[BBF Standards] BrickIt 0.1 data model

[Raik Gruenberg]

Hi Jason,

Jason Morrison wrote:
> Raik,
> 
> Thanks for getting BrickIt started, posting this!  I have a fair amount 
> of flight/airport time this weekend, during which I intend to dive into 
> the Brickit source and have a look around.

Probably good to have the excellent Django tutorial available next to it.
  http://www.djangoproject.com/documentation/tutorial01/
  http://www.djangoproject.com/documentation/tutorial02/

Part 1 and 2 cover all I've done so far, which is still very limited.

> 
> I am curious: what are your thoughts on storing BioBrick data in a 
> relational db schema such as in BrickIt vs rdf triples?

Very good question. I see it as a temporary fix. I am not aware of any rdf-web 
framework or anything even remotely matching django (or similar db-centric 
competitors) in ease and functionality. And we needed something up and running 
right now... The limitations are pretty obvious though. Besides, your page
http://openwetware.org/wiki/User:Jason_Morrison/Thoughts_on_semantic_wikis#Ideas_about_producing_views_on_RDF
has lots of links I still need to follow...

Having said that, BrickIt could actually help making the transition:

Step 1: it's trivial to let brickit serve RDF pages. E.g. you could get a N3 
view from yourbrickit.somewhere/parts.n3#BBa0001 by some very simple code not 
even using any rdf library. Perhaps we should demo that for the Washington meeting.

Step 2: would be to let BrickIt *import* RDF-formatted Biobricks although 
treating it as any fixed format. This should still be quite easy using, e.g. the 
redland library and would enable data exchange between registries, without 
resorting to (IMO over-complicated web-services). Good formal arguments for this 
kind of solution are here: http://en.wikipedia.org/wiki/REST

potential Step 3: Swap (or complement) the Brickit database for a RDF store. 
Django is quite exceptionally well designed -- database backend, DB-API, and 
visual representation are strictly decoupled. So one could continue to use the 
Django URL-routing and templating system (and custom HTML pages) but fill them 
from the RDF store. Obviously a project in its own right. This would essentially 
create an open-source alternative to http://www.freebase.com/, should be first 
discussed on the django mailing list.

Freebase and existing rdf stores seem still to only work with local data rather 
than following links to the outside, which is kind of missing the point of a 
semantic *web*. That needs to be fixed... my attempt at that was the crow 
project some years back but i am sure there are other solutions coming up.

Concerning semantic wikis -- looks interesting but we need to still ensure that 
ontology, data and representation are strictly uncoupled.

Greetings,
Raik

> 
> Jason
> 
> On Feb 6, 2008 5:32 AM, Raik Gruenberg <raik.gruenberg at crg.es 
> <mailto:raik.gruenberg at crg.es>> wrote:
> 
>     next announcement:
> 
>     Some of you may remember the BrickIt web server: BrickIt aims to
>     create a
>     portable web-based registry that helps synthetic biologists to plan,
>     organize
>     and track their local biobrick samples. The reason why I am posting
>     this here is
>     that a data model is part of the open-source project:
> 
>      http://brickit.wiki.sourceforge.net/Data+model
> 
>     I've bundled the current version of the project into a first release
>     for easier
>     download and evaluation. BrickIt 0.1 corresponds to the version we
>     use at the
>     CRG. It is still alpha stage but already useful for smaller groups
>     of users
>     (which is the target audience anyway) and, due to the limited
>     functionality,
>     rather stable.
> 
>     Please sign up with the (very low traffic) brickit mailing list, if
>     you are
>     interested in the project:
>     https://lists.sourceforge.net/lists/listinfo/brickit-general
> 
>     Or check out the wiki:
>       http://brickit.wiki.sourceforge.net/
> 
>     Greetings,
>     Raik
> 
>     --
>     ________________________________
> 
>     Dr. Raik Gruenberg
>     http://www.raiks.de/contact.html
>     ________________________________
> 
>     _______________________________________________
>     Standards mailing list
>     Standards at biobricks.org <mailto:Standards at biobricks.org>
>     http://biobricks.org/mailman/listinfo/standards_biobricks.org
> 
> 
> 
> 
> -- 
> Jason Morrison
> jason.p.morrison at gmail.com <mailto:jason.p.morrison at gmail.com>
> http://jayunit.net
> (585) 216-5657

-- 
________________________________

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