Synthetic Biology:Semantic web ontology

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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

Compiled from meetings and Registry_of_Standard_Biological_Parts

• 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
• 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.

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

• Semantic Web
• RDF
• RDF Schema
• OWL
• Query Languges
• Rule Languages (SWRL)
• Web Services
• Agents
• Examples
• Software
• Notes

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
• DOI & LSID info

Contact: Ilya Sytchev

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