[BBF Standards] [Fwd: pobol first draft]

[Raik Gruenberg]

CC to the list for the other Pobol fans ;-)
Note, this is still very much work in progress.
/Raik

-------- Original Message --------
Subject: pobol first draft
Date: Sun, 04 May 2008 02:20:30 +0200
From: Raik Gruenberg <raik.gruenberg at crg.es>
To: mgaldzic at u.washington.edu
CC: Mackenzie Cowell <macowell at gmail.com>,  Jason Morrison 
<jason.p.morrison at gmail.com>

Hi Michael, Mac, Jason,

attached is a first OWL-formatted draft of our minimal ontology: see
partsrdf.owl. I've written this from scratch as N3 file (see partsrdf.n3) and
converted it to the xml format using the RDF validator at
http://www.rdfabout.com/demo/validator/

The owl file loads into Protege and Swoop for perhaps easier editing. I would
suggest that we continue to ship N3 versions though for better readability (they
say XML was invented as a human readable format, yeah right...).

What is still missing are restrictions, like that a Biobrick must have exactly
one sequence and format and so on. So far I have just fixed the range of values
of each property (owl:range) and what kind of properties a class can have
(owl:domain, note this goes into the property not the class definition).

More explanations: "a owl:FunctionalProperty" means this property can only occur
ones per object. And "a owl:InverseFunctionalProperty" means this property has
to be unique for each object.

Apart from the restrictions, I didn't find out yet how to define a datatype
"list of Biobrick instances" for the subParts property (aka composition). N3
allows to formulate lists of values like this:

BBa0102  bbf:subParts  (BBa0001 BBa0002).

But I didn't find any documentation how to enforce that in an ontology. Hints
anyone?

Last note, I changed some property names (dnaSequence rather than sequence,
isCircular rather than Circular, subFamilyOf rather than parent) to better
conform with informal owl conventions. These are open to debate of course.
Ah, and I forgot the selfScar and constraint in Format...

Anyway, work in progress obviously. I've some last traveling to do starting
tomorrow and, probably, won't touch these files for the week to come. Feel free
to fill in the missing bits. Could anyone please set up a google code project
for this to get version control? Or this site may be an interesting alternative:
http://www.knoodl.com
Other ideas?

Greetings,
Raik

PS: also attached is an incomplete example Biobrick file using this ontology in
N3 and XML format.


Michal Galdzicki wrote:
> i am very impressed as to how well this workshop went. and happy to
> participate, i will make a better diagram of the pobol class
> structures and try to explain some of the theory that goes into it.
> mac: yell at me if i dont post anything by sunday :)
> 
> It's a pleasure to work with you guys,
> mike
> 
> On Wed, Apr 30, 2008 at 9:50 PM, Mackenzie Cowell <macowell at gmail.com> wrote:
>> Hi Raik,
>>
>> I had a great time at the SSSB workshop.  I think we accomplished a lot more
>> than anyone expected. Michal and I have put up a little bit of info on the
>> pobol page on OWW.  We still need to fill in the rationale for all the
>> classes (my job) and perhaps make a better diagram of the data model.  I
>> would also like to put together an example xml document of what a real part
>> (F2620 or JCA's promoter family?) would look like in pobol format.
>>
>> Besides that, what's the next step in moving forward with implementing pobol
>> in freebase and in brickit?
>>
>> I'll see you on the technical standards list!
>>
>>
>> Mac
> 

-- 
________________________________

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


-- 
________________________________

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