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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Filtering by gene does not return Reactome models #121

Closed ukemi closed 2 years ago

ukemi commented 3 years ago

When filtering by gene, Reactome models are not returned. It doesn't matter whether the GP acts as a monomer or in a complex. @deustp01 @vanaukenk

Example: MANBA Hsap should return gomodel:R-HSA-8853383 from instance Instance: gomodel:R-HSA-8853710

goodb commented 3 years ago

This is because of the use of gene classes from the REACTO ontology (subclasses of Neo entities). The search could be adapted to traverse to the gene ids. tagging @tmushayahama

vanaukenk commented 2 years ago

This issue came up again during @pmasson55 's presentation at the 2012 Fall GOC meeting.

He was trying to search for human MICAL1 using the UniProtKB accession Q8TDZ2 to retrieve the corresponding Reactome model: http://noctua.geneontology.org/editor/graph/gomodel:R-HSA-983231 but the search doesn't work because MICAL1 is represented as a REACTO complex with FAD.

@tmushayahama would it be possible to update the gene product search from the Noctua landing page to also find the UniProtKB accessions for gene products that are part of the REACTO ontology? What work would we need to do?

Thx.

dustine32 commented 2 years ago

@vanaukenk Heh, just made this minerva model search API ticket like 5 min ago: https://github.com/geneontology/minerva/issues/430

dustine32 commented 2 years ago

@vanaukenk Oh, just saw you already referenced it. Thanks! I blame the lag on how many tabs I have open :)

vanaukenk commented 2 years ago

No worries @dustine32 - awesome that you're already on it!

vanaukenk commented 2 years ago

This is a duplicate of https://github.com/geneontology/minerva/issues/430 where I think the work would actually need to be done, so I'm closing this ticket.