Hi I am trying to get all the abstracts of a list of SNPs from pubmed. I have got gene symbol for each SNP ID. I am not extractly sure which annotation package should I use to map to PMID. What is the function I can use to map from gene symbol (or affy snp id) to PMID? Thank you. Liu [[alternative HTML version deleted]]

Hi Liu, The thing you want to use for this is an annotation package. If you have gene symbols that implies that there are genes, so that would mean that you could use the appropriate organism annotation package like this: library(org.Hs.eg.db) symbols = c("A25","ACA7B") ## extract the entrez gene IDs (central ID for these packages) egids = unlist(mget(symbols, org.Hs.egALIAS2EG, ifnotfound=NA)) egids ## then get the PMIDs for each EG mget(egids, org.Hs.egPMID, ifnotfound=NA) ## or if you like data.frames egids = unlist(mget(symbols, org.Hs.egALIAS2EG, ifnotfound=NA)) egTab = toTable(org.Hs.egALIAS2EG[symbols]) pmidTab = toTable(org.Hs.egPMID[egids]) merge(egTab, pmidTab) Of course, using gene symbols is fraught with peril as they are not guaranteed to be unique! So I would really not recommend using them that way. If you have a real ID like an entrex gene ID or an ensembl ID, I would recommend using that instead. You can read more about these by looking at the AnnotationDbi vignette here: http://www.bioconductor.org/help/bioc- views/release/bioc/html/AnnotationDbi.html Let us know if you need more help, Marc On 10/22/2010 08:42 AM, Qian Liu wrote: > Hi I am trying to get all the abstracts of a list of SNPs from pubmed. I > have got gene symbol for each SNP ID. > I am not extractly sure which annotation package should I use to map to > PMID. > What is the function I can use to map from gene symbol (or affy snp id) to > PMID? > > Thank you. > Liu > > [[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 >