What is OBO-Edit?

OBO-Edit is an open source, platform-independent application for viewing and editing ontologies. It was originally designed for use with OBO ontologies, but it can now handle several other ontology formats as well.

OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes.

This tutorial provides a good introduction to the use of OBO-Edit, especially for some of the more advanced features, such as the reasoner and cross-products.

A Brief History of OBO-Edit

OBO-Edit began life as GO-Edit, a tool designed exclusively for use in editing the Gene Ontology. As more and more projects began to adopt the Gene Ontology standards for ontologies, GO-Edit became more flexible to accommodate the needs of more diverse ontologies. Eventually, GO-Edit became so general that it was renamed DAG-Edit, because DAG-Edit "ontologies" were a special sort of Directed Acyclic Graph.

DAG-Edit was a useful, fairly configurable tool. However, the code carried a lot of baggage from its former life as GO-Edit. And at its heart, DAG-Edit was really a program for editing labeled, directed graphs, not an ontology editor. DAG-Edit users began to have more and more complex needs for their ontologies. The Open Biomedical Ontologies project developed a new, much more expressive file format for describing ontologies. It was time for DAG-Edit to undergo another transformation.

So DAG-Edit became OBO-Edit, hopefully to be renamed for the last time. OBO-Edit is faster, more memory efficient, and more fully featured than its ancestors. OBO-Edit is a complete (if simple) ontology editor, with full support for the OBO ontology format (as well as several other ontology file formats, such as GO and OWL).

OBO-Edit 2: The Sequel

In October 2007, the decision was made to split the OBO-Edit code into three modular and reusable projects, known as bbop, obo, and oboedit. At the same time, the user interface of OBO-Edit was radically improved and revised (a process that is still under way).

This user guide has been updated to correspond to OBO-Edit 2. If you notice anything missing, out of date, or otherwise inaccurate in it, please use our bug tracker at http://sourceforge.net/tracker/?group_id=36855&atid=418257 to report the discrepancy.

People

OBO-Edit was orginally developed by John Day-Richter.

Amina Abdulla, Jennifer Deegan, Heiko Dietze, Nomi Harris, Chris Mungall, Nicolas Rodriguez and Nicole Washington have contributed additional programming.

Many OBO-Edit Working Group members have contributed to testing, documentation, etc., including Tanya Berardini, Marcus Chibucos, Karen Christie, Laurel Cooper, Wasila Dahdul, Alex Diehl, Harold Drabkin, Karen Eilbeck, Erika Feltrin, Rebecca Foulger, Melissa Haendel, Midori Harris, Wacek Kusnierczyk, Terry Meehan, David Osumi-Sutherland, Paola Roncaglia, Ramona Walls, and others.