Synthetic Biology:Semantic web ontology: Difference between revisions
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==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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*What kinds of devices/systems have been built? | *What kinds of devices/systems have been built? | ||
*Search for "similar" parts | *Search for "similar" parts | ||
* | *? | ||
==Implementation== | ==Implementation== | ||
*Possible initial architecture of the Registry: [http://www.w3.org/2005/Talks/0517-boit-tbl/# | *Possible initial architecture of the Registry: [http://www.w3.org/2005/Talks/0517-boit-tbl/#%5B20%5D Adapting SQL Databases] (slide 20) | ||
**Persistent RDF store (MySQL + Jena) | **Persistent RDF store (MySQL + Jena) | ||
*Possible final architecture of the Registry: [http://www.w3.org/2005/Talks/0517-boit-tbl/# | *Possible final architecture of the Registry: [http://www.w3.org/2005/Talks/0517-boit-tbl/#%5B19%5D Triple Store] (slide 19) | ||
==Meetings== | ==Meetings== | ||
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*[[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 | *[[Synthetic_Biology:Semantic_web_ontology/SWRL|Rule Languages]] | ||
*[[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]] | ||
==Miscellaneous== | ==Miscellaneous== | ||
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*[[Synthetic Biology:BioBricks|BioBricks]]: protocols and standards. | *[[Synthetic Biology:BioBricks|BioBricks]]: protocols and standards. | ||
*[[Synthetic Biology:Abstraction hierarchy | BioBricks abstraction hierarchy]] | *[[Synthetic Biology:Abstraction hierarchy | BioBricks abstraction hierarchy]] | ||
Contact: [[User:Ilya|Ilya Sytchev]] | Contact: [[User:Ilya|Ilya Sytchev]] | ||
Revision as of 16:49, 9 April 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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