[Feedback] Site Feedback: Gramene Ontology data on ftp site

[Marcela K. Monaco]

Hi Cathy,

I'm so sorry that our release notes have not been updated and have mislead
you.

Gramene's ontology DB is built from various ontology sources including
AmiGO and Ensembl gene/marker tables.  Our FTP files were last created on
August of 2014.

I am bit puzzled myself about the records displayed on the FTP files as
looking closely at an example (AT3G18710), they differ slightly different
from other resources:

AmiGO:
http://amigo.geneontology.org/amigo/gene_product/TAIR:locus:2093974

UniProt:
http://www.uniprot.org/uniprot/Q9LSA6

QuickGO:
http://www.ebi.ac.uk/QuickGO/GProtein?ac=Q9LSA6

and so are our own and Ensembl Plants records (Ontology section)...

http://ensembl.gramene.org/Arabidopsis_thaliana/Gene/Summary?db=core;g=AT3G18710;r=3:6434083-6435561;t=AT3G18710.1
OR
http://plants.ensembl.org/Arabidopsis_thaliana/Gene/Summary?g=AT3G18710;r=3:6434083-6435561;t=AT3G18710.1;db=core

Marcela



On Fri, Oct 24, 2014 at 1:22 PM, feedback at gramene.org <feedback at gramene.org>
wrote:

> URL         : http://gramene.org/
>
> Subject     : Site Feedback: Gramene Ontology data on ftp site
>
> Name        : Cathy Gresham
>
> Email       : gresham at igbb.msstate.edu
>
> Organization: Mississippi State University Institute for Genomics,
> Biocomputing and Biotechnology
>
> Comments    :
>
> I was looking at the ontology go data at
> ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/ontology/go
>
> I looked at the release notes from
> http://gramene.org/release-notes-42
>     It says that the ontology has not been updated since release 31 May -
> 2010.
>
>  Does this mean the IEA annotations have not been reviewed | run since
> that date?  The annotations have an assign date of Aug. 2014.
>
>   I looked at one record and the uniprot_id 2 entrez gene_id mapping seems
> to be different between the Gramene IEA record and the UniProt website.
> This is easily explained if the GO annotations have not been updated since
> May 2010.
>
> Thanks,
> Cathy
>
> http://www.warelab.org/bugs/view.php?id=5053
>
>
> _______________________________________________
> Feedback mailing list
> Feedback at gramene.org
> http://brie4.cshl.edu/mailman/listinfo/feedback
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/feedback/attachments/20141104/11ee44fe/attachment.html>