allow ISS annotation in admin mode

[ValWood]

Curating a paper today with @CuzickA

There was some bioinformatics analysis demonstrating that A9JX75_PHANO is a likely chitin binding protein with various evidences.

We haven't needed to do this in pombase because (almost) all our ISS's are usually done already in Artemis (in fact we are usually removing them, as EXP evidence becomes avaiable rather them adding them).

That said, once we stop adding non-experiemntal data in Artemis we will also need this functionality for PomBAse.

We don't want this available for users because largely we only really want users to make annotations based on experimental evidence ( @CuzickA agrees the same for PHIBase too), but occasionally there will be a strongly supported ISS annotation and we can add this in admin mode.

[kimrutherford]

I've changed the code to support this.

@jseager7 you'll need to add this to each of the GO annotation types in the canto_deploy.yaml:

     admin_evidence_codes:
       - ISS

For example:

   - name: molecular_function
     category: ontology
     abbreviation: F
     very_short_display_name: 'function'
     short_display_name: 'molecular function'
     display_name: 'GO molecular function'
     feature_type: 'gene'
     can_have_with: 1
     evidence_codes:
       - IDA
       - IGI
       - IMP
       - IPI
       - EXP
     admin_evidence_codes:
       - ISS
...

[kimrutherford]

Val, which evidence codes should I add for pombe? Just ISS?

[ValWood]

ISS, ISM and ISO (in fact we should probably use only ISO and ISM, which are more specific than ISS)

we will need to allow free text for the "with" field because I usually use SGD: but can be UniProt: or Interpro:/Pfam: for ISM

[kimrutherford]

we will need to allow free text for the "with"

I've opened a separate issue for that: #1857

Is allowing ISS, ISM and ISO not helpful if you can't put free text in the "with" field?

[ValWood]

no because it won't be a valid GO annotation. ISS isn't allowed without "with"

[kimrutherford]

OK. Allowing free text for "with" is going to take longer than adding admin-only evidence codes.

@jseager7 don't worry about changing the configuration yet. It's not useful until #1857 is done.

[ValWood]

I have 'stolen' this from James and assigned to Kim.

Because we removed the ability to curate in Artemis this is now higher priority for PomBase than for PHI-base. I make quite a lot of annotations this way. we would also need a way to do this using GO_REF:0000024

It isn't super urgent as I can make the annotations in the new tab-delimited file but I suspect that curating a 17 column format like this might be a bit tedious.

[kimrutherford]

How awful would it be to add these non-pombe withs in the extension internal with a new admin-only extension like?:

  with_external_id(SGD:0000001)

This could be done with a configuration change.

[mah11]

Fine with me, but maybe I shouldn't be the deciding factor ...

[ValWood]

Fine with me too, but don't worrry immediately, because most of these ISS/O annotations have GO_REF:0000024 so they can't be done in Canto anyway.

I'll see how I go on with the flat-file for a while and keep this on the radar.