The BioBricks Foundation:Standards/Technical/PoBoL: Difference between revisions
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== 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 12:35, 1 May 2008
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
- Implement pobol in freebase.com (Currently in progress)
- emit part entries in pobol
- Implement pobol in BrickIt
- emit part entries in pobol
- absorb part entries in pobol
- Possibly implement pobol in the MIT Registry
- emit part entries in pobol
- demonstrate part exchange between Freebase & Brickit via pobol
Class Diagrams
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)
- 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
