Synthetic Biology:Semantic web ontology: Difference between revisions
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==Overview== | ==Overview== | ||
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]. | 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]]. | ||
==Meetings== | ==Meetings== | ||
*First meeting | |||
Tuesday (9/20/05) at 3pm, room 68-674 | :Tuesday (9/20/05) at 3pm, room 68-674; [[Synthetic Biology:SWO1minutes|minutes]] | ||
[[Synthetic Biology:SWO1minutes| | *Second meeting | ||
: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| | |||
== | ==Resources== | ||
*[[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]] | ||
*[[Synthetic_Biology:Semantic_web_ontology/RDF_Schema|RDF Schema]] | **[[Synthetic_Biology:Semantic_web_ontology/RDF_Schema|RDF Schema]] | ||
*[[Synthetic_Biology:Semantic_web_ontology/OWL|OWL]] | **[[Synthetic_Biology:Semantic_web_ontology/OWL|OWL]] | ||
*[[Synthetic_Biology:Semantic_web_ontology/Query|Query Languges]] | **[[Synthetic_Biology:Semantic_web_ontology/Query|Query Languges]] | ||
*[[Synthetic_Biology:Semantic_web_ontology/SWRL|Rule Languages (SWRL)]] | **[[Synthetic_Biology:Semantic_web_ontology/SWRL|Rule Languages (SWRL)]] | ||
*[[Synthetic_Biology:Semantic_web_ontology/Web Services|Web Services]] | *[[Synthetic_Biology:Semantic_web_ontology/Web Services|Web Services]] | ||
*[[Synthetic_Biology:Semantic_web_ontology/REST|REST]] | *[[Synthetic_Biology:Semantic_web_ontology/REST|REST]] | ||
| Line 42: | Line 25: | ||
*[[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]] | ||
*[[Synthetic_Biology:Semantic_web_ontology/ | *[[Synthetic_Biology:Semantic_web_ontology/Knowledge_representation|Knowledge representation]] | ||
==Miscellaneous== | ==Miscellaneous== | ||
*[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.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://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 | ||
**[[SynBERC:MIT|MIT SynBERC]] | |||
*[[Registry_of_Standard_Biological_Models|Registry of Standard Biological Models]] | |||
**[[ | |||
*[[ | |||
*[[DOI|DOI & LSID info]] | *[[DOI|DOI & LSID info]] | ||
*[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) | ||
*[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]] | ||
Latest revision as of 00:31, 26 September 2007
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
- Architecture of the World Wide Web, Volume One
- Design Issues for the World Wide Web
- 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
- 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
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