Ontolog Forum

William Bug

William Bug, M.S., M.Phil.

Ontological Engineer

Biomedical Informatics Research Network (BIRN)


National Center for Microscopy & Imaging Research (NCMIR)

Dept. of Neuroscience, School of Medicine

University of California, San Diego

La Jolla, CA 92093, USA.


William Bug obtained his B.S. in Biology from MIT in 1984. Immediately following, he received graduate training as a biophysical neuropharmacologist studying the molecular mechanisms of learning and memory at the Center for Neurobiology & Behavior at Columbia University.

Since the early 1990s, Mr. Bug has been working in biomedical knowledge management, first designing and developing multi-workstation LIMS systems for the pharmaceutical industry. This was followed by a period as head of product development for the oldest and largest biomedical citation database, The Biological Abstracts (BIOSIS). During his time at BIOSIS, Mr. Bug became involved in the development and use of complex biomedical controlled vocabularies as a means to constructing high-quality information retrieval systems for research biologists and clinicians. Having worked in this capacity as the first popular World Wide Web search engines (e.g., InfoSeek, Lycos, AltaVista, Excite, HotBot, etc.) emerged to dominate over the venerable engines in place for decades in the online and enterprise information retrieval industry (e.g., Dialog, OVID, Silverplatter, DataStar, etc.) at a time when the company he worked for - and his primary job responsibilities - depended on those earlier search engines, he learned first hand how critical it was to stay on the leading edge of innovation, when working in a technology driven discipline.

Following BIOSIS, Mr. Bug has worked as server technologies lead analyst for the National Software Testing Labs and as lead ontological engineer for the bioinformatics firm, DoubleTwist, Inc.. He then returned to his first passion, neuroscience, and has, since 2001, worked in the field of neuroinformatics developing Java-based brain atlas client server software, as well as a web service based image retrieval system.

In parallel with this application development work, Mr. Bug has retained a role in knowledge management within neuroscience. He is currently lead ontological engineer both for the Biomedical Informatics Research Network ( BIRNLex lexically-enhanced ontology (, and the ontology underlying the Neuroscience Information Framework (NIF - Both are OWL-DL ontologies used to power broadly scoped federated query mediation infrastructures. The former is focussed mainly on federating biomedical research database searches, where the data is annotated using the BIRNLex ontology. The latter includes research databases and other public data respositories, along with a registry of such resources, and a literature corpus all focussed on basic and clinical neuroscience research, where again the underlying ontology provides a unified semantic framework on which to cast federated queries and classify the results returned.

Recent Publications:

Smith B., et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007 Nov;25(11):1251-5.

Fong L., et al. (2007) An Ontology-Driven Knowledge Environment For Subcellular Neuroanatomy. OWL ED 2007.

Ruttenberg A., et al. (2007) Advancing translational research with the Semantic Web. BMC Bioinformatics. 2007 May 9;8 Suppl 3:S2.

Gustafson C., et al. (2007) NeuroTerrain--a client-server system for browsing 3D biomedical image data sets. BMC Bioinformatics. 2007 Feb 5;8:40.

Bug, W. et al. 2006. Brain Spatial Normalization: Indexing Neuroanatomical Databases. 2006. In Neuroinformatics, Chaquito, C., ed., from Methods Mol. Biol., Walker, J., series ed., Humana Press

Bug W. (2005) The impact of the NIH public access policy on literature informatics: What role can the neuroinformaticists play? Neuroinformatics. 2005;3(2):81-91.