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Now on CPAN (but out of date).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

http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-moose/

to setup, follow the usual perl module procedure

 perl Makefile.PL
 make test

Object Model

The basic structure is:

Node
- InstanceNode - not used in most OBO ontologies
- RelationNode - e.g. part_of, is_a
- ClassNode - things that are instantiated
  - ClassExpression - a logical expression defining a class intensionally.
  - TermNode - named classes
Statement
- LinkStatement - edge in a graph

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

check for inconsistencies in a GAF (currently using the go-taxon links - see Category:Taxon )
make new inferences in a GAF (currently using the Function-Process_Links)

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:

http://github.com/cjfields/biome/tree/master

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