OWL for Clinical Informatics Manchester BioHealth Informatics Group in cooperation with Northwest Institute of BioHealth Informatics (NIBHI) for Siemens

OWL for Clinical OWL for Clinical InformaticsInformaticsManchester BioHealth Informatics Group in cooperation with Northwest Institute of BioHealth Informatics (NIBHI)

for Siemens Health

Alan Rector, Jeremy Rogers, Nick Drummond, Matthew Horridge,

With Uli Sattler, Ian Horrocks, Sean Bechhofer, Carole Goble, Robert Stevens, Amanda Hughs, Georgina Moulton, …

Open GALEN

BioHealthInformaticsGroup

© University of Manchester

2

Day 1Day 1

► Introductions

► Brief history of Manchester Group

► Review of OWL from a biomedical viewpoint

► Background on DLs (Uli Sattler)

► Normalisation and Modularisation


3

PracticalitiesPracticalities

► Lunch & Coffee

► Rest Rooms

► Restaurants

► Transport

► Emergency contacts► My Mobile +44 771 511 7126

Brief History of BHIG/MIGBrief History of BHIG/MIG

5

The VisionThe Vision

Best Practice

Clinical Terminology

Data Entry

Clinical Record

Decision Support

Best Practice

Data Entry

Electronic Health

Records

Decision Support &Aggregated

Data

GALEN Clinica

l Terminology

HealthCard

Mr Ivor BigunMr Ivor BigunDun RoaminDun RoaminAnytownAnytownAny countryAny country4431 3654 902734431 3654 90273


6

Where we started:Where we started:A VisionA Vision

► Useful and Usable clinical systems► Information when and where you need it

► In your own language

► Aggregated data as a byproduct of clinical► Management

► Remuneration

► Quality asssurance

►Audit

►Clinical Governance

► Research and Intelligence

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Simplicity for developers...Simplicity for developers...

"Open fixation of a fracture of the neck of the left femur"

MAIN fixing

ACTS_ON fracture

HAS_LOCATION neck of long bone

IS_PART_OF femur

HAS_LATERALITY left

HAS_APPROACH open

Rigour for implementorsRigour for implementorsA Model Driven Architecture for Data EntryA Model Driven Architecture for Data Entry

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FRACTURE SURGERY FRACTURE SURGERY

Simplicity for End Simplicity for End Users...Users...

Structured Data Entry

File Edit Help

TibiaTibia FibulaFibula AnkleAnkle More...More...

RadiusRadius UlnaUlna WristWrist More...More...HumerusHumerus

FemurFemur

LeftLeft RightRight

More...More...Gt Gt TrochTroch

ShaftShaft NeckNeck

FemurFemur

LeftLeft

NeckNeck

ReductionReduction FixationFixation

OpenOpen ClosedClosedOpenOpen

FixationFixation

2 steps to heaven...

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……in their own languagein their own language

“open fixation of fracture of collum of left femur”

“open fractuurvan collum femur van linkerfemoraal van bot fixeren”

“Áíïé÷ôüò ÓôåñÝùóç on Ðáèïëïãéêüò ÄïìÞ Óþìáôïò of Ïóôü of Êüëï of Áñéóôåñüò Ìçñéáßï Ïóôü caused by Êüôáãìá”

“ fixation on patologisk struktur of ben of inre kroppsdeldel of lateral position femur caused by fraktur #surgicallyOpen (Adjective)# #leftSelection (Adjective)# #Collum (Noun)#”


10

Clinergy: Commercial Clinergy: Commercial version of Pen&PAD version of Pen&PAD

► Nice product, bad timing.


11

FormsForms


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and more formsand more forms


13

Generated TextGenerated Text

And And automatic automatic (Read) code (Read) code generationgeneration


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The basic mechanismThe basic mechanism

► Forms for all disorders have a duration and a severity

► Forms for cardiovascular disroders include BP, Pulse, Chest Exam, …

►Forms for Angina include detailed description of chest pain

►Forms for unstable angina include …

► Ontology has two functions► As a consistent source of concepts/codes/entities

► As an index to the fragments from which to assemble forms


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Ontology Indexed reusable resources:Ontology Indexed reusable resources:example of data collection forms for trialsexample of data collection forms for trials

Renin dependent Hypertension at

St Stevens Hospitals for the National

Hypertension Survey

Hypertension Renin Dependent

Hypertension`In St Stevens Hospital

National Hypertension Survey

systolic & diastolicpressure

Serum Potassium

foot pulses


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Key Lessons from Key Lessons from PEN&PADPEN&PAD

► Semantic representation works► To beat the combinatorial explosion

► To make complex systems maintainable

► One change - one place

►Predictable evolution

► Separate Problem space from Solution Space

► Separate Model of use from Model of meaning► Initially drove interface directly from ontology

►Re-use reduced

►Change difficult

►Semantics muddled

► The need for ‘views’ or ‘Perspectives’► Anything big enough for everyone is too big for anyone


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GALEN & GALEN-in-USEGALEN & GALEN-in-USE

► Funded to focus on terminology► Scaling up the terminology

► Making use and training easier► From thee months to three days

► The Intermediate Representation and “dissections”

► Key Lessons► The formalism is the “assembly language”

► Separating language and representation saves time and money

► Language generation essential

► Exemplar Software► The Classification Workbench and SPET

► The KNOME - highly interactive classification and terminology engine

► The TIGGER - ontology life cycle management based on intermediate representations and “dissections”


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Separation incorporated in the GALEN Server

A single point of access for language, classification, code conversion, and indexing - well separated internally

API

Reference Management

Multilingual Dictionaries

MultilingualModule

Common Reference Model

ConceptModule

Code Store

Code ConversionModule

ClientApplication

Server

Client

Extrinsics Store

IndexingModule


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The UK Drug OntologyThe UK Drug Ontology

► Now subsumed into UK Drug Dictionary and other projects

► Capturing and information from the British National Formulary for use in Decision Support

► Key lessons

► Untangling works

►Forms and routes dealt with in days rather than years

► Even the experts would rather work in an intermediate representation

► Pre-coordinated delivery works

►But you can’t predict which abstractions developers need

► DLs provide an effective skeleton for indexing guidelines


20

CO-ODE/HyOntUseCO-ODE/HyOntUse

► Protégé-OWL tools► Taming OWL and making it as useful as GRAIL


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CLEFCLEF

► Developing a clinical repository

► Text Extraction

► The Chronicle

► Our best inferred notion of what has happened to the patient

►As opposed to a log of what the health system has recorded

► Query formulation by text generation

► What you see is what you meant

► Knowledge intensive work just beginning

► Early phases have focused on ethics, text extraction, and query formulation


22

PseudonymiseIn Hospital

Depersonalise

ExtractInformation

Integrate &Aggregate

Construct‘Chronicle’

Chronicle

Ethical oversightcommittee

PseudonymisedRepository

Knowledgeenrichment

Summarise& Formulate

Queries

Individual Summaries& Queries

ReidentifyBy Hospital

HazardMonitoring

PrivacyEnhancementTechnologies

PseudonymiseIn Hospital

Depersonalise

ExtractInformation

Integrate &Aggregate

Construct‘Chronicle’

Chronicle

Ethical oversightcommittee

PseudonymisedRepository

Knowledgeenrichment

Summarise& Formulate

Queries

Individual Summaries& Queries

ReidentifyBy Hospital

HazardMonitoring

PrivacyEnhancementTechnologies

Data Acquisition Cycle

Data Access Cycle

CLEF CLEF CycleCycle


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1975 1980 1985 1990 1995 2000

DiedGrade III infiltrating

ductal carcinoma left breast

NodesLiverSpleenKidneyBone

NodesLiverSpleenKidneyBone

T1>N1>M0

T1N3cM0

T1>N3cM1

>Stage IIA Stage IIIc Stage IV

SSSSSSS S S SS SSStaging CT

RRecurrence

R R R

TAMOXIFEN ARIMIDEX

RADIO

CHEMO

The CLEF Chronicle:The CLEF Chronicle:Inferred best view of the patient historyInferred best view of the patient history


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What you see is what you meant What you see is what you meant query constructionquery construction


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Other activityOther activity

► Terminfo / HL7 / NHS Terminology-Info model binding

► SNOMED-HL7v3

► SNOMED/GALEN-openEHR

► Generic methodology ripe for deployment

► Many BioInformatics initiatives► Robert Stevens on Thursday


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In the department - In the department - amongst other thingsamongst other things

► Description logics and OWL

► Semantic Web and E-Science and Workflows► myGrid and Taverna

► Bioinformatics

► E-Health and Health Intelligence

► Semantic Hypermedia

► Data quality research

► Statistical disclosure control ► Cathie Marsh Centre

Documents

OWL for Clinical Informatics Manchester BioHealth Informatics Group in cooperation with Northwest Institute of BioHealth Informatics (NIBHI) for Siemens