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VT
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SNAP and SPAN:with 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 WebStandardisierte Terminologien
UMLSSNOMEDICD-10Gene OntologyDigital Anatomistusw.
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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
Unified 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 NetworkSemantic Network
bestehend aus 134 Semantic TypesSemantic 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 ConceptFunctional ConceptQualitative ConceptQuantitative ConceptSpatial Concept
Body Location or RegionBody Space or JunctionGeographic AreaMolecular Sequence
Amino Acid SequenceCarbohydrate SequenceNucleotide Sequence
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BREMEN
is an Idea or Concept
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Idea or ConceptFunctional ConceptQualitative ConceptQuantitative ConceptSpatial Concept
Body Location or RegionBody Space or JunctionGeographic AreaMolecular Sequence
Amino Acid SequenceCarbohydrate SequenceNucleotide 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 OntologyBetter: 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 processesContinuants and occurrents
In preparing an inventory of realitywe 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
t i m
e
process
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SNAPshot Video (SPAN)ontology ontology
substance
t i m
e
process
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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
t1
t3
t2
here time exists outside the ontology, as an index or time-stamp
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each SNAPi section through reality
includes everything which exists (present tense)
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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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FunctionsThe function of the
heart is to pump blood
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SNAP
Fiat part of substanceExtremity (hand, arm)
Bodily System
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SPAN: Entities extended in time
SPANEntity extended in time
Portion of Spacetime
Fiat part of process *First phase of a clinical trial
Spacetime worm of 3 + Tdimensions
occupied by life of organism
Temporal interval *projection of organism’s life
onto temporal dimension
Aggregate of processes *Clinical trial
Process[±Relational]
Circulation of blood,secretion of hormones,course of disease, life
Processual Entity[Exists in space and time, unfolds
in time phase by phase]
Temporal boundary ofprocess *
onset of disease, death
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SPAN: Entities extended in time
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SPAN: Entities extended in time
FunctioningThe heart’s 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
John’s lifesubstance John
physiological processes
sustaining in existence
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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
Substances
Qualities, Roles,Functions…
Space Regions
Processuals
Processes
Events
Space-Time Regions
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Signatures of meta-relations
SNAP Component SPAN Component
Substances
Qualities, Roles,Functions…
Space Regions
Processuals
Processes
Events
Space-Time Regions
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Signatures of meta-relations
SNAP Component SPAN Component
Substances
Qualities, Roles,Functions…
Space Regions
Processuals
Processes
Events
Space-Time Regions
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Signatures of meta-relations
SNAP Component SPAN Component
Substances
Qualities, Roles,Functions…
Space Regions
Processuals
Processes
Events
Space-Time Regions
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Signatures of meta-relations
SNAP Component SPAN Component
Substances
Qualities, Roles,Functions…
Spatial Regions
Processuals
Processes
Events
Space-Time Regions
participation
realization
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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
SNAP
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execution
expression
exercise
realization
application
course
SPAN
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Material examples:
performance of a symphonyprojection of a filmexpression of an emotionutterance of a sentenceapplication of a therapycourse of a diseaseincrease of temperature
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How are SNAP and SPAN joined together?
Semantic roles …
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SNAP-SPAN
Participation
Perpetration (+agentive)
Initiation
Perpetuation
Termination
Influence
Facilitation
Hindrance
Mediation
Patiency(-agentive)
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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)