documentation:vocabulary:naaccr
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documentation:vocabulary:naaccr [2020/03/10 10:19] ekorchmar |
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| Source tables used for ingestion of NAACCR into OMOP CDM are derived using SEER API. | Source tables used for ingestion of NAACCR into OMOP CDM are derived using SEER API. | ||
| - | === Internal hierarchy === | + | === Internal ontology === |
| - | All NAACCR concepts form ontology from __Schema__ over __Variable__ to __Value__ level. All relationships are stated explicitly through levels, meaning that __Values__ have relations directly to __Schema__ level. Concepts on variable level are also united in kind of hierarchy indicated by relationship_id 'Has parent item' and 'Date of variable'. __Variables__ that belong to mpore than one __Schema__ have stated relations to all of them. Such __Variables__ also don't specify a schema name in their code. | + | All NAACCR concepts form ontology from __Schema__ over __Variable__ to __Value__ level. All relationships are stated explicitly through levels, meaning that __Values__ have relations directly to __Schema__ level. Concepts on __Variable__ level are also united in kind of hierarchy indicated by relationship_id 'Has parent item' and 'Date of variable'. __Variables__ that belong to mpore than one __Schema__ have stated relations to all of them. Such __Variables__ also don't specify a schema name in their code. |
| Currently, source ontology does not participate in forming [[documentation:cdm:concept_ancestor|CONCEPT_ANCESTOR table]], but is fully present in [[documentation:cdm:concept_relationship|CONCEPT_RELATIONSHIP table]]. | Currently, source ontology does not participate in forming [[documentation:cdm:concept_ancestor|CONCEPT_ANCESTOR table]], but is fully present in [[documentation:cdm:concept_relationship|CONCEPT_RELATIONSHIP table]]. | ||
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| === Code format === | === Code format === | ||
| - | All NAACCR codes are ontological, meaning they are built by concatenating all preceding ontological levels to capture meaning. | + | All NAACCR codes are ontological, meaning they are built by concatenating all preceding ontological levels to capture meaning. Schema codes coincide with schema names, Variables and values are numeric. |
| - | Example of code for value representing extent of tumor of colon: | + | ^ Type of concept ^ concept_code ^ concept_name ^ |
| + | | Site-specific variable | brain@2900 | Functional Neurologic Status - Karnofsky Performance Scale (KPS) | | ||
| + | | Site-nonspecific variable | 2810 | CS Extension | | ||
| + | | Site-specific value | **colon**@**2810**@**050** | (Adeno)carcinoma, noninvasive, in a polyp or adenoma | | ||
| + | | Site-nonspecific value | 1004@99 | [TNM Clinical Stage Group] Unknown, not staged | | ||
| - | | **colon**@**2810**@**050** | (Adeno)carcinoma, noninvasive, in a polyp or adenoma| | + | Site-specific value code contains parent schema name (**colon**), variable code (**2810**) and proper value code (**050**). For non-specific values and variables, schema name is omitted. |
| - | Value code contains parent schema name (**colon**), variable code (**2810**) and proper value code (**050**). | + | //Note: site-specific values may belong to site-nonspecific variables, as this is a case in this example// |
| === Concept classes === | === Concept classes === | ||
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| | NAACCR Value | Concepts representing permissible values for most variables | | | NAACCR Value | Concepts representing permissible values for most variables | | ||
| | NAACCR Procedure | Medical procedures belonging to specific schemas | | | NAACCR Procedure | Medical procedures belonging to specific schemas | | ||
| - | | Permisssible Range | Concepts representing certain numeric ranges as answers | | + | | Permisssible Range | Concepts representing allowed numeric ranges for variables. Numeric values outside specified range must be treated as specific codes or conversion artifacts. See [[https://github.com/OHDSI/OncologyWG/wiki/NAACCR-Crosswalk|"3. Populate Modifier record in Measurement for values as numbers"]] proposal for details| |
| === Domains by class === | === Domains by class === | ||
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| | NAACCR Value | Meas Value, Procedure, Observation, Drug | Concepts representing permissible values for most variables. Meas value is the most common, other domains are chosen depending on parent variable domain | | | NAACCR Value | Meas Value, Procedure, Observation, Drug | Concepts representing permissible values for most variables. Meas value is the most common, other domains are chosen depending on parent variable domain | | ||
| | NAACCR Procedure | Procedure, Observation | Procedure domain is default. Observation domain is for concepts indicating special procedure context (e.g. procedure not performed) | | | NAACCR Procedure | Procedure, Observation | Procedure domain is default. Observation domain is for concepts indicating special procedure context (e.g. procedure not performed) | | ||
| - | | Permisssible Range | Meas Value | Concepts representing certain numeric ranges as answers | | + | | Permisssible Range | Meas Value | Currently, numeric concepts don't have a dedicated domain | |
| === Standard status and mapping, by class === | === Standard status and mapping, by class === | ||
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| * Documentation regarding [[https://www.naaccr.org/implementation-guidelines/#ICDO3|joint NAACCR and ICDO3 implementation]] | * Documentation regarding [[https://www.naaccr.org/implementation-guidelines/#ICDO3|joint NAACCR and ICDO3 implementation]] | ||
| * Specifications for upcoming [[https://github.com/OHDSI/OncologyWG/wiki/Episode|Episode table]], which meant to harbor some of NAACCR variable concepts | * Specifications for upcoming [[https://github.com/OHDSI/OncologyWG/wiki/Episode|Episode table]], which meant to harbor some of NAACCR variable concepts | ||
| - | * [[http://datadictionary.naaccr.org/default.aspx | NAACCR dicitonary browser]] | + | * [[http://datadictionary.naaccr.org/default.aspx|NAACCR dicitonary browser]] |
| + | * [[https://github.com/OHDSI/OncologyWG/wiki/ETL-Instructions-for-Mapping-NAACCR-Treatment-Data-into-the-OMOP-CDM|Detailed ETL instructions]] on [[projects:workgroups:oncology-sg|Oncology Workgroup]] Wiki | ||
| + | * Illustrated [[https://github.com/OHDSI/OncologyWG/wiki/NAACCR-Crosswalk|crosswalks]] for ETL process | ||
documentation/vocabulary/naaccr.txt · Last modified: 2024/09/02 11:52 by jcruz
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