documentation:vocabulary:naaccr
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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 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. | ||
| + | |||
| + | 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]]. | ||
| === 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 | |
| - | === External links === | + | === Standard status and mapping, by class === |
| - | * [[https://www.naaccr.org/data-standards-data-dictionary/|NAACCR home site]] | + | |
| - | * [[https://staging.seer.cancer.gov/cs/software/02.05.50/|SEER API]] used to derive source tables | + | |
| + | NAACCR concepts currently do not have active mappings to concepts from other vocabularies, excluding some NAACCR variables which are mapped to Standard concepts in [[documentation:vocabulary:episode|Episode]] vocabulary. | ||
| + | ^ Schema level ^ Description ^ | ||
| + | | NAACCR Schema | Non-standard without mapping | | ||
| + | | NAACCR Proc Schema | ::: | | ||
| + | ^ Variable level ^^ | ||
| + | | NAACCR Variable | Standard and non-standard concepts; non-standard concepts may have mapping to standard concepts | | ||
| + | ^ Value level ^^ | ||
| + | | NAACCR Value | Standard and non-standard unmapped concepts | | ||
| + | | NAACCR Procedure | Standard concepts, always map to self | | ||
| + | | Permisssible Range | Non-standard without mapping | | ||
| + | |||
| + | === External relations === | ||
| + | __NAACCR Schema__ concepts have specific relations to precoordinated standard ICDO Condition concepts from [[documentation:vocabulary:icdo3|ICDO3]] concepts sourced from SEER. These relations indicate relation between neoplasm diagnoses and NAACCR schemas containing variables supporting further detalization of diagnoses and treatment history. They are intended to be used in extended ETL logic. | ||
| + | |||
| + | ^ Source vocabulary ^ Source concept_class_id ^ relationship_id ^ Target vocabulary ^ Target concept_class_id ^ | ||
| + | | NAACCR | NAACCR Schema | Schema to ICDO | ICDO3 | ICDO3 Condition | | ||
| + | | NAACCR | NAACCR Proc Schema | Proc Schema to ICDO | ICDO3 | ICDO3 Condition | | ||
| + | ^ Reverse relations ^^^^^ | ||
| + | | ICDO3 | ICDO Condition | ICDO to Schema | NAACCR | NAACCR Schema | | ||
| + | | ICDO3 | ICDO Condition | ICDO to Proc Schema | NAACCR | NAACCR Proc Schema | | ||
| + | |||
| + | === External links === | ||
| + | * [[https://www.naaccr.org/data-standards-data-dictionary/|NAACCR]] home site | ||
| + | * [[https://staging.seer.cancer.gov/cs/software/02.05.50/|SEER API]] used to derive source tables | ||
| + | * 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 | ||
| + | * [[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: 2020/03/10 11:50 by ekorchmar
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