Jim Balhoff

How would you like to define inferred annotations? It's a little complicated since technically every annotation results from an inference process (e.g., even to just infer 'enables' from 'enabled by')....

@tmushayahama @vanaukenk this is becoming urgent, since these changes are starting to propagate through RO and GO.

Here is a [query that gives 440 edges](https://api.triplydb.com/s/YdgJlk62cg). It takes about 40 seconds (so it almost times out with our current settings): ```sparql PREFIX owl: PREFIX rdf: PREFIX rdfs: PREFIX...

Table of 440 results |cam |mf_name |rel_name |bp_name | |----------------------------------------------|--------------------------------------------------------------------------------------------------------------------|-----------------------------------------------|----------------------------------------------------------------------------------------------------------------| |http://model.geneontology.org/568b0f9600000024|DNA-binding transcription repressor activity, RNA polymerase II-specific |negatively regulates |transcription by RNA polymerase II | |http://model.geneontology.org/5666dc6c00000018|DNA-binding transcription repressor activity, RNA...

@pgaudet that's a very good question! I checked the first one to see if it was marked "delete", but it doesn't seem to be.

@pgaudet that model is here: https://github.com/geneontology/noctua-models/blob/master/models/5966411600000233.ttl It's marked "delete" there, so it isn't loaded into Noctua. But that change happened 7 months ago: https://github.com/geneontology/noctua-models/commit/c1415f553f8767d9d35a3ea90d26384dfecba4a2#diff-87d08b64703ef6e9e9b656c1d6ad4d34e7aa4997ab3f2d6a4232d330ab256c9d @kltm could the triplestore be very...

@kltm that model says "development" in the endpoint: https://api.triplydb.com/s/RuwQG_fGT

@kltm I think the "internal" endpoint has a content problem. Compare these queries: - internal: - prod:

When there are multiple ECO codes, according to the spec we can only have one on each GPAD line. Would you want a criterion applied to prefer one over another?...

I think this is the model: http://noctua.geneontology.org/editor/graph/gomodel:SYNGO_2270