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Question: how to find a list of deleted GO ?

Rama Balakrishnan rama at genome.Stanford.EDU
Fri Apr 6 11:55:41 PDT 2007


GOIDs are never deleted, they are obsoleted. All the Obsolete IDs  
should be in the gene_ontology_edit.obo file.

Regarding how to retrieve these IDs from the GO database, I am not  
familiar with the database schema.  I have copied the GO database  
group on this email. You will hear from them.

You can download the gene_ontology_edit  file from the CVS and search  
for the IDs you are interested in.
http://www.geneontology.org/GO.downloads.ontology.shtml
You will see a table on this web page, and you can click on the OBO  
v1.2 file to download.

Obsolete terms can be identified by looking at the 'def' line and  
'is_obsolete:true' tag (see example below).

[Term]
id: GO:0000008
name: thioredoxin
namespace: molecular_function
alt_id: GO:0000013
def: "OBSOLETE. A small disulfide-containing redox protein that  
serves as a general protein disulfide oxidoreductase. Interacts with  
a broad range of proteins by a redox mechanism, based on the  
reversible oxidation of 2 cysteine thiol groups to a disulfide,  
accompanied by the transfer of 2 electrons and 2 protons. The net  
result is the covalent interconversion of a disulfide and a  
dithiol." [GOC:kd]
comment: This term was made obsolete because it represents gene  
products. To update annotations, consider the molecular function term  
'thiol-disulfide exchange intermediate activity ; GO:0030508'.
is_obsolete: true

Hope this helps. Please let us know if you have any questions.

Best,

Rama


On Apr 6, 2007, at 5:44 AM, Chisato Yamasaki wrote:

> I have one basic question about GO database.
>
> I am looking for the list of deleted GO IDs to check our annotation.
> Could anyone tell me where to find the information ?
>
> Thank you very much for your help in advance.
>
> Regards,
> Chisato Yamasaki
>
> H-InvDB: http://www.h-invitational.jp/
> Japan Biological Information Research Center, JBIRC
>
> Waterfront Bio-IT Research Building, 2-42 Aomi,
> Koto-ku, Tokyo 135-0064, Japan.
> Tel: +81-3-3599-8800, Fax: +81-3-3599-8801,
> E-mail: cyamasak at jbirc.aist.go.jp
> ---

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