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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==Registry features==
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Compiled from meetings and [[Registry_of_Standard_Biological_Parts]]
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*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.
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*Superpart Search: search for parts that contain the given parts
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*What about sub- and superpart searches in distributed registries?
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*Search for function (case insensitive): repressor, reporter, inverter, etc.
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*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
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*What kinds of devices/systems have been built?
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*Search for "similar" parts
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*Find all parts of the form promoter.Q04400 where promoter can be any promoter. It would also be nice to specify whether you want any parts, just available parts or available and working parts.
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==Implementation==
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*Possible initial architecture of the Registry: [http://www.w3.org/2005/Talks/0517-boit-tbl/#(20) Adapting SQL Databases] (slide 20)
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**Persistent RDF store (MySQL + Jena)
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*Possible final architecture of the Registry: [http://www.w3.org/2005/Talks/0517-boit-tbl/#(19) Triple Store] (slide 19)
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==Meetings==
==Meetings==
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===First meeting===
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*First meeting
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Tuesday (9/20/05) at 3pm, room 68-674<br/>
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:Tuesday (9/20/05) at 3pm, room 68-674; [[Synthetic Biology:SWO1minutes|minutes]]
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[[Synthetic Biology:SWO1minutes|Minutes]]
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*Second meeting
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===Second meeting===
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:Friday (9/23/05) at 10am, room 68-121; [[Synthetic Biology:SWO2minutes|minutes]]
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Friday (9/23/05) at 10am, room 68-121<br/>
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[[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]]
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*[[Synthetic_Biology:Semantic_web_ontology/RDF|RDF]]
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**[[Synthetic_Biology:Semantic_web_ontology/RDF|RDF]]
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*[[Synthetic_Biology:Semantic_web_ontology/RDF_Schema|RDF Schema]]
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**[[Synthetic_Biology:Semantic_web_ontology/RDF_Schema|RDF Schema]]
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*[[Synthetic_Biology:Semantic_web_ontology/OWL|OWL]]
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**[[Synthetic_Biology:Semantic_web_ontology/OWL|OWL]]
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*[[Synthetic_Biology:Semantic_web_ontology/Query|Query Languges]]
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**[[Synthetic_Biology:Semantic_web_ontology/Query|Query Languges]]
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*[[Synthetic_Biology:Semantic_web_ontology/SWRL|Rule Languages (SWRL)]]
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**[[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]]
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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==
*[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]
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*[http://www.w3.org/DesignIssues/Overview.html Design Issues for the World Wide Web]
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**[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)
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*[[Receiver Definition]] - F2620 is a receiver device that responds to the presence of a signaling molecule in the extracellular media by activating transcription from a regulated promoter
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*[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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*[[Synthetic Biology:BioBricks|BioBricks]]: protocols and standards.
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**[[SynBERC:MIT|MIT SynBERC]]
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**[[Synthetic_Biology:BioBricks/Naming_a_new_biological_part|Naming]]
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*[[Registry_of_Standard_Biological_Models|Registry of Standard Biological Models]]
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*[[Synthetic Biology:Abstraction hierarchy | BioBricks abstraction hierarchy]]
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*[[Flakey_DE_Stuff#Physical_and_Functional_Composition_of_Standard_Biological_Parts|Physical and Functional Composition of Standard Biological Parts]]
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*[[Registry of Standard Biological Parts|Registry of Standard Biological Parts]] - feature requests, improvements, etc
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*[[DOI|DOI & LSID info]]
*[[DOI|DOI & LSID info]]
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*[http://slam.bs.jhmi.edu/gd/ GeneDesign &beta;2.0]
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*[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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