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RobokopU24 / Feedback

Feedback on the ROBOKOP project
https://robokop.renci.org
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primary/original knowledge source #112

Closed cbizon closed 1 year ago

cbizon commented 1 year ago

One of these has been deprecated in biolink. Remove it and replace with the other.

EvanDietzMorris commented 1 year ago

This should have been done a long time ago.. is there an example of original knowledge source in a recent graph?

cbizon commented 1 year ago

I think that this is recent? /projects/stars/Data_services/biolink3/graphs/RobokopPlus/2d06121815f417d7

{"subject":"CAID:CA11116955","predicate":"biolink:is_nearby_variant_of","object":"NCBIGene:5861","biolink:original_knowledge_source":"infores:snpeff","distance_to_feature":89756,"id":"5c665f00c306186c"}
{"subject":"CAID:CA285456728","predicate":"biolink:is_nearby_variant_of","object":"ENSEMBL:ENSG00000260858","biolink:original_knowledge_source":"infores:snpeff","id":"94ee3df6adb639a0"}
{"subject":"CAID:CA270988704","predicate":"biolink:is_nearby_variant_of","object":"NCBIGene:645693","biolink:original_knowledge_source":"infores:snpeff","distance_to_feature":96414,"id":"12383498534f23f6"}

Seems like it's only snpeff since grep original_knowledge_source edges.jsonl | grep -v snpeff doesn't return anything.

EvanDietzMorris commented 1 year ago

It looks like this was already fixed but we are still using an old version of the GWAS Catalog (due to EFO terms being missing from the node normalizer) which includes the old format still. It is possible to re-process the SNPEFF/supplementation stage for gwas catalog to fix this for the next graph release, if we don't expect to be able to normalize the gwas catalog soon.

cbizon commented 1 year ago

Discusssed 3/15, on track to be complete 3/17

EvanDietzMorris commented 1 year ago

this should be fully fixed in all current graphs