documentation:vocabulary:icdo3
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documentation:vocabulary:icdo3 [2020/01/03 17:01] ekorchmar |
documentation:vocabulary:icdo3 [2020/01/08 09:37] ekorchmar added short description for automation logic |
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| 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. | 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. | + | 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 these codes or terms: usually codes for Histology and Topography are provided separately. |
| 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 ^ NOTE ^ | ^ CONCEPT_CODE ^ CONCEPT_NAME ^ NOTE ^ | ||
| - | |||
| | 8933/3-NULL | Neoplasm defined only by histology: Adenosarcoma | Condition misses topography definition | | | 8933/3-NULL | Neoplasm defined only by histology: Adenosarcoma | Condition misses topography definition | | ||
| | NULL-C50.9 | Neoplasm defined only by topography: Breast, NOS| Condition misses histology definition | | | NULL-C50.9 | Neoplasm defined only by topography: Breast, NOS| Condition misses histology definition | | ||
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| 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]]. |
| === 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 equivalence 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. Concepts without equivalence mappings are kept standard and have hierarchical relations to SNOMED concepts. No internal hierarchy for ICDO3 is currently created. |
| === Relationship === | === Relationship === | ||
documentation/vocabulary/icdo3.txt ยท Last modified: 2021/03/22 10:54 by ekorchmar
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