| 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----- Sent: Monday, July 31, 2006 7:57 AM 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 412-478-4552
-----Original Message----- 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
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
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)
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