Metric : Total genes in GO CAM models

pombase / pombase-chado

PomBase code for accessing Chado

MIT License

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Metric : Total genes in GO CAM models #1176

Closed ValWood closed 3 months ago

ValWood commented 4 months ago

It would be nice once you have figured out the "Shrec turtles" to have a simple metric

"number of genes in models"

It will motivate us! Aiming for 1000 by the end of the grant, (but I think that might be a bit optimistic, because we are doing the low hanging fruit first)

kimrutherford commented 3 months ago

It's not quite what you asked for, but I've added the code to the query system to allow querying for genes that are in models.

On my desktop I have a "Genes in GO-CAM models" in the commonly used queries list in the advanced search.

This could be added to pombase.org at any time with a config change.

ValWood commented 3 months ago

This. is a good start. Remind me what the process is for production models to get into pombe (if you know). do we get them after a Noctua update, or after a GO update?

kimrutherford commented 3 months ago

Remind me what the process is for production models to get into pombe (if you know). do we get them after a Noctua update, or after a GO update?

Currently we have to manually edit these files:

pombe-embl/supporting_files/production_gocam_id_mapping.tsv (model ID to gene ID mapping)
pombe-embl/supporting_files/production_gocam_term_id_mapping.tsv (model ID to process term mapping)

But I've been working today on automating the update of the files using:

http://snapshot.geneontology.org/products/upstream_and_raw_data/noctua_pombase.gpad.gz which has the pombe GO-CAM IDs and the genes in the models
API https://api.geneontology.org/api/go-cam/{ID} to get the process terms and model titles

kimrutherford commented 3 months ago

This number should increase to 160 tomorrow:

And there will be 15 models in PomBase.

ValWood commented 3 months ago

Excellent CC @PCarme

kimrutherford commented 3 months ago

This number should increase to 160 tomorrow:

kimrutherford commented 3 months ago

"Genes in GO-CAM models" is now available from the commonly used queries list on pombase.org.

Is the wording "Genes in GO-CAM models" OK? It was the first thing I thought of. Let me know if you have any suggestions for improving it.

ValWood commented 3 months ago

Let's say "genes in GO-CAM pathway models"

kimrutherford commented 3 months ago

Let's say "genes in GO-CAM pathway models"

That's done now.

Is there anything else to do here?

ValWood commented 3 months ago

nope