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Re: ontologies for BioRDF and LODD datasets

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 22 Apr 2010 15:14:56 -0400
To: François Scharffe <francois.scharffe@inria.fr>
Cc: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
Message-id: <4BD0A030.7090403@yale.edu>
The first question: what is drug? Dailymed seems to deal with marketed 
drugs at the FDA level, while drugbank seems to deal with drugs at the 
chemical/pharmacological/pharmaceutical level. There seems to be 
overlapping as well as unique parts between the two. Is the wikipedia 
definition of drug enough (http://en.wikipedia.org/wiki/Drug)? Do we 
want philosophical, universal, practical, and/or context-specific 
definition(s) of drug? Is herb belong to food or drug or both? If we 
take the cultural context into account, the answer may vary. I don't 
know if I've explained partly the proliferation of URI's (at least in 
the context of drugs). What kind of solution(s) do we want, how much 
time are we willing to wait, what kind of applications/use cases do we 
want to develop? For example, some people are concerned about herb-drug 
interactions ....

Just want to bring people's attention to the following meeting:


Submission of abstracts are welcome 
(http://www.hkbu.edu.hk/~cgcm2010/abstracts.php). A limited number of 
travel grants may be offered to graduate students/postdocs.



François Scharffe wrote:
> Hi,
> I've recently played around with BioRDF and LODD datasets. I must say 
> I'm impressed by the number of datasets available. It's good to see 
> how the linked data can lead to interesting queries allowing to 
> discover new information. I particularly like the TCM examples [1].
> I have a concern regarding the vocabularies used to published datasets.
> On one side it seems there are plenty of biomedical ontologies like 
> the ones on the bioportal, but on the other side there are many 
> datasets that each use its own native schema without referring to 
> these ontologies.
> Is there for example a reason why 'drugs' concepts in Dailymed and 
> Drugbank are different ? Why not reusing an existing ontology 
> describing drugs ? Is there actually a set of datasets reusing the 
> same ontology/ies ?
> I'm actually working on ontology alignment so I'd be glad to help in 
> the aligning task. I must however admit that I'm not very 
> knowledgeable in the biomediacal domain.
> Cheers,
> François
> [1] http://code.google.com/p/junsbriefcase/wiki/RDFTCMData
Received on Thursday, 22 April 2010 19:15:38 UTC

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