[Fwd: Re: rfc number request]
Raik Gruenberg
please find attached
RFC 30: Draft of an RDF-based framework for the exchange and integration of
Synthetic Biology data
It summarizes why RDF is the solution to all our data exchange problems ;-) and
how this could work out in practice. It's kind of a "meta RFC" that tries to
address your "meta issues". I hope this will stimulate some good discussion.
Sorry about the length of this RFC. We had lots of discussions scattered in
e-mails about this topic -- I now tried to put all cards on the table so that I
can consequently shut up for a while ;-).
Michal Galdzicki and the Seattle crowd just contacted me yesterday. They have
taken on the task of writing up the current state of the PoBoL data model. We
all know that this is going to change but I also think it's a good idea to
document the last common snapshot.
I've lost the overview but it looks to me as if we have gone from zero activity
to somewhat parallel efforts between the Seattle people around Herbert and the
Berkeley people around Chris and Doug. On the other hand that also means we have
activity from a good team that is more on the side of data "providers" and a
good team that perhaps more represents data "consumers". Which is great, a
synthesis of that should carry us quite far!
Have a nice weekend!
Greetings,
Raik
Reshma Shetty wrote:
>
> Hi Raik,
>
> [Yeah Drew and I are both on this list.]
>
> You get BBF RFC 30 for this one.
> You already know, but directions for writing RFCs can be found here: http://openwetware.org/wiki/The_BioBricks_Foundation:RFC
>
> Thanks,
>
> Reshma
>
> On Wed, Apr 22, 2009 at 3:58 AM, Raik Gruenberg <raik.gr...@crg.es <mailto:raik.gr...@crg.es>> wrote:
>
> Hi Drew (or Reshma?),
>
> after our e-mail exchange on Sunday, I've started writing up a RFC
> to make the point that we should embrace RDF for data exchange. I
> would like to ask for a RFC number for
>
> title:
> Draft of a RDF-based framework for the exchange and integration of
> Synthetic Biology data
>
> author:
> only me so far, others are hopefully jumping on board for a later
> replacement RFC
>
> Raik Grünberg
> raik.gr...@crg.es <mailto:raik.gr...@crg.es>
>
> Thanks!
> Raik
>
> -- ________________________________
>
> Dr. Raik Gruenberg
> http://www.raiks.de/contact.html
> ________________________________
>
>
--
________________________________
Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________
--
________________________________
Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________
Douglas Densmore
comments soon in the "RFC30 comments" thread. As you know we are
working on our own RFC draft over here which is going to be a merge of
what Clotho (Anderson lab and me) and JBEI (Tim Ham) are doing. This
is actually a high level spec, which is not going to specify how the
system is actually implemented, stored, or shared but rather a
proposal for a core data model (essential objects, fields, and
relations) which is extensible. It is also going to be a collection of
scenarios that we feel it addresses which are essential for Berkeley
and JBEI. It will be less "biobrick centric" but still support
biobricks. Clotho is migrating to a system where you can swap in and
out data models and database connections and have it configure itself
dynamically at runtime (more to come this summer). I am doing this to
hedge my bets:)
I agree that we are more on the data consumers side. I would love to
hook Clotho up to whatever folks have done and give it a try (it is
very easy to write plug-ins for Clotho). I have started to connect to
JBEI this way just to test it out as well as connecting to a database
Cesar Rodriguez is setting up at Stanford. If anyone has something set
up you want me to connect to, let me know and I will work it into our
iGEM plan this summer. I have seven students this summer:)
Doug
>
> > Hi Drew (or Reshma?),
>
> > after our e-mail exchange on Sunday, I've started writing up a RFC
> > to make the point that we should embrace RDF for data exchange. I
> > would like to ask for a RFC number for
>
> > title:
> > Draft of a RDF-based framework for the exchange and integration of
> > Synthetic Biology data
>
> > author:
> > only me so far, others are hopefully jumping on board for a later
> > replacement RFC
>
> > Raik Grünberg
> > Thanks!
> > Raik
>
> > -- ________________________________
>
> > Dr. Raik Gruenberg
> > http://www.raiks.de/contact.html
> > ________________________________
>
> --
> ________________________________
>
>
> --
> ________________________________
>
> Dr. Raik Gruenberghttp://www.raiks.de/contact.html
> ________________________________
>
> 5KViewDownload
>
> rfc30.pdf
> 143KViewDownload
>
> rfc30.tex
> 31KViewDownload