Bioinformatics: Proteomics/Mass-Spectroscopy and Sequence Analysis.
Databases: Morphological Image Databases, Metric Databases.
Data Integration: Data Warehousing, Semantic Web, LSIDs, Ontologies.
After founding a dot-com, I have chosen to work only on research with active application to biology. This research is covered by two overarching projects, MoBIoS and Morphster.
The MoBIoS project concerns metric-space search methods and their integration into database management systems. The impetus driving MoBIoS is the thesis that the unique challenge in managing biological data is that sorting biological data, (e.g. sequences, spectra, 3-D molecular models), is often not possible, and even when it is possible it does not reflect the biological relationships among the objects. Thus, database management systems, (e.g. mySQL, Oracle), can not index the data and have no direct way of searching that data. Much of the power of a database is simply lost.
The Morphster project concerns distributed data integration, data provenance and morphological image data management. The larger context is the uniting of information standards across the NSF grand challenge to assemble the tree of life (ATOL), NIH model organism efforts (e.g. ZFIN), and global biodiversity information efforts (GBIF, TDWG). Morphster's targetted effort is the creation of a productivity tool for systemtic biologists. The tool enables users to create, organize and annotate an image database. Resulting Iiustrated ontologies may be published on the Ontobrowser web site. The interface metaphor is succintcly described as image-driven ontology editing. Users may import annotation vocabulary from diverse externally defined ontologies and extend those ontologies as needed. Existing ontologies already tested with Morphster include Nomina Anatomica, anatomical is-part-of ontologies for both fish and mouse, emerging vocabularies for comparing anatomies, CARO, and describing phenotypes, PATO. Primary accomplishments to date include a round-trip translation mechism between the OBO and OWL ontology languages and the integration of OBO ontologies into the Semantic Web.