[go] synonym category

[Midori Harris]

On Wed, 5 Sep 2007, Chris Mungall wrote:

>
> On Aug 30, 2007, at 11:01 AM, Midori Harris wrote:
>
>> Hi,
>> 
>> For SF 1195550, I have added *lots* of synonyms for enzyme activity terms. 
>> Because these synonyms are all derived from EC (obtained via Expasy), it's 
>> been suggested that we flag them by creating a synonym category. For the 
>> moment I've done so in a file in the go/scratch/ directory 
>> (go_EC_synonyms.obo). Before I put them in the live gene_ontology_edit.obo 
>> file, I have some questions:
>> 
>> - Will any scripts, e.g. the obo2obo script that generates the 
>> gene_ontology.obo (1.0 format) file, need to be changed?
>
> in theory, no (although the mapping will be lossy), but we should of course 
> do the usual check.
>
>> - Should we make an announcement on the GO or GO-friends list?
>
> do you mean pre-announce to warn people? Probably, yes. But you probably 
> don't want to hear this as the longer we delay it the harder it will be to 
> integrate this back in...

I'm hoping it won't be a big deal to feed it to obomerge, so I'm happy to 
err on the side of warning.

> Note that of course people shouldn't be downloading go_edit.obo, this was 
> intended to be the editor's version, not the obof1.2 version. Before we do 
> this  change I would like to sort out this situation

Fine (and good luck ...)

>
>> At the last GOC meeting we agreed to use a synonym category to denote 
>> Obol-friendly "structured synonyms,"
>
> note that obol uses any exact synonym, it doesn't need anything explicitly 
> designated.
>
> but it's always good to give additional information on why a particular 
> synonym was chosen if the implementation cost is negligible. I'm not sure it 
> is here - once we start designating structured synonyms we are compelled to 
> maintain them are we not?

I'm actually agnostic on the "structured synonyms" ... the only reason I 
mentioned them here was to remind everyone that they've heard of synonym 
categories in that context.

m

>
>> but that category has not yet gone live. The "EC synonym" category would 
>> therefore be the first to be added to the gene_ontology_edit.obo file.
>> 
>> SF link:
>> https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1195550&group_id=36855
>> 
>> Thanks,
>> Midori
>