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README.rdoc

Biological Extensions to the InterMine Webservice Client Library

This library is a set of extensions to the InterMine Webservices client, providing access for data in biological formats. It directly extends the InterMine classes, providing extra methods to the Query class.

Example

Get all sequences for proteins on “h”, “r”, “eve”, “bib” and “zen”:

require "rubygems"
require "intermine/service"
require "intermine/bio"

s = Service.new("www.flymine.org/query")
syms = %w{h r eve bib zen} 

puts s.query(:Gene).select(:proteins).where(:symbol => syms).fasta

Process the locations of these genes one at a time:

s.query.select(:Gene).where(:symbol => syms).bed do |line|
  process line
end

Who is this for?

InterMine data warehouses are typically constructed to hold Biological data, and as this library facilitates programmatic access to these data, this install is primarily aimed at bioinformaticians. In particular, users of the following services may find it especially useful:

* FlyMine (http://www.flymine.org/query)
* YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
* RatMine (http://ratmine.mcw.edu/ratmine)
* modMine (http://intermine.modencode.org/release-23)
* metabolicMine (http://www.metabolicmine.org/beta)

These extensions are aimed at bioinformaticians looking to integrate these sources of data into other workflows.

For details on constructing queries, see the intermine documentation.

Support

Support is available on our development mailing list: dev@intermine.org

License

This code is Open Source under the LGPL. Source code for all InterMine code can be checked out from svn://subversion.flymine.org/flymine

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