Re: scientific publishing task force update

Dear John,

I do hope your kidney stones "pass" with as little pain as possible.   
Ouch!  :-(

The general nature of your comment - echoed by others on this thread  
- that our description of biological reality is an evolving target is  
of course true.  There'd be little point - or attraction - for most  
of us in pursuing a career in biomedical research were this not the  
case.

This is one of the biggest challenges in biomedical KR - to devise  
deterministic, computable semantic frameworks capable of - or better  
yet, that thrive on - the evolving nature of human knowledge.  I do  
think SW tech brings some unique advantages to the table, where this  
particular issue is concerned.

Having said that, unless one is a devout Kantian willing to run smack  
into brick walls to prove a point, there are certain real world  
entities being described in biomedical ontologies, and the specifics  
of those entities - from the sulci and gyri of mammalian brains down  
to the atomic constituents of opsin isoforms - do have very real -  
and classifiable properties.  The shared, universal features of these  
real-world entities - the objects and processes (or endurants/ 
perdurants or occurants/continuants - depending on the formalism you  
prefer) - are what is specified in the foundational ontologies, and  
these don't tend to change very often.

Unfortunately, as wonderfully demonstrated in the very important  
citations added to this thread (the original Soldatova & King Nature  
Biotech. editorial from September 2005 and the series of responses  
from the Jan 2006 issue of that same journal), there is considerable  
disagreement on whose view of foundational universals one would best  
be served by.  There at a minimum, three distinct camps - the formal  
philosophical ontologists, the AI/Robotics/KR C.S. folks, and the  
computational linguistics folks - the latter of which generally favor  
no ontology at all, but rather using empiracly derived statistical  
clustering & categorization.  From my point of view, these three  
approaches can, should (and even occasionally have) work together.

My fear is the SW community may end up creating its own thread of  
activity in this domain - one more URI dependent and less lexicon  
dependent than computational linguistics, and one eschewing top-down  
ontological frameworks for a totally empirical, bottom up approach.   
I've heard this view espoused in some arenas, which is what raised  
the concern for me.  I know the majority of the SW community come  
from a very formal C.S. foundation, and are clearly aware of the  
various approaches to KR, so I was a bit taken aback to hear this  
view expressed.

To my mind, the folks participating at this level - working out  
standards and SOPs/"best practices" should be striving to bring these  
disparate, yet completely compatible forms of KR together - a view I  
believe one does see emerging to some extent - and can be culled from  
reading the collection of citations from Nature Biotech. listed  
above.  Establishing an at least compatible collection of  
foundational ontologies - and fundamental relations - is one of the  
tasks that must be addressed, I believe.

I do think the constellation of researchers focussed on biomedical KR  
are moving into a qualitatively new epoch - one where top-down and  
bottom-up KR techniques can and will be more compatible - and can be  
realized in a synergistic combination that neither approach can  
achieve on its own.  From my experience over the last decade - and  
more recently on the BIRN project - it is clear there is a meeting of  
the minds emerging across the divide of more empirically-oriented,  
bench top biologists who moved into KR in the mid 1990s (epitomized  
by the GO Consortium participants), the more formal medical  
informaticsts, and the most formal philosophical ontologists who've  
focused on biomedical KR.

In particular, the emerging focus on primary data KR and provenance  
is going to truly transform what can be computed on large, federated  
collections of biomedical data.  In the context of the BIRN project,  
we've been moving toward an understanding that the scientific process  
in biology consists of providing descriptions of phenotype, a process  
one can formalize by providing structure, deterministic descriptions  
of scientific observations.  The combined formalism emerging from the  
OBO community - use of PATO (phenotypic traits & attributes) and FuGO  
(formal descriptions of assays, reagents, devices, and environment)  
to create formal, normalized (as opposed to pre-coordinated)  
descriptions of primary research data forms the "best practice" for  
moving forward with primary data KR capable of ultimately supporting  
complex, knowledge mining.

Again, SW Tech can be a critical valuable tool - given the unique  
benefits it brings with it - toward achieving this goal.

Cheers,
Bill

On Jun 13, 2006, at 2:01 PM, John Rumble wrote:

> An unwritten rule about higher level ontologies is that they  
> reflect our knowledge today, not tomorrow. As knowledge evolves,  
> the upper level ontologies, especially, must also evolve. The  
> example of the concept "protein" is very apropos here. We can view  
> it from  functional, structural, integrative angles, and I am sure  
> there are a bunch more. Then think about how our "concept" of a  
> protein in each of those views has evolved over the last 10 years,  
> 20 years, 75 years. The problem is evident.
>
> At whatever level an ontology is developed, someone smarter or with  
> more insight or standing on the shoulder of giants will use that  
> onotlogy as a building block for a new and better higher level view  
> of nature. We have not reached the end of science yet.
>
> In my days of leading similar standards developments, some of the  
> best progress we made was when we banned discussions of (1) higher- 
> level ontologies (though we called them something else back in  
> those old days) and (2) acronyms.
>
> For those of you who have requested more references on my previous  
> e-mail about experiment description, it will have to wait a few  
> more days. Unfortunately bioinformatics have not solved my kidney  
> stone issues, which severely limit my ability to pull the requested  
> information together.
>
> John
>
> Dr. John Rumble
> Technical Director
> Information International Associates
> Oak Ridge TN
> www.infointl.com
> jrumble@iiaweb.com
> jumbleusa@earthlink.net
> 301 963 7903 (Home Office)
> 301 502 5729 (Cell)
> 865 298 1251 (Oak Ridge Office)
>

Bill Bug
Senior 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







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