It is important that research data is properly annotated using a standard terminology in order for the data and findings to be retrieved effectively by computational search. Standard terminologies, or ontologies, have been widely adopted in bioinformatics and software tools for their development are needed.
Many biological ontologies are developed by loosely-organised groups who develop their ontology remotely. These groups tend to be formed from scientists and bio-informaticians from research groups with a common interest, who want to create a resource that will be useful to the community. This project created such a resource.
Until recently, technological support for bio-ontology development relied on stand-alone editors running on users’ desktops for creating new ontology versions (e.g. OBO-Edit, COBrA and Protégé) and on private email, email lists and perhaps Wikis for the distribution of ontology files and discussions. Clearly, much better use could be made of the storage, versioning and visualisation techniques being developed by the database and e-Science communities.
The tool developed in this project, BioSphere, is an online ontology editor supporting multiple users and is underpinned by a server that stores versions (in OWL-XML) and provides a discussion portal. The project built on existing Grid technology, adding novel graphical user interface components that rendered multiple views of an ontology. The data from which each user's version of the ontology is created is stored with mark-up that maintains the version history (multiple users each with multiple versions) in a single XML database file. Effective strategies for version management, and the corresponding user interface design were demonstrated in this project.