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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
