[go] GO Slims

[Rama Balakrishnan]

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