go-perl

GO Consortium

go-perl [external website] is a set of perl modules for parsing, manipulating and exporting ontologies and annotations. It includes parsers for OBO and GO association file formats. It is also an object model, centered around graphs [external website], with methods for graph traversal. For more details, see the go-perl introduction [external website].

go-perl comes bundled with various XSL [external website] transforms (which can also be used independently of perl, provided you have obo-xml files), as well as various scripts such as map2slim [external website] that can be used as standalone tools.

Installation should be simple, provided you have some experience with perl and CPAN - there are only a few dependencies. See the INSTALL [external website] files for details.

go-db-perl

GO Consortium [external website]

go-db-perl extends the functionality of go-perl (on which it depends) with GO Database access functionality.

go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools

Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI/DBD modules. Follow the INSTALL instructions in the Makefile.PL

go-db-perl is in use both to drive AmiGO and internally within Ensembl

BioPerl

Open-Bio[external website]

BioPerl is a set of perl modules for use in bioinformatics. It includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies

BioConductor

bioconductor[external website]

BioConductor is a package for statistical analysis of genomic data using the R language. It includes modules for analysis of GO datasets:

• goTools -- Wrapper functions for description/comparison of oligo ID list using Gene Ontology database
• ontoTools -- tools for working with ontologies and graphs

org.geneontology.oboedit

GO Consortium [external website]

OBOEdit is best known as a standalone application for editing ontologies. In fact the UI components are cleanly separated from the datamodel and data adapters, so these can be reused in other applications. The oboedit foward-chaining reasoner can also be used independently (for example, for traversing ontology graphs).

org.geneontology.oboedit is used in tools such as the Ontology Lookup Service and Phenote

See the wiki for instructions on downloading the source

Ontology Lookup Service

European Bioinformatics Institute [external website]

The OLS is best known as a web interface to the Open Bio-Ontologies (OBO) collection. The OLS codebase can also be used as a web service or as a colection of J2EE compliant libraries

The OLS code depends on org.geneontology.oboedit

LexGrid

European Bioinformatics Institute [external website]

LexGrid is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services. LexGrid can parse obo-format, as well as other formats such as OWL.

OWLAPI

University of Mancheser [external website]

The OWLAPI is a java application programmer interface for OWL-based ontologies. The latest version of the API contains an OBO-Format parser. The OWLAPI underpins ontology browsing and editing tools and platforms such as SWOOP and Protege4

Note that this API, or any other OWL-based API can be used without an integrated OWL parser, if you download a pre-converted OWL file generated from OBO. See OBO Ontologies List for all OBO ontologies converted to OWL.

(We do not list the full complement of OWL-based APIs here, only ones of direct relevance to GO)

Blip

BBOP [external website]

Blip (Biomedical LogIcal Programming) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations.

Blip underpins the Obol tool