Download Why a revision of the living organisms hierarchy? 1) A systematic

Why a revision of the living organisms hierarchy?
1) A systematic revision of the living organisms hierarchy is necessary at this time.
Specific problems include:
a. Incomplete and/or inappropriate assignment of Linnaean taxonomic terms
(e.g. E. coli) to medically important non-linnaean categories (e.g. Gram
negative bacillus)
b. Inaccurate and often incomplete Linnaean hierarchy
i. Inaccurate assignment
ii. Gaps in “middle hierarchy”
b. Many macro-organisms are represented only by common names
i. Inhibits proper translation
c. There are conflicting schema for the organization of parasites, fungi.
There is a need to create logical categories where there is no widely
agreed-upon Linnaean taxonomy (e.g., protozoa)
Why new organism model?
The living organisms (LO) hierarchy is presented as a classic subtype hierarchy with ISA
serving as the organizing attribute. Browsing the LO hierarchy, we find Escherichia coli
ISA Genus Escherichia. This is not strictly correct as a species is not a subtype of genus.
As described by Schulz et al, it is more appropriate to think that Escherichia coli (as
represented in a medical record) is a population of bacteria representative of the species
(taxon) Escherichia coli. In essence, the SNOMED LO hierarchy as currently rendered
conflates “a population of Escherichia coli” with “the taxon Escherichia coli”.
All concepts in the LO hierarchy are primitive. No defining attributes have been
sanctioned and no concepts have been defined. Essentially this means that autoclassification cannot be used as a means for organizing the hierarchy under some
clinically important concepts such as “gram negative bacteria (organism).” The present
circumstance in SNOMED means that a modeler assigns the gram negative bacteria
supertype for each bacteria modeled. The current list of descendants for concepts such
as “gram negative bacteria” is incomplete and inconsistently assigned (especially as
concerns taxonomic level).
2) Living organism hierarchy has no underlying model for defining individual
concepts
a. Current use – organisms are a primitive-only value list
b. Connections to decision support based on laboratory findings cannot be
done at this time (gram -)
c. Connection to new observables model cannot be done with current model
d. Living organism hierarchy is currently based on several different models.
None are complete and none are accurate none are up to date.
i. Linnaean
ii. Bergey key
3) The current living organisms hierarchy is rendered entirely as primitive concepts.
There are no defining attributes applied.
a. Autoclassification is not supported
b. Accurate and logical attachment / association between organisms and
either findings or procedures is not supported.
Figure 1. Current proposed living organisms model. This version is better aligned with the proposed
model for observables (procedures, findings) than were previous versions and is better aligned with Basic
Formal Ontology (and BioTop). Retains essential features and capabilities of previous draft(s).
Strategy
1) Render the CURRENT hierarchy accurately and completely using existing FSN
conventions.
a. Correct stated relationships
b. Remove stated relationships to common terms (e.g., “Gram negative
bacteria”)
c. Move CDC “groups” to navigational (controversial, big job, many
difficulties possible)
d. Provide definitions according to new model.
i. Hierarchy analysis and correction from top down will limit the
number of concepts that actually must be defined (see figure 1).
2) Automate creation of the taxon hierarchy DURING editing of the current LO
hierarchy
a. Automate linkage using “bearer_of” attribute and newly created taxon
concept.
b. Limitations
i. Species level (perhaps strain, certain CDC categories) concepts do
not INCLUDE the taxon level in the fsn (by convention). FSNs
for these concepts will have to be created manually.
3) Automate removal of taxon names from fsns of primary Linnaean hierarchy.
a. Minor editorial change. Ultimate use and meaning of these concepts in
medical records has not changed (it never did mean “the taxon” but rather
meant “the population that represents the taxon).
Impact on current users…
1)