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Re: Evidence

From: William Bug <William.Bug@DrexelMed.edu>
Date: Wed, 13 Jun 2007 09:02:25 -0400
Message-Id: <D3303003-E61B-451A-AF55-B6C51C67C300@DrexelMed.edu>
Cc: Waclaw Kusnierczyk <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>, Barry Smith <phismith@buffalo.edu>, Matthias Samwald <samwald@gmx.at>
To: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
Sorry I've been out of touch on this and other HCLS IG activities,  
but I've been - and will continue to be for some time - tied up with  
other tasks.

I believe both issues as originally raised by Matthias aer extremely  
important:
	a) creating a cogent and concise means of inter-relating entities  
that is - as best we can implement it - tied to a realist view of  
biomedical reality
	b) dealing in a consistent and - as much as is practical - formal  
way with evidence - which includes dealing in a consistent manner  
with "information" entities.

I think Vipul, Matt Williams, Chimezie, Daniel and others have all  
raised important issues in regards to evidence.  I would also cite  
two active threads in the HCLS IG that have direct bearing on this  
issue:

	1) Again beating the old (maybe not quite dead) horse of the  
experiment we began in BioONT back last September, I would cite the  
following HCLS IG Wiki page:
		http://esw.w3.org/topic/HCLS/OntologyTaskForce/ 
OboPhenotypeSyntaxExperiment
	    If the top of the page is familiar (or too dense), just jump to  
the section starting roughly 1/3 down the page entitled:
		"The OBO Phenotype Syntax + PATO Quality way to represent  
experimental observations/research statements/claims"
	    This "experiment" draws on a significant body of work both in  
the GO/OBO community, as well as ongoing community ontology  
development seeking to apply BFO to this issue of providing a  
consistent and coherent representation of biological reality - most  
especially - in this context - OBO-RO (http://www.obofoundry.org/ 
ro/), PATO (http://www.obofoundry.org/cgi-bin/detail.cgi?id=quality),  
and OBI (http://www.obofoundry.org/cgi-bin/detail.cgi?id=obi)

	2) SWAN
		http://www.ncbi.nlm.nih.gov/sites/entrez? 
Db=PubMed&Cmd=ShowDetailView&TermToSearch=17493287&ordinalpos=1&itool=En 
trezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
		http://www.mind-informatics.org:8081/swan/

My sense is these two efforts are both very relevant to this  
discussion.  SWAN obviously encompasses a complete, functional system  
currently in use by the AlzForum designed to describe hypotheses in  
the context of "evidentiary" statements.  The "experiment" Wiki page  
takes a more constrained approach than SWAN to describing evidence  
for "experimental assertions" drawing from the community biomedical  
ontology efforts defined above (as well as other resources).  I see  
this approach and the SWAN approach as very much complimentary and  
synergistic, each bearing their own advantages and disadvantages.  In  
this experiment, there are still many details to be worked through  
more explicitly, some of which relate directly to this issue Matthias  
raised initially (how and when should we reference RDBMS-based  
records for bio-molecular entities).  Still, there is much more there  
beyond this single issue of citing RDBMS records - as is true in SWAN  
- that addresses issues related to providing a formal framework for  
"experimental evidentiary assertions".   Note too that though the  
example on this Wiki page draws from an existing publication (very  
much a kin to the publication evidence used by GO annotators and  
other informatics projects such as NeuronDB at Yale), the approach is  
intended for use directly in annotating data repositories as well.

I would also note there is currently an ongoing discussion on the obo- 
phenotype list of this very topic - i.e., how to reference a UniProt  
record in a biomedical ontological framework - a thread Alan, and OBO  
investigators have all been contributing to (see the "Phenote for  
expression" thread at http://sourceforge.net/mailarchive/forum.php? 
forum_name=obo-phenotype).

I agree with Matt W. and Adrian's suggestion we must consider the  
extensive and long standing body of work related to "evidence-based  
science".  As Vipul and Daniel have both remarked, we must seek to  
use such approaches in a manner that can accommodate the way evidence  
is established in thin clinic.  However, whether your requirement is  
to include/exclude classified individuals, or doubt/question  
interpretations of rules for deriving "evidence" from experimental or  
clinical observation, it still will be necessary to provide a shared  
(hopefully formal) definition of the relevant entities - e.g., in the  
context of Karen's query such entities (considered in a BFO context)  
as "Smoking Behavior", "Assessment for Smoking Behavior" - which may  
include nominalized and qualified, numeric restrictions in the OWL  
sense (which certainly can be used to represent the required  
classification requirements).  To then give a "name" to such sub- 
types - as is done in when applying a diagnostic label to a specific  
EKG waveform or blood sample data point ("high sodium"), can  
certainly be done in OWL.

In regards to information entities, as Waclaw pointed out, there is  
an ongoing collaboration between the BFO developers and BFO users/ 
developers such as those working on the OBI ontology to provide a  
means to characterize such entities in a BFO context.  As has been  
mentioned, this is still a work-in-progress, and one in which we -  
the HCLS IG - can actively participate.

Finally, to extend Daniel's radiological evidentiary statement  
example, in the biomedical imaging domain (both in the clinic and in  
research domain), often we are relying on algorithmic means to first  
identify biologically-relevant objects in the digital images.  These  
algorithms also bring with them many caveats and assumptions, which  
also need to be addressed when expressing this "evidence" in a formal  
context.  This latter issue is one we are seeking to address in the  
BIRN project using BFO, OBO-RO, and OBI to establish as best we can a  
formal means of expressing the experimental observations (both "raw"  
and "derived") upon which one can build more complex assertions.

Cheers,
Bill

On Jun 12, 2007, at 3:53 PM, samwald@gmx.at wrote:

>
> Hi Waclaw,
>
>
>> Matthias, if you look carefully at BFO, you'll see that roles are
>> entities.  This means that evidences, as roles, are entities.
>
> Of course. I just wanted to differentiate that an experiment is not  
> an instance of any class called 'evidence' (in other words, an  
> experiment 'is not' evidence). Instead, it should be associated  
> with an 'evidence-role'.
>
> cheers,
> Matthias
>
> cheers,
> Matthias Samwald
>
> ----------
>
> Yale Center for Medical Informatics, New Haven /
> Section on Medical Expert and Knowledge-Based Systems, Vienna /
> http://neuroscientific.net
> -- 
> Psssst! Schon vom neuen GMX MultiMessenger gehört?
> Der kanns mit allen: http://www.gmx.net/de/go/multimessenger
>



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 Wednesday, 13 June 2007 13:00:28 GMT

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