[go] GO Slims

[Judith Blake]

Yes it's unfortunate that we didn't get this discussed at the latest 
meeting.

I agree that we want to have the slims as separate files, with 
interoperability with the basic GO file, but for the moment, we can 
update/add slims.  the format is such that we can pull them into a 
separate file when we are set up to do that in a way the is productive.

Judy





Rama Balakrishnan wrote:
> Hi Midori,
>
> Great!  I can add the Candida slims to the obo file.
>
> Thanks,
>
> Rama
>
> On Oct 11, 2007, at 3:01 AM, Midori Harris wrote:
>
>> Hi Rama,
>>
>> This is timely -- I've exchanged some email over the past few days 
>> with Darren Natale at PIR on essentially the same subject. They have 
>> a slim that they would like to have incorporated into GO. I forwarded 
>> the initial request and some follow-up info to the GO managers for 
>> comment. So far, Michael and Suzi have said they are happy to have GO 
>> add the PIR slim, and no one else on the managers' list has commented.
>>
>> For the time being, I'm inclined to add the slims to the 
>> gene_ontology_edit.obo file to keep them in sync with the rest of the 
>> ontology. From what John said in the earlier exchange, it seems it 
>> won't be very difficult to convert to separate files for slims 
>> whenever we see fit.
>>
>> I know that Amelia plans to update the GO slim script in the next 
>> week or two, so any new slims we add to the gene_ontology_edit.obo 
>> file will appear in the slim directory. That script can presumably 
>> also be adapted to find the slims in one or more external files 
>> if/when we go that route.
>>
>> Midori
>>
>> On Wed, 10 Oct 2007, Rama Balakrishnan wrote:
>>
>>>
>>> The topic of adding more GO Slims was slated for discussion at the 
>>> GOC meeting, but somehow did not happen.  There was a proposal to 
>>> maintain the slims in a separate file instead of adding categories 
>>> into the current OBO as we do it now.  But no conclusion was made.
>>>
>>> CGD (and others, please see below) would like to make their GO Slims 
>>> available. Since no conclusion was made, can we proceed using the 
>>> current system (maintaining categories within the obo file)?
>>>
>>> Background:
>>> Currently we store the various GO slims as categories in the 
>>> gene_ontology_edit.obo file. I believe there is a script that parses 
>>> this file and puts each GO slim on the FTP site. This mechanism was 
>>> put in place to keep the GO slims current with the ontology (to make 
>>> sure obsolete terms are removed from the GO slims, term merges are 
>>> represented correctly and so on).
>>>
>>>
>>> A curator from the Candida Genome Database emailed us asking how to 
>>> post the Candida GO slim that CGD has just developed. I understand 
>>> Alex from MGI, Michelle from TIGR all have GO slims that they want 
>>> to add.  There was an email discussion on the GO mailing list about 
>>> this topic. Here is a link to that thread-
>>>
>>> http://genetics.stanford.edu/go-email/email-go/go-arc/go-2007/0451.html
>>>
>>> Thanks,
>>>
>>> Rama
>