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RE: Evidence

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Thu, 21 Jun 2007 10:47:45 -0400
Message-ID: <DBA3C02EAD0DC14BBB667C345EE2D1248402E2@PHSXMB20.partners.org>
To: "M. Scott Marshall" <marshall@science.uva.nl>, "Alan Ruttenberg" <alanruttenberg@gmail.com>
Cc: <public-semweb-lifesci@w3.org>, "Pat Hayes" <phayes@ihmc.us>

Scott,

I was wondering if you could summarize your points and post it on the wiki.

http://esw.w3.org/topic/HCLS/Evidence

Thanks,

---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
> -----Original Message-----
> From: M. Scott Marshall [mailto:marshall@science.uva.nl]
> Sent: Thursday, June 21, 2007 10:24 AM
> To: Alan Ruttenberg
> Cc: Kashyap, Vipul; public-semweb-lifesci@w3.org; Pat Hayes
> Subject: Re: Evidence
> 
> I see evidence as a special type of provenance for "facts",
> "observations", and "conclusions" in a knowledgebase.
> 
> Motivation for evidence is the desire to represent information about an
> experiment, such as the hypothesis. If we want to work with hypotheses,
> then we need to represent hypothetical information. But how? A uniform
> approach would treat all information as propositional or hypothetical
> rather than to have a separate class so that "hypothesis" can be
> promoted to "fact" but I digress.. :) However we represent it, we would
> like to know how our hypothetical fact is supported by evidence, such as
> protocols and methods.
> 
> Alan Ruttenberg wrote:
> > Maybe we can bring this back to the main subject: What problems are we
> > trying to solve by recording evidence? What are the ways we would know
> > that we've made a mistake?
> >
> > (I suspect that there will be a variety of answers to this, and I'm very
> > curious to hear what people think)
> 
> I'll try to answer this:
> We want to record evidence in order to evaluate and weigh the quality of
> data/information, as well as steer and/or evaluate any conclusions that
> are made on the basis of that data. This is especially important in an
> environment for computational experiments. My test: If we can apply our
> own criterion to evaluate our confidence in a given fact, even when it
> is in someone else's knowledgebase, we have succeeded with our
> representation of the evidence. So, an example of how to represent such
> criterion reason with it about example evidence would be nice..
> 
> Evidence in Text mining
> -----------------------
> Suppose that we are trying to distill knowledge provided by a
> scientific article into some representation. Example: "Is the article
> about proteinX?". If so, "How relevant is proteinX to the article?" and
> so forth. If the distillation process is carried out by a person, then
> who? In the case of text mining, we might like to know what algorithms
> and techniques, queries, pattern recognizers (Bayesian or lexical
> patterns?), threshold values, etc. were used to extract knowledge. If a
> person used a text mining workflow to support the distillation process,
> then we would like the URL to the workflow WSDL (from which we can
> usually discover the other details) and to know who the person was.
> 
> In general, we would like to know the resources involved in producing a
> particular piece of data (or "fact"). We would like to know the actors,
> roles, conditions, algorithms, program versions, what rules were fired,
> and information resources.
> 
> An important challenge in the future will be to combine results from
> manual and automated processes. Most of us would tend to view "facts"
> that result from an automated process as more hypothetical or
> questionable than the same coming from a human expert. On the road to
> automation, however, we should eventually reach the point that the
> quality of "text mining"-supported (i.e. not generated!) annotations
> will be generally higher than manual-only annotation.
> 
> Evidence in Microarrays
> -----------------------
> I don't intend to start a debate about the particulars of microarrays
> but I think that evidence comes up in practice here throughout the
> entire process of measurement and analysis. Gene expression, as measured
> by microarrays, is actually a measurement of changes in mRNA levels at a
> particular time, which *indicates* how much change in the process of
> expression has occurred under *specific* *conditions*. So, already we
> have an example of terminology that is not ontologically accurate when
> incorrectly applied (to microarrays) - technically, measuring mRNA
> levels is not equivalent to measuring the quantity of protein product
> ("expression"). But the term has been in use for so long that it remains
> acceptable to refer to microarray analysis as "expression analysis". :)
> 
> In the case of "gene expression", the statistical process of microarray
> analysis only provides a probability that a gene is up or down regulated
>   (e.g. in the common reference model). However, there is a series of
> decisions and conditions that lead up to the "call" (up, down,
> unchanged) for a particular gene and thus the resulting set of
> differentially expressed genes for the array. The following conditions
> can all be relevant to decisions in how much weight to give to the
> resulting data:
> 
> * Experimental design - organism, conditions, disease, phenotype, ..
> * Source of cells, enzymes, ..
> * Materials handling (thawed? how often?)
> * Protocols used such as RNA extraction
> * Operator
> * Array layout and design - including choice of oligos
> * Instrumentation details - array spotter/printer, laser type and
> calibration, ..
> * Ozone levels (I'm not kidding!)
> * Image analysis ("Feature Extraction") software and settings
> * Type of normalization
> * Criteria for discarding data as "outliers"
> * Criteria for classifying gene as differentially expressed (p-value
> cutoff, ANOVA, ..)
> 
> Again, the point that I'm trying to make about microarrays is that
> evidence (as well as uncertainty), can be represented and used, even for
> the measurements ("observations") themselves. But this is not done in
> practice. Even if you wanted to simply "pool" microarray data (most
> people don't), it is very difficult to do because some of the most
> important metadata (e.g. experimental design), if available, is often in
> free text format.
> 
> -scott
> 
> p.s. My introduction to HCLS summarizes the way that I look at evidence
> a lot more succinctly than the above:  ;)
> http://lists.w3.org/Archives/Public/public-semweb-
> lifesci/2006Feb/0131.html
> 
> --
> M. Scott Marshall
> http://staff.science.uva.nl/~marshall
> http://adaptivedisclosure.org
> 
> 






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Received on Thursday, 21 June 2007 14:52:01 GMT

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