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documentation:vocabulary:dmd [2016/06/30 13:05] dimshitc1 created |
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- | 1. Ingredients | + | **Overall Structure of vocabulary is meets criteria described here:** |
+ | http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug | ||
+ | |||
+ | All the drug concepts have only relationship_id = 'Maps to' relates to RxNorm Extended or RxNorm concepts | ||
+ | |||
+ | RxNorm and RxNorm extended concept then have all usual relationships and drug_strenght tables (between Ingredient and Drug, Brand Name and Branded Drug and other) | ||
+ | |||
+ | **1. Ingredients**\\ | ||
all Ingredients and VTMs Maps to RxNorm or RxNorm Extension Ingredients | all Ingredients and VTMs Maps to RxNorm or RxNorm Extension Ingredients | ||
if there is VTM containing several ingredients, we map them to each ingredient | if there is VTM containing several ingredients, we map them to each ingredient | ||
- | 18035211000001104 Co-dydramol -> 1125315 Acetaminophen (RxNorm) | + | 18035211000001104 Co-dydramol -> 1125315 Acetaminophen (RxNorm) |
- | 18035211000001104 Co-dydramol -> 1189596 dihydrocodeine (RxNorm) | + | 18035211000001104 Co-dydramol -> 1189596 dihydrocodeine (RxNorm) |
--example with RxNorm Extension when it will be build | --example with RxNorm Extension when it will be build | ||
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some ingredients don't have exact mapping because RxNorm uses more precise version, like | some ingredients don't have exact mapping because RxNorm uses more precise version, like | ||
- | 10157211000001104 Melissa extract 44507591 Melilotus indicus whole extract 1 | + | 10157211000001104 Melissa extract -> 44507591 Melilotus indicus whole extract 1 |
- | 10157211000001104 Melissa extract 42904087 Melilotus officinalis top extract 2 | + | 10157211000001104 Melissa extract -> 42904087 Melilotus officinalis top extract 2 |
- | 10157211000001104 Melissa extract 42899425 Melissa officinalis extract 3 | + | 10157211000001104 Melissa extract -> 42899425 Melissa officinalis extract 3 |
- | 10157211000001104 Melissa extract 46234336 Melissa officinalis flowering top extract 4 | + | 10157211000001104 Melissa extract -> 46234336 Melissa officinalis flowering top extract 4 |
then anlysing drugs containing these ingredients we find out wich ingredient RxNorm uses more often | then anlysing drugs containing these ingredients we find out wich ingredient RxNorm uses more often | ||
--can give an example only after script run | --can give an example only after script run | ||
- | 2. Concept Classes | + | **2. Concept Classes**\\ |
Original dm+d classes (VTM, AMP, AMPP, etc.) are placed in column source_concept_class_id. | Original dm+d classes (VTM, AMP, AMPP, etc.) are placed in column source_concept_class_id. | ||
Concept_class_id is standardized and defined by the rules described here: | Concept_class_id is standardized and defined by the rules described here: | ||
http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug | http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug | ||
- | 3. Brand Names | + | **3. Brand Names**\\ |
- | Dm+d doesn't provide Brand Name as a separate concept, so we parsed drug descriptions in order to get Brand names | + | Dm+d doesn't provide Brand Name as a separate concept, so we parsed drug descriptions in order to get Brand names. |
- | for example "Vastarel MR 35mg tablets (Imported (France))" ->HAS Brand_name (Has ing)-> "OMOP246916 Vastarel MR" (RxE) OR | + | We use here not a clear Brand Name but any Name differs from Dose Form and Ingredient but used as a part of Drug name by Supplier, for example |
+ | relationship_id = 'RxNorm has ing' | ||
+ | Boots Cold and Flu Relief with Ibuprofen tablets (The Boots Company Plc) -> "Boots Cold and Flu Relief with Ibuprofen", | ||
+ | Aquasol A Parenteral 100,000units/2ml solution for injection vials (Imported (United States)) -> Aquasol A Parenteral | ||
+ | Vastarel MR 35mg tablets (Imported (France)) -> "Vastarel MR" | ||
+ | Stromectol 3mg tablets (Imported (France)) 20 tablet -> RxNorm ing of-> Stromectol | ||
+ | -- add example of RxNorm extension Brand Name concept when it'll be done | ||
- | Stromectol 3mg tablets (Imported (France)) 20 tablet -> HAS Brand_name (Has ing)-> 19081723 Stromectol (RxNorm) | + | **4. Drug Packs:**\\ |
- | + | ||
- | 4. Drug Packs: | + | |
built Drug Packs with RxNorm like relationships | built Drug Packs with RxNorm like relationships | ||
- | 5. Dm+d vocabulary contains devices such as bandages, syringes, food supplements, etc. | + | **5. Devices**\\ |
+ | Dm+d vocabulary contains devices such as bandages, syringes, food supplements, etc. | ||
Please see http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:domains for Domain rules definition. | Please see http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:domains for Domain rules definition. | ||
Devices don't have RxNorm Extension equivalents and relationships, they present in OMOP vocabulary as standard concepts | Devices don't have RxNorm Extension equivalents and relationships, they present in OMOP vocabulary as standard concepts | ||
+ | |||
+ | **6. Supplier**\\ | ||
+ | Supplier info added, made relationships between Marketed Drug Product and Supplier: relationships 'Has supplier' и 'Supplier of' as discribed | ||
+ | and between Marketed Drug Product and related Drug-concept relationship_id in ('Has marketed form', 'Marketed form of') | ||
+ | |||
+ | **7. Drug_strength issues**\\ | ||
+ | Most part of the drugs are parsed into ds_stage and then into drug_strenght tables but some of them can't be, some examples of these unparsable drugs | ||
+ | No dosage given: | ||
+ | Generic Glucosamine QCV tablets | ||
+ | Generic ARTISS solution for sealant 2ml pre-filled syringes | ||
- | 6. Supplier | + | |
- | + | Concentration is given not for all ingredients: | |
- | 7. | + | Dithranol 0.4% in Zinc and Salicylic acid paste, |
+ | Apple mistletoe 1mg/1ml with Copper carbonate solution for injection ampoules. | ||
+ | Concentration given is useless | ||
+ | Generic Resolve effervescent granules 8.09g sachets | ||
+ | actually contains combination of | ||
+ | Paracetamol, Ascorbic acid, Sodium bicarbonate, Potassium bicarbonate, Citric acid, Sodium carbonate, | ||
+ | so this 8.09g is totally useless in purpose of drug_strenght building | ||
+ | |||
+ | **8. Percents recalculation** | ||
+ | mostly is obvious, but \\ | ||
+ | sometimes they don't give exact quantitative factor info so define it by the Drug form, for example | ||
+ | "Avoca 95% silver nitrate applicators (Bray Group Ltd) 100 applicator 10 x 10 applicators" | ||
+ | and this is "95% w/w (weight / weight) silver nitrate pencil " , in other words 0,95 mg / mg. | ||
+ |