[BBF Standards] functional composition of BioBrick parts?

[Julius B. Lucks]

Hi All,

I agree with the separation of the task at hand:

>
> 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?
>

But I would rephrase #1 to say

1.) What is the data model needed to describe a biobrick?

Once the data model is firmly in place, the format should follow as  
the one that best implements that data model.  For example, if we  
settle on an RDF-like 'everything is a relationship triplet'  
approach, then some format that can handle these triplets would be  
most appropriate.  In addition, with a model like this, there are XML- 
based and more human-readable formats that can both implement the  
model equally well.

I think that tying our selves to a format too early will make us not  
have a clear model in mind, and will cause us to hack up the format.   
It is best to do model, then format.

So things to think about in a model are what type of relationships to  
we want to convey?

* Inheritance (where was a particular part derived from, and by who =  
link + data)
* Characterization (something quantitative about that part by itself  
= data)
* Plays well with others (what other parts can this one interact with  
- with possible data associated with this interaction = link + data)
* ...

Other ideas?

Cheers,

Julius


> 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
> ________________________________
>
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