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Re: bams class style model

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Mon, 19 Mar 2007 15:45:10 -0400
Message-Id: <3EF029B6-460B-41F3-8FFA-084228AFB6AF@gmail.com>
Cc: William.Bug@DrexelMed.edu, public-semweb-lifesci@w3.org
To: jbarkley@nist.gov

I think that having more than one name for something is a necessary  
evil, but that it's undesirable to mint them unless we have a good  
reason to (and I can't think of one off the top of my head).

-Alan


On Mar 19, 2007, at 3:42 PM, jbarkley@nist.gov wrote:

>
> I reasoned as follows:
>
> If a part should be a class, then a different name for that part  
> should be an
> equivalentClass. Likewise, if something were an individual, then  
> sameAs should
> be used.
>
> I'll be happy to use whatever representation people think works  
> best for the
> demo.
>
> jb
>
>
> Quoting William Bug <William.Bug@DrexelMed.edu>:
>
>> Sorry I was unable to attend today's meeting.
>>
>> Alan reminds me of another question I had re: this BAMS OWL file,  
>> John.
>>
>> I understand why you'd not want to tuck the ID and abbreviation
>> values into annotation properties.  Is there a reason not to add them
>> as DatatypeProperties?  This would help to make the core subsumptive
>> 'is_a' graph more meaningful but still keep these values accessible
>> to both reasoners and to a SPARQL engine - correct?
>>
>> Cheers,
>> Bill
>>
>> 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
>>>>
>>>>
>>>>
>>>
>>>
>>
>> Bill Bug
>> Senior Research Analyst/Ontological Engineer
>>
>> Laboratory for Bioimaging  & Anatomical Informatics
>> www.neuroterrain.org
>> Department of Neurobiology & Anatomy
>> Drexel University College of Medicine
>> 2900 Queen Lane
>> Philadelphia, PA    19129
>> 215 991 8430 (ph)
>> 610 457 0443 (mobile)
>> 215 843 9367 (fax)
>>
>>
>> Please Note: I now have a new email - William.Bug@DrexelMed.edu
>>
>>
>>
>>
>>
>
>
Received on Monday, 19 March 2007 19:46:00 UTC

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