A synthetic biology library for the Semantic Web

Award Information
Agency:
Department of Health and Human Services
Branch
n/a
Amount:
$99,967.00
Award Year:
2010
Program:
STTR
Phase:
Phase I
Contract:
1R41LM010745-01
Award Id:
n/a
Agency Tracking Number:
R41LM010745
Solicitation Year:
2010
Solicitation Topic Code:
NLM
Solicitation Number:
PA09-081
Small Business Information
926 N ST NW REAR, STUDIO #1, WASHINGTON, DC, 20001-
Hubzone Owned:
N
Minority Owned:
N
Woman Owned:
N
Duns:
171840031
Principal Investigator:
EVREN SIRIN
(202) 688-0596
evren@clarkparsia.com
Business Contact:
KENDALL CLARK
(202) 408-8770
kendall@clarkparsia.com
Research Institution:
University Of Washington

Office of Sponsored Programs
SEATTLE, WA, 98195-9472
() -
Nonprofit college or university
Abstract
DESCRIPTION (provided by applicant): The goal of the proposed research is to determine the feasibility of, and create prototype software for, a library of reusable synthetic biology components using Semantic Web technologies OWL, RDF, SPARQL and SWRL. Thislibrary will dramatically increase the availability of information about reusable components for synthetic biology, including machine-readable descriptions of the semantic meaning of the components. Such information, amenable to automated reasoning, intelligent retrieval, and other services, will increase the utility of the synthetic biology library for researchers as well as for commercial vendors engaged in designing synthetic biology products. Such a library will hasten the industrialization of synthetic biology, with a host of resulting benefits to public health, including better living machines designed and manufactured more quickly and efficiently. In order to achieve these results, in Phase I we will extend BioBricks standard biological component descriptions with semantically-rich descriptions, using OWL ontologies, to support better integration, both with other components, via model checking and verification-style analysis services, as well as with the wealth of biological background knowledgethat presently exists in OWL ontology form. We will extend OWL reasoning systems to interpret these semantically rich BioBrick descriptions, including Semantic Web query support via SPARQL and rule support via SWRL. Phase I deliverables include use case and requirements from bioengineering; gap analysis between these requirements and existing technologies; a final report detailing lessons learning and preliminary designs for Phase II; and a prototype library containing OWL-extended BioBrick descriptions andOWL, SPARQL, and SWRL reasoning and query services; and a faceted BioBrick browser for intuitive interaction with the library's entries. In short, better information sharing and analysis infrastructure will provide productivity increases for synthetic biology researchers and practitioners, which will in turn hasten the widescale industrial adoption and use of synthetic biology techniques, leading to new advances in bioengineered therapeutic, energy, and food technologies. PUBLIC HEALTH RELEVANCE: The relevance of the proposed research to public health is that a Semantic Web-enabled library for synthetic biology will increase the design quality and efficiency-via computer-aided decision support and seamless information sharing-of synthetic biology RandD and industrial activity, thus hastening the advent of industrialscale synthetic biology. That advent will directly benefit public health by way of better living machines to address therapeutics, energy, food, and other vital areas.

* information listed above is at the time of submission.

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