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: fD 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 <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>:
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 [EMAIL PROTECTED] 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: [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
>> [mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>] ëï\ Matthias Samwald
>>
¢ëó ±º: 2008îN5åé26ì 21:22
>> ùæåèêl: [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>; 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/
>>
>>
>>
>>
>>
>>
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