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. Semantic Web technologies 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.

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

Resources

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

Miscellaneous

• Architecture of the World Wide Web, Volume One
• Design Issues for the World Wide Web
  • What do HTTP URIs Identify?
• Decentralized Information Group @ CSAIL
• 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
• 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)
• The Data Center at the Massachusetts Institute of Technology is a new initiative charged with researching and developing the languages, protocols, and technologies to integrate data and models across global networks.

Contact: Ilya Sytchev