Transcript ECO R European Centre for Ontological Research Strategies for Referent Tracking in Electronic Health Records Dr. W.

ECO
R
European Centre for
Ontological Research
Strategies for Referent
Tracking in Electronic
Health Records
Dr. W. Ceusters
European Centre for Ontological Research
Saarland University
Saarbrücken - Germany
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European Centre for
Ontological Research
The story of
Jane Smith
an old case, well
known in the
literature ...
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July 4th, 1990:
Jane goes shopping:
Jane’s favourite supermarket
The freezer section of
Jane’s favourite
supermarket
The only available
warning sign used
outside
A very suspiciously
shaped upper leg
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European Centre for
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A visit to the hospital
City Health Centre
(City HC)
Dr. Peters
Dr. Longley
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Diagnosis: a severe spiral fracture
of the femur
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The City HC’s medical record
European Centre for
Ontological Research
• Main principles:
– a faithful record of the clinicians’ observations:
what they have heard, seen, thought and done.
– captures in a structured form all of the ‘clinically
significant’ information in the narrative notes,
where by clinically significant they mean the
information which is within the medical domain
rather than the domain of everyday life.
Rector AL, Nowlan WA, Kay S, Goble CA, Howkins TJ.
A framework for modelling the electronic medical record.
Methods Inf Med. 1993 Apr;32(2):109-19.
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City HC’s EHR model
Rector AL, Nowlan WA, Kay S, Goble CA, Howkins TJ.
A framework for modelling the electronic medical record.
Methods Inf Med. 1993 Apr;32(2):109-19.
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CityHC’s representation formalism
(for statements in records)
Categories: “represent
concepts and are analogous to
classes in other formalisms”
Individuals:
“concrete instances
of categories which
persist in space and
time”
Occurrences: “are
Rector AL, Nowlan WA, Kay S, Goble CA,
Howkins TJ.
A framework for modelling the electronic
medical record.
Methods Inf Med. 1993 Apr;32(2):109-19.
specific occurrences of
individuals and must be
situated in space and time.
The most important
group of occurrences are
observations — i.e. agents’
observations of individuals.”
ECO
R Mixing statements and entities
European Centre for
Ontological Research
• “Every occurrence level statement concerning the
Jane Smith’s Fracture of the Femur is an
observation of the corresponding individual.”
• “The existence of the individual Jane Smith’s
Fracture of Femur does not imply that Jane Smith
has, or has ever had, a fracture of the femur, but
merely that some observation has been made
about Jane Smith regarding a fracture of the
femur.”
• “(The only observation recorded about Jane
Smith’s Fracture of the Femur might be that she
did not have it.)”
ECO
R But, there are
Different
patients.
Same supermarket?
some
problems
...
European Centre for
Ontological Research
PtID
Date
Maybe the same (irrelevant ?) freezer
section ?
ObsCode
Narrative
Or different
supermarkets,
but always
26442006
closed
fracture of shaft of femur
Same patient,
same
hypertension
code:
81134009
Fracture,
closed, spiral
in the freezer
sections
?
Same (numerically
identical)
hypertension
?
5572
04/07/1990
5572
04/07/1990
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
298
Same patient, different
21/03/1992
26442006
closed fracturedates,
of shaft ofsame
femur fracture
Same
patient,
21/03/1992
9001224
Accident
in publicsame
buildingdate,
(supermarket)
codes:
same
03/04/1993patient,
58298795
Other lesion
on other specified
region
2patients,
different
fracture
codes:
Same
different
Differentdates,
same
fracture
codes:
(numerically
identical)
17/05/1993
79001
Essential
hypertension
same (numerically
Different codes.Same
Same(numerically
(numerically
identical)headfracture
? ?
22/08/1993
2909872
Closed fracture of radialfracture
identical) fracture ?
identical)
polyp
?
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
0939
20/12/1998
255087006
malignant polyp of biliary tract
2309
2309
47804
5572
298
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European Centre for
Ontological Research
Main problem areas
for CityHC’s EHR
• 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.
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Ontological 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
– ...
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Proposed solution:
European Centre for
Ontological Research
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
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European Centre for
Ontological Research
Ontology
• ‘Ontology’: the study of being as a science
• ‘An ontology’ is a representation of some preexisting 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
– ...
ECO An ontological analysis
R Universals
European Centre for
Ontological Research
EHR system
HC
Freezer section
continuants
City HC’s EHR system
City HC
The freezer section of Jane’s favourite supermarket
Jane Smith
Person
Dr. Peters
Dr. Longley
Femur
Jane’s left femur
Jane’s left femur
Jane’s left femur fracture
Fracture
Jane’s fracture’s image
Image
t
occurrents
Jane’s fracture as seen by Dr. Peters
Jane’s fracture as seen by Dr. Longley
Jane’s falling
Jane’s femur breaking
Dr. Peter’s examination of Jane’s fracture
Dr. Peter’s ordering of an X-ray
Shooting the pictures of Jane’s leg
Jane’s fracture’s healing
Dr. Peter’s diagnosis making
Dr. Longley’s examination of Jane’ s fracture
Freezer section dismantled
Jane dies
Instances of
Jane’s fracture
ECO
Ontological recategorisation
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European Centre for
Ontological Research
Fracture
Of Femur
CityHC
Dr. Peters
City HC
exists on
4th July
1990
Dr. Peters
located at
City HC on
4th July
1990
Jane
Smith
Jane Smith’s
consultation
with
Dr. Peters at
City HC on
4th July
1990
Jane
Smith’s
Fracture
Of Femur
Dr. Peters’
assessment of
Jane Smith’s
fracture of
femur
at
City HC on
4th July
1990
Severe
Jane
Smith’s
Fracture
Of Femur’s
severity
Spiral
Jane
Smith’s
Fracture
Of Femur’s
shape
ECO
R Essentials of Referent Tracking
European Centre for
Ontological Research
• 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.
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Ontological Research
Architecture of a
Referent Tracking System (RTS)
• RTS: system in which all statements referring to
particulars contain the IUIs for those particulars
judged to be relevant.
• Ideally set up as broad as possible:
– some metrics:
• % of particulars referred to by means of IUI
• % of HCs active in a region
– Geographic region
– functional region: defined by contacts amongst patients
• % of patients referred to within a region
• Services:
– IUI generator
– IUI repository: statements about assignments and reservations
– Referent Tracking ‘Database’ (RTDB): index (LSID) to statements
relating instances to instances and classes
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European Centre for
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IUI generation
• Universally Unique IDs:
– recently standardized through ISO/IEC 98348:2004,
– specifies format and generation rules enabling
users to produce 128-bit identifiers that are
either guaranteed or have a high probability of
being globally unique
– Meaningless strings
– Central management or certification not needed
to guarantee uniqueness
• (But use as IUI requires this)
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European Centre for
Ontological Research
IUI asignment
• = 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.
ECO
R Criteria for IUI assignment (1)
European Centre for
Ontological Research
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 !
•
–
More difficult: subjective symptoms
•
–
Only the plan exists and possibly the statements made about
the future execution of the plan
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, one out of 2 electrons in a György’s box
But: this is not a matter of choice, not ‘any’ out of ...
ECO
R Criteria for IUI assignment (2)
European Centre for
Ontological Research
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
ECO
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Assertion of assignments
European Centre for
Ontological Research
• IUI assignment is an act of which the execution
has to be asserted in the IUI-repository:
– <da, Ai, td>
• da
• Ai
• td
IUI of the registering agent
the assertion of the assignment <pa, pp, tap, c>
» pa
» pp
IUI of the author of the assertion
IUI of the particular
» tap
time of the assignment
» c
optional description for identification
time of registering Ai in the IUI-repository
• Neither td or tap give any information about when
#pp started to exist ! That might be asserted in
statements providing information about #pp .
ECO
R Management of the IUI-repository
European Centre for
Ontological Research
• Adequate safety and security provisions
– Access authorisation, control, read/write, ...
– Pseudonymisation
• Deletionless but facilities for correcting
mistakes.
• Registration of assertion ASAP after IUI
assignment
• (virtual, e.g. LSID) central management with
adequate search facilities.
ECO
Representation in the EHR
R
European Centre for
Ontological Research
Fracture
Of Femur
Severe
CityHC
Dr. Peters
Jane
Smith
Jane Smith’s
consultation
with
Dr. Peters at
City HC on
4th July
1990
4th July 1990
Jane
Smith’s
Fracture
Of Femur
Dr. Peters’
assessment of
Jane Smith’s
fracture of
femur
at
City HC on
4th July
1990
Jane
Smith’s
Fracture
Of Femur’s
severity
Spiral
Jane
Smith’s
Fracture
Of Femur’s
shape
particulars
• 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
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PTP statements particular to particular
European Centre for
Ontological Research
• ordered sextuples of the form
sa
ta
r
o
P
tr
<sa, ta, r, o, P, tr>
is the IUI of the author of the statement,
a reference to the time when the statement is made,
a reference to a relationship (available in o) obtaining between the
particulars referred to in P,
a reference to the ontology from which r is taken,
an ordered list of IUIs referring to the particulars between which
r obtains, and,
a reference to the time at which the relationship obtains.
• P contains as much IUIs as required by the arity of r. In most cases, P will
be an ordered pair such that r obtains between the particular represented by the
first IUI and the one referred to by the second IUI.
• As with A statements, these statements must also be accompanied by a
meta-statement capturing when the sextuple became available to the referent
tracking system.
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Ontological Research
PTCL statements –
particular to class
<sa, ta, inst, o, p, cl, tr>
sa
ta
inst
o
p
cl
tr
is the IUI of the author of the statement,
a reference to the time when the statement is made,
a reference to an instance relationship available in o
obtaining between p and cl,
a reference to the ontology from which inst and cl are
taken,
the IUI referring to the particular whose inst
relationship with cl is asserted,
the class in o to which p enjoys the inst relationship,
and,
a reference to the time at which the relationship obtains.
ECO
PTCO statements
R
particular to concept code
European Centre for
Ontological Research
<sa, ta, cbs, p, co, tr>
sa
ta
cbs
p
co
tr
is the IUI of the author of the statement,
a reference to the time when the statement is made,
a reference to the concept-based system from which co
is taken,
the IUI referring to the particular which the author
associates with co,
the concept-code in cbs which the author associates with
p, and,
a reference to the time at which the author considers the
association appropriate,
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R
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Interpretation of
PTCO statements
• must be interpreted as simple indexes to
terms in a dictionary.
• All that such a statement tells us, is that
within the linguistic and scientific community
in which cbs is used, the terms associated
with co may - i.e. are acceptable to - be
used to denote p in their determinative
version.
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R
European Centre for
Ontological Research
A SNOMED-CT example
• <IUI-0945, 18/04/2005, SNOMED-CT v0301, IUI1921, 367720001, forever>
• #IUI-0945: author of the statement
• #IUI-1921: the left testicle of patient #IUI-78127
• 367720001: the SNOMED concept-code to which “left testis” is
(in SNOMED) attached as term
• So we can denote #IUI-1921 by means of
• that left testis
• that entire left testis
• that testicle, that male gonad, that testis
•
that genital structure
•
that physical anatomical entity
• BUT NOT: that SNOMED-CT concept
ECO
Pragmatics of IUIs in EHRs
R
European Centre for
Ontological Research
• 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 tranfert or reference mechanism makes the statements
visible through the RTDB
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R
European Centre for
Ontological Research
PtID
Advantage: better
reality representation
Date
ObsCode
Narrative
5572
04/07/1990
26442006
IUI-001
closed fracture of shaft of femur
5572
04/07/1990
81134009
IUI-001
Fracture, closed, spiral
5572
12/07/1990
26442006
IUI-001
closed fracture of shaft of femur
5572
12/07/1990
9001224
5572
04/07/1990
79001
IUI-005
Essential hypertension
0939
24/12/1991
255174002
IUI-004
benign polyp of biliary tract
2309
21/03/1992
26442006
IUI-002
closed fracture of shaft of femur
2309
21/03/1992
9001224
IUI-007
Accident in public building (supermarket)
47804
03/04/1993
58298795
Other lesion on other specified region
5572
17/05/1993
79001
IUI-005
Essential hypertension
298
22/08/1993
2909872
IUI-003
Closed fracture of radial head
298
22/08/1993
9001224
5572
01/04/1997
26442006
IUI-012
closed fracture of shaft of femur
5572
01/04/1997
79001
IUI-005
Essential hypertension
0939
20/12/1998
255087006
IUI-004
malignant polyp of biliary tract
IUI-007
Accident in public building (supermarket)
IUI-007
Accident in public building (supermarket)
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R
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Ontological 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 cbs
– Systematic “inconsistent” descriptions in or
cross terminologies may indicate poor definition
of the respective terms
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R
European Centre for
Ontological 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