Erica Wood
Erica Wood
Also, see: https://github.com/RTXteam/RTX/issues/2290
The bad edges comes from SemMedDB, which is a KG2 problem
Running ``` match (n)-[e]-(m) where n.id in ["CHV:0000001598", "CHV:0000050438", "DOID:0060041", "DOID:12849", "EFO:0003756", "EFO:0003758", "HP:0000717", "HP:0000729", "ICD9:299.0", "MESH:D000067877", "MESH:D001321", "MONDO:0005258", "MONDO:0005260", "NCIT:C88412", "NCIT:C97161", "OMIM:209850", "OMIM:MTHU004240", "OMIM:MTHU038054", "OMIM:MTHU043125", "OMIM:MTHU043132", "PSY:04850", "PSY:04855", "UMLS:C0004352",...
I'm not sure what to do about `SEMMEDDB:TREATS`, since it is mapped in Biolink to a mixin. ``` + /home/runner/kg2-venv/bin/python3 -u -u /home/runner/work/RTX-KG2/RTX-KG2/RTX-KG2/validate_predicate_remap_yaml.py /home/runner/work/RTX-KG2/RTX-KG2/RTX-KG2/curies-to-urls-map.yaml /home/runner/work/RTX-KG2/RTX-KG2/RTX-KG2/predicate-remap.yaml https://raw.githubusercontent.com/biolink/biolink-model/v4.2.0/src/biolink_model/schema/biolink_model.yaml /home/runner/kg2-build/biolink_model.yaml /home/runner/kg2-venv/lib/python3.7/site-packages/rdflib_jsonld/__init__.py:12: DeprecationWarning: The...
> For `SEMMEDDB:administered_to` and `SEMMEDDB:ADMINISTERED_TO`, I favor the more generic `biolink:treats_or_applied_or_studied_to_treat` since I suspect a lot of edges picked up by SemMedDB will actually be investigational (i.e., "we tried administering...
Per my meeting with Steve today, I should add an exception for `SEMMEDDB:administered_to` and `SEMMEDDB:ADMINISTERED_TO`. I did this in b1d7501.
This seems to be solved in KG2.10.3: Closing.
I think the intention (@saramsey, correct me if I'm wrong) is to switch those edges to `biolink:treats` in the next version of KG2pre if we can tag them as "off...
The "treats" refactor was done before I arrived for the summer, so I am unfamiliar with the details of it. @saramsey likely has more information regarding its execution in KG2pre
> I do note that there used to be DRUGBANK:treats, but it is commented out in predicate-remap.yaml. @ecwood do you know if that is meaning that we are losing out...