Re: introduction to OA of pharmacogenomics in product labeling

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)

CONFIDENTIALITY NOTICE: This message is intended only for the addressee(s),
may contain information that is considered
to be sensitive or confidential and may not be forwarded or disclosed to
any other party without the permission of the sender.
If you have received this message in error, please notify the sender
immediately.