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implementation_international_drug_vocabulary [2020/06/23 19:26]
aostropolets
implementation_international_drug_vocabulary [2021/06/09 10:15] (current)
adavydov
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-===== International ​drugs vocabulary implementation process =====+===== International ​drug vocabulary implementation process =====
 The most straightforward way to standardize a local drug [[documentation:​vocabulary|Vocabulary]] is to utilize [[documentation:​international_drugs|RxNorm Extension]] logic to extend standard Drug concept pool and map source drug products to concepts in RxNorm and RxNorm Exterension. The most straightforward way to standardize a local drug [[documentation:​vocabulary|Vocabulary]] is to utilize [[documentation:​international_drugs|RxNorm Extension]] logic to extend standard Drug concept pool and map source drug products to concepts in RxNorm and RxNorm Exterension.
  
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 Brand Names that are simple combinations of generic international name of active substance and manufacturer name (e.g. "​Aspirin Bayer"​) should not appear as attributes for Drug Products. Manufacturer information should be stored as a concept with Supplier class. Brand Names that are simple combinations of generic international name of active substance and manufacturer name (e.g. "​Aspirin Bayer"​) should not appear as attributes for Drug Products. Manufacturer information should be stored as a concept with Supplier class.
  
-Concepts that belong to the source vocabulary, but do not belong to Drug domain by OMOP CDM conventions,​ should be classified as '​Device'​. Typically, these belong to different ​substance ​groups: +Concepts that belong to the source vocabulary, but do not belong to Drug domain by OMOP CDM conventions,​ should be classified as '​Device'​. Typically, these belong to different groups ​- check the list [[documentation:vocabulary:​drug|here]].
-  * Radiographic contrasts and dyes (barium sulfate, radiolabeled iodides) +
-  * Formulas for infant feeding +
-  * Parenteral nutrition (aminoacids and/or lipid mixes) +
-  * Solution for dialysis, catheter maintenance etc. +
-  * Blood products for transfusion,​ blood plasma, autologous and non-autologous transplants of any kind +
-  * Cosmetics, sunscreens, non-medicated shampoos and soaps, etc. +
-  * Surgical materials like bone cements +
-  * Topical/​external disinfectants+
    
 Animal drugs can be handled as Drugs or Devices, depending on what their role in patient data can be expected to be. Animal drugs can be handled as Drugs or Devices, depending on what their role in patient data can be expected to be.
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 This table should contain the mapping between source codes and Standard Concepts for Ingredients,​ Brand Names, Dose Forms, Suppliers and Units. All other relationships will be ignored. This table should contain the mapping between source codes and Standard Concepts for Ingredients,​ Brand Names, Dose Forms, Suppliers and Units. All other relationships will be ignored.
  
-^Field^Required^Type^Description^ +^ Field              ^ Required ​ ^ Type         ​^ Description ​                                                                                                                                                                                                                                                                                                                                                                                ​
-|concept_code_1|Yes|VARCHAR(255)|The source code| +| concept_code_1 ​    ​| Yes       ​| VARCHAR(50 | The source code                                                                                                                                                                                                                                                                                                                                                                             | 
-|concept_id_2|Yes|INTEGER|The existing target Concept| +| vocabulary_id_1 ​   | Yes       | VARCHAR(20) ​ | The source vocabulary ​                                                                                                                                                                                                                                                                                                                                                                      
-|precedence|No| ​INTEGER|For multiple concept_code_1/​concept_id_2 combination the order of precedence in which they should be considered for equivalence testing. The mapping with the highest prevalence among the drugs will be used for writing a record to the CONCEPT_RELATIONSHIP table. A missing precedence will be interpreted as precedence 1. Every precedence value should be unique per concept_code_1| +| concept_id_2 ​      ​| Yes       ​| INTEGER ​     | The existing target Concept ​                                                                                                                                                                                                                                                                                                                                                                ​
-|conversion_factor|No|NUMERIC|The factor used to convert the source code to the target Concept. This is usually defined for units|+| precedence ​        ​| No        SMALLINT ​    | For multiple concept_code_1/​concept_id_2 combination the order of precedence in which they should be considered for equivalence testing. The mapping with the highest prevalence among the drugs will be used for writing a record to the CONCEPT_RELATIONSHIP table. A missing precedence will be interpreted as precedence 1. Every precedence value should be unique per concept_code_1 ​ 
 +| conversion_factor ​ | No        | NUMERIC ​     | The factor used to convert the source code to the target Concept. This is usually defined for units                                                                                                                                                                                                                                                                                         ​|
  
 This table should contain all mappings from the new to existing Concepts and their precedence. This table should contain all mappings from the new to existing Concepts and their precedence.
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 ^Field^Required^Type^Description^ ^Field^Required^Type^Description^
-|concept_code_1|Yes|string(255)|One source code of the pair| +|concept_code_1|Yes|VARCHAR(50)|One source code of the pair| 
-|concept_code_2|Yes|string(255)|The other source code of the pair|+|concept_code_2|Yes|VARCHAR(50)|The other source code of the pair|
  
 This table should contain relationships for each Drug Concept: To the Ingredients (always), the Dose Form (if appropriate),​the Supplier (if appropriate) and the Brand Name (if appropriate). All other relationships will be derived and ignored if they exist in the table. The relationships don't need to be symmetrical,​ only the one initiating from the Drug Concept is required. This table should contain relationships for each Drug Concept: To the Ingredients (always), the Dose Form (if appropriate),​the Supplier (if appropriate) and the Brand Name (if appropriate). All other relationships will be derived and ignored if they exist in the table. The relationships don't need to be symmetrical,​ only the one initiating from the Drug Concept is required.
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 ^Field^Required^Type^Description^ ^Field^Required^Type^Description^
-|drug_concept_code|Yes| VARCHAR(255)|The source code of the Drug or Drug Component, either Branded or Clinical| +|drug_concept_code|Yes| VARCHAR(50)|The source code of the Drug or Drug Component, either Branded or Clinical| 
-|ingredient_concept_code|Yes| VARCHAR(255)|The source code for one of the Ingredients|+|ingredient_concept_code|Yes| VARCHAR(50)|The source code for one of the Ingredients|
 |amount_value|No|NUMERIC|The numeric value for absolute content (usually solid formulations)| |amount_value|No|NUMERIC|The numeric value for absolute content (usually solid formulations)|
 |amount_unit|No| VARCHAR(255)|The verbatim unit of the absolute content (solids)| |amount_unit|No| VARCHAR(255)|The verbatim unit of the absolute content (solids)|
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 |denominator_value|No|NUMERIC|The denominator value for a concentration (usually liquid formulations). It should contain a number for Quantified products, and null for everything else.| |denominator_value|No|NUMERIC|The denominator value for a concentration (usually liquid formulations). It should contain a number for Quantified products, and null for everything else.|
 |denominator_unit|No|VARCHAR(255)|The verbatim denominator unit of a concentration (usually liquid formulations)| |denominator_unit|No|VARCHAR(255)|The verbatim denominator unit of a concentration (usually liquid formulations)|
-|box_size|No| ​NUMERIC ​|The number of units per box|+|box_size|No|SMALLINT|The number of units per box|
  
 This table contains the dose of each ingredient in each drug, as well as the box_size. For drugs which have no strength information or have only for some of the containing ingredients,​ the ds_stage record must be omitted. '​0'​ values in ds_stage are only allowed for inert drugs. This table contains the dose of each ingredient in each drug, as well as the box_size. For drugs which have no strength information or have only for some of the containing ingredients,​ the ds_stage record must be omitted. '​0'​ values in ds_stage are only allowed for inert drugs.
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 |pack_concept_code|Yes|VARCHAR(50)|The source code of the Pack, either Branded or Clinical| |pack_concept_code|Yes|VARCHAR(50)|The source code of the Pack, either Branded or Clinical|
 |drug_concept_code|Yes|VARCHAR(50)|The component drug product in the Pack| |drug_concept_code|Yes|VARCHAR(50)|The component drug product in the Pack|
-|amount|No| ​NUMERIC ​|The number of units of the drug product in a pack| +|amount|No| ​SMALLINT ​|The number of units of the drug product in a pack| 
-|box_size|No| ​NUMERIC ​|The number of packs if the pack is boxed (several packs in a larger container|+|box_size|No| ​SMALLINT ​|The number of packs if the pack is boxed (several packs in a larger container|
  
 This table contains the composition of a Clinical or Branded Pack: The Clinical or Branded Drug and, number of doses in each box and number of boxes in each pack. If it is a boxed Pack, it will also contain the box size, since Packs have no records in DS_STAGE like the other drug products. Packs are allowed to have branded drugs as components, although usually Brand Name is only attributed to packs as a whole. Supplier may only be attributed to the pack as a whole. This table contains the composition of a Clinical or Branded Pack: The Clinical or Branded Drug and, number of doses in each box and number of boxes in each pack. If it is a boxed Pack, it will also contain the box size, since Packs have no records in DS_STAGE like the other drug products. Packs are allowed to have branded drugs as components, although usually Brand Name is only attributed to packs as a whole. Supplier may only be attributed to the pack as a whole.
implementation_international_drug_vocabulary.1592940415.txt.gz · Last modified: 2020/06/23 19:26 by aostropolets