https://github.com/intermine/intermine-ws-bio-ruby
Bio Extensions for the Ruby WS client
https://github.com/intermine/intermine-ws-bio-ruby
Last synced: 3 months ago
JSON representation
Bio Extensions for the Ruby WS client
- Host: GitHub
- URL: https://github.com/intermine/intermine-ws-bio-ruby
- Owner: intermine
- License: lgpl-3.0
- Created: 2011-10-17T00:13:53.000Z (about 14 years ago)
- Default Branch: master
- Last Pushed: 2011-10-17T00:14:14.000Z (about 14 years ago)
- Last Synced: 2025-03-13T02:16:08.477Z (10 months ago)
- Language: Ruby
- Homepage: www.intermine.org
- Size: 102 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rdoc
Awesome Lists containing this project
README
= 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