ontologyTerm.getXrefs().add(primaryPubmedRef); ontologyTerm.getXrefs().add(pubmedRef); ontologyTerm.getXrefs().add(pubmedRef); // MI not MOD } else if ( GO.equalsIgnoreCase(database) ) { Xref goRef = XrefUtils.createXrefWithQualifier(GO, GO_MI_REF, database + ":" + accession, Xref.SEE_ALSO, Xref.SEE_ALSO_MI); ontologyTerm.getXrefs().add(goRef); // MI not MOD } else if ( RESID.equalsIgnoreCase(database) ) { Xref resXref = XrefUtils.createXrefWithQualifier(RESID, RESID_MI_REF, accession, Xref.SEE_ALSO, Xref.SEE_ALSO_MI); ontologyTerm.getXrefs().add(resXref); } else if ( SO.equalsIgnoreCase(database) ) { Xref soRef = XrefUtils.createXrefWithQualifier(SO, SO_MI_REF, database + ":" + accession, Xref.SEE_ALSO, Xref.SEE_ALSO_MI); ontologyTerm.getXrefs().add(soRef); // MI not MOD }else if ( Xref.PUBMED.equalsIgnoreCase(database) ) { if (pubmedPrimary == null){ ontologyTerm.getXrefs().add(primaryPubmedRef); ontologyTerm.getXrefs().add(pubmedRef); ontologyTerm.getXrefs().add(resXref); }else if ( Xref.CHEBI.equalsIgnoreCase(database) ) { Xref chebiRef = XrefUtils.createXrefWithQualifier(Xref.CHEBI, Xref.CHEBI_MI, accession, Xref.SEE_ALSO, Xref.SEE_ALSO_MI); ontologyTerm.getXrefs().add(chebiRef); // MOD xref } else if ( Annotation.URL.equalsIgnoreCase(database) ) { ontologyTerm.getAnnotations().add(AnnotationUtils.createAnnotation(Annotation.URL, Annotation.URL_MI, accession));
/*** * This method will copy properties of cv term source in cv term target and will override all the other properties of Target cv term. * @param source : the cv term source to copy from * @param target : the cv term target to copy to */ public static void copyAndOverrideCvTermProperties(CvTerm source, CvTerm target){ if (source != null && target != null){ target.setShortName(source.getShortName()); target.setFullName(source.getFullName()); // copy collections target.getAnnotations().clear(); target.getAnnotations().addAll(source.getAnnotations()); target.getXrefs().clear(); target.getXrefs().addAll(source.getXrefs()); target.getIdentifiers().clear(); target.getIdentifiers().addAll(source.getIdentifiers()); target.getSynonyms().clear(); target.getSynonyms().addAll(source.getSynonyms()); } }
CvTerm cellType = organism.getCellType(); if (!cellType.getIdentifiers().isEmpty() || !cellType.getXrefs().isEmpty()){ Collection<psidev.psi.mi.jami.model.Xref> allPubmeds = XrefUtils.collectAllXrefsHavingDatabaseAndQualifier(cellType.getXrefs(), psidev.psi.mi.jami.model.Xref.PUBMED_MI, psidev.psi.mi.jami.model.Xref.PUBMED, psidev.psi.mi.jami.model.Xref.PRIMARY_MI, psidev.psi.mi.jami.model.Xref.PRIMARY);