W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > June 2007

RE: Reviewing the Banff demo ontology infrastructure

From: Daniel Rubin <rubin@med.stanford.edu>
Date: Mon, 11 Jun 2007 03:38:02 -0700
Message-Id: <>
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>,<samwald@gmx.at>, <public-semweb-lifesci@w3.org>
Cc: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>,<ogbujic@ccf.org>

At 09:43 PM 6/10/2007, Kashyap, Vipul wrote:

>Thanks for the well organized e-mail, This is clearly one area where 
>community can provide some feedback. Chimezie had similar constructs 
>related to
>"Patient Records" in his POMR. Let's try to distill out some issues so that
>HCLSIG/BIONT can give some feedback on this:
>1. Some notion of "records" is important at least in healthcare due to
>    temporal issues and provenance, for e.g., what if another physician
>    assigns a different diagnosis to the same patient. The patient's disease
>    is still the same, but there are two versions of the diagnosis in his
>    Record.
>2. Similarly, the same biological fact could be viewed differently by two
>    different versions of the biological record"
>3. That said, we have to figure out a way to partition the world into two
>    parts: biological or clinical facts/hypotheses; and records that record
>    those facts and hypotheses.
>    For e.g. as you suggest:
>                 > 'Protein_2 encoded_by Gene_1'
>                 > 'Gene_1 described_by gene_record_1'
>    A similar example for the healthcare scenario would be:
>             Patient_1 suffers_from Disease_1
>             Disease_1 described_by Snomed_code_1
>4. The representation of evidence:
>    Is evidence a collection of facts that supports the hypothesis or
>    Inference processes that derive the hypotheses from the facts:
>    - An example of the former is existence of a cross_reaction, similarity
>      of substrate specificity
>    - An example of the latter is "inferred from genomic analysis.."
>    In the healthcare context, evidence for a diagnosis is typically
>    phenotypic clinical observations that drive diagnoses or could also
>    be Pubmed publications as in Evidence based medicine.
>    It will be great to reconcile the two. And of course there are
>    Uncertainty related issues here as well!

"Evidence" is important, but is complex. If evidence is from 
collection of facts, then exactly how do those facts provide the 
evidence (there are many types of analyses you can do on raw data to 
produce evidence). So evidence is a function of the facts, the 
analysis method, the method of inference, and perhaps even the 
observer (e.g., if the evidence is a radiology image or physical 
exam, there is inter-observer variation).
And it's definitely necessary to relate the hypotheses to the 
evidence with probabilities.

>5. Of course this leads to the problems in using process related artifacts
>    from BFO ontologies. I think HCLSIG has a role to play for further
>    validation and use of BFO constructs, which are currently not well baked
>    IMO. Guidelines on how to use BFO constructs is not clear, for instance.
> > These issues will be discussed in the BioRDF (BioOnt?) teleconference
> > tomorrow.
>[VK] I guess there's an overlap with BIONT here... Was wondering if we could
>move the discussion out to the next BioRDF call (6/18) as it will give time to
>notify the BIONT and Clinical types who might be interested...

This is certainly relevant to the clinical domain (e.g., I'm 
interested in it from the radiology perspective)


>Also, Mattias (and Chimezie), was wondering if it would make sense to create
>a new wiki on this topic and link it to the BFO Process discussion Wiki and of
>course point to it from the BIONT wiki as well?
>The information transmitted in this electronic communication is 
>intended only for the person or entity to whom it is addressed and 
>may contain confidential and/or privileged material. Any review, 
>retransmission, dissemination or other use of or taking of any 
>action in reliance upon this information by persons or entities 
>other than the intended recipient is prohibited. If you received 
>this information in error, please contact the Compliance HelpLine at 
>800-856-1983 and properly dispose of this information.
Received on Monday, 11 June 2007 10:38:11 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 17:20:27 UTC