Synthetic Biology:Semantic web ontology
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.
- 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
- 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)
Tuesday (9/20/05) at 3pm, room 68-674
Friday (9/23/05) at 10am, room 68-121
- Architecture of the World Wide Web, Volume One
- Object-oriented biology - application of object-oriented paradigm to Gene
- BioBricks: protocols and standards.
- BioBricks abstraction hierarchy
Contact: Ilya Sytchev
This site is hosted on OpenWetWare and can be edited by all members of the Synthetic Biology community.
Making life better, one part at a time.