documentation:vocabulary:icd9cm
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documentation:vocabulary:icd9cm [2015/09/13 12:27] cgreich [Concept Relationships] |
documentation:vocabulary:icd9cm [2016/06/04 23:16] cgreich |
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| ===== ICD9CM ===== | ===== ICD9CM ===== | ||
| - | ICD9CM, usually 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. | + | 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. |
| ==== Transformation ===== | ==== Transformation ===== | ||
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| |Condition/Meas|Deprecated codes| | |Condition/Meas|Deprecated codes| | ||
| |Condition/Procedure|Deprecated codes| | |Condition/Procedure|Deprecated codes| | ||
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| - | Please refer to [[http://www.ohdsi.org/web/athena/vocabcontent#ICD9CM|Concepts of ICD-9-CM]] for details of the composition of this vocabulary. | ||
| ==== Concept Relationships ==== | ==== Concept Relationships ==== | ||
| - | There are types of relationships for ICD9CM: Mapping and hieararchical relationships. | + | There are two types of relationships for ICD9CM: Mapping and hieararchical relationships. |
| === ICD9CM to SNOMED map === | === ICD9CM to SNOMED map === | ||
| - | These are recorded as "Maps to" relationships. These are manually curated based on input from UMLS (connection through common CUIs) and through MedDRA through ICD9CM to MedDRA maps in combination to MedDRA to SNOMED maps (see there). | + | 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. |
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| + | 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 [[documentation:vocabulary:mapping|Mapping description]]. | ||
| - | === ICD9CM to SNOMED map for for Concepts that do not represent entities at the time of recording === | + | === Instructions for ETL === |
| - | For example, Concepts for history of, family history of, need for vaccination, etc. refer to observations that are recorded at a certain time, but the medical entity they are referring to, such as the disease for which family history is recorded, occurred at a different unspecified time earlier. These codes are mapped to SNOMED Observation Concepts using the "Maps to" relationship, and to the relevant medical entity to the "Maps to value" relationship. For example, ICD9CM 249.21 "Secondary diabetes mellitus with hyperosmolarity, uncontrolled" is mapped to Concept 195771 "Secondary diabetes mellitus" as well as 444369 "Hyperosmolality". These multiple mappings can sometimes involve target Concepts of different domains. For example, ICD9CM 679.10 "Fetal complications from in utero procedure" is mapped to the Procedure 4043197 "Procedure on uterus" as well as the Condition 436489 "Complication of obstetrical surgery AND/OR procedure". | + | 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 === | === Hierarchical relationships between 3, 4 and 5-characer Concepts === | ||
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| ==== Hierarchy ==== | ==== Hierarchy ==== | ||
| - | ICD9CM Concepts are non-Standard Concepts and therefore do not participate in the hierarchy of the OMOP Standardized Vocabularies CONCEPT_ANCESTOR table. However, the relationships between corresponding 3, 4 and 5-character Concepts exist as Concept Relationships in the CONCEPT_RELATIONSHIP table (see above). | + | 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
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