Software

Software written or maintained by BBOP.

Current software

AmiGO

AmiGO is the official tool for searching and browsing the Gene Ontology database.

AmiGO 2

The next generation of AmiGO.

Apollo

Apollo is a genomic annotation viewer and editor. It was originally developed as a collaboration between the Berkeley Drosophila Genome Project (part of the FlyBase consortium) and The Sanger Institute in Cambridge, UK.

Chado

Chado is a relational database schema that underlies many GMOD installations.

GOOSE

Allows nearly arbitrary SQL to be executed over the BBOP or EBI mirror of the GO database. It includes query templates, highlighted output, and downloads.

OBO-Edit

OBO-Edit is an open source ontology editor written in Java. This project is supported by the Gene Ontology Consortium.

Obolib obo2owl converter

The obolib obo2owl converter implements the official oboformat 1.4 obo to owl specification.

It converts all of obo to owl, and a subset of owl back to obo.

Oort

The OBO Ontology Release Tool (Oort) is an application to help manage ontologies and manage the ontology release process

OWLSim

The OWLSim package provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes.

PAINT

Phylogenetic Annotation and INference Tool (PAINT) is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree.

Phenote

Phenote is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies.

TermGenie

TermGenie is a web application for ontology content generation. It generates new terms according to pre-defined templates, and uses OWL reasoners to place the term in the correct place in the ontology