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[Gofriends] Best practice for integration of GO annotation ?

K. Shameer shameer at ncbs.res.in
Wed Mar 4 22:23:36 PST 2009


Hello Haris,

Thanks for the link to flat file 'GO.terms_and_ids'. I have used a script
to convert different ontology files from  obo and use it for assignement
earlier and it was pretty much faster than using modules. But, I also need
to obtain parent terms and descendent terms for genes from model organism,
in such a situation - this flat-file will not be useful. I would like to
know how can I obtain parent terms/child terms in different levels in a
pretty faster mode. I know about different perl modules are available for
this purpose, but I found them very slow - you guys had any similar issues
? any faster module to recommend ?

Thanks,
Shameer

> Hello,
>
> Thank you for your interest in GO. Although the OBO format version of GO
> is authoritative, if you need only term names and IDs, we have a simple ID
> -> name, ontology mapping file available:
>
>    http://www.geneontology.org/doc/GO.terms_and_ids
>
> Tab-delimited flat files of GO annotations from the GO repository from
> this web page:
>
>    http://www.geneontology.org/GO.current.annotations.shtml
>
> Or, if you prefer, the same files are available by FTP and anonymous CVS,
> as described here:
>
>    http://www.geneontology.org/GO.downloads.ftp.cvs.shtml
>
> The file format is documented here:
>
>    http://www.geneontology.org/GO.format.annotation.shtml
>
> Midori
>
> ============================
> Midori A. Harris, Ph.D.
> GO Editor
> EMBL - EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD UK
>
> Tel: +44 (0) 1223 494667
> Fax: +44 (0) 1223 494468
> Email: midori at ebi.ac.uk
>
> On Wed, 4 Mar 2009, K. Shameer wrote:
>
>> Hello GOFriends,
>>
>> I am looking for a best-practice method used by GO friends for
>> integration
>> of GO annotation for genes in model organism. I need to store the GO
>> data
>> for several model organisms in a local databases and retrieve the
>> annotation as a part of a web server based on requirement. I obtained GO
>> IDs using BioMart, using the GO IDs, I tried different perl modules to
>> obtain GO term from ID, but I find the processing is really slow - its
>> taking approximately 15 seconds to get term using a GO ID. Is there a
>> better approach to get the Gene ID, GO ID, GO Terms for model organisms
>> as
>> a flat file ? I am also curious to know how GO friends obtain GO
>> annotations for genomes of interest - any best practices ?
>>
>> Thanks in advance,
>> Khader Shameer
>> NCBS - TIFR
>> Bangalore
>>
>> _______________________________________________
>> Gofriends mailing list
>> Gofriends at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/gofriends
>>
>





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