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A Convergence of Need

Joining up clinical care and biomedical research CLEF/ CLEF-Services Alan Rector et al. rector@cs.man.ac.uk www.clinical-escience.org. National Policy for IT (NPfIT). Evidence based health care. Clinical Practice, Audit & Governance. Clinical trials recruitment & support.

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A Convergence of Need

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  1. Joining up clinical care and biomedical researchCLEF/CLEF-ServicesAlan Rector et al.rector@cs.man.ac.ukwww.clinical-escience.org

  2. National Policyfor IT (NPfIT) Evidence based health care Clinical Practice, Audit & Governance Clinical trials recruitment & support A Convergence of Need Post genomic research more & better clinical information

  3. Knowledgeenrichment (workflows+) HazardMonitoring Ethical oversightcommittee StatisticalDisclosureControl FormulateQueries Integrate &Aggregate(provenance) PseudonymisedRepository ExtractInformation Depersonalisetext Chronicle Construct‘Chronicle’ (inference) PseudonymiseIn Hospital Trials & Research Cycle Individual Summaries & Queries Patient Care Cycle ReidentifyBy Hospital(if agreed) Making itWork

  4. The repository so far: 20,000 patients, 1.7 million EHR nodes, 880,000 data values 365,000 narratives, ready for Information Extraction

  5. The coded data are not sufficient to meet the needs of research queries: “…located in the lower or middle lobe of the lung..” Location of the tumour is not held in structured form: it is only found consistently in the narrative of radiology reports IE and the Chronicle are needed to enrich the original structured data

  6. Chest 8/5/96 Chest 30/5/96 Chest 6/8/97 … Once again numerous nodules are seen in the right lower lobe. … … A further new lung nodule is seen in the left upper zone. … … There is a lobulated mass adjacent to suture material in the right lower zone. … Date: 8/5/96 Sign-1: Name: mass Locus-1: Name: lower zone Location-1: Sign: Sign-1 Locus: Locus-1 Date: 30/5/96 Sign-2: Name: nodules Locus-2: Name: lower lobe Location-2: Sign: Sign-2 Locus: Locus-2 Date: 6/8/97 Sign-3: Name: lung nodule Locus-3: Name: upper zone Location-3: Sign: Sign-3 Locus: Locus-3 Information Extraction Information Extraction Engine

  7. Date: 30/5/96 Sign-2: Name: nodules Locus-2: Name: lower lobe Location-2: Sign: Sign-2 Locus: Locus-2 Date: 8/5/96 Sign-1: Name: mass Locus-1: Name: lower zone Location-1: Sign: Sign-1 Locus: Locus-1 Date: 6/8/97 Sign-3: Name: lung nodule Locus-3: Name: upper zone Location-3: Sign: Sign-3 Locus: Locus-3 Problem: Name: lung cancer Location: lower lobe of lung ICD-O-T code: C34.3 Information Integration Chronicler

  8. CLEF WYSIWYM Query Writer – L2 Login Query OMIM Exit Relevant Subjects Patients with [this type of tumour] at [this site] AND [another characteristic]. monitored for risk of reidentification AND [this genetic marker]. Treatment Profiles Patients who received [radiotherapy] [daily], compared with patients who received [radiotherapy] [every other day] and those who received [no radiotherapy].  Patients who received [this type of treatment], compared with patients who received [this type of treatment].  Links out to other bioscience resources e.g. OMIM, PubMed, Gene Ontology Outcome Measures Percentage of patients [alive] after [1 year] and after [2 years] and after [5 years]. Percentage of patients in [this condition] after [this interval of time]. Feedback Text Result of running query displayed as generated text… Generated text confirms the nature of the query For all patients with adenocarcinoma of the breast, compare the survival at 1, 2 and 5 years for those patients who had daily radiotherapy, those who had radiotherapy on alternate days, and those who had no radiotherapy …or graphically Submit SAFE Submit For communities ofbiomedical E-Scientists:Safe & easy analysis e-Scientists use query writer Patients with [adenocarcinoma] of [this laterality] of [this part] of [breast] Patients with [adenocarcinoma] at [this site] bladderblood brain breastcervixcolonendometriumkidneylarynxlunglymphnodeoesophagusovarypancreas prostaterectumskinstomachtestistongue AND [BRCA1 (OMIM 113705)]. QUERY RESULT1792 patients diagnosed with adenocarcinoma of the breast were found. 788 had radiotherapy daily, 513 had it on alternate days and 491 had no radiotherapy. After 5 years, 20% (n=158) of patients who had a daily treatment were alive. After 5 years, 10% (n=49) who had alternate day treatment were alive. After 5 years, 5% (n=27) of the patients who had no treatment were alive.

  9. Query construction: specifying the age range

  10. Query construction: selecting a cancer tissue diagnosis

  11. The final query: ready to submit to the repository query service

  12. Visualisation of Chronicle: A timeline of index events R R R R Grade III infiltrating ductal carcinoma left breast Died RADIO CHEMO TAMOXIFEN ARIMIDEX Nodes Liver Spleen Kidney Bone Nodes Liver Spleen Kidney Bone Staging CT S S S S S S S S S S S S S T1>N1>M0 T1N3cM0 T1>N3cM1 >Stage IIA Stage IIIc Stage IV Recurrence 1975 1980 1985 1990 1995 2000

  13. CLEF Chronicle • Inferred “best view” of what is known about a patient • What was done and why? • What happened and why? • Includes detailed provenance - sources & inferences • Enriched by information on analyses, conclusions, workflows, related searches, etc. • Workflows • Designed for scalable retrieval, aggregation, and alignment • Simulations and real data for testing of alternatives • Virtual view of EHR ... or ... • Persistent network using Semantic Web/Grid Technology ...or... • Temporal DB

  14. Pain:5735 Ulcer:1945 locus attends locus finding attends attends Breast:1492 Clinic:1024 plans plans plans plans about locus Radio:1812 Chemo:6502 locus target finding treats treats Mass:1666 Cancer:1914 A CLEF Chronicle Patient:1382 Clinic:4096 Clinic:2010 Biopsy:1066

  15. Schema Status compare target Goal LOCUS INVESTIGATION has-locus has-locus subpart Age has-locus PATIENT INTERVENTION Sex indication GeneticGenomicImaging… GeneticProfile REGIMEN involves recommend treats/indicates recommend DRUG finding Time causes after indicatedBy causes about CONSULT PROBLEM Size Clinical Course PATHOLOGY Diagnostic Status Evidence for Presence / absence Status Other Feature

  16. Personal data Privacy:Policy and Legal Level • in the UK • Common Law of Confidentiality • Data Protection Act 1998 • Human Rights Act 1998 • Section 60 of Heath & Social Care Act 2001 • BMA Guidance Oct 1999 • GMC Guidance Sept 2000 • at a European Level • European Community Directive 95/46/EC (1995) • Council of Europe Recommendation R(97)5 (1997)

  17. Personal data Privacy • The UK Data Protection Act defines "personal data" as: • "data which relate to a living individual who can be identified (a) from those data, or (b) from those data and other information which is in the possession of, or is likely to come into the possession of, the data controller“ • This is likely to apply to any clinically useful information about living patients • Patient consent would be required for CLEF to acquire the data into its repository, and for each new kind of research access to the data • This is not scalable

  18. Anonymised data Privacy • If legitimately processed for research or statistical purposes, “can be kept indefinitely and are exempt from the subject access rights if the results of the work are not made available in a form from which data subjects can be identified” • If CLEF could make sure the data is anonymous, consent would not be required and the data could be used for any reasonable research purpose • This is the only scalable approach • But.. no anonymisation can be perfect

  19. Socio-Technical Response: brief summary • De-identify the data • make overt identifying data unusable • Several layers of pseudonymisation • No source should be able to generate or obtain a central CLEF ID • CLEF should never be able to get to source IDs • Collaborating with e-science/Grid projects , BioBank, NHS,... 2) De-personalise the parts of the record which risk re-identifying the data • depersonalising text requires specialised tools 3) Still treat the data as having some small potential risk of re-identification • regulate, restrict and monitor access – FAME-Permis • statistical disclosure control • Cathie Marsh Centre for Census and Survey Research

  20. CLEF to CLEF-Services from development to use • Trials: Initially • Institute of Genetic Medicine, Londoncollaborationsponsored by the London Development Agency • Close links to Clinical Trials Centres - MRC / UCL / CRUK • Genetic effects on outcome and treatment response • Start with cancer, but ... • Aim for re-use in cardiovascular disease, mental health, diabetes... • Trialists and statisticians • New forms of data require new forms of analysis • Technical deployment: build • An E-Science/Grid environment • Collaborative and collection based research • Re-usable components within a Grid Services architecture • Build on and extend myGrid • Collaborate with CaGrid, PsyGrid, eDiamond, ...

  21. To link Grid & NHS computing NHS Information (NPfIT) Research Information genetics biosciences clinical trials and longitudinal studies knowledge management decision support data mining health improvement patient centred medicine clinical service framework clinical governance outcome: effectiveness/ efficiency evidence Information forpatients & public Security Images, Language, GenomicsArchitecture, Web/Grid Services, Terminology, Standards To realise the research potential of the nhs

  22. Software componentsSteps towards wide deployment • Reducing the effort of re-use • Common services & standards for... • Language technology • Repositories • Chronicles • Workbench analysis and workflows • Build on myGrid & other E-Science / Grid efforts • Knowledge resource management as Grid Services • Build on CO-ODE/HyOntUse

  23. The key is collaboration • Post-genomic research & cancer • NCRI – designed to fill gaps in planning matrix • NTRAC/NCTR, NCRN, CaGrid, eDiamond • PsyGrid • BioBank • NHS, DoH and Industry • DTI – Funding for linkage to industry and NHS • International • US NCICB, Mouse/Human Anatomy projects • Cancer Networks & National Programme • E-Science & Standards • myGrid, CO-ODE/HyOntUse, ESNW, Semantic Web/Grid,... • HL7, CEN TC251, ISO TC215 • Semantic Mining NoE in 6th Framework • Bioinformatics • OBO (GO, GONG, MGED), EBI, SAEL, ...

  24. CLEF Consortium • Clinical • Royal Marsden Hospital Trust • London Institute for Genetic Medicine • North and North Central London Cancer Networks • Technical and E-Science • University of Manchester (E-Science & knowledge) • Biohealth Information Forum – link to myGrid • Cathie Marsh Centre for Census and Social Statistics • E-Science Centre including link to Security projects (FAME-Permis) • University College London (Electronic Health Records) • Centre for Health Informatics and Multiprofessional Education • E-Science Centre including link to Security projects • University of Sheffield (Language technology) • Natural Language Group, Department of Computer Science • Cambridge University (Privacy and policy) • Judge Institute for Management Studies, • University of Brighton (Language technology and HCI) • Information Technology Research Institute, • Clinical and Industrial/NHS steering committees • DTI Funded companion project

  25. CLEF/CLEF-SERVICESEmpowering the e-Clinical ResearchMaking new research possibleMaking existing research more effective by Removing barriers to data sharingJoining up health care and biomedical researchRe-usable components for clinical e-science www.clinical-escience.org

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