Linked Data efforts for data standards in biopharma and healthcare

Kerstin Forsberg (@kerfors on Twitter, SlideShare etc.)Informatics Analyst and Lifetime LearnerAZ IT | R&D Information

Länkade Data i Sverige 2016, LDSV2016

See alsohttp://kerfors.blogspot.se/2016/04/linked-data-in-sweden-2016.html

”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

Use standardized standards

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Web of (Linked) DataAn 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

”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

• 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 RDFKnowledge awareness and community building

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CDISC Interchange Europe 2011 and 2012presentations from Roche and AstraZeneca

Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information

6 Kerstin Forsberg | WHO UMC, Jan 21 2015 AZIT | R&D Information

CDISC in RDFFrom Human Readable to Machine Processable

RDF triples describing one variable/data elementand linking to related standard parts

MeSH in RDFExample http://id.nlm.nih.gov/mesh/D015242for Ofloxacin in MeSH

ICD-11 in OWLiCAT tool, but Excel spreadsheets still rules :-(

8 Author | 00 Month Year Set area descriptor | Sub level 1

“Pushing back” to get MedDRA in RDFAZ Vocabulary Management team shared this with MedDRA MSSO

9Courtland Yockey, Informatics AnalystAstraZeneca 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

“Pushing back” to get ATC codes in RDFAZ Vocabulary Management team created a RDF representation of ATC codes using the SKOS Schema

10Courtland Yockey, Informatics AnalystAstraZeneca R&D Information, USA

4 example RDF Triplesrepresenting part of a ATC code

Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information

”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

Semantic WebStandards

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 DataOpen 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 DataPrinciples

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