cannot import existing annotations from GO database into a GO_CAM

[Pauldenny]

When trying to import existing annotations from GO database for P25051 e.g. these IEAs noctua seems unable to find them.

[Pauldenny]

Kimberley @vanaukenk suggested this issue is a result of AMIGO2 including only EXP annotations for some species - would it be possible for these species to be added to the shortlist for which other non-EXP annotations could be included? I am working on antimicrobial resistance, which can involve many non-reference / non-MOD species:

E. coli [taxID=562] - Not just the K12 MOD Staphylococcus aureus [1280] Klebsiella pneumoniae (High priority organism - WHO GLASS report 2022) [573] Acinetobacter baumanii [470] Pseudomonas aeruginosa - particularly high risk for multi-drug resistance [287] Enterobacteriaceae [543]

NB - the reason for the high-level taxa requested is that many papers use bacterial species further down the taxonomic "tree" and so it's simpler to capture these as they will share a taxonomic parent, rather than try to second-guess an even larger number of more specific taxa?

[pgaudet]

Hi @Pauldenny @vanaukenk correctly identified the issue you are observing - we only have EXP annotations for P25051

https://amigo.geneontology.org/amigo/gene_product/UniProtKB:P25051

I dont think we can load the additional data in the very short term, so you'll have to make that annotation again in Noctua.

WRT strains versus species, I am also in favor of GO central being strain-specific, and moving all 'strain' annotations up to the species. However that involves Uniprot chaning their reference proteomes, as far as I know.

Again, this is on the radar, but it may take a ltitle while to get done. However these use cases are extremely valuable in deciding which way to go.

Thanks for your patience - sorry we cannot help more in the immediate future.

@kltm anything you'd like to add? or correct if I stated anything incorrectly.