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Question: how to find a list of deleted GO ?
suzi at berkeleybop.org
Sun Apr 8 15:27:54 PDT 2007
ah, so nice to have documentation to point at (and build upon)
On Apr 6, 2007, at 12:01 PM, Chris Mungall wrote:
> Common queries on the GO Database can be found here:
> Querying by obsolete IDs:
> If your question isn't answered here let us know
> On Apr 6, 2007, at 11:55 AM, Rama Balakrishnan wrote:
>> 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).
>> 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.
>> 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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