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Question: how to find a list of deleted GO ?
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.
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).
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
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'.
Hope this helps. Please let us know if you have any questions.
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.
> 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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