public ONDEXConcept lookupPublication(String id) { Holder h = lookupConcept(pubIndex, publication, id); ONDEXConcept c = h.concept; if (h.isNew) c.createConceptAccession(id, pmid, false); return c; }
public synchronized ConceptAccession getAccession ( String accession, DataSource dataSrc, boolean isAmbiguous, ONDEXConcept concept ) { // TODO: is the ID unique? Is it concept-unique? return this.cacheGet ( ConceptAccession.class, accession, () -> concept.createConceptAccession ( accession, dataSrc, isAmbiguous ) ); }
private void assignAccessions(ONDEXConcept c, Set<String> accs) { for (String acc : accs) { String[] split = dataSourceLookup.recognize(acc); if (split != null) { String cvStr = split[0], value = split[1]; DataSource dataSource = dataSourceLookup.get(cvStr); if (dataSource != null) { c.createConceptAccession(value, dataSource, false); } } else { unmatchedKeys.add(acc); } } }
private void assignAccessions(ONDEXConcept c, Set<String> accs) { for (String acc : accs) { String[] split = dataSourceLookup.recognize(acc); if (split != null) { String cvStr = split[0], value = split[1]; DataSource dataSource = dataSourceLookup.get(cvStr); if (dataSource != null) { c.createConceptAccession(value, dataSource, false); } } else { unmatchedKeys.add(acc); } } }
/** * Creates the corresponding ONDEXConcept on the given graph. * * @return created publication ONDEXConcept */ public ONDEXConcept createONDEXConcept(int index) { if (!taxids[index].isEmpty()) { ONDEXConcept c = graph.getFactory().createConcept(taxids[index], dataSource, cc, et); // publication associated Attribute c.createAttribute(taxidAttributeName, taxids[index], false); c.createConceptAccession(taxids[index], external, false); return c; } else { throw new RuntimeException("Organism without valid taxid tag!"); } } }
/** * Extracts all target information and creats a new Ondex concept * * @param eElement * @return */ private ONDEXConcept createTarget(Element eElement) { // check for existing targets String key = getTagValue("target__chemblid", eElement); if (!targets.containsKey(key)) { // new target concept ONDEXConcept c = graph.getFactory().createConcept(key, dsCHEMBL, ccTarget, evidencetype); c.createConceptName(getTagValue("target__name", eElement), true); c.createConceptAccession(key, dsTARGET, false); targets.put(key, c); } return targets.get(key); }
/** * Copies all accessions from old concept to new concept. * * @param oldC * old ONDEXConcept * @param newC * new ONDEXConcept */ private void copyAccessions(ONDEXConcept oldC, ONDEXConcept newC) { // iterate over all old accessions for (ConceptAccession acc : oldC.getConceptAccessions()) { // clone old accession on new concept newC.createConceptAccession(acc.getAccession(), acc.getElementOf(), acc.isAmbiguous()); } }
@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(), dataSourceAraC, cc, etIMPD); concept.createAttribute( attTaxId, MetaData.TAXID, false); int monomerPos = protein.getUniqueId().indexOf("-MONOMER"); if (monomerPos != -1){ concept.createConceptAccession(protein.getUniqueId().subSequence(0, monomerPos).toString(), super.dataSourceTAIR, true); String nameWithoutMonomer = protein.getUniqueId().subSequence(0, monomerPos).toString(); if ( !protein.getSynonym().contains(nameWithoutMonomer)) concept.createConceptName(nameWithoutMonomer,false ); } protein.setConcept(concept); }
public static void correctUniprotAccession(OVTK2PropertiesAggregator viewer) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); ConceptClass prot = graph.getMetaData().getConceptClass("Protein"); DataSource nc_np = graph.getMetaData().getDataSource("NC_NP"); for (ONDEXConcept p : graph.getConceptsOfConceptClass(prot)) { List<String> newAcc = new ArrayList<String>(); for (ConceptAccession ca : p.getConceptAccessions()) { if (ca.getElementOf().equals(nc_np)) { if (ca.getAccession().contains(".")) { newAcc.add(ca.getAccession().split("\\.")[0]); } } } for (String str : newAcc) { p.createConceptAccession(str, nc_np, true); } } }
@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 actionPerformed(ActionEvent e) { this.setVisible(false); editor.acc.setAmbiguous(box.isSelected()); // has the DataSource of accession changed? DataSource dataSource = (DataSource) selection.getSelectedItem(); if (!editor.acc.getElementOf().equals(dataSource)) { // delete old one ConceptAccession old = editor.concept.getConceptAccession(editor.acc.getAccession(), editor.acc.getElementOf()); editor.concept.deleteConceptAccession(editor.acc.getAccession(), editor.acc.getElementOf()); // create one with new DataSource editor.acc = editor.concept.createConceptAccession(old.getAccession(), dataSource, old.isAmbiguous()); } } }
/** * Creates an accession on concept only if it does not already exists * * @param target * - relation * @param newAcc * - attribute to create * @throws AccessDeniedException * @throws EmptyStringException * @throws NullValueException */ public static void addNewAccession(ONDEXConcept target, ConceptAccession newAcc) throws NullValueException, EmptyStringException, AccessDeniedException { if (target.getConceptAccession(newAcc.getAccession(), newAcc.getElementOf()) == null) target.createConceptAccession(newAcc.getAccession(), newAcc.getElementOf(), true); }
@Override public void nodeToConcept(AbstractNode node) { Publication pub = (Publication) node; if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD)) return; ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD); if (pub.getPubMedId() != 0){ concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false); } if (pub.getTitle() != null && !pub.getTitle().equals("")){ concept.createAttribute(attTitle, pub.getTitle(), false); } pub.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Publication pub = (Publication) node; if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceBioC, ccPublication, etIMPD)) return; ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceBioC, ccPublication, etIMPD); if (pub.getPubMedId() != 0){ concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false); } if (pub.getTitle() != null && !pub.getTitle().equals("")){ concept.createAttribute(attTitle, pub.getTitle(), false); } pub.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Publication pub = (Publication) node; if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceAraC, ccPublication, etIMPD)) return; ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceAraC, ccPublication, etIMPD); if (pub.getPubMedId() != 0){ concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false); } if (pub.getTitle() != null && !pub.getTitle().equals("")){ concept.createAttribute(attTitle, pub.getTitle(), false); } pub.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Publication pub = (Publication) node; if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD)) return; ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD); if (pub.getPubMedId() != 0){ concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false); } if (pub.getTitle() != null && !pub.getTitle().equals("")){ concept.createAttribute(attTitle, pub.getTitle(), false); } pub.setConcept(concept); }
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; } }