Conduits Between Anatomical Hierarchies in SNOMED Dr. Jeff R. Wilcke Dr. Penny Livesay Dr. Larry Freeman Veterinary Medical Informatics VMRCVM 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 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 SNOMED – SNOVET SNOVET included two kinds of codes/concepts 1) 2) Concepts and codes that were the same as SNOMED Concepts and codes that were added for special veterinary needs Veterinary Medical Informatics VMRCVM 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 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 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 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 Laminitis definition (SRT) Equine laminitis (disorder) Is a Disease of foot Veterinary Medical Informatics VMRCVM Laminitis definition (SRT) Equine laminitis (disorder) Is a Disease of foot Associated topography right “hand” Veterinary Medical Informatics VMRCVM 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 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 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 Comparative Anatomy “Conduits” Identify structures with common comparative “heritage”. Determine subtypes of common parent(s) necessary for speciesbased anatomical comparisons. Map individual species “parts” to the template. Veterinary Medical Informatics VMRCVM The “Scheme” Each concept should have a definition that is contextindependent. Create logical and true relationships between concepts Veterinary Medical Informatics VMRCVM 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 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 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 The “Scheme” Disruption and redefinition of the existing "human-based" nomenclature should be strictly minimized. Veterinary Medical Informatics VMRCVM 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 Gaster (parent of all stomachs) Gaster Compartmented Stomach Non-compartmented stomach Camelid Ruminant Veterinary Medical Informatics VMRCVM Glandular Glandular/ Squamous Whole Gaster Gaster Structure Glandular Portion Of Gaster Gaster Part Whole Non-compartmented Stomach Non-Compartmented Stomach Structure Non-compartmented Stomach Part Whole Non-compartmented Simple Stomach Non-compartmented Simple Stomach Structure Whole Complex Non-compartmented Stomach Non-compartmented Compound Stomach Structure Complex Non-Compartmented Stomach Part Non-compartmented Simple Stomach Part Squamous Epithelial Portion Glandular Portion Dog Stomach* Stomach T-57000* (Human) Mouse Stomach* Horse Stomach* *members of species-specific hierarchy Is a Part of Analogue 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 Is a Part of Rumen Omasum Analogue Abomasum Peaceful Co-existance Upper Gastrointestinal Tract Structure Stomach Structure (Human Stomach) Gaster Structure Non-compartmented Stomach Structure Veterinary Medical Informatics VMRCVM Peaceful Co-existance Man Mouse Dog Conduit Cattle Rat Veterinary Medical Informatics VMRCVM 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