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geneontology / neo

noctua entity ontology
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RNAcentral IDs incorrectly use OBO PURL namespace #100

Closed balhoff closed 2 years ago

balhoff commented 2 years ago

I believe this is the cause of ShEx violations caused by missing root types, noted here: https://github.com/geneontology/neo/issues/99 https://github.com/geneontology/minerva/issues/481

kltm commented 2 years ago

@balhoff Regarding https://github.com/geneontology/neo/pull/101 What is a positive or negative test we can use to prove that this worked when we go for our next update?

balhoff commented 2 years ago

@kltm after this change, NEO should no longer contain a term http://purl.obolibrary.org/obo/RNAcentral#_URS000229B2C9_9606. It should now contain a term http://rnacentral.org/rna/URS000229B2C9_9606.

kltm commented 2 years ago

Some browsing on early products seems to essentially confirm that the change is in place:

$ zgrep -a "URS000229B2C9_9606" blazegraph-go-lego-reacto-neo.jnl.gz | grep -a -c purl
0
$ zgrep -a "URS000229B2C9_9606" blazegraph-go-lego-reacto-neo.jnl.gz | grep -a -c rnacentral
1
kltm commented 2 years ago

Can close once in production (Thursday, if no incident) so that other issues know to revisit.

kltm commented 2 years ago

This should be out.