Comments (4)
goodb
commented on September 24, 2024
@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.
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kltm
commented on September 24, 2024
I'm not sure if this has happened; tagging @cmungall
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goodb
commented on September 24, 2024
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.
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dustine32
commented on September 24, 2024
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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Related Issues (20)
- Update extension validation rules TSV
- Update extension validation rules for acts_o_population_of HOT 3
- Create test files for additional annotation metadata HOT 31
- No extension is an island HOT 4
- Resolve Shex failures in MGI annotations due to invalid identifiers for binding input HOT 38
- add taxon metadata for each model HOT 5
- Create test files for WB import HOT 12
- Write translated models out in N-Quads format HOT 1
- Proteoforms shouldn't be split into separate models HOT 14
- Handle pipe-separation in translation of with/from field HOT 1
- Handling interacting taxon data
- Add date and contributor to ALL annotation individuals? Not just evidence and Axiom? HOT 4
- Emit comment in annotation properties HOT 1
- Collapse comma-delimited objects of chain relations
- Add providedBy to all individuals HOT 2
- Add gene symbol to model title HOT 14
- Param to set modelstate HOT 1
- Comment missing some text from the GPAD HOT 1
- Set import model states to production so annotations are in GPAD outputs from dev HOT 5
- Processing annotation contributors for multiple GPAD lines with single annotation id HOT 5
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