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ECOREuropean Centre forOntological Research
Requirements for natural language understanding in
referent-tracking based electronic patient records.
CS seminar, Bolzano, Dec 5, 2005
Dr. W. CeustersEuropean Centre for Ontological Research
Saarland University, Saarbrücken - Germany
ECOREuropean Centre forOntological Research
Presentation overview
• ECOR and me
• The Electronic Health Record (EHR)
• Problems with terminologies and their use in the EHR
• Realist ontology
• Referent Tracking
• Opportunities for narural language understanding
ECOREuropean Centre forOntological Research
Short personal history
1959 - 20051977
1989
1992
1998
2002
2004
ECOREuropean Centre forOntological Research
Electronic Health Record
• ISO/TS 18308:2003– Electronic Health Record (EHR):
• A repository of information regarding the health of a subject of care, in computer processable form.
– EHR system:• the set of components that form the mechanism by which
electronic health records are created, used, stored, and retrieved. It includes people, data, rules and procedures, processing and storage devices, and communication and support facilities.
• More common meaning of EHR system: – only the “software being executed”
ECOREuropean Centre forOntological Research
The Medical Informatics dogmaTo structure or NOT to be
• Fact: computers can only deal with a structured representation of reality:– structured data:
• relational databases, spread sheets
– structured information:• XML simulates context
– structured knowledge:• rule-based knowledge systems
• Conclusion: a need for structured data entry
(???)
ECOREuropean Centre forOntological Research Structured EHR data entry
• Current technical solutions:– Data entry forms
• provide the structure• various paradigms:
– Rigid, pre-fixed– Adaptable to user-preferences, but fixed when used– Dynamically adapting to entered data in context
– Terminologies, coding and classification systems: • provide the language to be used• Exchange of information preserving meaning• Statistics and epidemiology
ECOREuropean Centre forOntological Research The International
Classification of diseases (WHO).• ...
• Chapter II: Neoplasms (C00-D48)• Chapter III: Diseases of the Blood and Blood-forming organs and
certain disorders involving the immune mechanism (D50-D89)• Excludes : auto-immune disease (systemic) NOS (M35.9)• ....• Nutritional Anemias (D50-D53)• D50 Iron deficiency anaemia• Includes: ...• D50.0 Iron deficiency anaemia secondary to blood loss (chronic)• Excludes : ...• D50.1 ...• D51 Vit B12 deficiency anaemia• Haemolytic Anemias (D55-D59) • ...• Chapter IV: ...
ECOREuropean Centre forOntological Research Main problems
• Internal and external consistency of terminologies.
• What do the terms in a terminology stand for ?
ECOREuropean Centre forOntological Research
Problems with terminologies (1)
Lack of face value
Agrammatical constructions
Shift in ontological category (or ambiguous meaning)
ECOREuropean Centre forOntological Research
Problems with terminologies (2)
‘ventricle’ used in 2 different meanings
ECOREuropean Centre forOntological Research
Problems with terminologies (3)
• Mixing of differentiae• Ontological nonsense
ECOREuropean Centre forOntological Research
Problems with terminologies (4)
Incomplete classification
ECOREuropean Centre forOntological Research
What’s wrong with current use of terminologies in the
EHR ?
ECOREuropean Centre forOntological Research
Current mainstream thinking
datainformation
knowledge
wisdom
- representation
- representation
- representation
(- representation)
Questions not often enough asked:• What part of our data corresponds with
something out there in reality ?• What part of reality is not captured by our
data, but should because it is relevant ?
RealityWhat is there on the side of the patient
ECOREuropean Centre forOntological Research
5572 04/07/1990 26442006 closed fracture of shaft of femur
5572 04/07/1990 81134009 Fracture, closed, spiral
5572 12/07/1990 26442006 closed fracture of shaft of femur
5572 12/07/1990 9001224 Accident in public building (supermarket)
5572 04/07/1990 79001 Essential hypertension
0939 24/12/1991 255174002 benign polyp of biliary tract
2309 21/03/1992 26442006 closed fracture of shaft of femur
2309 21/03/1992 9001224 Accident in public building (supermarket)
47804 03/04/1993 58298795 Other lesion on other specified region
5572 17/05/1993 79001 Essential hypertension
298 22/08/1993 2909872 Closed fracture of radial head
298 22/08/1993 9001224 Accident in public building (supermarket)
5572 01/04/1997 26442006 closed fracture of shaft of femur
5572 01/04/1997 79001 Essential hypertension
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
A look at the database:Use of SNOMED codes for ‘unambiguous’
understanding
*
*
*
* cause, not disorder
How many disorders have patients 5572, 2309 and 298 each had thus far in their lifetime ?
How many numerically different disorders are listed here ?
How many different types of disorders are listed here ?
ECOREuropean Centre forOntological Research Would it be easier if you
could see the code labels ?
5572 04/07/1990 26442006 closed fracture of shaft of femur
5572 04/07/1990 81134009 Fracture, closed, spiral
5572 12/07/1990 26442006 closed fracture of shaft of femur
5572 12/07/1990 9001224 Accident in public building (supermarket)
5572 04/07/1990 79001 Essential hypertension
0939 24/12/1991 255174002 benign polyp of biliary tract
2309 21/03/1992 26442006 closed fracture of shaft of femur
2309 21/03/1992 9001224 Accident in public building (supermarket)
47804 03/04/1993 58298795 Other lesion on other specified region
5572 17/05/1993 79001 Essential hypertension
298 22/08/1993 2909872 Closed fracture of radial head
298 22/08/1993 9001224 Accident in public building (supermarket)
5572 01/04/1997 26442006 closed fracture of shaft of femur
5572 01/04/1997 79001 Essential hypertension
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
ECOREuropean Centre forOntological Research
5572 04/07/1990 26442006 closed fracture of shaft of femur
5572 04/07/1990 81134009 Fracture, closed, spiral
5572 12/07/1990 26442006 closed fracture of shaft of femur
5572 12/07/1990 9001224 Accident in public building (supermarket)
5572 04/07/1990 79001 Essential hypertension
0939 24/12/1991 255174002 benign polyp of biliary tract
2309 21/03/1992 26442006 closed fracture of shaft of femur
2309 21/03/1992 9001224 Accident in public building (supermarket)
47804 03/04/1993 58298795 Other lesion on other specified region
5572 17/05/1993 79001 Essential hypertension
298 22/08/1993 2909872 Closed fracture of radial head
298 22/08/1993 9001224 Accident in public building (supermarket)
5572 01/04/1997 26442006 closed fracture of shaft of femur
5572 01/04/1997 79001 Essential hypertension
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
Same patient, same hypertension code:Same (numerically identical) hypertension ?
Different patients, same fracture codes:Same (numerically identical) fracture ?
Same patient, different dates, same fracture
codes: same (numerically identical)
fracture ?
Same patient, same date,2 different fracture codes:
same (numerically identical) fracture ?
Same patient, different dates, Different codes. Same (numericallyidentical) polyp ?
A look at the problems ...Different patients. Same supermarket? Maybe the same (irrelevant ?) freezer section ?Or different supermarkets, but always in the freezer sections ?
ECOREuropean Centre forOntological Research Main problem areas
for current EHRs• Statements refer only very implicitly to the concrete
entities about which they give information.• Idiosyncracies of concept-based terminologies
– tell us only that some instance of the class the codes refer to, is refered to in the statement, but not what instance precisely.
– Are usually confused about classes and individuals.• “Country” and “Belgium”.
• Mixing up the act of observation and the thing observed.
• Mixing up statements and the entities these statements refer to.
ECOREuropean Centre forOntological Research
Consequences
• Very difficult to:– Count the number of (numerically) different diseases
• Bad statistics on incidence, prevalence, ...• Bad basis for health cost containment
– Relate (numerically same or different) causal factors to disorders:
– Dangerous public places (specific work floors, swimming pools),
– dogs with rabies,
– HIV contaminated blood from donors,
– food from unhygienic source, ...
• Hampers prevention
– ...
ECOREuropean Centre forOntological Research Proposed solution:
Referent Tracking
• Foundation:
Realist ontology
ECOREuropean Centre forOntological Research Ontology
• ‘Ontology’: the study of being as a science• ‘An ontology’ is a representation of some pre-
existing domain of reality which– (1) reflects the properties of the objects within its
domain in such a way that there obtains a systematic correlation between reality and the representation itself,
– (2) is intelligible to a domain expert– (3) is formalized in a way that allows it to support
automatic information processing
• ‘ontological’ (as adjective):– Within an ontology.– Derived by applying the methodology of ontology– ...
ECOREuropean Centre forOntological Research Proposed solution:
Referent Tracking
• Purpose:– explicit reference to the concrete individual entities
relevant to the accurate description of each patient’s condition, therapies, outcomes, ...
• Method:– Introduce an Instance Unique Identifier (IUI) for each
relevant individual (= particular, = instance).– Distinguish between
• IUI assignment: for instances that do exist• IUI reservation: for entities expected to come into existence in
the future
ECOREuropean Centre forOntological Research
An ontological analysis
continuantsCity hospital
The freezer section of Jane’s favourite supermarket
Jane’s left femur
Jane’s left femur fracture
Jane Smith
Dr. Peters
Jane’s left femur
Jane’s fracture’s image
Dr. Longley
City hospital’s EHR system
t Jane’s fallingJane’s femur breakingDr. Peter’s examination of Jane’s fractureDr. Peter’s ordering of an X-rayShooting the pictures of Jane’s leg
occurrents
Jane’s fracture’s healingDr. Peter’s diagnosis making
Jane diesFreezer section dismantledDr. Longley’s examination of Jane’ s fracture
UniversalsEHR system
HC
Freezer section
Person
Femur
Fracture
Image
ECOREuropean Centre forOntological Research
Essentials of Referent Tracking
• Generation of universally unique identifiers;• deciding what particulars should receive a IUI;• finding out whether or not a particular has already
been assigned a IUI (each particular should receive maximally one IUI);
• using IUIs in the EHR, i.e. issues concerning the syntax and semantics of statements containing IUIs;
• determining the truth values of statements in which IUIs are used;
• correcting errors in the assignment of IUIs.
ECOREuropean Centre forOntological Research
IUI assignment
• = an act carried out by the first ‘cognitive agent’ feeling the need to acknowledge the existence of a particular it has information about by labelling it with a UUID.
• ‘cognitive agent’:– A person;– An organisation;– A device or software agent, e.g.
• Bank note printer,• Image analysis software.
ECOREuropean Centre forOntological Research
Criteria for IUI assignment (1)1. The particular’s existence must be determined:
– Easy for persons in front of you, body parts, ...– Easy for ‘planned acts’: they do not exist before the
plan is executed !• Only the plan exists and possibly the statements made about
the future execution of the plan
– More difficult: subjective symptoms• But the statements the patient makes about them do exist !
– However: • no need to know what the particular exactly is, i.e. which
universal it instantiates• No need to be able to point to it precisely
– One bee out of a particular swarm that stung the patient, one pain out of a series of pain attacks that made the patient worried
– But: this is not a matter of choice, not ‘any’ out of ...
ECOREuropean Centre forOntological Research
Criteria for IUI assignment (2)
2. The particular’s existence ‘may not already have been determined as the existence of something else’:
• Morning star and evening star• Himalaya• Multiple sclerosis
3. May not have already been assigned a IUI.
4. It must be relevant to do so:• Personal decision, (scientific) community guideline, ... • Possibilities offered by the EHR system• If a IUI has been assigned by somebody, everybody else
making statements about the particular should use it
ECOREuropean Centre forOntological Research Representation in the EHR
• Relevant particulars referred to using IUIs• Relationships that obtain between particulars
at time t expressed using relations from an ontology (type OBO)
• Statements describing for each particular, at time t:– Of what universal from an ontology it is an instance
of– AND/OR (if one insists):– By means of what concept from a concept-based
system it can sensibly be described
ECOREuropean Centre forOntological Research
A shift in mind set
• Not:– ‘this patient has a fracture of the left tibia ’
• But:
– #12 #234 #876– #234 is_located_in #876– #876 is_part_of #12– #876 is_instance_of left_tibia– ...
this this
•With Relationships and universals from a realist ontology
concepts from a terminology
{
ECOREuropean Centre forOntological Research Pragmatics of IUIs in EHRs
• IUI assignment requires an additional effort• In principle no difference qua (or just a little bit more) effort
compared to using directly codes from concept-based systems– A search for concept-codes is replaced by a search for the
appropriate IUI using exactly the same mechanisms• Browsing• Code-finder software• Auto-coding software (CLEF NLP software Andrea Setzer)
– With that IUI comes a wealth of already registered information– If for the same patient different IUIs apply, the user must make
the decision which one is the one under scrutiny, or whether it is again a new instance
• A transfert or reference mechanism makes the statements visible through the RTDB
ECOREuropean Centre forOntological Research Advantage: better
reality representation
5572 04/07/1990 26442006 closed fracture of shaft of femur
5572 04/07/1990 81134009 Fracture, closed, spiral
5572 12/07/1990 26442006 closed fracture of shaft of femur
5572 12/07/1990 9001224 Accident in public building (supermarket)
5572 04/07/1990 79001 Essential hypertension
0939 24/12/1991 255174002 benign polyp of biliary tract
2309 21/03/1992 26442006 closed fracture of shaft of femur
2309 21/03/1992 9001224 Accident in public building (supermarket)
47804 03/04/1993 58298795 Other lesion on other specified region
5572 17/05/1993 79001 Essential hypertension
298 22/08/1993 2909872 Closed fracture of radial head
298 22/08/1993 9001224 Accident in public building (supermarket)
5572 01/04/1997 26442006 closed fracture of shaft of femur
5572 01/04/1997 79001 Essential hypertension
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
IUI-001
IUI-001
IUI-001
IUI-003
IUI-004
IUI-004
IUI-005
IUI-005
IUI-005
IUI-007
IUI-007
IUI-007
IUI-002
IUI-012
ECOREuropean Centre forOntological Research
Other Advantages
• mapping as by-product of tracking– Descriptions about the same particular using
different ontologies/concept-based systems
• Quality control of ontologies and concept-based systems– Systematic “inconsistent” descriptions in or
cross terminologies may indicate poor definition of the respective terms
ECOREuropean Centre forOntological Research
How to make this practicalfor the text-based parts
of an EHR ?
Referent tracking
in the linguistic sense !
ECOREuropean Centre forOntological Research The problem summarised
• natural language is the only medium that is able to communicate clinical information about individual patients without loss of necessary detail;
• (virtual) structured data repositories are required to make subsequent analyses possible;
• any transformation from free language to coding and classification systems results in information loss that is unacceptable for individual patient care, but at the other hand is a conditio sine qua non for population based studies;
• today’s graphical user interfaces can deal reasonably well with picking lists build around controlled vocabularies that fulfil a bridging function from free language towards coding and classification systems but are incompatible with referent tracking
ECOREuropean Centre forOntological Research
The ultimate scenario
#IUI-1 ‘affects’ #IUI-2#IUI-3 ‘affects’ #IUI-2#IUI-1 ‘causes’ #IUI-3
Referent TrackingDatabase
EHR
CAG repeat
Juvenile HD
persondisorder
continuantOntology
Natural LanguageUnderstandingTechnology
ECOREuropean Centre forOntological Research
Jim Cimino’s Woods Hole case
First sentence:
Jane Smith is a 30 year old, Native American female who presents to the emergency room with the chief complaint of cough and chest pain.
ECOREuropean Centre forOntological Research
Step 1: identify the phrases referring to particulars
Jane Smith is a 50 year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
ECOREuropean Centre forOntological Research
Jane Smith is a 50 year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
Step 2: indentify to what particulars these phrases refer
Jane Smith Jane Smith’s age
Jane Smith’s race Jane SmithJane Smith’s gender Jane Smith’s showing up at ...
A specific emergency room of health facility XYZ
Jane Smith’s complaining primarily about ...
A temporal part of Jane Smith’slife marked by happenings of coughs
Jane Smith’s chest
A specific pain experienced by Jane Smith
ECOREuropean Centre forOntological Research
Compare with simple clinical coding in juxtaposition
Jane Smith is a 50 year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
“Jane Smith” CS1-age
CS1-native-americanCS1-female-gender
CS1-emergency room
CS1-chief-complaint
CS1-coughing CS1-chest-pain
CS2-woman
CS2-painCS2-chest
ECOREuropean Centre forOntological Research
Compare with the output of the perfect semantic analyser we all would dream of
CS3-50 years oldHas-Age
CS3-woman
Is-A
CS3-native american
Is-ACS3-complaining
“Jane Smith”
Has-Sayer
CS3-chest pain
Has-Saying
CS3-coughing
Has-Saying
CS3-consultation
Has-happening-during
CS3-Em.RoomHas-Loc
Has-participant
Compare with the output of the NAIVE !!! semantic analyser we all would dream of
ECOREuropean Centre forOntological Research
What it (more or less) should be with traditional coding
CS3-complaining
CS3-chest pain
Has-Saying
CS3-coughing
Has-Saying
“chest-pain”
Has-’referent’
“coughing”Has-’referent’
ECOREuropean Centre forOntological Research
What it (more or less) should be with referent tracking
CS3-complaining
CS3-chest pain
Has-Saying
CS3-coughing
Has-Saying
“chest-pain”
Has-referent
“coughing”
Has-referent
J.S.’ complaining at t1
J.S.’ chest pain at t-1
J.S.’ coughing at t-1
Has-code
Has-code
Has-code
ECOREuropean Centre forOntological Research Most important difference:
Use of generic terms
Use of concrete particulars
Jane Smith is a 50 year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
Jane Smith is a 50 year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
Jane Smith Jane Smith’s age
Jane Smith’s race Jane SmithJane Smith’s gender Jane Smith’sshowing up at ...
A specific emergency room of health facility XYZ
Jane Smith’s complaining primarily about ...
A temporal part of Jane Smith’slife marked by happenings of coughs
Jane Smith’s chest
A specific pain experienced by JaneSmith
Jane Smith is a 50 year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
“Jane Smith” CS1-age
CS1-native-americanCS1-female-gender
CS1-emergency room
CS1-chief-complaint
CS1-coughing CS1-chest-pain
Jane Smith is a 50 year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
Jane Smith is a 50 year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
“Jane Smith” CS1-age
CS1-native-americanCS1-female-gender
CS1-emergency room
CS1-chief-complaint
CS1-coughing CS1-chest-pain
CS2-woman
CS2-painCS2-chest
CS2-womanCS2-woman
CS2-painCS2-painCS2-chestCS2-chest
CS3-50 years oldHas-Age
CS3-50 years oldHas-Age
CS3-woman
Is-A
CS3-woman
Is-A
CS3-native american
Is-A
CS3-native american
Is-ACS3-complaining
“Jane Smith”
Has-Sayer
“Jane Smith”
Has-Sayer
CS3-chest pain
Has-Saying
CS3-chest pain
Has-Saying
CS3-coughing
Has-Saying
CS3-coughing
Has-Saying
CS3-consultation
Has-happening-during
CS3-consultation
Has-happening-during
CS3-Em.RoomHas-Loc CS3-Em.RoomHas-Loc
Has-participantHas-participant
ECOREuropean Centre forOntological Research Step 3: are relevant and
necessary particulars missing ?• Referred to:
– Jane Smith– Jane Smith’s age– Jane Smith’s race– Jane Smith’s gender– Jane Smith’s showing up at ...– The specific emergency room in the health facility– Jane Smith’s primarily complaining ...– The temporal part ... coughs– Jane Smith’s chest– Jane Smith’s particular pain
• Missing:– The health facility– The healthcare worker she consulted– The particular coughs (under the condition she tells the objective truth)– The underlying disorder (under whatever state of affairs)
ECOREuropean Centre forOntological Research
Step 4: IUI assignment
• Assumptions: – the RTS contains already:
• IUI-1 Jane Smith
Coi = <IUIa, ta, CS3, IUI-1, woman, tr>
• IUI-1.1 Ri = <IUIa, ta, depends-on, BFO, {IUI-1.1, IUI-1}, tr>
Coi = <IUIa, ta, CS1, IUI-1.1, age, tr>
• IUI-1.2 Coi = <IUIa, ta, CS1, IUI-1.2, cherokee, tr>
Ri = <IUIa, ta, depends-on, BFO, {IUI-1.2, IUI-1}, tr>
• IUI-1.3 Coi = <IUIa, ta, CS3, IUI-1.3, chest pain, tr>
Ri = <IUIa, ta, is-located-in, BFO, {IUI-1.3, IUI-1}, tr>
– All dates in the statements are 2 years earlier than now
• What to do with:• Jane Smith• Jane Smith’s race (CS1: native American)• Jane Smith’s gender (CS1: female)• Jane Smith’s chest pain (CS3: chest pain)• Jane Smith’s age (50)
ECOREuropean Centre forOntological Research Conclusion
• Referent tracking can solve a number of problems in an elegant way.
• Existing (or emerging) technologies can be used for the implementation.
• Old technologies (cbs) can play an interesting role.
• Big Brother feeling is to be expected but with adequate measures easy to fight.
• The proof of the pudding is in the eating– Pilote is going to be set up
• Collaboration sought for dealing with NLU