search

monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
57 stars 26 forks source link

OMIA uses obsolete disease class #998

Closed cmungall closed 3 years ago

cmungall commented 4 years ago

image

uses this obsolete class http://purl.obolibrary.org/obo/DOID_2214

cmungall commented 4 years ago

https://github.com/monarch-initiative/dipper/blob/fcbe342a7de4a2bf0ef9ce3b0f6daec304461d3b/translationtable/GLOBAL_TERMS.yaml#L80

TomConlin commented 4 years ago

OMIAs string "group_category:4" is what dipper translated to "inherited blood coagulation disease".

I do not find the string "group_category:4" in OMIAs data file directly because it is constructed from parts as the ingest attempts to replicate the functionality of a relational database engine where the '4' is an internal database key for ...

sqlite> select * from  group_category where cat_id = 4;
4|Inherited bleeding disorder

which seem it may map to

"inherited bleeding disorder, platelet-type" http://purl.obolibrary.org/obo/MONDO_0000009

although the appending of the ", platelet-type" suffix implies alternative exist but I do not see them in MONDO.

TomConlin commented 4 years ago

noting this solution has been sitting in the omia local translation table commented out for the last couple of years with the question; is the MONDO term too specific.

https://github.com/monarch-initiative/dipper/blob/79c9735f0120d0309ab446d9f9a93e2d88f4a0e3/translationtable/omia.yaml#L41

kshefchek commented 3 years ago

fixed with #999