documentation:vocabulary:atc
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documentation:vocabulary:atc [2021/10/02 15:18] ptalapova [Relationships] |
documentation:vocabulary:atc [2021/10/06 15:54] (current) ptalapova [Sources] |
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| ==== Sources ===== | ==== Sources ===== | ||
| - | ATC source codes are obtained from [[https://www.whocc.no/atc_ddd_index|WHOCC ATC/DDD Index 2021]] and, in OMOP, stored in the table of [[https://drive.google.com/file/d/1CJY739Obztme3mlnk89TttbT0_1zQ1rS/view?usp=sharing|class_drugs_scraper]] | + | ATC source codes are obtained from [[https://www.whocc.no/atc_ddd_index|WHOCC ATC/DDD Index 2021]] and, in OMOP, stored in the table of [[https://drive.google.com/file/d/1VX2HRw71Wac7BIN_gh5EOUxNwAF-DqwW/view?usp=sharing|class_drugs_scraper]] |
| ==== Transformation ===== | ==== Transformation ===== | ||
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| === ATC-specific relationships (internal) ==== | === ATC-specific relationships (internal) ==== | ||
| - | ^ relationship_id ^ reverse ^ target\\ vocabulary_id ^ description ^ | + | ^ relationship_id ^ reverse ^ target\\ vocabulary_id ^ description ^ |
| - | | ATC - RxNorm | RxNorm - ATC | RxNorm, RxNorm Extension | - connects ATC Classes and Drug Products, but not Ingredients\\ - technically non-hierarchical, however, semantically it resembles 'Subsumes' - 'Is a' | | + | | ATC - RxNorm | RxNorm - ATC | RxNorm, RxNorm Extension | ■ connects ATC Classes and Drug Products, but not Ingredients\\ ■ technically non-hierarchical, however, semantically it resembles the 'Subsumes' relationship_id with the reverse of 'Is a' | |
| - | | ATC - RxNorm pr lat | RxNorm - ATC pr lat | RxNorm, RxNorm Extension | - connects:\\ -- Monocomponent ATC Classes with their full semantic equivalents in the form of main active Standard Ingredients\\ -- the 1st Active Ingredient of Multicomponent ATC Classes with Standard Ingredients\\ - used as a Primary unambiguous link for ATC Classes with a clear and well-defined Ingredient \\ - non-hierarchical \\ - semantically, it is an equivalent to ‘Maps to’ relationship_id, and usually (except for exemptions) has such a pair in concept_relationship_stage | | + | | ATC - RxNorm pr lat | RxNorm - ATC pr lat | RxNorm, RxNorm Extension | ■ //ATC - RxNorm primary lateral// connects:\\ -- Monocomponent ATC Classes with their full semantic equivalents in the form of main active Standard Ingredients\\ -- the 1st Active Ingredient of Multicomponent ATC Classes with Standard Ingredients\\ ■ used as a Primary unambiguous link for ATC Classes with a clear and well-defined Ingredient \\ ■ non-hierarchical \\ ■ semantically, it is an equivalent to ‘Maps to’ relationship_id, and usually (except for exemptions) has such a pair in concept_relationship | |
| - | | ATC - RxNorm sec lat | RxNorm - ATC sec lat | RxNorm, RxNorm Extension | - connects the 2nd Active Ingredient OR any subsequent Active Ingredient of a Multicomponent ATC Class to Rx/RxN Standard Ingredient\\ - non-hierarchical\\ - used as a Secondary unambiguous link for ATC Classes with clear and well-defined Ingredient(s)\\ - the presence of this link is a prerequisite for creating a ‘Maps to’ relationship_id | | + | | ATC - RxNorm sec lat | RxNorm - ATC sec lat | RxNorm, RxNorm Extension | ■ //ATC - RxNorm secondary lateral// connects the 2nd Active Ingredient OR any subsequent Active Ingredient of a Multicomponent ATC Class to Rx/RxN Standard Ingredient\\ ■ non-hierarchical\\ ■ used as a Secondary unambiguous link for ATC Classes with clear and well-defined Ingredient(s)\\ ■ the presence of this link is a prerequisite for creating a ‘Maps to’ relationship_id | |
| - | | ATC - RxNorm pr up | RxNorm - ATC pr up | RxNorm, RxNorm Extension | - connects the 1st Ingredient Groups of Multicomponent ATC Classes to respective Rx/RxN Standard Ingredients.\\ - applied to Multicomponent ATC Classes, which names:\\ -- starts either from the Ingredient Group or the word of combinations\\ -- contains only one Ingredient Group, which is mentioned somewhere in the middle\\ - hierarchical (applied at the post-processing, gives +1 level of separation)\\ - used as Primary ambiguous link, in which ATC Class is represented with a particular group of Ingredients with a common trait\\ - can be used for a well-defined but diverse group of ingredients (e.g. diastase, tree pollen, feather) | | + | | ATC - RxNorm pr up | RxNorm - ATC pr up | RxNorm, RxNorm Extension | ■ //ATC - RxNorm primary upward// connects the 1st Ingredient Groups of Multicomponent ATC Classes to respective Rx/RxN Standard Ingredients\\ ■ applied to Multicomponent ATC Classes, which names:\\ -- starts either from the Ingredient Group or the word of combinations\\ -- contains only one Ingredient Group, which is mentioned somewhere in the middle\\ ■ hierarchical (applied at the post-processing, gives +1 level of separation)\\ ■ used as Primary ambiguous link, in which ATC Class is represented with a particular group of Ingredients with a common trait\\ ■ can be used for a well-defined but diverse group of ingredients (e.g. diastase, tree pollen, feather) | |
| - | | ATC - RxNorm sec up | RxNorm - ATC sec up | RxNorm, RxNorm Extension | - connects the 2nd Ingredient Group OR any subsequent Ingredient Group OR NOT mentioned and unspecified list of Ingredients, which can be in combination with Primary lateral or Primary upward ATC Classes, to respective Rx/RxN Ingredients.\\ - hierarchical (applied at the post-processing, gives +1 level of separation)\\ - refers to the Secondary ambiguous link for Multicomponent ATC Classes | | + | | ATC - RxNorm sec up | RxNorm - ATC sec up | RxNorm, RxNorm Extension | ■ //ATC - RxNorm secondary upward// connects the 2nd Ingredient Group OR any subsequent Ingredient Group OR NOT mentioned and unspecified list of Ingredients, which can be in combination with Primary lateral or Primary upward ATC Classes, to respective Rx/RxN Ingredients\\ ■ hierarchical (applied at the post-processing, gives +1 level of separation)\\ ■ refers to the Secondary ambiguous link for Multicomponent ATC Classes | |
| === Possible combinations of ATC-specific relationships used at the Ingredient level === | === Possible combinations of ATC-specific relationships used at the Ingredient level === | ||
| Line 65: | Line 65: | ||
| The ATC vocabulary is the hierarchical terminology, in which "the lowest" 5th ATC Drug Classes, reflecting real Drug Products, are connected to "higher" ATC Classes (from the 4th to 1st) via the //one-step// ancestry. In OMOP, the original ATC hierarchy is extended by Standard Drug Products of RxNorm and RxNorm Extension vocabularies, which are assigned to be descendants of the 5th ATC Classes. | The ATC vocabulary is the hierarchical terminology, in which "the lowest" 5th ATC Drug Classes, reflecting real Drug Products, are connected to "higher" ATC Classes (from the 4th to 1st) via the //one-step// ancestry. In OMOP, the original ATC hierarchy is extended by Standard Drug Products of RxNorm and RxNorm Extension vocabularies, which are assigned to be descendants of the 5th ATC Classes. | ||
| - | ==== The OMOP conversion of ATC Administation Routes ==== | + | ==== The OMOP conversion of ATC Administration Routes ==== |
| ^ atc.adm_r ^ omop.adm_r ^ | ^ atc.adm_r ^ omop.adm_r ^ | ||
| | implant | implant | | | implant | implant | | ||
documentation/vocabulary/atc.1633187937.txt.gz · Last modified: 2021/10/02 15:18 by ptalapova
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