Search Mailing List Archives
Question: how to find a list of deleted GO ?
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
narrow: molecular function unknown
Thank you very much for all of your help again.
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:
>> 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
More information about the go-discuss