conduits between anatomical hierarchies in snomed
DESCRIPTION
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” - PowerPoint PPT PresentationTRANSCRIPT
Veterinary Medical Informatics
VMRCVM
Conduits Between Anatomical Hierarchies in SNOMED
Dr. Jeff R. WilckeDr. Penny LivesayDr. 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/concepts1) Concepts and codes that were the
same as SNOMED2) 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 footAssociated 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 species-based anatomical comparisons.
Map individual species “parts” to the template.
Veterinary Medical Informatics
VMRCVM
The “Scheme” Each concept should have a
definition that is context-independent.
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 StomachNon-compartmented
SimpleHuman being, dog, cat, guinea pig, rabbit
CompoundRat, mouse, horse, pig
Compartmented Camelid
Camels, llamasRuminant
Cattle, sheep, goats
* Naming convention is subject to debate
Veterinary Medical Informatics
VMRCVM
Gaster (parent of all stomachs)
Gaster
Non-compartmented stomach
CompartmentedStomach
Camelid
Ruminant
Glandular
Glandular/Squamous
Part ofIs a
Gaster Structure
Gaster Part
Whole Gaster
Glandular PortionOf Gaster
Non-Compartmented StomachStructure
Non-compartmentedCompound Stomach
Structure
Non-compartmentedSimple Stomach Structure
Stomach T-57000*(Human)
Dog Stomach* Mouse Stomach* Horse Stomach*
Squamous Epithelial
Portion
Glandular Portion
Analogue
Whole ComplexNon-compartmented
Stomach
Complex Non-Compartmented
Stomach Part
Non-compartmented Stomach Part
Whole Non-compartmented
Stomach
Whole Non-compartmentedSimple Stomach
Non-compartmentedSimple Stomach Part
*members of species-specific hierarchy
Part ofIs a
Glandular PortionOf Gaster
Gaster Structure
Gaster Part
Whole Gaster
Reticulum AbomasumRumen OmasumDistal C3C1 C2 Proximal C3
Ruminant StomachStructure
Camelid StomachStructure
Compartmented StomachStructure
Analogue
Whole RuminantStomach
Ruminant Stomach
Part
WholeCamelid Stomach
Camelid Stomach
Part
Compartmented StomachPart
Whole Compartmented Stomach
Fermenting Portion Of Compartmented Stomach
Veterinary Medical Informatics
VMRCVM
Stomach Structure(Human Stomach)
Upper Gastrointestinal TractStructure Gaster Structure
Non-compartmented StomachStructure
Peaceful Co-existance
Veterinary Medical Informatics
VMRCVM
Peaceful Co-existance
ManMouse
Cattle
Dog
Rat
Conduit
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.