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Minerva changes in prep for switch of URIs, see geneontology/go-site#617
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Makefil added to clarify how the json ld contexts are built.

Now using go and obo context only
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@cmungall
cmungall committed May 18, 2018
1 parent 654c4df commit b22e285
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Showing 4 changed files with 31 additions and 26 deletions.
4 changes: 4 additions & 0 deletions Makefile
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@@ -0,0 +1,4 @@
# See: https://github.com/geneontology/go-site/issues/617
# Note: we will later switch to doing this as part of the GO release
minerva-core/src/main/resources/go_context.jsonld:
wget --no-check-certificate https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/go_context.jsonld -O $@
12 changes: 6 additions & 6 deletions minerva-core/src/main/java/org/geneontology/minerva/curie/DefaultCurieHandler.java
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Expand Up @@ -33,13 +33,13 @@ public static CurieMappings loadMappingsFromFile(File jsonld) throws FileNotFoun

public static CurieMappings loadDefaultMappings() {
final Map<String, String> curieMap = new HashMap<String, String>();
// TODO: we believe we only need obo_context and go_context
// See: https://github.com/geneontology/go-site/issues/617
loadJsonldResource("obo_context.jsonld", curieMap);
// TODO: we believe we only need obo_context and go_context
// See: https://github.com/geneontology/go-site/issues/617
loadJsonldResource("monarch_context.jsonld", curieMap);
loadJsonldResource("amigo_context_gen.jsonld", curieMap);
loadJsonldResource("amigo_context_manual.jsonld", curieMap);
loadJsonldResource("go_context.jsonld", curieMap);
loadJsonldResource("go_context.jsonld", curieMap);
//loadJsonldResource("monarch_context.jsonld", curieMap);
//loadJsonldResource("amigo_context_gen.jsonld", curieMap);
//loadJsonldResource("amigo_context_manual.jsonld", curieMap);
return new CurieMappings.SimpleCurieMappings(curieMap);
}

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17 changes: 5 additions & 12 deletions minerva-core/src/main/resources/go_context.jsonld
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Expand Up @@ -20,7 +20,6 @@
"MEROPS_fam": "http://merops.sanger.ac.uk/cgi-bin/famsum?family=",
"GO_REF": "http://purl.obolibrary.org/obo/go/references/",
"VEGA": "http://vega.sanger.ac.uk/id/",
"EnsemblProtists": "http://www.ensemblgenomes.org/id/",
"ZFIN": "http://identifiers.org/zfin/",
"AspGD_REF": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=",
"RO": "http://purl.obolibrary.org/obo/RO_",
Expand All @@ -33,7 +32,6 @@
"SGN": "http://identifiers.org/sgn/",
"BFO": "http://purl.obolibrary.org/obo/BFO_",
"Genesys-pgr": "https://www.genesys-pgr.org/acn/search?q=",
"NCBI_gi": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=",
"UniMod": "http://www.unimod.org/modifications_view.php?editid1=",
"UM-BBD_reactionID": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=",
"PubChem_Substance": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=",
Expand All @@ -42,7 +40,7 @@
"InterPro": "http://identifiers.org/interpro/",
"UniRule": "http://www.uniprot.org/unirule/",
"MGCSC_GENETIC_STOCKS": "http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=",
"dictyBase": "http://identifiers.org/dbsnp/",
"dictyBase": "http://identifiers.org/dictybase/",
"PO_GIT": "https://github.com/Planteome/plant-ontology/issues/",
"AspGD_LOCUS": "http://identifiers.org/aspgd.locus/",
"SGD": "http://identifiers.org/sgd/",
Expand All @@ -51,13 +49,10 @@
"PAMGO_MGG": "http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=",
"AgBase": "http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=",
"AraCyc": "http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=",
"GONUTS": "http://gowiki.tamu.edu/wiki/index.php/",
"EcoCyc_REF": "http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=",
"EnsemblPlants": "http://www.ensemblgenomes.org/id/",
"CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
"HGNC": "http://identifiers.org/hgnc/",
"dictyBase_gene_name": "http://dictybase.org/gene/",
"ENSEMBL_ProteinID": "http://www.ensembl.org/id/",
"TAIR": "http://identifiers.org/tair.locus/",
"EnsemblFungi": "http://www.ensemblgenomes.org/id/",
"Wikipedia": "http://en.wikipedia.org/wiki/",
Expand All @@ -75,7 +70,6 @@
"MIPS_funcat": "http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=",
"GR_REF": "http://www.gramene.org/db/literature/pub_search?ref_id=",
"MaizeGDB": "http://maizegdb.org/gene_center/gene/",
"EnsemblMetazoa": "http://www.ensemblgenomes.org/id/",
"HAMAP": "http://hamap.expasy.org/unirule/",
"SGN_ref": "http://www.sgn.cornell.edu/chado/publication.pl?pub_id=",
"TO_GIT": "https://github.com/Planteome/plant-trait-ontology/issues/",
Expand All @@ -84,7 +78,6 @@
"MaizeGDB_REF": "http://maizegdb.org/data_center/reference?id=",
"GEO": "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=",
"PO": "http://purl.obolibrary.org/obo/PO_",
"ENSEMBL_TranscriptID": "http://www.ensembl.org/id/",
"PomBase": "http://identifiers.org/pombase/",
"ENA": "http://www.ebi.ac.uk/ena/data/view/",
"PIRSF": "http://pir.georgetown.edu/cgi-bin/ipcSF?id=",
Expand All @@ -101,6 +94,7 @@
"WB_REF": "http://www.wormbase.org/db/misc/paper?name=",
"TGD_LOCUS": "http://db.ciliate.org/cgi-bin/locus.pl?locus=",
"MA": "http://purl.obolibrary.org/obo/MA_",
"UniProtKB": "http://identifiers.org/uniprot/",
"MGI": "http://identifiers.org/mgi/",
"GRINDesc": "https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=",
"DDANAT": "http://purl.obolibrary.org/obo/DDANAT_",
Expand All @@ -114,7 +108,7 @@
"Gene3D": "http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=",
"PATRIC": "http://patric.vbi.vt.edu/gene/overview.php?fid=",
"FB": "http://identifiers.org/flybase/",
"UniProtKB": "http://identifiers.org/uniprot/",
"PAINT_REF": "http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR",
"CASREF": "http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=",
"ENSEMBL": "http://identifiers.org/ensembl/",
"SMART": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=",
Expand Down Expand Up @@ -160,19 +154,18 @@
"SEED": "http://www.theseed.org/linkin.cgi?id=",
"SO": "http://purl.obolibrary.org/obo/SO_",
"Soy_gene": "http://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=",
"PECO_GIT": "https://github.com/Planteome/plant-environment-ontology/issues/",
"CORUM": "http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=",
"RHEA": "http://www.rhea-db.org/reaction.xhtml?id=",
"dbSNP": "http://identifiers.org/dbsnp/",
"MaizeGDB_Locus": "http://identifiers.org/maizegdb.locus/",
"MO": "http://mged.sourceforge.net/ontologies/MGEDontology.php#",
"PLANA_REF": "http://purl.obolibrary.org/obo/plana/references/",
"BRENDA": "http://purl.obolibrary.org/obo/BTO_",
"BRENDA": "http://www.brenda-enzymes.info/php/result_flat.php4?ecno=",
"ASAP": "https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=",
"CAS": "http://identifiers.org/cas/",
"H-invDB_locus": "http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=",
"UM-BBD_ruleID": "http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=",
"taxon": "http://purl.obolibrary.org/obo/NCBITaxon_",
"NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_",
"ComplexPortal": "https://www.ebi.ac.uk/complexportal/complex/",
"JSTOR": "http://www.jstor.org/stable/",
"GRIMS": "https://www.genesys-pgr.org/acn/search2?q=IRGC+",
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24 changes: 16 additions & 8 deletions minerva-core/src/test/java/org/geneontology/minerva/curie/DefaultCurieHandlerTest.java
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Expand Up @@ -24,14 +24,22 @@ public void testAll() {
assertTrue(handler.getInternalMappings().containsKey("PMID"));
assertFalse(handler.getInternalMappings().containsKey("BLABLA"));
}

@Test
public void testObo() {
InputStream stream = DefaultCurieHandler.loadResourceAsStream("obo_context.jsonld");
assertNotNull(stream);
CurieMappings mappings = CurieMappingsJsonld.loadJsonLdContext(stream);
assertFalse(mappings.getMappings().isEmpty());
}

@Test
public void testGo() {
InputStream stream = DefaultCurieHandler.loadResourceAsStream("go_context.jsonld");
assertNotNull(stream);
CurieMappings mappings = CurieMappingsJsonld.loadJsonLdContext(stream);
assertFalse(mappings.getMappings().isEmpty());
}

@Test
public void testObo() {
InputStream stream = DefaultCurieHandler.loadResourceAsStream("obo_context.jsonld");
assertNotNull(stream);
CurieMappings mappings = CurieMappingsJsonld.loadJsonLdContext(stream);
assertFalse(mappings.getMappings().isEmpty());
}

@Test
public void testMonarch() {
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