Synthetic Biology:Semantic web ontology

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==Overview==
==Overview==
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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]].
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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]. 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 [[Synthetic Biology:Abstraction hierarchy | BioBricks abstraction hierarchy]].
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==Design==
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==Meetings==
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*[[Synthetic_Biology:Semantic_web_ontology/Registry_requirements|Registry requirements]]
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*[[Synthetic_Biology:Semantic_web_ontology/Registry_architecture|Registry architecture]]
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===Meetings===
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*First meeting
*First meeting
:Tuesday (9/20/05) at 3pm, room 68-674; [[Synthetic Biology:SWO1minutes|minutes]]
:Tuesday (9/20/05) at 3pm, room 68-674; [[Synthetic Biology:SWO1minutes|minutes]]
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:Friday (9/23/05) at 10am, room 68-121; [[Synthetic Biology:SWO2minutes|minutes]]
:Friday (9/23/05) at 10am, room 68-121; [[Synthetic Biology:SWO2minutes|minutes]]
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==References==
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==Resources==
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*[[Synthetic_Biology:Semantic_web_ontology/Design|Design]]
*[[Synthetic_Biology:Semantic_web_ontology/Semantic_Web|Semantic Web]]
*[[Synthetic_Biology:Semantic_web_ontology/Semantic_Web|Semantic Web]]
**[[Synthetic_Biology:Semantic_web_ontology/RDF|RDF]]
**[[Synthetic_Biology:Semantic_web_ontology/RDF|RDF]]
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*[[Synthetic_Biology:Semantic_web_ontology/Examples|Examples]]
*[[Synthetic_Biology:Semantic_web_ontology/Examples|Examples]]
*[[Synthetic_Biology:Semantic_web_ontology/Software|Software]]
*[[Synthetic_Biology:Semantic_web_ontology/Software|Software]]
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*[[Synthetic_Biology:Semantic_web_ontology/Notes|Notes]]
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*[[Synthetic_Biology:Semantic_web_ontology/Knowledge_representation|Knowledge representation]]
==Miscellaneous==
==Miscellaneous==
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*[http://www.w3.org/DesignIssues/Overview.html Design Issues for the World Wide Web]
*[http://www.w3.org/DesignIssues/Overview.html Design Issues for the World Wide Web]
**[http://www.w3.org/DesignIssues/HTTP-URI.html What do HTTP URIs Identify?]
**[http://www.w3.org/DesignIssues/HTTP-URI.html What do HTTP URIs Identify?]
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*[http://dig.csail.mit.edu/ Decentralized Information Group] @ CSAIL
*[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
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*[[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]]
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*[http://slam.bs.jhmi.edu/gd/ GeneDesign β2.0]
 
*[http://researchweb.watson.ibm.com/journal/sj/402/haas.html 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)
*[http://researchweb.watson.ibm.com/journal/sj/402/haas.html 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)
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*[http://mitdatacenter.org/ 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: [[User:Ilya|Ilya Sytchev]]
Contact: [[User:Ilya|Ilya Sytchev]]

Current revision

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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. 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

Miscellaneous

Contact: Ilya Sytchev

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