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

From: kei cheung <kei.cheung@yale.edu>
Date: Thu, 10 Aug 2006 15:53:30 -0400
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
Cc: "Miller, Michael D (Rosetta)" <Michael_Miller@Rosettabio.com>, donald.doherty@brainstage.com, w3c semweb hcls <public-semweb-lifesci@w3.org>
Message-id: <44DB8EBA.4070908@yale.edu>

Hi All,

I have written two examples demonstrating the need for ontological 
mapping between NeuronDB and CoCoDat. These examples are now included in 
the following ontology task:

http://esw.w3.org/topic/HCLS/OntologyTaskForce/Create_Bridging_Ontology_between_NeuronDB_and_CoCoDat_databases_and_UMLS_Common_Vocabulary

It would be great to see if we can come up with a semantic web approach 
to facilitate such ontological mappings between NeuronDB and CoCoDat.

Cheers,

-Kei


Kashyap, Vipul wrote:

>May I propose cataloging methodically all possible inter-ontology relationships
>
>Here is an initial list. Feel free to add to them 
>
>Let A1, ... , An be concepts in ontology O1 and B1, ..., Bn be concepts in
>ontology O2. The following possibilities exist:
>
>A1 = B1
>A1 subset of B1 (analogous to B1 subset of A1)
>A1 = some OWL expression involving B1, ..., Bn
>(e.g., A1 subset of B1 AND B2)
>A1 subset of some OWL expression involving B1, ..., Bn
>Some OWL-expression involving A1, ..., An 
>= Some OWL-expression involving B1, ..., Bn
>Some OWL-expression involving A1, ..., An 
>subset of Some OWL-expression involving B1, ..., Bn
>
>A1 instance of B1 (This takes us beyond OWL-DL)
>All variations above replacing subset-of by instance-of
>
>Overlaps can be expressed as follows:
>
>If A1 overlaps B1, then A1 and B1 will not be inconsistent
>This can also be expressed using two conditional probability
>statements:
>
>Prob( x=A1 | x=B1) = p1
>Prob( x=B1 | x=A1) = p2
>
>Note p1 not necessarily = p2.
>
>I may have missed some possbilities. So feel free to complete them.
>May be we should open this up as a task in BIONT?
>
>If interested in inter-ontology mappings you may want to check out:
>http://lsdis.cs.uga.edu/~kashyap/publications/MKIS00.pdf 
>
>Cheers,
>
>---Vipul
>
>  
>
>>-----Original Message-----
>>From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-
>>request@w3.org] On Behalf Of Miller, Michael D (Rosetta)
>>Sent: Tuesday, August 08, 2006 1:50 PM
>>To: kei cheung; donald.doherty@brainstage.com
>>Cc: w3c semweb hcls
>>Subject: RE: [HCLS] RE: scientific publishing task force update
>>
>>
>>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
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>
>>>
>>>
>>>      
>>>
>
>
>  
>
Received on Thursday, 10 August 2006 19:53:38 GMT

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