[BioC] libraries or commands to help with parsing or handling web based database queries

ALAN SMITH alansmith2 at gmail.com
Mon Feb 19 18:41:47 CET 2007


Hello Bioconductors
I am having a very hard time figuring out how to make web based
database query results into a nice neat table (if such a thing is
possible in R).  I am constantly searching the metabolite database
METLIN by copying and pasting addresses.  I have to search this
database with several hundred entries, often, and would like to
automate the process to remove the HUGE amount of time I spend doing
this carpel tunnel creating routine.  I have found several ways to get
the pages source like.

library(RCurl)
test<-getURL("http://metlin.scripps.edu/metabo_list.php?mass_min=112.04885&mass_max=112.0555")
#OR
url.show("http://metlin.scripps.edu/metabo_list.php?mass_min=112.04885&mass_max=112.0555")

Once I get the URL info I notice that the data I am interested in is
between  </form>  and  </table>.

Are there any packages or methods in R to remove the information I am
interested in?  I am having problems manipulating STRINGS in R like
selecting all of the text between two strings.  I am not a programmer.

Thanks,
Alan

Note I am able to use KEGGSOAP without any trouble.



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