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Re: Evidence

From: SATYA SANKET SAHOO <satya30@uga.edu>
Date: Wed, 13 Jun 2007 12:33:18 -0400 (EDT)
To: public-semweb-lifesci@w3.org, public-semweb-lifesci-request@w3.org
Message-Id: <20070613123318.AUO91674@punts5.cc.uga.edu>

I am avidly following this interesting discussion. I had the following points:

>   I am following part of this thread and feel like
>   popping in. Maybe it helps.
>   In clinical trials and 'evidence' based medicine the
>   word evidence is strictly defined and may not be
>   compatible with the word 'evidence' used in logic:
>   if <evidence> then <conclusion>.
>   I support the idea of connecting the interpretation
>   of the raw data (the source data) with the data
>   itself. Pixels cannot be evidences on their own,
>   without knowing what the pixels mean. So, an
>   important fact is the thrust in the interpreter.

Satya: Connecting source data with result data along with the processing information used to derive the results and 'trust' sound very similar to 'provenance' information. Can we or not differentiate between 'evidence' and 'provenance'? 

This is especially pertinent in case of experimental data and results derived from it. For example, when a list of peptides is derived from a 'biochemical sample' using mass spectrometry (ms) the evidence that accompany these results are:
1. The details of the original sample (organism, type of cells, cleavage enzyme used etc.)
2. The ms instrument used, the settings of the instruments and as pointed out earlier in this discussion, the algorithms used in processing the ms data - these entail a lot of contextual information regarding how the results are processed or interpreted (measure of confidence etc.)

>   In Evidence Based Medicine (EBM) we use a
>   classification of evidences, based on the source of
>   the statement. If I, as an expert in the field,
>   state "Aspirine is beneficial in the treatment of
>   cardial ischemia in 70% of the cases" than this is
>   considered as a statement with evidence class 4 (the
>   lowest). You have to take my world for it, you have
>   to trust me.  If you do a randomized double blind
>   clinical trial and you know (via statistical
>   analysis) the sensitivity, the specificty and the
>   confidence interval, the same statement is based on
>   evidence class 1 (the highest).
>   So, I think that in the definition of evidence you
>   need to have more than the raw data. Raw data is in
>   the 'real world' domain, evidence is a concept from
>   the 'logic' domain. The interpretation of the raw
>   data bridges that 'semantic' gap.
>   Summarizing I think that evidence
>   - is always about something (the statement)
>   - relies on the interpretation of raw data
>   - has a level, based on the thrust in the
>   interpreter
>   We are using the concepts statement, interpretation,
>   interpreter, raw data, level and thrust to describe
>   something that we call "evidence".

Satya: Through the ProPreO ontology, listed on OBO (http://knoesis.wright.edu/students/satya/ProPreO-060707.owl), we have used three primary concepts of:
1. The object (data) to which 'evidence' is associated with
2. The agent which took part in creating this data (including analytical instruments, software applications etc.)
3. The 'task' or 'process' by which the result was generated (like proteolysis etc.)
to associate the 'evidence' characteristics with the proteomics data. 

But, instead of 'evidence' we use the term 'provenance' :)

Satya Sahoo

Kno.e.sis Center
Wright State University

>   Dirk
>   ______________________________________
>   Dr. Dirk Colaert MD
>   Advanced Clinical Application Research Manager
>   Agfa Healthcare               mobile: +32 497 470
>   871
>Waclaw Kusnierczyk                           To Daniel Rubin                 
><Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>         <rubin@med.stanford.edu>     
>Sent by:                                     cc public-semweb-lifesci@w3.org 
>public-semweb-lifesci-request@w3.org    Subject Re: Evidence                 
>12/06/2007 21:27                        
>   Daniel Rubin wrote:
>   >
>   > At 07:15 AM 6/11/2007, Matt Williams wrote:
>   >
>   >> I changed the subject line to make it more
>   specific.
>   >>
>   >> I think that Evidence is a tricky, slippery
>   subject. It seems to be
>   >> both traces (i.e. records of something) and in
>   many cases, inferences.
>   >> Those inferences probably shouldn't be called
>   evidence, but they are
>   >> the reason that some data are considered
>   evidence, and others not, and
>   >> hence often get included.
>   >
>   > Actually, sometimes the interpretation *is* part
>   of the evidence--best
>   > example is medical imaging wherein the radiologist
>   interpretation of the
>   > images are part of the primary evidence (the image
>   is the "raw"
>   > evidence, but you have no result without the
>   radiology interpretation of
>   > the image).
>   I'd think of the image as of a piece of evidence (of
>   whatever the
>   patient may suffer from), and the radiologist's
>   interpretation (a
>   written or spoken statement thereof) as another
>   piece of evidence (of
>   that the radiologist must have judged the image as a
>   piece of evidence
>   for whatever the patient may suffer from).  And the
>   interpretation is
>   only indirectly evidence for whatever the patient
>   may suffer from, and
>   only if we trust or otherwise know the
>   qualifications of the
>   radiologist.  If we doubt, the interpretation is no
>   evidence;  and if we
>   know the interpretation is wrong, it is evidence
>   that the radiologist
>   made a mistake (and perhaps is not a good one), but
>   certainly not
>   evidence that the patient suffers from this or that.
>   > Interpretation also transforms raw data into
>   recoded variables that is
>   > also used as evidence, for example in interpreting
>   raw EKG tracings to
>   > give the label of "ventricular tachycardia" or
>   recording a sodium of 150
>   > as "high sodium."
>   This is a similar case, though if we are based on
>   firm rules (e.g., if X
>   > 10 then X is high), this recoding is hardly an
>   interpretation, it is
>   just a lossy translation from quantitative to
>   qualitative form.
>   But both 'evidence' and 'interpretation' are terms
>   used with many
>   meanings, and perhaps instead of trying to answer
>   the question 'what is
>   evidence?' it is better to define the term:
>    'evidence', for our
>   purposes, means ...
>   vQ
Received on Wednesday, 13 June 2007 19:38:16 UTC

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