Managing SNOMED

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Managing SNOMED

• NAHLN
• January 2004
• Las Vegas

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Nomenclature Tasks

• Do I know how you should do this?
• NO!!!!!!

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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

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Interface options (Ferrari)

• Data entry concept requests
• Queries of LIMS data
• Natural language interface?
• Description logic approach

High Powered Terminology Server
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 pre-processing

• Disadvantages
• Expense
• Server
• Terminology software
• SNOMED functionality inadequate at this time.
• Probably requires full time nomenclaturologist ?

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Interface options (Chevy)

• Store subsets (pick lists) in LIMS System
• Query server
• a complete copy of SNOMED
• Your SNOMED workshop

Lims Server
Low End Terminology Server (Full copy of SNOMED)

• Advantages
• Terminology operations

• Disadvantages
• Several many subsets
• Subset updates as second step with new release
  (problematic if manual)
• Somebody must build subsets

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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.

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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.

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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

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NAHLN Subsets?

• SNOMED (-) hierarchies that are NOT of interest.
• Someone has to decide whats not of interest
• Someone familiar with SNOMED should build the
  subsets
• Desired functionality -gt 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)

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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
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Veterinary SubsetsShared resource

• We need to develop a root veterinary subset
• Manual process (cant 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.

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Subsets
All of SNOMED
Cardiovascular disease subset Algorithm
Vet Subset
Cardiovascular Diseases
Intersection Veterinary Cardiovascular Diseases
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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

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NAHLN Extension(s)?

• Conditions of husbandry
• Probably should be core
• Descriptions (more synonyms)
• Local
• Network-wide

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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.

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List a SNOMED definition
ISA relationships always defining 116680003
ISA
Group by RelationshipsGroup CharacteristicType 0
is defining
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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

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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

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Mapping

• Mapping is directional
• Largely the result of differing granularity
  between target and source
• 11 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 11)

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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 11, the single map is
  bidirectional.

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Mapping for NAHLN

• 11 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

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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

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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.

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SNOMED -gt 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.

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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.

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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.)

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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.

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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

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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.

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Nomenclature Updates

• Retired Concepts
• Concept referral mechanism
• New Concepts
• Retired Descriptions
• New Descriptions
• New relationships

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Queries

• Query full copy of SNOMED
• Queries based on description have highest yield.
• Indexes
• Query portion that has been recorded?

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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.

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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.

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Existing Extension(s)

• US Drug extension
• List of drugs marketed in the United States
• UK Drug extension