GO Moose

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GO Moose aka GOBO is a replacement for the nearly 10-year old go-perl library. It is a perl library for handling ontologies constructed using the Moose framework.

See GOBO CPAN docs.


Installation

Now on CPAN (but out of date).

To install:

 sudo cpan GOBO

Developers: Obtaining the source

 svn co https://geneontology.svn.sourceforge.net/svnroot/geneontology/go-moose

Can be browsed here

to setup, follow the usual perl module procedure

 perl Makefile.PL
 make test

Object Model

The basic structure is:

Database connectivity

The plan is to have some kind of bridge or mapping to GODB, Chado and OBD DBIx-Class layers.

Currently GO-Moose can be used in conjunction with .obo files and GAF files.

Utilities

The main utility so far is go-gaf-inference.pl

This can be used to

In the future there will be additional sources of inconsistency and inference

Interoperation with BioPerl

There is currently an experimental project going on to implement bioperl2 using Moose:

The aim is to maximize compatibility and even use the exact same objects.

GOBO could move under this project (e.g. in the Biome::Ontology namespace)

GOBO: http://upload.wikimedia.org/wikipedia/commons/5/5e/Arctium_lappa02.jpg