1 vt. 2 snap and span: with a preamble on medical ontology barry smith

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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)