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

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Tue, 8 Aug 2006 20:58:02 -0400
To: "Miller, Michael D \(Rosetta\)" <Michael_Miller@Rosettabio.com>, "kei cheung" <kei.cheung@yale.edu>, <donald.doherty@brainstage.com>
Cc: "w3c semweb hcls" <public-semweb-lifesci@w3.org>, "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
```
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
> > 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:
> > >>
> > >>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 Wednesday, 9 August 2006 00:58:24 UTC

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