ontologyTerm.getXrefs().add(primaryPubmedRef);
ontologyTerm.getXrefs().add(pubmedRef);
ontologyTerm.getXrefs().add(pubmedRef);
} 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);
} 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);
}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);
} else if ( Annotation.URL.equalsIgnoreCase(database) ) {
ontologyTerm.getAnnotations().add(AnnotationUtils.createAnnotation(Annotation.URL, Annotation.URL_MI, accession));