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The PomBase community curation tool
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user interface: populate gene names when known from a previous session (curation streamlining and speed increase)) #219

Closed pombase-admin closed 5 months ago

pombase-admin commented 12 years ago

This isn't urgent as it wont usually affect users so much, but it would be nice if a paper has been annotated previously, that the names appeared in the gene names box (at present I usually just add a single "random" name, as when I get to the session, most of the names will be there....

Original comment by: ValWood

pombase-admin commented 12 years ago

This will be quite quick to do as most of the code is in place already.

Original comment by: kimrutherford

pombase-admin commented 11 years ago

This might speed things a little the names which are prepopulated should include i) genes from a previous curation (even from Artemis) ii) genes from BioGRID annotation if this isn't easily possible will reconsider priority

Original comment by: ValWood

ValWood commented 5 years ago

Action If any genes are already associated with a session in Chado (via artemis or biogris), prepopulate the session

ValWood commented 6 months ago

sources of "known genes"

  1. Publication keywords (will need to ignore if it has a synonym match, unless can be resolved by bioGRID)
  2. Structure (should be able to map exactly using uniprot ID)
  3. Previous (legacy) annotation - precise using the systematic ID
kimrutherford commented 6 months ago

Structure (should be able to map exactly using uniprot ID)

This needs a little bit of work first. The genes and PMIDs from PDB aren't loaded into Chado at the moment because there isn't a clean way to store things like method, resolution and chain. The PDB details are in this file: https://curation.pombase.org/dumps/latest_build/pombe-embl/external_data/protein_structure/systematic_id_to_pdbe_mapping.tsv (pombe-embl/external_data/protein_structure/systematic_id_to_pdbe_mapping.tsv in SVN) Those details are processed when Chado is processed to make the website. So first step is to load at least the gene to PMID mapping from PDB into Chado. I've made a separate issue about this:

kimrutherford commented 6 months ago

I have a prototype of this running on my desktop.

image

Unfortunately it dumps you straight into the Canto front page without asking for more genes. Fixing that will take a bit of thought. Canto only prompts for genes when you first enter a session because there are no genes yet. When the session it's hard-wired to go to the front page. There's probably a workaround for that.

image

ValWood commented 6 months ago

This will be great. I can't test because the login required is orcid sandbox, and I don't have a password for this and the passed recovery doesn't work. I would go ahead and add it. It won't be a problem even if the wrong gene is occasionally added.

kimrutherford commented 6 months ago

I would go ahead and add it.

I will do but first I'll try to arrange for Canto to go to the edit genes pages when there are existing genes, rather than to the front page.

kimrutherford commented 6 months ago

I will do but first I'll try to arrange for Canto to go to the edit genes pages when there are existing genes, rather than to the front page.

Val, could you suggest improvements for the message here? It only appears once, the first time you get to this page.

Warning: this session has been populated with PMID:35101096 genes known from other sources.
Use the "Add more genes from PMID:35101096" link to add missing genes

image

kimrutherford commented 6 months ago

could you suggest improvements for the message here?

Warning: this session has been populated with ...

Maybe "Note:" rather the "Warning:" would be a better tone?

kimrutherford commented 6 months ago

I've updated the test Canto with this change. PMID:35101096 is an example if you'd like to try it.

ValWood commented 6 months ago

I agree "Note" perhaps Note: this session has been populated with genes from PMID:35101096 abstract, keywords and other sources. Use the "Add more genes" link to add missing genes. You can also add, or remove, genes at any time during curation.

ValWood commented 6 months ago

tested, wonderful

kimrutherford commented 6 months ago

Should we say "UniProt keywords" in the message?

ValWood commented 6 months ago

These aren't UniProt Keywords they're PubMed

kimrutherford commented 6 months ago

Yes, sorry. Should we say "PubMed keywords"?

ValWood commented 6 months ago

OK, that might be helpful (and encourage people to add them!)

kimrutherford commented 6 months ago

OK, done. And I've released this change in the main Canto.

Should we close this issue?

ValWood commented 6 months ago

OK I will announce

ValWood commented 5 months ago

I just tried https://www.pombase.org/reference/PMID:27538348 in Canto and I didn't see any genes populated (I expected minimally to see those curated by BioGrid)

kimrutherford commented 5 months ago

Action: include BioGRID genes/publications

kimrutherford commented 5 months ago

Action: include BioGRID genes/publications

That's done, but not in time for the load.

I'll check it worked OK on Thursday morning.

kimrutherford commented 5 months ago

That's done, but not in time for the load.

I'll check it worked OK on Thursday morning.

I've just restarted the load after a failure so this will be done by the morning after all.

(Mondo has new release with an exciting new relation "has material basis in germline mutation in" which caused problems. It's all fixed now)

kimrutherford commented 5 months ago

Action: include BioGRID genes/publications

Done!

Example from the test Canto for PMID:27538348:

image

ValWood commented 5 months ago

nice!