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nomenclature for changes from the reference sequence

From: Michael Miller <mmiller@systemsbiology.org>
Date: Thu, 30 Jun 2011 08:34:52 -0700
Message-ID: <f88f3ae0d69bebeaa218357236d68419@mail.gmail.com>
To: public-semweb-lifesci@w3.org
hi all,

in a previous bioRDF call, lena (i think) brought up the question of how
to encode how a given sequence varies from the reference sequence.  in
'Clinical Laboratory Reports in Molecular Pathology', pgs 7 and onward
there's a nice detailed requirement for this (based on human but can
probably be extended):

http://www.archivesofpathology.org/doi/pdf/10.1043/1543-2165%282007%29131%
5B852%3ACLRIMP%5D2.0.CO%3B2

this came from the HL7 Clinical Genomics mailing list.

cheers,
michael


Michael Miller
Software Engineer
Institute for Systems Biology

----- Original Message -----
From: "Amnon Shabo" <SHABO@il.ibm.com>
To: <clingenomics@lists.hl7.org>
Sent: Monday, June 27, 2011 9:25 AM
Subject: Harmonizing GTR with proposals from the literature


>
> Dear CGers,
> Thanks to Mollie who referred us to publications describing molecular
> testing reports, we can refine our GTR specification if needed.
> For example, one of the publications I glanced through is a paper titled
> "Clinical Laboratory Reports in Molecular Pathology" (see
>
http://www.archivesofpathology.org/doi/pdf/10.1043/1543-2165%282007%29131%
5B852%3ACLRIMP%5D2.0.CO%3B2)
>
> In this paper there are sample reports, for example, I extracted the
> following report on Fragile X Genotyping results, for your convenience:
>
> (Embedded image moved to file: pic31376.gif)
>
> Looking at the headings, it's similar in essence to the basic outline of
> the GTR as represented through the "Test Details Section" with different
> names perhaps, e.g, we use findings rather than results, or methodology
> rather than procedure. As for the "Comment" heading, we use
> Recommendations
> which is more informative to the content of this piece I believe but
we'd
> be glad to hear your thoughts. Interpretations are separated to clinical
> and analytic interpretations which is actually a good idea as I can see
> research reports using merely the analytic interpretations, but I wonder

> if
> this specialization of Interpretation should not be optional.
>
> Note that the GTR "Test Details Sections" is the parent template of
> specialized sections by testing type, e.g., Genetic Variations,
> Cytogenetics, etc. In this way, we can further refine those sections and
> bind their attributes to corresponding value sets (such as the LOINC
value
> sets) and still be consistent with the same outline as described by this
> abstract section template  "Test Details Section".
>
> Let's review this paper and others (e.g., "Clinician Perspectives about
> Molecular Genetic Testing for Heritable Conditions and Development of a
> Clinician-Friendly Laboratory Report" at
> http://moldiag.highwire.org/cgi/reprint/11/2/162) and compare its
guidance
> to the GTR and if you think we should make changes to the GTR outline or
> any other component of the GTR, please post your proposals to our
mailing
> list and we could also discuss it in our weekly conf. calls.
> Thanks,
> Amnon.
>
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Received on Thursday, 30 June 2011 15:35:19 UTC

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