public int getNcbiTaxId() { return organism.getNcbiTaxId(); }
public BioSource psiToIntact(Organism psiObject) { if (psiObject == null) return null; psiStartConversion(psiObject); int taxId = psiObject.getNcbiTaxId(); BioSource bioSource = new BioSource(); bioSource.setTaxId(String.valueOf(taxId)); bioSource.setOwner(getInstitution()); IntactConverterUtils.populateNames(psiObject.getNames(), bioSource, aliasConverter); // cell type final CellType cellType = psiObject.getCellType(); if (cellType != null) { CvCellType intactCellType = cellTypeConverter.psiToIntact(cellType); bioSource.setCvCellType(intactCellType); } // tissue final Tissue tissue = psiObject.getTissue(); if (tissue != null) { CvTissue intactTissue = tissueConverter.psiToIntact(tissue); bioSource.setCvTissue(intactTissue); } if (psiObject.getCompartment() != null){ log.warn("Organism having a compartment : "+psiObject.getNcbiTaxId()+". Compartment is not converted in IntAct and is ignored."); } psiEndConversion(psiObject); return bioSource; }
String ncbiId = Integer.toString(organism.getNcbiTaxId()); String name = null;
psidev.psi.mi.xml.model.Organism o = xmlInteractor.getOrganism(); List<CrossReference> organismXrefs = new ArrayList<CrossReference>(); String taxId = String.valueOf(o.getNcbiTaxId());
jOrganism.setNcbiTaxId( mOrganism.getNcbiTaxId() );
jOrganism.setNcbiTaxId( mOrganism.getNcbiTaxId() );
if (organism != null) { HostOrganism hostOrganism = new HostOrganism(); hostOrganism.setNcbiTaxId(organism.getNcbiTaxId()); hostOrganism.setNames(organism.getNames()); hostOrganism.setCellType(organism.getCellType());
final Integer taxID = org.getNcbiTaxId(); mapNames(nodeTable, node.getSUID(), org.getNames(), "Species ");