Term list(s) vs.
SNOMED -CT® subset.
2nd AAHA Software Vendors Summit – April 21, 2009
Lists of words…
• Nomenclature
•
The system or set of names for things
• Vocabulary
•
A collection or list of words with explanations of their
meanings
• Classification
• The result of classifying; a systematic distribution, allocation,
or arrangement, in a class or classes; esp. of things which
form the subject-matter of a science or of a methodic inquiry.
(SNOMED)
Lists of words…
• Terminologies are about information
sharing, retrieval, aggregation and
analysis.
• It’s difficult if not impossible to justify the
effort required to “do terminology right”
from a data entry perspective.
• A functional terminology must attend to
both perspectives.
What do we need?
• Nomenclature ONLY
• Provides a simple list for data entry
• Vocabulary / Classification
• We can be CERTAIN that the “term” (description
in SNOMED) means what we think it means.
• We can develop rules that allow us to combine
concepts to express ideas more complicated than
those contained in the nomenclature.
• We can use the knowledge base supported by the
vocabulary/classification to search, retrieve and
analyze our data.
Why a controlled nomenclature?
• Aggregation of text-based content from
multiple sources
• Multiple individuals
• Multiple institutions
• Any time you rely on a computer to
manipulate language and “meaning” is
critical.
Why a controlled vocabulary /
nomenclature?
• Controlled vocabularies should
automate recognition of and accurate
substitution of synonyms.
• Controlled vocabularies should facilitate
retrieval and categorization.
Complaints about SNOMED
• It’s too…
• Big
• Complicated
• Expensive
• Yes but…
• We can make it smaller (sort of), and use small pieces (for
most purposes).
• Use it in simple and straightforward ways
• But nothing, it’s expensive.
• Not the license fees, the cost of making it work.
Why pick something as big and
complicated as SNOMED?
• Viable nomenclatures must be maintained.
• SNOMED is the ONLY actively maintained
nomenclature that has veterinary content.
• Veterinary medicine CANNOT afford:
• to build it’s own competent nomenclature
• to continue to live without a competent
nomenclature
SNOMED history
2000
1965
Reduce storage size
Reduce Storage size
Storage not an issue
Categorize information
Multiple code-based
mono-hierarchies
Poly-hierarchical
categorization
Functional Subsets
Pathology content
“All Medicine”
Veterinary content
separate, then
integrated
SNOVET DOES NOT
EXIST
Integrated content
Natural language,
artificial intelligence,
decision support
“Computability” for
retrieval.
Development history
•
SNOP
•
•
SNOMED
•
•
Disorders, Morphology, Living organisms, social context
Veterinary content re-integrated
SNOMED RT
•
•
Same structure as SNOMED
Mix of existing SNOMED, additional veterinary content
SNOMED III
•
•
•
Morphologies, Etiologies, Locations
SNOVET
•
•
•
Morphologies
Logic based approach to SNOMED. Axes became hierarchies. Most
significantly, the poly-hierarchic approach to classification.
SNOMED CT
•
SNOMED RT on steroids. Post merger with CTv3.
What do we get ?
• Sound technical solution to synonyms.
• Ability to “localize” the synonyms
• Compatibility with other “lists”
• Ability to merge AAHA-based records with others
(e.g., a cardiology specialty subset)
• Functional Sub-setting
• Enhanced queries
Solution to synonymy
• Obvious duplicates in AAHA draft list:
•
•
•
HYPERGLYCEMIA, BLOOD GLUCOSE INCREASED
• AAHA Category = Hematology, Lymphatic, Endocrine
HYPERGLYCEMIA, BLOOD GLUCOSE INCREASED
• AAHA Category = Metabolic
(NOT) Obvious duplicates in AAHA draft list
•
Thyroid gland mass
• AAHA Category = Hematology, Lymphatic, Endocrine
•
Mass, thyroid
• AAHA Category = Neoplasm
•
In SNOMED, both = 237557003 = Mass of thyroid gland (finding)
“Local” Synonyms
• It is POSSIBLE to allow practitioners to
add their own favorite description of a
concept.
• Analysis / transmission by conceptID.
Compatibility with other lists
• AAHA list can be part of “mixed animal”
system
• AAHA list would integrate (could be
used to query) a more granular
specialty list.
Functional Sub-setting
• We only need PORTIONS of SNOMED
• DIFFERENT portions of SNOMED needed for
different contexts in HIS.
• Retain the ability to use ALL of SNOMED to
search, retrieve, analyze data produced using
sub-sets.
• Be prepared to transfer (copy) from SNOMED
to subset as needs change.
Functional
Subsets
All of SNOMED
“Cardiovascular disease” subset Algorithm
Vet
Subset
Cardiovascular Diseases
Intersection = Veterinary Cardiovascular Diseases
SNOMED Subset
• “…a set of Concepts, Descriptions, or
Relationships that are appropriate to a
particular language, dialect, country,
specialty, organization, user or context.”
• “…simplest form, the Subset Mechanism is a
list of SNOMED identifiers (SCTIDs).”
• “…may be used to derive tables that contain
only part of SNOMED CT.”
• Can be selected by clever query, if underlying
definitions in SNOMED are sound.
Existing Subset(s)
• Non-human subset
• This subset assists applications that desire to exclude
concepts which are not human medical concepts (i.e., paw
and fin).
• Note that this is NOT a veterinary subset as that subset
would include terms shared with humans such as brain and
eye.
• Pathology subsets (3)
• CAP Cancer checklists
• Allergen subsets
Subsets
All veterinary content
Root Veterinary Subset
(large)
100 k ?
Bacteria
Living organism automated
subset
8500 concepts
Abnormal Morphologies
Body structure automated
subset
4000 concepts
Respiratory Findings
Findings/disorders
automated subset
850
Severities
Automated from qualifiers
5
AAHA Subset(s)
• SNOMED then remove hierarchies that are
NOT of interest.
• Someone has to decide what’s “not of interest”
• Someone familiar with SNOMED
• Someone with domain knowledge
• Desired functionality
• We think it’s important to distribute a subset of the
hierarchy above the AAHA subset with relationships
– Facilitate retrieval queries, may be possible to use the hierarchy to
control “lists in correct context” (this does not currently exist.
Subset development (Ideal)
• Build a competent Veterinary Subset of
SNOMED
• Veterinary subset a resource shared by the
profession.
• Managed by central “authority”
• Distributed by SNOMED?
• Use algorithm approaches to create
“microsubsets”
What we’re doing instead…
• Intellectual investment (by AAHA) in a list of
terms representing desirable small animal
medical content.
• “Mapping” by VTSL and EHRTF
• Add “missing” content through SNOMED
Extension mechanism.
• AAHA terms expressed as SNOMED
descriptions.
• Permanent identifiers
Mapping (why we didn’t just map AAHA’s list).
• Mapping is directional
• Largely the result of differing granularity between “target”
and “source”
• 1:1 – Concept is the same
– Term may be identical or synonym – remember to distinguish on
CONCEPT not on string
• Narrow to Broad – Source concept is more specific than target
• Broad to Narrow – Source concept is more general than target
• Two maps may be needed for bi-directional functionality
(unless entire map is 1:1)
Mapping
• 1:1 maps will represent a majority
• Broad (source) to narrow (SNOMED)
• Good argument that SNOMED needs more
content
• Narrow (source) to broad (SNOMED)
• SNOMED may need/want the content
• Map to a post-coordinated concept may be
required
AAHA terminology development
• There is no “final version”
• Walk don’t run
• No syntax (post-coordination) just yet
• Breadth first, depth later
SNOMED Extensions
• Enable authorized organizations (VTSL maintains
two namespaces) to add Concepts, Descriptions,
Relationships and Subsets to complement those that
are centrally maintained as the core content of
SNOMED CT.
• specialized terminology needs of an organization.
• ISIS / ZIMS
• USDA
• FDACVM
• Extensions maintain unique identification across
organizations.
SNOMED Extensions
• Distinguishable from the main body of SNOMED CT
• in the thesaurus
• when stored in a patient record, query or decision support
protocol.
• Distinguishable from other Extensions, in the same
way as they are distinguishable from the main body
of SNOMED CT.
• Able to be distributed and processed in the same way
as equivalent components from the main body of
SNOMED CT without requiring specific adaptations
of SNOMED-enabled applications.
Existing Extension(s)
• US Drug extension
• List of drugs marketed in the United States
• Veterinary drugs have not been maintained
in some time.
• UK Drug extension
What are we doing to the AAHA Diagnostic Terms list?
• Two reviews by VTSL veterinarians, third review by
AAHA team.
• Determining what each term MEANS
• Mapping each term to SNOMED
• Editing the terms
•
•
•
•
Slightly more natural English
Separating list of synonyms into individual descriptions
Limiting commas to one “use” only
Converting to sentence case
• Providing SNOMED identifiers for each description
AAHA Terms (version changes)
• AAHA terms will have SNOMED-based
identifiers
• AAHA terms will be mapped to SNOMED
concepts
• Phrasings more like natural English
• Only one use of commas
• “Within-term” synonyms will be separate
descriptions.
Future project(s)
• Plan / build user request system
• Characterize AAHA content
• Patient findings
• Laboratory findings
• Morphologies
• Add, then “clean up” upper hierarchy
• Hierarchy to display "in appropriate context"
•
(Liver things show up when vet wants liver things).
• Create similar specialty-based subsets
• Increased specificity/granularity
• Cardiology, Neurology, etc.
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Term list(s) vs SNOMED -CT® subset.