[BBF Standards] Initial Draft Documents for PICA

[Raik Gruenberg]

Hi guys,

I haven't been attending the workshop. Perhaps my opinion would be completely 
different if I would have witnessed your discussions and perhaps/likely I am 
getting all wrong but here is my birds-eye first impression on the PICA proposal 
from just browsing over the documents:

I think it fails in several respects:

1) It is too complicated. Pulling in all those outside ontologies means you are 
directly from the start juggling with vocabularies comprising hundreds of terms 
and relations at extreme detail level. Basically we are starting with more terms 
than Biobricks. Which also means that two annotators will probably not use the 
same terms for the same thing.

2) It fails to solve the immediate problem at hand. I don't see a suggestion how 
to communicate a new biobrick to the Registry with the minimal information that 
we are used to expect already right now (sequence, format, user, experience, 
chassis, classification, etc)

3) It deters outside developers. What may be interesting as a research topic for 
a group of full-time bioinformaticians who are specialising in ontology 
building, looks certainly not inviting to a weekend hacker with a funny Biobrick 
idea (like, say, link Biobricks to Freebase or Facebook).

I would prefer to start with a very slim core biobrick description -- after the 
discussions we already had on the mailing list, an owl definition of this could 
be hacked up by two people in 2 days. Any further relations should be developed 
*together* with the actual data and tools, tested, and may be step-by-step 
incorporated into the core if they turn out to be useful in practice.

Links to outside vocabularies should of course be possible and its a good idea 
to borrow concepts or ensure compatibility where appropriate but this shouldn't 
be the most important goal right now. A "owl:sameAs" link can be added anytime 
later.

Greetings,
Raik


Ralph Santos wrote:
> Hi,
> 
> Pursuant to a discussion at the BBF Technical Standards Workshop on March 1 in San Francisco, I've put up some draft documents on a data model and language I'm calling PICA (for "Part Interaction and Composition Assertion").  It's not intended to be a complete standard proposal, and the documents are in very early draft form (not really appropriate to build anything off of them yet), but they do illustrate the main concepts behind the framework, namely establishing an abstract view of biological parts and providing annotations declaring part information based on generic vocabulary of internal features (using Sequence Ontology terms) and behaviors cited in terms of the molecular species that interact with and/or are produced by the part.
> 
> I've placed the documents here:
> 
>   http://openwetware.org/wiki/PICA_Framework_Draft_Proposal_Documents
> 
> I'll update them as I build out the rest of the proposal package.  I'd appreciate any comments/questions/criticisms/suggestions on any of the material that people would care to share with me.
> 
> Thanks,
> ---ralf
>   
> 
> _______________________________________________
> Standards mailing list
> Standards at biobricks.org
> http://biobricks.org/mailman/listinfo/standards_biobricks.org
> 
> 

-- 
________________________________

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