Re: Evidence

Ditto - thanks to Matthias, Vipul, and Matt for leading the charge  
and investing the time.

Excellent point re: namespaces, Eric.  It's becoming quite clear what  
a critical role these need to play in a shared, interoperable formal  
semantic ecosystem.

I'm pretty busy with a meeting coming up early next week but will  
pick up and get back to that page after that meeting.

One quick note:
	I would say we want to not only consider bfo:process, but also very  
the closely related dependent-continuants - bfo:function (and/or  
bfo:disposition), and bfo:role.  There is some question at this point  
as to how these three need to co-exist in a BFO-based framework, but  
as I believe Waclaw had pointed out, they are all bone fide entities,  
and definitions (formal and informal) of one can't really exist  
without the others.  bfo:function and bfo:role play a critical role  
in providing a functional-context for process-related entities.

Cheers,
Bill

On Jun 13, 2007, at 12:47 PM, Eric Neumann wrote:

>
> Thanks Vipul for putting this up!
>
> Eric
>
>
> -----Original Message-----
> From: Kashyap, Vipul [mailto:VKASHYAP1@PARTNERS.ORG]
> Sent: Wed 6/13/2007 12:33 PM
> To: Eric Neumann; William Bug; public-semweb-lifesci hcls
> Cc: Waclaw Kusnierczyk; Barry Smith; Matthias Samwald
> Subject: RE: Evidence
>
> OK! The wiki page is now ready...
>
>
>
> Matthias, Thanks for getting this started!
>
>
>
> Matt, have incoporated your view point, feel free to modify it if  
> required...
>
>
>
> http://esw.w3.org/topic/HCLS/Evidence
>
>
>
> Bill, please add your references to this web page... I think HCLS +  
> BIONT can
> make some sold recommendations around the
>
> following interrelated topics:
>
>
>
> 1.      The use of BFO:Process across multiple HCLS contexts
> 2.      The representation and reasoning with Evidence across  
> multiple HCLS
> contexts
>
>
>
> For the latter, we can also coordinate with the Uncertainty  
> Reasoning Working
> Goup URW3...
>
>
>
> Please update the wiki page soon... Will probably share this wiki  
> page with the
> URW3 working group.
>
>
>
> 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: Eric Neumann [mailto:eneumann@teranode.com]
> Sent: Wednesday, June 13, 2007 11:17 AM
> To: Kashyap, Vipul; William Bug; public-semweb-lifesci hcls
> Cc: Waclaw Kusnierczyk; Barry Smith; Matthias Samwald
> Subject: 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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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