Transcript Beside the Digital Anatomist: Integrating Veterinary

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
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http://sig.biostr.washington.edu/projects/da/
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Veterinary Medical Informatics
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SNOMED History

College of American Pathologists
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1963 SNOP
• Systematized Nomenclature of Pathology
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1974 SNOMED
• Systematized Nomenclature of Medicine

1993 “SNOVET” amalgamation
• Tools inadequate to the task
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1999 SNOMED-RT
• Tools are adequate, now someone must repair the
content.
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SNOMED – SNOVET
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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
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SNOMED – SNOVET

Reconciliation outcomes
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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.
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SNOMED III
Hand = T-D8700
 Forefoot = T-D8700V
 Forepaw = T-D8700V
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Forepaw and forefoot were not
concepts in their own right, but stored
as synonyms with a “V” designator in a
“type of synonym” field.
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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.
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Veterinary Disease
“Laminitis of the right front foot of a
horse”
 Equine Laminitis (D0-54200)
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Associated topography : forefoot (T-D9702)
• Has laterality : Right (G-A100)
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Laminitis definition (SRT)
Equine laminitis (disorder)
Is a Disease of foot
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Laminitis definition (SRT)
Equine laminitis (disorder)
Is a Disease of foot
Associated topography right “hand”
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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.
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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)
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Comparative Anatomy
“Conduit”
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Mechanism:
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A set of concepts and relationships
connecting species-specific anatomical
hierarchies.
Goal:
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To accurately compute the anatomical
analogies and differences among
species.
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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.
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The “Scheme”
Each concept should have a
definition that is contextindependent.
 Create logical and true relationships
between concepts
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The “Scheme”
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Allow the rapid and easy addition of
anatomical variations
as they are called into use by
comparative anatomy.
 as they are discovered, defined
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The “Scheme”

Express comparable anatomical sites
across a wide range of species,
including man
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analogous structures should be
grouped under a parent that defines
their similarities.
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The “Scheme”

Enable data processing that
excludes the comparative anatomy
axis where no such depth or
complexity is desired
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the searcher wants to see only human
(or equine, bovine, canine)
topographical sites.
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The “Scheme”
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Disruption and redefinition of the
existing "human-based"
nomenclature should be strictly
minimized.
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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
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Gaster
(parent of all stomachs)
Gaster
Compartmented
Stomach
Non-compartmented
stomach
Camelid
Ruminant
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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
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Peaceful Co-existance
Man
Mouse
Dog
Conduit
Cattle
Rat
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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.
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Veterinary Medical Informatics
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