The BioBricks Foundation:Standards/Technical/PoBoL: Difference between revisions

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PoBoL ("<u>P</u>r<u>o</u>visional <u>B</u>i<u>o</u>Brick <u>L</u>anguage") is the name given to an initial attempt at defining a minimal data model for BioBrick repository entries.  It was developed during the [http://www.sys-bio.org/sbwWiki/workshops/standardsandspecifications08 Standards and Specifications in Synthetic Biology] workshop in Seattle on April 26-27, 2008.   
PoBoL ("<u>P</u>r<u>o</u>visional <u>B</u>i<u>o</u>Brick <u>L</u>anguage") is the name given to an initial attempt at defining a minimal data model for BioBrick repository entries.  It was developed during the [http://www.sys-bio.org/sbwWiki/workshops/standardsandspecifications08 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.
"Pobol" means "people" in Welsh; the developers thought that it was a fitting name for this community-defined format.
== Goals ==
* Implement pobol in [http://www.freebase.com/view/guid/9202a8c04000641f8000000004ff9406 freebase.com]
# emit part entries in pobol
* Implement pobol in [http://brickit.wiki.sourceforge.net/ BrickIt]
# emit part entries in pobol
# absorb part entries in pobol
* Possibly implement pobol in the [http://partsregistry.org MIT Registry]
# emit part entries in pobol
* demonstrate part exchange between Freebase & Brickit via pobol
== Class Diagrams ==


[[Image:pobol1.gif]]
[[Image:pobol1.gif]]


[[Image:pobol2.gif]]
[[Image:pobol2.gif]]
== Test Cases ==
The following are suggested test cases for the pobol data model and are derived directly from a discussion on the [http://biobricks.org/pipermail/standards_biobricks.org/2008-April/000212.html 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

Revision as of 21:30, 30 April 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

  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

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
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