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Ontologie-basierte Qualitätssicherung

medizinischer Terminologien

Barry Smith

with thanks to Werner Ceusters, Anand Kumar and Cornelius

Rosse

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Problems with UMLS

Each is a ‘fusion’ of several source vocabularies, some of dubious quality

They were fused without an ontological system being established first

They contain circularities, taxonomic gaps, and unnatural ad hoc determinations

They are representations of concepts, not of reality

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UMLS Metathesaurus traps

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Problem: Confusion of concepts and entities in reality

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Blood Pressure Ontology

The hydraulic equation:

BP = CO*PVR

arterial blood pressure (BP) is directly proportional to the product of blood flow (cardiac output, CO) and peripheral vascular resistance (PVR).

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UMLS-Semantic Types:

blood pressure is an Organism Function,

cardiac output is a Laboratory or Test Result or Diagnostic Procedure

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UMLS-Semantic Types:

BP = CO*PVR thus asserts that

blood pressure is proportional either to a laboratory or test result or to a diagnostic procedure

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SNOMED-CT

900,000 ‘concepts’

Description Logic infrastructure

NIH + NHS gesegnet

College of American Pathologists

SNODENT

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Confused treatment of is_a and part_of

beide_Hoden is_a Hoden

beide_ Gebärmuttern is_a Gebärmutter

teilweise_Entfernung_der_Blase

is_a Entfernung_ der_Blase.

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Confused treatment of is_a and part_of

Halbextraktion_aus_Steißlage is_a Extraktion_aus_Steißlage

Extraktion_aus_Steißlage is_a vollständige_Steißgeburt

____________________________

Halbextraktion_aus_Steißlage is_a vollständige_Steißgeburt

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Confused treatment of objects and processes

diagnostische_endoskopische_Untersuchung_eines_Mediastinums_NOS

is_a Mediastinoskop.

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Confusion of object with knowledge about object

Kontrazeption is_a funktionaler_Befund

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Just plain confusion

labial vein is_a vein of head

labial vein is_a vulval vein

Dupuytren-Krankheit,_

Knoten_ohne_Kontraktur

is_a

Kontraktur_der_Palmarfaszie

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Problems with logical combination

‘Veterinary proprietary drug AND/OR biological’ *

Such terms not designate natural kinds. (Which biological classes exist is not a matter of logical combination of terms or concepts)

*has 2532 children in SNOMED-CT

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Confusion of part_of and overlaps_with

Struktur_des_Nervus_tibialis

is_a

Oberschenkelteil

Struktur_des_Nervus_tibialis

is_a

Unterschenkelstruktur

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Missed subsumption detection

Missing: is_a neoplasm of heart

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Are these just isolated examples of errors?

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Why Description Logicsare not enough

SNOMED-RT

amputation of toe is_a amputation of foot

Hahn-Schulz improvements re part-of in SNOMED-CT

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National Cancer InstitutecaCORE

Cancer Informatics Infrastructure Backbone

caBIO Cancer Bioinformatics Infrastructure Objects:Biomedical objects to facilitate the communication and integration of information from the various initiatives supported by the NCICB

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caBIO architecture

Connectivity at programming interface level

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Instead of building an ontology of cancer

the NCI builds an ontology (or a ‘model’) of the data in the NCI’s own computers

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NCI Thesaurus

a biomedical thesaurus created specifically to meet the needs of the NCI

semantically modeled cancer-related terminology built using Description Logic

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Search for “cancer”

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Missed subsumption detection

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Recall SNOMED confusion of ‘part’ and ‘structure’

Struktur_des_Nervus_tibialis

is_a

Oberschenkelteil

Struktur_des_Nervus_tibialis

is_a

Unterschenkelstruktur

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Confusion of ‘part’ and ‘structure’ and ‘system’ and

‘substance’

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NCI Thesaurus Root concepts

Anatomic Structure, Anatomic System, or Anatomic Substance ?Or ? Does the NCI not know to which categoryAny item classified there belongs ?Anatomic Substance ? If yes, why is geneproduct not subsumed by it ? If no, why aredrugs and chemicals not subsumed by it ?

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Conceptual entity

Definition: none

Semantic type: – Conceptual entity– Classification

Subconcepts:– Action:

• definition: action; a thing done

– And: • Definition: an article which expresses the relation of

connection or addition, used to conjoin a word with a word, ...

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Action is_a Conceptual Entity

And is_a Conceptual Entity

Swimming is healthy and contains 8 letters

Conceptual entity

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Definition of “cancer gene”

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NCI Thesaurus architecture

Disease

BreastBreast neoplasmDisease-has-associated-anatomy

ISA

Findings-And-Disorders-Kind Anatomy-Kind

“Formal subsumption” or

“inheritance”

“Associative” relationships providing

“differentiae”

“Kinds” restrict the domain and range of

associative relationships

What diseases have a diameter of over 3 cm ?

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Confusion of objects and the states in which they participate

Disease

BreastBreast neoplasmDisease-has-associated-anatomy

ISA

Findings-And-Disorders-Kind Anatomy-Kind

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Cancer Data Standards Repository (caDSR)

“One of the problems confronting the biomedical data management community is the panoply of ways that similar or identical concepts are described.”

The real problem is that concepts are being described. 

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Problems with the concept orientation

Ad hoc readings of statements of the type C1-relationship-C2– California is-part-of United States //

California isa name

Concepts do not necessarily correspond to anything in reality: sorcerer, unicorn, leprechaun, ...

Language can make strings of words look as if it were terms– Middle lobe of left lung

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“Ontology”In information science:

– An ontology is a description (like a formal specification of a program) of the concepts and relationships that can exist for an agent or a community of agents.

In philosophy:

– Ontology is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality.

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Why are conceptsnot enough?

– only by looking at referents in reality can we work out how the concepts used by different communities relate to each other

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Ontology as Bridge for Understanding Cancer Information

Diseases Pathological Processes Body site for diseases Diseases by staging Risk factors

Anatomy Is-a, part-of Granular relationship

Biological Processes Ontology Classification Swiss-Prot

proteins Annotation: function, structure, mutation

SNOMED

GO

FMA

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Levels of granularity inbiomedical ontology

Population environment screening

Person Race, age, disease, symptom

ADL, working, treatment, prevention

Organ Liver, lung, organ part, sign Heart beat, digestion, surgery

Tissue Elasticity,Turgor, Strength Resorption, protection

Cell Bone cell, Alveolar cellCell size, bacterium

Fagocytosis, Cell growth, Reparation, hormone production

Subcellular Cell membrane, ProteinDNA, Oncogene, Protooncogene,Virus, oncogenic molecule

TranscriptionSplicingMutationGene regulation

Granularity level Continuants Occurrents

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SWISS-PROT and OMIM databases have little capability to support reasoning which crosses levels of granularity

also, like SNOMED and GO, they offer no facility for reasoning about time and instances

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TNM Staging Information

– T1: The tumor invades the submucosa, the second layer of the large intestine.

– T2: The tumor invades the muscularis propria.

…

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We need an ontological framework with the facility to deal with instance-based information

drawn from Patient Records

TNM Staging Information Risk factors (Age, Family history)Localization of Tumor (Organ affected,

Tissues involved)Pathology (Gross and Miscroscopic

pathology, Vessels involved, Nerves involved, Cell types, Nuclear characteristics)

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Basic Formal Ontology glues the whole thing together

at different levels of granularity, from molecular to whole organism level

at different stages in time