public void buildOntology(Map<String, T> id2Terms, Map<String, T> name2Terms) { // 1. convert and index all terms (note: at this stage we don't handle the hierarchy) for ( Iterator iterator = ontBean.getTerms().iterator(); iterator.hasNext(); ) { Term term = ( Term ) iterator.next(); // convert term into a OboTerm T ontologyTerm = createNewTerm(term); final Collection<TermSynonym> synonyms = term.getSynonyms(); if( synonyms != null ) { for ( TermSynonym synonym : synonyms ) { ontologyTerm.getSynonyms().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, synonym.getSynonym())); } } id2Terms.put(term.getIdentifier(), ontologyTerm); name2Terms.put(term.getName(), ontologyTerm); } }
protected void processSynonyms(Term term, T ontologyTerm) { Collection<TermSynonym> synonyms = term.getSynonyms(); if (synonyms != null){ for (TermSynonym synonym : synonyms){ Term synonymType = synonym.getSynonymType(); //PSI-MOD-label for MOD if (synonymType != null){ if (SHORTLABEL_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || MOD_SHORTLABEL_IDENTIFIER.equalsIgnoreCase(synonymType.getName())){ ontologyTerm.setShortName(synonym.getSynonym()); } else if (ALIAS_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || MOD_ALIAS_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || RESID_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || RESID_MISNOMER_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || RESID_NAME_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || RESID_SYSTEMATIC_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || UNIPROT_FEATURE_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || EXACT_KEY.equalsIgnoreCase(synonymType.getName())){ ontologyTerm.getSynonyms().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, synonym.getSynonym())); } } } } }
protected void processSynonyms(Term term, OntologyTerm ontologyTerm) { Collection<TermSynonym> synonyms = term.getSynonyms(); if (synonyms != null){ for (TermSynonym synonym : synonyms){ Term synonymType = synonym.getSynonymType(); //PSI-MOD-label for MOD if (synonymType != null){ if (SHORTLABEL_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || MOD_SHORTLABEL_IDENTIFIER.equalsIgnoreCase(synonymType.getName())){ ontologyTerm.setShortName(synonym.getSynonym()); } else if (ALIAS_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || MOD_ALIAS_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || RESID_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || RESID_MISNOMER_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || RESID_NAME_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || RESID_SYSTEMATIC_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || UNIPROT_FEATURE_IDENTIFIER.equalsIgnoreCase(synonymType.getName()) || EXACT_KEY.equalsIgnoreCase(synonymType.getName())){ ontologyTerm.getSynonyms().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, synonym.getSynonym())); } } } } }
currentOrganism.getAliases().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, currentOrganism.getCommonName())); currentOrganism.getAliases().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, currentOrganism.getScientificName())); currentOrganism.setScientificName(organism.getCommonName()); fullNameLength = organism.getCommonName().length(); currentOrganism.getAliases().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, organism.getCommonName()));
currentOrganism.getAliases().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, currentOrganism.getCommonName())); currentOrganism.getAliases().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, currentOrganism.getScientificName())); currentOrganism.setScientificName(organism.getCommonName()); fullNameLength = organism.getCommonName().length(); currentOrganism.getAliases().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, organism.getCommonName()));
private BioactiveEntity createNewBioactiveEntity(Entity entity) { CvTerm entityType = retrieveMoleculeTypeFrom(entity); BioactiveEntity bioactiveEntity = new DefaultBioactiveEntity(entity.getChebiAsciiName(), entity.getChebiAsciiName(), entityType); // == Chebi ID bioactiveEntity.setChebi( entity.getChebiId() ); // == Secondary CHEBI IDs for(String secondaryId : entity.getSecondaryChEBIIds()){ bioactiveEntity.getIdentifiers().add(XrefUtils.createChebiSecondary(secondaryId)); } // == Smile bioactiveEntity.setSmile( entity.getSmiles() ); // == Inchi / Inchi Key bioactiveEntity.setStandardInchi( entity.getInchi() ); bioactiveEntity.setStandardInchiKey( entity.getInchiKey() ); // == SYNONYMS for(DataItem syn : entity.getSynonyms()){ bioactiveEntity.getAliases().add(AliasUtils.createAlias( Alias.SYNONYM, Alias.SYNONYM_MI, syn.getData())); } // == IUPAC names for(DataItem syn : entity.getIupacNames()){ bioactiveEntity.getAliases().add(AliasUtils.createAlias( Alias.IUPAC , Alias.IUPAC_MI , syn.getData())); } return bioactiveEntity; }
public static psidev.psi.mi.jami.model.Organism createOrganismFromEntry(UniProtEntry entity){ if(entity.getNcbiTaxonomyIds() == null || entity.getNcbiTaxonomyIds().isEmpty()){ return OrganismUtils.createUnknownOrganism(); } else if(entity.getNcbiTaxonomyIds().size() > 1){ throw new IllegalArgumentException( "Uniprot entry ["+entity.getPrimaryUniProtAccession().getValue()+"] " +"has multiple organisms."); } else { String id = entity.getNcbiTaxonomyIds().get(0).getValue(); try{ psidev.psi.mi.jami.model.Organism o = new DefaultOrganism( Integer.parseInt( id ) ); if(entity.getOrganism().hasCommonName()) o.setCommonName(entity.getOrganism().getCommonName().getValue()); if(entity.getOrganism().getScientificName() != null) o.setScientificName(entity.getOrganism().getScientificName().getValue()); if(entity.getOrganism().hasSynonym()) o.getAliases().add(AliasUtils.createAlias(Alias.SYNONYM, Alias.SYNONYM_MI, entity.getOrganism().getSynonym().getValue())); return o; }catch(NumberFormatException n){ throw new IllegalArgumentException("Uniprot entry ["+entity.getPrimaryUniProtAccession().getValue()+"] " + "has a TaxonomyID which could not be cast to an integer: ("+id+").",n); } } } }