1 the ontologically privileged status of the past barry smith

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The Ontologically Privileged Status of the Past

Barry Smith

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Universals vs. instances

Assertions in scientific texts pertain to universals in reality

Assertions in a lab report pertain (also) to instances of these universals

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Universals are those invariants in realitywhich make possible

• the use of general terms in scientific inquiry

• the use of standardized therapies in clinical care

• the use of standardized procedures in business transactions

• ...

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universals instances / particulars

scientific texts, dictionaries

diaries, biographies, histories, journalism

medical ontologies, terminologies

clinical records, lab reports, X-ray images

macroeconomic surveyscredit card transaction

records

databases

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universals / concepts instances / particulars




clinical records


records

databases

relate indiscriminately to past, present and future

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clinical records, lab reports, X-ray images


records

relate only to the past

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universals instances / particulars




clinical records


records

databases

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clinical records


records

databases

9UMLS Semantic Network

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Pleural Cavity

Pleural Cavity

Interlobar recess

Interlobar recess

Mesothelium of Pleura


Pleura(Wall of Sac)

Pleura(Wall of Sac)

VisceralPleura

VisceralPleura

Pleural SacPleural Sac

Parietal Pleura

Parietal Pleura

Anatomical SpaceAnatomical Space

OrganCavityOrganCavity

Serous SacCavity

Serous SacCavity

AnatomicalStructure

AnatomicalStructure

OrganOrgan

Serous SacSerous Sac

MediastinalPleura

MediastinalPleura

TissueTissue

Organ PartOrgan Part

Organ Subdivision

Organ Subdivision

Organ Component

Organ Component

Organ CavitySubdivision


Serous SacCavity

Subdivision

Serous SacCavity

Subdivision

Foundational Model of Anatomy

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Pleural Cavity

Pleural Cavity

Interlobar recess

Interlobar recess



Pleura(Wall of Sac)

Pleura(Wall of Sac)

VisceralPleura

VisceralPleura

Pleural SacPleural Sac

Parietal Pleura

Parietal Pleura

Anatomical SpaceAnatomical Space

OrganCavityOrganCavity

Serous SacCavity

Serous SacCavity

AnatomicalStructure

AnatomicalStructure

OrganOrgan

Serous SacSerous Sac

MediastinalPleura

MediastinalPleura

TissueTissue

Organ PartOrgan Part

Organ Subdivision

Organ Subdivision

Organ Component

Organ Component



Serous SacCavity

Subdivision

Serous SacCavity

Subdivision

part

_of

is_a

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Gene

Ontology

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Gene

Ontology

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Holy grail of biomedical informatics = integration of genomic and EHR

data Main obstacles

1. Poor facility for dealing with time and instances / particulars in current ontologies

2. Poor facility for dealing with instances / particulars in current clinical record systems

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Current ontologies are about meanings (‘concepts’, ‘conceptualizations’)

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The Ontologically Privileged Status of Universals

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The Ontologically Privileged Status of Universals (a.k.a. Concepts)

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?

The concept diabetes mellitus becomes ‘associated with a diabetic patient’

concept patient concept diabetes

what it is on the

side of the patient?

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?

The concept diabetes mellitus becomes ‘associated with a diabetic patient’

concept patient concept diabetes

what it is on the

side of the patient?What is the relation here? Not a relation between concepts

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A contains B =defthe concept A stands in a containment relation

to the concept B

A causes B =def the concept A stands in a causative relation to

the concept B

A is_a B =def. ‘A’ is more specific in meaning than ‘B’

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GALEN

vomitus contains carrot

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UMLS Semantic Network:

Food causes Experimental Model of Disease

Biomedical or Dental Material causes Mental or Behavioral Dysfunction

Manufactured Object causes Disease or Syndrome

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vomitus contains carrot

The authors of ontologies have not paid attention to the question whether these are all or some assertions

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because they have not paid attention to instances

some instances of vomitus contain instances of carrot

all instances of vomitus contain instances of carrot

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IFOMIS proposal:

move from associative relations between concepts/meanings to

strictly defined relations between the universals (types, kinds) in

reality

embraced also by Gene Ontology Consortium

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Key idea

Ontological relations like

contains, part_of, causes

are relations between universals,

but to define them properly we need to take account of instances and of time

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Three kinds of relations

<universal, universal>: is_a, part_of, ...

<instance, universal>: this throb here and now instance_of the class throb

<instance, instance>: Mary’s heart part_of Mary at t

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part_of

A part_of B =def.given any particular a and any time t, if a is an instance of A at t,then there is some instance b of B such that a is an instance-level part_of b at t

HAS ALL-SOME FORM

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transformation_of

c at t1

C

c at t

C1

time

same instance

mature RNA transformation_of pre-RNAadult transformation_of child

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transformation_of

A transformation_of B =def

for all a, t, if a is an instance of A at t then there is some t´ earlier than t which is such that a is an instance of B at t´

HAS ALL-SOME FORM

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transformation_ofin short:

A transformation_of B =def. any instance of A was

at some earlier time an instance of B

Contrast:

A transforms_into B

child transforms_into adult

The ontologically privileged status of relations

pointing towards the past

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C

c at t c at t1

C1

embryological development

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C

c at t c at t1

C1

tumor development

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Advantages of the methodology of enforcing commonly accepted

coherent definitions

promote quality assurance (better coding)

guarantee automatic reasoning across ontologies and across data at different granularities

yields direct connection to times and instances in EHR

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The story of Jane Smith

(with thanks to Werner Ceusters)

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Jane’s favourite supermarket

July 4th, 1990: Jane goes shopping:

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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A visit to the hospital City Health Centre Dr. Peters

(City HC) Dr. Longley

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Diagnosis: a severe spiral fracture of the femur

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The City HC’s medical record

captures in a structured form all of the ‘clinically significant’ information in the narrative notes

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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Structured Medical Record

www.medappz.com/

04/07/1990 – 17:10Dr. Peters

Jane SmithOrthopedics

Emergency visit: 04/07/1990 – 17.00

Severe

Left upper leg

Since fall on floor

Constant

26442006 closed fracture of shaft of femur

81134009 fracture, closed, spiral

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CityHC’s representation formalismfor statements in records

Occurrences: “are specific occurrences of individuals and must be situated in space and time. The most importantgroup of occurrences are observations — i.e. agents’ observations of individuals.”

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City HC’s EHR model

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Rector et al:“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.)”

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5572 04/07/1990 26442006 closed fracture of shaft of femur

5572 04/07/1990 81134009 Fracture, closed, spiral


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



47804 03/04/1993 58298795 Other lesion on other specified region


298 22/08/1993 2909872 Closed fracture of radial head




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 ?

ProblemsDifferent patients. Same supermarket? Maybe the same (irrelevant ?) freezer section ?Or different supermarkets, but always in the freezer sections ?

Same patient, different dates, Different codes. Same (numericallyidentical) polyp ?

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Main problems of EHRsStatements refer only implicitly to the concrete

entities about which they give information.Codes are general: they tell us only that some

instance of the class the codes refer to, is referred to in the statement, but not what instance precisely.

Mixing up the act of observation and the thing observed.

Mixing up statements and the entities these statements refer to.

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ConsequencesDifficult 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), HIV contaminated blood from donors, food from unhygienic source, ...

• Hampers prevention

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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 particular / instance

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CUI (coo-ey): Concept Unique Identifier (e.g. a SNOMED code)

UUI (oo-ey): Universal Unique Identifier

IUI (you-ey): Instance Unique Identifier (e.g. a Social Security Number)

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Referent tracking

a response to the hard NLP problem of reference resolution in running text

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OntologyAn 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

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Basic Formal OntologyContinuants Occurrents / Events

endure identically through time while undergoing changes, including gaining and losing parts

unfold themselves through time in successive temporal phases

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Basic Formal OntologyContinuants Occurrents

Independent: things, substances

Always dependent on their bearers (participants/agents)Dependent:

functions, qualities, shapes, roles ...

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An ontological analysis

continuantsCity HC

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 HC’s EHR system

t

UniversalsEHR system

HC

Freezer section

Person

Femur

Fracture

Image

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

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Essentials of Referent Tracking

Deciding what particulars should receive a IUI;Finding out whether or not a particular has already

been assigned a IUI; Using IUIs in the EHR, resolve issues concerning

the syntax and semantics of statements containing IUIs;

Correcting errors in the assignment of IUIs;Dealing with relation between IUI-identified

instances and corresponding universals

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Architecture of aReferent Tracking System (RTS)

Ideally set up to be as geographically broad in scope as possible

Services:– IUI generator– IUI repository: statements about assignments and

reservations– Referent Tracking Database (RTDB): statements

relating instances to instances and universals

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IUI generationUniversally Unique IDs:

– recently standardized through ISO/IEC 9834-8:2004,

– specifies format and generation rules enabling users to produce 128-bit identifiers that have a very high probability of being globally unique

– Meaningless strings

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IUI assignment= an act of labelling carried out by the first

cognitive agent needing to acknowledge the existence of a particular it has information about

cognitive agent:– A person– An organisation– A device or software agent, e.g.

• Bank note printer• Image analysis software• Credit card transaction reader

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Criteria for IUI assignment (1)

The particular’s existence must be determined:– Easy for persons in front of you, for body parts, for X-

ray images– More difficult for subjective symptoms– 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

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Criteria for IUI assignment (2)The particular should not have been already

determined as something else:• Morning star / evening star• May not have already been assigned a IUI.

Must be salient/relevant/significant:• Personal decision, (scientific) community guideline, ... • Reflects a possibility offered by the EHR system• Once a IUI has been assigned, everybody making

statements about this particular should use it

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IUI assignmentsThe act of IUI assignment can be represented as:

<da , Ai , td>

da = IUI of the registering agent

Ai = <pa, pp, tap, c>

pa = IUI of the author of the assertion

pp = IUI of the particular

tap = time of assignment

c = optional description

td = time of registering Ai in the IUI-repository

Neither ‘td’ nor ‘tap’ give any information about when

#pp began to exist.

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Management of IUI-repositoryAdequate safety and security provisions

– Access authorisation, control, read/write, ...– Pseudonymisation

Deletionless but with facilities for correcting mistakes.

Central management with adequate search facilities.

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Representation in the EHR

Relevant particulars referred to using IUIs

Relationships that obtain between particulars at time t expressed using strictly defined relations from an ontology

Statements describing for each particular at time t of what universal from an ontology it is an instance

CityHC Dr. PetersJane

Smith

JaneSmith’s

FractureOf Femur

FractureOf Femur

SevereSpiral

Jane Smith’sconsultation withDr. Peters atCity HC on 4th July1990

Dr. Peters’assessment ofJane Smith’sfracture offemur atCity HC on 4th July1990

JaneSmith’s

FractureOf Femur’s

severity

JaneSmith’s

FractureOf Femur’s

shape

4th July 1990

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PtoP (particular to particular) statements ordered sextuples of the form: <sa, ta, r, o, P, tr>

sa the IUI of the author of the statement,

ta the time when the statement is made,

r a relationship obtaining between the particulars referred to in P,o the ontology from which r is taken,P an ordered list of the IUIs of the particulars between which r obtains, tr the time at which r obtains.

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PtoCL (particular to class) statements

<sa, ta, inst, o, p, cl, tr>



inst an instance relationship available in o obtainingbetween p and cl,

o the ontology from which inst and cl are taken,p the IUI of the particular whose inst relationship with cl

is asserted,cl the class in o to which p enjoys the inst relationship, tr the time at which the relationship obtains.

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PtoCO (particular to concept code)

statements <sa, ta, cbs, p, co, tr>



cbs the concept-based system from which co is taken,p the IUI of the particular which the author associates

with co,co the concept-code in cbs which the author associates with p, tr a reference to the time at which the author considers the

association appropriate,

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Interpretation of PtoCO statements

Such statements tell us that within the linguistic and scientific community in which cbs is used, the terms associated with co may be used to denote p

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A SNOMED-CT example <IUI-0945, 18/04/2005, SNOMED-CT v0301, IUI-

1921, 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

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Pragmatics of IUIs in EHRsIUI assignment requires (just a bit) more effort compared to

current use of general 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 some IUIs there comes a wealth of already registered information

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IUIs in structured EHRs

www.medappz.com/

04/07/1990 – 17:10Dr. Peters

Jane SmithOrthopedics

Emergency visit: 04/07/1990 – 17.00

Severe

Left upper leg

Since fall on floor

Constant

26442006 closed fracture of shaft of femur

81134009 fracture, closed, spiral

Replaced by the IUI for thepatient’s left upper legThat IUI might be found byusing “left upper leg” as asearch term to query theRTDB

Both replaced by the IUI for that fractureBy means of PTCO statements is the IUI relatedto the SNOMED-codes

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Advantage: betterreality

representation5572 04/07/1990 26442006 closed fracture of shaft of femur

5572 04/07/1990 81134009 Fracture, closed, spiral




0939 24/12/1991 255174002 benign polyp of biliary tract



47804 03/04/1993 58298795 Other lesion on other specified region


298 22/08/1993 2909872 Closed fracture of radial head




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

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Other AdvantagesMappings between ontologies and coding

systems created as by-product of tracking– Descriptions about the same particular using

different systems e.g. in different hospitals

Quality control of ontologies and concept-based systems– Systematically inconsistent descriptions within

or across terminologies may indicate poor definition of the respective terms

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Other advantages

credit card transaction records already constitute a referent tracking database

can give a global picture of economic patterns in a given society

Our proposal will provide for something analogous in the realm of healthcare

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Other AdvantagesReferent tracking can be used in decision

support when making diagnoses

We can consider the results of assignment of different clinical codes to one and the same collection of IUIs assembled over a period (and thereby uncover new patterns of symptoms, e.g. in a case of multiple sclerosis)

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ConclusionReferent tracking can solve a number of

problems in an elegant way.Existing (or emerging) technologies can be

used for the implementation.Old technologies can play an interesting

role.Big Brother feeling is to be expected, but

with adequate measures easy to fight.Pilot is being established

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Generalizing beyond healthcare1) intelligence/security: tracking movements of people and

goods2) tracking copies of papers, music-files, over the internet.

Numbers can be assigned by producers of the files, but also by the people who forward them (buying and selling numbers)

3) creation of tag-technology for all forms of hardware/collectibles

4) gaming (turning spam into a game): collaborative, distributed story writing

5) gambling/play mixture: a question is asked, and every tenth, twentieth, ... person who calls the TV studio is allowed to answer. But calling costs you $1. Referent tracking allows this idea to be realized over email/internet.

1 the ontologically privileged status of the past barry smith

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