Display term names for "consider" list for obsolete GO terms

[vanaukenk]

Hi,

When a term is OBSOLETE, it would be very helpful to also display the term name for the GO terms to consider in the Comment section of the term page. See, for example, the list of three GO terms for 'chaperone activity' at: http://amigo.geneontology.org/amigo/term/GO:0003754

Users could then see straight away what other terms might be most relevant to their search.

Thanks,
--Kimberly

[kltm]

This is a more complicated loader request; it will require:

• parsing the comment section, removing the consider section when writing into the field
• looking up the IDs to get name information
• populating three fields (name list, id list, and map)
• perl client code addition for display

Feels like a 2.3 feature request.

[cmungall]

I think this should be straightforward. No parsing of comments required. Everything is there in the ontology and should be loaded into golr.

I note that currently obsoletes resolved to a 404 which is not good
http://amigo.geneontology.org/amigo/term/GO:0003754

[kltm]

Are we loading consider?

No matter what is loaded into golr, as things stand now, it would require the perl code to take multiple passes at the backend to try and find the right document (in this case we're not searching, we're just pulling the identifier, which I think is a much better idea).

The best way to do this might be with an "acceptable identifier" field that could be used; primary choice would be the one that also had the same id, next a unique one that didn't, finally a user choice if there are somehow multiple ones.

No matter what, non-trivial code changes that would need more testing, so likely 2.3 and not 2.2.

[kltm]

To answer my own question, yes, we are loading consider.
property: [getAnnotationPropertyValues, consider]

The perl backend still would have to be changed a bit, and I think it would be better done with a new single field.

[cmungall]

Not following you about multiple passes. Should be easy, can discuss today. But yes 2.3 is fine.

[kltm]

This has been discussed offline with @cmungall. While the labels are a desired feature, the extra mechanism needed (label-id maps for consider) is lower priority at this point and will be considered for 2.3.

[selewis]

I have to admit to punting on this in the paint/touchup code. It uses
replaced by, or failing that those that were merges and are found as
synonyms, but I ran out of steam in adding 'consider' to the report I give
the curators.

-S

On Tue, Jan 27, 2015 at 1:27 PM, kltm [email protected] wrote:

This has been discussed offline with @cmungall
https://github.com/cmungall. While the labels are a desired feature,
the extra mechanism needed (label-id maps for consider) is lower priority
at this point and will be considered for 2.3.

—
Reply to this email directly or view it on GitHub
https://github.com/kltm/amigo/issues/156#issuecomment-71731457.

[kltm]

@selewis is your comment for this (amigo) issue, or should it be in the touchup tracker?

[selewis]

I was thinking touchup, but it would be good if we had a coherent approach to this that we agree on.

[kltm]

@selewis there is only one way that it can be done in AmiGO/GOlr: we will be able to add this once we have the additional search/lookup and maps created in the loader.