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geneontology
A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
A couple of issues come up when trying to search GO-CAMs on the GO site. https://geneontology.cloud/browse 1. For some organisms: c.elegans, D.mel, there is not a valid DBxref for the...
Create a GO-CAM -> TSV file for end user consumption. This could fill the ecological niche of our previous SIF effort. TBD: - [ ] is this a one-off, or...
We have a user that is trying to cross-reference >1000 Reactome terms to GO, and cannot find some of these in the reactome2go: http://current.geneontology.org/ontology/external2go/reactome2go. The list includes - degradation of...
Currently, species information can be found in multiple locations. Off the top of my head: metadata/datasets/*.yaml['species_code'] ./scripts/downloads-page-gen.py ./metadata/go-reference-species.yaml Until these are aligned, I'll be tagging fixes for issues around this...
discussed on GO PIs call This issue is resolved by making a PR on xrefs.yaml where the gene redirects go to the Alliance, not the MOD Note: uniprot is unaffected.
[prefixmaps](https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/ingest/ingest_go.py) uses: https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml to retrieve the `rdf_uri_prefix` for its mapping of genes and gene products in use at GO. The official expansions in the db-xrefs.yaml `rdf_uri_prefix` field are sometimes different...
- do the generic_urls (http://flybase.org -> https://www.alliancegenome.org/members/flybase ?) also need to be changed? 796 1559 2320 2331 2331 2755 2862 2904 - 1566 1572 are the MGI:MGI and may not...
Spawned off of #847: Need to review the Annotation Downloads (bottom of geneontology.github.io/_docs/download-go-annotations.md, which links to http://current.geneontology.org/products/pages/downloads.html) and remove unneeded entries
The following yamls are missing at least one species_code, and probably should have them: cgd.yaml ecocyc.yaml genedb noctua paint Sounds like /scripts/downloads-page-gen.py is looking for this line and hoping it's...
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Metadata
A collection of metadata, tools, and files associated with the Gene Ontology public web presence.