IMIA 2005 A Journey through the 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

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

IMIA 2005

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

IMIA 2005

acknowledgements:

Massimo BATTAGLIA M.D.

Ivano APOLLONI

… and all the LOAkers

IMIA 2005

sources for the ontology of BSp&J:

UMLS FMA

IMIA 2005

IMIA 2005fragment of UMLS Semantic Network

IMIA 2005

Body Spaceor Junction

Body Space

Body Junction

quiddities

IMIA 2005

some quiddities:

cavities inside joint

Synovial cavity of vertebral arch joint

junctions between cavities

Esophagogastric Junction

IMIA 2005

some Body Spaces:

Lumen of colon

Ocular orbit

Perichoroidal space

Laryngeal cavity

IMIA 2005

some Body Spaces:

Cavity of pulmonary alveolus

Hepatic perisinusoidal space

Interalveolar pore

IMIA 2005

some Junctions:

Right neurocentral junction of eleventh thoracic vertebra

Thoraco-abdominal junction

Labial commissure of mouth

IMIA 2005

problems with UMLS

• false IS_A assignments

• Junctions, Borders and Jointscollapsed in a single cathegory

IMIA 2005

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

IMIA 2005

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)

IMIA 2005

boundaries

• bona-fide boundaries

• fiat boundaries

(Smith and Varzi)

IMIA 2005

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)

IMIA 2005

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)

IMIA 2005

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)

IMIA 2005

bona-fide boundary

IMIA 2005

fiat boundary

IMIA 2005

IMIA 2005

junctions

• bona-fide junctions

• fiat junctions

IMIA 2005

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

IMIA 2005

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

IMIA 2005

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

IMIA 2005

an ontology of body junctions

IMIA 2005

Body junction

Bona-fide junctionConfluenceJunction between cavitiesJunction between anatomical structuresCommissureBorder

Fiat junctionConventional anatomical surfaceConventional anatomical line

an ontology of body junctions

IMIA 2005

Body space

Lumen

CavityCavity inside organ

Cavity inside joint

Orifice

an ontology of body spaces

IMIA 2005

some lumina:

Lumen of aorta

Lumen of urinary bladder

Lumen of esophagus

IMIA 2005

Lumen of esophagus

http://www.health.utah.edu

IMIA 2005

some examples of macroscopic cavities inside organs

Cavity of left atrium

Cavity of incisor tooth

IMIA 2005

Cavity of left atrium

http://www.vh.org

IMIA 2005

Cavity of incisor tooth

http://animated-teeth.com

IMIA 2005

some examples of microscopic cavities inside organs

Cavity of endoplasmic reticulum vesicle

Cavity of lysosome

IMIA 2005

Cavity of endoplasmic reticulum vesicle

5

Cavity of lysosome7

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

IMIA 2005

some cavities inside joint:

Carpal tunnel

Synovial cavity of hip joint

IMIA 2005

some orifices:

Pyloric orifice

Orifice of parotid duct

Orifice of prostatic duct

Tympanic orifice of right auditory tube

IMIA 2005

IMIA 2005

IMIA 2005

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

IMIA 2005

sources for ROME:

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

IMIA 2005

IMIA 2005

IMIA 2005

IMIA 2005

IMIA 2005

IMIA 2005

is it a realist ontology?

• objective reality representation

• subjectivity taken into account

anatomy

diagnosis

IMIA 2005

what is needed

• a refined mereological treatment

• a good lawyer

IMIA 2005