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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
© University of Manchester
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
© University of Manchester
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
7
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
8
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...
9
……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)#”
© University of Manchester
10
Clinergy: Commercial Clinergy: Commercial version of Pen&PAD version of Pen&PAD
► Nice product, bad timing.
© University of Manchester
11
FormsForms
© University of Manchester
12
and more formsand more forms
© University of Manchester
13
Generated TextGenerated Text
And And automatic automatic (Read) code (Read) code generationgeneration
© University of Manchester
14
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
© University of Manchester
15
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
© University of Manchester
16
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
© University of Manchester
17
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”
© University of Manchester
18
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
© University of Manchester
19
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
© University of Manchester
20
CO-ODE/HyOntUseCO-ODE/HyOntUse
► Protégé-OWL tools► Taming OWL and making it as useful as GRAIL
© University of Manchester
21
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
© University of Manchester
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
© University of Manchester
23
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
© University of Manchester
24
What you see is what you meant What you see is what you meant query constructionquery construction
© University of Manchester
25
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
© University of Manchester
26
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