Merge pull request #104 from mcwdsi/resolve-duplicate-ndcs

fixed duplicate NDCs, updated script to hopefully prevent them in the…

Author: hoganwr

src/scripts/update-dron-from-rxnorm.sql

@@ -256,7 +256,9 @@ WHERE r.RELA = 'has_inactive_ingredient'
   AND c2.RXAUI = r.RXAUI2
   AND c2.RXCUI = bd.rxcui;
 
--- Add NDCs for branded drugs not already in that table.
+-- Add NDCs for branded drugs not already in ndc_branded_drug or ndc_clinical_drug.
+--  Note that by starting with branded drugs, we prefer branded drug association 
+--   in hte event that an NDC is associated with both a branded & a clinical drug.
 INSERT OR IGNORE INTO ndc_branded_drug
 SELECT DISTINCT
     NULL AS curie,
@@ -269,9 +271,10 @@ LEFT JOIN ndc_branded_drug AS n
 WHERE s.RXCUI = bd.rxcui
   AND s.SAB = 'RXNORM'
   AND s.ATN = 'NDC'
-  AND n.curie IS NULL;
+  AND n.curie IS NULL
+  AND s.ATV not in (select ndc from ndc_clinical_drug);
 
--- Add NDCs for clinical drugs not already in that table.
+-- Add NDCs for clinical drugs not already in ndc_clinical_drug or ndc_branded_drug.
 INSERT OR IGNORE INTO ndc_clinical_drug
 SELECT DISTINCT
     NULL AS curie,
@@ -285,4 +288,29 @@ WHERE s.RXCUI = cd.rxcui
   AND s.SAB = 'RXNORM'
   AND s.ATN = 'NDC'
   AND n.curie IS NULL
-  AND s.ATV not in (select ndc from ndc_branded_drug);
+  AND s.ATV not in (select ndc from ndc_branded_drug);
+
+-- In the event that there is an NDC in ndc_clinical_drug, and that is now--
+--  in the current version of RxNorm that we are processing--
+--  associated with a branded drug, then we will isnert a row in 
+--  ndc_branded_drug for this new association. Later, we will deal 
+--  with the redundancy.
+INSERT INTO ndc_branded_drug
+SELECT DISTINCT
+    n.curie as curie,
+    n.ndc as ndc,
+    bd.curie as drug
+FROM rxnorm.RXNSAT as s, 
+     branded_drug as bd, 
+     ndc_clinical_drug AS n
+ WHERE s.ATV = n.ndc
+   AND s.RXCUI = bd.RXCUI
+   AND s.SAB = 'RXNORM'
+   AND s.ATN = 'NDC';
+
+-- Here, we delete anything that got duplicated in the previous step.
+-- If we updated the NDC to a new branded_drug association, then 
+--  we created a new row in ndc_branded_drug, and to avoid duplicawtion
+--  now here will remove all such dups from ndc_clinical_drug
+DELETE from ndc_clinical_drug
+WHERE ndc in (select ndc from ndc_branded_drug); 

src/templates/ingredient.tsv

@@ -2514,7 +2514,7 @@ CHEBI:7465	naltrexone	7243
 CHEBI:7466	nandrolone	7244
 CHEBI:74669	1,2-dioleoyl-sn-glycero-3-phosphocholine	1424656
 CHEBI:746859	travoprost	283809
-CHEBI:746867	remibrutinib	2724365
+CHEBI:746867	Remibrutinib	2724365
 CHEBI:746908	lurbinectedin	2374729
 CHEBI:7470	Naphazoline	7247
 CHEBI:7476	naproxen	7258