EMPWR.ORG
From HMS Genetics Department Wiki
EMPWR: Computational Exploration of Molecules in the Context of Biological Pathway Networks
Joanne Luciano
Principal Investigator
Project Summary
This project seeks to computationally explore biomolecules in the context of networks of different biological pathways. The methods employed are built upon the combination of two complementary technologies, BioPAX and the instance Store. BioPAX is an emerging standard for the representation of biological pathway data exchange such as metabolic pathways, signal transduction pathways, and gene regulatory networks. It is an ontology written in the Web Ontology Language (OWL) to describe genes, proteins, enzymes, and small molecules in metabolic, signal transduction, and molecular interaction pathways. The recently developed instance Store takes an ontology and the data it describes formally represented in OWL and uses reasoning technology to ask questions and make inferences about these data. Joanne wishes to use the developing instance Store in conjunction with complex BioPAX data to explore biological pathway data to make novel and interesting biological inferences. The combination of these two technologies, along with data represented in this language makes scalable computational biological exploration possible. Methodology employed will first identify appropriate sources of data and then convert them to the BioPAX OWL format. Once this is complete, systematic biological exploration can commence. This will create a cycle that will raise questions and inspire further modifications and improvements. The benefits are threefold: it will create the technology necessary to support new discoveries, a better understanding of current technology, and the potential for new discovery.
Intellectual Merit
The combination of these two nascent technologies will enable the knowledge captured in the BioPAX OWL schema to realize its full potential and enable scientific discovery through seamless integration of multiple disparate data sources. A common language facilitates the creation and interoperability of analysis tools. The instance Store allows BioPAX to be more easily understood by humans and allows for easy manipulation of the data.
Broader Impact
Understanding and reasoning over these data will enhance life science research in drug discovery, where it will provide a way of exploring the context in which a particular drug target lies; disease research such as cancer, to facilitate the understanding of the cancer pathways, thus leading to better diagnosis and treatment; and environmental research such as bioremediation, by providing integrated data that will facilitate analyses of metabolic pathways such as Flux Balance Analysis. Moreover, this work will have major impact on the development of Semantic web technology because the life sciences provide the vast quantities of data and use cases that are needed to both test and drive forward the development of next generation Web technology. The World Wide Web Consortium has recently recognized the Life Sciences by holding a Workshop in Cambridge, Massachusetts to learn about its relevance. It has since begun an official life science initiative. In addition, the proposed work will have major impact on multiple challenging areas in biological research because biological pathways are present in all living organisms.
Collaborators
EMPWR is funded by the United States National Science Foundation Award Number IIS-0542041
