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Question: how to find a list of deleted GO ?

Suzanna Lewis 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:
> 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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