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A Journey throughthe Cavities of the Human Body

Domenico M. PISANELLI

CNR – Laboratory of Applied Ontology, Rome, Italy

IMIA 2005

A Journey throughthe Cavities of the Human Body

an ontology of Body Spaces & Junctions

Domenico M. PISANELLI

CNR – Laboratory of Applied Ontology, Rome, Italy

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Laboratory of Applied Ontology of CNR-ISTC www.loa-cnr.it

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acknowledgements:

Massimo BATTAGLIA M.D.

Ivano APOLLONI

… and all the LOAkers

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sources for the ontology of BSp&J:

UMLS FMA

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Body Spaceor Junction

Body Space

Body Junction

quiddities

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some quiddities:

cavities inside joint

Synovial cavity of vertebral arch joint

junctions between cavities

Esophagogastric Junction

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some Body Spaces:

Lumen of colon

Ocular orbit

Perichoroidal space

Laryngeal cavity

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some Body Spaces:

Cavity of pulmonary alveolus

Hepatic perisinusoidal space

Interalveolar pore

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some Junctions:

Right neurocentral junction of eleventh thoracic vertebra

Thoraco-abdominal junction

Labial commissure of mouth

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problems with UMLS

• false IS_A assignments

• Junctions, Borders and Jointscollapsed in a single cathegory

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false IS_A assignments

Lumen of bronchus IS_A Bronchi

Ocular orbit IS_A Eye

Finger Joint IS_A Wrist

Canal of Guyon IS_A Wrist

Esophagogastric Junction IS_A Gastrointestinal System

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Junctions, Borders and Joints

Junctions are boundaries between different anatomical structures (e.g. abdominopelvic junction)

Borders delimit anatomical structures (e.g. inferior border of tympanic plate)

Joints are systems(e.g. knee)

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boundaries

• bona-fide boundaries

• fiat boundaries

(Smith and Varzi)

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bona-fide boundaries

“Inner boundaries involving spatial discontinuity (holes, fissures, slits) or qualitative heterogeneity (of material constitution, texture, electric charge) we shall call bona fide boundaries.”

(Smith and Varzi)

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bona-fide boundaries

“The distinction between fiat and bona fide boundaries applies not only to inner boundaries but to outer boundaries, too. The surfaces of extended objects such as planets or tennis balls are of the bona fide sort.”

(Smith and Varzi)

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fiat boundaries

“National borders, by contrast, as well as county- and property-lines and the borders of postal and electoral districts, provide examples of outer boundaries of the fiat sort, at least in those cases where they lie skew to any qualitative differentiations or spatial discontinuities (coastlines, rivers) in the underlying territory.”

(Smith and Varzi)

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bona-fide boundary

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fiat boundary

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junctions

• bona-fide junctions

• fiat junctions

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bona-fide borders or junctions

Free border of nail of third toe

Posterior border of vomer

Neurocentral junction of lumbar vertrebra

Neurocentral junction of cervical vertrebra

Cerebellopontine Angle

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Cerebellopontine Angle

http://www.mrcophth.com

Anatomy of the cerebellopontine angle showing the relationship of the various cranial nerves. 1.Sensory root of trigeminal nerve 2.Pons 3.Vestibulocochlear nerve 4.Facial nerve 5.Abducent nerve 6.Medulla oblongata 7.Motor root of trigeminal nerve 8.Basilar sulcus

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fiat junctions

Reid’s base line

http://education.yahoo.com/reference/gray/illustrations/figure?id=1193

http://education.yahoo.com/reference/gray/illustrations/figure?id=1193

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an ontology of body junctions

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Body junction

Bona-fide junctionConfluenceJunction between cavitiesJunction between anatomical structuresCommissureBorder

Fiat junctionConventional anatomical surfaceConventional anatomical line

an ontology of body junctions

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Body space

Lumen

CavityCavity inside organ

Cavity inside joint

Orifice

an ontology of body spaces

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some lumina:

Lumen of aorta

Lumen of urinary bladder

Lumen of esophagus

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Lumen of esophagus

http://www.health.utah.edu

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some examples of macroscopic cavities inside organs

Cavity of left atrium

Cavity of incisor tooth

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Cavity of left atrium

http://www.vh.org

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Cavity of incisor tooth

http://animated-teeth.com

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some examples of microscopic cavities inside organs

Cavity of endoplasmic reticulum vesicle

Cavity of lysosome

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Cavity of endoplasmic reticulum vesicle

5

Cavity of lysosome7

http://www.sci.port.ac.uk

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some cavities inside joint:

Carpal tunnel

Synovial cavity of hip joint

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some orifices:

Pyloric orifice

Orifice of parotid duct

Orifice of prostatic duct

Tympanic orifice of right auditory tube

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Reference

Ontology for

MEdicine

version 3.2• developed in RACER v. 1-17-20• can be exported in DAML+OIL, OWL• can be browsed by Rice, OilEd, Protégé

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sources for ROME:

ON 9 GALEN-CORE UMLS UMLS-SN HL7 reference model

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is it a realist ontology?

• objective reality representation

• subjectivity taken into account

anatomy

diagnosis

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what is needed

• a refined mereological treatment

• a good lawyer

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