Computational knowledge integration in biopharmaceutical research
Led several projects in bioinformatics and knowledge engineering at Millennium. He was formerly with the Washington University Genome Center.
Molecular and computational biologist who developed J. Mill. and the Knowledge Intermediary program at Millennium.
Postdoctoral fellow at the Applied Biodynamics Lab, Boston University. His work applies mathematics and statistics to complex biological systems such as intracellular networks.
Leads computational biology at Ingenuity. He previously led Ingenuity's efforts in natural language processing.
Ingenuity's CTO and cofounder of the Stanford University Medical Media & Information Technologies Center. He founded Digital Alchemy.
Managed efforts in R&D and business development at Ingenuity. He previously led projects in collaborative technology innovation with Affymetrix and Stanford University.
Oversees product strategy and management at Ingenuity, Inc. He previously ran knowledge engineering and acquisition operations at Ingenuity.
Lead software architect focusing on scalable interoperability. He developed Millenium software integration architecture, and was formerly with The Math Works.
Molecular and computational biologist currently working in the Knowledge Management practice at Millennium.
The PARIS software project manager. Previous work includes parallel computing, computer vision, knowledge representation and user interface.
Trained in oncology and molecular biology and has worked extensively in computational biology at Millennium and the EBI.
Heads Millennium's Knowledge Management practice. He was formerly an executive consultant with IBM Business Consulting.
Led development of Millennium's bioinformatics, cheminformatics and knowledge engineering programmes from their inception. He was previously at the NCBI, where he helped develop GenBank.
Tim Clark, 12 Dana Street, Brookline, MA 02445, USA Tel: +1 617 947 7098 E-mail: tim.clark{at}acm.org
An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software components rely on mutually supporting integration techniques. These include a richly structured ontology, statistical analysis of experimental data against stored conclusions, natural language processing of public literature, secure document repositories with lightweight metadata, web services integration, enterprise web portals and relational databases. This approach has already begun to increase scientific productivity in our enterprise by creating an organisational memory (OM) of internal research findings, accessible on the web. Through bringing together these components it has also been possible to construct a very large and expanding repository of biological pathway information linked to this repository of findings which is extremely useful in analysis of DNA microarray data. This repository, in turn, enables our research paradigm to be shifted towards more comprehensive systems-based understandings of drug action.
Keywords: ontology, knowledge base, pharmaceutical, drug discovery, microarray, biochemical pathway