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Re: Banff demo

From: Mark Montgomery <markm@kyield.com>
Date: Mon, 14 May 2007 07:33:24 -0700
Message-ID: <005d01c79634$d514e290$a100a8c0@Inspiron>
To: "Alan Ruttenberg" <alanruttenberg@gmail.com>
Cc: "Tim Berners-Lee" <timbl@w3.org>, <public-semweb-lifesci@w3.org>, "William Bug" <William.Bug@DrexelMed.edu>

Sorry for the grammar in my last post folks- fast fingers and spell check + 
on the run = gibberish.

I may be able to finally add some value to the discussion, and am happy to 
assist with papers, demo, or anywhere else if I can add value. I don't do 
much coding these days, but I am an expert (if anyone is-questionable) on 
e-commerce, e-learning, economic modeling and adoption with several notable 
firsts coming out of our small shop since '95 (don't be first- martyrdom is 
tough on loved ones). I just filed a patent amendment to our Kyield system 
so it will hopefully be published soon for anyone with deeper interest- 
brings together over a decade of work, much of which is relative to this 

Regarding sources- While I review a fair volume in my VC work, I don't 
consider myself an expert in LS R&D, much less any of the dozens of 
specialties within the broad area of study- they should be the primary voice 
on sources needed. I have received correspondence however that suggests talk 
and some pressure recently on the FDA in making more of their data available 
(from academia and corp.), which apparently many believe would accelerate 
prevention and therapy if not cures on many fronts. So that would be one 
huge example in the public sector. But we can expect that as has been the 
case all along, when it comes to intelligent data representing knowledge, 
much of it will remain private. The medium threatens many industries 
(whether real or imagined the result is similar), and the battles have been 
brutal at times.

We have two primary interests and goals here from my perspective:

1) Immediate- demonstrating the acceleration of R&D within the broad and 
highly complex environment known as life science. It's pretty clear to me 
and most engaged here (apparently) that ontological languages are already 
playing an essential role in this goal, but the combination of lack of 
sources (Alan Brain Institute addressed as shown in your example- $100 
million), trained technicians, and adoption of standards remain challenges.

For drug development and genomics among others, we know that high volume 
data manipulation and collaboration can and do lead to accelerated 
discovery. A big part of the problem is one of culture, which is the most 
important aspect of knowledge systems in my and others' view. On one hand we 
have sub-cultures that will share anything and destroy organizations- and 
even cost the lives of large numbers of people, while on the other extreme 
we have sub-cultures that are so intent on protecting agency turf that it 
creates the same result. Both of these extremes have been evident within the 
same broader U.S. Government over the past few years as partial causes of 
major disasters- an excellent body of case history. I have made the argument 
with members of congress, agency heads, CIOs, etc. that our Kyield system 
could have prevented same, simply due to embracing more intelligent systems 
as discussed here in combination with equally intelligent organizational 
design. Lots of talk- little action.

So I argue in enterprise architecture to manage culture intelligently first 
and always. Otherwise the tools won't be used properly if used at all, and 
once cultures deteriorate sufficiently then a negative spiral of decision 
making can occur- and that can be catastrophic- in any type of organization.

My guess is that even private life science companies could share far more 
data safely than many believe, within the right structure of course. But as 
my old friend and colleague Russell Borland said a decade ago in one of our 
GWIN forums on the topic- free only works if everything is free. Sacrifice 
and investment need compensation as bills need to be paid. Structure 

One of the main themes currently in life sciences in the VC world is an 
attempt to show the giants that collaboration with smaller firms would be a 
more intelligent path. I'm thinking that this specific target would be ripe 
for this type of demo perhaps in showing how a similar collaboration between 
entities can actually lead to a hypothetical discovery.

This WG is I think doing an excellent job of helping to demonstrate the 
potential for acceleration of solutions with a more intelligent web, whether 
public, private, or some combination thereof. And I think that life science 
is among the best communities to target the broader technology for adoption. 
The industry cluster has serious problems that affect us all, not least of 
which is that it requires $1 billion to bring the average drug to market, 
meaning that very few can even begin the journey, and also very likely that 
most affective therapies die long before potential value can be known.

2) Mid-term- demonstrating to other clusters, including multi-disciplinary, 
the value of semantic technologies to life science that can then be applied 
to their industry or discipline. Based on my own discussions with a couple 
of other industry leaders, I'd say we have a lot left to be done to show the 
value relative to their perceived needs.

One additional comment- the cost of entry is not what matters to those of us 
with battle scars in IT investment. What matters is total cost of ownership, 
scale, and sustainability in order to achieve the objective.

- .02, MM

----- Original Message ----- 
From: "Alan Ruttenberg" <alanruttenberg@gmail.com>
To: "Mark Montgomery" <markm@kyield.com>
Cc: "William Bug" <William.Bug@DrexelMed.edu>; 
Sent: Sunday, May 13, 2007 10:24 AM
Subject: Re: Banff demo

> On May 12, 2007, at 9:05 AM, Mark Montgomery wrote:
>> Nice work folks on the slide presentation folks. Haven't been able  to 
>> access the demo, but the goal is obvious. I agree that it's a  good 
>> foundation to build upon, although it would indeed be nice to  have 
>> additional sources to work with. Access to sources is likely  to be a 
>> perm challenge.
> Well, we've got quite a lot to do in the way of making available the 
> existing public resources before we are data starved. However, I  agree 
> that specific resources that we would like may be hard to  acquire due to 
> licensing issues. Do you any specific sources in mind?
>>  Of course the communications on value with some will be more 
>> challenging than expressed here- I can almost hear the typical  CIO's 
>> cynical reply after years of reduced budgets, 70-80% of which  is 
>> required for sustaining legacy-living little if any for  innovation, but 
>> R&D divisions I would hope be more receptive.
> I would. I think we're at the stage of starting to show the  possibility 
> of doing things that are not available in any single  public resource. Not 
> too long from now I hope we'll be able to do  things that haven't ever 
> been done in easily deployable systems.
> In terms of value, I think that the first message is that this  technology 
> is, at least to deploy, very inexpensive. Hardware to run  the thing at 
> this scale is ~3K. All the data is free, and there is an  open source 
> version of Virtuoso. On the other hand, cost of  development of new 
> resources is still high, and we are starved for  people who know the 
> technology well. Hopefully we'll help accelerate  that process as we put 
> more of the documentation about how we  converted each resource up on the 
> wiki, a project for the next few  weeks.
> I do hope we can more explicitly develop the value proposition to 
> companies in the future. From my perspective, for the moment the the 
> challenge is showing value.
>> Congrats- a good step. - MM
> Thanks, and for your comments,
> Regards,
> Alan
>> ----- Original Message -----
>> From: William Bug
>> To: Alan Ruttenberg
>> Cc: public-semweb-lifesci@w3.org
>> Sent: Saturday, May 12, 2007 1:51 AM
>> Subject: Re: Banff demo
>> Vunderbar!
>> Thanks to all who worked hard to pull this off!
>> It's hard to get the full impact just perusing the slides, but it  looks 
>> to me that you pulled together a very compelling demo that  examined 
>> several questions of biological relevance to  neuroscientists studying 
>> neurodegenerative disease (AD in particular).
>> I also really like the list breakdown of tools to target different 
>> aspects of the overall development - e.g., Pellet, Jena, Perfuse, etc.
>> I think this will be a fantastic base to build off for ISMB (and SfN).
>> Kudos!
>> Cheers,
>> Bill
>> On May 11, 2007, at 2:18 PM, Alan Ruttenberg wrote:
>>> I have updated the page http://esw.w3.org/topic/HCLS/Banff2007Demo  with 
>>> slides, pointers to the triple store etc.
>>> -Alan
>> Bill Bug
>> Senior Research Analyst/Ontological Engineer
>> Laboratory for Bioimaging  & Anatomical Informatics
>> www.neuroterrain.org
>> Department of Neurobiology & Anatomy
>> Drexel University College of Medicine
>> 2900 Queen Lane
>> Philadelphia, PA    19129
>> 215 991 8430 (ph)
>> 610 457 0443 (mobile)
>> 215 843 9367 (fax)
>> Please Note: I now have a new email - William.Bug@DrexelMed.edu
Received on Monday, 14 May 2007 14:33:46 UTC

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