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documentation:international_drugs [2017/09/06 18:00]
aostropolets [Challenges and problems]
documentation:international_drugs [2019/07/24 14:09] (current)
ekorchmar
Line 40: Line 40:
  
 Currently not supported in the Standardized Vocabularies:​ Currently not supported in the Standardized Vocabularies:​
-^Concept Class^Composed of^Note^ +^ Concept Class        ^ Composed of  ^ Note                                                                                                                                                             ​
-|Precise Ingredient|Ingredient|Ingredient used instead| +| Precise Ingredient ​  ​| Ingredient ​  ​| Ingredient used instead; Precise Ingredients are mapped to Ingredients inside CONCEPT_RELATIONSHIP table                                                         
-|Multiple Ingredient|Ingredients|Single ingredients used instead| +| Multiple Ingredient ​ | Ingredients ​ | Single ingredients used instead ​                                                                                                                                 
-|Dose Form Group|Dose Form|Explicit Dose Forms used instead|+| Dose Form Group      | Dose Form    | Explicit Dose Forms used instead; Dose Form Groups exist as Classification concepts and bear relation to standard concepts only inside native RxNorm vocabulary  ​|
  
 The Concepts are connected through hierarchical and lateral relationships. The Concepts are connected through hierarchical and lateral relationships.
  
 ==== Combined target structure ==== ==== Combined target structure ====
-To incorporate a new set of drug information,​ a structure ​should be achieved ​that contains every Concept only once and preserves the RxNorm structure, no matter which vocabulary the additional Concept is coming from. In a way, it should create a mixed RxNorm/drug vocabularies union.+To incorporate a new set of drug information,​ a structure that contains every Concept only once and preserves the RxNorm structure, no matter which vocabulary the additional Concept is coming from should be achieved. This means that for each source drug concept a standard concept that follows RxNorm logic is created and correctly placed inside a hierarchy. In a way, it should create a mixed RxNorm/drug vocabularies union.
  
 In order to achieve this, any two equivalent Concepts have to be matched through its components: Ingredients to Ingredients,​ Forms to Forms, Supplier to Supplier, etc. Concepts are defined as matching if all components match. For example, a Clinical Drug matches another Clinical Drug if it contains the same Ingredients at the same strength and the same Dose Form.  In order to achieve this, any two equivalent Concepts have to be matched through its components: Ingredients to Ingredients,​ Forms to Forms, Supplier to Supplier, etc. Concepts are defined as matching if all components match. For example, a Clinical Drug matches another Clinical Drug if it contains the same Ingredients at the same strength and the same Dose Form. 
 +
 +For specifics, see [[:​implementation_international_drug_vocabulary|International drugs vocabulary implementation process]]
  
 ==== Rules for adding Concepts ==== ==== Rules for adding Concepts ====
Line 67: Line 69:
 Units used in the strength determination are not added. They must be mapped to a Standard UCUM Concept instead. If a unit is not present in the UCUM vocabulary it has to be added. Units used in the strength determination are not added. They must be mapped to a Standard UCUM Concept instead. If a unit is not present in the UCUM vocabulary it has to be added.
  
-==== Challenges and problems ==== +=== Implementation ​=== 
-To implement a tool to create and maintain the above structure, a number of issues need to be taken care of:+Concepts from source vocabularies must be added following [[:implementation_international_drug_vocabulary|International drugs vocabulary implementation process]].
  
-  * **Excipients:​** There is no general agreement of what is an active agreement and what is an excipient. Therefore, some of the ingredients need to be declared as “semiactive”,​ such as gelatine. Therefore they should be excluded from a list of a drug's ingredients. +=== Result ===
-  * **Forms:** These are not used the same way across drug vocabularies. For example, RxNorm has a Form "​Cream",​ but also "​Ophthalmic cream",​ "​Vaginal cream",​ "​Rectal cream",​ "Oral cream" and "​Cutaneous cream",​ making this Form ambiguous. Instead of a one-to-one mapping, a one to many mapping with an order of precedence is required to establish matching equivalence between Forms. +
-  * **Strength:​** RxNorm normalizes weight units to "​mg"​ and volume units to mL, but other vocabularies might not. There might be units like "​µg",​ "​gram-%"​ or "​volume-%"​. Special unit conversion tables are needed instead of simple unit mappings. This approach becomes infeasible if units are used where the conversion is dependent on the molecule, like "​mol"​ or "​equivalent"​. +
-  * **Ingredient forms:** Ingredients might have ambiguous chemical forms, which RxNorm calls "​Ingredient"​ and "​Precise Ingredient"​ (e.g. a salt of the active compound). They have to be mapped to the right RxNorm Ingredient. If there is no RxNorm Ingredient to map to and the drug vocabulary to be added contains several ambiguous forms of the same Ingredient, one of them has to be declared Standard. Another problem might occur due to the strength is given for a precise ingredient, rather than a standard ingredient.+
  
 +Concepts belonging to source drug vocabularies have 'Maps to' relations to standard concepts in RxNorm and RxNorm Extension vocabularies.
  
-==== Implementation ==== +Equivalence relationship ​to valid non-standard concepts ​(like Brand Names and Dose forms) is indicated ​by entry in CONCEPT_RELATIONSHIP table with RELATIONSHIP_ID = '​Source - RxNorm eq'​. ​Such relations ​are built for attributes like Dose Forms and Brand Names.
-=== 1. Registering a new drug vocabulary === +
- +
-If a drug vocabulary gets added for the first time, it needs to get listed in the VOCABULARY table. +
- +
-=== 2. Creation of input tables === +
-The new vocabulary should be prepared in the following tables: +
- +
-**DRUG_CONCEPT_STAGE** +
- +
-^ Field                    ^ Required ​ ^ Type         ^ Description ​                                                                                                                                                                                ^ +
-| concept_name ​            | Yes       | string(255) ​ | An unambiguous,​ meaningful and descriptive name for the Concept ​                                                                                                                            | +
-| domain_id ​               | Yes       | string(20) ​  | A foreign key to the DOMAIN table. The standard content is '​Drug',​ but for non-drugs it could be '​Device'​ of '​Observation' ​                                                                 | +
-| vocabulary_id ​           | Yes       | string(20)   | A foreign key to the VOCABULARY table. The value of this field should be identical for all records, indicating the new vocabulary being added. ​                                             | +
-| concept_class_id ​        | Yes       | string(20) ​  | One of the above listed RxNorm Concept Classes ​                                                                                                                                             | +
-| concept_code ​            | Yes       | string(50) ​  | The code in the source vocabulary. If the source vocabulary does not contain a code, e.g. for ingredients or dose forms, they will be created automatically (see below OMOP created codes | +
-| source_concept_class_id ​ | No        | string(20) ​  | Concept class that is given by the source vocabulary ​                                                                                                                                       | +
-| possible_excipient ​      | No        | string(1) ​   | A flag only relevant to ingredients,​ indicating whether or not they are not active ingredients and could be omitted from an ingredient list.                                                | +
-| valid_start_date ​        | No        | date         | Date when the Concept became valid. This may or may not coincide with the date the product went to market. ​                                                                                 | +
-| valid_end_date ​          | No        | date         | Date when the Concept became invalid. Market withdrawal does not mean a Concept is invalid. ​                                                                                                | +
-| invalid_reason ​          | No        | string(1) ​   | Flag indicating wether the Concept is active (today'​s date between valid_start and valid_end_date),​ or upgraded ('​U'​) or deprecated ('​D'​). ​                                                 | +
- +
-This table is expected to contain as a minimum the comprehensive list of Concept Classes: +
- +
-  * Drug Product (Branded Drug, Clinical Drug, Marketed Product etc.) +
-  * Form +
-  * Brand Name +
-  * Ingredient +
-  * Unit +
-  * Supplier +
- +
-If may contain Branded or Clinical Drug Forms or Components, but if not they will be derived (see below). Note that units should not have their own concept ​in the DRUG_CONCEPT_STAGE table. Instead, they should be used as verbatim. If the precise Concept Class is not known, it can be included as "Drug Product"​ and the correct Concept Class will be assigned during the incorporation automatically based on the availability of Strength, Dose Form, Brand Name, Quantity and Box Size information. +
- +
-Concepts that belong to the source vocabulary, but are not classified as human drugs, should be classified as '​Device'​ or '​Observation'​. Typically, these are radiopharmaceuticals,​ contrast material, surgical material, desinfectants,​ supplements or nutrients. Animal drugs can be handled as Drugs or Devices, depending on the local regulations of the country. +
- +
-**RELATIONSHIP_TO_CONCEPT** +
-This table should contain the mapping between source codes and Standard Concepts for Ingredients,​ Brand Names, Dose Forms, Suppliers and Units.It also may contain mapping from source drugs to Standard Concepts for related ATC classes. All other relationships will be ignored. +
- +
-^Field^Required^Type^Description^ +
-|concept_code_1|Yes|string(255)|The source code| +
-|concept_id_2|Yes|integer|The existing target Concept| +
-|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. Only precedence=1 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|float|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. It should also contain links between Ingredients and Drug Classification Concepts, particularly for the new Ingredients. Since ATC is used as an international standard, relationships to ATC are very desirable. +
- +
-Units should be mapped to Standard Concept Units. Weight units should be converted to milligram, volume units should be mapped to milliliter, molar - to millimole ​with the right conversion factor. The source_code field should contain the verbatim string of the unit.  +
- +
-**INTERNAL_RELATIONSHIP_STAGE** +
- +
-^Field^Required^Type^Description^ +
-|concept_code_1|Yes|string(255)|One source code of the pair| +
-|concept_code_2|Yes|string(255)|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 need not be symmetrical,​ only the one initiating from the Drug Concept is required. +
- +
-**DS_STAGE** +
- +
-^Field^Required^Type^Description^ +
-|drug_concept_code|Yes|string(255)|The source code of the Drug or Drug Component, either Branded or Clinical| +
-|ingredient_concept_code|Yes|string(255)|The source code for one of the Ingredients| +
-|amount_value|No|float|The numeric value for absolute content (usually solid formulations)| +
-|amount_unit|No|string(255)|The verbatim unit of the absolute content (solids)| +
-|numerator_value|No|float|The numerator value for a concentration (usually liquid formulations)| +
-|numerator_unit|No|string(255)|The verbatim numerator unit of a concentration (liquids)| +
-|denominator_value|No|float|The denominator value for a concentration (usally liquid formulations). It should contain a number for Quantified products, and null for everything else.| +
-|denominator_unit|No|string(255)|The verbatim denominator unit of a concentration (liquids)| +
-|box_size|No|integer|The amount 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 might be omitted. ​'0' in ds_stage is only allowed for inert drugs. +
-Drug ingredients should match those in internal_relationship_stage. +
-If ingredients are mapped to the same one in relationship_to_concept their dosages should be summed up. +
-A drug should not contain ingredients in solid (amount) and liquid (numerator/​denominator) form. It might be either source data bias or drug pack. +
- +
-**PС_STAGE** +
- +
-^Field^Required^Type^Description^ +
-|pack_concept_code|Yes|string(255)|The source code of the Pack, either Branded or Clinical| +
-|drug_concept_code|Yes|string(255)|The component drug product in the Pack| +
-|amount|No|integer|The number of units of the drug product in drug_concept_code| +
-|box_size|No|integer|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 the number 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. +
- +
-=== 4. Concept Codes === +
-Source ​systems my designate codes for different levels or Concept Classes. For all Concepts that are inferred or do not come with a code has to be assigned. The codes are constructed of the word "​OMOP"​ and a running number. The running number should be unique across all vocabularies. That means, each time a new vocabulary is added or refreshed, the next Concept Code should be the one of the last (without the '​OMOP'​ string) +1. +
- +
-=== 5. Quality of input tables === +
- +
-The input tables need to have the following quality requirements:​ +
- +
-^ Rule                                                                                                                                           ^ If rule is violated ​                                                                                                                                                                                                   ^ +
-| Each record should be unique in all tables. ​                                                                                                   | The processing will fail.                                                                                                                                                                                              | +
-| Concept Codes should be unique and should not repeat for different products. ​                                                                  | The processing will fail.                                                                                                                                                                                              | +
-| Combinations of product components should be unique. These are Ingredient-strength(s) combination,​ Dose Form, Brand Name, Quantity, Box size.  | Only the highest Concept Code is retained, and the other ones are treated as non-standard Concepts and mapped to the highest. ​                                                                                         | +
-| Each product should have links (records in INTERNAL_RELATIONSHIP_STAGE) to all their Ingredients. ​                                             | The product will be treated as if it had only the linked Ingredients. If no Ingredients are linked, the product will be processed into the CONCEPT_STAGE table, but as an orphan without any related Concept Classes. ​ | +
-| Ingredients should be linked to their Standard Counterparts. ​                                                                                  | These Ingredients are treated as new Standard Ingredients. ​                                                                                                                                                            | +
-| Dose Forms should be linked to their Standard Counterparts. ​                                                                                   | The processing will fail.                                                                                                                                                                                              | +
-| Brand Names should be linked to their Standard Counterparts. ​                                                                                  | These Brand Names will be treated as new Concepts. ​                                                                                                                                                                    | +
-| All % in source dosages should be converted into mg/ml (mg) unless it is a gas.                                                                | A drug would not be mapped to it's Standard Conept ​                                                                                                                                                                    | +
-| Marketed Product (a drug that has relationship to it's supplier in INTERNAL_RELATIONSHIP_STAGE) should have both dosage and Dose Form          | The product won't be processed into CONCEPT_STAGE table                                                                                                                                                              | +
-| Boxed drug should have both dosage and Dose Form.                                                                                              | The product won't be processed into CONCEPT_STAGE table. ​                                                                                                                                                              | +
-| Product ingredients should match in INTERNAL_RELATIONSHIP_STAGE and DS_STAGE ​                                                                  | The processing will fail.                                                                                                                                                                                              | +
- +
- +
-=== 5. Processing === +
- +
-If all 4 tables DRUG_CONCEPT_STAGE,​ INTERNAL_RELATIONSHIP_STAGE,​ RELATIONSHIP_TO_CONCEPT and DS_STAGE ​are available, the new terminology can be built+
- +
-** Inferring of missing Concept Classes ** +
- +
-All missing Concept Classes are inferred from the existing ones, from bottom upwards.  +
- +
-^Concept Class^Defined by^ +
-|Clinical Drug Component|Ingredient-strength. Note that Clinical Components are always single-Ingredient. This is in contrast to all other Concept Classes| +
-|Branded Drug Component|Ingredient-strength(s),​ Brand Name| +
-|Clinical Drug Form|Ingredient(s),​ Dose Form| +
-|Branded Drug Form|Ingredient(s),​ Dose Form, Brand Name| +
-|Clinical Drug|Ingredient-strength(s),​ Dose Form| +
-|Branded Drug|Ingredient-strength(s),​ Dose Form, Brand Name| +
-|Quantified Clinical Drug|Ingredient-strength(s),​ Dose Form, Quantity| +
-|Quantified Branded Drug|Ingredient-strength(s),​ Dose Form, Brand Name, Quantity| +
-|Clinical Drug Box|Ingredient-strength(s),​ Dose Form, Box size| +
-|Branded Drug Box|Ingredient-strength(s),​ Dose Form, Brand Name, Box size| +
-|Quantified Clinical Box|Ingredient-strength(s),​ Dose Form, Quantity, Box size| +
-|Quantified Branded Box|Ingredient-strength(s),​ Dose Form, Brand Name, Quantity, Box size| +
- +
-Even though all drug classes are inferred, only those will be written to the CONCEPT table that have no mapping to an equivalent Standard Concept. +
- +
-** Matching ** +
-This step is necessary to add inferred equivalence relationships between new and existing Standard Concepts. All matches are created. Links in the RELATIONSHIP_TO_CONCEPT table are ignored.  +
- +
-The matching considers all components (Ingredient-strength(s),​ Dose Form, Brand Name, Quantity, Box size) in the order of precedence and optionally ​for records where possible_excipient is set to 1. A 10% mismatch between strength values is still considered a match. Matching beteween normal and Quantified products compares the Numerator Value of the non-quantied to the Numerator divided by the Denominator Value. +
- +
-** Result **  +
-All records in the DRUG_CONCEPT_STAGE table are written to the CONCEPT_STAGE table as follows. The standard_concept field is set to '​S'​ for all products and Ingredients and Brand Names that have no match to existing Standard Concepts. Dose Forms are always written as non-standard. +
- +
-All records linking drug products to their Ingredients, ​Dose Forms and Brand Names are written to the CONCEPT_RELATIONSHIP_STAGE table. Note that this can be a one or two step connection:​ +
- +
- * Ingredients,​ Dose Forms and Brand Names that have no equivlent to RxNorm (and are therefore Standard Concepts): These are converted from the INTERNAL_RELATIONSHIP_STAGE table.  +
- * Ingredients,​ Dose Forms and Brand Names that have an RxNorm equivalent (at least one) are not written into the CONCEPT_RELATIONSHIP_STAGE table, but the RxNorm equivalent instead, using the records from the RELATIONSHIP_TO_CONCEPT table with the relationship_id = 'Has standard ing', 'Has standard brand' and 'Has standard form' ​.+
  
 Relationships between Drug Products or derivatives (Drug Forms and Components) are connected through CONCEPT_RELATIONSHIP_STAGE records with the the following relationship_id values: Relationships between Drug Products or derivatives (Drug Forms and Components) are connected through CONCEPT_RELATIONSHIP_STAGE records with the the following relationship_id values:
Line 325: Line 185:
 | Supplier ​            | Marketed Product ​    | Supplier of           | | Supplier ​            | Marketed Product ​    | Supplier of           |
  
-From the pack_content,​ build the name of the Branded and Clinical ​Packs.+Name of the Branded and Clinical ​Pack concepts is built by combining names of the contents.
  
 Relationships between any Drug Concept Class and a Classfication Concept Class is recorded through the "Drug has drug class" and "Drug class of drug" generic relationship pair. Relationships between any Drug Concept Class and a Classfication Concept Class is recorded through the "Drug has drug class" and "Drug class of drug" generic relationship pair.
  
-Finally, a new DRUG_STRENGTH_STAGE table should be created from DS_STAGE and the the unit conversions in RELATIONSHIP_TO_CONCEPTso the content can be added to the DRUG_STRENGTH tableThis includes ony Drug Concepts ​that have no mapping to an existing Standard Concept and are now Standard themselvesThe ingredient_concept_code field is either the RxNorm equivalentor from the newly added vocabularyif unavailable. ​+** Inferring of missing Concept Classes ** 
 + 
 +After RxNorm Extension Standard concept with the fullest attribute set is created ​for each source entity, all missing preceding Concept Classes are inferred ​from the existing onesfrom bottom upwards 
 + 
 +^Concept Class^Defined by^ 
 +|Clinical ​Drug Component|Ingredient-strength. Note that Clinical Components ​are always single-IngredientThis is in contrast to all other Concept Classes| 
 +|Branded Drug Component|Ingredient-strength(s)Brand Name| 
 +|Clinical Drug Form|Ingredient(s)Dose Form| 
 +|Branded Drug Form|Ingredient(s),​ Dose Form, Brand Name| 
 +|Clinical Drug|Ingredient-strength(s),​ Dose Form| 
 +|Branded Drug|Ingredient-strength(s),​ Dose Form, Brand Name| 
 +|Quantified Clinical Drug|Ingredient-strength(s),​ Dose Form, Quantity| 
 +|Quantified Branded Drug|Ingredient-strength(s),​ Dose Form, Brand Name, Quantity| 
 +|Clinical Drug Box|Ingredient-strength(s),​ Dose Form, Box size| 
 +|Branded Drug Box|Ingredient-strength(s),​ Dose Form, Brand Name, Box size| 
 +|Quantified Clinical Box|Ingredient-strength(s),​ Dose Form, Quantity, Box size| 
 +|Quantified Branded Box|Ingredient-strength(s),​ Dose Form, Brand Name, Quantity, Box size|
  
-To maintain the continuity of OMOPXXX concept_codes created in this processthey are all stored in the EXISTING_DS table, which is being maintain like a standard OMOP CDM vocabulary ​table.+Even though all drug classes are inferredonly those will be written to the CONCEPT ​table that have no mapping to an existing equivalent Standard Concept.
documentation/international_drugs.1504720802.txt.gz · Last modified: 2017/09/06 18:00 by aostropolets