Comments (11)
@cmungall Should we derive here or work with SGD to provide a better source for us?
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I think right now we should remove the gpi entry from sgd.yaml. neo will fall back on the GAF. Which is good enough for a well-annotated genome for SGD.
After that we can try another solution. SGD provide a BGI for the Alliance, providing a GPI should not be hard and we can have some shared conversion code.
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Sounds like there's a plan? Let me know if there's something SGD specifically needs to do. Thanks
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@cmungall geneontology/go-site#953 correct?
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Merged and waiting for effect over the weekend.
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Update: No sgd Noctua gpad, but our existing annotations to Uniprot accessions are being rejected in the Form summary page (good I suppose) and SGD IDs are autofilling in. What steps do we need to take now to get a Noctua gpad?
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Well, if the IDs are SGD, the next time the models are reduced to GPADs in the pipeline they should come out naturally (assuming everything else is okay).
If I'm missing the answer you're wanting, feel free to tag me and we can get some of the others to take a look at it.
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next time the models are reduced to GPADs in the pipeline
This is a "daily/24h" occurrence or you mean the monthly release?
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This is a daily occurrence, which should be completed sometime in the evening, every day. The pickup location is the snapshot
set of URLs, but progress can be seen here:
https://build.geneontology.org/job/geneontology/job/pipeline/job/snapshot/
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Thanks for the info, I'll bet we missed today's cutoff. We'll check it later. Thanks!
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ah well it looks like this is fine now
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Related Issues (20)
- Add some minimal QC to the NEO pipeline HOT 14
- Some Reactome Identifiers are not resolving HOT 11
- NEO GOlr / Solr load does not use "modern" loader, so does not build all closures for "modern" AmiGO
- Xenbase entities do not seem to propagate to the NEO build from the Xenbase GPI HOT 6
- Would like phage proteins to be available HOT 2
- Request to load more phage proteins HOT 2
- Many ChEBI chemicals not available for metabolic models HOT 17
- Isoform display in label (originally on the visual tool) HOT 4
- Clarify and implement rules on inclusion of RNA gene products / RNA central HOT 4
- RNAcentral IDs incorrectly use OBO PURL namespace HOT 5
- Some IDs we expect are not found in Noctua HOT 5
- Transient Xenbase issue dropped GPI file HOT 1
- unresolved IDs HOT 10
- Xenbase identifiers are not correct getting labels (in NEO?) HOT 5
- Some e.coli entries not found HOT 18
- In some cases bad identifiers are getting into the load HOT 5
- Ecoli data is gone from NEO as the upstream source changed HOT 13
- add additional species names to gene labels HOT 5
- Add FB Developmental and Anatomy Ontology HOT 14
- Unknown reduction in entities in NEO build HOT 15
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