Ontology views for collaborative ontology development and resource integration

Research into genetics, and into the ways in which organisms develop, produces large volumes of data. This data is of many different types, takes many forms and is generated by many different communities of scientists. As a result, it can be difficult to relate data and findings to one another. Part of the problem is in the terms used to talk about the data, and to describe it when it is stored in databases. The Gene Ontology is an exemplary solution to the problem of terminology - it is a shared, curated, community-based ontology (a set of terms and definitions). This ontology has been used with great success to describe the activities of gene products, i.e. proteins, and has enabled a range of new computational analyses. Ontologies for anatomy, phenotype and clinical studies are also important. Many of these are either active areas for ontology development where consensus has yet to be reached, or have ontologies whose organisation needs to be kept under review. At the very least, any ontology that is in use will be curated and subject to minor extensions and alterations. In all cases, effective collaborative ontology development is essential to progress and appropriate tools are needed. This project will implement tools to support the collaborative development of biological ontologies by expert biologists. To improve on existing tools that do not support collaboration among experts across different locations, we propose a Grid-based portal that provides access to a database of ontologies that the user accesses securely through a familiar web browser. The portal will provide tools for displaying, editing and searching over the ontologies in the database. These tools are installed and maintained by the developers so freeing the user from these tasks.

This project will implement tools to support the collaborative development of biological ontologies by expert biologists. Current technological support for bio-ontology development relies on stand-alone ontology editors for creating new ontology versions, and ad-hoc ways of distributing ontology files and reviewing their contents. To improve on this situation, we propose a Grid-based portal that provides access to a database of ontologies that the user accesses securely through a familiar web browser. The portal will provide tools for displaying, editing and searching over the ontologies in the database. These tools are installed and maintained by the developers so freeing the user from these tasks (noted barriers to the adoption of new tools). Each user will create a view of the ontology as they edit and extend it. Each user's view, and the versions they create within it, will be stored efficiently by modifying the source XML document, rather than saving previous versions in their entirety. Computationally, two view mechanisms will be used in combination: XML views are created by from the source XML document by rewriting XPath queries. These queries return OWL 1.1 ontologies derived from the source XML. The second view mechanism to be used is ontology views. These are subsets of the entire ontology, for example, all the concepts within a given distance of a selected term. Ontology views are small, connected sub-graphs that help the user understand the local structure of the ontology. These notions of view subsume existing features of the Gene Ontology such as 'GO-slims' and the 'subset' mechanism. Having allowed each user to create views, the tool will allow users to see the intersection of their view with that of the entire development group in order to identify the common core of the ontology. Similarly, the tool will allow two users to locate those parts of the ontology where they agree or disagree.