Poster Sessions

PROT-6

William Lau

W. W. Lau, L. Shum, C. A. Johnson

A collaborative annotation system for proteomics data using Semantic MediaWiki: Experience from the Human Salivary Proteome Project

A consortium of three research centers supported by the NIDCR has recently completed a catalog of 1,116 proteins in human saliva from healthy individuals. The mass spectrometry-based experimental data generated from the project have been imported into a wiki-based annotation system. A number of knowledge bases, including PubMed and SwissProt, have also been incorporated to enrich the data provided by the research groups. In addition, bioinformatics tools, such as multiple sequence alignment and protein signature identification, have been implemented to deliver users with dynamically generated, supplemental information about the proteins. The purpose of this resource is to facilitate community-driven annotation and vibrant discussion of the salivary proteins. Furthermore, data in the system have semantic markups in RDF format, thereby permitting machine-based reasoning to discover new knowledge. A commercial knowledge discovery engine, known as AKS2 (Alma Bioinformatics, Madrid, Spain), has been integrated into the wiki to support exploration of relationships among biomedical entities. The rich features of the system provide researchers across geographical locations, such as in the case of the Human Salivary Proteome Project, to coordinate their efforts, share results, perform curation, and discover new knowledge, in a user-centric manner customized to the needs and culture of the community.