[BioC] Mapping NCBI accession numbers to GO terms

[James F. Reid]

Hi Steve,

Term(names(get(get("NM_172496", org.Mm.egREFSEQ2EG), org.Mm.egGO)))
            GO:0001843            GO:0005515
"neural tube closure"     "protein binding"

HTH,
J.

On 05/21/2010 12:31 PM, Steve Taylor wrote:
> 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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>>
>> [[alternative HTML version deleted]]
>>
>
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