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Conduits Between Anatomical Hierarchies in SNOMED

Conduits Between Anatomical Hierarchies in SNOMED. Dr. Jeff R. Wilcke Dr. Penny Livesay Dr. Larry Freeman. Digital Anatomist. “motivated by the belief that anatomy is the basis of all the biomedical sciences”

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Conduits Between Anatomical Hierarchies in SNOMED

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  1. Conduits Between Anatomical Hierarchies in SNOMED Dr. Jeff R. Wilcke Dr. Penny Livesay Dr. Larry Freeman

  2. Digital Anatomist • “motivated by the belief that anatomy is the basis of all the biomedical sciences” • “goal is to represent anatomy in a comprehensive and consistent way, which should meet the needs of all biomedical applications that require anatomical knowledge.” • Completely anthropocentric • http://sig.biostr.washington.edu/projects/da/ Veterinary Medical Informatics VMRCVM

  3. SNOMED History • College of American Pathologists • 1963 SNOP • Systematized Nomenclature of Pathology • 1974 SNOMED • Systematized Nomenclature of Medicine • 1993 “SNOVET” amalgamation • Tools inadequate to the task • 1999 SNOMED-RT • Tools are adequate, now someone must repair the content. Veterinary Medical Informatics VMRCVM

  4. SNOMED – SNOVET • SNOVET included two kinds of codes/concepts • Concepts and codes that were the same as SNOMED • Concepts and codes that were added for special veterinary needs Veterinary Medical Informatics VMRCVM

  5. SNOMED – SNOVET • Reconciliation outcomes • Concepts and codes that were the same, retained concept name and code • Concepts that were truly unique to veterinary medicine had their own codes and given a “V” flag so that they could easily be removed from human systems. • Concepts that were “analogues” were added as synonyms but not given their own unique codes and the synonym got a “V” flag. Veterinary Medical Informatics VMRCVM

  6. SNOMED III • Hand = T-D8700 • Forefoot = T-D8700V • Forepaw = T-D8700V • Forepaw and forefoot were not concepts in their own right, but stored as synonyms with a “V” designator in a “type of synonym” field. Veterinary Medical Informatics VMRCVM

  7. SNOMED-RT • Hand = T-D8700 • ForeFoot = T-D9702 • ForePaw is a synonym for Forefoot • IMPLICATION of this is that the forefoot of a horse = the forepaw of a rat and these are both “kinds of” hand. Veterinary Medical Informatics VMRCVM

  8. Veterinary Disease • “Laminitis of the right front foot of a horse” • Equine Laminitis (D0-54200) • Associated topography : forefoot (T-D9702) • Has laterality : Right (G-A100) Veterinary Medical Informatics VMRCVM

  9. Laminitis definition (SRT) Equine laminitis (disorder) Is a Disease of foot Veterinary Medical Informatics VMRCVM

  10. Laminitis definition (SRT) Equine laminitis (disorder) Is a Disease of foot Associated topography right “hand” Veterinary Medical Informatics VMRCVM

  11. So where are we? It’s Christmas eve. We’re peering into a box. We’re sure there’s a bicycle in there, but have not reached the part of the instructions that indicate we’ve found it. Veterinary Medical Informatics VMRCVM

  12. Comparative Anatomy of the Stomach Stomach (body structure) Parent(s): Abdominal viscus (body structure) Digestive organ (body structure) Hollow viscus (body structure) Child(ren): Avian stomach (body structure) Glandular stomach (body structure) Non-glandular stomach (body structure) Ruminant stomach (body structure) Veterinary Medical Informatics VMRCVM

  13. Comparative Anatomy “Conduit” • Mechanism: • A set of concepts and relationships connecting species-specific anatomical hierarchies. • Goal: • To accurately compute the anatomical analogies and differences among species. Veterinary Medical Informatics VMRCVM

  14. Comparative Anatomy “Conduits” • Identify structures with common comparative “heritage”. • Determine subtypes of common parent(s) necessary for species-based anatomical comparisons. • Map individual species “parts” to the template. Veterinary Medical Informatics VMRCVM

  15. The “Scheme” • Each concept should have a definition that is context-independent. • Create logical and true relationships between concepts Veterinary Medical Informatics VMRCVM

  16. The “Scheme” • Allow the rapid and easy addition of anatomical variations • as they are called into use by comparative anatomy. • as they are discovered, defined Veterinary Medical Informatics VMRCVM

  17. The “Scheme” • Express comparable anatomical sites across a wide range of species, including man • analogous structures should be grouped under a parent that defines their similarities. Veterinary Medical Informatics VMRCVM

  18. The “Scheme” • Enable data processing that excludes the comparative anatomy axis where no such depth or complexity is desired • the searcher wants to see only human (or equine, bovine, canine) topographical sites. Veterinary Medical Informatics VMRCVM

  19. The “Scheme” • Disruption and redefinition of the existing "human-based" nomenclature should be strictly minimized. Veterinary Medical Informatics VMRCVM

  20. Kinds of Stomach • Non-compartmented • Simple • Human being, dog, cat, guinea pig, rabbit • Compound • Rat, mouse, horse, pig • Compartmented • Camelid • Camels, llamas • Ruminant • Cattle, sheep, goats * Naming convention is subject to debate Veterinary Medical Informatics VMRCVM

  21. Gaster (parent of all stomachs) Gaster Compartmented Stomach Non-compartmented stomach Glandular Camelid Glandular/ Squamous Ruminant Veterinary Medical Informatics VMRCVM

  22. Whole Gaster Gaster Structure Glandular Portion Of Gaster Gaster Part Whole Non-compartmented Stomach Non-Compartmented Stomach Structure Non-compartmented Stomach Part Whole Complex Non-compartmented Stomach Whole Non-compartmented Simple Stomach Non-compartmented Simple Stomach Structure Non-compartmented Compound Stomach Structure Complex Non-Compartmented Stomach Part Squamous Epithelial Portion Non-compartmented Simple Stomach Part Glandular Portion Dog Stomach* Stomach T-57000* (Human) Mouse Stomach* Horse Stomach* Analogue Part of Is a *members of species-specific hierarchy

  23. Whole Gaster Gaster Structure Glandular Portion Of Gaster Gaster Part Whole Compartmented Stomach Compartmented Stomach Structure Compartmented Stomach Part Fermenting Portion Of Compartmented Stomach Whole Ruminant Stomach Whole Camelid Stomach Camelid Stomach Structure Ruminant Stomach Structure Ruminant Stomach Part Camelid Stomach Part C1 C2 Proximal C3 Distal C3 Reticulum Rumen Omasum Abomasum Analogue Part of Is a

  24. Upper Gastrointestinal Tract Structure Gaster Structure Non-compartmented Stomach Structure Stomach Structure (Human Stomach) Peaceful Co-existance Veterinary Medical Informatics VMRCVM

  25. Peaceful Co-existance Man Mouse Dog Conduit Cattle Rat Veterinary Medical Informatics VMRCVM

  26. Goals • Convince our friends in “two-legged” medicine that they can’t live without an accurate comparative anatomy. • Convince these same friends that we should be paid to provide it. • Enlist interested veterinary anatomists in the effort. Veterinary Medical Informatics VMRCVM

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