Synthetic Biology:Semantic web ontology

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Overview

This is a part of the effort to provide a standardized, extensible, scalable and machine-processable interface for the Registry of Standard Biological Parts. The ideas of the Semantic Web seem to provide a solution to this problem. The success of developing a Synthetic Biology ontology depends in part on a good definition of the BioBricks abstraction hierarchy.

Design

• Registry requirements
• Registry architecture

Meetings

First meeting

Tuesday (9/20/05) at 3pm, room 68-674
Minutes

Second meeting

Friday (9/23/05) at 10am, room 68-121
Minutes

References

• Semantic Web
  • RDF
  • RDF Schema
  • OWL
  • Query Languges
  • Rule Languages (SWRL)
• Web Services
• REST
• Agents
• Examples
• Software
• Notes

Miscellaneous

• Architecture of the World Wide Web, Volume One
• Object-oriented biology - application of object-oriented paradigm to Gene (from nodalpoint.org)
• SynBERC: Synthetic Biology Engineering Research Center is a multi-institution research effort to lay the foundation for synthetic biology, which aims to build biological components and assemble them into integrated systems to accomplish specific tasks
  • MIT SynBERC
• Registry of Standard Biological Models
• DOI & LSID info
• GeneDesign β2.0
• IBM DiscoveryLink provides users with a virtual database to which they can pose arbitrarily complex queries, even though the actual data needed to answer the query may originate from several different sources, and none of those sources, by itself, is capable of answering the query (data integration)

Lowercase semantic web

• Microformats
• Structured Blogging plugins to create and syndicate structured information, such as reviews and events

Contact: Ilya Sytchev

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