Customized annotation and ontology files for BiNGO

[ashwani Kumar]

Hi All,

I need to use BiNGO (followed by Enrichment Map) plugin for a set of E. coli genes (few hundreds) for which there are no GO terms available. I looked for those genes into the literature and prepared a set of GO terms for them. Now, I would like to prepare customized gene_association.anno and gene_ontology.obo files. I followed the instructions provided on BiNGO website but I am getting some errors (screenshot attached with this email.).  

Could anybody please help me out with gene_association.anno and gene_ontology.obo files?

Any help is highly appreciated.

Thanks,

Ashwani

[konika]

Hi Ashwani

The gene_association.anno and gene_ontology.obo files are available for download from the geneontology website (http://www.geneontology.org/).

One is in download annotation section while other in download ontology section. You can get the .obo files also from http://www.obofoundry.org/ (if you want the biological process terms only etc.)

You then need to store these file and load them by selecting 'custom files' while running BiNGO. These are used to get updated annotations.

Hope this helps!

Konika

[ashwani Kumar]

Hi Konika,

Thanks for the reply. I had used the gene_association and antology files just like the way you explained. But the problem is, for a set of genes either I don't have GO terms or they are just the predicted once. So, for that set of genes, I went back to literature and generated a set of possible biological processes. Now, I want to introduce this information into the data I have for E. coli (association and ontology files) or I can simply generate gene_association and geneontology.obo files and feed it to BiNGO. While doing so, I followed the instructions provided on BiNGO website but its really not working for me and I am getting errors I attached in my last email.

SO, I need help in generating customized gene_associataion and .obo files.

Thanks,

Ashwani

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-helpdesk?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[Vijaykumar Muley]

Hi Ashwani,
gene_association file just enlist the proteins and the GO terms
associated with them in structured way. Since your proteins are not
listed, you have to add them in the file. So you will need, GO
identifiers, names, type P (process), C, F, then evidence code such as
(IEA) for your proteins.
Once you add this information in gene_association file, you need to
describe the relationship between your new terms as well as already
existing GO terms in the .obo file.
Then only it will work.
I hope this will help

On 5/26/13, ashwani Kumar <ashwan...@gmail.com> wrote:
> Hi Konika,
>
> Thanks for the reply. I had used the gene_association and antology files
> just like the way you explained. But the problem is, for a set of genes
> either I don't have GO terms or they are just the predicted once. So, for
> that set of genes, I went back to literature and generated a set of
> possible biological processes. Now, I want to introduce this information
> into the data I have for E. coli (association and ontology files) or I can
> simply generate gene_association and geneontology.obo files and feed it to
> BiNGO. While doing so, I followed the instructions provided on BiNGO
> website but its really not working for me and I am getting errors I
> attached in my last email.
>
> SO, I need help in generating customized gene_associataion and .obo files.
>
> Thanks,
> Ashwani
>
>
> On Sat, May 25, 2013 at 7:05 AM, konika <komu...@gmail.com> wrote:
>
>> Hi Ashwani
>> The gene_association.anno and gene_ontology.obo files are available for
>> download from the geneontology website (http://www.geneontology.org/).
>> One is in download annotation section while other in download ontology
>> section. You can get the .obo files also from

>> http://www.obofoundry.org/(if you want the biological process terms only

--
--
Vijaykumar Yogesh Muley, *Ph.D.*
Centre of Excellence (CoE) in Epigenetics,
Indian Institute of Science Education and Research (IISER),
Sixth Floor, Central Tower, Sai Trinity Building, Pashan, Pune 411021, INDIA
Ph.No. +91 9881390632
http://www.iiserpune.ac.in/~coee/wiki/index.php/Vijaykumar_Muley
http://scholar.google.co.in/citations?user=FoyJkwcAAAAJ&hl=en&oi=ao

------------------------------------------------------------------
Life : A journey from Cell to Cell
------------------------------------------------------------------

[ashwani Kumar]

Hi Vijay,

Nice to hear from you and thanks for the suggestion. I tried to generated association and .obo files like they have instructed on their website (http://www.psb.ugent.be/cbd/papers/BiNGO/Customize.html), but did not work out. I guess, now only way is  to incorporate my data into gene_association and .obo files, as you suggested. 

@Konika, Thanks for the suggestion. I would seek your help again if need so.

Thanks,

Ashwani

[rajasekargutha]

i have downloaded respected files but not working for me