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Re: introduction to OA of pharmacogenomics in product labeling

From: Paolo Ciccarese <paolo.ciccarese@gmail.com>
Date: Fri, 15 Mar 2013 10:48:20 -0400
Message-ID: <CAFPX2kCNHt5JLNWUHWi-b_5PkYBtzB=qdRJtQPnh0=13-2GawA@mail.gmail.com>
To: Robert Sanderson <azaroth42@gmail.com>
Cc: Richard Boyce <rdb20@pitt.edu>, public-openannotation@w3.org
Rob,



> * Collections
>
> To date we haven't looked into formalizing collections of annotations.
>  It certainly could be an oa:Composite or oa:List (all of these items,
> or all of the items in a certain order), but whether that's the most
> appropriate syntax for this sort of thing or not hasn't really been
> discussed.
>
>
I am not sure the current definition of oa:Composite fits this:
*A multiplicity construct that conveys to a consuming application that all
of the constituent resources are required for the Annotation to be
correctly interpreted. *

The topic is certainly something we need to discuss soon.

Best,
Paolo


>
> On Fri, Mar 15, 2013 at 1:57 PM, Richard Boyce <rdb20@pitt.edu> wrote:
> > Dear Open Annotators,
> >
> > My name is Rich Boyce, I am an Assistant Professor at the University of
> > Pittsburgh Department of Biomedical Informatics. I have been following
> the
> > work of this group for awhile because and am interested in applying Open
> > Data Annotation to my research on medication safety. This email is to
> notify
> > the group of a new resource that I have created using the most recent
> Open
> > Data Annotation guidelines. I am seeking feedback on the resource from an
> > Open Data Annotation perspective since the guidelines are so fresh and
> this
> > is my first attempt at developing a resource using them.
> >
> > Currently, I am leading a project that involves annotating
>  pharmacogenomics
> > statements in United States product labeling. Drug product labels are
> > available in electronic form from the DailyMed website [1] and the FDA
> has
> > created indexed product labels sections that make some statement about a
> > pharmacogenomics biomarker [2]. Pharmacists have several use cases for
> the
> > product label statements and find this indexing approach unsatisfactory.
> To
> > address this issue, a team of pharmacists at the U of Pittsburgh are
> > annotating the indexed statements using a new semantic model [3]. This
> past
> > week, I  created an RDF data set [4] following the Open Data Annotation
> > guidelines [5] for ~140 annotations that are undergoing final validation.
> > Would anyone be interested in reviewing this data set and letting me
> know if
> > it seems to follow the guidelines as intended?
> >
> > Kind regards,
> > -Rich Boyce
> >
> > Richard D Boyce, PhD
> > Assistant Professor of Biomedical Informatics
> > Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research
> and
> > Training Program
> > Scholar, Comparative Effectiveness Research Program
> > University of Pittsburgh
> > rdb20@pitt.edu
> > Office: 412-648-9219
> > Twitter: @bhaapgh
> >
> >
> >
> > 1. dailymed.nlm.nih.gov
> >
> > 2.
> >
> http://www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htm
> >
> > 3. Boyce, RD., Freimuth, RR., Romagnoli, KM., Pummer, T., Hochheiser, H.,
> > Empey, PE. Toward semantic modeling of pharmacogenomic knowledge for
> > clinical and translational decision support. Proceedings of the 2013 AMIA
> > Summit on Translational Bioinformatics. San Francisco, March 2013.
> >
> > 4.
> >
> https://code.google.com/p/swat-4-med-safety/source/browse/trunk/analyses/pharmgx-statement-annotation/data/all-NON-VALIDATED-annotations-from-092012-BETA-OA-model-03142013.xml
> >
> > 5. http://www.openannotation.org/spec/core/
> >
> > --
>
>



-- 
Dr. Paolo Ciccarese
http://www.paolociccarese.info/
Biomedical Informatics Research & Development
Instructor of Neurology at Harvard Medical School
Assistant in Neuroscience at Mass General Hospital
Member of the MGH Biomedical Informatics Core
+1-857-366-1524 (mobile)   +1-617-768-8744 (office)

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Received on Friday, 15 March 2013 14:48:50 GMT

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