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 [[BioBricks_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]. 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]].
==Registry features==
==Registry features==
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*[[Registry_Wish_List]]
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*[[Registry Wish List]]
*Subpart Search: search for parts that match a portion of this part or this sequence of parts. Software agent would take a part name and using the ontology definitions would query other registries via their semantic web interfaces (no need to know about schema: e.g., just say "need all <#part>s that match a <#component> of the given <#part>"). Software agent can search anyone's registry if they use a common ontology: simply follow URLs (or use query language) and add triples to the local RDF store.
*Subpart Search: search for parts that match a portion of this part or this sequence of parts. Software agent would take a part name and using the ontology definitions would query other registries via their semantic web interfaces (no need to know about schema: e.g., just say "need all <#part>s that match a <#component> of the given <#part>"). Software agent can search anyone's registry if they use a common ontology: simply follow URLs (or use query language) and add triples to the local RDF store.
*Superpart Search: search for parts that contain the given parts
*Superpart Search: search for parts that contain the given parts
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*[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  
*[http://www.nodalpoint.org/node/1645 Object-oriented biology] - application of object-oriented paradigm to Gene  
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*[[Receiver_Definition]]
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*[[Receiver Definition]]
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*[[BioBricks|BioBricks]]: protocols and standards.
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*[[Synthetic Biology:BioBricks|BioBricks]]: protocols and standards.
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*[[BioBricks_abstraction_hierarchy | BioBricks abstraction hierarchy]]
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*[[Synthetic Biology:Abstraction hierarchy | BioBricks abstraction hierarchy]]
Contact: [[User:Ilya|Ilya Sytchev]]
Contact: [[User:Ilya|Ilya Sytchev]]
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{{Synthetic biology bottom}}

Revision as of 23:06, 3 January 2006

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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.

Registry features

  • Registry Wish List
  • Subpart Search: search for parts that match a portion of this part or this sequence of parts. Software agent would take a part name and using the ontology definitions would query other registries via their semantic web interfaces (no need to know about schema: e.g., just say "need all <#part>s that match a <#component> of the given <#part>"). Software agent can search anyone's registry if they use a common ontology: simply follow URLs (or use query language) and add triples to the local RDF store.
  • Superpart Search: search for parts that contain the given parts
  • What about sub- and superpart searches in distributed registries?
  • Search for function (case insensitive): repressor, reporter, inverter, etc.
  • What are the available (instances of) parts? Are they used in any devices already? (saves time for constructing expression device). Problem: different names for exactly same DNA sequence
  • What kinds of devices/systems have been built?
  • Search for "similar" parts
  • ?

Implementation

  • Possible initial architecture of the Registry: Adapting SQL Databases (slide 20)
    • Persistent RDF store (MySQL + Jena)
  • Possible final architecture of the Registry: Triple Store (slide 19)

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

Miscellaneous

Contact: Ilya Sytchev

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