Pharmaceutical Industry and Linked Data

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  • 1. 2010 11 24 ymchu@topquadrant.co.kr : http://www.topquadrant.co.kr : http://blog.topquadrant.co.kr

2. R&D ICT LODD(Linked Open Drug Data) Competitive Intelligence Use Case 3. R&D (therapy) , Safty & efficacy( , side effect, ) Multidisciplinary , , , 4. ICT (ICT) , , , DB ... Knowledge Management Multidisciplinary collaboration data -> 5. Information Interoperability Clinical Trials + Clinical Research(experiments) + Biomedical literature + electronic health records... + geographical data, medical vocabulary..., (interoperability) source : Mats Sundgren , New needs for interoperability in Clinical Research , AstraZeneca, health conference 2010 6. The Semantic Web is a vision: the idea of having data on the Web defined and linked in a way that it can be used by machines not just for display purposes, but for automation, integration and reuse of data across various applications.[W3C 2001] 2010-12-07 7. RDF(Resource Description Framework) RDFS, OWL, SKOS(Simple Knowledge OrganizationSystem), FOAF(Friends of a Friend), etc... Sparql URI(Uniform Resource Identifier) Linked Data 8. RDF - RDF(Resource Description Framework)create subjectpredicateobject (Triple) 9. - integrationgraph representation using RDF data modelSource: Ivan Herman 10. SPARQL as a Unifying SourceApplication Sparql query return dataSPARQL EngineDB X DBX DB X DBSource: Ivan Herman 11. Linked DataData Silos on the WebImage: Bob Jagensdorf, http://flickr.com/photos/darwinbell/,CC-BY Many common things are represented in multiple data sets Linking identifiers connects these data sets Linked data opens the doors of the silos 12. Linked Data Tim Berners-Lee, Linked Data- Design Issues(2006), http://www.w3.org/DesignIssues/LinkedData.html1. Use URIs as names for things2. Use HTTP URIs so that people can look up those names3. When someone looks up a URI, provide useful RDF Information4. Include RDF statements that link to other URIs so that they can discoverrelated thingsLinked data URI , RDF HTTP 13. Linked Data RDF Data LinkLinked DataLinked DataSearchBrowsers MashupsEnginesThingThingThingThing ThingThingThingThingThing Thingtypedtypedtyped typed linkslinkslinks linksA BCDE : Chris Bizer / The Emerging Web of Linked Data 14. W3C Linking Open Data ProjectW3C SWEO Community (Semantic Web Education & Outreach Interest Group) RDF , RDF , (data common) Over 500 million RDF triples Around 120,000 RDF links between data sources 15. LOD Cloud 2008. 2 16. LOD Cloud 2009. 7July 2009 17. LOD Cloud 2010. 92010-12-07 18. LOD Cloud Life Science 19. Linked Data LODDLinking Open Drug Data(LODD) Health Care Life Science , Drug clinical practice(LinkedCT), disease, gene LinkedData Drug Discovery, drug development, clinical practice 20. Linked Data LODDThe Linked Clinical Trials(LinkedCT) NIH 158 http://linkedct.org 6 DrugBank FDA 5000 small molecule biotech drugs http://www4.wiwiss.fu-berlin.de/drugbank/drugbankDiseasome 4300 disorders disease genes, (from OMIM:The Online Mendelian Inheritance in Man) http://www4.wiwiss.fu-berlin.de/diseasomeDailyMed NLM high quality information , , , , , , http://www4.wiwiss.fu-berlin.de/dailymed/ 21. Competitive Intelligence Use Case -> LinkedCT AD 1) Pfizer Varenicline http://data.linkedct.org/resource/trials/NCT00744978 2) http://dbpedia.org/resource/Vareniclinehttp://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB01273 3) DailyMed nicotineaddiction 4) . 5) (LinkedCT) 22. Competitive Intelligence Use Case nicotine addiction AD(Alzheimers Disease) 6) DrugBank Varenicline alpha-4 beta-2 neuronal nicotinicacetylcholine receptor agonist 7) Desiasome AD nicotine addiction 8) Diseasome 9) SWAN (http://hypothesis.alzforum.org/swan) AD nicotinic receptors (LinkedCT) 23. USE CASE view Linked Data , , , , , (interlinking) , (exploring) Knowledge Base Innovation Internal Information External Information DailyMed, LinkedCT, DrugBank , 24. Open Innovation R&D Sourcing requires data standards to enable rapid data integrationData Requirements for Clinical Trials all the different departments, regulators and partners have to look at data in the same way standards applicable across any enterprise within the BioPharma business 25. LODD,LODBioRDF, etc(DBPedia, from LifeGeo-data, etcScience from otherdomain)domains) externalLinked Data Information InteroperabilityinternalPatient Scientific Data Internal heterogeneous InformationResearch ReportsInformationdifferent vocabularies 26. Linked Data 27. Key Capability , , Linked Data LOD(, LODD) , 28. ymchu@topquadrant.co.kr : http://www.topquadrant.co.kr : http://blog.topquadrant.co.kr