Linked-spls-initial-hcls-presentation-06082012

Biomedical Informatics1

Linked Structured Product Labels (LinkedSPLs) -Towards a reference linked data source for drug product labeling

Richard Boyce, University of Pittsburgh

Department of Biomedical Informatics


Overview• About product labels• What are Structured Product Labels• Some use cases• Linked DailyMed was a great start• How LinkedSPLs is an improvement• Some best practices used and needed• Discussion


Why are product labels important?• Product labels are intended to be a reference for

prescribing clinicians [1]

1. Marroum PJ, Gobburu J. The product label: how pharmacokinetics and pharmacodynamics reach the prescriber. Clin Pharmacokinet. 2002;41(3):161-169.

2. Ko, Y. et al. Prescribers’ knowledge of and sources of information for potential drug-drug interactions: a postal survey of US prescribers. Drug Saf. 31, 525-536 (2008).

3. Boyce RD, Collins C, Clayton M, Kloke J, Horn J. Inhibitory Metabolic Drug Interactions with Newer Psychotropic Drugs: Inclusion in Package Inserts and Influences of Concurrence in Drug Interaction Screening Software. Annals of Pharmacotherapy. (In Press).


Why is the product label apparently so influential? • Authoritative• Simple (for a drug expert) to follow• Often the only source of information besides

FDA approval documentation for new drugs• No standard for searching the scientific

literature• No standard for judging the quality of

published studies


Structured Product Labels (SPL)• All package inserts for currently marketed drugs

are available in this format [1-3]

1. http://www.fda.gov/OHRMS/DOCKETS/98fr/FDA-2005-N-0464-gdl.pdf2. http://www.fda.gov/ForIndustry/DataStandards/StructuredProductLabeling/default.htm3. http://dailymed.nlm.nih.gov/dailymed/downloadLabels.cfm


Want to see one?• Perphenazine and Amitriptyline HCL:

– http://tinyurl.com/d93ttm5


FDA dictates the kinds of claims that should be present in each section [1]

1. FDA. Code of Federal Regulations 21 Part 201.56, chapter Requirements on content and format of labeling for human prescription drug and biological products. Washington, DC: US Government Printing Office, 2010. http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=201.57


DailyMed – the public source of SPLs• dailymed.nlm.nih.gov/• Provides an HTML view of SPLs using XSLT• Current statistics:

– Human prescription products: ~17K

– Human OTC: ~16K

– Homeopathic: ~3K

– Animal: 1k

– Other: ~500


DailyMed uses Permanent URLs

"SPL IDs are not static, so a label's URL may change if the label is updated. However, we provide permanent URLs to view or download the latest version of an SPL”• a permanent URL to view a label.

– http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid={setId}

• a permanent URL to download a label as a ZIP file.– http://dailymed.nlm.nih.gov/dailymed/downloadzipfile.cfm?setI

d={setid}

• Try it for setid ‘ca5598e4-4226-45ab-abd1-e961707ae457’


SPLs on the Semantic Web 1/2• The DailyMed node:

– http://www4.wiwiss.fu-berlin.de/dailymed/

– 164,276 triples; 4,039 drugs (http://tinyurl.com/6qzd2lo)

• A great start but…– does not appear to handle drug products with more

than one active ingredient correctly

– clearly incomplete

– incorrect encoding (Latin instead of Unicode)

– how often is it updated and where is the versioning information?

– where are the HTML tables and Image tags?


SPLs on the Semantic Web 2/2• The LinkedSPL node:

– http://purl.org/net/nlprepository/linkedSPLs

– 527K triples; 17K drugs

– Active ingredients linked to ChEBI (via dc:subject)

• Also, links to DrugBank (706) and bio2rdf (1412) via dailymed:subjectXref

• Some improvements now implemented– correctly handles drug products with more than one active

ingredient

– Complete for prescription drugs

– correct encoding

– updated weekly and versioning information present

– HTML tables and Image tags retained in raw form


Goals for LinkedSPLs• I want this the resource to:

1. be a model of best practices for publishing linked open drug data in terms of provenance, data quality, and timeliness

2. Become the reference linked data source for drug product labels for the NLP and Semantic Web communities


Use Case 11. An NLP researcher developing an

algorithm for extracting entities or knowledge from the product label

– May require only a particular section or set of sections

– Would like to stratify sampling of the product labels by product and drug features

• E.g., drug class, drug targets, pharmacokinetic properties, manufacturer, date of first release

– The training data represents knowledge that is most useful if linked back to the SPL


Use Case 21. A Semantic Web researcher wants to link

to product labeling– May require only a particular section or set of

sections– Wants to enable querying of the product

labels by product and drug features• E.g., drug class, drug targets, pharmacokinetic

properties, manufacturer, date of first release

– Data quality and provenance important


Some best practices used and needed• PURLs not yet fully implemented

– Makes for long URIs and server dependance

• Some initial use of provenance meta-data– See next slide

• Revision history not yet implemented– Can be derived from DailyMed RSS feed

• Not sure of all of the NLP and SW community requirements

• Looking for collaborators


My initial effort at provenanced2r:documentMetadata [

foaf:primaryTopic <http://purl.org/net/nlprepository/linkedSPLs>;meta:d2rUser "Richard D. Boyce";meta:d2rUserHomepage <http://www.linkedin.com/in/boycer>;meta:d2rOperator "Richard D. Boyce";meta:license <http://creativecommons.org/licenses/by-nc-sa/3.0/>

;meta:dataset <http://thedatahub.org/dataset/linked-structured-

product-labels>;prv:performedAt "2012-04-10T12:00:00Z"^^xsd:dateTime;prv:performedBy <http://www.linkedin.com/in/boycer>;

rdfs:comment "Please note that DailyMed updates (http://dailymed.nlm.nih.gov/dailymed/rss.cfm) are brought into the LinkedSPL resources once per week.";


Discussion/questions


Acknowledgements• The Drug Interaction Knowledge Base team

– John Horn Pharm.D, Carol Collins MD, Greg Gardner, Rob Guzman

• W3C LODD and Scientific Discourse Task Force

Linked-spls-initial-hcls-presentation-06082012

Health & Medicine

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