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intermine

1.03.00

Webservice Client Library for InterMine Data-Warehouses

This library provides an interface to the InterMine webservices API. It makes construction and execution of queries more straightforward, safe and convenient, and allows for results to be used directly in Ruby code. As well as traditional row based access, the library provides an object-orientated record result format (similar to ActiveRecords), and allows for fast, memory efficient iteration of result sets.

Example

Get all protein domains associated with a set of genes and print their names:

require "intermine/service"

Service.new("www.flymine.org/query").
    new_query("Pathway")
    select(:name).
    where("genes.symbol" => ["zen", "hox", "h", "bib"]).
    each_row { |row| puts row[:name]}

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)

How to use this library:

We have tried to construct an interface to this library that does not require you to learn an entirely new set of concepts. As such, as well as the underlying methods that are common to all libraries, there is an additional set of aliases and sugar methods that emulate the DSL style of SQL:

SQL style

service = Service.new("www.flymine.org/query")
service.model.
   table("Gene").
   select("*", "pathways.*").
   where(:symbol => "zen").
   order_by(:symbol).
   outerjoin(:pathways).
   each_row do |r|
     puts r
   end

Common InterMine interface

service = Service.new("www.flymine.org/query")
query = service.new_query("Gene")
query.add_views("*", "pathways.*")
query.add_constraint("symbol", "=", "zen")
query.add_sort_order(:symbol)
query.add_join(:pathways)
query.each_row do |r|
  puts r
end

For more details, see the accompanying documentation and the unit tests for interface examples. Further documentation is available at www.intermine.org.

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

installgem install intermine -v 1.03.00
Authors

Alex Kalderimis

18,067 total downloads 504 for this version
Owners

B939a41c70402cb3e5551fc3d4d2556e

Licenses

LGPL

Gemfile
gem 'intermine', '~> 1.03.00'
Versions
  1. 1.04.00 July 8, 2013 (59 KB)
  2. 1.03.00 July 4, 2013 (58.5 KB)
  3. 1.02.00 June 27, 2013 (58.5 KB)
  4. 1.01.01 June 27, 2013 (58 KB)
  5. 1.01.00 March 1, 2013 (58 KB)
Show all versions (20 total)
Runtime Dependencies
  1. json >= 0