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Question: how to find a list of deleted GO ?

Chris Mungall cjm at fruitfly.org
Fri Apr 6 12:01:06 PDT 2007


Common queries on the GO Database can be found here:
http://wiki.geneontology.org/index.php/Example_Queries

Querying by obsolete IDs:
http://wiki.geneontology.org/index.php/Example_Queries#Obsolete_terms

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.
> 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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