update Ribbon AGR slim to be compatible

[nathandunn]

TODO

• [x] make sure the slims line up: https://github.com/geneontology/ribbon/blob/master/src/data/agr.js
• [x] fix just the CC portion: https://github.com/geneontology/ribbon/blob/master/src/data/expression.js
• [x] create agr_ui PR

via reference for agr_slim: http://snapshot.geneontology.org/ontology/go.obo

fixes here: https://agr-jira.atlassian.net/browse/AGR-1163 .

[lpalbou]

Just an update on that: I have talked with Chris and we will simplify the BioLink API call on the API side (e.g. /slimmer/function?subset=agr_slim&subject=xxx), hence the files agr.js and I believe expression.js would be deprecated in favor of this API call. It would also ensure that a slim is always the same wherever you use it.

There will also be a /ontology/slim/{id} to retrieve metadata on a specific slim, should you need it.

[nathandunn]

👍

We are still allowing folks to pass in a slim, though, right?

Nathan

On Sep 11, 2018, at 9:51 AM, lpalbou notifications@github.com wrote:

Just an update on that: I have talked with Chris and we will simplify the BioLink API call on the API side (e.g. /slimmer/function?subset=agr_slim&subject=xxx), hence the files agr.js and I believe expression.js would be deprecated in favor of this API call. It would also ensure that a slim is always the same wherever you use it.

There will also be a /ontology/slim/{id} to retrieve metadata on a specific slim, should you need it.

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[cmungall]

See also https://github.com/biolink/biolink-api/issues/40

I answer your Qs there

[lpalbou]

Yes, including for backward compatibility, but for consistency it will be far better to use the new route.

@sibyl229 if you want the data fetched by the API to have a different structure, or if you have any problem with it, please let us know ?

[sibyl229]

Thanks @lpalbou . I should be fine I think. I'm fetching data from WormBase database.

[lpalbou]

As the PR on BioLink / Ontobio will take some time, I have corrected the agr.js file manually and done this intermediary PR: https://github.com/geneontology/ribbon/pull/65

@selewis was right, there is an obsolete term, GO:0000988 (obsolete transcription factor activity, protein binding). I am unsure how the slimmer will work on an obsolete term so this should be fixed. Following comments on jira, I have removed it from the slim at the moment.

Notes:

• this AGR slim is indeed larger, we'll have to see how it renders on AGR
• terms are now ordered in each aspect (MF / BP / CC)