On Thu, May 20, 2010 at 10:49 AM, January Weiner <
january.weiner@mpiib-berlin.mpg.de> wrote:

> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

