Trapping A Better Mouse:
Taxonomy of living
organisms in SNOMED
Submitted by
Penny Livesay BS, MA,
DVM
Proposal
To organize SNOMED's taxonomy into a
systematic and consistent Linnean
hierarchy
 To remove all non-taxonomic information
about living organisms from the taxonomic
hierarchy
 To represent such information, when
useful, reproducible, and retrievable,
elsewhere in the nomenclature—for
instance, by qualifier values.

Methods



All existing taxonomic terms are being reviewed
and standardized according to the Integrated
Taxonomic Information System (ITIS). Where
ITIS is not yet complete, the Smithsonian
mammalian taxonomy website is being used as a
secondary reference.
All organisms will be represented by their
scientific names as FSNs. Common names of
organisms will be given as descriptions where
appropriate.
Will not attempt to represent all known
organisms now, but will create a skeletal
representation at least to the level of subfamilies
for all families. Additional genera and species will
be added as time allows or as requested by
What is ITIS?
 “A
partnership of federal agencies
formed to satisfy their mutual needs
for scientifically credible taxonomic
information”
– USDA
– EPA
– Smithsonian Institute
– Department of the Interior
– Department of Commerce
SNOMED's taxonomy of living
organisms presently consists of:
Linnean taxonomic terms (“Canis
familiaris”)
 Common names for organisms (“Dog”)
 Non-taxonomic information

– Use and Circumstances
 Laboratory
fur-bearing animal
– Pathogenicity
 Parasite,
pyogenic bacterium
– Life cycle stage of organisms
 Worm
eggs
Common names as FSNs:
why is this a problem?

Some organisms have many common
names
– Butorides virescens = green heron, greenbacked heron, little green heron, crab-catcher,
fly-up-the-creek, green bittern, poke,
shitepoke, skeow, skow, and swamp squaggin

May be impossible to verify what
organism is meant
– Ex: Comte de Paris star frontlet (organism) ???

A single common name may refer to more
than one species:
– Ex: Yellowhammer (organism) MAY BE A
Emberiza citrinella, MAY BE A Colaptes auratus
Non-taxonomic terms in a
taxonomic hierarchy:
why is this a problem?


In an ISA hierarchy, the relationships are
"defining," that is, a subtype is always and
necessarily a "kind of" its parent
The present interpolation of non-taxonomic terms
in a taxonomic hierarchy violates this convention,
as these terms are often context-dependent rather
than defining. An elephant may be a domestic
animal in India; a dog may be a food animal in
Korea
– Question: Is a canary a “Wild bird--chordate” or a
“Domestic fowl”?
– Answer: Neither. It is Serinus canaria
Work in progress
 Extending
and correcting SNOMED’s
taxonomic coverage of birds and
mammals
 Retiring common names as FSN’s
and referring them as synonyms to
the appropriate scientific names
Proposed further changes
 To
represent contextual information
about living organisms outside the
taxonomic hierarchy
– Contexts of domesticity (domestic, feral,
wild)
– Contexts of use (food, laboratory,
companion, service, breeding, etc)
– Contexts of life stage (oocyst, larva,
spore, trophozooite, etc)
– Contexts of medical significance
(parasite, renotrophic organism,
pathogen)???
Life, qualified?
 Qualifier
values offer one possible
means to convey non-taxonomic
information about living organisms,
just as qualifiers such as onsets,
severities, or courses can be used to
describe a disease
An unqualified mink
Mink
ISA Domestic animal species, nonprimate (organism)
A qualified mink
Mustela vison (syn. Mink)
ISA Genus Mustela
 Qualifier values
– Context of use
 Fur-bearing
animal
 Laboratory animal
 Etc.
– Context of domestication
 Wild
 Domestic
 Feral
What about “infectious agents”?
The taxonomy of parasites, bacteria and
other potentially pathogenic
microorganisms is also a mixture of
scientific names, common names, and
contextual information
 Attempting to convey “contexts of
pathogenicity” creates errors in logic:

– Ex: Helminth ISA Parasite in SNOMED-but
most helminths are not parasitic
– Ex: Fungus ISA Infectious agent in SNOMED—
but most fungi are not infectious