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ICD9CM, often spelled “ICD-9-CM”, is a coding system in the USA, which is based on the WHO ICD9 coding system but has multiple additions and modifications.


The procedures for transforming Concepts from the source to the OMOP Standard Vocabularies can be found here.

Concept Names

All Concepts are assigned the longest of all available names.

Concept Code

All ICD9CM codes are represented in the format containing the dot. For example, the Concept for “Eating disorder, unspecified” is stored under the concept_code “307.50”.

Standard Concepts

All ICD9CM codes are non-Standard.

Concept Classes

ICD9CM Concept Classes identify each Concept as part of the general coding scheme of diagnoses and disorders, the codes for health status and contact with health services (V codes, starting with the letter “V”) and those for external causes of injury (E codes, starting with the letter “E”). In addition, the Concept Classes distinguish between billing and non-billing codes. These are defined according to the Health Care Services Coding System of the Centers of Medicare and Medicaid Services (CMS). Billing codes are those that are used for reimbursement of services, while non-billing codes are Chapter, Category or Sub Category codes.

Concept ClassNotes
3-dig billing V code
3-dig billing code
3-dig nonbill V code
3-dig nonbill code
4-dig billing E codeThere are no 3-digit E codes
4-dig billing V code
4-dig billing code
4-dig nonbill E code
4-dig nonbill V code
4-dig nonbill code
5-dig billing E codeThere are no 5-digit codes that are non-billing
5-dig billing V code
5-dig billing code
ICD9CM V codeLegacy class of deprecated Concepts
ICD9CM codeLegacy class of deprecated Concepts


For each ICD9CM Concept, the Domain is inferred from the SNOMED Concept it is mapped to. If a ICD9CM Source Concept is mapped to more than one target SNOMED Concept, a combination Domain is assigned.

ConditionBulk of ICD9CM codes
Meas/ProcedureDeprecated codes
Condition/MeasDeprecated codes
Condition/ProcedureDeprecated codes

Concept Relationships

There are two types of relationships for ICD9CM: Mapping and hieararchical relationships.


ICD9CM concepts are non-Standard Concepts and therefore are mapped to Standard Concepts through records in the CONCEPT_RELATIONSHIP table. All such mappings point to SNOMED-based concepts. Most of these SNOMED Concepts are in the Condition Domain, but despite the fact that ICD9CM is a “Classification of Disease” some of them get mapped to Procedure, Measurement and Observation Domain Concepts. All mappings are manually maintained by a team of curators.

Most mappings establish one-to-one equivalence between the Concepts. However, some ICD9CM Concepts are pre-coordinated (consist of several semantic components), contain negations, declarations about conditions at an unspecified time in the past (e.g. medical history of), declarations about people other than the patient (e.g. family history), lab test findings, mixed mother/child conditions or Observations. All these cases are properly handled as described in the Mapping description.

Instructions for ETL

All ICD9CM concepts are non-Standard. That means, they have to be mapped to the corresponding Standard Concepts using the CONCEPT_RELATIONSHIP table (“Maps to” and occasionally “Maps to value” records). Most of them map to single Condition Concepts, generating one-to-one records in the CONDITION_OCCURRENCE table, but some of them create multiple records or mappings to other domains.

Hierarchical relationships between 3, 4 and 5-characer Concepts

These are constructed for those Concepts where the shorter code is entirely subsumed by longer one. Note that these relationships also exist between 3 and 5-digit codes according to these rules, which deviates from the preferred convention that “Subsumes” and “Is a” relationships only exist between directly related Concepts.


ICD9CM Concepts are non-Standard Concepts and therefore do not participate in the hierarchy of the CONCEPT_ANCESTOR table.

documentation/vocabulary/icd9cm.txt · Last modified: 2016/06/04 23:16 by cgreich