Linking clinical data standards

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Presentation material for the CDISC Interchange Europe 2011, conference in Brussels, for the track "eHR and the World Beyond", 13 April

Transcript of Linking clinical data standards

  • 1.Linking Clinical Data StandardsPresented by Kerstin ForsbergAstraZeneca R&D, Clinical Information Strategykerstin.l.forsberg@astrazeneca.comkerfors on Twitter, LinkedIn, SlideShare, Blogspot, citulikeKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 1

2. Things I want to show you Beyond a Web of Documents Web of Data Forerunners The UK and US Government Two things to remember Triples and Global Identifiers Three live examples From the Linking Open Data cloudKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 2 3. Things for CDISC, and for us inthe industry, to consider How this relates to the Innovative MedicineInitiative (IMI) projects Pragmatic first steps for CDISC, together with NCI Linking Clinical Data Standards Opportunities across the industry Linking Clinical Study Metadata Linking Clinical DataKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 3 4. Acknowledgements Bosse Andersson, for sharing insights from AstraZenecas engagement in Semantic Web Health Care andEU project The Large Knowledge Collider Life Sciences (HCLS) Interest Group Linked Life Data Linking Open Drug Data Wayne Kubick, CDISC and Oracle, for good email discussions last summer Martin Agfjord, Gothenburg University, for the Bachelor Thesis work Chimezie Ogbuji, Case Western Reserve Universitys Center for ClinicalInvestigation and previously Cleveland Clinics, for the explorative work usingthe Patient Controlled Health Records (PCHR) Ontology for Clinical Data Sam Hume, Simon Lundberg, Dan Ringenbach, Lee Evans,Gunnar Magnusson for being healthy volunteersKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond4 5. Web of DocumentsWeb 3.0 Image Source: Frederic Martin Web of DataKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond5 6. Forerunners: The UK and US Governmentdata.gov onlineOpen Government data.gov relaunchJanuary 1, 2009December 8, 2009Openness will strengthen May 21, 2010May 21, 2009our democracy and promoteDirective released6.4 billion RDF triplesefficiency and effectivenessin Government. --- President Obama January 19, 2010 June30,2009 Putting Government Data onlinedata.gov.uk online Illustration by Prof .Jim Hendler The Semantic Web 2010 Status UpdateKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 6 7. Linking Open Data cloudKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 7 8. Whats a Triple? subjectpredicat object An example from a text bookThe sky has the colorblue Three example of facts from the Open Linked Data cloud Payment number 8605670 netAmount120.00Clinical Trial number NCT00755378 enrollment 58 The Brussels Capital RegionpopulationTotal1080790Three example representing some of the standards for these three facts The net amount of the payment. This is the effective cost toThe property netAmountcommentthe payer after any reclaimable tax has been deducted.The type of entity Active Ingredient subClassOfType of entity Chemical Substance The data property populationTotaldomain Type of object Populated Place Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 8 9. And, whats RDF? And, how is XMLrelated to this?Common Model for Datasubjectpredicat object Resource Description Framework Alternative serialization formatsKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 9 10. Whats a Global Identifier?Linked Data Principles 1. Use URIs (Uniform Resource Identifiers)to identify things. . 2. Use HTTP URIs so that these things can be referred to and looked up ("dereferenced") by people and machines. Three examples of identifiers from the Open Linked Data cloud http://spending.lichfielddc.gov.uk/spend/8605670http://data.linkedct.org/resource/trial/NCT00755378http://dbpedia.org/resource/BrusselsThree examples of identifiers used in the standards behind the three exampleshttp://reference.data.gov.uk/def/payment#netAmount http://www.w3.org/2001/sw/hcls/ns/transmed/TMO_0000http://dbpedia.org/ontology/populationTotalKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 10 11. And, whats the difference betweenURI and URL?Brussels Capital Region is a real world entity Identified by this URI http://dbpedia.org/resource/Brussels Locator (URL) of the people friendly view of the data about the Brussels Capital Region http://dbpedia.org/page/BrusselsLinked Data Principles Locator (URL) of the machine-processeable data about the Brussels Capital Region3. Provide useful, structured, http://dbpedia.org/data/Brussels.rdf information about the thing when its URI is lock-up:ed (de-referenced). Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond11 12. So, whats the fourth Linked Data principle?http://data.nytimes.com/N78748399240553400231owl:sameAshttp://dbpedia.org/resource/Brussels owl:sameAs http://sws.geonames.org/2800866/Linked Data Principles4. Include links to other, relatedURIs in the exposed data to improve discovery of other related information.Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 12 13. Semantic Web standards is a key topic across the IMI projectsInnovative Medicine Initiative EHR4CRDDMoREOpenPHACTSElectronic Health Records Drug Disease ModelThe Open Pharmacologicalfor Clinical Research Resources Concepts Triple StoreRICORDOResearching Interoperability using Core Reference Datasets and Ontologies for the Virtual Physiological HumanKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond13 14. Pragmatic first steps for CDISC,together with NCI Learn from others, such as the UK and USGovernment Apply the Linked Data principles Start with the SDTM CT:s e.g. the Trial Summary Parameters Strive for a 5-star rating of Linked Open Data Pragmatic first steps, more detailsKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond14 15. Opportunities across the industry Applying the four Linked Data principles for Linking Clinical Study Metadata Linking Clinical Subject DataKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 15 16. A scenario:Linking Clinical Study MetadataInternal categorization to support Design & Interpretation decisionshttp://clinial.data.astrazeneca.com/id/study/D8180C00011owl:sameAs http://data.linkedct.org/resource/trials/NCT00755378 What would we like to see on aWhat would we likewebpageinternal to see as the linked data description of data presenting linked it? describing a clinical study?More ideas Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 16 17. So, why Im so enthusiastic aboutall of this! Well applied Linked Data principles and cautioussteps building on existing insights would improve the research utility of clinicaldatasets Organized for associations Prepared for not yet defined use Ready for automation where computers can function alongside us to Mitigate the complexity in clinical research Improve the productivity in clinical data management Live examples Pragmatic first steps More ideasKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 17 18. ExtrasKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 18 19. Three Live Examples1. Net amount for an expenditure from a local authority in UK2. Enrollment number for a study from ClinicalTrial.gov3. Population of Brussels Capital Region from Wikipedia123 2 of 10 Triples2 of 48 Triples4 of 992 Triples Three different approaches to standardization Pragmatic first stepsMore ideasKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond19 20. Expenditure amount for a localauthority in UK1Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 20 21. Expenditure amount for a localauthority in UK1Live view using the Web Data Inspector2 of 10 Triples Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 21 22. An example of a top-down approach tostandardization for Linked DataThe Linked Data Cube Vocabulary Live view using the Web Data InspectorKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 22 23. UK government: Top-down approach to standardization for Spending DataStatistical Data perspective Linked Data Cube VocabolaryPayment OntologyLive example indexKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond23 24. Enrollment number for a studyfrom ClinicalTrial.gov2Semantic Web Health Careand Life Sciences (HCLS)Interest GroupLinking Open Drug Data(Life Science part of theLinking Open Data cloud)Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 24 25. Enrollment number for a studyfrom ClinicalTrial.gov2Live view using the Web Data Inspector Semantic Web Health Care and Life Sciences (HCLS) Interest Group Linking Open Drug Data (Life Science part of the Linking Open Data cloud)2 of 48 TriplesKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond25 26. An example of first using the source datastructure as the standard 2Live view using the Web Data Inspector2 of 48 TriplesDatabase keyVariabel nameTable nameKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 26 27. and then as a next step look for a common standardSemantic Web Health Care Live view using the Web Data Inspector and Life Sciences (HCLS)Interest GroupTranslational Medicine Ontology(a.k.a. Pharma Ontology)Live example indexKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 27 28. Population of Brussels CapitalRegion from Wikipedia3Live view using the Web Data InspectorKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond28 29. Linking between different sources aboutthe same entity using different identifiers3Live view using the Web Data InspectorKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond29 30. Bottom-up standardization: Communitycurated, and a central shallow Ontologyhttp://dbped