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Re: Cross Language with topic maps [was Re: 答复: KB note]

From: Kei Cheung <kei.cheung@yale.edu>
Date: Fri, 30 May 2008 13:05:10 -0400
To: "Huajun Chen @ Zhejiang University" <huajunsir@gmail.com>
Cc: eric neumann <ekneumann@gmail.com>, Jack Park <jack.park@sri.com>, public-semweb-lifesci@w3.org, kc28@email.med.yale.edu, twclark@nmr.mgh.harvard.edu
Message-id: <484033C6.70700@yale.edu>

Just a few clarifications. First of all, I'm not an expert in TCM. Also, 
herbal medicine is not just restricted to TCM, but it has a global 
interest (in other Asian and European countries). TCM includes other 
areas than herbal medicine, such as acupuncture .... Right now we try to 
limit our scope to herbal medicine as it has a potentially strong 
connection with western drugs and it may be easier for us to start.

I agree that it's hard to do the mapping and it's not possible (and 
there is no need) to do all the mappings. Huajun said: "But in some 
cases, it may work." What are these cases? I've been pondering on this a 
little bit. I also found the following article interesting:


I'm particularly attracted to the "TCM formulas" section. It mentions 
that "TCM regards treating the kidney as particularly important in aging 
disorders." In TCM, "zang" refers to "yin" organs" and "fu" refers to 
"yang" organs. It's interesting that brain is not mentioned as one of 
these organs. In fact, some Chinese herbalists told me that the 
brain/mind is tightly linked with zangs (yin organs). It is also 
interesting that there are differences between Zang Fu anatomy and 
western anatomy:


For possible mappings (although some of the mappings may seem to be 
fuzzy/uncertain) between TCM and mainstream medicine, mappings between 
Zhang Fu anatomy and western anatomy may be a possible place to start. 
Just a suggestion. I agree that it may still be difficult ...

Another thing that interests me  in the TCM formulas section of the 
above paper is that it mentions several formulas for Alzheimer's (there 
any many other formulas). Basically a formula is a mixture of herbs. As 
Huajun mentioned, a chemical compound database for these herbs may be of 
interest to western drug researchers. Also, as Matthias pointed out this 
might help lead to novel drug discovery strategies in AD. In the case of 
Huperzine A, it may be interesting to see if there is any difference in 
terms of potency between the natural (herb) form of Huperzine A vs. the 
synthetic form of Huperzine A. It may also be interesting to compare the 
mixture approach (TCM formulas) vs. the reductionist approach adopted by 
western drug research. I wonder how much of David Ho's cocktail drug 
approach to treating HIV/AIDS was influenced (or not influenced at all) 
by this mixture approach. I heard that some western drug researchers 
working in the US/Europe have applied some of the TCM philosophy in 
their drug research ...

Just my two cents,


Huajun Chen @ Zhejiang University wrote:
> In some cases, this approach works, but in perhaps more cases, it doesn't.
> I don't think we need and could find out correspondence between all
> concepts in Chinese medicine and Western medicine, as TCM has a
> different concept framework for describing many things. I also do not
> think we can figure out a universal, common ontology that can span
> over these two language systems (It may still be doable to some
> extend, but it would be very hard).
> By cross-culture data integration, i do not mean cross-language
> ontology translation (which is also an challenge, important, and
> useful of course). Instead, it might be more essential and doable to
> find out connection hubs or correlation points between them.  For
> example, the disease description may serve as one such  type of
> connection point. Another example is the chemical compound database
> for herb.  We only do translation and mapping at the hub nodes, so
> that a TCM researcher can explore relevant western medicine resource
> (still in English), and a western medicine researcher can explore
> relevant TCM resource (maybe still in Chinese if they can understand).
> Best, huajun
> On 5/29/08, eric neumann <ekneumann@gmail.com> 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="男性" lang="zh-Hans"
>> ...
>> Eric
>> 2008/5/28 Jack Park <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
>>>>> -----邮件原件-----
>>>>> 发件人: public-semweb-lifesci-request@w3.org
>>>>> [mailto:public-semweb-lifesci-request@w3.org] 代表
>> Matthias Samwald
>>>>> 发送时间: 2008年5月26日 21:22
>>>>> 收件人: kc28@email.med.yale.edu; Tim Clark
>>>>> 抄送: M. Scott Marshall; public-semweb-lifesci@w3.org
>>>>> 主题: 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/
Received on Friday, 30 May 2008 17:06:08 UTC

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