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geneontology / noctua-form-legacy

Simple annoton editor workbench for Noctua.
BSD 3-Clause "New" or "Revised" License
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Confirm most up-to-date annotations are available from Search database function #78

Closed vanaukenk closed 5 years ago

vanaukenk commented 6 years ago

Hi @tmushayahama

Today I was working on a model and wanted to see what MF annotations already existed for the C. elegans gene mat-3.

When I used the Search database option, I didn't see any MF annotations available, even though I can see one MF annotation in AmiGO:

http://amigo.geneontology.org/amigo/gene_product/WB:WBGene00003134

Can you double-check to see why that might be?

Thx!

tmushayahama commented 6 years ago

@vanaukenk Search database use golr and I think it is update with the pipeline monthly. @kltm @cmungall I am using the url from global golr server and it is http://noctua-golr.berkeleybop.org for production site, is that correct?

image

tagging @thomaspd

kltm commented 6 years ago

@tmushayahama If you are doing an annotation import, you quite probably want to be using the production GO GOlr servers. I.e.:

http://golr-aux.geneontology.io/ (recommended for bulk operations) http://golr-aux.geneontology.io/ (the AmiGO UI server)

The NEO/Noctua load does not have annotations. (I would note that the Function Companion does not use any of the above servers, but another one that is loaded on a different schedule; that is a bug.)

tmushayahama commented 6 years ago

@kltm thanks. So search database is just function companion. Do I need to change to http://golr-aux.geneontology.io/ ?

kltm commented 6 years ago

If you are trying to do a search of the current public annotations via Solr, that would be the best choice.

tmushayahama commented 6 years ago

@kltm what is the solution to the question from @vanaukenk about this endpoint not being up to date? Is function companion up to date?

@vanaukenk when you use the function companion with the same search, what results do you get?

vanaukenk commented 6 years ago

@tmushayahama if I use the function companion from the Workbenches menu of the graph editor, and filter on 'mat-3', I do see the protein binding annotation for mat-3 available for import, and importing it seems to work fine.

vanaukenk commented 5 years ago

The mat-3 'protein binding' annotation has disappeared from the Search database functionality of the form, although it is still accessible from the Function Companion.

vanaukenk commented 5 years ago

@tmushayahama - can you confirm that the Search database functionality of the form is searching the current set of production GO annotations?
@kltm - can the Function Companion and the form Search database functionality please search the same set of annotations?

kltm commented 5 years ago

@vanaukenk I'll look into this: geneontology/noctua#586

vanaukenk commented 5 years ago

Thank you @kltm !

vanaukenk commented 5 years ago

@tmushayahama @kltm It looks like this issue still exists.
I was just trying to add an MF annotation using the Noctua form and can't find the MF I want in the Search database entries, even though that annotation exists in AmiGO, WB, and Protein2GO. I can find the annotation if I use the Function Companion. @tmushayahama - let's discuss tomorrow.