pisanelli

Slide1: 

A Journey through the Cavities of the Human Body Domenico M. PISANELLI CNR – Laboratory of Applied Ontology, Rome, Italy

Slide2: 

A Journey through the Cavities of the Human Body an ontology of Body Spaces & Junctions Domenico M. PISANELLI CNR – Laboratory of Applied Ontology, Rome, Italy

Slide3: 

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

Slide4: 

acknowledgements: Massimo BATTAGLIA M.D. Ivano APOLLONI … and all the LOAkers

sources for the ontology of BSp&J:: 

sources for the ontology of BSp&J: UMLS FMA

Slide7: 

fragment of UMLS Semantic Network

Slide8: 

Body Space or Junction Body Space Body Junction quiddities

some quiddities:: 

some quiddities: cavities inside joint Synovial cavity of vertebral arch joint junctions between cavities Esophagogastric Junction

some Body Spaces:: 

some Body Spaces: Lumen of colon Ocular orbit Perichoroidal space Laryngeal cavity

some Body Spaces:: 

some Body Spaces: Cavity of pulmonary alveolus Hepatic perisinusoidal space Interalveolar pore

some Junctions:: 

some Junctions: Right neurocentral junction of eleventh thoracic vertebra Thoraco-abdominal junction Labial commissure of mouth

Slide13: 

problems with UMLS false IS_A assignments Junctions, Borders and Joints collapsed in a single cathegory

Slide14: 

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

Slide15: 

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)

Slide16: 

boundaries bona-fide boundaries fiat boundaries (Smith and Varzi)

Slide17: 

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)

Slide18: 

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)

Slide19: 

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)

Slide20: 

bona-fide boundary

Slide21: 

fiat boundary

Slide23: 

junctions bona-fide junctions fiat junctions

Slide24: 

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

Slide25: 

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

Slide26: 

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

Slide27: 

an ontology of body junctions

Slide28: 

Body junction Bona-fide junction Confluence Junction between cavities Junction between anatomical structures Commissure Border Fiat junction Conventional anatomical surface Conventional anatomical line an ontology of body junctions

Slide29: 

Body space Lumen Cavity Cavity inside organ Cavity inside joint Orifice an ontology of body spaces

some lumina:: 

some lumina: Lumen of aorta Lumen of urinary bladder Lumen of esophagus

Slide31: 

Lumen of esophagus http://www.health.utah.edu

Slide32: 

some examples of macroscopic cavities inside organs Cavity of left atrium Cavity of incisor tooth

Slide33: 

Cavity of left atrium http://www.vh.org

Slide34: 

Cavity of incisor tooth http://animated-teeth.com

Slide35: 

some examples of microscopic cavities inside organs Cavity of endoplasmic reticulum vesicle Cavity of lysosome

Slide36: 

Cavity of endoplasmic reticulum vesicle 5 Cavity of lysosome 7 http://www.sci.port.ac.uk

some cavities inside joint:: 

some cavities inside joint: Carpal tunnel Synovial cavity of hip joint

some orifices:: 

some orifices: Pyloric orifice Orifice of parotid duct Orifice of prostatic duct Tympanic orifice of right auditory tube

Slide41: 

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

sources for ROME:: 

sources for ROME: ON 9 GALEN-CORE UMLS UMLS-SN HL7 reference model

Slide48: 

is it a realist ontology? objective reality representation subjectivity taken into account anatomy diagnosis

Slide49: 

what is needed a refined mereological treatment a good lawyer