Synthetic Biology:SWO2minutes

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Held on Friday (9/23/05) at 10am, room 68-121.



Basic terms for describing the biological parts and their properties.


Abridged minutes of the 2nd meeting on a semantic web ontology for synthetic biology. I only included the stuff that was finalized on rather than the intermediary material. Please feel free to add anything I have left out or to use the discussion page to add any new thoughts.

  • To recap, the fundamental unit of a semantic web is a triplet, subject--(property)-->value
  • Based on meeting 1 the decision was taken to start with the most "atomic" units of a semantic web for synthetic biology, with the expectation that if these are correct the higher levels will follow easily. Additionally, starting with the atomic units should make it easier to later interface with the anthologies of other groups.
  • To make the discussion more specific, there was a decision made to focus on one specific part of the antology, that describing the physical location and properties of a biological instance(DNA, protein, cell, etc).

Certain properties were assigned that are intended to define a biological instance or a NFKAAPC (Node formerly known as a physical container).

Biological Instance

  • What am I - DNA/Cell etc.
  • What is my physical location - Container info.
  • What is my immediate(?) ancestor

Physical container a.k.a NFKAAPC

  • What do I contain (this makes the link between a biological instance and a physical container bidirectional)
  • What kind of container am I
  • What contains me - physical container, organization
  • What is my location/contact info.