On 05/21/2010 04:45 AM, James F. Reid wrote: > Hi Steve, > > Term(names(get(get("NM_172496", org.Mm.egREFSEQ2EG), org.Mm.egGO))) > GO:0001843 GO:0005515 > "neural tube closure" "protein binding" I'm partial to library(org.Mm.eg.db) # organism-specific library library(GO.db) # GO ontology ## a vector of REFSEQ ids. in org.*eg.db packages the 'Lkey' is the ## 'eg' part of the package name, i.e., the ENTREZ gene id, while ## 'Rkey' is the part of the thing that is getting mapped to, ## 'mappedRkeys' are those keys that are in the present map ## so here we get the first three REFSEQ ids, to be used as ## an example rids <- mappedRkeys(head(org.Mm.egREFSEQ2EG, 3)) Then the maps egids <- org.Mm.egREFSEQ2EG[rids] # REFSEQ to ENTREZ id goids <- org.Mm.egGO[mappedLkeys(egids)] # ENTREZ to GO id terms <- GOTERM[mappedRkeys(goids)] # GO to TERM we could see what we've got, e.g., toTable(terms) or maybe unique(toTable(terms)[,c("go_id", "Term")]) or more explicitly r2eg <- toTable(egids) eg2go <- toTable(goids) go2term <- unique(toTable(terms)[,c('go_id', 'Term')]) merge(merge(r2eg, eg2go), go2term) The first few lines of which are > head(merge(merge(r2eg, eg2go), go2term)) go_id gene_id accession Evidence Ontology Term 1 GO:0001666 235623 NM_001001144 IMP BP response to hypoxia 2 GO:0003674 19783 NG_005612 ND MF molecular_function 3 GO:0003674 22746 NM_001001130 ND MF molecular_function 4 GO:0005515 235623 NM_001001144 IPI MF protein binding 5 GO:0005575 19783 NG_005612 ND CC cellular_component 6 GO:0005575 22746 NM_001001130 ND CC cellular_component An alternative to map a single key might be Term(names(org.Mm.egGO[[ org.Mm.egREFSEQ2EG[["NM_172496"]] ]])) Martin > > 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 >>>> Charit?platz 1 >>>> D-10117 Berlin, Germany >>>> Web : www.mpiib-berlin.mpg.de >>>> Tel : +49-30-28460514 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at 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]] >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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