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Linking clinical data standards
 

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

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

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  • Thanks Michel - see my blog post following-up questions and thoughts http://kerfors.blogspot.com/2011/05/linking-clinical-data-standards.html
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    Linking clinical data standards Linking clinical data standards Presentation Transcript

    • 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
    • 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
    • Things for CDISC, and for us inthe industry, to consider• How this relates to the Innovative Medicine Initiative (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
    • Acknowledgements Bosse Andersson, for sharing insights from AstraZeneca’s engagement in Semantic Web Health Care and EU 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 Clinical Investigation and previously Cleveland Clinics, for the explorative work using the Patient Controlled Health Records (PCHR) Ontology for Clinical Data Sam Hume, Simon Lundberg, Dan Ringenbach, Lee Evans, Gunnar Magnusson for being ”healthy volunteers”Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 4
    • Web of Documents Web 3.0 Image Source: Frederic Martin Web of DataKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 5
    • Forerunners: The UK and US Government data.gov online “Open Government data.gov relaunchJanuary 1, 2009 December 8, 2009 “Openness will strengthen May 21, 2010 May 21, 2009 our democracy and promote Directive” released 6.4 billion RDF triples efficiency and effectiveness in Government.” --- President Obama January 19, 2010 June30,2009 Putting Government Data online data.gov.uk online Illustration by Prof .Jim Hendler The Semantic Web 2010 Status Update Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 6
    • Linking Open Data cloudKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 7
    • What’s a Triple? subject predicat object An example from a text book The sky has the color blue Three example of facts from the Open Linked Data cloud Payment number 8605670 netAmount 120.00Clinical Trial number NCT00755378 enrollment 58 The Brussels Capital Region populationTotal 1080790 Three example representing some of the standards for these three facts “The net amount of the payment. This is the effective cost to The property netAmount comment the payer after any reclaimable tax has been deducted.”The type of entity Active Ingredient subClassOf Type of entity Chemical Substance The data property populationTotal domain Type of object Populated Place Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 8
    • And, what’s RDF? And, how is XMLrelated to this? Common Model for Data subject predicat object Resource Description Framework Alternative serialization formatsKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 9
    • What’s 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/8605670 http://data.linkedct.org/resource/trial/NCT00755378 http://dbpedia.org/resource/BrusselsThree examples of identifiers used in the standards behind the three examples http://reference.data.gov.uk/def/payment#netAmount http://www.w3.org/2001/sw/hcls/ns/transmed/TMO_0000 http://dbpedia.org/ontology/populationTotal Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 10
    • And, what’s the difference between URI 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/Brussels Linked 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 Beyond 11
    • So, what’s the fourth Linked Data principle? http://data.nytimes.com/N78748399240553400231 owl:sameAshttp://dbpedia.org/resource/Brussels owl:sameAs http://sws.geonames.org/2800866/ Linked Data Principles 4. Include links to other, related URIs in the exposed data to improve discovery of other related information. Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 12
    • Semantic Web standards is a key topic across the IMI projects Innovative Medicine Initiative EHR4CR DDMoRE OpenPHACTSElectronic Health Records Drug Disease Model The Open Pharmacological for Clinical Research Resources Concepts Triple Store RICORDO Researching Interoperability using Core Reference Datasets and Ontologies for the Virtual Physiological Human Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 13
    • Pragmatic first steps for CDISC,together with NCI• Learn from others, such as the UK and US Government• 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 Beyond 14
    • 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
    • A scenario: Linking Clinical Study Metadata Internal categorization to support Design & Interpretation decisionshttp://clinial.data.astrazeneca.com/id/study/D8180C00011 owl:sameAs http://data.linkedct.org/resource/trials/NCT00755378 What would we like to see on a What would we likewebpage internal 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
    • So, why Im so enthusiastic aboutall of this!• Well applied Linked Data principles and cautious steps building on existing insights …• … would improve the research utility of clinical datasets  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
    • ExtrasKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 18
    • 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 Wikipedia 1 2 3 2 of 10 Triples 2 of 48 Triples 4 of 992 Triples Three different approaches to standardization Pragmatic first steps More ideasKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 19
    • Expenditure amount for a local authority in UK1 Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 20
    • Expenditure amount for a local authority in UK1 Live view using the Web Data Inspector 2 of 10 Triples Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 21
    • 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
    • UK government: Top-down approach to standardization for Spending Data Statistical Data perspective Linked Data Cube Vocabolary Payment OntologyLive example index Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 23
    • Enrollment number for a study from ClinicalTrial.gov2 Semantic Web Health Care and Life Sciences (HCLS) Interest Group Linking Open Drug Data (Life Science part of the Linking Open Data cloud) Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 24
    • Enrollment number for a study from ClinicalTrial.gov2 Live 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 Triples Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 25
    • An example of first using the source data structure as the ”standard” …2 Live view using the Web Data Inspector 2 of 48 Triples Database key Variabel name Table name Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 26
    • … and then as a next step look for a common standard Semantic Web Health Care Live view using the Web Data Inspector and Life Sciences (HCLS) Interest Group Translational Medicine Ontology (a.k.a. Pharma Ontology)Live example index Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 27
    • Population of Brussels Capital Region from Wikipedia3 Live view using the Web Data Inspector Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 28
    • Linking between different sources about the same entity using different identifiers3 Live view using the Web Data Inspector Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 29
    • Bottom-up standardization: Communitycurated, and a central shallow Ontology http://dbpedia.org/ontology/PopulatedPlace http://dbpedia.org/ontology/populationTotal http://dbpedia.org/ontology/populationAsOfKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 30
    • Pragmatic first steps for CDISC,together with NCI• Learn from others, such as the UK and US Government• 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 DataKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 31
    • Linked Open Data star schemeKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 32
    • Pragmatic first stepsLearn from others, two examples• AGFA  Clinical drug administration forms mapped to SNOMED CT and FDA codes using the SKOS (Simple Knowledge Organization System) vocabulary http://www.agfa.com/w3c/2009/drugAdministrationForms#• EU Project – LarKC • Published CDISC CT:s as part of Linked Life Data http://linkedlifedata.com/resource/umls/id/C1879952 http://linkedlifedata.com/resource/umls/id/C0013153Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 33
    • Pragmatic first steps, start with Trial Summary Parameters0 Existing text strings published in a long file in Excel txt format (soon also as ODM/XML) Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 34
    • Pragmatic first steps, start with Trial Summary Parameters1 Establish a CDISC URI scheme Proposal: Build on http://data.gov.uk/resources/uris Examples: http://reference.data.cdisc.org/ct/sdtm/ROUTE#ORAL or alt. using the C-code from NCI Thesaurus http://reference.data.cdisc.org/ct/sdtm/C66729#C382882 Model CDISC SDTM CT:s as RDF Triples Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 35
    • Pragmatic first steps, start with Trial Summary Parameters1 Establish a CDISC URI scheme Proposal: Build on http://data.gov.uk/resources/uris Examples: http://reference.data.cdisc.org/ct/sdtm/ROUTE#ORAL or alt. using the C-code from NCI Thesaurus http://reference.data.cdisc.org/ct/sdtm/C66729#C382882 Model CDISC SDTM CT:s as RDF Triples 3 Publish in RDF/XML 4 De-reference/look-up service so people and applications can get descriptions of individual code lists and code. 5 Create a so called SPARQL endpoint so that CDISC standards published as triples can be queried directly using the RDF query language. Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 36
    • Some thoughts and ideas explored• Applying the four Linked Data principles  Linking Clinical Study Metadata • A scenario • Explore the use of – BRIDG Domain Model (to be published in OWL/RDF) – Translational Medicine Ontology - TMO (a.k.a. Pharma Ontology)  Linking Clinical Data • Best practice for URI scheme and minting URI:s • Explorative work: using the Computer-Based Patient Record (CPR) Ontology for Clinical DataKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 37
    • A scenario: Linked Clinical Study Metadata Internal categorization to support Design & Interpretation decisionshttp://clinial.data.astrazeneca.com/id/study/D8180C00011 owl:sameAs http://data.linkedct.org/resource/trials/NCT00755378 What would we like to see on a What would we likewebpage internal 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 38
    • Explore the use of BRIDG and TMOfor common classes and properties Semantic Web Health Care and Life Sciences (HCLS) Interest Group Translational Medicine Ontology (a.k.a. Pharma Ontology)Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 39
    • Linking Clinical Data: Explore URIscheme and minting URI:sProposal: Build on http://data.gov.uk/resources/urisKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 40
    • Explorative work: using the Computer-BasedPatient Record (CPR) Ontology for Clinical Data Acknowledgements: Chimezie Ogbuji, Case Western Reserve Universitys Center for Clinical Investigation, previously Cleveland Clinics. Martin Agfjord, IT University, GöteborgKerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 41
    • If you want to learn more An Intro To The Semantic Web: Why You Need To http://data.gov.uk/linked-data Know About It Sooner Than Later , by Samantha Wong Image Source: Frederic Martin http://www.data.gov/semantic The Semantic Web 2010 Status Update by Prof .Jim Hendler Open data: accountability, citizen utility and economic opportunity. Linked Spending Data – How and Why Bother Guide to the Payments Ontology How DBpedia Treats Linked Open Data star scheme by example Wikipedia as a Database Presentation: Linking Open Drug DataStatistical Data in RDF Interest Group for Semantic Web in Health Care and Life Science The RDF Data Cube http://www.w3.org/blog/hcls vocabulary The Linking Open Data cloud diagram Excellent article “More than Words: Biomedical Ontologies” Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 42
    • And now – An Evening with TinTinat the Brussels Comic Strip Center!Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 43