Clean up SynGO metadata and reimport into production and development branches of noctua-models

[kltm]

Currently, there are some SynGO models that use a "SYNGO" namespaced identifier for contributors. These models should be purged from our system by:

• [ ] ensuring that all SynGO curators are in the users.yaml file
• [ ] ensuring that all SynGO curators are properly marked as GO Noctua editors
• [ ] upgrade all SYNGO identifiers in models to their appropriate ORCID

See https://github.com/geneontology/noctua/issues/658#issuecomment-614942166 for originating thread.

Tagging @dustine32

This time around, it might be good to see if the SynGO models pass ShEx. I'd like to see the "main" ShEx (or elsewhere) contain shapes that describe our metadata rules as well, such as kinds of allowed contributors (this), correct timestamping, etc.

[dustine32]

Thanks @kltm ! I'll get the list of SynGO curators (name, ORCID) from the latest annotation JSON.

[dustine32]

Here's the list of ORCIDs from the annotation JSON:

http://orcid.org/0000-0002-0269-0311
http://orcid.org/0000-0002-9681-3318
http://orcid.org/0000-0002-5676-366X
http://orcid.org/0000-0002-2094-7491
http://orcid.org/0000-0002-2666-0758
http://orcid.org/0000-0003-0575-6950
http://orcid.org/0000-0002-5265-6306
http://orcid.org/0000-0002-1558-1958
http://orcid.org/0000-0003-0912-1514
http://orcid.org/0000-0001-7806-5662
http://orcid.org/0000-0003-3185-5709
http://orcid.org/0000-0002-2514-0216
http://orcid.org/0000-0001-9783-5183
http://orcid.org/0000-0002-1585-539X
http://orcid.org/0000-0002-0808-7003
http://orcid.org/0000-0002-7620-2704
http://orcid.org/0000-0002-3670-7863
http://orcid.org/0000-0002-5615-1014
http://orcid.org/0000-0003-2533-9548
http://orcid.org/0000-0003-0662-9523
http://orcid.org/0000-0002-1190-4481
http://orcid.org/0000-0001-7351-8706
http://orcid.org/0000-0002-8862-2562
http://orcid.org/0000-0002-9900-4233
http://orcid.org/0000-0001-9377-7414
http://orcid.org/0000-0003-2949-9725
http://orcid.org/0000-0003-1542-3498
http://orcid.org/0000-0001-5259-4945
http://orcid.org/0000-0002-0755-5899
http://orcid.org/0000-0001-5518-6584
http://orcid.org/0000-0001-9425-2935
http://orcid.org/0000-0002-3898-5197
http://orcid.org/0000-0002-9848-0262
http://orcid.org/0000-0002-4419-210X
http://orcid.org/0000-0002-9880-1214
http://orcid.org/0000-0003-0938-8534
http://orcid.org/0000-0002-4973-5732
http://orcid.org/0000-0003-0593-3443
http://orcid.org/0000-0002-6153-3586

No names are provided in the JSON (probably a good thing) but all 39 of these are already in users.yaml. @kltm Shall I go ahead and PR users.yaml with noctua-edit permissions added for these?

[kltm]

I'd like to confirm with @vanaukenk that we're happy with this path first--that's a lot of "official" curators to add and give full access to the system at once--but yes, that is the plan.

[kltm]

@dustine32 And as a note, I'd model the permissions for allow-edit as here: https://github.com/geneontology/go-site/blob/c75ccb9858e3944446491ec34340a378ee036945/metadata/users.yaml#L70

[dustine32]

@kltm OK, great, I'll hold!

Looking at that allow-edit example made me wonder if anything will choke if we add allow-edit but the users don't have anything in accounts:? Ex:

-
  authorizations:
    noctua:
      go:
        allow-edit: true
  groups:
    - 'https://syngo.vu.nl'
  nickname: 'Arthur de Jong'
  organization: 'Kaeser Lab, Department of Neurobiology, Harvard Medical School, Boston, USA'
  uri: 'http://orcid.org/0000-0002-7620-2704'

[kltm]

@dustine32 Hey, that's a great point and may actually be a perfectly fine workaround. Essentially, while they are authorized editors, they have no practical way of logging into the system. Problem solved. Now, that said, I'm not actually sure what the schema and sanity checkers will think of that, but I think we should probably pass the buck to them. I would feel comfortable that you can start a branch/PR for these changes--worse case is we'll revisit them later with modification.

[dustine32]

Sounds fun! Here's the PR https://github.com/geneontology/go-site/pull/1467

[vanaukenk]

Next step: contact SynGO to see what their plans/expectations are for future curation in Noctua to decide how best to handle an update of SynGO-related metadata.

[pgaudet]

We do have a process, drop and relload their json file @vanaukenk @dustine32 can we close this?