- From: Pat Hayes <phayes@ihmc.us>
- Date: Thu, 29 May 2008 12:01:50 -0700
- To: Jack Park <jack.park@sri.com>
- Cc: w3c semweb hcls <public-semweb-lifesci@w3.org>, Tim Clark <twclark@nmr.mgh.harvard.edu>
- Message-Id: <p06230956c464acd84f9f@[192.168.1.11]>
At 2:32 PM -0700 5/28/08, Jack Park wrote: >Thanks for the question, Kai. > >Topic maps in RDF: >There exists an OWL DL variant of the XML topic maps standard (XTM) [1] >There may be others. Certainly a search on "owl topic map" reveals interest. > >I have an OWL Full variant of the TMRM "subject >maps" standard, ISO 13250-5. The TMRM (topic >maps reference model) departs from the XML topic >maps standard (which I helped create) by >reducing topic mapping to its core >functionality, releasing the standard from XML >serialization schemes. We are now back to the >frame-based representations many people are >familiar with. But, I have yet to find a way to >use DL because the properties of each OWL class >or instance (we call them "subjects") must also >be subjects; the co-reference of a property as a >class instance has evaded me: I have yet to make >it validate. But, validation as OWL Full flys >quite easily. Each property instance is then >contained in a p-list rather than thinking in >terms of restrictions. Wierd, but it does answer >SPARQL queries. > >Topic maps do not and should not interfere with >the semantic web; they bring other >characteristics to knowledge representation and >organization that, I think, enhance the semantic >web's capabilities. For one thing, they offer >two opportunities: they automatically organize >all entities of the semantic web in a >subject-centric fashion, and, in so doing, they >offer the opportunity to federate (a kind of >merge) ontologies of all kinds. For instance, it >may be that the NCI cancer ontology has a few >terms (classes) that are also found (perhaps >even under a different name) in, say, a >Parkinson's ontology. We can merge all >ontologies, no matter the names, so long as we >are able to identify that different classes >happen to be representing the same subject >(entity, concept, whatever you wish to call it), >the two entities are merged. One can do that in OWL also. In fact one can do that in any notation which has (1) globally scoped names, such as URIs, and (2) an equality operator, to assert identity; in OWL, that is owl:sameAs. BTW, one can also (of course) have multiple names for the same entity, and (in OWL Full) link the various names to such things as email messages, comments, etc.. I don't see what 'extra' topic maps bring as far as all this is concerned. All the actual work is in doing that identification, which is still more an art than a science. Recording it once it is made is easy. In this context, I think your use of the word 'automatically' above may be rather misleading. Pat > Those that don't merge remain still linked in >their graphs. This allows for potential "aha!" >moments (some might say "Black Swan Events"), as >an emergent behavior. I don't mean to sound like >I'm making arm-waving claims; I am merely >sketching some possibilities. It's also the case >that you don't need topic maps to do that. Topic >maps represent, more than anything, a slightly >different way to think about the problem space. > >Cheers, >Jack >[1] http://xml.coverpages.org/CreganTMs-OWL200505.pdf > >Kei Cheung wrote: >>Hi Eric et al, >> >>I'm glad that umls, topic map, ... were >>mentioned. We have to do more than literal >>translation or linguistics. It's semantics! >> >>Traditional Chinese medicine embodies rich >>dialectical thought, such as that of the >>holistic connections and the unity of yin and >>yang. It deals with many facets of human >>anatomy and physiology: ”f”D zang-fu (organs), >>åä meridians (main and collateral channels), üÜ >>qi (vital energy), åå blood, *Ë‘ *jing (essence >>of life), body fluid, the inside and outside of >>the body, as well as the connections between >>the whole and the parts. >> >>I wonder if there is a Chinese counterpart of >>umls that have semantic correspondence to the >>English umls. Topic map is also interesting. I >>also wonder if there is a direct mapping >>between topic map and semantic web (rdf/owl) >>.... >> >>I agree that we should narrow the scope of our >>problem a little bit. Otherwise, things tend to >>fall apart if we try to be too ambitious. I >>hope we can start thinking more about this >>Huperzine use case, for example. I also hope >>such a use case is holistic in the sense that >>it is both scientifically and technologically >>interesting. >> >>Thanks, >> >>-Kei >> >>eric neumann wrote: >>>Why not simply use to following trick on top of universal symbols? >>> >>><umls:male rdfs:label="male" lang="en" >>>rdfs:label="Mann" lang="ge" >>>rdfs:label="mâle" lang="fr" >>>rdfs:label="íjê´" lang="zh-Hans" >>>... >>>> >>> >>>Eric >>> >>>2008/5/28 Jack Park <jack.park@sri.com <mailto:jack.park@sri.com>>: >>> >>> >>> In cross-language data integration, it may be a simple matter of >>> using a >>> multitude of language-scoped labels in an ontology. Another approach >>> that has been mentioned on this list many moons back by the late Bill >>> Bugg was that of applying topic maps to the federation of >>> heterogeneous >>> resources, including disparate ontologies that don't easily merge, and >>> data sets. Bill was referring to some of my work. Topic maps >>> provide the >>> ability to apply as many different names to some entity as >>> necessary for >>> all participants to successfully locate what they seek. At the same >>> time, topic maps can federate each entity with external comments, >>> dialogues (such as this email message), bookmarks (tags) and >>> relationships with other entities. >>> >>> Jack >>> >>> Xiaoshu Wang wrote: >>> > Huajun Chen@Zhejiang University wrote: >>> >> Another challenge is cross-language data integration, which is >>> actually a >>> >> job that ontology should do. >>> >> >>> > I honestly disagree. Ontology is about the semantics of *being* >>> but that >>> > of symbols. It doesn't matter if how "gene" is called, named, or >>> > written. It symbolize the same objective entities. A URI such as >>> > http://www.example.com is not written in English. It is just a >>> bunch of >>> > symbols. Let's not introduce linguistic issues into data >>> integration, >>> > which already have a lot of issues. >>> > >>> > Xiaoshu Wang >>> >> Best wishes, huajun >>> >> >>> >> -----" åèå¥åè----- >>> >> …¢åèêl: public-semweb-lifesci-request@w3.org >>> <mailto:public-semweb-lifesci-request@w3.org> >>> >> [mailto:public-semweb-lifesci-request@w3.org >>> <mailto:public-semweb-lifesci-request@w3.org>] ë“ï\ Matthias Samwald >>> >> …¢ëó ±º”: 2008îN5åé26ì™ 21:22 >>> >> ùæåèêl: kc28@email.med.yale.edu >>> <mailto:kc28@email.med.yale.edu>; Tim Clark >>> >> è¥ëó: M. Scott Marshall; public-semweb-lifesci@w3.org >>> <mailto:public-semweb-lifesci@w3.org> >>> >> éÂÃ’: Re: KB note >>> >> >>> >> >>> >> >>> >>> Speaking of national boundaries, I wonder if alternative >>> medicine (e.g., >>> >>> herbal >>> >>> medicine) would also be of interest to this community. For >>> example, >>> >>> Huperzine >>> >>> is a drug derived from the herb Huperzia serrata. I also >>> wonder if there >>> >>> are >>> >>> hypotheses regarding the study of herbs in the possible >>> treatment of >>> >>> neurological diseases. >>> >>> >>> >> I would also be very motivated to help in this kind of research. >>> >> Specifically, Huperzine A would be a very interesting use-case >>> for our >>> >> developments. It is a herbal compound with a history in folk >>> medicine and is >>> >> >>> >> available OTC in most countries, yet it rivals the effectiveness of >>> >> currently leading Alzheimer medications such as Tacrine. It >>> also has a dual >>> >> mode of action that does not only involve acetylcholinesterase >>> inhibition, >>> >> but also modulation of the NMDA receptor. The implications of >>> this for the >>> >> treatment of Alzheimer's are still a rather hot topic. >>> >> >>> >> The integration of knowledge from traditional medicine, plant >>> >> taxonomy/phylogeny/biochemistry and receptor binding databases >>> (PDSP Ki >>> >> database, IUPHAR) could lead to the identification of some >>> extremely novel >>> >> therapeutic strategies. Finding candidate molecules in such a >>> way might be >>> >> much more effective than weeding through libraries of compounds >>> generated by >>> >> >>> >> combinatorial synthesis etc. The challenge lies in the >>> integration of some >>> >> very heterogenous datasets that come from vastly different >>> disciplines, >>> >> which is exactly the field of research where Semantic Web >>> technologies are >>> >> most effective. >>> >> >>> >> I guess the major problem for this kind of research is that >>> there are no >>> >> funding programmes that span China, the US and Asia... >>> >> >>> >> Cheers, >>> >> Matthias Samwald >>> >> >>> >> DERI Galway, Ireland // Semantic Web Company, Austria >>> >> http://www.deri.ie/ >>> >> http://www.semantic-web.at/ >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> -- --------------------------------------------------------------------- IHMC (850)434 8903 or (650)494 3973 home 40 South Alcaniz St. (850)202 4416 office Pensacola (850)202 4440 fax FL 32502 (850)291 0667 cell http://www.ihmc.us/users/phayes phayesAT-SIGNihmc.us http://www.flickr.com/pathayes/collections
Received on Thursday, 29 May 2008 19:02:37 UTC