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.
Now on CPAN (but out of date).
sudo cpan GOBO
Developers: Obtaining the source
Can be browsed here
to setup, follow the usual perl module procedure
perl Makefile.PL make test
The basic structure is:
- LinkStatement - edge in a graph
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.
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:
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)