Hello All, Could anybody be able to assist me in trying to use R to retrieve PubMed abstracts for a list of Unigene IDs? I thank you in advance for your kind assistance. Lawrence _____________________________________________ Lawrence-Paul Petalidis Department of Pathology Division of Molecular Histopathology University of Cambridge Visiting Researcher Human Genome Mapping Project Resource Centre

>Hello All, Could anybody be able to assist me in trying to use R to >retrieve PubMed abstracts for a list of Unigene IDs? Have a look at the "pubmed" function in package "annotate". To map UG ids to LL ids that are required by "pubmed", use the package "XXXXLLMappings", where XXXX is the name of an organism (e. g. humanLLMappings). > >I thank you in advance for your kind assistance. >Lawrence > >_____________________________________________ >Lawrence-Paul Petalidis >Department of Pathology >Division of Molecular Histopathology >University of Cambridge > >Visiting Researcher >Human Genome Mapping Project Resource Centre > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Here is an example: library("humanLLMappings") library("annotate") ## developmental version library("XML") llIds <- lookUp(c("Hs.390608", "Hs.444776"), "humanLLMappings", "UG2LL") pmids <- lookUp(unlist(llIds), "humanLLMappings", "LL2PMID") abs <- pubmed(unlist(pmids), "data") abs <- getPMInfo(abs) # The first abstract in the list abs[[names(abs)[[1]]]][["abstract"]]

Hi, there are a number of functions in the annotate package, there is a Vignette entitled: HowTo: Automated Querying of PubMed Data and some of the lab materials also has examples of how to do a number of different things like obtaining abstracts and searching them using regular expressions. Robert On Thu, Nov 20, 2003 at 11:11:23AM -0500, John Zhang wrote: > > >Hello All, Could anybody be able to assist me in trying to use R to > >retrieve PubMed abstracts for a list of Unigene IDs? > > Have a look at the "pubmed" function in package "annotate". To map UG ids to LL > ids that are required by "pubmed", use the package "XXXXLLMappings", where XXXX > is the name of an organism (e. g. humanLLMappings). > > > > >I thank you in advance for your kind assistance. > >Lawrence > > > >_____________________________________________ > >Lawrence-Paul Petalidis > >Department of Pathology > >Division of Molecular Histopathology > >University of Cambridge > > > >Visiting Researcher > >Human Genome Mapping Project Resource Centre > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Biostatistics > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+