VCell Kisao Ontology.

Classes creation.

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

@@ -0,0 +1,49 @@
+package cbit.util.kisao;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+
+public class KisaoOntology {
+
+	private List<KisaoTerm> terms = new ArrayList<>();
+	private static KisaoOntology instance;
+
+
+	public static KisaoOntology getInstance() {
+		if (instance == null) {
+			instance = new KisaoTermParser().parse();
+		}
+		return instance;
+	}
+
+	public void addTerm(KisaoTerm curr) {
+		terms.add(curr);
+	}
+	public List<KisaoTerm> getTerms() {
+		return Collections.unmodifiableList(terms);
+	}
+
+	public KisaoTerm getTermById(String id) {
+		for (KisaoTerm term : terms) {
+			if (term.getId().equalsIgnoreCase(id)) {
+				return term;
+			}
+		}
+		return null;
+	}
+
+	public void createRelations() {
+		for (KisaoTerm term : terms) {
+			List<String> isas = term.getIsaRef();
+			for (String isa : isas) {
+				KisaoTerm termIsa = getTermById(isa);
+				if (termIsa != null) {
+					term.addIsa(termIsa);
+				}
+			}
+		}
+	}
+
+}

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

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+package cbit.util.kisao;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+public class KisaoTerm {
+
+	private String id, name, def;
+	private List<KisaoTerm> isaList = new ArrayList<KisaoTerm>();
+	private List<String> isaRef = new ArrayList<String>();	// used only during parsing, as proxy for still unknown terms
+
+	KisaoTerm() {
+	}
+
+	@Override
+	public String toString() {
+		return "KisaoTerm [id=" + id + ", name=" + name + ", def=" + def + "]";
+	}
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((id == null) ? 0 : id.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;
+		}
+		KisaoTerm other = (KisaoTerm) obj;
+		if (id == null) {
+			if (other.id != null) {
+				return false;
+			}
+		} else if (!id.equals(other.id)) {
+			return false;
+		}
+		return true;
+	}
+
+	public String getId() {
+		return id;
+	}
+	void setId(String id) {
+		this.id = id;
+	}
+
+	public String getName() {
+		return name;
+	}
+	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);
+	}
+	void addIsa(KisaoTerm is_a) {
+		isaList.add(is_a);
+	}
+
+	void addIsaRef(String synonym) {
+		isaRef.add(synonym);
+	}
+	List<String> getIsaRef() {
+		return isaRef;
+	}
+
+public boolean is_a(KisaoTerm otherTerm) {
+		if (this.equals(otherTerm)) {
+			return true;
+		}
+		for (KisaoTerm isa : isaList) {
+			if (isa.equals(otherTerm)) {
+				return true;
+			}
+		}
+		for (KisaoTerm isa : isaList) {
+			return isa.is_a(otherTerm);
+		}
+		return false;
+	}
+
+}
+

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

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+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));
+		String line = null;
+		boolean inPreamble = true;
+		boolean inState = false;
+		KisaoOntology ontology = new KisaoOntology();
+		KisaoTerm curr = null;
+
+		try {
+			while ((line = isr.readLine()) != null) {
+
+				if (line.matches(TERM_PATTERN)) {
+					inState = true;
+					curr = new KisaoTerm();
+				}
+				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()) {
+						curr.setId(matcher.group(1));
+					}
+
+					matcher = NAME_PATTERN.matcher(line);
+					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));
+					}
+				}
+			}
+		} catch(Exception e) {
+			e.printStackTrace();
+		}
+
+		ontology.createRelations();
+		return ontology;
+	}
+}