The Ontologically Privileged Status of the Past - PowerPoint PPT Presentation

Loading...

PPT – The Ontologically Privileged Status of the Past PowerPoint presentation | free to view - id: 75d8e4-ZTZjZ



Loading


The Adobe Flash plugin is needed to view this content

Get the plugin now

View by Category
About This Presentation
Title:

The Ontologically Privileged Status of the Past

Description:

The Ontologically Privileged Status of the Past Barry Smith – PowerPoint PPT presentation

Number of Views:50
Avg rating:3.0/5.0
Slides: 76
Provided by: md79
Category:

less

Write a Comment
User Comments (0)
Transcript and Presenter's Notes

Title: The Ontologically Privileged Status of the Past


1
The Ontologically Privileged Status of the Past
Barry Smith
2
Universals vs. instances
  • Assertions in scientific texts pertain to
    universals in reality
  • Assertions in a lab report pertain (also) to
    instances of these universals

3
Universals are those invariants in reality
  • which 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
  • ...

4
universals instances / particulars
scientific texts, dictionaries diaries, biographies, histories, journalism
medical ontologies, terminologies clinical records, lab reports, X-ray images
macroeconomic surveys credit card transaction records
databases databases
5
universals / concepts instances / particulars
scientific texts, dictionaries diaries, biographies, histories, journalism
medical ontologies, terminologies clinical records
macroeconomic surveys credit card transaction records
databases databases
relate indiscriminately to past, present and
future
6
universals / concepts instances / particulars
scientific texts, dictionaries diaries, biographies, histories, journalism
medical ontologies, terminologies clinical records, lab reports, X-ray images
macroeconomic surveys credit card transaction records

relate only to the past
7
universals instances / particulars
scientific texts, dictionaries diaries, biographies, histories, journalism
medical ontologies, terminologies clinical records
macroeconomic surveys credit card transaction records
databases databases
8
universals / concepts instances / particulars
scientific texts, dictionaries diaries, biographies, histories, journalism
medical ontologies, terminologies clinical records
macroeconomic surveys credit card transaction records
databases databases
9
UMLS Semantic Network
10
Anatomical Space
Anatomical Structure
Organ Cavity Subdivision
Organ Cavity
Organ
Serous Sac
Organ Component
Serous Sac Cavity
Tissue
Serous Sac Cavity Subdivision
Pleural Sac
Pleura(Wall of Sac)
Pleural Cavity
Parietal Pleura
Visceral Pleura
Interlobar recess
Mediastinal Pleura
Mesothelium of Pleura
Foundational Model of Anatomy
11
Anatomical Space
Anatomical Structure
Organ Cavity Subdivision
Organ Cavity
Organ
Serous Sac
Organ Component
Serous Sac Cavity
Tissue
Serous Sac Cavity Subdivision
is_a
Pleural Sac
Pleura(Wall of Sac)
Pleural Cavity
part_of
Parietal Pleura
Visceral Pleura
Interlobar recess
Mediastinal Pleura
Mesothelium of Pleura
12
  • Gene
  • Ontology

13
  • Gene
  • Ontology

14
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

15
Current ontologies are about meanings
(concepts, conceptualizations)
16
The Ontologically Privileged Status of Universals
17
The Ontologically Privileged Status of
Universals (a.k.a. Concepts)
18
The concept diabetes mellitus becomes
associated with a diabetic patient
  • concept patient concept diabetes
  • what it is on the
  • side of the patient

?
?
19
The concept diabetes mellitus becomes associated
with a diabetic patient
  • concept patient concept diabetes
  • what it is on the
  • side of the patient

?
?
20
A is_a B def. A is more specific in meaning
than B
  • A contains B def
  • the 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

21
GALEN
  • vomitus contains carrot

22
  • UMLS Semantic Network
  • Food causes Experimental Model of Disease
  • Biomedical or Dental Material causes Mental or
    Behavioral Dysfunction
  • Manufactured Object causes Disease or Syndrome

23
vomitus contains carrot
  • The authors of ontologies have not paid
    attention to the question whether these are all
    or some assertions

24
because they have not paid attention to instances
  • some instances of vomitus contain instances of
    carrot
  • all instances of vomitus contain instances of
    carrot

25
IFOMIS proposal move from associative
relations between concepts/meanings to strictly
defined relations between the universals (types,
kinds) in realityembraced also by Gene Ontology
Consortium
26
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

27
Three kinds of relations
  • ltuniversal, universalgt is_a, part_of, ...
  • ltinstance, universalgt this throb here and now
    instance_of the class throb
  • ltinstance, instancegt Marys heart part_of Mary
    at t

28
  • 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

29
transformation_of
mature RNA transformation_of pre-RNAadult
transformation_of child
30
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
31
transformation_of
  • in 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

32
embryological development
33
tumor development
C1
C c at t
c at t1
34
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

35
The story of Jane Smith(with thanks to Werner
Ceusters)
36
July 4th, 1990 Jane goes shopping
37
A visit to the hospital
  • City Health Centre Dr. Peters
  • (City HC) Dr. Longley

38
Diagnosis a severe spiral fracture of the femur
39
The City HCs 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
Apr32(2)109-19.
40
Structured Medical Record
41
CityHCs representation formalismfor statements
in records
Occurrences are 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.
42
City HCs EHR model
43
  • Rector et al
  • Every occurrence level statement concerning the
    Jane Smiths Fracture of the Femur is an
    observation of the corresponding individual.
  • The existence of the individual Jane Smiths
    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
    Smiths Fracture of the Femur might be that she
    did not have it.)

44
Problems
45
Main problems of EHRs
  • Statements 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.

46
Consequences
  • 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), HIV contaminated blood from
    donors, food from unhygienic source, ...
  • Hampers prevention

47
Proposed solutionReferent Tracking
  • Purpose
  • explicit reference to the concrete individual
    entities relevant to the accurate description of
    each patients condition, therapies, outcomes,
    ...
  • Method
  • Introduce an Instance Unique Identifier (IUI) for
    each relevant particular / instance

48
  • 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)

49
Referent tracking
  • a response to the hard NLP problem of reference
    resolution in running text

50
Ontology
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
51
Basic Formal Ontology
Continuants Occurrents / Events
endure identically through time while undergoing changes, including gaining and losing parts unfold themselves through time in successive temporal phases
52
Basic Formal Ontology
Continuants Occurrents
Independent things, substances Always dependent on their bearers (participants/agents)
Dependent functions, qualities, shapes, roles ... Always dependent on their bearers (participants/agents)
53
An ontological analysis
continuants
54
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

55
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

56
IUI generation
  • Universally Unique IDs
  • recently standardized through ISO/IEC
    9834-82004,
  • specifies format and generation rules enabling
    users to produce 128-bit identifiers that have a
    very high probability of being globally unique
  • Meaningless strings

57
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

58
Criteria for IUI assignment (1)
  • The particulars 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

59
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

60
IUI assignments
  • The act of IUI assignment can be represented as
  • ltda , Ai , tdgt
  • da IUI of the registering agent
  • Ai ltpa, pp, tap, cgt
  • 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.

61
Management of IUI-repository
  • Adequate safety and security provisions
  • Access authorisation, control, read/write, ...
  • Pseudonymisation
  • Deletionless but with facilities for correcting
    mistakes.
  • Central management with adequate search
    facilities.

62
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

63
PtoP (particular to particular) statements
ordered sextuples of the form ltsa, ta, r, o, P,
trgt
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.
64
PtoCL (particular to class) statements
ltsa, ta, inst, o, p, cl, trgt sa the IUI of the
author of the statement, ta the time when the
statement is made, inst an instance
relationship available in o obtaining between 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.
65
PtoCO (particular to concept code) statements
ltsa, ta, cbs, p, co, trgt sa the IUI of the
author of the statement, ta the time when the
statement is made, 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,
66
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

67
A SNOMED-CT example
  • ltIUI-0945, 18/04/2005, SNOMED-CT v0301,
    IUI-1921, 367720001, forevergt
  • 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

68
Pragmatics of IUIs in EHRs
  • IUI 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

69
IUIs in structured EHRs
70
Advantage betterreality representation
IUI-003
71
Other Advantages
  • Mappings 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

72
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

73
Other Advantages
  • Referent 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)

74
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 can play an interesting role.
  • Big Brother feeling is to be expected, but with
    adequate measures easy to fight.
  • Pilot is being established

75
Generalizing beyond healthcare
  • 1) intelligence/security tracking movements of
    people and goods
  • 2) 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.
About PowerShow.com