VCell Kisao Ontology.

Proof of concept.

vcell-core/src/main/java/cbit/util/kisao/KisaoOntology.java

@@ -45,5 +45,12 @@ public void createRelations() {
 			}
 		}
 	}
+
+	public static void main(String[] args) {
+
+		KisaoTerm sedmlSolverKisaoTerm = KisaoOntology.getInstance().getTermById("KISAO_0000027");
+		System.out.println(sedmlSolverKisaoTerm);
+		System.out.println("Done");
+	}
 
 }

vcell-core/src/main/java/cbit/util/kisao/KisaoTerm.java

@@ -6,7 +6,7 @@
 
 public class KisaoTerm {
 
-	private String id, name, def;
+	private String id, name;
 	private List<KisaoTerm> isaList = new ArrayList<KisaoTerm>();
 	private List<String> isaRef = new ArrayList<String>();	// used only during parsing, as proxy for still unknown terms
 
@@ -15,7 +15,7 @@ public class KisaoTerm {
 
 	@Override
 	public String toString() {
-		return "KisaoTerm [id=" + id + ", name=" + name + ", def=" + def + "]";
+		return "KisaoTerm [id=" + id + ", name=" + name + "]";
 	}
 	@Override
 	public int hashCode() {
@@ -61,13 +61,6 @@ void setName(String name) {
 		this.name = name;
 	}
 
-	public String getDefinition() {
-		return def;
-	}
-	void setDef(String def) {
-		this.def = def;
-	}
-
 	public List<KisaoTerm> getIsa() {
 		return Collections.unmodifiableList(isaList);
 	}

vcell-core/src/main/java/cbit/util/kisao/KisaoTermParser.java

@@ -1,26 +1,25 @@
 package cbit.util.kisao;
 
 import java.io.BufferedReader;
-import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 
 public class KisaoTermParser {
+
 	final String Kisao_OBO = "kisao_2020_12_13.obo";
+
 	final String TERM_PATTERN = "\\[Term\\]";
 	final Pattern ID_PATTERN = Pattern.compile("id:\\s*(.+)");
 	final Pattern NAME_PATTERN = Pattern.compile("name:\\s*(.+)");
-	final Pattern DEF_PATTERN = Pattern.compile("def:\\s*(.+)");
 	final Pattern ISA_PATTERN = Pattern.compile("is_a:\\s*(\\S+)");
 
 	KisaoOntology parse() {
-		InputStream is2 = KisaoTermParser.class.getClassLoader().getResourceAsStream(Kisao_OBO);
-		BufferedReader isr = new BufferedReader(new InputStreamReader(is2));
+		InputStream is = KisaoTermParser.class.getClassLoader().getResourceAsStream(Kisao_OBO);
+		BufferedReader isr = new BufferedReader(new InputStreamReader(is));
 		String line = null;
-		boolean inPreamble = true;
 		boolean inState = false;
 		KisaoOntology ontology = new KisaoOntology();
 		KisaoTerm curr = null;
@@ -34,10 +33,10 @@ KisaoOntology parse() {
 				}
 				if (line.matches("^$") && curr != null) {
 					inState = false;
-					inPreamble = false;
 					ontology.addTerm(curr);
 					curr = null;
 				}
+
 				if(inState) {
 					Matcher matcher = ID_PATTERN.matcher(line);
 					if (matcher.find()) {
@@ -48,10 +47,6 @@ KisaoOntology parse() {
 					if (matcher.find()) {
 						curr.setName(matcher.group(1));
 					}
-					matcher = DEF_PATTERN.matcher(line);
-					if (matcher.find()) {
-						curr.setDef(matcher.group(1));
-					}
 					matcher = ISA_PATTERN.matcher(line);
 					if (matcher.find()) {
 						curr.addIsaRef(matcher.group(1));