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RE: Reviewing the Banff demo ontology infrastructure

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Mon, 11 Jun 2007 00:43:33 -0400
Message-ID: <DBA3C02EAD0DC14BBB667C345EE2D1244287AF@PHSXMB20.partners.org>
To: <samwald@gmx.at>, <public-semweb-lifesci@w3.org>
Cc: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, <ogbujic@ccf.org>


Matthias,

Thanks for the well organized e-mail, This is clearly one area where the HCLSIG
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!
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...

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?

Cheers,

---Vipul





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Received on Monday, 11 June 2007 04:44:17 GMT

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