Transcript Document
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
I 3 : Identity, Identifiers, Identification
Referent Tracking and its Applications
WWW2007 – Banff, May 8th, 2007 Werner CEUSTERS
Center of Excellence in Bioinformatics and Life Sciences Ontology Research Group University at Buffalo, NY, USA
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Imagine being in Saudi-Arabia, ready to open this window …
R T U
Center of Excellence in Bioinformatics & Life Sciences
This specific guy (#1) This specific ‘silver’ Audi (#2) This specific brick (#3)
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
But we are not here …
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New York State Bioinformatics & Life Sciences
This specific image of #2 (#5) This specific image of #3 (#6)
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
… as well as second order #4 stands-for? #1 #6 stands-for? #3
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New York State Center of Excellence in Bioinformatics & Life Sciences
Not just first order is “in reality”, But so is second order
R T U
Center of Excellence in Bioinformatics & Life Sciences
An image of #9 (the hotel from which we would be looking to this car) (#10)
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
A different look on #8 as first order entity
(What would be #7 ?)
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R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Close your eyes … Try to imagine that specific ‘silver’ car …
• If everybody succeeded, there is #11, #12, #13, … • i.e. a ‘mental image’ inside
each
of the attendees in this room
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New York State Center of Excellence in Bioinformatics & Life Sciences
A wealth of distinct, though closely related things
• The guy (of flesh and blood) standing next to that ‘silver’ car • The images of that guy embodied in the projections on the screen a bit earlier • The bits in the PP-file on this laptop that cause PP and the OS on this laptop and … to project an image of that guy on the screen • The mental images of that guy in each of you, as well as the mental images of the images of that guy • …
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
The essence of Referent Tracking
• Keeping track of entities in reality • By means of singular and globally unique identifiers (#1, #2, #3, …) • That function as surrogates for these enities in information systems, documents, etc Ceusters W. and Smith B. Tracking Referents in Electronic Health Records. In: Engelbrecht R. et al. (eds.) Medical Informatics Europe, IOS Press, Amsterdam, 2005;:71-76
R T U
Center of Excellence in Bioinformatics & Life Sciences
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Unfortunately, it is not that easy …
• What is ‘
THIS
’ … – The car ?
– The door ?
– The reflected image of the hotel ?
– That pixel on this image ?
– …
#12
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New York State Center of Excellence in Bioinformatics & Life Sciences
What is really needed …
• A ‘formal’ mechanism to – Assign numbers to entities – Specify : – what the entities are how they are related – Keep inventories of numbered entities – Let ‘systems’ know what number is assigned to an entity, and what entity is denoted by an assigned number
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Does mainstream SW thinking acknowledges this ?
• The answer is clearly:
NO !
– Overemphasis on syntactic regimentation • XML, RDF(s), OWL, … each have a semantics but users tend to assign more semantics to expressions therein than is actually carried.
– Unwarranted trust in the power of description logics – Expressions in SW languages or ontologies are said to refer to ‘concepts’ – A complete mess in the terminology adhered to: • Instance, object, resource, class, …
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Our proposal
A combination of three theories/paradigms/...
1. Basic Formal Ontology what entities exist and how they are related 2. Granular Partition Theory how representations relate to reality 3. Referent Tracking how particular entities can be described unambiguously
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
BFO & GPT: a realist view of the world
1. The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; 2. Cognitive agents build up through observations
cognitive representations
of the world; 3. To make these representations publicly accessible in some enduring fashion, these agents create
representational artifacts
that are fixed in some medium.
Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
A realist view of the world
• The world consists of – entities that are • Either
particulars
or
universals
;
Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA
R T U
New York State Bioinformatics & Life Sciences
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
A realist view of the world
• The world consists of – entities that are • Either
particulars
or
universals
; • Either
occurrents
or
continuants
; • Either
dependent
or
independent
; and, – relationships between these entities of the form •
Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
A widespread misconception
• ‘A variety of clinical terminology standards exist in the health care system, giving meaning to raw data and allowing for
semantic interoperability
. Systemized Nomenclature of Medicine (SNOMED) clinical terms are one example of a
clinical reference terminology
semantic interoperability.’ that provides for
Pharmacotherapy. 2005;25(8):1116-1125.
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New York State
what is described: how many disorders are listed?
in relation to three different events
PtID
5572
Date
04/07/1990 might or might not refer to the same
ObsCode Narrative
location.
closed fracture of shaft of femur 5572 5572 04/07/1990 12/07/1990 patient denote three times the 26442006
same
closed fracture of shaft of femur disease.
5572 5572 0939 2309 2309 47804 5572 298 298 5572 5572 0939 12/07/1990 04/07/1990 9001224 79001 Accident in public building (supermarket) Essential hypertension 24/12/1991 255174002 21/03/1992 21/03/1992 22/08/1993 22/08/1993 01/04/1997 26442006 9001224 58298795 different dates, then 79001 2909872 If two different fracture codes observations made on the same Essential hypertension day for the same patient, they Closed fracture of radial head dates for the same patient, 9001224 they may still refer to the same tumor. 26442006 code is used for the Accident in public building (supermarket) are used in relation to Other lesion on other specified region might not refer to the 01/04/1997 20/12/1998 79001 255087006 Essential hypertension malignant polyp of biliary tract
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Consequences
• Very difficult to: – Count the number of (numerically) different diseases • Bad statistics on incidence, prevalence, ...
• Bad basis for health cost containment – Relate (numerically the 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 – ...
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Proposed Solution: Referent Tracking Now! That should clear up a few things around here !
•
Purpose
: –
explicit
reference to the concrete individual entities relevant to the accurate description of each patient’s condition, therapies, outcomes, ...
Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. J Biomed Inform. 2006 Jun;39(3):362-78.
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New York State Center of Excellence in Bioinformatics & Life Sciences
Numbers instead of words
•
Method
: – Introduce an
Instance Unique Identifier
(IUI) for each relevant particular (individual) entity 78
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New York State Center of Excellence in
#1 #2 #3 #4 instance-of at t 1 instance-of at t 1 person liver inst-of at t 2 #10 inst-of at t 2 #20
‘John Smith’s liver
instance-of at t 1 tumor inst-of at t 2 #30
tumor
instance-of at t 1 treating inst-of at t 2 #40
was treated with
#5 clinic instance-of at t 1 device #6 inst-of at t 2 #5 #6
RPCI’s irradiation device’
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
EHR – Ontology “collaboration”
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Advantage: better reality representation
PtID
5572 5572 5572 5572 5572 0939 2309 2309 47804 5572 298 298 5572 5572 0939
Date
04/07/1990 04/07/1990 12/07/1990 12/07/1990 04/07/1990 24/12/1991 21/03/1992 21/03/1992 03/04/1993 17/05/1993 22/08/1993 22/08/1993 01/04/1997 01/04/1997 20/12/1998
ObsCode
26442006
IUI-001
81134009 26442006 9001224 79001 255174002 26442006 9001224 58298795 79001 2909872 9001224 26442006 79001 255087006
7 distinct disorders IUI-001 IUI-001 IUI-007 IUI-005 IUI-004 IUI-002 IUI-007 IUI-006 IUI-005 IUI-003 IUI-007 IUI-012 IUI-005 IUI-004 Narrative
closed fracture of shaft of femur Fracture, closed, spiral closed fracture of shaft of femur Accident in public building (supermarket) Essential hypertension benign polyp of biliary tract closed fracture of shaft of femur Accident in public building (supermarket) Other lesion on other specified region Essential hypertension Closed fracture of radial head Accident in public building (supermarket) closed fracture of shaft of femur Essential hypertension malignant polyp of biliary tract
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
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.
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
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):
instances to instances and classes index (LSID) to statements relating
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
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.
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
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
it instantiates the particular exactly is, i.e. which universal 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 ...
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Criteria for IUI assignment (2)
2.
3.
4.
The particular’s existence ‘
may not already have been determined as the existence of something else
’: • • • Morning star and evening star Himalaya Multiple sclerosis May not have already been assigned a IUI.
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
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Assertion of assignments
• IUI assignment is an act of which the execution has to be asserted in the IUI-repository: –
D i =
•
IUI d
IUI of the registering agent •
A i
the assertion of the assignment
< IUI p , IUI a , t ap >
»
IUI a
IUI of the author of the assertion »
IUI p
IUI of the particular »
t ap
time of the assignment •
t d
• Neither
t d
time of registering A i in the IUI-repository or
t ap
give any information about when #
IUI p
started to exist ! That might be asserted in statements providing information about #
IUI p
.
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences •
PtoP statements - particular to particular
ordered sextuples of the form
R i =
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.
t r
•
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.
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
PtoU statements – particular to universal
U i =
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
u
are taken, the IUI referring to the particular whose
inst
relationship with
u
is asserted, the universal in
o
to which
p
enjoys the
inst
relationship, and, a reference to the time at which the relationship obtains.
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
PtoN-statements
N i =< IUI a , t a , nt j , n i , IUI p , t r >
• The person referred to by IUI a asserts at time t a that
n i
is the name of the nametype
nt j
that designates in the real world the particular referred to by IUI p at t r . This template will further be referred to as
PtoN
template.
• Would assert that “Werner” is my first name, and “Ceusters” is my last name.
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New York State Bioinformatics & Life Sciences
Ontology EHR
continuant disorder CAG repeat Juvenile HD person #IUI-1 ‘affects’ #IUI-2 #IUI-3 ‘affects’ #IUI-2 #IUI-1 ‘causes’ #IUI-3 ...
Referent Tracking Database
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New York State Center of Excellence in Bioinformatics & Life Sciences
RT for Digital Rights Management
R T U
New York State Center of Excellence in Bioinformatics & Life Sciences
Conclusion
The Semantic Web