[BBF Standards] Questions about functional composition, functional definition, data exchange

[Raik Gruenberg]

Ralph Santos wrote:
> For my part, it seems quite reasonable.  I've taken the liberty of 
> building on your edits to feather out "Biobrick Classification" into 
> intrinsic and extrinsic classification and tried to cite illustrative 
> examples (including some borrowed from Barry's comments).

Great, thanks for updating the Wiki!

> 
> Some of what I wrote overlaps with what Raik wrote about 
> characterization, and that was actually intentional, though I'm not very 
> satisfied with what I wrote to resolve the situation.

mhm, I don't yet understand the difference yet very well. Perhaps you could 
clarify that a bit.

> 
> I was thinking of cases which probably won't actually be encountered for 
> quite a while, in particular:
> 
> * Forming queries for functional performance regardless of the presence 
> of empirical findings, or negative queries regarding functional 
> performance, i.e. "Return me biobricks where specificity is unreported"
> * Dealing with biobricks where multiple findings have been reported, and 
> one has or wishes to choose a performance parameter of record, i.e. the 
> "X" lab has made the definitive measure on the Hill Coefficient of 
> Biobrick Y.

Triple-based systems can perform such queries quite easily. See freebase.com for 
some examples.

Greetings,
Raik

> 
> This may be overthinking things at this stage.
> 
> ---ralf
> 
> 
> Raik Gruenberg wrote:
>> Following Ralph's and Barry's mail, I've sub-devided the data model 
>> section into 4 sub-topics -- Please have a look at:
>> http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical#What_is_the_data_model_needed_to_describe_a_biobrick.3F 
>>
>>
>> The idea is to tackle the problem in stages:
>>     * 1 minimal Biobrick information
>>     * 2 Biobrick classification
>>     * 3 Characterization
>>     * 4 Further annotation
>>
>> Point 1 should be relatively straightforward to decide on and would 
>> cover the basic needs for sending around and assembling Biobricks. I 
>> would aim to have a draft ready for the Seattle meeting. Point 2 may 
>> be already slightly more tricky but, again, we should try to have a 
>> draft for Seattle.
>> Point 3 and 4 will probably need some more discussion. Here it may be 
>> more important to have some obvious examples and then agree on a 
>> procedure for evolving the model over time (technology permitting).
>>
>> Does that sound reasonable?
> 
> 
> 

-- 
________________________________

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