Linking Open Drug Data (HCLSIG LODD)

1
Linking Open Drug Data(HCLSIG LODD)

• Christian BizerFreie Universität Berlin

2
Overview

• Linked Data Principles
• What is Linked Data?
• Linked Data Deployment on the Web
• What data is out there?
• Linking Open Drug Data
• Status and plans of the HCLSIG LODD task

3
The Classic Web

• Single information space,
• build on
• URIs
• globally unique IDs
• retrieval mechanism
• Hyperlinks
• are the glue that holds everything together

Search Engines
Web Browsers
HTML
HTML
HTML
hyper-links
hyper-links
A
C
B
4
Linked Data

• Use Semantic Web technologies to
• publish structured data on the Web,
• set links between data from one data source to
  data within other data sources.

Thing
Thing
Thing
Thing
Thing
Thing
Thing
Thing
Thing
Thing
typedlinks
typedlinks
typedlinks
typedlinks
A
C
E
D
B
5
Data objects are identified with HTTP URIs
rdftype
foafPerson
pdcygri
foafname
Richard Cyganiak
foafbased_near
dbpediaBerlin
pdcygri http//richard.cyganiak.de/foaf.rdfcyg
ridbpediaBerlin http//dbpedia.org/resource/Be
rlin Forms an RDF link between two data sources.
6
Dereferencing URIs over the Web
rdftype
foafPerson
pdcygri
foafname
Richard Cyganiak
foafbased_near
dbpediaBerlin
7
Dereferencing URIs over the Web
rdftype
foafPerson
pdcygri
foafname
Richard Cyganiak
foafbased_near
dbpediaBerlin
skossubject
dbpediaHamburg
dbpediaMuenchen
skossubject
8
Applications

• What can I do with this?

Linked Data Browsers
Linked DataMashups
Search Engines
Thing
Thing
Thing
Thing
Thing
Thing
Thing
Thing
Thing
Thing
typedlinks
typedlinks
typedlinks
typedlinks
A
E
C
D
B
9
(No Transcript)
10
Falcons
11
DBpedia Mobile

• Geospatial entry point into the Web of Data
• Starts with DBpedia, Revyu and Flickr data

12
DERI Semantic Web Pipes
13
2. Linked Data Deployment on the Web

• W3C Linking Open Data Community Effort
• Bio2RDF Project

14
W3C Linking Open Data Project

• Community effort to
• publish existing open license datasets as Linked
  Data on the Web
• interlink things between different data sources

15
The LOD Cloud

• More than 2 billion RDF triples
• More than 3 million links between datasets.

16
Organizations publishing Linked Data

• Universities and Research Institutes
• Massachusetts Institute of Technology (USA)
• University of Southampton (UK)
• Freie Universität Berlin (DE)
• DERI (IRE)
• KMi, Open University (UK)
• University of London (UK)
• Universität Hannover (DE)
• University of Pennsylvania (USA)
• Universität Leipzig (DE)
• Universität Karlsruhe (DE)
• Joanneum (AT)
• University of Toronto (CA)

• Companies
• BBC (UK)
• OpenLink (UK)
• Zitgist (USA)
• Talis (UK)
• Garlik (UK)
• Mondeca (FR)
• Cyc Foundation (USA)

17
The Bio2RDF Project

• Goals
• Make bioinformatics data available in RDF format
  on the Web.
• Promote the linked data vision within the
  bioinformatics community.
• Answer questions which were not possible or
  practical to ask before.
• Participants
• Université Laval, Canada
• Queensland University of Technology, Australia

18
The Bio2RDF Cloud

• 27 data sources
• 260 million records
• 2,7 billion RDF triples

19
3. Linking Open Drug Data

• HCLSIG task started October 1st, 2008
• Primary Objectives
• Survey publicly available data sets about drugs
• Publish and interlink these data sets on the Web
• Explore interesting questions that could be
  answered if the data sets are linked.

20
Questions that LODD might help to answer

• Physicians and Pharmacists
• What are alternative drugs for a given indication
  (disease)?
• What are equivalent drugs (generic version of a
  brand name, or the chemical name of a active
  ingredient)?
• Are there ongoing clinical trials for a drug?
• Consumers
• What background information is available about a
  drug?
• Which alternative drugs are available?
• What are the contraindications of a drug?
• What are the results of clinical trials for a
  drug?
• Pharmaceutical Companies
• What are other companies with drugs in similar
  areas?
• Which companies have a similar therapeutic focus?

21
Public Drug Data Sources

• Source Mark Sharp, et al A Framework for
  Characterizing Drug Information Sources, 2008

22
esw.w3.org/topic/HCLSIG/LODD/Data/DataSetEvaluatio
n
23
Potential Links between LODD Data Sets
24
LODD Participants

• Kristin Tolle (Microsoft)
• Eric Prud'hommeaux (W3C)
• Don Doherty (Brainstage)
• Susie Stephens (Lilly)
• Bosse Anderssen (AZ)
• Scott Marshall (University of Amsterdam)
• Chris Bizer (Freie Universitat Berlin)
• Glen Newton (National Research Council Canada)
• Michel Dumontier (Carleton University)
• TN Bhat (NIST)
• Oktie Hassanzadeh (University of Toronto)
• You?

25
Thanks!

• References
• Linking Open Drug Data HCLSIG Taskhttp//esw.w3.o
  rg/topic/HCLSIG/LODD/
• Linking Open Data Community Effort
  http//esw.w3.org/topic/SweoIG/TaskForces/Communit
  yProjects/LinkingOpenData
• Bio2RDF Project http//bio2rdf.wiki.sourceforge.n
  et/
• Tutorial How to Publish Linked Data on the
  Webhttp//www4.wiwiss.fu-berlin.de/bizer/pub/Link
  edDataTutorial/