Examples of OntologyTerm

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

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    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());
      for(Synonym s : term.getSynonyms()){
        //if(id.equals("CHEBI:16243")) System.out.println(s);
        //System.out.println("\t" + s);
        if(s.getType().equals("RELATED InChI")) {
          inchi = s.getSyn();
        } else if(s.getType().equals("RELATED SMILES")) {
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Examples of uk.ac.cam.ch.wwmm.oscar3.terms.OntologyTerm

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    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());
     
      if(term.getDef() != null) {
        sxd.addPara().appendChild(term.getDef());
        if(term.getDef().matches(".*[Rr]eaction.*")) reacts++;
      }
      termID++;
      if(termID % 100 == 0) {
        System.out.println(termID);
        //Serializer ser = new Serializer(new FileOutputStream(new File("/home/ptc24/tmp/goscixml", "g" + termID + ".xml")));
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Examples of uk.ac.cam.ch.wwmm.oscar3.terms.OntologyTerm

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      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;
        for(Synonym s : term.getSynonyms()){
          if(s.getType().equals("RELATED SMILES")) {
            smiles = s.getSyn();
          }
        }
        if(smiles != null && smiles.contains("*")) {
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Examples of uk.ac.cam.ch.wwmm.oscar3.terms.OntologyTerm

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    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();
        }
      }
      if(smiles != null && !smiles.contains("*")) {
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