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fix ontology term URIs #22

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goodb opened this issue Jan 31, 2019 · 4 comments
Closed

fix ontology term URIs #22

goodb opened this issue Jan 31, 2019 · 4 comments
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@goodb
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goodb commented Jan 31, 2019

GO terms used in exported ttl
use an identifier.org uri like http://identifiers.org/GO:0000302

they should always be using purls like
http://purl.obolibrary.org/obo/GO_0000302

@goodb
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goodb commented Jan 31, 2019

@kltm I'm making an assumption that the URIs we see in the Noctua-generated models are what we want to see. e.g. http://www.wormbase.org/db/gene/gene?name=WBGene00004055 for a worm gene class (assuming in neo). Thats correct right, we can't just use identifiers.org e.g. @dustine32 currently has @prefix WB: <http://identifiers.org/wormbase/> which I think is wrong.

@kltm
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kltm commented Jan 31, 2019

I'm not sure if this has happened; tagging @cmungall

@goodb
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goodb commented Jan 31, 2019

Based on what is coming out of noctua (prod) not noctua-dev, the identifiers.org pattern seems correct for the gene products, e.g. http://identifiers.org/mgi/MGI:108078 . But, definitely need to use the purls for ontology classes and relations.

@dustine32
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Commit 7577d7d hooks up the ontobio URI expander, which uses go_context.jsonld. This appears to fix the gene product (e.g. http://identifiers.org/mgi/MGI:2444777), ontology class (e.g. http://purl.obolibrary.org/obo/GO_0045132), and relation (e.g. http://purl.obolibrary.org/obo/BFO_0000050).

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