[BBF Standards] functional composition of BioBrick parts?

[Raik Gruenberg]

Hi guys,

nice to see the discussion starting. Thanks Deepak!

I somewhat share the reservation about completely new file formats, but the 
non-readability and general nastiness of XML is also an issue. A good solution, 
IMO, would be to use the Turtle format (formerly "notation 3" or N3) developed 
by the semantic web folks. It is concise, human-readable and editable (i used it 
myself some years ago) *AND* is equivalent to XML. That means there is a well 
defined translation back and for and many libraries and tools do the conversion. 
Being semantic web, it also solves the linking problem (everything is a link).

I'll cook up some small example and send it around later today. Quick Preview:

# ... skipping namespace definition for rdf, bbf, harvard ...

# define a biobrick hosted at this address
:BBa_0001
	rdf:type	bbf:biobrick;
	bbf:sequence	"AAACCCGGG";
	bbf:contains	[:BBa_0003, harvard:BBa_J1000, :BBa_00010];
.

# add information to biobrick defined elsewhere
harvard:BBa_J1000
	rdf:sameAs	:BBa_0999;
.

OK, one can argue about human-readability but it's at least possible to 
understand and edit these documents (and much better than the equivalent xml).

Besides, shall we set up a scratch board page on OWW?

Greetings,
Raik

Herbert Sauro wrote:
> 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 
> seeing however a proliferation of human readable formats in systems 
> biology, both visual and text based but which are largely 
> interchangeable through SBML or CellML.
> 
> Herbert Sauro
> 
> Bryan Bishop wrote:
>> 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/
>>
>> I wonder how this might be useful.
>>
>> - Bryan
>> ________________________________________
>> Bryan Bishop
>> http://heybryan.org/
>>
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> 
> 
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> 

-- 
________________________________

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