Hi there, I met some questions about arabidopsis annotation package(ath1121501, version 1.10), I will be truly grateful if any of you can help me with some questions. (1) I tried to get PUBMED ID for probesets (Affy) that have known function and known pubmed ID from website. However, the "ath1121501PMID" returns NA for them. For example, probeset "264328_at" has no pubmed ID in the package, but it has 5 Pubmed ID form NCBI website. ################## For example: > mget("264328_at",ath1121501PMID) $"264328_at" [1] NA ##I used 5 pubmed ID from NCBI website x=pubmed(c("7658471","11130712","14593172","12036262","14742873")) a <- xmlRoot(x) buildPubMedAbst(a[[1]]) ########################## So does this mean that package "ath1121501" contains only incomplete Pubmed ID, thus it can't be used to annotate gene? (2) I noticed that there were a newer version of "ath1121501" (version 1.11) at Bioconductor 1.8, does this one contain the complete list of all available pubmed ID? However, it is built on R 2.3 which is not publicly available now. Is there any way that I can obtain it? Thank you very much! Bests, Fangxin -------------------- Fangxin Hong Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong at salk.edu (Phone): 858-453-4100 ext 1105

Hi Fangxin, On Tue, 14 Mar 2006 fhong at salk.edu wrote: > > Hi there, > I met some questions about arabidopsis annotation package(ath1121501, > version 1.10), I will > be truly grateful if any of you can help me with some questions. > > (1) I tried to get PUBMED ID for probesets (Affy) that have known function > and known pubmed ID from website. However, the "ath1121501PMID" returns NA > for them. For example, probeset "264328_at" has no pubmed ID in the > package, but it has 5 Pubmed ID form NCBI website. > > ################## > For example: > > mget("264328_at",ath1121501PMID) > $"264328_at" > [1] NA > > ##I used 5 pubmed ID from NCBI website > x=pubmed(c("7658471","11130712","14593172","12036262","14742873")) > a <- xmlRoot(x) > buildPubMedAbst(a[[1]]) > ########################## > > So does this mean that package "ath1121501" contains only incomplete > Pubmed ID, thus it can't be used to annotate gene? > The package ath1121501 (version 1.10.0) is built by the public data we collected on September 29, 2005. Any updated information on the data website after September 29, 2005 would not be included in the package ath1121501 (version 1.10.0). > (2) I noticed that there were a newer version of "ath1121501" (version > 1.11) at > Bioconductor 1.8, does this one contain the complete list of all available > pubmed ID? However, it is built on R 2.3 which is not publicly available > now. Is there any way that I can obtain it? > The package ath1121501 (version 1.11.0) is also built by the 2005-09-25 data. The primary reason we re-built these packages (version 1.11.0) is to reflect the modification of "environment" data structure in R developmental version. The information are the same between version 1.10.0 and 1.11.0 of the package ath1121501. The coming BioConductor 1.8 release will update the meta data packages (version 1.12.0). > > Thank you very much! > > Bests, > Fangxin > > -------------------- > Fangxin Hong Ph.D. > Plant Biology Laboratory > The Salk Institute > 10010 N. Torrey Pines Rd. > La Jolla, CA 92037 > E-mail: fhong at salk.edu > (Phone): 858-453-4100 ext 1105 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA