Synthetic Biology:Semantic web ontology: Difference between revisions
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This is a part of the effort to provide a standardized, extensible, scalable and machine-processable interface for the [http://parts.mit.edu/ 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 [[Synthetic Biology:Abstraction hierarchy | BioBricks abstraction hierarchy]]. | This is a part of the effort to provide a standardized, extensible, scalable and machine-processable interface for the [http://parts.mit.edu/ 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 [[Synthetic Biology:Abstraction hierarchy | BioBricks abstraction hierarchy]]. | ||
== | ==Design== | ||
*[[Synthetic_Biology:Semantic_web_ontology/Registry_requirements|Registry requirements]] | |||
*[[Synthetic_Biology:Semantic_web_ontology/Registry_architecture|Registry architecture]] | |||
* | |||
==Meetings== | ==Meetings== | ||
Line 47: | Line 35: | ||
*[http://www.w3.org/TR/webarch/ Architecture of the World Wide Web, Volume One] | *[http://www.w3.org/TR/webarch/ Architecture of the World Wide Web, Volume One] | ||
*[http://www.nodalpoint.org/node/1645 Object-oriented biology] - application of object-oriented paradigm to Gene (from nodalpoint.org) | *[http://www.nodalpoint.org/node/1645 Object-oriented biology] - application of object-oriented paradigm to Gene (from nodalpoint.org) | ||
*[http://www.synberc.org/ SynBERC]: [[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 | *[http://www.synberc.org/ SynBERC]: [[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 | ||
**[[SynBERC:MIT|MIT SynBERC]] | **[[SynBERC:MIT|MIT SynBERC]] | ||
*[[Registry_of_Standard_Biological_Models|Registry of Standard Biological Models]] | *[[Registry_of_Standard_Biological_Models|Registry of Standard Biological Models]] | ||
*[[DOI|DOI & LSID info]] | *[[DOI|DOI & LSID info]] |
Revision as of 12:09, 7 September 2006
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
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
- 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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