log.trace( "defDbxref: " + defDbxref.getDatabase() + "defDbxref ID: " + defDbxref.getDatabaseID() ); if ( defDbxref.getDatabase().equalsIgnoreCase( "PMID" ) || defDbxref.getDatabase().equalsIgnoreCase( "pubmed" ) ) { identifier = defDbxref.getDatabaseID(); database = CvDatabase.PUBMED; } else if ( defDbxref.getDatabase().equalsIgnoreCase( "PMID for application instance" ) ) { identifier = defDbxref.getDatabaseID(); database = CvDatabase.PUBMED; qualifier = CvXrefQualifier.SEE_ALSO; } else if ( defDbxref.getDatabase().equalsIgnoreCase( CvDatabase.GO ) ) { identifier = defDbxref.getDatabase() + ":" + defDbxref.getDatabaseID(); database = CvDatabase.GO; qualifier = CvXrefQualifier.IDENTITY; } else if ( defDbxref.getDatabase().equalsIgnoreCase( CvDatabase.INTACT ) ) { identifier = defDbxref.getDatabase() + ":" + defDbxref.getDatabaseID(); database = CvDatabase.INTACT; qualifier = CvXrefQualifier.IDENTITY; } else if ( defDbxref.getDatabase().equalsIgnoreCase( CvDatabase.RESID ) ) { identifier = defDbxref.getDatabaseID(); database = CvDatabase.RESID; } else if ( defDbxref.getDatabase().equalsIgnoreCase( CvDatabase.SO ) ) { identifier = defDbxref.getDatabase() + ":" + defDbxref.getDatabaseID(); database = CvDatabase.SO; qualifier = CvXrefQualifier.IDENTITY; } else if ( defDbxref.getDatabase().equalsIgnoreCase( "MOD" ) || defDbxref.getDatabase().equalsIgnoreCase("PSI-MOD") ) { identifier = defDbxref.getDatabase() + ":" + defDbxref.getDatabaseID();
retval.setDbName(safeTrim(xref.getDatabase())); if (retval.getDbName() != null && retval.getDbName().length() > 255) { logger.warn("dbxref dbname longer than allowed database column length - truncating " + retval.getDbName()); if (xref.getDatabaseID() != null && !xref.getID().trim().equals("none")) { retval.setAccession(safeTrim(xref.getDatabaseID())); if (xref.getDesc() != null && !xref.getDesc().trim().equals("none")) { retval.setDescription(safeTrim(xref.getDesc())); if (retval.getDescription() != null && retval.getDescription().length() > 2000) { logger.warn("dbxref description longer than allowed database column length: " + retval.getDescription());
if (MOD_STRING_ANNOTATIONS.contains(safeTrim(xref.getDatabase()))) { annot.setAnnotationType(safeTrim(xref.getDatabase())); annot.setAnnotationStringValue(safeTrim(xref.getDesc())); annot.setParentTerm(trm); retval.add(annot); } else if (MOD_NUMERIC_ANNOTATIONS.contains(safeTrim(xref.getDatabase()))) { annot.setAnnotationType(safeTrim(xref.getDatabase())); annot.setAnnotationDoubleValue(safeTrim(xref.getDesc())); annot.setParentTerm(trm); retval.add(annot);
private int getPubmedIndex( Object[] dbxrefArray ) { int index = 0; for ( int i = 0; i < dbxrefArray.length; i++ ) { Dbxref defDbxref = ( Dbxref ) dbxrefArray[i]; if ( defDbxref.getDatabase().equalsIgnoreCase( "PMID" ) ) { return i; } } return index; }
Annotation annot = toAnnotation( CvTopic.SEARCH_URL, dbxref.getDesc() ); if ( annot != null ) { cvObject.addAnnotation( annot );
private OBOClass getRootObject() { if (rootObj != null) { return rootObj; } /* [Term] id: MI:0000 name: molecular interaction def: "Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions." [PMID:14755292] subset: Drugable subset: PSI-MI slim synonym: "mi" EXACT PSI-MI-short [] */ rootObj = new OBOClassImpl( "molecular interaction", "MI:0000" ); rootObj.setDefinition( "Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions." ); //[PMID:14755292]" Dbxref dbxref = new DbxrefImpl( "PMID", "14755292" ); dbxref.setType( Dbxref.DEFINITION ); rootObj.addDefDbxref( dbxref ); addPsimiShortSyn(rootObj, "mi"); return rootObj; }//end of method
retval.setDbName(safeTrim(xref.getDatabase(), true)); if (retval.getDbName() != null && retval.getDbName().length() > 255) { logger.warn("dbxref dbname longer than allowed database column length - truncating " + retval.getDbName()); if (xref.getDatabaseID() != null && !xref.getID().trim().equals("none")) { retval.setAccession(safeTrim(xref.getDatabaseID(), true)); if (xref.getDesc() != null && !xref.getDesc().trim().equals("none")) { retval.setDescription(safeTrim(xref.getDesc(), true)); if (retval.getDescription() != null && retval.getDescription().length() > 2000) { logger.warn("dbxref description longer than allowed database column length: " + retval.getDescription());
if (MOD_STRING_ANNOTATIONS.contains(safeTrim(xref.getDatabase()))) { annot.setAnnotationType(safeTrim(xref.getDatabase())); annot.setAnnotationStringValue(safeTrim(xref.getDesc())); annot.setParentTerm(trm); retval.add(annot); } else if (MOD_NUMERIC_ANNOTATIONS.contains(safeTrim(xref.getDatabase()))) { annot.setAnnotationType(safeTrim(xref.getDatabase())); annot.setAnnotationDoubleValue(safeTrim(xref.getDesc())); annot.setParentTerm(trm); retval.add(annot);
private boolean checkIfUniqueResid( Object[] dbxrefArray ) { int countResid = 0; for ( Object aDbxrefArray : dbxrefArray ) { Dbxref defDbxref = ( Dbxref ) aDbxrefArray; if ( defDbxref.getDatabase().equalsIgnoreCase( "RESID" ) ) { countResid++; } } return countResid == 1; }
dbxref.setType( Dbxref.DEFINITION );
retval.setDbName(safeTrim(xref.getDatabase())); if (retval.getDbName() != null && retval.getDbName().length() > 255) { logger.warn("dbxref dbname longer than allowed database column length - truncating " + retval.getDbName()); if (xref.getDatabaseID() != null && !xref.getID().trim().equals("none")) { retval.setAccession(safeTrim(xref.getDatabaseID())); if (xref.getDesc() != null && !xref.getDesc().trim().equals("none")) { retval.setDescription(safeTrim(xref.getDesc())); if (retval.getDescription() != null && retval.getDescription().length() > 2000) { logger.warn("dbxref description longer than allowed database column length: " + retval.getDescription());
if (MOD_STRING_ANNOTATIONS.contains(safeTrim(xref.getDatabase(), true))) { annot.setAnnotationType(safeTrim(xref.getDatabase(), true)); annot.setAnnotationStringValue(safeTrim(xref.getDesc(), true)); annot.setParentTerm(trm); retval.add(annot); } else if (MOD_NUMERIC_ANNOTATIONS.contains(safeTrim(xref.getDatabase(), true))) { annot.setAnnotationType(safeTrim(xref.getDatabase(), true)); annot.setAnnotationDoubleValue(safeTrim(xref.getDesc(), true)); annot.setParentTerm(trm); retval.add(annot);
if (MOD_STRING_ANNOTATIONS.contains(safeTrim(xref.getDatabase()))) { } else if (MOD_NUMERIC_ANNOTATIONS.contains(safeTrim(xref.getDatabase()))) {
if (MOD_STRING_ANNOTATIONS.contains(safeTrim(xref.getDatabase(), true))) { } else if (MOD_NUMERIC_ANNOTATIONS.contains(safeTrim(xref.getDatabase(), true))) {
if (MOD_STRING_ANNOTATIONS.contains(safeTrim(xref.getDatabase()))) { } else if (MOD_NUMERIC_ANNOTATIONS.contains(safeTrim(xref.getDatabase()))) {