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

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

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

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

  2. 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

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

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

  5. sources for the ontology of BSp&J: • UMLS • FMA

  6. fragment of UMLS Semantic Network

  7. Body Space Body Space or Junction Body Junction quiddities

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

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

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

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

  12. problems with UMLS • false IS_A assignments • Junctions, Borders andJoints • collapsed in a single cathegory

  13. 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

  14. 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)

  15. boundaries • bona-fide boundaries • fiat boundaries • (Smith and Varzi)

  16. 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)

  17. 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)

  18. fiatboundaries “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)

  19. bona-fide boundary

  20. fiat boundary

  21. junctions • bona-fide junctions • fiat junctions

  22. 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

  23. Cerebellopontine Angle 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 http://www.mrcophth.com

  24. 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

  25. an ontology of body junctions

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

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

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

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

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

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

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

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

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

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

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

  37. 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

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

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

  40. what is needed • a refined mereological treatment • a good lawyer

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