Transcript Mapping to SNOMED

Managing SNOMED
NAHLN
January 2004
Las Vegas
Nomenclature Tasks
Do I know how you
should do this?
NO!!!!!!
Nomenclature Tasks
Install nomenclature
Interface to terminology



Subsetting to enhance efficiency
Mapping from existing controlled vocabulary
Displaying preferred descriptions
System wide
User specific??????
Message processing
Requests from users for concept addition
Updates (ongoing)
Queries
Interface options (Ferrari)
Data entry concept requests
Queries of LIMS data
Natural language interface?
Description logic approach
Lims Server
CIS Server
Etc.
Advantages




Offload nomenclature from
production system CPU / data
storage
Single update with new release of
nomenclature
Access to “all” at all times
Minimal SNOMED “preprocessing”
“High Powered” Terminology Server
Disadvantages

Expense
Server
Terminology “software”


SNOMED functionality inadequate
at this time.
Probably requires full time
nomenclaturologist… 
Interface options (Chevy)
Store subsets (pick lists) in LIMS
System
Query server


a complete copy of SNOMED
Your SNOMED “workshop”
Lims Server
Advantages

Terminology “operations”
“Low End” Terminology Server
(Full copy of SNOMED)
Disadvantages



Several – many subsets
Subset updates as second step
with new release (problematic if
manual)
Somebody must build subsets
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).”
“…Mechanism may be used to derive
tables that contain only part of SNOMED
CT.”
Functional Sub-setting
We only need PORTIONS of SNOMED
DIFFERENT portions of SNOMED for
various parts of LIMS.
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.
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
NAHLN Subsets?
SNOMED (-) hierarchies that are NOT of interest.




Someone has to decide what’s “not of interest”
Someone familiar with SNOMED should build the subsets
Desired functionality -> Subset the relationships?
It would be nice to have a Non-human-only subset
Organisms



Species
Breeds
Bacteria, viruses, parasites, etc.
Diseases of interest
Some portion of laboratory tests (classification scheme
for LOINC?)
Reportable diseases (depending on jurisdiction)
Subsets
Veterinary Subset
(large)
SNOMED – (human
only)
100 k - 200k+
concepts
Bacteria
Living organism
automated subset
6500 concepts
Abnormal
Morphologies
Body structure
automated subset
4000 concepts
Respiratory Findings
Findings/disorders
automated subset
850
Severities
Automated from
qualifiers
5
Veterinary Subsets
Shared resource
We need to develop a “root” veterinary
subset



Manual process (can’t be automated at this
time).
Prune SNOMED to remove human ONLY
content.
Prune SNOMED aggressively to remove
excessive granularity.
Automated subsetting works on ALL
SNOMED or the Veterinary subset.
Subsets
All of SNOMED
“Cardiovascular disease” subset Algorithm
Vet
Subset
Cardiovascular Diseases
Intersection = Veterinary Cardiovascular Diseases
Subset development (Ideal)
Build a complete 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”
NAHLN Extension(s)?
Conditions of husbandry

Probably should be core
Descriptions (more synonyms)


Local
Network-wide
ConceptID
Recursion for gathering all
descendants of a concept.
• Build subsets
• breeds, species
• all disorders
• all cardiovascular disorders
• etc.
• Query for concept and all its
specializations
• everything that “ISA”
respiratory disease.
SET NewChildList = ConceptID
SELECT Distinct ConceptID1
FROM RelationshipsTable
WHERE RelationshipsType =116680003
AND ConceptID2 IN (Childlist)
SET NewChildList = Returns from query
APPEND returns from query to Childlist
Returns? – Yes
No
Output Childlist
“List” a SNOMED definition
TargetConceptID
(Gather IsA parents)
ISA relationships always defining
116680003 = “ISA”
SELECT ConceptID2
FROM RelationshipsTable
WHERE ConceptID1 = (TargetConceptID)
AND RelationshipsType =116680003
(Gather non isa Children)
Group by RelationshipsGroup
CharacteristicType =0 is defining
SELECT ConceptID2, RelationshipType,
RelationshipsGroup
FROM RelationshipsTable
WHERE ConceptID1 = (TargetConceptID)
AND CharacteristicType = 0
AND NOT RelationshipsType =116680003
(Output)
Why map?
SNOMED is not optimized for data entry.
Your own local vocabulary may be the
preferred data entry instrument.



Capture data via local term (description string)
Convert to SNOMED concept
Transmit to repository
SNOMED Maps
SNOMED provides a number of maps to
nomenclatures of human interest




ICD-9
ICD-10
ICD-0
LOINC (special case we MIGHT use)
SNOMED is source
Mapping
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 for NAHLN
NAHLN Maps (e.g., CAHFS) will use local
nomenclature as source, SNOMED as
target
Map builder qualifications:


Understand structure of source and target
Understand content of source and target
IF the map is completely 1:1, the single
map is bidirectional.
Mapping for NAHLN
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
Post-coordination
(for NAHLN mapping)
What is post-coordination?

Create a new concept by adding specificity to
and existing SNOMED concept.
Source has:

“Acute pasteurella pneumonia”
Target (SNOMED) has:

“pasteurella pneumonia”
Create:

Pasteurella pneumonia + has course = acute
Post-coordination
(for NAHLN mapping)
Pasteurella pneumonia + has course = acute
Where do you put your new creation?

Extend the concepts table (1 new)
Identifier outside of SNOMED itself (namespace
mechanism)

Extend the “relationships table”
An extension (not part of core)
Processed as if it is part of the original table.
SNOMED -> LOINC map?
SNOMED can be used to provide a
categorization hierarchy for LOINC codes
through the map.
Probably unnecessary unless vocabulary
server approach is employed.
Species and Breeds
It is our INTENTION that the living
organisms hierarchy should accurately
reflect the current state of the art re:
animal taxonomy.
Each entry has taxonomic rank identified
in FSN
Relationship type 3 (additional) to support
a relationship that identifies taxonomic
rank.
Species and Breeds
Gather species and breeds


Select the root for the hierarchy
Perform recursive search for children
Identify taxonomic rank


Process string of FSN
Fact relationship
“has taxonomic rank” = breed (etc.)
Concept Addition
Users WILL discover concepts that are not
present in the nomenclature
Licensed users can make requests to
SNOMED directly
Channels have been established for timely
addition.
Concept Addition
When we (AVMA Secretariat) receive a
request for concept addition:

We confirm that the concept is really missing
Often there is a synonym present
Requested “description” can be added


We prepare a SNOMED-style definition for the
concept
Concepts are added to the nomenclature by a
veterinarian on SNOMED staff
Nomenclature Updates
New version of SNOMED scheduled for
every 6 months.

Expect change rate to decline with time
NLM updating may be less frequent.
NLM updating will certainly lag behind
SNOMED releases.
Nomenclature Updates
Retired Concepts

Concept “referral” mechanism
New Concepts
Retired Descriptions
New Descriptions
New relationships
Queries
Query full copy of SNOMED


Queries based on description have highest
yield.
Indexes
Query portion that has been recorded?
SNOMED Extensions
Enable authorized organizations 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.
Extensions maintain unique identification across
organizations for data transmission and sharing.
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 SNOMEDenabled applications.
Existing Extension(s)
US Drug extension

List of drugs marketed in the United States
UK Drug extension