[BioC] Mapping NCBI accession numbers to GO terms

[Steve Taylor]

Hi,

I too would like a simple way of getting from Refseq to GOTERM(s).

What's the best package (and an example if possible) for getting the actual term information (rather than the GO ID as below) from a Refseq ID?

Thanks,

Steve

>
>> Hello,
>>
>> I'm not sure how to retrieve GO terms associated with the NCBI
>> accession numbers (such as "NM_172496").
>>
>> I have found references to GOLOCUSID, but I cannot find this
>> environment. I have GOstats and I can access GOTERM, but not
>> GOLOCUSID.
>>
>>
> Perhaps this will get you going:
>
>> library(org.Mm.eg.db)
>> get("NM_172496", org.Mm.egREFSEQ2EG)
> [1] "12808"
>> names(get("12808", org.Mm.egGO))
> [1] "GO:0001843" "GO:0005515"
>
>> sessionInfo()
> R version 2.12.0 Under development (unstable) (2010-05-03 r51901)
> x86_64-apple-darwin10.3.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  tools     utils     methods
> [8] base
>
> other attached packages:
> [1] org.Mm.eg.db_2.4.1   org.Hs.eg.db_2.4.1   RSQLite_0.9-0
> [4] DBI_0.2-5            AnnotationDbi_1.11.1 Biobase_2.9.0
> [7] weaver_1.15.0        codetools_0.2-2      digest_0.4.2
>
>
>
>> Anyways, I also failed to map NCBI accession numbers to Entrez IDs
>> using BioIDMapper:
>>
>
> Not bioconductor; please contact the author of that package for concerns
> about it.
>
>
>>
>> library(BioIDMapper)
>> data(glist)
>>> head( bio.convert( glist, 1, 24 ) )
>> Parsing data from UniProt
>> 200  IDs have been processed
>> 159  IDs have been processed
>> Parsing data from UniProt
>> 22  IDs have been processed
>>   No ID found in database. 0 IDs have been processed
>> Done...
>>   P_GI       ACC        P_ENTREZGENEID
>> 1 "54125119" "A6YK35\r" NA
>> 2 "54125311" "A6YK35\r" NA
>> 3 "54125051" "A6YK35\r" NA
>> 4 "54125369" "A6YK35\r" NA
>> 5 "54125435" "A7J4K5\r" NA
>> 6 "54125083" "A6YK35\r" NA
>>>
>>
>> Best regards,
>>
>> confused January
>>
>> --
>> -------- Dr. January Weiner 3 --------------------------------------
>> Max Planck Institute for Infection Biology
>> Charitéplatz 1
>> D-10117 Berlin, Germany
>> Web   : www.mpiib-berlin.mpg.de
>> Tel     : +49-30-28460514
>>
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