Hi, There are two ways to do this in biomaRt. The result will be the same but the second way is a very general one and will allow you to extract anything you want that is available from the BioMart databases. 1) Using the simple getGO function: > mart=martConnect() connected to: ensembl_mart_35 #Now retrieve the GO annotation for your id, note that you can also give a vector of id's > getGO(id="NM_001533",type="refseq",species="hsapiens",mart=mart) id GOID description evidence 1 NM_001533 GO:0000166 nucleotide binding IEA 2 NM_001533 GO:0003723 RNA binding TAS 3 NM_001533 GO:0006397 mRNA processing IEA 4 NM_001533 GO:0005654 nucleoplasm TAS 5 NM_001533 GO:0030530 heterogeneous nuclear ribonucleoprotein complex TAS 6 NM_001533 GO:0005634 nucleus IEA martID 1 ENSG00000104824 2 ENSG00000104824 3 ENSG00000104824 4 ENSG00000104824 5 ENSG00000104824 6 ENSG00000104824 >martDisconnect(mart) 2) Using the more powerful getBM function: #List the available BioMart databases > listMarts() [1] "ensembl_mart_35" "vega_mart_35" "snp_mart_35" "msd_mart_4" "uniprot_mart_17" #Select a BioMart to use with the function useMart() and verify database connection. > mart=useMart("ensembl_mart_35") connected to: ensembl_mart_35 #List the available datasets in the selected BioMart database. > listDatasets(mart) dataset version 1 ptroglodytes_gene_ensembl CHIMP1 2 ggallus_gene_ensembl WASHUC1 3 rnorvegicus_gene_ensembl RGSC3.4 4 scerevisiae_gene_ensembl SGD1 5 tnigroviridis_gene_ensembl TETRAODON7 6 xtropicalis_gene_ensembl JGI3 7 frubripes_gene_ensembl FUGU2 8 cintestinalis_gene_ensembl CINT1.95 9 agambiae_gene_ensembl MOZ2a 10 amellifera_gene_ensembl AMEL2.0 11 btaurus_gene_ensembl BDGP4 12 celegans_gene_ensembl CEL140 13 mmusculus_gene_ensembl NCBIM34 14 cfamiliaris_gene_ensembl BROADD1 15 dmelanogaster_gene_ensembl BDGP4 16 drerio_gene_ensembl ZFISH5 17 hsapiens_gene_ensembl NCBI35 18 mdomestica_gene_ensembl JGI3 #Update the mart object by selecting a dataset > mart = useDataset(dataset = "hsapiens_gene_ensembl",mart = mart) Reading database configuration of: hsapiens_gene_ensembl Checking attributes ... ok Checking filters ... ok Checking main tables ... ok #List the available attributes for this dataset. This shows you all the attributes that can be retrieved. > listAttributes(mart) [1] "chr_name" [2] "chrom_start" [3] "chrom_end" [4] "chrom_strand" . #List the available filters for this dataset. This shows all possible filters that can be used on this dataset. > listFilters(mart) [1] "chr_name" [2] "gene_chrom_start" [3] "gene_chrom_end" [4] "in_encode" . #Now you can do a query e.g. Get the GO id, evidence code, and description for refseq id as filter and with values NM_001533. Note that you can also give a vector of identifiers as values. > getBM(attributes=c("go_id", "go_description","evidence_code"), filter="refseq_dna",values="NM_001533",mart=mart) refseq_dna go_id go_description 1 NM_001533 GO:0000166 nucleotide binding 2 NM_001533 GO:0003723 RNA binding 3 NM_001533 GO:0006397 mRNA processing 4 NM_001533 GO:0005654 nucleoplasm 5 NM_001533 GO:0030530 heterogeneous nuclear ribonucleoprotein complex 6 NM_001533 GO:0005634 nucleus evidence_code 1 IEA 2 TAS 3 IEA 4 TAS 5 TAS 6 IEA best, Steffen > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >