[go] synonym category

[Chris Mungall]

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...

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

> At the last GOC meeting we agreed to use a synonym category to  
> denote Obol-friendly "structure 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?

> 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
>