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A synthetic biology library for the Semantic Web

Award Information

Agency:
Department of Health and Human Services
Branch:
N/A
Award ID:
Program Year/Program:
2010 / STTR
Agency Tracking Number:
R41LM010745
Solicitation Year:
2010
Solicitation Topic Code:
NLM
Solicitation Number:
PA09-081
Small Business Information
CLARK AND PARSIA, LLC
926 N ST NW REAR STUDIO #1 WASHINGTON, DC -
View profile »
Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No
 
Phase 1
Fiscal Year: 2010
Title: A synthetic biology library for the Semantic Web
Agency: HHS
Contract: 1R41LM010745-01
Award Amount: $99,967.00
 

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.

Principal Investigator:

Evren Sirin
202-688-0596
evren@clarkparsia.com

Business Contact:

Kendall Clark
202-408-8770
kendall@clarkparsia.com
Small Business Information at Submission:

CLARK AND PARSIA, LLC
926 N ST NW REAR STUDIO #1 WASHINGTON, DC 20001-

EIN/Tax ID: 154218794
DUNS: N/A
Number of Employees: N/A
Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No
Research Institution Information:
University Of Washington
Office of Sponsored Programs
SEATTLE, WA 98195-9472
Contact: