Re: bams class style model

Just had a discussion with John, summary:

Minor, stylistic: Class names are often written as singular e.g.  
Cells -> Cell.

Single URI for each class, based on the id. The name of the thing  
goes to the label, and an annotation property records the abbreviation.

part_has_cell, cell_has_molecule_within,   
part_has_molecule_in_region,  become subproperties of ro:location_of  
(from relation ontology)

We had a discussion of the allValuesFrom restrictions.
The first was re: his previous mail. He was using separate  
allValuesFrom which were being interpreted as a conjunction. Instead  
he would
change these to a single allValueFrom of the union.
The second question was whether the allValuesFrom was appropriate.   
It seemed appropriate in some cases, not in others.
For the part/part relations, we assumed that the atlas was  
exhaustive, so the restriction makes sense.
We're not as sure about source/target, part/cell, cell/molecule  
relations. These are probably not exhaustive, so
someValueFrom alone would seem to make more sense. He will ask  
Mikhail and adjust the model accordingly.

The "by_" classes will be removed.

-Alan


On Mar 19, 2007, at 10:15 AM, Alan Ruttenberg wrote:

>
> Hi John,
>
> Great progress!
>
> I think I would choose a single name and then have e.g,  id and  
> abbreviation be properties of it. You can use annotation properties  
> for these. Then remove the "by" layer of the ontology - these lists  
> can be regenerate on demand via e.g. a sparql query.
>
> I notice that you use has_part and part_of in the definitions.  
> Remember that each is a all-some statement, so perhaps verify that  
> that is true. e.g. a has_part some b = every a has some b as a  
> part. a part_of some b = every a is part of some b. Sometimes only  
> one or the other direction is true.
>
> Speak to you soon,
>
> Best,
> Alan
>
>
> On Mar 19, 2007, at 8:18 AM, John Barkley wrote:
>
>>
>> For another one of my action items, I put on the wiki demo page:
>> http://esw.w3.org/topic/HCLS/HCLSIG_DemoHomePage_HCLSIG_Demo
>> a reference to the initial bams class style model and an updated  
>> bams instance
>> style model. In both, I made the properties "has_source" and  
>> "has_target"
>> transitive. Please let me know if this is not correct.
>>
>> There are no instances in the class style model. It is in the  
>> style of the
>> Pizza tutorial
>> (http://www.co-ode.org/resources/tutorials/ProtegeOWLTutorial.pdf).
>> You may notice that the model is OWL Full, but that's only because  
>> there is an
>> annotation property "has_bams_URL". Reasoners generally ignore  
>> annotation
>> properties.
>>
>> jb
>>
>>
>>
>
>

Received on Monday, 19 March 2007 20:31:59 UTC