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geneontology / annotation_extensions

Documentation, tickets & usage reports for annotation extension relations.
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inconsistency in relations #51

Open dosumis opened 9 years ago

dosumis commented 9 years ago

From @rbalakri on August 6, 2015 21:51

HI,

the gorel.obo file contains names that sometimes have an underscore (_) between words, sometimes not? Should 'happens_during' have an underscore?

GOREL:0000027 in_presence_of GOREL:0000752 has_direct_input GOREL:0000001 happens during BFO:0000051 has part RO:0002502 depends on

Rama

Copied from original issue: geneontology/go-ontology#12002

dosumis commented 9 years ago

Hi Rama,

This is a historical thing. All relations originally had underscores in the names. I'd have preferred if we'd kept it that way, but for RO/BFO it was agreed that these should be removed. Never happened for GOREL relations. We could do it, although you'd continue to see the readable old-style OBO ids (AKA shorthand) in GAF/GPAD.

Interesting that happens_during still has a GOREL ID. We should be using the one from RO. Thought I'd cleaned all these up, but seems not.

Cheers, David

BTW - better to put gorel issues on the annotation extensions github, as the rest of them are there.

Cheers, David

dosumis commented 9 years ago

From @rbalakri on August 7, 2015 17:40

Hi David, Thanks. I thought there was a technical reason to keep underscore (easy for scripts to parse). You are saying the standard format should no underscores.

Rama

dosumis commented 9 years ago

happens_during ID issue fixed (was OK in OWL - but stray xref gave it wrong it in OBO).

Should probably remove underscores from names in order to be consistent. But this is low priority.

dosumis commented 9 years ago

From @paolaroncaglia on August 11, 2015 13:39

Hi @dosumis and @rbalakri , There doesn't seem to be an easy way to transfer tickets from one tracker to the other. If this is the case, please either make a copy on the annotation tracker (it should be linked to it anyway?), or please deal with this issue here. Let me know if I can be of any help. Thanks! Paola

dosumis commented 9 years ago

From @mah11 on August 11, 2015 13:43

Following the derail rather than the original topic ... I looked into moving tickets for our PomBase trackers and found that indeed, GitHub doesn't have anything built in to do it. The feature has been requested:

https://github.com/holman/ama/issues/413

and there's apparently a third-party hack that you may want to look into:

https://github.com/google/github-issue-mover

dosumis commented 9 years ago

From @cmungall on August 11, 2015 18:1

On 11 Aug 2015, at 6:43, Midori Harris wrote:

https://github.com/google/github-issue-mover

I'v used this, it works fine