documentation:vocabulary:icdo3
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documentation:vocabulary:icdo3 [2020/01/03 16:16] ekorchmar |
documentation:vocabulary:icdo3 [2021/03/22 10:54] (current) ekorchmar Updated to match current version |
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| === Concept Classes === | === Concept Classes === | ||
| There are three concept classes in ICDO3 vocabulary. | There are three concept classes in ICDO3 vocabulary. | ||
| - | == ICDO Topography == | + | |
| + | **1. ICDO Topography** | ||
| Concepts that represent various body sites. | Concepts that represent various body sites. | ||
| - | ICDO Topography concepts correspond to malignant neoplastic Condition concepts in [[ICD10]] vocabulary and use the same 4 character alphanumeric codes. | + | ICDO Topography concepts generally correspond to codes of malignant neoplastic condition concepts in [[ICD10]] vocabulary and use the same format 4 character alphanumeric codes. |
| ^ CONCEPT_CODE ^ VOCABULARY_ID ^ CONCEPT_NAME ^ CONCEPT_CLASS_ID ^ | ^ CONCEPT_CODE ^ VOCABULARY_ID ^ CONCEPT_NAME ^ CONCEPT_CLASS_ID ^ | ||
| | C15.2 | ICDO3 | Abdominal esophagus | ICDO Topography | | | C15.2 | ICDO3 | Abdominal esophagus | ICDO Topography | | ||
| | C15.2 | ICD10 | Malignant neoplasm: Abdominal part of oesophagus | ICD10 code | | | C15.2 | ICD10 | Malignant neoplasm: Abdominal part of oesophagus | ICD10 code | | ||
| - | Note: benign neoplasms, in-situ neoplasms or neoplasms of uncertain behavior will still use same ICD10 codes for topography. | + | | C15 | ICDO3 | Esophagus | ICDO Topography | |
| + | Benign neoplasms, in-situ neoplasms or neoplasms of uncertain behavior will still use same ICD10 codes for malignant neoplasm to represent topography. Conversion tables from ICD10 conditions to ICDO3 topography codes are [[https://seer.cancer.gov/tools/conversion/ICD03toICD9CM-ICD10-ICD10CM.xls|provided by SEER]]. | ||
| - | == ICDO Histology == | + | All topography concepts are valid and are either standard or mapped to Standard SNOMED concepts from 'Spec Anatomic Site' Domain. |
| + | |||
| + | **2. ICDO Histology** | ||
| Concepts that represent various morphologies of neoplastic diseases. Histology codes are built from 2 parts separated by slash. First part consists of 4 digits and encodes morphology. Last digits encodes behavior of the neoplasm. | Concepts that represent various morphologies of neoplastic diseases. Histology codes are built from 2 parts separated by slash. First part consists of 4 digits and encodes morphology. Last digits encodes behavior of the neoplasm. | ||
| Some cancer registries may store behavior of the neoplasm in a separate field. In OMOP morphology and behavior are treated as a single combined entity. | Some cancer registries may store behavior of the neoplasm in a separate field. In OMOP morphology and behavior are treated as a single combined entity. | ||
| - | == ICDO Condition == | + | Outdated or unconfirmed histology concepts are deprecated in OMOP standard vocabularies but have Concept replaced by links to active counterparts whenever possible. All valid Histology concepts are either mapped to Standard concepts in SNOMED or are Standard themselves. |
| - | Concepts that are formed by combining Histology and Topography concepts together to represent actual disease. Since number of all possible combinations is enormous and no universal validation list exists, only limited number of valid combinations is included. | + | |
| - | Codes of ICDO conditions are formed by concatenating Histology and Topography codes over hyphen. Source data are not expected to have such codes: usually codes are provided separately. | + | **3. ICDO Condition** |
| + | Concepts that are formed by combining Histology and Topography concepts together to represent actual diagnosus. Since number of all possible combinations is enormous and no universal validation list exists, only limited number of valid combinations is included. | ||
| + | |||
| + | Codes of ICDO conditions are formed by concatenating Histology and Topography codes over hyphen. Condition names are concatenated from names of their attributes without any modifications from names of topography and histology. Source data is not expected to have neither these combined codes nor terms: usually codes for Histology and Topography are provided in separate fields. | ||
| Some ICDO Condition concepts feature only Histology or only Topography, as seen from their names and codes. These codes are created for each existing histology and topography to accommodate for incomplete source data. | Some ICDO Condition concepts feature only Histology or only Topography, as seen from their names and codes. These codes are created for each existing histology and topography to accommodate for incomplete source data. | ||
| - | ^ CONCEPT_CODE ^ CONCEPT_NAME ^ | + | ^ CONCEPT_CODE ^ CONCEPT_NAME ^ NOTE ^ |
| - | | 8933/3-NULL | Neoplasm defined only by histology: Adenosarcoma| | + | | 8933/3-NULL | Neoplasm defined only by histology: Adenosarcoma | Condition misses topography definition | |
| - | | NULL-C50.9 | Neoplasm defined only by topography: Breast, NOS| | + | | NULL-C50.9 | Neoplasm defined only by topography: Breast, NOS| Condition misses histology definition | |
| + | | 8560/3-C34.9 | Adenosquamous carcinoma of lung, NOS | Fully defined condition | | ||
| + | |||
| + | //Note: If condition definition misses histology attribute, it is often beneficial to treat topography code as pure ICD10 code// | ||
| All ICDO conditions have equivalence mappings or hierarchical relations built to SNOMED concepts from SNOMED Clinical Finding sub-hierarchy. This way ICDO3 Condition concepts form seamless extension of SNOMED hierarchy. | All ICDO conditions have equivalence mappings or hierarchical relations built to SNOMED concepts from SNOMED Clinical Finding sub-hierarchy. This way ICDO3 Condition concepts form seamless extension of SNOMED hierarchy. | ||
| - | Relations for conditions are built automatically, using manual relations of Topographies and Histologies to corresponding SNOMED concepts. Existing mappings, list of combinations and logic for building the condition hierarchy can be found on projects [[https://github.com/OHDSI/Vocabulary-v5.0/tree/master/ICDO3|github]]. | + | Relations for conditions are built automatically, using manual relations of Topographies and Histologies to corresponding SNOMED concepts. All SNOMED condition that have exact match on attribute set are taken as mapping targets and all concepts that have more generic attribute set are made ancestors. Existing mappings, list of combinations and logic for building the condition hierarchy can be found on projects [[https://github.com/OHDSI/Vocabulary-v5.0/tree/master/ICDO3|github]]. |
| + | |||
| + | Conditions built from outdated or unconfirmed histologies may still be standard with hierarchy participation if no other mapping is available. | ||
| === Standard status and hierarchy === | === Standard status and hierarchy === | ||
| - | Since all concepts in ICDO3 vocabulary map to or form hierarchical relations with concepts in SNOMED CT, ICDO3 in OMOP can be seen as seamless extension of SNOMED hierarchy. Concepts without equivalency mappings are kept standard and have hierarchical relations to SNOMED concepts. No internal hierarchy for ICDO3 is created. | + | Since all concepts in ICDO3 vocabulary map to or form hierarchical relations with concepts in SNOMED CT, ICDO3 in OMOP can be seen as seamless extension of SNOMED hierarchy. Condition concepts without equivalence mappings are kept standard and have hierarchical relations to SNOMED concepts. |
| + | |||
| + | |||
| + | Hierarchical levels of both topography and histology attributes are present and have hierarchical relationships to subsuming attributes. Hierarchical attributes are valid, non-standard and do not participate in combination forming. | ||
| === Relationship === | === Relationship === | ||
| - | All ICDO3 concepts have either hierarchical or mapping relations to SNOMED. | + | All ICDO3 concepts excluding hierarchical levels of attributes have either hierarchical or mapping relations to SNOMED concepts. |
| - | Additionally, ICDO Condition have specific relations to ICDO Histology and ICDO Topography they originate from. Standard ICDO Conditions inherit SNOMED-specific relations to attributes from their ancestors. | + | Additionally, ICDO Condition have specific relations to ICDO Histology and ICDO Topography they originate from. Standard ICDO Conditions inherit and mimic SNOMED-specific relations to attributes from their ancestors. |
| === Domains === | === Domains === | ||
| Line 50: | Line 64: | ||
| | ICDO Histology | Morph Abnormality | Observation | | | ICDO Histology | Morph Abnormality | Observation | | ||
| | ICDO Condition | Clinical Finding | Condition | | | ICDO Condition | Clinical Finding | Condition | | ||
| - | //Note: domain_id for topography concepts is currently assigned wrong and will be updated closest release// | ||
| === External links === | === External links === | ||
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| * [[https://seer.cancer.gov/icd-o-3/|NIH SEER]]: ICDO3 coding guidelines and validation list | * [[https://seer.cancer.gov/icd-o-3/|NIH SEER]]: ICDO3 coding guidelines and validation list | ||
| * [[https://confluence.ihtsdotools.org/display/DOCEG/SNOMED+CT+Editorial+Guide|SNOMED CT editorial guide]]: used to create attribute extensions and manage hierarchy | * [[https://confluence.ihtsdotools.org/display/DOCEG/SNOMED+CT+Editorial+Guide|SNOMED CT editorial guide]]: used to create attribute extensions and manage hierarchy | ||
| + | * [[https://seer.cancer.gov/tools/conversion/ICD03toICD9CM-ICD10-ICD10CM.xls|Conversion tables from ICD10 conditions to ICD-O topography]]: Recommended for use for ETL | ||
documentation/vocabulary/icdo3.1578068168.txt.gz · Last modified: 2020/01/03 16:16 by ekorchmar
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