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]. 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 [[ | 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== | ||
*[[ | *[[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 | ||
*[[ | *[[Receiver Definition]] | ||
*[[BioBricks|BioBricks]]: protocols and standards. | *[[Synthetic Biology:BioBricks|BioBricks]]: protocols and standards. | ||
*[[ | *[[Synthetic Biology:Abstraction hierarchy | BioBricks abstraction hierarchy]] | ||
Contact: [[User:Ilya|Ilya Sytchev]] | Contact: [[User:Ilya|Ilya Sytchev]] | ||
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{{Synthetic biology bottom}} | {{Synthetic biology bottom}} | ||
Revision as of 20:06, 3 January 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.
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
- Architecture of the World Wide Web, Volume One
- Object-oriented biology - application of object-oriented paradigm to Gene
- Receiver Definition
- BioBricks: protocols and standards.
- BioBricks abstraction hierarchy
Contact: Ilya Sytchev
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