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geneontology / go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
http://geneontology.org
BSD 3-Clause "New" or "Revised" License
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Searching issues for Gene Ontology: Causal Activity Models on GO site #2016

Open hattrill opened 1 year ago

hattrill commented 1 year ago

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 entity

Screenshot 2023-05-26 at 09 54 03

Screenshot 2023-05-26 at 09 54 20

When clicking on Gene Products get errors like this:

Resolution request 'wormbase/WBGene00012019' is NOT A NAMESPACE; INVALID Compact Identifier resolution request for 'wormbase/WBGene00012019'

Resolution request 'flybase/FBgn0262582' is NOT A NAMESPACE; INVALID Compact Identifier resolution request for 'flybase/FBgn0262582'

Seems to be ok for mouse.

  1. When searching with a species, it just uses an exact text search e.g. Drosophila -> 1 model ; D.mel -> 7 models Screenshot 2023-05-26 at 09 57 06 Screenshot 2023-05-26 at 09 57 16

Models for species should be retrieved by mapping to the taxon ID for consistency mapping species name/synonyms mapping to Taxon ID in model.

kltm commented 1 year ago

Drawing the eye of @pgaudet . There are some known problems with the GO-CAM (formally http://geneontology.org/go-cam). It has been frozen for some time now, but if fixes are not trivial, maybe we can prioritize one of the projects that would replace it (AmiGO-ization or the replacement widget).