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opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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PATRIC gene IDS #669

Closed mjenior closed 5 years ago

mjenior commented 5 years ago

Are there any plans to expand the list of gene annotation databases to include PATRIC ID namespace in future versions?

Midnighter commented 5 years ago

A prerequisite for that would be the inclusion of PATRIC at https://registry.identifiers.org/ which hasn't happened as far as I can tell. (Please correct me if I'm wrong.) In general, including namespaces is a trivial task as long as there is evidence that the COBRA community uses that namespace.

mjenior commented 5 years ago

Totally agree, I don't think it really matters. It's only in the interest a greater level of inclusion for scoring models in MEMOTE if the quality metrics it reports catch on as standards in the field. PATRIC's automated reconstruction tools provide decent starting draft reconstructions, so I would expect those annotations to be used with some frequency.

Just a thought, so I will go ahead and close the issue.

Midnighter commented 5 years ago

Alright, maybe you can push for inclusion of PATRIC at identifiers.org. It's a pretty easy process I think.

mjenior commented 4 years ago

Ok great! I'll check it out and create a pull request.