VT

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VT
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Medical Ontology

• Barry Smith
• bsmith_at_ifomis.uni-leipzig.de

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The Importance of Getting Documentation Right

• Health Level 7 Reference Information Model (HL7
  RIM)

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Ontology of HL7 RIM based on Speech Act Theory

• the medical record is not a collection of facts,
  but "a faithful record of what clinicians have
  heard, seen, thought, and done." Its Act class
  represents what is known as "speech-acts" in
  linguistics and philosophy.

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The Ontology of HL7 RIM

• Act as statements or speech-acts are the only
  representation of real world facts or processes
  in the HL7 RIM. The truth about the real world is
  constructed through a combination (and
  arbitration) of such attributed statements only,
  and there is no class in the RIM whose objects
  represent "objective states of affairs" or "real
  processes" independent from attributed
  statements.
• As such, there is no distinction between an
  activity and its documentation. Every Act
  includes both to varying degrees.

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The failure to distinguish between facts and
their representations (or between objects and
concepts) is endemic in linguistics

• One of the cornerstones of the objectivist
  paradigm is the independence of metaphysics from
  epistemology. The world is as it is, independent
  of any concept, belief, or knowledge that people
  have. Minds, in other words, cannot create
  reality. I would like to suggest that this is
  false and that it is contradicted by just about
  everything known in cultural anthropology.
  George Lakoff

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Why is this important?

• HL7 ... there is no distinction between an
  activity and its documentation. ...

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HL7 Corporate SponsorsGE IBMMicrosoft Oracle
SiemensSun MicrosystemsErnst Young Eli
Lilly
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HL7 Merchandizing
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Federally mandated ontological confusion

• All US federal agencies are required to adopt
  HL7 messaging standards to ensure that each
  federal agency can share information that will
  improve coordinated care for patients

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Ontologie als Zweig der Philosophie

• die Wissenschaft von den Arten und Strukturen
  von Objekten, Qualitäten, Prozessen, Ereignissen,
  Funktionen und Relationen in allen Bereichen der
  Wirklichkeit

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Aristotle
Der erste Ontologe

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Eine biologische Ontologie
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Linnaeus

• 1763 Genera Morborum
• (Nosologie
• oder
• Ontologie der Krankheitsarten)

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Q Warum Ontologie in der medizinischen
Informatik?

• A Das Turm von Babel-Problem der
  Informationssysteme

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Turm von Babel

• Jedes Informationssystem basiert auf einer
  eigenen Terminologie
• Wie können wir die Inkompatibilitäten lösen, die
  entstehen, wenn Daten aus verschiedenen Quellen
  kombiniert werden?
• Vgl. Wie können wir Anatomie und Physiologie
  integrieren?

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Wie lösen Medizinstudenten dieses Problem?

• Vielfach erst durch die Begegnung mit dem
  Patienten
• Der Patient und die in ihm ablaufenden Prozesse
  dienen als Kristallisationspunkt für eine
  sinnvolle Ordnung sonst isoliert stehender
  (gelernter) Fakten.
• (Aus Wissen-dass wird Wissen-wie)

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Dem Computer fehlt praktisches Wissen

• Wie können in Medizininformations-systemen
  isolierte Datenartefakte zu konsistentem und
  anwendbarem Wissen integriert werden?

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Ursprünglicher Traum der Ontologie in der
Informatik

• Eine einzige allumfassende Taxonomie aller
  Gegenstandsarten, die als zentrales
  integrierendes Kategoriensystem für alle
  Informationssysteme dient.
• Dieser Traum ist ausgeträumt ...

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Gegenwärtige Lösungen

• Standardisierte Terminologien
• UMLS
• SNOMED
• ICD-10
• Gene Ontology
• Digital Anatomist
• usw.

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Standardisierte Terminologien

• sollen Zugriff auf biomedizinische Literatur und
  Faktendatenbanken erleichtern
• Beispielsweise um Verbindungen zwischen
  spezifischen Genen und spezifischen
  Körperreaktionen auffindbar zu machen
• Eine neue Art medizinischer Forschung soll
  dadurch ermöglicht werden

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Database and terminology standardization

• is desparately needed in medical and
  bioinformatics
• to enable the huge amounts of existing data to
  be fused together automatically

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To reap the benefits of standardization

• we need to make ONE SYSTEM out of many different
  terminologies
• But how?
• Through government edict? (Scandinavia)
• Through efforts of international standards
  bodies (ISO, CEN )?
• Through UMLS Metathesaurus?

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Zentrale Schaltstelle

• UMLS
• Universal Medical Language System
• National Library of Medicine
• Bethesda, MD

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UMLS Metathesaurus

• eine riesige Kombination verschiedener
  maschinenlesbarer Quellterminologien
• 800,000 Begriffe
• 10 Mio. Beziehungen

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Beispiele für Quell-Terminologien

• SNOMED-RT
• Systematized Nomenclature of Medicine
• MeSH
• Medical Subject Headings

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is_a trees

• hormone
• peptide hormone digestive hormone
• adrenocorticotropin glycopeptide hormone
• 
  follicle-stimulating hormone

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• is_a ist ein / ist von der Art
• Diabetes Milletus is_a Disease

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Bad Coding

• deriving from over-simplification
• and from failure to pay attention to ontological
  principles
• Z.B. SNOMED
• both_testes is_a testis
• (beide_Hoden ist_ein Hoden)

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Terminological Incompatibilities
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Representation of Blood in SNOMED
Blood is_a Tissue
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Representation of Blood in MeSH
Blood is_a Bodily Fluid
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Bad CodingIncompatibilitiesContext-Dependence

• Standardized Terminologies must be used properly

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people are lazy and idiosyncratic

• Sie machen Schreibfehler
• Jeder pflegt seine eigene Terminologie, die sich
  mehr oder weniger von der anderer Akteure
  unterscheidet
• Sie verwenden verschiedene natürlich-sprachliche
  Darstellungen der gleichen medizinischen
  Phänomena

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The codes are not formulated on the basis of
clear principles

• Therefore inconsistent
• Unintuitive
• Difficult to train people to use them
• Application often depends on context-dependent
  knowledge

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The IFOMIS Contribution

1. help to improve standardizations through
   constructive criticism based on ontological
   principles
2. show practical use of ontological research
3. help to make natural language the code

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The IFOMIS Contribution

• help to improve standardizations through
  constructive criticism based on ontological
  principles
• show practical use of ontological research in
• 3. help to make natural language the code

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UMLS Metathesaurus

• eine riesige Kombination verschiedener
  maschinenlesbarer Quellterminologien
• UMLS Semantic Network
• bestehend aus 134 Semantic Types
• soll Ordnung in diesem Wust schaffen

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UMLS Semantic Network

• entity event
• physical conceptual
• entity entity

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conceptual entity

• Organism Attribute
• Finding
• Idea or Concept
• Occupation or Discipline
• Organization
• Group
• Group Attribute
• Intellectual Product
• Language

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conceptual entity

• Organism Attribute
• Finding
• Idea or Concept
• Occupation or Discipline
• Organization
• Group
• Group Attribute
• Intellectual Product
• Language

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• Idea or Concept
• Functional Concept
• Qualitative Concept
• Quantitative Concept
• Spatial Concept
• Body Location or Region
• Body Space or Junction
• Geographic Area
• Molecular Sequence
• Amino Acid Sequence
• Carbohydrate Sequence
• Nucleotide Sequence

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Geneva

• is an Idea or Concept

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• Idea or Concept
• Functional Concept
• Qualitative Concept
• Quantitative Concept
• Spatial Concept
• Body Location or Region
• Body Space or Junction
• Geographic Area
• Molecular Sequence
• Amino Acid Sequence
• Carbohydrate Sequence
• Nucleotide Sequence

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Confusion of Ontology and Epistemology

• Physical Entity
• Chemical Entity
• Chemical Chemical
• Viewed Viewed
• Structurally Functionally

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Confusion of Ontology and Epistemology

• the hydraulic equation
• BP COPVR
• arterial blood pressure is directly proportional
  to the product of blood flow (cardiac output, CO)
  and peripheral vascular resistance (PVR).
• Cardiac Output in UMLS A Finding

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UMLS-Semantic Types

• blood pressure is an Organism Function,
• cardiac output is a Laboratory or Test Result or
  Diagnostic Procedure
• BP COPVR thus asserts that
• blood pressure is proportional either to a
  laboratory or test result or to a diagnostic
  procedure

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The goal

• Formulate clear principles for building
  ontologies
• Reconstitute the UMLS Semantic Types on the basis
  of these principles

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Zusammenarbeit mit der National Library of
Medicine

• Revision der UMLS Semantic Types und der Gene
  Ontology

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GO the Gene Ontology

• 3 large telephone directories of standardized
  designations for gene functions and products
• organized into hierarchies via is_a and part_of

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GO

• can in practice be used only by trained
  biologists (with know how)
• whether a GO-term truly stands in the is_a
  relation depends e.g. on the type of organism
  involved
• glycosome is part-of cytoplasm only for
  Kinetoplastidae
• Computers have no counterpart of such
  context-dependent know-how

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GO divided into three disjoint term hierarchies

• the cellular component ontology,
• e.g. flagellum, chromosome, cell
• the molecular function ontology,
• e.g. ice nucleation, binding, protein
  stabilization
• the biological process ontology,
• e.g. glycolysis, death

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Definition of Molecular Function

• the action characteristic of a gene product.
• On March 2003 all nodes in the Molecular
  Function ontology (except the root) had
  activity added to their names
• -- confusion of function with functioning
• (how deal with dormant/suppressed functions?)

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Definition of Biological Process

• A phenomenon marked by changes that lead to a
  particular result, mediated by one or more gene
  products

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How are the 3 ontologies related?

• Function the action characteristic of a gene
  product.
• Process phenomenon marked by changes that lead
  to a particular result, mediated by one or more
  gene products
• No part-whole relations across ontologies?

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The GO isa relatio

• in its intended meaning indicates a necessary
  relationship.
• That is, when we say eukaryotic cell isa cell,
  we mean that every eukaryotic cell is a cell.
• Confusion of necessarily, universally, and
  permanently
• (No time in GO)

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part_of

• The Relation part-of The intended meaning of
  part-of as explained in the GO Usage Guide is
  can be a part of, not is always a part of

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Uses of part_of

• membrane part-of cell, intended to mean a
  membrane is a part-of any cell
• flagellum part-of cell, intended to mean a
  flagellum is part-of some cells
• replication fork part-of cell cycle, intended
  to mean a replication fork is part-of the
  nucleoplasm only during certain times of the cell
  cycle
• regulation of sleep part-of sleep, should be
  corrected to regulation of sleep is co-located
  with and is causally involved with the sleep
  process.

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Bodies and Bodily Systems
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INTEGUMENTARY (SKIN) SYSTEM
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MUSCULO-SKELETAL SYSTEM
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CONNECTIVE SYSTEM
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The Connective System

• The connective system contains all the bona fide
  boundaries in the interior of the body the
  membranes and layers of fat which create an
  internal framework of support for the organs
• This system performs active work by maintaining
  the internal sub-environments in the necessary
  conditions

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DIGESTIVE SYSTEM
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RESPIRATORY SYSTEM
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URINARY SYSTEM
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IMMUNE SYSTEM
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CIRCULATORY SYSTEM
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CIRCULATORY SYSTEM (Principal Organs)
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NERVOUS SYSTEM
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The autonomic part of the nervous system

• This is the oldest part of the nervous system
  from the standpoint of evolution. It regulates
  the vegetative functions of the body.
• Vegetative means
• automatic, not dependent on ones mind.

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Example

• I decide to run. I can decide to start or stop
  running because running is controlled by the
  somatic part of the nervous system.
• BUT when Im running my heart is beating more
  quickly because my muscles need more oxygen for
  their work
• The autonomous part of the nervous system is
  responsible for these changes.
• You cannot decide to start or stop digesting the
  food that is already in your stomach
• Digestion and heart-beat are vegetative processes

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The autonomous part of the nervous system
(regulatory links to other systems)
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ENDOCRINESYSTEM
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The endocrine system

• is like a system of the radio transmitters which
  are broadcasting to the every cell of the body.
• Their waves are hormones.
• The medium of transmission is the blood.
• The cell have receivers specific receptors
  for particular hormones

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ENDOCRINE SYSTEM
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IMMUNE SYSTEM
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Bodily Systems are Component Parts of Bodies
respiratory
digestive
circulatory
immune
skeletal
musculatory
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A system for keeping your tools safe
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A system for keeping your jewels safe
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Bodily Systems interconnect
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plus NERVOUS SYSTEM (Regulatory Links)
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Thus bodily systems are separated from each other
by fiat boundaries
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MUSCULO-SKELETAL SYSTEM
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Why one system?
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Rather than two
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MUSCLE SYSTEM
SKELETAL SYSTEM
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because without muscle the skeletal system would
fall apart and without bone the muscles would
have nothing to attach themselves
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Why talk of one nervous system rather than two?

• Is the boundary between the autonomous and
  vegetative system porous
• (can you train yourself to control vegetative
  processes?)

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Bodily systems are like arms and legs
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but the fiat boundaries separating them from
their surroundings are much more complicated
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plus NERVOUS SYSTEM (Regulatory Links)
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Where to fit bodily systems into an ontology?
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Bodily systems are SNAP entities
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Substances and processes exist in time in
different ways
substance
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SNAP and SPAN

• Substances and processes
• Continuants and occurrents
• In preparing an inventory of reality
• we keep track of these two different categories
  of entities in two different ways

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Need for different perspectives

• Not one ontology, but a multiplicity of
  complementary ontologies
• Cf. Quantum mechanics particle vs. wave
  ontologies

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SNAPshot Video (SPAN)ontology
ontology
substance
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SNAP and SPAN

• stocks and flows
• commodities and services
• product and process
• anatomy and physiology
• synchrony and diachrony

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SNAP and SPAN

• SNAP entities
• - have continuous existence in time
• - preserve their identity through change
• - exist in toto if they exist at all
• SPAN entities
• - have temporal parts
• - unfold themselves phase by phase
• - exist only in their phases/stages

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SPQR entities

• States, powers, qualities, roles
• functions, dispositions, plans, shapes
• SPQR entities are all dependent on substances

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SOME SYSTEMS ARE SPQR ENTITIES

• legal systems
• languages (as systems of competences)
• religions (as systems of beliefs)

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The SPAN Ontology
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SNAP ontology

• many sharp boundaries
• SPAN ontology
• many smeered boundaries
• Fiat boundaries can be drawn in each
• (Cf. Ingvars theory of 4-D shapes)

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Mesoscopic reality

• is divided at its joints into substances
• animals, bones, rocks, potatoes
• and into parts of substances
• ARMS
• LEGS
• and
• BODILY SYSTEMS

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Processes

• Processes merge into one another
• Process kinds merge into one another
• few clean joints either between instances or
  between types

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boundaries are mostly fiat
everything is flux
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SNAP Entities existing in toto at a time
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Three kinds of SNAP entities

• Substances
• SPQR entities
• Spatial regions, Contexts, Niches

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Functions The function of the heart is to pump
blood
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SNAP
Fiat part of substance Extremity (hand,
arm) Bodily System
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SPAN Entities extended in time
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SPAN Entities extended in time
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SPAN Entities extended in time
Functioning The hearts pumping of blood
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Granularity
spatial region
substance
parts of substances are always substances
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Granularity
spatial region
substance
parts of spatial regions are always spatial
regions
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Granularity
process
parts of processes are always processes
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MORAL

• Relations crossing the SNAP/SPAN border are never
  part-relations

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Relations crossing the SNAP/SPAN border are never
part-relations
Johns life
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How do you know whether an entity is SNAP or SPAN?
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problem cases

• traffic jam
• forest fire
• anthrax epidemic
• hurricane Maria
• waves
• shadows

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forest fire

• an object (complex substance)
• Compare a pack of monkeys jumping from tree to
  tree
• the Olympic flame
• a process or a thing?
• anthrax spores are little monkeys

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System (OED)

• An organized or connected group of objects.
• A set or assemblage of things connected,
  associated, or interdependent, so as to form a
  complex unity a whole composed of parts in
  orderly arrangement according to some scheme or
  plan

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Roman Ingarden

• Theory of Relatively Isolated Systems

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Roman Ingarden

• organisms, in order to be able to sustain
  themselves effectively as identical through time,
  must be at least in some respects bounded off
  from the surrounding world and partially isolated
  or, better, shielded from it.

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Each complex multi-cellular organism

• is a relatively isolated causal system which is
  organized in modular fashion in such a way as to
  contain within itself numerous further relatively
  isolated causal systems on successively lower
  levels.
• The latter are hierarchically ordered and at the
  same time both partially interconnected (they
  collaborate in their functioning) and also
  partially segregated from each other via
  coverings or membranes which protect their
  interiors from certain external influences and
  also allow other kinds of influences and
  substances to pass through them.

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MODULARITY Bodily Systems

• can be viewed at different levels of granularity

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NERVOUS SYSTEM
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Relative Isolation

• The container formed by the skin or hide around a
  bodily system may be topologically highly
  complicated

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The whole body

• is surrounded by a well-defined enclosurefor
  man this is the skin, for the majority of
  animalsthe hide.
• The skin or hide is itself a complex organ which
  is composed of many layers and has many functions
  in the life-process, precisely because it forms
  the boundary between the body and the external
  world. Thus it is a permeable membrane, which
  participates in the expulsion of water and
  waste-products.

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Organisms

• order to be able to sustain themselves
  effectively as identical through time, must be at
  least in some respects bounded off from the
  surrounding world and partially isolated or
  shielded from it.

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Each multi-cellular organism

• is a system of relatively isolated causal systems
  organized in modular fashion in such a way as to
  contain within itself further relatively isolated
  causal systems on successively lower levels.
• The systems within this modular hierarchy are
  both partially interconnected (they collaborate
  in their functioning)
• and also partially segregated via coverings or
  membranes which protect their interiors from
  certain external influences and also allow other
  kinds of influences and substances to pass
  through them

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Bodily systems

• are not absolutely closed off from each other
  they are partially open and partially shielded.
• There are paths between them along which a
  certain restricted spectrum of causal influences
  and substances may flow.
• Each sense organ is a partially open system
  which is attuned to a special selection of
  outside processes and at the same time also
  shielded in other respects.

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Two kinds of fiat boundaries
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Bodily systems have fiat boundaries
Endocrine system unified as a system of scattered
radio transmitters is unified through
transmitted waves
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What gives a bodily system its unity?

• Why do we divide up the bodily systems in this
  way rather than in that?
• Because each performs some CRITICAL FUNCTION if
  functioning ceases the organism will die

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Digital Anatomist

• Tissue
• is an organ part,
• which consists of similarly specialized cells
  and intercellular matrix,
• aggregated according to genetically determined
  spatial relationships.

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Millikan

• An item X has proper function F if and only if
• (i) X is a reproduction of some prior item that,
  because of the possession of certain reproduced
  properties, actually performed F in the past
• (ii) X exists because of this performance.

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Critical Element

• An item X is a critical element for an organism Y
  if and only if
• (i) X is an element of Y
• (ii) there is a proper function F of X
• (iii) X performs F and no other part of Y
  performs F
• (iv) the continuing to exist of the organism Y is
  causally dependent on the continued performance
  by X of F.

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Definition of Bodily System

• X is a bodily system for organism Y if and only
  if
• (i) X is a critical element for Y
• (ii) X is not a proper part of any larger
  critical element for Y.

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Evidence

• The visual system is not classified in medical
  science as a bodily system in its own right
• (It is a module of the nervous system)
• because it is non-critical
• part of the bodys redundancy

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Problems

• Prostheses (Heart pacemakers )
• Are they parts of the body or analogous to
  foreign bodies in the interior of the body
• Solve this problem by adding condition of
  reciprocal dependence
• (Pacemaker does not change in light of its
  functioning and of the functioning of associated
  systems)

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Problems

• Kidney dialysis
• (is the operation of the kidney a critical
  function?)
• Cryptobiosis the condition that some creatures
  (e.g. shrimp) surivive in after drying out and
  shutting down
• this means that they can survive even though
  their bodily systems are not functioning

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Problems

• Reproductive system
• Not critical to the life of the individual
• critical to the life of the species
• of the population?
• Mother and baby share an endocrine system?

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Problems

• Maximality
• Is the endocrine system one system or seven?
• Rosse Digital Anatomist

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Questions

• If these systems are critical, how could they
  evolve?
• By splitting from prior systems?

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Questions

• Does every system contain at least one organ?
• How is organ to be defined?
• Are muscles organs?
• Are bones organs?

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Questions

• How many of these systems are present in all
  organisms?
• In all multi-cellular organisms?
• In all vertebrates?
• How many of these systems have analogues in other
  sorts of systems
• (antivirus software in computer systems)

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Questions

• In a good parsing of the body into bodily systems
  
• should all bodily systems be mereologically
  disjoint?
• should the parsing exhaust the body?

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Systems are SPAN entities
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The Monarchic System of Government
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The Monarchic System of Government