Closed colleenXu closed 1 year ago
The primary code changes would be in knowledge_graph.js, with some code in the query_graph_handler index.js to pass the API_LIST in.
@tokebe are you available to test Rohan's PRs to see if the issue is addressed?
This issue is related to the Translator priority of "having primary_knowledge_source
set for each Edge". I'll review @rjawesome's PRs ASAP.
First, I'll list my review of the current main-branch behavior:
primary_knowledge_source
(see screenshot below). So I'll be checking if this is fixed with the PRs. source
property in its x-bte annotation that's assigned as the primary_knowledge_source
(dbsnp) while litvar itself is listed as an aggregator_knowledge_source
(see screenshot below). So I'll check the behavior with the PRs and probably remove the "primary knowledge source" tag for Litvar.primary_knowledge_source
(see screenshot below). So I'll be checking if this is fixed with the PRs.Deployed to prod 🚀
I'm not sure that primary_knowledge_source is marked on all Edges. These are missing it...
MESH:C006303
-> Gene), I see that BTE isn't assigning CTD as the primary source. This is happening for all instances + my local instance (all main branches). This is related to this PR as wellClosing in favor of https://github.com/biothings/biothings_explorer/issues/627
When @tokebe and I were reviewing the PR for issue #463 , we noticed some issues with older code.
This code was meant to address "situation C": non-TRAPI apis that are generating knowledge/inferred-associations from data and should therefore be labeled as "primary knowledge sources". They also do not provide their edge-attributes in TRAPI format (if the ydid, we could ingest their edge-attributes the same way we ingest edge-attributes from TRAPI APIs).
The desired refactoring is:
kgEdge.inforesCuries
(is this the infores of the API?) should be put into the value of a "primary knowledge source" edge-attribute along with thekgEdge.sources
. Then there's a separate "aggregator knowledge source" edge-attribute withinfores:biothings-explorer
as the value.~Related: we want to discuss with @andrewsu if a BioThings API of a primary knowledge source then also counts as a primary knowledge source (maybe it doesn't because of the parsing / organizing of the data that happens?).~
Discussed with Andrew 2023-01-23. He said this is correct, that BioThings APIs usually are NOT primary knowledge sources because of the parsing / organizing of data that is done. So the small list above is correct (we only want those labeled as primary knowledge sources).
Many BioThings APIs may be in this situation, like
* BioThings BindingDB * BioThings GTRx * BioThings Rhea * BioThings SEMMEDDB * BioThings DDInter * BioThings iDISK * BioThings pfocr * DISEASES