Linked Data efforts for data standards in biopharma and healthcare

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Presentation at the "Linked Data in Sweden, 2016" meeting

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Linked Data efforts for data standards in biopharma and healthcare

  1. 1. Linked Data efforts for data standards in biopharma and healthcare Kerstin Forsberg (@kerfors on Twitter, SlideShare etc.) Informatics Analyst and Lifetime Learner AZ IT | R&D Information Länkade Data i Sverige 2016, LDSV2016 See also http://kerfors.blogspot.se/2016/04/linked-data-in- sweden-2016.html
  2. 2. ”Standardized the Standards” In traditional standard organizations • CDISC in RDF • HL7 FHIR in RDF • MeSH in RDF • ICD-11 in OWL • Others standards e.g. ATC, WHO Drug and MedDRA 2 Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information
  3. 3. Use standardized standards 3 Web of (Linked) Data An Intro To The Semantic Web: Why You Need To Know About It Sooner Than Later , by Samantha Wong Image Source: Frederic Martin Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information http://yosemiteproject.org/ In new cross-functional communities
  4. 4. ”Standardized the Standards” Observations • Pushing back to traditional standard organizations requires knowledge awareness and community building • Much of the work done in new cross- functional communities e.g. Yosemite project and PhUSE • Many use github • Excel spreadsheets still rules :-( 4 Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information
  5. 5. • CDISC2RDF, Oct 2012 a pre-competitive project with AZ, Roche, W3C et al. to show case Semantic Web standards and Linked Data principles. • FDA meeting Nov 2012: Solutions for Study Data Exchange Standards Meeting – W3C Semantic Web presentation. • June 2013 the Semantic Technology project, a FDA/PhUSE working group for Emerging Technologies, with 25+ repr. from FDA, CDISC, Pharma:s, CRO:s and software vendors. • Oct 2013 press release: Representing existing standards (SDTM, CDASH, SEND, ADaM) in RDF. • Dec 2014, Public review of CDISC in RDF Guide. • July 2015, Published on http://www.cdisc.org/rdf and https://github.com/phuse-org/rdf.cdisc.org CDISC (clinical study data standards) in RDF Knowledge awareness and community building 5 CDISC Interchange Europe 2011 and 2012 presentations from Roche and AstraZeneca Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information
  6. 6. 6 Kerstin Forsberg | WHO UMC, Jan 21 2015 AZIT | R&D Information CDISC in RDF From Human Readable to Machine Processable RDF triples describing one variable/data element and linking to related standard parts
  7. 7. MeSH in RDF Example http://id.nlm.nih.gov/mesh/D015242 for Ofloxacin in MeSH
  8. 8. ICD-11 in OWL iCAT tool, but Excel spreadsheets still rules :-( 8 Author | 00 Month Year Set area descriptor | Sub level 1
  9. 9. “Pushing back” to get MedDRA in RDF AZ Vocabulary Management team shared this with MedDRA MSSO 9 Courtland Yockey, Informatics Analyst AstraZeneca R&D Information, USA A very simple SKOS-rendering of MedDRA • term  skos:Concept • hierarchy level  skos:ConceptScheme • SMQ  skos:Collection Approach should be augmented with VoID representation of MedDRA versions and term properties distinguishing active from inactive terms. Skos:Collection is likely not sufficient to support SMQ versioning nor context of terms in an SMQ (e.g. weight) Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information
  10. 10. “Pushing back” to get ATC codes in RDF AZ Vocabulary Management team created a RDF representation of ATC codes using the SKOS Schema 10 Courtland Yockey, Informatics Analyst AstraZeneca R&D Information, USA 4 example RDF Triples representing part of a ATC code Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information
  11. 11. ”Standardized the Standards” Observations • Pushing back to traditional standard organizations requires knowledge awareness and community building • New cross-functional communities e.g. Yosemite project and PhUSE • Many use github • Excel spreadsheets still rules :-( 11 Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information
  12. 12. Semantic Web Standards  A stack of standards to represent data and semantics based on Resource Description Framework (RDF). RDF is a framework for creating statements in a form of so-called triples  OWL and SKOS: RDF-based standards to represent vocabularies of terms representing identified entities and concepts  SPARQL: query language for RDF triples Building Linked Data Applications  Use of Semantic Web standards and Linked Data principles enabling us to ask questions and solve business problems across a heterogeneous information landscape across open and closed sources Capture Business Questions and Sources Domain Expert Concept Map Build Formal Ontolog! Challenge with Linked Open Data Model Business Questions (SPARQL) Interact with RDF answer in a Faceted Browser Web of Data Open and Closed  Open data sources applying the Linked Data principles and semantic web standards as a Web of Data  Central is the Wikipedia’s structured content via DBpedia used by e.g. Google’s KnowledgeGraph and IBM’s Watson.  Closed data sources now also form internal Webs of Data Linked Data Principles  Use URIs (Uniform Resource Identifiers) as names for things.  Use HTTP URIs so that people can look up (dereference) those names.  When someone looks up a URI, provide useful information.  Include links to other URIs so that they can discover more things Linked Data in One slide Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information

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