- 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 > > >(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 Wednesday, 9 August 2006 00:58:24 UTC