[BioC] Gene Ontology Annotations from Gene Names

[Joseph Shaw]

Hi Jim,

Thanks for your reply!

The organism is Campylobacter jejuni (strain: NCTC11168). How can I
check if this is a viable option?

According to the reference manual for AnnotationForge, the
makeOrgPackageFromNCBI() function makes an organism package from
annotations available from NCBI, but, according to the function
arguments an author and maintainer are required; I'm not sure exactly
what this applies to.

Also, the function returns nothing; if this is the case, how can you
access the created organism package?

Joseph

On Wed, Feb 5, 2014 at 3:51 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi Joseph,
>
> What's the organism? You might be able to create an org-level package using
> orgPkgFromNCBI() in the AnnotationForge package.
>
> Best,
>
> Jim
>
>
>
> On 2/4/2014 7:09 PM, Joseph Shaw [guest] wrote:
>>
>> I am hoping to get appropriate GO mappings for a list of genes used in a
>> microarray experiment with a view to identifying significantly regulated
>> processes.
>>
>> I was planning on using the Bioconductor package GOstats to identify these
>> processes; however, the organism under study is not a supported organism. I
>> have attempted to use the blast2GO software to generate the gene to GO
>> mapping, but this approach seems to be very time consuming (after generating
>> the corresponding .fasta files, it took over 1 hour to BLAST just 10 genes).
>>
>> Currently, the gene identifiers I am using are simply the gene names, but
>> it shouldn't be too difficult to derive a list of corresponding alternative
>> identifiers (assuming they are publicly available) should it be advantageous
>> to the GO mapping process.
>>
>> Is there any faster way to achieve this gene to GO mapping (either through
>> Bioconductor packages or otherwise)?
>>
>> Any assistance is appreciated.
>>
>> Joseph
>>
>>   -- output of sessionInfo():
>>
>> -
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>