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intermine-bio
= 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")
puts s.query("Gene").select("proteins").where(:symbol => %w{h r eve bib zen}).fasta
Process the locations of these genes one at a time:
s.query.select("Gene").where(:symbol => %w{h r eve bib zen}).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: [email protected]
== 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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