Linking Open Drug Data (HCLSIG LODD)

Christian Bizer: Linking Open Drug Data (LODD)

Linking Open Drug Data

(HCLSIG LODD)

Christian BizerFreie Universität Berlin


Overview

1. Linked Data Principles What is Linked Data?

2. Linked Data Deployment on the Web What data is out there?

3. Linking Open Drug Data Status and plans of the HCLSIG LODD task


The Classic Web

B C

HTML HTMLHTML

Web Browsers

Search Engines

hyper-links

Single information space,build on

1. URIs globally unique IDs

retrieval mechanism

2. Hyperlinks are the glue that holds

everything together

A

hyper-links


Linked Data

B C

Thing

typedlinks

A D E

typedlinks

typedlinks

typedlinks

Thing

Thing

Thing

Thing

Thing Thing

Thing

Thing

Thing

Use Semantic Web technologies to

1. publish structured data on the Web,2. set links between data from one data source

to data within other data sources.


Data objects are identified with HTTP URIs

pd:cygri

Richard Cyganiak

dbpedia:Berlin

foaf:name

foaf:based_near

foaf:Personrdf:type

pd:cygri = http://richard.cyganiak.de/foaf.rdf#cygri

dbpedia:Berlin = http://dbpedia.org/resource/Berlin

Forms an RDF link between two data sources.


Dereferencing URIs over the Web

dp:Cities_in_Germany

3.405.259dp:population

skos:subject

Richard Cyganiak

dbpedia:Berlin

foaf:name

foaf:based_near

foaf:Personrdf:type

pd:cygri


Dereferencing URIs over the Web

dp:Cities_in_Germany

3.405.259dp:population

skos:subject

Richard Cyganiak

dbpedia:Berlin

foaf:name

foaf:based_near

foaf:Personrdf:type

dbpedia:Hamburg

dbpedia:Muenchen

skos:subject

skos:subject

pd:cygri


Applications

B C

Thing

typedlinks

A D E

typedlinks

typedlinks

typedlinks

Thing

Thing

Thing

Thing

Thing Thing

Thing

Thing

Thing

Search Engines

Linked DataMashups

Linked DataBrowsers

What can I do with this?


Falcons


DBpedia Mobile

Geospatial entry point into the Web of Data

Starts with DBpedia, Revyu and Flickr data


DERI Semantic Web Pipes


2. Linked Data Deployment on the Web

1. W3C Linking Open Data Community Effort

2. Bio2RDF Project


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


The LOD Cloud

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


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)

Organizations publishing Linked Data

Companies BBC (UK)

OpenLink (UK)

Zitgist (USA)

Talis (UK)

Garlik (UK)

Mondeca (FR)

Cyc Foundation (USA)


The Bio2RDF Project

Goals1. Make bioinformatics data available in RDF format on the Web.2. Promote the linked data vision within the bioinformatics community. 3. Answer questions which were not possible or practical to ask before.

Participants Université Laval, Canada Queensland University of Technology, Australia


The Bio2RDF Cloud

27 data sources

260 million records

2,7 billion RDF triples


3. Linking Open Drug Data

HCLSIG task started October 1st, 2008

Primary Objectives

1. Survey publicly available data sets about drugs

2. Publish and interlink these data sets on the Web

3. Explore interesting questions that could be answered if the data sets are linked.


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?


Public Drug Data Sources

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


esw.w3.org/topic/HCLSIG/LODD/Data/DataSetEvaluation


Potential Links between LODD Data Sets


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?


Thanks!

References

Linking Open Drug Data HCLSIG Taskhttp://esw.w3.org/topic/HCLSIG/LODD/

Linking Open Data Community Effort http://esw.w3.org/topic/SweoIG/TaskForces/CommunityProjects/LinkingOpenData

Bio2RDF Project http://bio2rdf.wiki.sourceforge.net/

Tutorial: How to Publish Linked Data on the Webhttp://www4.wiwiss.fu-berlin.de/bizer/pub/LinkedDataTutorial/

Linking Open Drug Data (HCLSIG LODD)

Documents

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