Working with HPO

OntoLib supports you in working with the HPO in the following ways:

• The HpoOntology class supports the standard Ontology interface. Besides this, the “phenotypic abnormality” sub ontology is extracted on construction and is available through HpoOntology.getPhenotypicAbnormalitySubOntology().
• The classes HpoFrequencyTermIds, HpoModeOfInheritanceTermIds, and HpoSubOntologyRootTermIds provide shortcuts to important/special terms that come in handy when using the HPO.
• OntoLib provides means to parse disease-to-phenotype and disease-to-gene annotations from the HPO project into HpoDiseaseAnnotation and HpoGeneAnnotation objects.

This section will demonstrate these three features.

The HpoOntology Class

When iterating over all primary (i.e., not alternative) and non-obsolete term IDs, you should use the getNonObsoleteTermIds() method for obtaining a Set of these ``TermId``s

// final HpoOntology hpo = ...
System.err.println("Term IDs in HPO (primary, non-obsolete)");
for (TermId termId : hpo.getNonObsoleteTermIds()) {
  System.err.println(termId);
}

You can obtain the correct HpoTerm instance for the given TermId by consulting the resulting Map from calling getTermMap():

System.err.println("Term IDs+names in HPO (primary IDs, non-obsolete)");
for (TermId termId : hpo.getNonObsoleteTermIds()) {
  final HpoTerm term = hpo.getTermMap().get(termId);
  System.err.println(termId + "\t" + term.getName());
}

The “phenotypic abnormality” sub ontology, can be accessed with ease and then used just like all other Ontology objects.

// final HpoOntology hpo = ...
final Ontology<HpoTerm, HpoTermRelation> subOntology =
    hpo.getPhenotypicAbnormalitySubOntology();
System.err.println("Term IDs in phenotypic abnormality sub ontology");
for (TermId termId : subOntology.getNonObsoleteTermIds()) {
  System.err.println(termId);
}

Shortcuts to Important Term IDs

These can be accessed as follows.

System.err.println("ALWAYS_PRESENT\t", HpoFrequencyTermIds.ALWAYS_PRESENT);
System.err.println("FREQUENT\t", HpoFrequencyTermIds.FREQUENT);

System.err.println("X_LINKED_RECESSIVE\t", HpoModeOfInheritanceTermIds.X_LINKED_RECESSIVE);
System.err.println("AUTOSOMAL_DOMINANT\t", HpoModeOfInheritanceTermIds.AUTOSOMAL_DOMINANT);

System.err.println("PHENOTYPIC_ABNORMALITY\t", HpoSubOntologyRootTermIds.PHENOTYPIC_ABNORMALITY);
System.err.println("FREQUENCY\t", HpoSubOntologyRootTermIds.FREQUENCY);
System.err.println("MODE_OF_INHERITANCE\t", HpoSubOntologyRootTermIds.MODE_OF_INHERITANCE);

Parsing Annotation Files

You can parse the phenotype-to-disease annotation files as follows.

File inputFile = new File("phenotype_annotation.tab");
try {
  HpoDiseaseAnnotationParser parser = new HpoDiseaseAnnotationParser(inputFile);
  while (parser.hasNext()) {
    HpoDiseaseAnnotation anno = parser.next();
    // work with anno
  }
} except (IOException e) {
  System.err.println("Problem reading from file.");
} except (TermAnnotationException e) {
  System.err.println("Problem parsing file.");
}

The phenotype-to-gene annotation file can be parsed as follows.

File inputFile = new File("phenotype_annotation.tab");
try {
  HpoDiseaseAnnotationParser parser = new HpoDiseaseAnnotationParser(inputFile);
  while (parser.hasNext()) {
    HpoDiseaseAnnotation anno = parser.next();
    // ...
  }
} except (IOException e) {
  System.err.println("Problem reading from file.");
} except (TermAnnotationException e) {
  System.err.println("Problem parsing file.");
}