[BBF Standards] functional composition of BioBrick parts?

[Raik Gruenberg]

Hi all ,

I see two pretty independent questions waiting to be answered for the data 
exchange standardization:

1) What is the minimal data set needed to describe a biobrick? (including What 
is a Biobrick?)
2) What is the best format / technology for exchange?

It would be good if we could capture the main suggestions and arguments on a 
wiki page -- I would be happy to take care of that but didn't manage to create 
one on http://parts.mit.edu/registry. Could someone with the permissions please 
add some empty page to the community portal box (like the ones for the other RFC 
groups)?

Anyway, we have started discussing 2). Suggestions were roughly:

a) create a new XML format
b) adapt existing CellML, SBML XML formats
c) create a custom file format
d) use Turtle/N3 notation for semantic web documents

If we get a wiki page, we could put up a little section on each possibility and 
collect pro's and cons.

Does anyone have the needed permissions to create a page on the registry wiki? 
Or perhaps i just overlooked the right link?

Greetings,
Raik

Josh Perfetto wrote:
> My initial instinct is also that a separate ontology will be needed to
> properly describe BioBricks.  However I would expect it would be both
> -Josh
> 

> Yes definitely, there are a bunch of new ontologies coming up in systems 
> biology and I think they will have some relevance here, though I suspect 
> there could still be a need for something specifically related to 
> synthetic biology.
> 
> The existence of these ontologies makes human readable formats difficult 
> to deal with and XML is the proper place for them. However, as humans, 
> we also need a human readable face and I think there has to be some kind 
> of two way world, or at least each software application will present 
> parts and devices in their own human readable format even if the 
> back-end is ultimately XML. This is the way SBML and CellML work. We are 
> 
> Herbert Sauro

>> On Wednesday 30 January 2008, "Josh Perfetto" <josh at maulikai.com> wrote:
>>> Yes, I think ease of processing and the representational power of the
>>> format is more important nowadays than human readability.  We need
>>> standard representations that can be adopted by software developers
>>> to build powerful processing systems for BioBricks.  We can expect
>>> such software to present a more human-usable interface to manipulate
>>> the BioBricks than a file format ever could.

>> Have you ever heard of these 'ontologies' that have jumped up?
>> http://www.biomodels.net/
>> http://obofoundry.org/


-- 
________________________________

Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________