Joined up Health and Bio Informatics:

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Joined up Health and Bio Informatics

• Alan RectorBio and Health Informatics
  Forum/Medical Informatics GroupDepartment of
  Computer ScienceUniversity of Manchester
• rector_at_cs.man.ac.ukwww.cs.man.ac.uk/mig
  img.man.ac.ukwww.clinical-escience.orgmygrid.man
  .ac.uk

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The Problem

• The next steps in exploiting our exploding
  knowledge of basic biology depends on
  understanding its relation with health and
  disease.
• Health care is
• Deluged with information
• about generalities, policies, and theory
• Information and Knowledge Poor
• about specifics of patient care and outcomes

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A Convergence of Need

• Post genomic research

• Safe, high quality, evidence based health care

Knowledge is Fractal
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A convergence of Technologies

• Post genomic research

• Safe, high quality, evidence based health care

• Web/Grid/Semantic Web
• Ontologies Information fusion
• Language technology
• Data mining and case based reasoning
• Healthcare records standards
• Mobile devices

Open Collaborative Research
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A Unique Time

• E-Science
• The Grid
• The Semantic Web / Grid
• BioInformatics Genomics/Proteomics
• Massive investment in population medicine
• Massive investment in NHS computing
• Maturing Electronic Health Records

Ride the Whirlwind!
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Protocol/Collection-based research
Results in vivo
Research idea
Shared CollectionsModels Standards
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Stones in the Road

• Confidentiality, Privacy and Consent
• How to keep public confidence while enabling
  research
• Information capture
• Speed and ease of use require language technology
• doctors dictate!
• Information integration
• Need common ontologies which bridge bio and
  health information

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One Response CLEFJoining up Health Care
Bioscience in Cancer

• Clinical e-Science Framework
• Clinical care
• Clinical research
• Clinical bioscience
• Genotype meets Phenotype
• New technologies for healthcare
• A focus to adapt new technologies to healthcare
• New ways to do clinical research
• Faster, safer, easier, better
• Trial design, execution, archiving, reporting

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CLEFTowards and end-to-end solutionin an
ethical framework

• Patient care
• Formulation of clinical studies
• Information capture
• Information representation
• Information analysis and integration
• Knowledge hypothesis generation
• Clinical support

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CLEF A meeting of open technologies

• Organisational issues Information governance
• Consent, Models of access, balance of research
  and privacy
• Information capture quality
• Language technology Ontologies (OpenGALEN
  OWL) E Health Record (OpenEHR)
• Information use for Care
• E Health Record Decision support Ontologies
  Language generation
• Information Re-use for Research
• Pseudonymised E Health Record Ontologies
  Metadata/repositories

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CLEF Language Technology

• Extraction of simple information from clinical
  records
• Measures of reliability
• Pseudonomysation aids
• Language generation
• Validation
• What you see is what you meant
• Presentation

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CLEF Logic-based Ontologies Conceptual Lego
SNPolymorphism of CFTRGene causing Defect in
MembraneTransport of ChlorideIon causing Increase
in Viscosity of Mucus in CysticFibrosis
Hand which isanatomicallynormal
OpenGALEN OWL
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Bridging Scales with Ontologies
Species
Genes
Function
Disease
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Avoiding combinatorial explosions

• The Exploding Bicycle From phrase book to
  dictionary grammar
• 1980 - ICD-9 (E826) 8
• 1990 - READ-2 (T30..) 81
• 1995 - READ-3 87
• 1996 - ICD-10 (V10-19 Australian) 587
• V31.22 Occupant of three-wheeled motor vehicle
  injured in collision with pedal cycle, person on
  outside of vehicle, nontraffic accident, while
  working for income
• and meanwhile elsewhere in ICD-10
• W65.40 Drowning and submersion while in bath-tub,
  street and highway, while engaged in sports
  activity
• X35.44 Victim of volcanic eruption, street and
  highway, while resting, sleeping, eating or
  engaging in other vital activities

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Making it simple Tools

• Logic based ontology (OWL) is the assembler
• Write real ontologies in high level languages
• Intermediate representations
• Present real ontologies to be relevant to needs
• Views
• Scalable simplicity for end-users requires
  sophisticated architecture
• Swans paddle furiously under water
• Decoupled distributed environment
• Owned by the domain experts

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Summary

• Convergence of need in healthcare post genomic
  research
• Matched by convergence of technologies
• E-Science an opportunity for collaboration
• Faster, less costly, more effective translation
  from bioscience to health care
• Barriers to be overcome
• Information capture
• Privacy, confidentiality, consent
• Information integration sharing of meaning
• Common Ontologies are a key resource

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CLEF Consortiumwww.clinical-escience.org

• Bio Health Informatics Forum, Department of
  Computer Science, University of Manchester
• Centre for Health Informatics and
  Multiprofessional Education, University College
  London
• Natural Langauge Group, Department of Computer
  Science, University of Sheffield
• Judge Institute for Management Studies,
  University of Cambridge
• Information Technology Research Institute,
  University of Brighton
• Royal Marsden Hospital Trust
• North and North Central London Cancer Networks