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Question: how to find a list of deleted GO ?

Chisato Yamasaki cyamasak at jbirc.aist.go.jp
Mon Apr 9 02:46:37 PDT 2007


Dear Rama, Chris, Erick and Suzanna,

Thank you very much for your replies.
Now I am sure that GOIDs are never deleted, they are obsoleted.

In fact GO ID I was checking at AmiGO was below;
GO:0005554    molecular function unknown

I found the GO ID as only alt_id so htat I misunderstood that it was 
deleted.
Accession: GO:0003674
Ontology: molecular_function
Synonyms:
narrow: molecular function unknown
alt_id: GO:0005554

Thank you very much for all of your help again.

Best regards,
Chisato Yamasaki

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
---
----- Original Message ----- 
From: "Suzanna Lewis" <suzi at berkeleybop.org>
To: "Chris Mungall" <cjm at fruitfly.org>
Cc: "Rama Balakrishnan" <rama at genome.stanford.edu>; "GO Annotation list" 
<annotation at genome.stanford.edu>; "Benjamin Hitz" 
<hitz at genome.stanford.edu>; "Seth Carbon" <sjcarbon at fruitfly.org>; "Stan 
Dong" <qdong at genome.stanford.edu>
Sent: Monday, April 09, 2007 7:27 AM
Subject: Re: Question: how to find a list of deleted GO ?


> 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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