public OboCategory(String name){ super.setName( name ); }
private void addFooterInfo() { OBOPropertyImpl partOf = new OBOPropertyImpl("part_of"); partOf.setName("part of"); partOf.setTransitive(true); oboSession.addObject(partOf); }
String id = oboClass.getID(); String name = oboClass.getName(); Set<SynonymImpl> oboSynonyms = oboClass.getSynonyms(); Set<String> synonyms = synonymsToString(oboSynonyms); } else { for (Link link : oboClass.getParents()) { LinkedObject oboParent = link.getParent();
private Synonym createSynonym( String shortLabel, String shortLabelId ) { Synonym syn = new SynonymImpl(); syn.setText( shortLabel ); SynonymType synCat = new SynonymTypeImpl(); synCat.setID(shortLabelId); syn.setSynonymType( synCat ); syn.setScope( 1 ); return syn; }
OBOClass oboObj = new OBOClassImpl( dagObj.getFullName(), cvId); Dbxref dbxref = new DbxrefImpl( dbx, xref.getPrimaryId() ); dbxref.setType( Dbxref.DEFINITION ); } else if ( cvTopic.getShortLabel().equalsIgnoreCase( CvTopic.SEARCH_URL ) ) { String annotationText = "\""+annotation.getAnnotationText()+"\""; oboObj.addPropertyValue(new PropertyValueImpl("xref", CvTopic.SEARCH_URL+": "+annotationText)); } else if ( cvTopic.getShortLabel().equalsIgnoreCase( CvTopic.XREF_VALIDATION_REGEXP ) ) { String annotationText = "\\\""+annotation.getAnnotationText()+"\\\""; oboObj.addPropertyValue(new PropertyValueImpl("xref", CvTopic.XREF_VALIDATION_REGEXP+":"+annotationText)); } else if ( cvTopic.getShortLabel().equalsIgnoreCase( CvTopic.COMMENT ) && annotation.getAnnotationText() != null ) { oboObj.setComment( removeLineReturns(annotation.getAnnotationText() ));
public CvExporter() { ObjectFactory objFactory; objFactory = new DefaultObjectFactory(); oboSession = new OBOSessionImpl( objFactory ); cvToOboCache = new HashMap<CvClassIdentifier,OBOClass>(); defaultOntologyConfig = new IntactOntologyConfig(); cvToOboMapExternalConfig = new HashMap<String, ExternalOntologyConfig>(); initializeExternalOntologyConfig(); }
private void addLinkToRootFor(OBOClass oboObj) { OBOClass rootObject = getRootObject(); Link linkToRoot = new OBORestrictionImpl( oboObj ); OBOProperty oboProp = new OBOPropertyImpl( "part_of" ); linkToRoot.setType( oboProp ); rootObject.addChild( linkToRoot ); }
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
private void addHeaderInfo() { Collection<ExternalOntologyConfig> ontoConfigs = cvToOboMapExternalConfig.values(); oboSession.setDefaultNamespace( new Namespace( defaultOntologyConfig.getDefaultNamespace() ) ); oboSession.addPropertyValue(new PropertyValueImpl("auto-generated-by", "IntAct CvExporter")); oboSession.addSynonymType(new SynonymTypeImpl(defaultOntologyConfig.getAliasSynonymCategory(), defaultOntologyConfig.getAliasSynonymDefinition())); oboSession.addSynonymType(new SynonymTypeImpl(defaultOntologyConfig.getShortLabelSynonymCategory(), defaultOntologyConfig.getShortLabelSynonymDefinition())); for (ExternalOntologyConfig conf : ontoConfigs){ oboSession.addNamespace( new Namespace( conf.getDefaultNamespace() ) ); oboSession.addSynonymType(new SynonymTypeImpl(conf.getAliasSynonymCategory(), conf.getAliasSynonymDefinition())); oboSession.addSynonymType(new SynonymTypeImpl(conf.getShortLabelSynonymCategory(), conf.getShortLabelSynonymDefinition())); } }
public OBOClass getOBOCellType() { if (cellTypeObj != null) { return cellTypeObj; } cellTypeObj = new OBOClassImpl("cell type", "IAX:0002"); cellTypeObj.setDefinition("IntAct cell type base object"); addLinkToRootFor(cellTypeObj); oboSession.addObject(cellTypeObj); return cellTypeObj; }
private boolean isARootTerm(OBOClassImpl oboClass) { return oboClass.getParents().isEmpty(); }
private boolean isALeafTerm(OBOClassImpl oboClass) { return oboClass.getChildren().isEmpty(); } }
private Set<String> synonymsToString(Set<SynonymImpl> oboSynonyms) { Set<String> synonyms = new HashSet<String>(oboSynonyms.size()); for (SynonymImpl oboSynonym : oboSynonyms) { synonyms.add(oboSynonym.getText()); } return synonyms; }
@SuppressWarnings("unchecked") private Set<String> getSynonyms(LinkedObject oboParent) { Set<String> parentSynonyms; if (oboParent instanceof OBOClassImpl) { OBOClassImpl parentOboClass = (OBOClassImpl) oboParent; parentSynonyms = synonymsToString(parentOboClass.getSynonyms()); } else { parentSynonyms = Collections.EMPTY_SET; } return parentSynonyms; }
private void addChild(OBOClass parent, OBOClass child) { Link linkToIsA = new OBORestrictionImpl(child); linkToIsA.setType( OBOProperty.IS_A ); parent.addChild( linkToIsA ); }
private void addPsimiShortSyn(OBOClass oboObj, String synonym) { Synonym syn = new SynonymImpl(); syn.setText( synonym ); SynonymType synCat = new SynonymTypeImpl(); synCat.setID(synonym); syn.setSynonymType( synCat ); syn.setScope( 1 ); oboObj.addSynonym( syn ); }
ObjectFactory objFactory = new DefaultObjectFactory(); OBOSession session2export = new OBOSessionImpl( objFactory );
public OBOClass getOBOTissue() { if (tissueObj != null) { return tissueObj; } tissueObj = new OBOClassImpl("tissue", "IAX:0001"); tissueObj.setDefinition("IntAct tissue base object"); addLinkToRootFor(tissueObj); oboSession.addObject(tissueObj); return tissueObj; }
private Synonym createAlias( CvObjectAlias cvAlias, String aliasId ) { Synonym syn = new SynonymImpl(); syn.setText( cvAlias.getName() ); SynonymType synCat = new SynonymTypeImpl(); synCat.setID(aliasId); syn.setSynonymType( synCat ); syn.setScope( 1 ); return syn; }