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[go-helpdesk] Proteome subsets for E.coli from AmiGO

Tanya Berardini tberardi at acoma.stanford.edu
Tue Sep 6 14:53:55 PDT 2011


Hi Sharan,

Thanks for all the details. Unfortunately, I'm unable to reproduce your
exact results.

Here's what I did:

1. www.geneontology.org
 2. Click on AmiGO browser
3. Choose species (Escherichia coli ONLY); click "Set Filters" -> Results =
5435 Gene Products for CC
4. Click on "+" sign by (e.g.) "Cellular Components"
5. Click on histogram to the right of "Cellular Components"
6. Click on link to 4990 gene products for the term GO:0005623 ; cell 4990
gene products

Result:

"There are over 154 pages of gene products annotated to the term cell ;
GO:0005623 and its children. Due to limitations in the current AmiGO
software, requests of this size have been disabled. If this is problematic,
please contact the GO helpdesk about query limits. Otherwise, please select
from one of the options below."

The display on HTML of the almost 5K results is disabled.  However, you can
still download the entire result set by clicking on either of the two
alternative links presented in the next sentence.

"Download associations in RDF-XML or tab-delimited gene association format."

I clicked on the 'tab delimited gene association format' and downloaded a
file with 8115 lines, representing annotations to 4990 gene products.

I hope this text file is useful for your purposes.  You should be able to
use a similar approach to download the other subsets of data you are
interested in studying.

Please let me know if you require further assistance.

Best wishes,

Tanya



Tanya Berardini
TAIR Curator
www.arabidopsis.org


On Tue, Sep 6, 2011 at 12:59 PM, Sharan Srinivasan <sharans at umich.edu>wrote:

> Hi Tanya,
>
> Thanks for the reply. I'm trying to filter the E. coli proteome by the
> categories on AmiGO (Biological Process, Cellular Component, Molecular
> Function). Here was how I was getting to this data:
>
> 1. www.geneontology.org
> 2. Click on AmiGO browser
> 3. Choose species (Escherichia coli ...); click "Set Filters" -> Results =
> 3892 Gene Products
> 4. Click on "+" sign by (e.g.) "Cellular Components"
> 5. Click on histogram to the right of "Cellular Components"
>
> Here's where I am for reference (
> http://amigo.geneontology.org/cgi-bin/amigo/term-chart.cgi?term=GO:0005575&session_id=6211amigo1315322448
> ).
>
> 6. Click on 264631 Gene Products in line (GO:0005623 ; cell<http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0005623&session_id=6211amigo1315322448>
> ).
> Result:
> http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0005623&session_id=6211amigo1315322448
>
> This is where I'm told that AmiGO's limits render me unable to view the
> full results.
>
>
> I hope I was able to give you a clear idea of what I was doing (and the
> data I was trying to retrieve). Please let me know if you can point me in
> the right direction.
>
> Many thanks!
>
> Sharan Srinivasan
> University of Michigan
>
> On Tue, Sep 6, 2011 at 1:16 PM, Tanya Berardini <tberardi at arabidopsis.org>wrote:
>
>> Dear Sharan,
>>
>> Thank you for contacting GO with your question.
>>
>> Can you please elaborate on what you mean by E. coli 'proteome subsets'?
>> If you can tell me how you have tried to obtain this data (step by step is
>> good), I can point you in the right direction for getting the results that
>> you want.
>>
>> Thanks,
>>
>>
>> Tanya Berardini
>> TAIR Curator/GO Curator
>> www.arabidopsis.org
>> www.geneontology.org
>>
>>
>> ---------- Forwarded message ----------
>>> From: sharans at umich.edu
>>> To: go-helpdesk at mailman.stanford.edu
>>> Date: Tue, 6 Sep 2011 08:20:43 -0700
>>> Subject: GO Help query (from website)
>>>
>>> Email: sharans at umich.edu
>>> Name: Software (from Sharan Srinivasan)
>>> Text: Hi,
>>> I'm trying to download some proteome subsets from E. coli using AmiGO,
>>> but the query size limits my ability to obtain the full sets. Can I be given
>>> access to these please?
>>>
>>> Thanks,
>>> Sharan Srinivasan
>>>
>>>
>>
>
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