Re: updated bams model

hi alan,

> minor: remove "is_" in "is_direct_part_of", for consistency of naming.

ok.

> Looks like the "has_direct_part allValuesFrom unionOf" axioms aren't
> present. Did you decide against them?

Nope, I forgot to include them.

> If you like the ring of it you could
> use http://sciencecommons.org/2007/bams/swanson98.owl

I will. I should think it would be an advantage to have demo stuff in a 
common repository for the time being. I presume at some point, there will be 
a way for me to get it there.

> 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.

I will add this.

> 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'll try this, make the other modifications, and do another round of the 
model before I start the conversion.

thanks,

jb


----- Original Message ----- 
From: "Alan Ruttenberg" <alanruttenberg@gmail.com>
To: "John Barkley" <jbarkley@nist.gov>
Cc: <public-semweb-lifesci@w3.org>
Sent: Thursday, March 22, 2007 11:42 AM
Subject: Re: updated bams model


> 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-
> class-style-model-3-22-07.owl
> or
> 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
>
> Best,
> Alan
>
>
> 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
>>
>
>

Received on Friday, 23 March 2007 12:40:59 UTC