linked data in pharma it univ 2 april 2012
TRANSCRIPT
Kerstin Forsberg
AstraZeneca, R&D, Sweden
Clinical Information Strategy
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