Re: An application of the Semantic Web for finding alternative drug applications

Peter Ansell wrote:
> ----- "Kei Cheung" <kei.cheung@yale.edu> wrote:
>
>   
>> From: "Kei Cheung" <kei.cheung@yale.edu>
>> To: "eric neumann" <ekneumann@gmail.com>
>> Cc: "w3c semweb hcls" <public-semweb-lifesci@w3.org>
>> Sent: Thursday, September 11, 2008 6:42:33 AM GMT +10:00 Brisbane
>> Subject: Re: An application of the Semantic Web for finding alternative drug  applications
>>
>> Thanks for sharing the papers, Eric. I went through some of the papers
>> including the one you mentioned (interestingly there is a paper on 
>> wiki). I think they're interesting. They reminded me of "mining for the 
>> semantic web" (ontology learning?) and "mining from the semantic web"
>> (data mining). For biological networks, we need to do both semantic and 
>> topological queries. It might be difficult to achieve the latter using
>> SPARQL (e.g., finding protein hubs). Maybe we need some extensions of
>> SPARQL.
>>
>> Best,
>>
>> -Kei
>>     
>
> What are the limits to what you can do with bare SPARQL in this area? Does it help to have elementary rdfs subclass knowledge for the topological parts?
>
> Cheers,
>
> Peter
>
>   
Hi Peter,

When YeastHub [1] was being built, I was wondering whether Semantic Web 
(SW) technologies can help facilitate integrative biological network 
analysis including network topology. Later, a web-based tool called 
"tYNA" was created and published [2] which supports biological network 
analysis/visualization. tYNA was not implemented using SW, but I still 
wonder how some of its features can be implemented using SW.

[1] http://bioinformatics.oxfordjournals.org/cgi/reprint/21/suppl_1/i85
[2] http://bioinformatics.oxfordjournals.org/cgi/content/full/22/23/2968

Cheers,

-Kei

Received on Thursday, 11 September 2008 14:51:20 UTC