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Understanding SNOMED CT in a Veterinary Setting (February 9, 2004)
W. Kathleen Ellis, RHIT, RN, BSUniversity of IllinoisVeterinary Teaching Hospitaland 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’ 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 Is-a versus Attribute
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-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 post-coordinate 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 pre-coordinated 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 post-coordination or are incorrectly modeled • Assists in choosing a code with similar concepts
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 post-coordination When in doubt always select a more generalized concept (a parent) Questions? Go to the Forum and VCOPS Quick Review
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