- 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>
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 UTC