Re: [HCLS] RE: scientific publishing task force update

Good point, Michael.

I think there maybe ways to use some combination of NamedGraphs,  
SKOS, and Topic Maps to address different aspects of this general  
issue.  We're working on this in the BIRN project and expect it will  
help us - and others - make use of the OBO Foundry ontologies - and  
data/literature annotations using OBO Foundry ontology classes -  in  
the "messy" world we all have to function in.

The work you are doing Kei will be a very helpful example to have for  
review.

Cheers,
Bill

On Aug 8, 2006, at 1:50 PM, Miller, Michael D (Rosetta) wrote:

>
> Hi Kei,
>
>> It means that  things might not overlap at
>> the same level, but may overlap at different levels between different
>> ontologies (entity modeled at a higher level of granularity may be
>> mapped to one modeled at a lower level of granularity) .
>
> Excellent point, and I just want to add (explicitly!) that one also  
> has
> to consider that a concept in one ontology might overlap partially or
> completely two concepts in another ontology and if you map those two
> concepts back to the first ontology, they have interesting overlaps to
> not only the original concept but other concepts in the first  
> ontology,
> and so on.
>
> cheers,
> Michael
>
>> -----Original Message-----
>> From: public-semweb-lifesci-request@w3.org
>> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of kei cheung
>> Sent: Monday, July 31, 2006 7:57 AM
>> To: donald.doherty@brainstage.com
>> Cc: 'w3c semweb hcls'
>> Subject: Re: [HCLS] RE: scientific publishing task force update
>>
>>
>>
>> Hi Don et. al,
>>
>> I'm also catching up with all the exciting communications
>> that have been
>> going on within the HCLSIG forum. Different neuroscience
>> databases store
>> different but related types of information at possibly
>> different levels
>> of detail and granularity. It means that  things might not overlap at
>> the same level, but may overlap at different levels between different
>> ontologies (entity modeled at a higher level of granularity may be
>> mapped to one modeled at a lower level of granularity) . It would
>> therefore be important to be able to address these issues in our
>> integration framework (e.g., the one proposed by Eric).   I'm in the
>> process drafting a scenario involving integration CoCoDat and
>> NeuronDB.
>> I'll make it available to the group as soon as possible.
>>
>> Cheers,
>>
>> -Kei
>>
>> Donald Doherty wrote:
>>
>>> Kei is correct that there is overlap in the approach I think
>> we're taking to
>>> and Eric's ideas. My mentor Karl Pribram wrote about
>> neuroscience as a
>>> modern day "Tower of Babel" in his 1972 "Languages of the Brain."
>>>
>>> Not only is the situation is much the same today but I don't
>> believe that
>>> will ever change (nor would it be desirable if it did...we
>> need all of the
>>> ideas, viewpoints, etc. that we can get). So, there will
>> always be multiple
>>> ontologies that change over time (some slowly some not).
>>>
>>> That is why it seems especially important to provide a way
>> to build bridges
>>> between ontologies that enable individuals and organizations
>> to contemplate
>>> more than one semantic view of any given dataset.
>>>
>>> [Please ignore the above if this has been covered
>> already...I'm currently
>>> trying to catch up with about one and a half months of
>> email! I had to
>>> finish a prototype that is now in debug hell...but that's
>> another story.]
>>>
>>> Don
>>>
>>> -----
>>> Donald Doherty, Ph.D.
>>> Brainstage Research, Inc.
>>> www.brainstage.com
>>> donald.doherty@brainstage.com
>>> 412-478-4552
>>>
>>>
>>> -----Original Message-----
>>> From: public-semweb-lifesci-request@w3.org
>>> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of kei  
>>> cheung
>>> Sent: Thursday, June 15, 2006 1:04 PM
>>> To: Eric Neumann
>>> Cc: Phillip Lord; w3c semweb hcls
>>> Subject: Re: scientific publishing task force update
>>>
>>>
>>> Hi Eric et al,
>>>
>>> The more I think of, would your OntologyCovering task relate to Don
>>> Doherty's Bridging Ontology task
>>> (http://esw.w3.org/topic/HCLS/OntologyTaskForce/Create_Bridgi
>> ng_Ontology_bet
>>> ween_NeuronDB_and_CoCoDat_databases_and_UMLS_Common_Vocabular
>> y#preview)?
>>>
>>> In other words, can your Ontology Covering technique potentially be
>>> applied to mapping between NeuronDB and CoCoDat OWL ontologies?
>>>
>>> Just my 2-cent observation.
>>>
>>> Cheers,
>>>
>>> -Kei
>>>
>>> Eric Neumann wrote:
>>>
>>>
>>>
>>>> Following up to Phil's point, an alternative to building upper
>>>> ontologies (UO) first, is to consider constructing a "Covering Map"
>>>> between apparent overlapping sets of "related" ontologies.
>> These are
>>>> light weight, RDF associations that can help "pin-down" potentially
>>>> related items/classes from different ontologies. I also agree the
>>>> notion of "guides" is very powerful when dealing with a diverse
>>>> community, yet trying to get things up and running sooner
>> than later...
>>>>
>>>> I've written this up on the HCLS/OntologyTaskForce wiki:
>>>> http://esw.w3.org/topic/HCLS/OntologyTaskForce/OntologyCovering
>>>>
>>>> As BioRDF progresses in making more life sciences data available as
>>>> RDF, we will have to deal with such ontological issues more
>>>> frequently, so it's very useful for everyone to be discussing these
>>>> issues at this point.
>>>>
>>>> cheers,
>>>> Eric
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --- Phillip Lord <phillip.lord@newcastle.ac.uk> wrote:
>>>>
>>>>
>>>>
>>>>>>>>> "SC" == Steve Chervitz <Steve_Chervitz@affymetrix.com> writes:
>>>>>>>>>
>>>>>>>>>
>>>>>> They also wrote an interesting paper on the state of
>>>>>> bio-ontologies.
>>>>>>
>>>>>> Nature Biotechnology 23, 1095 - 1098 (2005)
>>>>>> doi:10.1038/nbt0905-1095 Are the current ontologies in biology
>>>>>> good ontologies?
>>>>>>
>>>>>> Larisa N Soldatova & Ross D King
>>>>>>
>>>>>>
>>>> SC> Also worth seeing: The MGED ontologies folks wrote a  
>>>> response to
>>>> SC> this article that comments on the bio-ontology development
>>>> SC> process, and addresses some statements Soldatova and King make
>>>> SC> about MO which the MO folks feel are inaccurate or misleading:
>>>>
>>>> SC> Stoeckert C et al. Nature Biotechnology 24, 21 - 22 (2006)
>>>> SC> doi:10.1038/nbt0106-21b Wrestling with SUMO and bio-ontologies
>>>> SC> http://www.nature.com/nbt/journal/v24/n1/full/nbt0106-21b.html
>>>>
>>>> Their paper did cause, how shall I say, somewhat of a stir.
>>>>
>>>>
>>>> SC> The reliance on and choice of upper level ontology seems to  
>>>> be a
>>>> SC> big bone of contention. Are there any good reviews on these
>>>> SC> discussing things like why there are so many of them and why
>>>> SC> can't they be combined? Seems like the current trend is to
>>>> SC> accept their existence and work towards making them
>>>> SC> interoperable:
>>>>
>>>>
>>>> If I were being cynical (those of you who know me will know how  
>>>> rare
>>>> this is), I would suggest that it's a case of "standards
>> are so good,
>>>> that we need one each".
>>>>
>>>> The issue is a slightly deeper one in bio-ontologies. It's not  
>>>> clear
>>>> that an upper ontology actually brings significant value to the
>>>> table. The claimed advantage of interoperability between ontologies
>>>> is, to my mind, somewhat bogus; they only really allow
>>>> interoperability when you are querying over the concepts in
>> the upper
>>>> ontology. Much more important is that they help to ease the
>> design of
>>>> an ontology; you have more idea where concepts should go, so you  
>>>> can
>>>> spend more time worrying about the details of what ever you are
>>>> modelling and less about the big picture.
>>>>
>>>> On the flip side, they tend to complicate some stages of ontology
>>>> development, mostly notably the first month when you have lots of
>>>> biologists tearing their hair out trying to work out what a
>> perjurant,
>>>> continuant, sortal, self-standing kind is.
>>>>
>>>> The juries still out in my opinion.
>>>>
>>>> Phil
>>>>
>>>> Eric Neumann, PhD
>>>> co-chair, W3C Healthcare and Life Sciences,
>>>> and Senior Director Product Strategy
>>>> Teranode Corporation
>>>> 83 South King Street, Suite 800
>>>> Seattle, WA 98104
>>>> +1 (781)856-9132
>>>> www.teranode.com
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>
>

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







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