Linked ATC and WHO Drug in a

Semantic Web enabled world

Kerstin Forsberg (@kerfors on Twitter, SlideShare etc.)

Informatics Analyst and Lifetime Learner

AZ IT | R&D Information

Representing and linking data, schemas, models,

data standards and terminologies

Web 1.0 (25 years) and Web 2.0 (the last 10 years)

2

Web of (Linked) Data

Web of Documents

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

Web 3.0 (RDF, foundation standard, 15 years)

3

Web of Data

Web of Documents

subject predicat object

Common Model (“Triples”)

Resource Description Framework

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

Web of Data

Fine granularity

Web of Data as RDF Triples for “Things”

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80+ RDF Triples (here are 4 of them)

describing Ticagrelor

Web of Data view of structured data

in Wikipedia pages

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

Linked Data, Semantic Web and Graphs

BBC http://www.bbc.co.uk/things/

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Linked Data, Semantic Web and Graphs

Nobel Prize http://www.nobelprize.org/nobel_organizations/nobelmedia/nobelprize_org/developer/

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Linked Data, Semantic Web and Graphs

Google Knowledge Graph /

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http://searchengineland.com/demystifying-knowledge-graph-201976

RDF @ NCBI

Example http://id.nlm.nih.gov/mesh/D015242

for Ofloxacin in MeSH

AstraZeneca engagements

• Public

- IMI Open PHACTS (Innovative Medicine Initiative, Open

Pharmacology Space)

- FDA/PhUSE and CDISC, Semantic technology project

- W3C Health Care and Life Science (HCLS)

• Internal

- iSIM

- i2 Semantic Framework

Semantic Web and Linked Data

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

The Innovative Medicines

Initiative

• EC funded public-private

partnership for

pharmaceutical research

• Focus on key problems

– Efficacy, Safety,

Education & Training,

Knowledge

Management

The Open PHACTS Project• Create a semantic integration hub (“Open

Pharmacological Space”)…

• Delivering services to support on-going drug

discovery programs in pharma and public domain

• Not just another project; Leading academics in

semantics, pharmacology and informatics, driven by

solid industry business requirements

• 23 academic partners, 8 pharmaceutical companies,

3 biotechs

• Work split into clusters:

• Tehnical Build

• Scientific Drive

• Community & Sustainability

• CDISC2RDF started Oct 2012 as 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.

Clinical standards in the Semantic WebCommunity building and knowledge sharing

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CDISC Interchange Europe 2011 and 2012

presentations from Roche and AstraZeneca

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

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

Clinical data standards in the Semantic Web

Example from CDISC SDTM, Adverse Event domain (AE)

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

“Pushing back” – Use standards for standardsAZ Vocabulary Management team shared this with MedDRA MSSO

13 Kerstin Forsberg | WHO UMC, Jan 21 2015 AZIT | R&D InformationCourtland 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)

“Pushing back” – Use standards for standardsAZ Vocabulary Management team created a RDF representation of

ATC codes using the SKOS Schema

14 Kerstin Forsberg | WHO UMC, Jan 21 2015 AZIT | R&D InformationCourtland Yockey, Informatics Analyst

AstraZeneca R&D Information, USA

4 example RDF Triples

representing part of a ATC code

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

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