conduits between anatomical hierarchies in snomed

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Conduits Between Anatomical Hierarchies in SNOMED

Dr. Jeff R. WilckeDr. Penny LivesayDr. Larry Freeman

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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/

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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.

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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

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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.

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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.

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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)

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 footAssociated 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” Mechanism:

A set of concepts and relationships connecting species-specific anatomical hierarchies.

Goal: 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 species-based anatomical comparisons.

Map individual species “parts” to the template.

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The “Scheme” Each concept should have a

definition that is context-independent.

Create logical and true relationships between concepts

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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

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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.

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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.

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The “Scheme” Disruption and redefinition of the

existing "human-based" nomenclature should be strictly minimized.

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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

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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

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Stomach Structure(Human Stomach)

Upper Gastrointestinal TractStructure Gaster Structure

Non-compartmented StomachStructure

Peaceful Co-existance

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Peaceful Co-existance

ManMouse

Cattle

Dog

Rat

Conduit

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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.