[BioRuby] use of CGI.escape in Bio::Pubmed.esearch
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Fri Nov 9 12:30:10 UTC 2007
Hi,
On Tue, 06 Nov 2007 10:54:00 +0100
Kaustubh Patil <kpatil at science.uva.nl> wrote:
> Hi,
>
> I would like to thank you for the BioRuby library, it is a very useful
> tool. I am doing some literature mining using Ruby and I use PubMed as
> my source. Here is some background for my question;
>
> It is not possible to search PubMed with logical operators, e.g.
> HIV+AND+drug or geneA+OR+geneB etc. using Bio::PubMed.esearch (it
> returns empty result).
Probably you mean
Bio::PubMed.esearch("HIV AND drug")
Bio::PubMed.esearch("geneA OR geneB")
More complicated example:
Bio::PubMed.esearch("((p53 AND apoptosis) 2007/11[dp]) OR bioperl")
You can use the same search terms as of NCBI PubMed seaech
without any care about URL encoding.
> It is due to the url encoding (i.e. CGI.escape) of the search term
> (approx. line 89 in pubmed.rb). If we remove this url encoding it is
> possible to make such queries.
>
> Now my question is, is it safe to remove this CGI.escape ?
I think it is unsafe and should not be removed.
--
Naohisa Goto
ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp
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