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README.md

MeSHy

unanticipated knowledge discovery through statistical ranking of MeSH term pairs


server: http://bat.infspire.org/tools/meshy
citation: http://www.ncbi.nlm.nih.gov/pubmed/21684350
code: we provide the main Perl script, and the server's CGI script and HTML page - you'll need a few more things...
usage:
before you run MeSHy, be sure to:
- download the latest PubMed's MeSH term tree and frequencies (see code for details)
- update (in the code) the total (approximate) number of PubMed articles
- have installed the following Perl modules:
	Getopt::Long
	LWP::Simple
	XML::LibXML::Reader
	Statistics::Descriptive
+ we use TableFilter (now: https://koalyptus.github.io/TableFilter/) for HTML output

meshy.pl

either --query query you want to perform in PubMed, enclose it in double quotes or --xml results from PubMed in XML format

other (optional) arguments --threshold if log_odds is between threshold, remove MeSH term [default=5.0] --chem use chemical terms [default=on] --max_doc define the maximum number of documents you want to handle [default=10,000]

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unanticipated knowledge discovery through statistical ranking of MeSH term pairs

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