exactMatch in MONDO

[pnrobinson]

Currently, phenol does not pull in "exactMatch" as used in MONDO. This is important to get exact OMIM matches.

It looks like the information is contained in the Node/Meta object from obographs. See org.monarchinitiative.phenol.io.obo.OboGraphTermFactory, line 35.

Meta meta = node.getMeta();

The meta object has a lot of information that can be accessed via

meta.getBasicPropertyValues()

See

Phenol does not currently capture this, but we could.

I would suggest we do so in a Dbxref object. For the above example, the MONDO term is MONDO:0002974, label="cervical cancer". The meta field of this term (from obographs) has a map "basicPropertlyValues". The term also has an xrefs list, one of whose values is NCIT:C9311.

Therefore, the question is what we map this to in phenol.

[pnrobinson]

@julesjacobsen Do you have an opinion about where to put the exactMatch property? The Term class in phenol is somewhat constrained and does not map 1:1 to the Node/Meta object from obographs. We should either extend the Term class to have basicPropertyValues or we would have to add this as an Xref or something like that.

[pnrobinson]

Probably related to https://github.com/monarch-initiative/phenol/issues/215

[pnrobinson]

This is working now. I added a test class "OntologyLoaderMondoTest", e.g.,

@Test
  void testGetExactSynomym() {
    Term maxillofacialDysostosis = mondo.getTermMap().get(TermId.of("MONDO:0007952"));
    List<TermSynonym> synonymList = maxillofacialDysostosis.getSynonyms();
    assertEquals(1, synonymList.size());
    TermSynonym syn = synonymList.get(0);
    assertEquals(TermSynonymScope.EXACT, syn.getScope());
    System.out.println(syn);
    List<TermXref> xreflist = syn.getTermXrefs();
    assertEquals(1, xreflist.size());
    TermXref xref = xreflist.get(0);
    assertEquals(TermId.of("OMIM:155000"), xref.getId());
  }

[pnrobinson]

I will commit this to develop because I only added a test class and did not change any other code.