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

[Ralph Santos]

Yes, that's looking pretty half-baked now.  I'll edit that part out and try to stick it back in the oven and hope it eventually becomes coherent.

---ralf

----- Original Message -----
From: Raik Gruenberg <raik.gruenberg at crg.es>
Date: Wednesday, February 13, 2008 2:57 pm
Subject: Re: [BBF Standards] Questions about functional composition, functional definition, data exchange
To: Ralph Santos <RASantos at lbl.gov>
Cc: Barry Canton <bcanton at mit.edu>, standards at biobricks.org

> 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
> ________________________________
>