add additional species names to gene labels

geneontology / neo

noctua entity ontology

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add additional species names to gene labels #116

Open balhoff opened 1 year ago

balhoff commented 1 year ago

See https://github.com/geneontology/go-site/issues/1955#issuecomment-1529033344

pgaudet commented 9 months ago

Species names are still not being displayed in Noctua.

For example, Taxon:42789 & model: http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A6494e2e900000134

balhoff commented 9 months ago

This seems to be controlled by the script https://github.com/geneontology/neo/blob/master/gpi2obo.pl. When it is called by the Makefile, a species code needs to be passed to be appended to the gene product name. There seems to be some unfinished work related to handling virus names here:

https://github.com/geneontology/neo/blob/b1a10399234c2638250286f8434093e494ccc100/Makefile#L41-L68

kltm commented 9 months ago

(Quiet shoutout to https://github.com/geneontology/project-management/issues/52)

pgaudet commented 8 months ago

Trying to quote @kltm

How the data gets in:

takes the GPI file, and convert it into an obo and load it
the GPI files are species-specific and the species 4-letter code is inserted at the processing of the GPI file to .obo.
therefore, GPI files with more than one species cannot include a species code and include the taxon ID

kltm commented 8 months ago

Noting that this seems to be the "next step" referred to in https://github.com/geneontology/neo/issues/77. Essentially, we stopped there before getting to this point.

pgaudet commented 3 weeks ago

Right now there is a single file per file - so this is complicated to load