The BioBricks Foundation:Standards/Technical/PoBoL

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Added feeds section)
Line 48: Line 48:
== Notes ==
== Notes ==
* http://syntheticbiology.org/Semantic_web_ontology/Software.html
* http://syntheticbiology.org/Semantic_web_ontology/Software.html
 +
 +
== Feeds ==
 +
A registry will likely want to expose a feed of its parts.  Atom is a good candidate for the feed format (it is an alternative to/improvement upon RSS 2.0 - see Wikipedia for a discussion)
 +
* Atom standard: http://en.wikipedia.org/wiki/Atom_(standard)
 +
* URN:UUID RFC: http://www.ietf.org/rfc/rfc4122.txt
 +
* URN:UUID Provider: http://www.itu.int/ITU-T/asn1/uuid.html

Revision as of 15:35, 1 May 2008

Contents

PoBoL ("Provisional BioBrick Language") is the name given to an initial attempt at defining a minimal data model for BioBrick repository entries. It was developed during the Standards and Specifications in Synthetic Biology workshop in Seattle on April 26-27, 2008.

"Pobol" means "people" in Welsh; the developers thought that it was a fitting name for this community-defined format.

Goals

  1. emit part entries in pobol
  1. emit part entries in pobol
  2. absorb part entries in pobol
  1. emit part entries in pobol


  • demonstrate part exchange between Freebase & Brickit via pobol

Class Diagrams

Image:pobol1.gif

Image:pobol2.gif


owl / rdf draft

raik?


Example: J23100 family

JCA's J23100 promoter family encoded as xml / owl here


Test Cases

The following are suggested test cases for the pobol data model and are derived directly from a discussion on the biobricks technical standards mailing list. As developers of the standard, we have an imperative to not just bake our cake, but try it too.

Data Entry test cases

  • ex: each BB should should have a unique ID, or list of required/optinal fields.

Search test cases

  • return all composite sequences having a specific BB
  • return all BB being a constitutive promoter in E.Coli - perhaps a test for registries, not for pobol

Data Flow and Data Exchange test cases

  • 1 Person / N Parts / 1 Registry
  • X Persons / N Parts / 1 Registry
  • X Persons / N Parts / M Registries
  • Registry 1 wants to import n1 parts from Registry 2

Notes

Feeds

A registry will likely want to expose a feed of its parts. Atom is a good candidate for the feed format (it is an alternative to/improvement upon RSS 2.0 - see Wikipedia for a discussion)

Personal tools