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added MINs from rxnconso (https://github.com/OHDSI/Vocabulary-v5.0/is… #640

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merged 1 commit into from
Jul 28, 2022
Merged

added MINs from rxnconso (https://github.com/OHDSI/Vocabulary-v5.0/is… #640

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27 changes: 18 additions & 9 deletions RxNorm/load_stage.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,8 @@ SELECT vocabulary_pack.CutConceptName(str),
THEN 'Clinical Dose Group'
WHEN 'SBDG'
THEN 'Branded Dose Group'
WHEN 'MIN'
THEN 'Multiple Ingredients'
END,
-- only Ingredients, drug components, drug forms, drugs and packs are standard concepts
CASE tty
Expand All @@ -94,6 +96,8 @@ SELECT vocabulary_pack.CutConceptName(str),
THEN NULL
WHEN 'BN'
THEN NULL
WHEN 'MIN'
THEN NULL
ELSE 'S'
END,
-- the code used in RxNorm
Expand Down Expand Up @@ -174,7 +178,8 @@ WHERE sab = 'RXNORM'
'PIN',
'DFG',
'SCDG',
'SBDG'
'SBDG',
'MIN'
);

-- Packs share rxcuis with Clinical Drugs and Branded Drugs, therefore use code as concept_code
Expand Down Expand Up @@ -282,20 +287,24 @@ INSERT INTO concept_stage (
valid_end_date,
invalid_reason
)
SELECT DISTINCT ON (rxcui) vocabulary_pack.CutConceptName(str) AS concept_name,
SELECT DISTINCT ON (rxa.rxcui) vocabulary_pack.CutConceptName(rxa.str) AS concept_name,
'RxNorm' AS vocabulary_id,
'Drug' AS domain_id,
'Multiple Ingredients' AS concept_class_id,
NULL AS standard_concept,
rxcui AS concept_code,
TO_TIMESTAMP(created_timestamp, 'mm/dd/yyyy hh:mm:ss pm')::DATE AS valid_start_date,
rxa.rxcui AS concept_code,
TO_TIMESTAMP(rxa.created_timestamp, 'mm/dd/yyyy hh:mm:ss pm')::DATE AS valid_start_date,
TO_DATE('20991231', 'yyyymmdd') AS valid_end_date,
NULL AS invalid_reason
FROM sources.rxnatomarchive
WHERE tty = 'MIN'
AND sab = 'RXNORM'
ORDER BY rxcui,
TO_TIMESTAMP(created_timestamp, 'mm/dd/yyyy hh:mm:ss pm');
FROM sources.rxnatomarchive rxa
LEFT JOIN sources.rxnconso rx ON rx.rxcui = rxa.rxcui
AND rx.sab = 'RXNORM'
AND rx.tty = 'MIN'
WHERE rx.rxcui IS NULL
AND rxa.tty = 'MIN'
AND rxa.sab = 'RXNORM'
ORDER BY rxa.rxcui,
TO_TIMESTAMP(rxa.created_timestamp, 'mm/dd/yyyy hh:mm:ss pm');

--4. Add synonyms - for all classes except the packs (they use code as concept_code)
INSERT INTO concept_synonym_stage (
Expand Down