Examples of OBOOntology

Examples of uk.ac.cam.ch.wwmm.oscar3.terms.OBOOntology

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    long time = System.currentTimeMillis();
    ResourceGetter rg = new ResourceGetter("uk/ac/cam/ch/wwmm/oscar3/chemnamedict/resources/");
   
    Set<String> stops = rg.getStringSet("ChEBIStop.txt");
   
    OBOOntology o = OBOOntology.getInstance();

    Map<String,Set<String>> relatedBySource = new HashMap<String,Set<String>>();
   
    for(String id : o.getTerms().keySet()) {
      if(!id.startsWith("CHEBI:")) continue;
      //if(id.equals("CHEBI:16243")) System.out.println("foo!");
      OntologyTerm term = o.getTerms().get(id);
      Set<String> names = new LinkedHashSet<String>();
      names.add(term.getName());
      String inchi = null;
      String smiles = null;
      //System.out.println(term.getName());
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Examples of uk.ac.cam.ch.wwmm.oscar3.terms.OBOOntology

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    }
  }
 
  private Bag<String> expandOntologyBag(Bag<String> ontologyBag) {
    Bag<String> results = new Bag<String>();
    OBOOntology oo = OBOOntology.getInstance();
    for(String id : ontologyBag.getSet()) {
      for(String parent : oo.getIdsForIdWithAncestors(id)) {
        results.add(parent, ontologyBag.getCount(id));
      }
    }
    return results;
  }
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Examples of uk.ac.cam.ch.wwmm.oscar3.terms.OBOOntology

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  /**
   * @param args
   */
  public static void main(String[] args) throws Exception {
    OBOOntology ontology = new OBOOntology();
    ontology.read(new File("/home/ptc24/gene_ontology.obo"));
    System.out.println(ontology.getTerms().size());
    int termID = 0;
    SciXMLDocument sxd = new SciXMLDocument();
    sxd.setTitle("GO terms");
    int reacts = 0;
    for(String id : ontology.getTerms().keySet()) {
      OntologyTerm term = ontology.getTerms().get(id);
      //SciXMLDocument sxd = new SciXMLDocument();
      //sxd.setTitle(term.getName());
      sxd.getNewDiv(term.getId());
      sxd.addPara().appendChild(term.getName());
     
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Examples of uk.ac.cam.ch.wwmm.oscar3.terms.OBOOntology

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  public ChEBIGenerics() {
    try {
      cache = new HashMap<String,List<String>>();
      sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
      ha = new HydrogenAdder(new ValencyHybridChecker());
      OBOOntology o = OBOOntology.getInstance();
     
      qacs = new HashMap<String, QueryAtomContainer>();
      qsmiles = new HashMap<String, String>();
      qid = new HashMap<String, String>();
     
      for(String id : o.getTerms().keySet()) {
        if(!id.startsWith("CHEBI:")) continue;
        OntologyTerm term = o.getTerms().get(id);
        String name = term.getName();
        if(badQueries.contains(name)) continue;
        if(name.startsWith("graph")) continue;
        if(name.matches(".*(muonium|protide|protium|protide|positronium).*")) continue;
        String smiles = null;
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Examples of uk.ac.cam.ch.wwmm.oscar3.terms.OBOOntology

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    }
    return qac;
  }
 
  private void test() {
    OBOOntology o = OBOOntology.getInstance();

    //System.out.println("----------------------------------------------");
    for(String id : o.getTerms().keySet()) {
      if(!id.startsWith("CHEBI:")) continue;
      OntologyTerm term = o.getTerms().get(id);
      String name = term.getName();
      String smiles = null;
      for(Synonym s : term.getSynonyms()){
        if(s.getType().equals("RELATED SMILES")) {
          smiles = s.getSyn();
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