VT

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VT
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SNAP and SPANwith a preamble on Medical Ontology

• Barry Smith

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IFOMIS

• Institute for Formal Ontology and Medical
  Information Science
• Faculty of Medicine
• University of Leipzig
• http//ifomis.de

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Aristotle
Der erste Ontologe

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Eine biologische Ontologie
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Linné

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

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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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Current Solutions to the Babel Problem

• Semantic Web
• Description Logic works well precisely for
  ontologies involving simple taxonomic trees
• Does NOT work well when time is involved
• when A is part-of B at t1 but not at t2
• when A is-a B at t1 but not at t2

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Current Solutions to the Babel Problem

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

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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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Central terminological switchboard

• 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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Examples of Source-Terminologies

• 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 Melletus 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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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

• help to improve standardizations through
  constructive criticism based on robust
  ontological principles

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UMLS Metathesaurus

• How to navigate?
• How to integrate the source terminologies?
• 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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BREMEN

• 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

• Chemical Entity
• Chemical Viewed Structurally
  Chemical Viewed Functionally
• Inorganic Chemical Organic Chemical
  Pharmacologic Substance

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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 relation

• 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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The goal

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

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Need to find ways to deal with (space and) time
in medical informatics

• Need to move away from Description Logic-inspired
  focus on simple taxonomic trees and simple
  partonomies
• Towards Dynamic Ontology
• Better towards Synchronic and Diachronic
  Ontology
• (Anatomy and Physiology)
• (Email ToC vs. Graph of Email Throughput)

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Need to find ways to deal with (space and) time
in medical informatics

• Functions vs. Realizations of Functions
• Function is still there even when not being
  realized
• need to be clear about the distinction between
  continuants and occurrents

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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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SNAP and SPAN
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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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Substances and processes exist in time in
different ways
substance
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SNAPshot Video (SPAN)ontology
ontology
substance
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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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Many SNAP Ontologies
t3
t2
t1
here time exists outside the ontology, as an
index or time-stamp
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each SNAPi section through reality
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mereology works without restriction (parthood is
everywhere determinate) in every SNAPi ontology
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SNAP Entities existing in toto at a time
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Three kinds of SNAP entities

• Substances
• Dependent SNAP entities (qualities, functions,
  roles, powers )
• Spatial regions, Contexts, Niches

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How to help GO

• Functions are continuants (SNAP entities)
• Functionings (the exercises of functions, the
  activities of GO) are occurrents (SPAN entities)

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Functions The function of the heart is to pump
blood
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(No Transcript)
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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 are SNAP and SPAN joined together?

via meta-ontological relations
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Perpetration

• A substance perpetrates an action (direct and
  agentive participation in a process)
• The referee fires the starting-pistol
• The captain gives the order

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Initiation

• A substance initiates a process
• The referee starts the race
• The attorney initiates the process of appeal

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Signatures of meta-relations
SNAP Component
SPAN Component
Processuals
Substances
Processes
Qualities, Roles, Functions
Events
Space Regions
Space-Time Regions
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Signatures of meta-relations
SNAP Component
SPAN Component
Processuals
Substances
Processes
Qualities, Roles, Functions
Events
Space Regions
Space-Time Regions
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Signatures of meta-relations
SNAP Component
SPAN Component
Processuals
Substances
Processes
Qualities, Roles, Functions
Events
Space Regions
Space-Time Regions
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Signatures of meta-relations
SNAP Component
SPAN Component
Processuals
Substances
Processes
Qualities, Roles, Functions
Events
Space Regions
Space-Time Regions
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Signatures of meta-relations
SNAP Component
SPAN Component
Processuals
Substances
Processes
Qualities, Roles, Functions
Events
Spatial Regions
Space-Time Regions
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Realization (role, function ? process)

• The most general relation between a dependent
  SNAP entity (role, function, power) and a process
• The power to legislate is realized through the
  passing of a law
• The role of antibiotics in treating infections
  is realized via the killing of bacteria

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Realization (SNAP-SPAN)

• the execution of a plan, algorithm
• the expression of a function
• the exercise of a role
• the realization of a disposition

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• plan
• function
• role
• disposition
• algorithm

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• execution
• expression
• exercise
• realization
• application
• course

SPAN
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Material examples

• performance of a symphony
• projection of a film
• expression of an emotion
• utterance of a sentence
• application of a therapy
• course of a disease
• increase of temperature

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How are SNAP and SPAN joined together?

Semantic roles
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SNAP-SPAN
Participation
Perpetration (agentive)
Influence
Patiency (-agentive)
Initiation
Termination
Facilitation
Perpetuation
Hindrance
Mediation
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How do you know whether an entity is SNAP or SPAN?
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problem cases

• forest fire
• anthrax epidemic
• hurricane Maria
• traffic jam
• ocean wave

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forest fire

• a process
• a pack of monkeys jumping from tree to tree and
  eating up the trees as they go
• the Olympic flame
• a process or a thing?
• (anthrax spores are little monkeys)