linked data in pharma it univ 2 april 2012

Kerstin Forsberg

AstraZeneca, R&D, Sweden

Clinical Information Strategy

kerstin.l.forsberg@astrazeneca.com

kerfors on Twitter, Google+, LinkedIn, Slideshare, Blogspot, citulike

Linked Data in Pharmaceutical R&D

PhD Informatics Seminar, IT University

What is this?

DBpedia

WikiData

Schema.org

Some recent headlines!

How DBpedia treats Wikipedia as a Database

Wikipedia’s Next Big Thing: Wikidata, A Machine-

Readable, User-Editable Database Funded By

Google, Paul Allen And Others

Yandex (Russia’s leading search engine) joins

Google, Yahoo! and Bing to collaborate on

Schema.org

What is this?

http://dbpedia.org/resource/IT_University

http://dbpedia.org/resource/Stockholm

http://education.data.gov.uk/id/school/123065

http://schema.org/CollegeOrUniversity

http://research.data.astrazeneca.com/id/clinicalstudy/D5890C00003

http://linkedct.org/resource/trial/nct00244608/

Pharmaceutical Research and Development

Complexity

QoL? Outcomes?

Costs?

Pathophysiology?

Biomarkers?

Targets? Phenotypes?

Association and interpretation

of all data needed

has become a too complex task

for individuals, or even teams to handle.

Health care, pharma, academia,

authorities and payers.

Shared datasets

Different decisions and different types

of applications.

Why is it so hard …

See slide 1-5 in the slide pack from Open PHACTS

presented at BioIT World Expo Europe – Oct 2011

by Prof. Carole Goble on SlideShare

http://www.slideshare.net/open_phacts/open-phacts-bioit-world-europe-cag-111013

Web of (Linked) Data

Web 3.0

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

Opportunities Organized for associations

Prepared for not yet defined use

Ready for automation where computers can

function alongside us to

Mitigate the complexity in discovering, accessing,

connecting and interpreting information

Improve the productivity in managing

information

Semantic Web Standard Stack

RDF Triples

Resource Description Framework (RDF):

a general model of how any piece of data and

representations of knowledge can be expressed as

so called triples.

subject predicate

Stockholm place

Stockholm Sweden

Stockholm Port cities in Sweden

Stockholm “+46-8”

object (or value)

type

capital

subject

areaCode

“http://en.wikipedia.org/wiki/Stockholm” primaryTopic Stockholm

RDF Triples

Triples can be aggregated into graphs with subject

and objects as nodes, and predicates as arcs.

place

Sweden

Stockholm Port cities in Sweden

“+46-8”

type

capital

subject

areaCode

“http://en.wikipedia.org/wiki/Stockholm” primaryTopic

RDF Triples

Graphs of triples can be extended across different

sources and for different purpose.

place

Sweden

Stockholm Port cities in Sweden

“+46-8”

type

capital

subject

areaCode

Country type

Gothenburg

subject

CDISC

CDISC

Interchange

EU 2012

“http://en.wikipedia.org/wiki/Stockholm” primaryTopic

RDF Triples

RDF Schema and the RDF based Web Ontology

Language (OWL) add a typing mechanism to classify

subjects and objects into hierarchies of types

place

Sweden

Stockholm Port cities in Sweden

“+46-8”

type

capital

subject

areaCode

Country type CDISC

CDISC

Interchange

EU 2012

“http://en.wikipedia.org/wiki/Stockholm” primaryTopic

Adm.Area

Place

subClass

subClass

subClass

Organization

type

Business

Event

type

Event

subClass

Thing subClass subClass

Gothenburg

subject

RDF Triples

Simple Knowledge Organization System (SKOS) is

a thin RDF based vocabulary that can be used to

build terminologies of broader/narrower concepts.

place

Sweden

Stockholm Port cities in Sweden

“+46-8”

type

capital

subject

areaCode

CDISC

CDISC

Interchange

EU 2012

“http://en.wikipedia.org/wiki/Stockholm” primaryTopic

Organization

type

Business

Event

type

Gothenburg

subject

Cities in

Sweden

broader

Populated

places in Europe

broader narrower

narrower

4 Principles for Linked Data … … and 5 stars for Linked Open Data

• 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.

Source: Linked Open Data star scheme by example

More resources introducing and describing the Linked Data idea

Linked Open Data cloud

Richard Cyganiak and Anja Jentzsch

http://lod-cloud.net/

Growing Linked Open Data Cloud

http://youtu.be/TXFYSWuEOOw

Linked Enterprise Data

Source: What does Open Data mean for Enterprises?

More resources introducing and describing the Linked Data idea

I’m encouraged by …

• … what actually can be done by applying Linked

Data principles, together with a stepwise

implementation and pragmatic application of

crucial building blocks, to …

• … improve the research and commercial

utility of information

• Organized for associations

• Prepared for not yet defined use

• Ready for automation where computers can

function alongside us to

Mitigate the complexity in discovering,

accessing, connecting and interpreting

information

Improve the productivity in managing

information

1

9

Health Care and Life Sciences (HCLS)

Interest Group

Linking Open Drug Data

EU project The Large Knowledge Collider

Linked Life Data

A 2-page summary of our learnings from

participating in these external projects:

Linked Data in Pharma, 2011, Bo Andersson

and Kerstin Forsberg