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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 10:34:49 -0400
Message-ID: <CAFPX2kCL+AQhUKutq0CJ8bbCVkZL3ix-SWBtvJgW4q9cW5qoDQ@mail.gmail.com>
To: Richard Boyce <rdb20@pitt.edu>
Cc: public-openannotation@w3.org
Dear Richard,
The first thing I notice right away are the OA definitions as
AnnotationProperty such as:
<AnnotationProperty rdf:about="&oa;annotatedBy"/>
While they are defined as ObjectProperties in OA:
http://www.w3.org/ns/oa#objectproperties

The SpecificResources and Selector seems accurate.

The 'annotation sets' like '&poc;pharmgx-spl-annotation-set-7'
seems very similar of what I was doing in Annotation Ontology with
ao:AnnotationSet:
http://code.google.com/p/annotation-ontology/wiki/v2AnnotationSets
Was oa:onResource -> ao;onResource and oa:item -> ao:item?
oa:onResource is not a Open Annotation term and oa:item is currently used
for different constructs.

We did not include anything to organize annotation in the current specs.
In Domeo and I still use the oa:AnnotationSet in combination with Open
Annotation.
In other words exactly the way you did it but with namespace ao (annotation
ontology).

Other options are ORE [http://www.openarchives.org/ore/] or Collections
Ontology [http://code.google.com/p/collections-ontology/wiki/StructureSet]

Anybody has comments on this?

<NamedIndividual rdf:about="&poc;pharmgx-spl-annotation-set-8">
        <rdf:type rdf:resource="http://purl.org/dc/dcmitype/Collection"/>
        <oa:annotatedAt rdf:datatype="&xsd;date">2013-03-14</oa:annotatedAt>
        <oa:annotatedBy>TRIADS Lab, University of
Pittsburgh</oa:annotatedBy>
        <oa:onResource
rdf:resource="file:///home/rdb20/Downloads/d2rq-0.8.1/linkedSPLs-dump.nt#structuredProductLabelMetadata/cb684ad9-0b72-406f-8a07-a419254ccd36"/>
        <oa:item rdf:resource="&poc;pharmgx-spl-annotation-item-10"/>
        <oa:item rdf:resource="&poc;pharmgx-spl-annotation-item-16"/>
    </NamedIndividual>



Best,
Paolo







On Fri, Mar 15, 2013 at 9:57 AM, 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 Pittsburghrdb20@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 14:35:20 GMT

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