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; }
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; }
private ONDEXConcept createTranscriptionFactor( String tfid, String[] additionalIdsFrom, String conceptName ) { ONDEXConcept tf = graph.getFactory().createConcept(tfid, dataSource, cc_tf, eviType); createAccessions(additionalIdsFrom, tf); if (conceptName != null && !conceptName.equalsIgnoreCase("na")) { tf.createConceptName(conceptName.trim(), true); } tf.createAttribute(taxidAn, String.valueOf(3702), false); return tf; }
@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(), dataSourceAraC, ccPathway, etIMPD); concept.addTag(concept); pathway.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) { 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); }
@Override public void nodeToConcept(AbstractNode node) { Protein protein = (Protein) node; ConceptClass cc = null; if (protein.isComplex()) cc = ccProteinComplex; else cc = ccProtein; ONDEXConcept concept = graph.getFactory().createConcept( protein.getUniqueId(), dataSourceBioC, cc, etIMPD); concept.createAttribute(attTaxId, Parser.taxidToUse, false); protein.setConcept(concept); }
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); } }
public int getOrCreateGeneID(String geneId) { if (poplarReg.containsGene(geneId)) { return poplarReg.getGene(geneId); } else { ONDEXConcept gene = og.getFactory().createConcept(geneId, dataSourcePHYTOZOME, ccGene, etIMPD); gene.createConceptAccession(geneId, dataSourcePHYTOZOME, false); gene.createConceptName(geneId, false); Integer ondexGeneId = gene.getId(); gene.createAttribute(anTaxID, Parser.POPLAR_TAX_ID, false); poplarReg.addGene(geneId, ondexGeneId); return ondexGeneId; } }
@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); }