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Re: updated bams model

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Thu, 22 Mar 2007 11:42:05 -0400
Message-Id: <8CD5FAFF-7119-489D-84FB-808270425716@gmail.com>
Cc: public-semweb-lifesci@w3.org
To: John Barkley <jbarkley@nist.gov>
This looks great, John, go for it!

minor: remove "is_" in "is_direct_part_of", for consistency of naming.
Looks like the "has_direct_part allValuesFrom unionOf" axioms aren't  
present. Did you decide against them?

consider a more stable namespace. I've been putting our stuff in  
http://sciencecommons.org/2007/. If you like the ring of it you could
use http://sciencecommons.org/2007/bams/swanson98.owl . Or, if Mihail  
is willing to stand behind it as being "authoritative", he could offer
a namespace, e.g http://brancusi.usc.edu/bkms/2007/bams/swanson98.owl.

Consider adding attributions in the form of dc:creator, dc:source  
annotations on the ontology, including dc:creator for you and  
Mihail,  and a dc:source for the xml file, and another for
Swanson: Rat Structures of the Brain ISBN: 0444827854, as well as an  
rdfs:comment explaining how the file came to be.

Afterwards let's circle back and hook things up a bit more with the  
OBO ontologies.
Here's what I'm thinking.

Cell can be caro:0000013 cell
Molecule can be subclass of caro:0000063 portion of cell substance,  
or removed and replaced with it.
Mouse Brain can be subclass of caro:0000074 solid compound organ
The rest of the brain parts can be subclasses of caro:0000019  
compound organ component
we can either lose Mouse_Brain_Part, or make it subclass of caro: 
0000019 and leave the parts, other than Brain as subclasses of it.

owl imports for OBO_REL and CARO would be added.

I'm attaching a picture of the portion of CARO I'm referring to, as  
well as a picture of your work, as I see it.

I've made it easier to use LSW as a browser.  Instructions:

get http://sw.neurocommons.org/software/lsw09.tar.gz (currently lsw- 
latest.tgz points to that version too)
tar xfz lsw0-9.tar.gz
cd lsw-0.9
bin/browse http://hissa.nist.gov/jb/biordf-demo/bams-from-swanson-98- 
bin/browse :caro

You have to kill (control-c or (quit) at prompt) lsw when you are  
done - it doesn't yet quit when the browser windows are closed.

CARO is http://purl.org/obo/owl/CARO


On Mar 22, 2007, at 9:33 AM, jbarkley@nist.gov wrote:

> I put the reference to the updated BAMS model on the wiki demo page:
> http://esw.w3.org/topic/HCLS/HCLSIG_DemoHomePage_HCLSIG_Demo
> This model incorporates Alan's suggestions in a prior email and  
> reflects
> consultations with Mihail Bota. Anticipating the action item for  
> me, I will
> start creating the OWL version of BAMS based on this model.
> I'm not sure if I will be able to make today's HCLS call.
> jb

(image/png attachment: 02-caro.png)

(image/png attachment: 05-Bams.png)

Received on Thursday, 22 March 2007 15:44:20 UTC

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