private ONDEXConcept createConcept(String nodelabel, String nodeId) { ONDEXConcept concept = graph.getFactory().createConcept(nodeId, dataSource, cc, et); concept.createConceptName(nodelabel, true); nodeID2Concept.put(nodeId, concept); return concept; }
public ONDEXRelation createRealtion(ONDEXConcept from, ONDEXConcept to, RelationType rt) { ONDEXRelation result = graph.getRelation(from, to, rt); if (result == null) { result = graph.getFactory().createRelation(from, to, rt, evidence); } return result; }
private static ONDEXRelation createRealtion(ONDEXGraph graph, ONDEXConcept from, ONDEXConcept to, RelationType ofType, EvidenceType ev) { ONDEXRelation result = graph.getRelation(from, to, ofType); if (result == null) { result = graph.getFactory().createRelation(from, to, ofType, ev); } return result; }
private ONDEXConcept createGene(String geneid, String[] additionalIdsFrom, String conceptName) { ONDEXConcept gene = graph.getFactory() .createConcept(geneid, dataSource, cc_gene, eviType); createAccessions(additionalIdsFrom, gene); if (conceptName != null && !conceptName.equalsIgnoreCase("na")) { gene.createConceptName(conceptName.trim(), true); } gene.createAttribute(taxidAn, String.valueOf(3702), false); return gene; }
@Override public void nodeToConcept(AbstractNode node) { Enzyme enzyme = (Enzyme) node; ONDEXConcept concept = graph.getFactory().createConcept(enzyme.getUniqueId(), dataSourceMetaC, ccEnzyme, etIMPD); enzyme.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Enzyme enzyme = (Enzyme) node; ONDEXConcept concept = graph.getFactory().createConcept(enzyme.getUniqueId(), dataSourceAraC, ccEnzyme, etIMPD); enzyme.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Enzyme enzyme = (Enzyme) node; ONDEXConcept concept = graph.getFactory().createConcept(enzyme.getUniqueId(), dataSourceMetaC, ccEnzyme, etIMPD); enzyme.setConcept(concept); }
@Override public void parse(File file) throws IOException { pheno0 = graph.getFactory().createConcept("Phenotype", ahd, phenotype, evidence); pheno0.createConceptName("Phenotype", true); super.parse(file); }
@Override public void nodeToConcept(AbstractNode node) { Enzyme enzyme = (Enzyme) node; ONDEXConcept concept = graph.getFactory().createConcept(enzyme.getUniqueId(), dataSourceBioC, ccEnzyme, etIMPD); enzyme.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Pathway pathway = (Pathway) node; ONDEXConcept concept = graph.getFactory().createConcept(pathway.getUniqueId(), dataSourceMetaC, ccPathway, etIMPD); concept.addTag(concept); pathway.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Gene gene = (Gene) node; ONDEXConcept concept = graph.getFactory().createConcept(gene.getUniqueId(), dataSourceAraC, ccGene, etIMPD); concept.createAttribute(attTaxId, MetaData.TAXID, false); gene.setConcept(concept); //super.addCommonDetailsToConcept(concept, node); }
@Override public void nodeToConcept(AbstractNode node) { Pathway pathway = (Pathway) node; ONDEXConcept concept = graph.getFactory().createConcept(pathway.getUniqueId(), dataSourceAraC, ccPathway, etIMPD); concept.addTag(concept); pathway.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { ECNumber ecNumber = (ECNumber) node; ONDEXConcept concept = graph.getFactory().createConcept(ecNumber.getUniqueId(), dataSourceMetaC, ccEC, etIMPD); concept.createConceptAccession(ecNumber.getUniqueId(), dataSourceEC, false); ecNumber.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { ECNumber ecNumber = (ECNumber) node; ONDEXConcept concept = graph.getFactory().createConcept(ecNumber.getUniqueId(), dataSourceAraC, ccEC, etIMPD); concept.createConceptAccession(ecNumber.getUniqueId(), dataSourceEC, false); ecNumber.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { ECNumber ecNumber = (ECNumber) node; ONDEXConcept concept = graph.getFactory().createConcept(ecNumber.getUniqueId(), dataSourceMetaC, ccEC, etIMPD); concept.createConceptAccession(ecNumber.getUniqueId(), dataSourceEC, false); ecNumber.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { ECNumber ecNumber = (ECNumber) node; ONDEXConcept concept = graph.getFactory().createConcept(ecNumber.getUniqueId(), dataSourceBioC, ccEC, etIMPD); concept.createConceptAccession(ecNumber.getUniqueId(), dataSourceEC, false); ecNumber.setConcept(concept); }
public synchronized ONDEXRelation getRelation ( ONDEXConcept from, ONDEXConcept to, RelationType type, EvidenceType evidence ) { String id = from.getPID () + to.getPID () + type.getId () + evidence.getId (); return this.cacheGet ( ONDEXRelation.class, id, () -> this.graph.getFactory ().createRelation ( from, to, type, evidence ) ); }
public void createTag(String conceptClass, String name) { ONDEXConcept c = graph.getFactory().createConcept(name, createDataSource(graph, "UC"), createCC(graph, conceptClass), createEvidence(graph, "M")); c.createConceptName(name, true); this.addTag(c); } }
public static void createContext(OVTK2PropertiesAggregator viewer, String name) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); ONDEXConcept context = graph.getFactory().createConcept(name, createDataSource(graph, "unknown"), createCC(graph, "Thing"), createEvidence(graph, "manual")); context.createConceptName(name, true); for (ONDEXConcept c : graph.getConcepts()) { c.addTag(context); } }
@Override public void nodeToConcept(AbstractNode node) { Reaction reaction = (Reaction) node; ONDEXConcept concept = graph.getFactory().createConcept( reaction.getUniqueId(), dataSourceAraC, ccReaction, etIMPD); if (reaction.getBalancedState() != null) concept.setAnnotation(reaction.getBalancedState()); concept.createConceptName(constructFormula(reaction), false); if (reaction.getDeltaGo() != null) { concept.createAttribute(deltaGo, reaction.getDeltaGo(), false); } reaction.setConcept(concept); }