[BioC] annotate() and genbank and XML

[Andrew Yee]

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.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=Nucleotide&id=NM_000610")
>
> 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
>>
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>
>