Add Biolink preferred prefix

[karafecho]

The Biolink folks recently added MPATH (https://www.ebi.ac.uk/ols4/ontologies/mpath) as a preferred prefix for the class biolink:PathologicalProcess, per request of folks at NIEHS. This issue is to request that we add MPATH to Node Normalizer. Thanks!

[gaurav]

Hi Kara! Do you need all 838 pathological entities in MPATH?

To incorporate these into NodeNorm, it'd be great to get them combined with the existing concept we have -- for example, MPATH:234 "basal cell carcinoma" looks like it should be combined with MONDO:0020804 "basal cell carcinoma" -- unless we want to be really careful about keeping human and non-human concepts separate (thoughts, @cbizon?).

I don't see any mappings in the mpath.obo file, but the MPATH paper claims that they have mappings from a bunch of sources:

From the point of view of application, the most important mappings for MPATH are to the Human Phenotype Ontology (125), the Mammalian Phenotype ontology (111), the Disease Ontology (231), SNOMED-CT (867) and the NCIt (566), reflecting the emphasis on the domain of anatomic pathology rather than disease.)

I'll look through the paper in more detail to see if I can figure out where those mappings are, and if I can't find them I'll contact the authors.

[karafecho]

Hi Guarav - The entities that NIEHS folks are mapping are pathological findings in rodents, so not disease per se, although they do map to MONDO when an entity does not map to MPATH. I agree with the authors of the MPATH paper, that any mappings should reflect an emphasis on the domain anatomic pathology rather than disease. Here are a few examples:

Morphology and Incidence | Morphology Ontology Link (or ID) | Morphology Ontology | Morphology (Original Term)

hepatocellular adenoma (0/50, 1/49, 0/50, 3/50, 8/49); hepatocellular carcinoma (1/50, 0/49, 0/50, 0/50, 3/49); hepatocellular adenoma or carcinoma (combined) (1/50, 1/49, 0/50, 3/50, 11/49) | http://purl.obolibrary.org/obo/MPATH_353 | Hepatocellular adenoma | Hepatocellular adenoma

hepatocellular adenoma (0/50, 1/49, 0/50, 3/50, 8/49); hepatocellular carcinoma (1/50, 0/49, 0/50, 0/50, 3/49); hepatocellular adenoma or carcinoma (combined) (1/50, 1/49, 0/50, 3/50, 11/49) | http://purl.obolibrary.org/obo/MPATH_357 | Hepatocellular carcinoma | hepatocellular carcinoma

acinar adenoma (10/50, 7/49, 8/50, 36/50, 22/49); acinar carcinoma (0/50, 0/49, 0/50, 3/50, 1/49); acinar adenoma or carcinoma (combined) (10/50, 7/49, 8/50, 38/50, 22/49) | http://purl.obolibrary.org/obo/MPATH_270 | Adenoma | acinar adenoma

Happy to chat, if that would be helpful.