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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