[go] AmiGO beta announcement

[Benjamin Hitz]

There's an ontology version?  You mean the CVS revision number?
It's updated "hourly" ... and the goterm database is loaded daily.

The way the loading works is that it checks out the ontology (and  
gas, etc.) with a "sticky date".

For the (current, not yet finished) golite
mysql at goad ontology]$ cvs status -v gene_ontology.edit
===================================================================
File: gene_ontology.obo Status: Up-to-date

    Working revision:    4.377
    Repository revision: 4.377   /anoncvs/go/ontology/ 
gene_ontology.obo,v
    Sticky Tag:          (none)
    Sticky Date:         2007.12.20.08.00.00
    Sticky Options:      (none)

    Existing Tags:
         metabolism_branch_oct_04        (branch: 3.557.2)


So anyone can get the exact file used with >cvs update -dA -D 2007-12-20

We use the date stamp so that it's easier to recreate a load at a  
different time.

Ben
On Dec 20, 2007, at 6:19 AM, Amelia Ireland wrote:

> Back in Gotham City, Valerie Wood wrote:
>
>> I agree with David, most analysis which use GO are not reproducible
>> because details about GO data (annotations and ontology) and software
>> used are ommitted. I think we should provide this info at the top  
>> of the
>> results output. Perhaps the load date for now, until we have proper
>> versioning?
>
> How about something saying 'Cite this data', with information about  
> the
> ontology version and the date when the annotations were updated? We  
> should
> also update the GO website page about citing GO to state that you  
> should
> specify this data when you use/publish data from AmiGO.
>
> Chris / Ben - can we get the ontology version data put into the  
> database
> as well as the date when the annotations were updated?
>
> -- 
> Amelia Ireland
> GO Editorial Office,
> European Bioinformatics Institute, UK.
> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp
>

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu