[BioC] How to match Locus IDs with Gene Ontology IDs?

[Robert Gentleman]

Hi

Earl F. Glynn wrote:
> I looked at several Bioconductor packages that deal with Gene Ontology (GO,
> goTools, ontoTools), and I don't seem to find functionality that does the
> following:
> 
> 
> 
> Given Locus ID NM_001533 I can go to NCBI

  I think that is a RefSeq ID and I am also pretty sure that LocusLink 
has been retired in favor of Entrez Gene (although we are a bit slow in 
moving).

> 
> http://www.ncbi.nlm.nih.gov/
> 
> and search "Nucleotide" for "NM_001533"
> 
> 
> 
> I can click on the NM_0015333 hit returned, and about 2/3rds of the way down
> the page under the CDS section, the go_component, go_function, and
> go_process subsections give Gene Ontology info for NM_0015333.
> 

  biomaRt might be your best choice

> 
> 
> Likewise, if I do the same thing with Locus ID BC001721, I see a hit and a
> CDS section, but no gene ontology information.  That's OK, I'm not expecting
> everything to have GO information.  (E.g, of the 45,101 probesets on the
> Mouse430_2 Affy chip, only about 4693 have GO Biological process
> information, 2573 have celleular info, and 4875 have molecular function
> info.  I'm not working with Affy data, but I know many IDs won't have GO
> info, but some will.)

  Again I do not believe that BC001721 is an Entrez Gene ID, and it does 
matter a bit.

   You can of course always use AnnBuilder to build your own annotation 
for a microarray (if that is what you are working off).

  Robert

> 
> 
> 
> If I have a long list of Locus IDs, e.g., NM_001533, BC001721, ., are there
> any Bioconductor packages that "connect" these identifiers to gene ontology
> identifiers, or perhaps some other identifier (say LocusLink, aka Enterez
> Gene) that is mapped to the Gene Ontology information?
> 
> 
> 
> Thanks for any suggestions on how this might be automated using Bioconductor
> and R.
> 
> 
> 
> Earl F. Glynn
> 
> Scientific Programmer
> 
> Bioinformatics Department
> 
> Stowers Institute for Medical Research
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org