Transcript Document

Understanding
SNOMED CT
in a Veterinary Setting
(February 9, 2004)
W. Kathleen Ellis, RHIT, RN, BS
University of Illinois
Veterinary Teaching Hospital
and VMDB HIM Consultant
Thanks to the following for their contributions:
• Dr. Allen Hahn (University of Missouri),
• Margaret Neterer, RHIA (Michigan State University),
• Bobbi Schmidt, RHIA (The Ohio State University)
• Celia Ruckel and Krissy Ruth (The Ohio State
University), and
• Dr. Art Siegel (University of Illinois)
Basic Terminology
• Concept: a clinical term
– assigned a unique concept ID
• Concept ID: a unique numeric value assigned to a concept
– Has no meaning by itself
– Should be used to store and transmit concepts
– Example: 53084003 = Bacterial Pneumonia (disorder)
• SNOMED ID: also known as a “Legacy Code”
– Alphanumeric value assigned to a concept
– Because of the limitations of using alphanumeric codes, CAP* began
using concept IDs
• *The College of American Pathologists; the licensing body for SNOMED
– SNOMED IDs are linked to the Concept ID
– Should no longer be used for storage and retrieval
– Example: DE-10100 (Bacterial Pneumonia)
Terminology continued
• CTV3 ID – ‘Read Codes’ from the UK; integrated into
SNOMED
• Concept Status – indicates if a code is active or retired,
retired codes are never deleted (Limited codes may be
used, but please post to the Forum)
• IsPrimitive – indicates the concept is not fully defined
(May use these if a fully defined code does not exist.)
Type of Concepts
•
•
•
•
Diseases/Disorders
Findings
Procedures
Body structures (normal and abnormal, includes
morphologies)
• Etc.
– NOTE: It’s important to choose a concept from the
appropriate hierarchy
• Avulsion is a ‘morphology’
• Avulsion is a ‘disorder’
• Avulsion is also a ‘procedure’
Hierarchies
• Concepts are related to one another by an ‘is-a’
type or an ‘attribute’
(see next slide)
• The relationships between concepts are their
hierarchies. These relationships are what gives the
concept its definition or meaning
– Before choosing a concept, look at its definition
to insure it is correct and complete
Is-a versus Attribute
• ‘Is-a’ relationships are
defined only by the
modeling team at CAP
– Bacterial pneumonia
• Is a
– Bact lower resp infect
– Infective pneumonia
• ‘Attributes’ are used by a coder
to link multiple concepts
together; when these are used
the end result must always be
an odd number
– Mycoplasma bact pneu is
defined as:
• Bacterial pneumonia
– Causative agent (Atribute)
– Mycoplasma
– Not:
• Bacterial pneumonia
– Mycoplasma
Parents & Children
Relationships of concepts to one
another are best looked at as Parents
and Children
Parent concepts
• Looking at bacterial pneumonia, one can
see it has two parents:
– bacterial lower respiratory infection, and,
– infective pneumonia
• One can go further up the parental tree by
clicking on either of the two parents,
infective pneumonia or bacterial lower
respiratory infection
Children concepts
• Looking at bacterial pneumonia and going
down the tree, one can see its many
children:
–
–
–
–
Anthrax pneumonia
Chlamydial pneumonia
Nocardial pneumonia
Etc.
Descriptions
• Many concepts have descriptions in their hierarchy.
Synonyms are listed under these descriptions. Do not
rely on these to define a concept. Many of these are
inaccurate and are under review.
• Example: Diagnosis of Pinworm Disease
– Concept = Enterobiasis (266162007)
• Enterobiasis is the human pinworm species
• Has synonyms of oxyuriasis, pinworm disease, etc.
• However, the definition for this concept does not meet veterinary
needs even though the synonym would make it appear as though
it does.
Pre- vs Post-Coordination
Pre-Coordination
• is merely a concept that already exists in
SNOMED CT
– Bacterial Pneumonia (Disorder) (53084003)
does not need further enhancement
Post-Coordination
• an already existing concept can be enhanced by using a
combination of 2 or more codes
– Mycoplasma Bacterial Pneumonia:
• There is no pre-coordinated concept, thus, several
concepts would need to be combined to build this
• Bacterial Pneumonia (Disorder) (53084003)
» Causative Agent (Attribute) (246075003)
» Mycoplasma (Organism) (78981005)
(see slide on ‘Attributes’)
Nesting of concepts
Order is important. The root concept is always
followed by the attribute and its value
• So one would ‘not’ say:
– Mycoplasma
– Causative agent
• Bacterial pneumonia
• Nor,
– Lung structure
– Finding site
• Bacterial pneumonia
Multiple Attributes and Values
Each ‘value’ must be accompanied by its own attribute,
e.g. multiple finding sites each need their ‘own’
attribute of finding site.
• Rupture of tendon of pastern joint left hindlimb of cow
– Ligament rupture (Disorder) (263134008)
• Finding site (Attribute) (363698007)
• Pastern joint (Body structure ) (214226000) [Value]
• Finding site (Attribute) (363698007)
• Hindlimb (Body structure) (116013008) [Value]
– Laterality (Attribute) (272741003)
– Left (7771000) (Qualifier value)
POST-COORDINATION
REDUNDANCY
If a concept is already built into the root concept
hierarchy then it would be redundant to postcoordinate that concept:
– Bacterial Pneumonia (Disorder) (53084003)
» Causative agent (Attribute) (246075003)
» Mycoplasma (Organism) (78981005)
»
Finding site (Attribute) (363698007)
»
Lung structure (Body structure) (39607008)
However:
• Some redundancy may occur if a more specific
value is preferred, e.g.
– Malignant neoplasm femur (Disorder)(93798006)
• Finding site (Attribute) (363698007)
• Distal shaft of femur (Body structure) (23480003)
‘Distal shaft of femur adds more detail to the concept’
Attributes
• See the SNOMED Clinical Terms User Guide
• See listing of approved attributes
• When linking concepts, it is helpful to locate an
already similarly linked existing code in Clue and
mimic it:
– Mycoplasma bacterial pneumonia
No pre-coordinated term exists. Following the rules,
this concept may be built using the attribute causative
agent (see Anthrax pneumonia as an example)
Anatomy
Be cautious when choosing body structure concepts for
veterinary usage. SNOMED is still developing
veterinary anatomy, thus, there are some inaccuracies
and some concepts are not yet added.
• Use ‘non-human’ body structures when possible
• Many concepts are modeled to human body structures, so
when choosing one of these ‘avoid’ species specific terms
such as 4th rib.
• Although hindlimb and forelimb are available as body
structures, they are rarely available when choosing a precoordinated concept: e.g., Malignant neoplasm of upper
limb not forelimb
Discussion Forum
• A discussion forum is available for questions
concerning concepts, functionality and syntax
related to veterinary medicine.
• This Forum was developed and is maintained by
Dr. Jeff Wilcke. Contact Dr. Wilcke to register for
access at: https://snomed.vetmed.vt.edu
• The Forum maintains a historical record of
discussions that can be used as a searchable
reference.
Guidelines
• As they are developed, VMDB will post
guidelines to the website at:
– http://www.vmdb.org
• These are meant only as a guide to assist the user
and subject to change as technologies develop
VCOPS
(Veterinary Coding Protocols)
http://www.vmdb.org
Always search VCOPS first when searching for a code. This helps ensure
that all veterinary users are coding common diagnoses/procedures in a
consistent manner.
• These have been developed over time by OSU and U of IL
• Maintains a history of codes that have been used to express concepts in
the past which have been changed or further developed in SNOMED
• Tracks codes requested on the Forum
• More easily helps locate concepts not intuitively found (slang)
• More easily locate concepts frequently used or that return huge results
on searches
• Provides guidance on how to code specific concepts that need postcoordination or are incorrectly modeled
• Assists in choosing a code with similar concepts
Quick Review
• Understand the concept
meaning before selecting
• Know the top level
hierarchy of code
chosen, e.g., disorder vs
procedure
• Follow SNOMED rules
for using attributes
• Enter root concept first
followed by postcoordination
• When in doubt always
select a more generalized
concept (a parent)
• Questions? Go to the
Forum and VCOPS
VMDB Submissions
Sanctioned Codes
• Submit only SNOMED sanctioned codes to
VMDB
• Although temporary codes may be assigned
internally, they must be replaced with a
SNOMED code before submitting
– Note: we suggest limiting the use of these as it
can become labor intensive to find and replace
these.
Confirmation of Diagnoses
Diagnoses may be submitted to VMDB as
confirmed, suspect, or probable
Do not submit rule out or differential diagnoses at
this time
This is an institutional decision. If the diagnosis is
submitted without these ‘flags’ they will be taken
in as confirmed.
Confirmed
• Definition:
– ‘ validated by factual proof’
• Per Merriam Webster, 10th Ed
Suspect
• Definition:
– ‘to imagine being true with slight evidence or
without proof’
• Per Merriam Webster, 10th Ed
Probable
• Definition:
– ‘supported by evidence strong enough to
establish presumption but not proof; likely to be
or become true or real’
• Per Merriam Webster, 10th Ed
Recheck vs Initial Diagnosis
• The first time a patient is diagnosed with a
particular condition is considered its initial
diagnosis, e.g. diagnosis of diabetes mellitus
• If the patient returns for a follow-up for the same
condition, it is considered a recheck for that
diagnosis
• Not a recheck:
• Otitis externa diagnosed initially, resolved, then patient returns
for a new diagnosis of otitis externa
Context Dependent Categories
• Are used to explain the context of a chosen concept
– History of
– Family history of
– Physical exam finding
• VMDB makes no recommendations as to whether or
not an institution wishes to collect this information or
how it should be collected
– However, at such time when VMDB is able to accept context
dependent concepts, they need to be transmitted via LOINC
(Logical Observation Identifiers Names and Codes) codes