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documentation:vocabulary:naaccr [2020/03/10 10:19]
ekorchmar
documentation:vocabulary:naaccr [2020/03/10 11:50]
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, noninvasivein 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 variablesschema 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 variablesas 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: 2020/03/10 11:50 by ekorchmar