Synthetic Biology:Semantic web ontology/Design

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Registry use cases

• 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.

Miscellaneous use cases

• Find a low-copy vector (1 to 2 per cell) which carries two antibiotic marker genes. (preferably one sensitive such rpsL, and one resistant such at Tetracycline, Chloramphenicol, etc.) and are FLANKED between two LoxP sites.

References

• Meetings
• Registry:Community_Portal - feature requests, improvements, etc (old site: Registry of Standard Biological Parts)
  • Registry improvements
• Questions and Answers
• BioBricks: protocols and standards.
  • Naming
  • Standardization - ways to classify biological parts
• BioBricks abstraction hierarchy
  • Composition model
  • Network layer model
• Physical and Functional Composition of Standard Biological Parts
• 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
• Registry of Standard Biological Models
• Bioinformatics Discussion Group

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