RE: Evidence

Thanks Vipul for volunteering!

-Eric


-----Original Message-----
From: Kashyap, Vipul [mailto:VKASHYAP1@PARTNERS.ORG]
Sent: Wed 6/13/2007 11:13 AM
To: Eric Neumann; William Bug; public-semweb-lifesci hcls
Cc: Waclaw Kusnierczyk; Barry Smith; Matthias Samwald
Subject: RE: Evidence
 
 

I volunteer to do that (as I was planning to do that anyway)

 

I believe this is another area, like Process which cuts across HCLS areas -
biological and clinical

This is another place we can coordinate with URW3 

 

Cheers,

 

---Vipul

 

=======================================

Vipul Kashyap, Ph.D.

Senior Medical Informatician

Clinical Informatics R&D, Partners HealthCare System

Phone: (781)416-9254

Cell: (617)943-7120

http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik

 

To keep up you need the right answers; to get ahead you need the right questions

---John Browning and Spencer Reiss, Wired 6.04.95

________________________________

From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Eric Neumann
Sent: Wednesday, June 13, 2007 11:08 AM
To: William Bug; public-semweb-lifesci hcls
Cc: Waclaw Kusnierczyk; Barry Smith; Matthias Samwald
Subject: RE: Evidence

 

 

Bill,

Thanks for sending out the urls-- always good for a discussion thread-group to
have the same common references! It may be necessary to identify not one, but a
few definitions of evidence to be used by different groups (e.g., researchers
def vs. HC compliance forms-- Dirk's point)-- remember, its about namspaces and
the ontological structures associated with each!

On the subject of 'evidence' has anyone started such a esw-wiki page for HCLS?
There's enough good input from several people over the last few days, that I
hope someone is willing to distill the ideas, and list them on such a page.

If no one is willing, I will try and do so, but I cannot guarantee it will be
done right away (i.e., people with more invested interest on this topic might
wish to start a page sooner and post its location to the group)...

Eric


-----Original Message-----
From: public-semweb-lifesci-request@w3.org on behalf of William Bug
Sent: Wed 6/13/2007 9:02 AM
To: public-semweb-lifesci hcls
Cc: Waclaw Kusnierczyk; Barry Smith; Matthias Samwald
Subject: Re: Evidence

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











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