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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Update all models with Assigned_by GO_Noctua to correct Assigned_by value #614

Open vanaukenk opened 5 years ago

vanaukenk commented 5 years ago

Hi,

In looking over some annotation stats with @pgaudet and @ukemi this morning, we found that there are still some production GO-CAM models that have GO_Noctua in the Assigned_by field of the output GPAD.

These annotations need to be converted to have the correct Assigned_by field.

The actual GPAD lines are in this spreadsheet:

https://docs.google.com/spreadsheets/d/1zE_zH3g0XHO6C7tJ-j7eKnwjwpMuOe6TCzPt1qB06Zc

Here's a summary of annotations and actions. @kltm - let me know if you want to touch base about any of this.

MGI - 1 line Action: Update Assigned_by to MGI

PR - 5 lines Action: Update Assigned_by to MGI Update contributor=GOC:krc -> contibutor=http://orcid.org/0000-0001-5501-853X

Zfin - 56 lines Action: Update Assigned_by to ZFIN

Also tagging @sabrinatoro so she's in the loop about these updates.

kltm commented 5 years ago

Previously, we've done data store "migrations" via queries provided by @balhoff by shutting down the store, running transforms on the quite store, dumping files to disk, rebuilding store from the models, restarting system. No steps hard, but a little time and some canned queries needed.

@vanaukenk Do you think it's likely that there will be some other things like this coming up or should we go ahead and do this earlier rather than later?

vanaukenk commented 5 years ago

@kltm - we could take another look at the Assigned_by field for all production models, just to be sure, before we make the changes. For development models, I'm not sure we need to do anything at this point, since a number of those models probably can just be deleted anyway.

kltm commented 5 years ago

@vanaukenk Perhaps we could use http://geneontology.org/go-cam or get a custom query from @dougli1sqrd ?