId) throws IOException, OWLExc OWLOntology o = m3.getModelAbox(mid); Set annotations = o.getAnnotations(); for( OWLAnnotation an : annotations ){ - Pair pair = JsonAnnotation.createSimplePair(an); + Pair pair = JsonTools.createSimplePair(an); if (pair != null) { modelMap.put(pair.getKey(), pair.getValue()); } @@ -659,7 +661,12 @@ private void export(M3BatchResponse response, String modelId, String userId) thr } private void exportLegacy(M3BatchResponse response, String modelId, String format, String userId) throws UnknownIdentifierException, IOException { - String exportModel = m3.exportModelLegacy(modelId, format); + ModelContainer model = m3.getModel(modelId); + if (model == null) { + throw new UnknownIdentifierException("Could not find a model for id: "+modelId); + } + final GafExportTool exportTool = GafExportTool.getInstance(); + String exportModel = exportTool.exportModelLegacy(modelId, model, format); initMetaResponse(response); response.data.exportModel = exportModel; } @@ -726,13 +733,13 @@ private Set extract(JsonAnnotation[] values, String userId, Batch result.add(create(f, shorthand, evidenceValue)); } else { - result.add(create(f, shorthand, jsonAnn.createAnnotationValue(f))); + result.add(create(f, shorthand, JsonTools.createAnnotationValue(jsonAnn, f))); } } else { IRI pIRI = IRI.create(jsonAnn.key); if (dataPropertyIRIs.contains(pIRI) == false) { - OWLAnnotationValue annotationValue = jsonAnn.createAnnotationValue(f); + OWLAnnotationValue annotationValue = JsonTools.createAnnotationValue(jsonAnn, f); result.add(f.getOWLAnnotation(f.getOWLAnnotationProperty(pIRI), annotationValue)); } } @@ -754,7 +761,7 @@ private Map> extractDataProperties(JsonAnnotati if (shorthand == null) { IRI pIRI = IRI.create(jsonAnn.key); if (dataPropertyIRIs.contains(pIRI)) { - OWLLiteral literal = jsonAnn.createLiteral(f); + OWLLiteral literal = JsonTools.createLiteral(jsonAnn, f); if (literal != null) { OWLDataProperty property = f.getOWLDataProperty(pIRI); Set literals = result.get(property); diff --git a/src/main/java/owltools/gaf/lego/server/handler/OperationsTools.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsTools.java similarity index 86% rename from src/main/java/owltools/gaf/lego/server/handler/OperationsTools.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsTools.java index 9d7eec09..c946fa73 100644 --- a/src/main/java/owltools/gaf/lego/server/handler/OperationsTools.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsTools.java @@ -1,15 +1,14 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; import java.util.List; import org.apache.commons.lang3.StringUtils; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.geneontology.minerva.server.external.ExternalLookupService; +import org.geneontology.minerva.server.external.ExternalLookupService.LookupEntry; import org.semanticweb.owlapi.model.OWLNamedObject; -import owltools.gaf.lego.json.MolecularModelJsonRenderer; -import owltools.gaf.lego.server.external.ExternalLookupService; -import owltools.gaf.lego.server.external.ExternalLookupService.LookupEntry; -import owltools.util.ModelContainer; - class OperationsTools { static void requireNotNull(Object value, String msg) throws MissingParameterException { diff --git a/src/main/java/owltools/gaf/lego/server/handler/PacketIdGenerator.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/PacketIdGenerator.java similarity index 88% rename from src/main/java/owltools/gaf/lego/server/handler/PacketIdGenerator.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/handler/PacketIdGenerator.java index e8281cce..9667686d 100644 --- a/src/main/java/owltools/gaf/lego/server/handler/PacketIdGenerator.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/PacketIdGenerator.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; public class PacketIdGenerator { diff --git a/src/main/java/owltools/gaf/lego/server/validation/BeforeSaveModelValidator.java b/minerva-server/src/main/java/org/geneontology/minerva/server/validation/BeforeSaveModelValidator.java similarity index 88% rename from src/main/java/owltools/gaf/lego/server/validation/BeforeSaveModelValidator.java rename to minerva-server/src/main/java/org/geneontology/minerva/server/validation/BeforeSaveModelValidator.java index e257f682..309dcbfa 100644 --- a/src/main/java/owltools/gaf/lego/server/validation/BeforeSaveModelValidator.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/validation/BeforeSaveModelValidator.java @@ -1,20 +1,19 @@ -package owltools.gaf.lego.server.validation; +package org.geneontology.minerva.server.validation; import java.util.ArrayList; import java.util.List; import java.util.Set; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.MolecularModelManager; +import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; import org.semanticweb.owlapi.model.OWLAnnotation; import org.semanticweb.owlapi.model.OWLAnnotationProperty; import org.semanticweb.owlapi.model.OWLNamedIndividual; import org.semanticweb.owlapi.model.OWLOntology; import org.semanticweb.owlapi.reasoner.OWLReasoner; -import owltools.gaf.lego.IdStringManager.AnnotationShorthand; -import owltools.gaf.lego.MolecularModelManager; -import owltools.gaf.lego.MolecularModelManager.UnknownIdentifierException; -import owltools.util.ModelContainer; - public class BeforeSaveModelValidator { static boolean USE_CONSISTENCY_CHECKS = false; diff --git a/src/main/resources/log4j.properties b/minerva-server/src/main/resources/log4j.properties similarity index 100% rename from src/main/resources/log4j.properties rename to minerva-server/src/main/resources/log4j.properties diff --git a/src/test/java/owltools/annotation/lego/generate/.gitignore b/minerva-server/src/test/java/org/geneontology/minerva/generate/.gitignore similarity index 100% rename from src/test/java/owltools/annotation/lego/generate/.gitignore rename to minerva-server/src/test/java/org/geneontology/minerva/generate/.gitignore diff --git a/src/test/java/owltools/gaf/lego/server/external/GolrExternalLookupServiceTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/external/GolrExternalLookupServiceTest.java similarity index 79% rename from src/test/java/owltools/gaf/lego/server/external/GolrExternalLookupServiceTest.java rename to minerva-server/src/test/java/org/geneontology/minerva/server/external/GolrExternalLookupServiceTest.java index 820a64fc..c7ab0b00 100644 --- a/src/test/java/owltools/gaf/lego/server/external/GolrExternalLookupServiceTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/external/GolrExternalLookupServiceTest.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.external; +package org.geneontology.minerva.server.external; import static org.junit.Assert.*; @@ -7,10 +7,12 @@ import java.util.List; import org.bbop.golr.java.RetrieveGolrBioentities; +import org.geneontology.minerva.server.external.CachingExternalLookupService; +import org.geneontology.minerva.server.external.ExternalLookupService; +import org.geneontology.minerva.server.external.GolrExternalLookupService; +import org.geneontology.minerva.server.external.ExternalLookupService.LookupEntry; import org.junit.Test; -import owltools.gaf.lego.server.external.ExternalLookupService.LookupEntry; - public class GolrExternalLookupServiceTest { @Test diff --git a/src/test/java/owltools/gaf/lego/server/external/ProteinToolServiceTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/external/ProteinToolServiceTest.java similarity index 75% rename from src/test/java/owltools/gaf/lego/server/external/ProteinToolServiceTest.java rename to minerva-server/src/test/java/org/geneontology/minerva/server/external/ProteinToolServiceTest.java index dfa664bd..939958cc 100644 --- a/src/test/java/owltools/gaf/lego/server/external/ProteinToolServiceTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/external/ProteinToolServiceTest.java @@ -1,7 +1,8 @@ -package owltools.gaf.lego.server.external; +package org.geneontology.minerva.server.external; import static org.junit.Assert.*; +import org.geneontology.minerva.server.external.ProteinToolService; import org.junit.Test; public class ProteinToolServiceTest { diff --git a/src/test/java/owltools/gaf/lego/server/handler/.gitignore b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/.gitignore similarity index 100% rename from src/test/java/owltools/gaf/lego/server/handler/.gitignore rename to minerva-server/src/test/java/org/geneontology/minerva/server/handler/.gitignore diff --git a/src/test/java/owltools/gaf/lego/server/handler/BatchModelHandlerTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchModelHandlerTest.java similarity index 97% rename from src/test/java/owltools/gaf/lego/server/handler/BatchModelHandlerTest.java rename to minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchModelHandlerTest.java index ce899a6e..787c5b27 100644 --- a/src/test/java/owltools/gaf/lego/server/handler/BatchModelHandlerTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchModelHandlerTest.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; import static org.junit.Assert.*; @@ -9,6 +9,31 @@ import java.util.Map; import java.util.Set; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.UndoAwareMolecularModelManager; +import org.geneontology.minerva.json.JsonAnnotation; +import org.geneontology.minerva.json.JsonEvidenceInfo; +import org.geneontology.minerva.json.JsonModel; +import org.geneontology.minerva.json.JsonOwlFact; +import org.geneontology.minerva.json.JsonOwlIndividual; +import org.geneontology.minerva.json.JsonOwlObject; +import org.geneontology.minerva.json.JsonOwlObject.JsonOwlObjectType; +import org.geneontology.minerva.json.JsonRelationInfo; +import org.geneontology.minerva.json.JsonTools; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.geneontology.minerva.server.StartUpTool; +import org.geneontology.minerva.server.external.CombinedExternalLookupService; +import org.geneontology.minerva.server.external.ExternalLookupService; +import org.geneontology.minerva.server.external.ExternalLookupService.LookupEntry; +import org.geneontology.minerva.server.external.ProteinToolService; +import org.geneontology.minerva.server.external.TableLookupService; +import org.geneontology.minerva.server.handler.M3BatchHandler.Entity; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3Argument; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3Request; +import org.geneontology.minerva.server.handler.M3BatchHandler.Operation; +import org.geneontology.minerva.util.IdStringManager; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Rule; @@ -17,32 +42,8 @@ import org.semanticweb.owlapi.model.OWLObjectProperty; import org.semanticweb.owlapi.model.OWLOntologyCreationException; -import owltools.gaf.lego.IdStringManager; -import owltools.gaf.lego.IdStringManager.AnnotationShorthand; -import owltools.gaf.lego.UndoAwareMolecularModelManager; -import owltools.gaf.lego.json.JsonAnnotation; -import owltools.gaf.lego.json.JsonEvidenceInfo; -import owltools.gaf.lego.json.JsonModel; -import owltools.gaf.lego.json.JsonOwlFact; -import owltools.gaf.lego.json.JsonOwlIndividual; -import owltools.gaf.lego.json.JsonOwlObject; -import owltools.gaf.lego.json.JsonOwlObject.JsonOwlObjectType; -import owltools.gaf.lego.json.JsonRelationInfo; -import owltools.gaf.lego.json.MolecularModelJsonRenderer; -import owltools.gaf.lego.server.StartUpTool; -import owltools.gaf.lego.server.external.CombinedExternalLookupService; -import owltools.gaf.lego.server.external.ExternalLookupService; -import owltools.gaf.lego.server.external.ExternalLookupService.LookupEntry; -import owltools.gaf.lego.server.external.ProteinToolService; -import owltools.gaf.lego.server.external.TableLookupService; -import owltools.gaf.lego.server.handler.M3BatchHandler.Entity; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3Argument; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3BatchResponse; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3Request; -import owltools.gaf.lego.server.handler.M3BatchHandler.Operation; import owltools.graph.OWLGraphWrapper; import owltools.io.ParserWrapper; -import owltools.util.ModelContainer; @SuppressWarnings("unchecked") public class BatchModelHandlerTest { @@ -125,8 +126,8 @@ public void testTypeOperations() throws Exception { M3Request r = BatchTestTools.addIndividual(modelId, "GO:0006915"); // apoptotic process r.arguments.assignToVariable = "i1"; r.arguments.values = new JsonAnnotation[2]; - r.arguments.values[0] = JsonAnnotation.create(AnnotationShorthand.comment, "comment 1"); - r.arguments.values[1] = JsonAnnotation.create(AnnotationShorthand.comment, "comment 2"); + r.arguments.values[0] = JsonTools.create(AnnotationShorthand.comment, "comment 1"); + r.arguments.values[1] = JsonTools.create(AnnotationShorthand.comment, "comment 2"); batch.add(r); r = new M3Request(); diff --git a/src/test/java/owltools/gaf/lego/server/handler/BatchTestTools.java b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchTestTools.java similarity index 85% rename from src/test/java/owltools/gaf/lego/server/handler/BatchTestTools.java rename to minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchTestTools.java index b09bb3f0..9284ceee 100644 --- a/src/test/java/owltools/gaf/lego/server/handler/BatchTestTools.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchTestTools.java @@ -1,24 +1,25 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; import static org.junit.Assert.*; import java.util.Map; import java.util.Set; -import owltools.gaf.lego.IdStringManager.AnnotationShorthand; -import owltools.gaf.lego.json.JsonAnnotation; -import owltools.gaf.lego.json.JsonEvidenceInfo; -import owltools.gaf.lego.json.JsonOwlFact; -import owltools.gaf.lego.json.JsonOwlIndividual; -import owltools.gaf.lego.json.JsonOwlObject; -import owltools.gaf.lego.json.JsonOwlObject.JsonOwlObjectType; -import owltools.gaf.lego.json.JsonRelationInfo; -import owltools.gaf.lego.json.MolecularModelJsonRenderer; -import owltools.gaf.lego.server.handler.M3BatchHandler.Entity; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3Argument; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3BatchResponse; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3Request; -import owltools.gaf.lego.server.handler.M3BatchHandler.Operation; +import org.geneontology.minerva.json.JsonAnnotation; +import org.geneontology.minerva.json.JsonEvidenceInfo; +import org.geneontology.minerva.json.JsonOwlFact; +import org.geneontology.minerva.json.JsonOwlIndividual; +import org.geneontology.minerva.json.JsonOwlObject; +import org.geneontology.minerva.json.JsonOwlObject.JsonOwlObjectType; +import org.geneontology.minerva.json.JsonRelationInfo; +import org.geneontology.minerva.json.JsonTools; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.geneontology.minerva.server.handler.M3BatchHandler.Entity; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3Argument; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3Request; +import org.geneontology.minerva.server.handler.M3BatchHandler.Operation; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; public class BatchTestTools { @@ -219,7 +220,7 @@ static String generateBlankModel(JsonOrJsonpBatchHandler handler) { } static JsonAnnotation[] singleAnnotation(AnnotationShorthand sh, String value) { - return new JsonAnnotation[]{ JsonAnnotation.create(sh, value)}; + return new JsonAnnotation[]{ JsonTools.create(sh, value)}; } } diff --git a/src/test/java/owltools/gaf/lego/server/handler/DataPropertyTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/DataPropertyTest.java similarity index 87% rename from src/test/java/owltools/gaf/lego/server/handler/DataPropertyTest.java rename to minerva-server/src/test/java/org/geneontology/minerva/server/handler/DataPropertyTest.java index e727159d..d836377d 100644 --- a/src/test/java/owltools/gaf/lego/server/handler/DataPropertyTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/DataPropertyTest.java @@ -1,4 +1,4 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; import static org.junit.Assert.*; @@ -7,6 +7,22 @@ import java.util.Set; import org.apache.commons.lang3.tuple.Pair; +import org.geneontology.minerva.ModelContainer; +import org.geneontology.minerva.MolecularModelManager; +import org.geneontology.minerva.UndoAwareMolecularModelManager; +import org.geneontology.minerva.UndoAwareMolecularModelManager.UndoMetadata; +import org.geneontology.minerva.json.JsonAnnotation; +import org.geneontology.minerva.json.JsonModel; +import org.geneontology.minerva.json.JsonOwlIndividual; +import org.geneontology.minerva.json.JsonRelationInfo; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.geneontology.minerva.server.handler.JsonOrJsonpBatchHandler; +import org.geneontology.minerva.server.handler.M3BatchHandler.Entity; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3Argument; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3Request; +import org.geneontology.minerva.server.handler.M3BatchHandler.Operation; +import org.geneontology.minerva.util.IdStringManager.AnnotationShorthand; import org.junit.Test; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.model.AxiomType; @@ -20,22 +36,7 @@ import org.semanticweb.owlapi.model.OWLOntology; import org.semanticweb.owlapi.model.OWLOntologyManager; -import owltools.gaf.lego.IdStringManager.AnnotationShorthand; -import owltools.gaf.lego.MolecularModelManager; -import owltools.gaf.lego.UndoAwareMolecularModelManager; -import owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata; -import owltools.gaf.lego.json.JsonAnnotation; -import owltools.gaf.lego.json.JsonModel; -import owltools.gaf.lego.json.JsonOwlIndividual; -import owltools.gaf.lego.json.JsonRelationInfo; -import owltools.gaf.lego.json.MolecularModelJsonRenderer; -import owltools.gaf.lego.server.handler.M3BatchHandler.Entity; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3Argument; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3BatchResponse; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3Request; -import owltools.gaf.lego.server.handler.M3BatchHandler.Operation; import owltools.graph.OWLGraphWrapper; -import owltools.util.ModelContainer; public class DataPropertyTest { diff --git a/src/test/java/owltools/gaf/lego/server/handler/M3ExpressionParserTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/M3ExpressionParserTest.java similarity index 92% rename from src/test/java/owltools/gaf/lego/server/handler/M3ExpressionParserTest.java rename to minerva-server/src/test/java/org/geneontology/minerva/server/handler/M3ExpressionParserTest.java index 8c4137b2..993a99fb 100644 --- a/src/test/java/owltools/gaf/lego/server/handler/M3ExpressionParserTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/M3ExpressionParserTest.java @@ -1,19 +1,20 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; import static org.junit.Assert.*; import java.io.IOException; +import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; +import org.geneontology.minerva.json.JsonOwlObject; +import org.geneontology.minerva.json.JsonOwlObject.JsonOwlObjectType; +import org.geneontology.minerva.server.external.ProteinToolService; +import org.geneontology.minerva.server.handler.M3ExpressionParser; +import org.geneontology.minerva.server.handler.OperationsTools.MissingParameterException; import org.junit.BeforeClass; import org.junit.Test; import org.semanticweb.owlapi.model.OWLClassExpression; import org.semanticweb.owlapi.model.OWLOntologyCreationException; -import owltools.gaf.lego.MolecularModelManager.UnknownIdentifierException; -import owltools.gaf.lego.json.JsonOwlObject; -import owltools.gaf.lego.json.JsonOwlObject.JsonOwlObjectType; -import owltools.gaf.lego.server.external.ProteinToolService; -import owltools.gaf.lego.server.handler.OperationsTools.MissingParameterException; import owltools.graph.OWLGraphWrapper; import owltools.io.ParserWrapper; diff --git a/src/test/java/owltools/gaf/lego/server/handler/SeedHandlerTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/SeedHandlerTest.java similarity index 80% rename from src/test/java/owltools/gaf/lego/server/handler/SeedHandlerTest.java rename to minerva-server/src/test/java/org/geneontology/minerva/server/handler/SeedHandlerTest.java index 11489df3..a5721dcf 100644 --- a/src/test/java/owltools/gaf/lego/server/handler/SeedHandlerTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/SeedHandlerTest.java @@ -1,17 +1,18 @@ -package owltools.gaf.lego.server.handler; +package org.geneontology.minerva.server.handler; import static org.junit.Assert.*; +import org.geneontology.minerva.UndoAwareMolecularModelManager; +import org.geneontology.minerva.UndoAwareMolecularModelManager.UndoMetadata; +import org.geneontology.minerva.json.MolecularModelJsonRenderer; +import org.geneontology.minerva.server.handler.JsonOrJsonpSeedHandler; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse; +import org.geneontology.minerva.server.handler.M3SeedHandler.SeedRequest; +import org.geneontology.minerva.server.handler.M3SeedHandler.SeedResponse; import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Test; -import owltools.gaf.lego.UndoAwareMolecularModelManager; -import owltools.gaf.lego.UndoAwareMolecularModelManager.UndoMetadata; -import owltools.gaf.lego.json.MolecularModelJsonRenderer; -import owltools.gaf.lego.server.handler.M3BatchHandler.M3BatchResponse; -import owltools.gaf.lego.server.handler.M3SeedHandler.SeedRequest; -import owltools.gaf.lego.server.handler.M3SeedHandler.SeedResponse; import owltools.graph.OWLGraphWrapper; import owltools.io.ParserWrapper; diff --git a/src/test/resources/gaf/gene_association.goa_chicken.gz b/minerva-server/src/test/resources/gaf/gene_association.goa_chicken.gz similarity index 100% rename from src/test/resources/gaf/gene_association.goa_chicken.gz rename to minerva-server/src/test/resources/gaf/gene_association.goa_chicken.gz diff --git a/src/test/resources/gaf/gene_association.jcvi.gz b/minerva-server/src/test/resources/gaf/gene_association.jcvi.gz similarity index 100% rename from src/test/resources/gaf/gene_association.jcvi.gz rename to minerva-server/src/test/resources/gaf/gene_association.jcvi.gz diff --git a/src/test/resources/ontology/protein/subset/9031.owl b/minerva-server/src/test/resources/ontology/protein/subset/9031.owl similarity index 100% rename from src/test/resources/ontology/protein/subset/9031.owl rename to minerva-server/src/test/resources/ontology/protein/subset/9031.owl diff --git a/src/test/resources/ontology/protein/subset/catalog-v001.xml b/minerva-server/src/test/resources/ontology/protein/subset/catalog-v001.xml similarity index 100% rename from src/test/resources/ontology/protein/subset/catalog-v001.xml rename to minerva-server/src/test/resources/ontology/protein/subset/catalog-v001.xml diff --git a/pom.xml b/pom.xml index 318cdff6..7fa75ee0 100644 --- a/pom.xml +++ b/pom.xml @@ -1,14 +1,37 @@ 4.0.0 - org.bbop + org.geneontology 0.2.2-SNAPSHOT - Minerva + minerva + pom + Minerva UTF-8 + 0.2.2-SNAPSHOT + + + doclint-java8-disable + + [1.8,) + + + + + org.apache.maven.plugins + maven-javadoc-plugin + + -Xdoclint:none + + + + + + + @@ -63,49 +86,24 @@ versions-maven-plugin 2.1 - - org.apache.maven.plugins - maven-assembly-plugin - 2.5.3 - - minerva-server - false - false - ${project.basedir}/bin - - src/main/assembly/minerva-server.xml - - - - true - owltools.gaf.lego.server.StartUpTool - - - - - - make-assembly - package - - single - - - - org.apache.maven.plugins maven-surefire-plugin 2.18.1 - - -Xmx2200M - - **/GolrExternalLookupServiceTest.java - **/SeedHandlerTest.java - + -Xmx2200M + + + + org.apache.maven.plugins + maven-assembly-plugin + 2.5.3 + + + @@ -132,51 +130,65 @@ - - org.bbop - OWLTools-Annotation - 0.2.2-SNAPSHOT - junit junit 4.11 test - - org.bbop - OWLTools-Core - 0.2.2-SNAPSHOT - test-jar - test - - + + + + + + com.google.code.gson + gson + 2.2.4 + + + org.bbop + OWLTools-Annotation + ${owltools.version} + + + org.bbop + OWLTools-Core + ${owltools.version} + test-jar + test + + + org.bbop + golr-client + ${owltools.version} + + org.bbop - golr-client - 0.2.2-SNAPSHOT - - - org.eclipse.jetty - jetty-server - 7.5.4.v20111024 - - - org.eclipse.jetty - jetty-servlet - 7.5.4.v20111024 - - - org.glassfish.jersey.containers - jersey-container-servlet-core - 2.5 - - - org.apache.httpcomponents - httpclient - 4.3.6 - test + OWLTools-Runner + ${owltools.version} - + + org.eclipse.jetty + jetty-server + 7.5.4.v20111024 + + + org.eclipse.jetty + jetty-servlet + 7.5.4.v20111024 + + + org.glassfish.jersey.containers + jersey-container-servlet-core + 2.5 + + + org.apache.httpcomponents + httpclient + 4.3.6 + + + @@ -190,4 +202,12 @@ ${bbopsnapshotrepository} + + + minerva-core + minerva-json + minerva-server + minerva-converter + minerva-cli +