Ontology/Vocabulary Activity

Brief Description

Ontologies are formal representations of concepts in a domain of discourse. A number of biomedical ontologies, including Gene Ontology and SNOMED-CT, have been developed in recent years. Many factors contribute to the success of an ontology, as measured by how widely it is being adopted. One of the major driving forces is community involvement. Currently, most ontologies are controlled by a relatively small number of individuals and updates are released periodically to the users. Community-driven ontologies usually have wider acceptance by scientists as they are more likely to conform to the shared view of the community. In collaboration with the director of CIT, Jack Jones, HPCIO is investigating different methods in which biomedical ontologies/vocabularies can be created by contributions from members in the scientific community. We will leverage Web 2.0 technologies, including wikis, to foster an environment for community-driven ontology development.

The Salivary Proteome Project is an effort supported by NIDCR and multiple centers in the countries are involved to characterize about 1,700 proteins secreted by the salivary glands. HPCIO is working with NIDCR to implement a wiki-based platform that will allow about 100 to 200 researchers in this area to collaboratively annotate these proteins with information such as their molecular functions.

List of Collaborators

• Eleni Kousvelari, DDS, D.Sc.; Associate Director for Biotechnology and Innovation; National Institute of Dental and Craniofacial Research

• Jack Jones, Ph.D.; Acting CIO, NIH; Acting Director, Center for Information Technology 

Major Accomplishments in FY 2007

We have evaluated several semantic extensions to MediaWiki, including Semantic MediaWiki and OmegaWiki that facilitate annotation and ontology development. For the Salivary Proteome Project, we have identified WikiProfessional as the potential annotation server and are investigating its usability for this project.  The process of modeling the data for storage and transport has begun.

Anticipated Major Accomplishments in FY 2008

In FY 2008, we shall have obtained a copy of WikiProfessional hosted by NIH. All the necessary data will be imported to the system and customization will be made in accord with the needs of the Salivary Proteome Project. We shall develop a prototype to facilitate community-driven ontology development and use.  A desirable goal of this resource is that it will be extensible to multiple research communities.  Integration of the community annotation service into the caGrid architecture should facilitate discovery of public data and publication of the community annotations.