Thanks for the reply. ?I guess on a broader level, is there a way to extract the sig_peptide field from http://www.ncbi.nlm.nih.gov/nuccore/NM_000610.3 I'm trying to figure out why the document reference in Carey's example doesn't contain "sig_peptide" yet is visible on that web page. Perhaps there is another method of getting the annotation for sig_peptide within GenBank? Thanks, Andrew On Wed, Sep 21, 2011 at 4:07 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > I don't see a sig_peptide field.? You should have a look at > > http://www.omegahat.org/RSXML/shortIntro.html > > and references therein. > > It has been a long time since I did anything with XML per se. We did a > certain amount of exposition in Chapter 8 > of the 2005 Springer monograph.? Since then more XPath support has come in > and many new ideas help distance users from > details of XML processing.? To illustrate a bit with your example, I trapped > the actual document reference > > zz = > xmlInternalTreeParse("http://www.ncbi.nih.gov/entrez/eutils/efetch.f cgi?tool=bioconductor&rettype=xml&retmode=text&db=Nucleotide&id=NM_000 610") > > and then performed an XPath query > >> getNodeSet(zz, "//Seq-interval_from") > [[1]] > <seq-interval_from>3244</seq-interval_from> > > [[2]] > <seq-interval_from>3328</seq-interval_from> > > [[3]] > <seq-interval_from>5695</seq-interval_from> > > and so on.? I don't recall how to do a relatively simple task like > "enumerate all tags in use in a document" but it can be done with the XML > package tools.? I think it will be more effective to isolate the use case > and see how to use eutils to solve it fairly directly as opposed to wading > through XML, but perhaps wading is inevitable. > > > On Wed, Sep 21, 2011 at 12:29 PM, Andrew Yee <yee at="" post.harvard.edu=""> wrote: >> >> Hi, I'm looking for some guidance in terms of parsing the XML output >> from a genbank query. >> >> result <- genbank('NM_000610', disp='data', type='uid') >> >> I'm trying to figure out how to use the XML package in order to parse >> out the "sig_peptide" field from the XML output from the genbank >> query. >> >> Any pointers or suggestions would be appreciated, as I'm new to XML. >> >> Thanks, >> Andrew >> >> >> >> > sessionInfo() >> R version 2.13.0 (2011-04-13) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] XML_3.2-0 ? ? ? ? ? ? annotate_1.29.4 ? ? ? AnnotationDbi_1.13.21 >> [4] Biobase_2.11.10 >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 ? ? RSQLite_0.9-4 tools_2.13.0 ?xtable_1.5-6 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >