RE: Evidence

Wow that's great-- so many willing volunteers! I'm expecting a real comprehensive and useful wiki page. ; )

Eric

-----Original Message-----
From: Matt Williams [mailto:matthew.williams@cancer.org.uk]
Sent: Wed 6/13/2007 11:13 AM
To: Eric Neumann; public-semweb-lifesci@w3.org
Subject: Re: Evidence
 
I was going to try and pull some ideas together and send them as and 
email; I'll do that, and as long as people aren't horrified by it (I 
expect discussion) I'll set up a wiki page.

Matt

Eric Neumann wrote:
>
> 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
>
>
>
>
>