Relations in Anatomy and Image Ontologies Dirk Marwede Institute for Formal Ontology and Medical Information Science, Saarland University, Saarbruecken,
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Relations in Anatomy and Image Ontologies
Dirk Marwede
Institute for Formal Ontology and Medical Information Science, Saarland University, Saarbruecken, Germany
Department of Diagnostic Radiology, Leipzig University, Germany
Overview
• OBO relation ontology
• Anatomical Entities (Foundational Model of Anatomy, FMA)
– Relations in Anatomy Ontology
• Diagnostic Domain of Medial Imaging
– Image Entity Types
– Relations between Image Entity Types
– Building an Imaging Ontology (RadiO)
OBO relation ontology• Three types of binary relations
– < class, class >: e.g. is_a lung is_a lobular organ
– < instance, class >: instance_ofThis particular „lung“ instance_of class lung
– < instance, instance >: instance-level relation, e.g. part_ofThis particular instance of „right lower lobe of lung“ part_of this
particular instance of „right lung“
• Relations between classes represent what is general in reality. – class level:
• lung is_a lobular organ
– instance level: • this particular instance of lung is_a particular instance of lobular organ
Anatomical Ontologies (FMA)
• Class level-relations
– Structural Relationships between Anatomical Entities
• Boundary (bounded_by)
• Partonomy (part_of, regional_part_of, constitutional_part_of,…)
• Spatial Association
– Location (located_in, contained_in, adjecent_to)– Orientation (coordinate, laterality)– Connectivity (continuous_with, attached_to)
– Properties of Anatomical Entities:
• Dimension • Physical Properties
Image Ontologies
• Medical Imaging is concerned with diagnosing diseases.
• How we come from an image to a diagnosis?
– What kind of entities exist on the image and how do they relate to each other ?
• Image Entity Types
– Anatomical Image Entities
– Pathological Image Entities
– Image Features
dependent entities
Image Entity Types – Pathological Image Entity
• Which diseases can be inferred from images?
• What kind of image features do diseases have?
• Does a disease have in any case identical image features?
• If not, what are criteria which give evidence for a disease?
Pathological Image Entities
Features
Class-Level Relations between Image Entity Types
• C image_of C1 – basic relation holding between two continuants. – C is an anatomical or pathological image entity, C1 is an anatomical or
pathological entity.
• C has_feature C1 – a property relation holding between two continuants. – C is an anatomical or pathological image entity, C1 is a feature attribute.
• C has_location C1 – basic location relation holding between two continuants. – C is a visual feature or pathological image entity and C1 is an anatomical
image entity
Class-level relations between Image Entity Types and the FMA
has_feature
Anatomical Image Entityimage_of
Anatomical Entity (FMA)
Pathological Image EntityFeature
has_location
has_feature
has_location
Subrelations of has_feature Relations to annotate properties to anatomical and pathological image entities
Visual features
Morphology featuresc has_shape c1 at time of examination.
Adrenal gland [Anatomic Image Entity] has_shape round [Attribute:Shape] at time of examination
c has_size c1 at time of examination.T1 vertebral body [Anatomical Image Entity] has_size decreased in height [Attribute:Size] at time of examination
c has_composition c1 at time of examination.Tumor [Pathological Image Entity] has_composition cystic [Attribute:Composition] at time of examination
Signal features
c has_density c1 at time of examination.Liver [Anatomical Image Entity] has_density hypodense [Attribute:Density] at time of examination (or contrast phase).
General features
c has_amount c1 at time of examination.Pulmonary nodule [Pathological Image Entity] has_amount multiple [Attribute:Amount] at time of examination.
Use of Relations in Medical Imaging [Pathological Image Entity] has_feature [GeneralFeature]
Pulmonary embolism has_timing acute
[Pathological Image Entity] has_location [Anatomical Image Entity]has_feature [MorphologyFeature]
Mass has_location upper right lobe of right lunghas_margin spiculatedhas_shape roundhas_composition solid
evidence for malignant neoplasm
[Anatomical Image Entity] has_feature [MorphologyFeature]
Thyroid gland has_size enlarged
[Anatomical Image Entity] has_feature [MorphologyFeature][Pathological Image Entity] has_location [Anatomical Image Entity]
Hilar lymph node has_composition calcifiedGranuloma has_location upper lobe of left lung
evidence for tuberculosis has_timing old
Disease Ontology
Imaging Ontology
Imaging Ontology
Imaging Ontology ?
Disease Ontology
Conclusions• Entities of two domains
– Body Entities– Image Entities (dependent entities)
• Construction of an Imaging Ontology
– Image Entity Types
• Anatomical Image entities • Pathological Image Entities • Features
– Class level relations between Image Entity Types (and the FMA)
• Application Ontology (RadiO) for Diagnostic Domain
– Annotating image features to Anatomical and Pathological Image entities.
– Criteria for Pathological Image Entities: Tracking the use of relations between image entity types to discriminate image features of diseases.
• Separating/linking of an Imaging Ontology from/to other Ontologies of Diseases/Diagnosis.
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