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Linking Open Drug Data (HCLSIG LODD)

This article provides an overview of linked data principles and deployment on the web, with a specific focus on linking open drug data. It discusses the status and plans of the HCLSIG LODD task, as well as the potential applications and benefits of linked data in the field of pharmaceuticals.

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Linking Open Drug Data (HCLSIG LODD)

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  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 E C D B

  5. Data objects are identified with HTTP URIs rdf:type foaf:Person pd:cygri foaf:name Richard Cyganiak foaf:based_near dbpedia:Berlin pd:cygri = http://richard.cyganiak.de/foaf.rdf#cygridbpedia:Berlin = http://dbpedia.org/resource/Berlin Forms an RDF link between two data sources.

  6. 3.405.259 dp:population skos:subject dp:Cities_in_Germany Dereferencing URIs over the Web rdf:type foaf:Person pd:cygri foaf:name Richard Cyganiak foaf:based_near dbpedia:Berlin

  7. 3.405.259 dp:population skos:subject dp:Cities_in_Germany Dereferencing URIs over the Web rdf:type foaf:Person pd:cygri foaf:name Richard Cyganiak foaf:based_near dbpedia:Berlin skos:subject dbpedia:Hamburg dbpedia:Muenchen skos:subject

  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. Falcons

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

  11. DERI Semantic Web Pipes

  12. 2. Linked Data Deployment on the Web • W3C Linking Open Data Community Effort • Bio2RDF Project

  13. 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

  14. The LOD Cloud • More than 2 billion RDF triples • More than 3 million links between datasets.

  15. 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)

  16. 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

  17. The Bio2RDF Cloud • 27 data sources • 260 million records • 2,7 billion RDF triples

  18. 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.

  19. 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?

  20. Public Drug Data Sources • Source: Mark Sharp, et al: A Framework for Characterizing Drug Information Sources, 2008

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

  22. Potential Links between LODD Data Sets

  23. 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?

  24. 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/

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