Examples with Ontology org.monarchinitiative.phenol.ontology.data.Ontology used on opensource projects

Example 1 with Ontology

use of org.monarchinitiative.phenol.ontology.data.Ontology in project loinc2hpo by monarch-initiative.

the class AnnotationQcCommand method run.

@Override
public void run() {
    System.out.println(annotPath);
    Loinc2HpoAnnotationParser parser = new Loinc2HpoAnnotationParser(annotPath);
    List<Loinc2HpoAnnotation> entries = parser.getEntries();
    System.out.println("[INFO] Got " + entries.size() + " LOINC annotations.");
    Ontology ontology = OntologyLoader.loadOntology(new File(hpJsonPath));
    System.out.println("[INFO] Got " + ontology.countNonObsoleteTerms() + " HPO terms in hp.json.");
    checkValidityOfHpoTerms(entries, ontology);
    Map<LoincId, LoincAnnotation> mymap = parser.loincToHpoAnnotationMap();
    System.out.println("[INFO] " + mymap.size() + " annotated LOINC terms");
    checkValidityOfLoincAnnotations(mymap);
}