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Re: introduction to OA of pharmacogenomics in product labeling

From: Robert Sanderson <azaroth42@gmail.com>
Date: Fri, 15 Mar 2013 14:44:50 +0000
Message-ID: <CABevsUFaKrsMNWWeCfktFiLJd4m8+zMmj5ApDbahsTXt5BCtxA@mail.gmail.com>
To: Richard Boyce <rdb20@pitt.edu>
Cc: public-openannotation@w3.org
Hi Richard,

Some quick notes, compiled during a meeting...

* The object of oa:annotatedBy is a resource, rather than a literal.

    <oa:annotatedBy>TRIADS Lab, University of Pittsburgh</oa:annotatedBy>
  Should instead be:
    <oa:annotatedBy rdf:resource="(uri)"/>
  And then you'd just have one block for the Agent, along the lines of:
    <rdf:description rdf:about="(uri")>
        <foaf:name>TRIADS Lab, University of Pittsburgh</foaf:name>
        [...]
    </rdf:description>

The relevant section of the spec is:
    http://www.openannotation.org/spec/core/core.html#ProvAgents


* NamedIndividual

This looks like a typo for rdf:description?  It appears to cover
multiple classes within the OA ontology.
Or is it in another ontology?

* 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.


Thanks for your interest and work on this, it's very interesting to see! :)

Rob


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/
>
> --
Received on Friday, 15 March 2013 14:45:19 GMT

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