W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2008

Re: Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

From: Kei Cheung <kei.cheung@yale.edu>
Date: Wed, 20 Aug 2008 22:58:40 -0400
Message-ID: <48ACD9E0.1000408@yale.edu>
To: Adrian Walker <adriandwalker@gmail.com>
CC: public-semweb-lifesci@w3.org, lstein@cshl.org, Euan Adie <e.adie@nature.com>

Hi Adrian et al,

Thanks for the information. I just wonder how clinical workflow might be 
different from or the same as biological workflow.

Also, I just noticed Licoln Stein was copied in this email. Below is my 
early response to Duncan's email:

"It looks like there are a number of ways for commenting on the paper. I 
don't know if Lincoln Stein is reading this list. If not, it may be 
worth contacting him to see if he is aware of the HCLSIG activities and 
to let him know that we found his paper interesting and have some 
constructive comments for his paper. If he thinks it's OK for us to 
submit a short correspondence (<1 page including references) to Nature, 
we may contact the Editor of Nature Genetics to see if such a 
correspondence would be of interest to them. Otherwise, we can just 
relay the comments via the Wiki and/or Nature Network. Please let me 
know what you think."

To add to this, more people may be motivated to provide comments if they 
can be published in journal. No matter what, I'm happy to see semantic 
web is part of the bioinformatics nation now!

Best,

-Kei

Adrian Walker wrote:

> Hi All --
>
> Here's another possible item for a cyberinfrastructure.
>
> It's a kind of Wiki for content, written as syllogism-flavored rules, 
> in *executable* English. 
>
> It's live on the  Web, and shared use is free.
>
> It also works as an SOA endpoint on the Web.
>
> Here are some examples of a biological and workflow nature that you 
> can view, run and change, using a browser:
>
> www.reengineeringllc.com/ibldrugdbdemo1.htm 
> <http://www.reengineeringllc.com/ibldrugdbdemo1.htm>   (Flash video 
> with audio)
> www.reengineeringllc.com/demo_agents/HclsDrugDb1.agent 
> <http://www.reengineeringllc.com/demo_agents/HclsDrugDb1.agent>
>
> www.reengineeringllc.com/demo_agents/MedMine2.agent 
> <http://www.reengineeringllc.com/demo_agents/MedMine2.agent>
>
> www.reengineeringllc.com/demo_agents/GeneSequenceOntology3.agent 
> <http://www.reengineeringllc.com/demo_agents/GeneSequenceOntology3.agent>
>
> www.reengineeringllc.com/demo_agents/RDFQueryLangComparison1.agent 
> <http://www.reengineeringllc.com/demo_agents/RDFQueryLangComparison1.agent>
>
> www.reengineeringllc.com/demo_agents/CriticalPath1.agent 
> <http://www.reengineeringllc.com/demo_agents/CriticalPath1.agent>
>
> www.reengineeringllc.com/demo_agents/ProcessSpecificationLanguage1.agent 
> <http://www.reengineeringllc.com/demo_agents/ProcessSpecificationLanguage1.agent>
>
> Apologies if you have seen this before, and thanks for comments.
>
>                                                     -- Adrian
>                   
> Internet Business Logic
> A Wiki and SOA Endpoint for Executable Open Vocabulary English over 
> SQL and RDF
> Online at www.reengineeringllc.com 
> <http://www.reengineeringllc.com>    Shared use is free
>
> Adrian Walker
> Reengineering
>
> On Wed, Aug 20, 2008 at 9:52 AM, Duncan Hull <duncan.hull@cs.man.ac.uk 
> <mailto:duncan.hull@cs.man.ac.uk>> wrote:
>
>
>     Hello Kei
>
>     Glad you liked the article.
>
>
>     On 20 Aug 2008, at 14:27, Kei Cheung wrote:
>
>
>
>             "To my knowledge, there is currently only one project that
>             aims to bring the pure semantic web to biomedical
>             research. That project is the Simple Semantic Web
>             Architecture and Protocol (SSWAP30)"
>
>             It's nice that Nature allows the community to add
>             descriptions about our various projects on the wiki page
>             associated with the article [2]; unfortunately, though,
>             most readers of the original article will probably not
>             have a look at that wiki.
>
>
>         Nature seems to allow one to write correspondence (1 page) to
>         comment about matters arising from research papers. See:
>
>         http://www.nature.com/ng/pdf/gta.pdf
>
>
>
>     I think in this case, this is what the wiki is for. So if Lincoln
>     Stein has not told the full story, people could try adding the
>     appropriate details to
>     http://nrgwiki.nature.com/cyberinfrastructureforbiology/show/HomePage
>
>     I see Susanna and Eric Jain have already contributed
>     http://nrgwiki.nature.com/cyberinfrastructureforbiology/recently_revised
>
>     Also, if anyone is having trouble accessing the original article
>     at http://dx.doi.org/10.1038/nrg2414 , as a "featured article" it
>     should be available free (for the first month only), provided you
>     sign in at http://www.nature.com/foxtrot/svc/login
>
>     Some discussion on this over at Nature Network too
>     http://network.nature.com/forums/bioinformatics/2235
>
>
>     Duncan
>
>     ---
>     http://duncan.hull.name
>
>
>
>
Received on Thursday, 21 August 2008 02:59:29 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:53 GMT