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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
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Noctua organism list #597

Open sandyl27 opened 5 years ago

sandyl27 commented 5 years ago

During the multiorganism meeting this week, we discussed allowing all SwissProt proteins to be avaliable in the form editor in Noctua.

There still needs to be more discussion on Trembl proteins.

@cmungall @jimhu-tamu @jrr-cpt

jrr-cpt commented 5 years ago

@cmungall This came up in the multiorganism working group. It is also relevant for a couple phage GO-CAM/Noctua models @sandyl27 and I are building. Can we have a set of lambda proteins added so that our models can be edited using the form? The lambda reference proteome is here: UP000001711.

@jimhu-tamu

cmungall commented 5 years ago

OK, looks like 61/66 are in swissprot/reviewed, so when we take care of swissprot loading #35 then you should be mostly covered - how important is it for you to have the remaining 5 (it wouldn't be massively hard to have an extra load for selected proteomes but I prefer to keep it simple)

sandyl27 commented 5 years ago

I just looked at the 5 unreviewed and I don't think we will be needing them!

jrr-cpt commented 5 years ago

As per latest multi-organism working group meeting, we should provide the list of desired proteins as a GPI (preferred) file until the load of all Swiss-Prot entries occurs.

Under gene-ontology/go-site/metadata/datasets/

@sandyl27 @jimhu-tamu our group will use gonuts.yaml

vanaukenk commented 2 years ago

It would be helpful to have in our general Noctua documentation a list and/or link of all organisms available for annotation.