Bbv

.gitignore

@@ -0,0 +1,5 @@
+config/pentaho.config
+config/aws.config
+config/pentaho.config
+config.config
+faers.config

README.md

@@ -3,3 +3,6 @@ Standardize FDA LAERS database and FAERS database drugs, indications, reactions
 and generate the unique case report counts and safety signal statistics 
 
 See the documentation folder for more information.
+
+Dependencies:
+Postgres 9.1+ (create table if not exists)

documentation/example-report-extract.sql

@@ -0,0 +1,180 @@
+-- Example of pulling reports for tizanidine
+
+
+
+/*
+python3 getDrugNameMatches.py -d 1 -s 'tizanidine|TIZANIDINE HYDROCHLORIDE|Zanaflex|ZANAFLEX (tizanidine hcl)|ZANAFLEX (tizanidine hydrochloride)|ZANAFLEX (tizanidine hcl 4mg) tablet|TERNELIN|SIRDALUD' -f drugs-unmapped-June2019.csv > /tmp/tizanidine-likely-mispelled.txt
+
+Searching for string matches to TIZANIDINE|TIZANIDINE HYDROCHLORIDE|ZANAFLEX|ZANAFLEX (TIZANIDINE HCL)|ZANAFLEX (TIZANIDINE HYDROCHLORIDE)|ZANAFLEX (TIZANIDINE HCL 4MG) TABLET|TERNELIN|SIRDALUD using input file drugs-unmapped-June2019.csv and 1 allowed character replacements.
+Input file drugs-unmapped-June2019.csv has 356124 lines.
+
+NOTE: There is a record that has no pipes - assuming end of file. Total number of lines processed: 356123. Total lines in file:356124
+
+
+Total length of unmapped drug strings input from the file (removing duplicates): 356108
+
+NOTE: these drug strings could not be processed because they contain more than one pipe symbol. These will need to be corrected BOTH in the database and in   the input file:
+"CELECOXIB;IBUPROFEN|NAPROXEN;PLA(IBUPROFEN)"|2
+"PROACTIV CLEANSER 2.5% BENZOYL PEROXIED GUTHY|RENKER"|2
+"|LISINOPRIL"|1
+"CELECOXIB;IBUPROFEN|NAPROXEN;PLACEBO"|1
+"|METOPROLOL"|1
+"ATORVASTATIN | LOVASTATIN| YEAST EXTRACT FROM MONASCUS PURPUREUS"|1
+"|ATENOLOL"|1
+"|SIMVAST ATIN"|1
+"|SPIRONOLACTONE"|1
+"|MONTELUKAST"|1
+"CADD SOLIS |V PUMP"|1
+"FARXIGA(DAPAG|IFLOZIN PROPANEDIOL) 5 MG TABLET"|1
+
+MATCH RESULTS:
+BIZANIDINE
+CANAFLEX
+DIZANIDINE
+FANAFLEX
+LANAFLEX
+LIZANIDINE
+PIZANIDINE
+RIZANIDINE
+SANAFLEX
+SIDALUD
+SIDALUD (SIRDALUD)
+SIRADALUD
+SIRALUD
+SIRALUD 2
+SIRDALUD (TIZANDINE HYDROCHLORIDE)
+SIRDALUD (TYIZANIDINE HYDROCHLORIDE)
+SIRDALUD /00740702/ (SIRDALUD - TIZANADINE HYDROCHLORIDE) 2MG (NOT SPE
+SIRDALUD /00740702/ (SIRDALUD - TIZANDINE HYDROCHLORIDE) (NOT SPECIFIE
+SIRDALUD/00740702/(SIRDALUD TIZANADINE HYDROCHLORIDE)
+SIRDALUL
+SIRDALUT
+TANAFLEX
+TAZANIDINE
+TAZANIDINE 4MG 2X/DAY
+TAZANIDINE HYDROCHLORIDE (TAZANIDINE HYDROCHLORIDE)
+TERNALIN
+TERNELIN (TERNELIN - TIZANADINE HYDROCHLORIDE)
+TERNELIN (TIAZANIDINE HYDROCHLORIDE)
+TERNELLIN
+THIZANIDINE HCL
+TIANIDINE 4 MG
+TIAZANIDINE (TIAZANIDINE)
+TICANIDINE
+TIDANIDINE
+TIDANIDINE HYDROCHLORIDE
+TIIZANIDINE
+TINZANIDINE
+TINZANIDINE HYDROCHLORIDE
+TIRANIDINE
+TISANIDINE
+TITANIDINE
+TIVANIDINE
+TIVANIDINE HCL
+TIXANIDINE
+TIZAMIDINE
+TIZANADINE 4 MG
+TIZANADINE HCL
+TIZANADINE HCL (UNKNOWN)
+TIZANADINE HYDROCHLORIDE
+TIZANDIDINE
+TIZANDINE 4MG
+TIZANDINE 8MG
+TIZANDINE HYDROCHLORIDE
+TIZANDINE HYDROCHLORIDE (TIZANDINE HYDROCHLORIDE)
+TIZANEDINE
+TIZANICINE
+TIZANIDANE
+TIZANIDENE
+TIZANIDIE
+TIZANIDIN ACTAVIS
+TIZANIDIN EOLAPATADINE
+TIZANIDIN TEVA 2MG
+TIZANIDINE HYDROCHLORIDE (TIZANADINE HYDROCHLORIDE)
+TIZANIDINE HYDROCHLORIDE (TIZANTIDINE HYDROCHLORIDE)
+TIZANIDINEM
+TIZANIDINI HYDROCLORIDUM
+TIZANIDINIE
+TIZANINDINE
+TIZANISINE
+TIZANITINE HCL
+TIZANNIDINE (ZARAFLEX)
+TIZANOIDINE
+TIZANTIDINE
+TIZATIDINE
+TIZENIDINE
+TIZENIDINE (UNKNOWN)
+TIZIANIDINE
+TIZIANIDINE HCL
+TIZINIDINE
+TIZNIDINE
+TIZONIDINE
+TRIZANIDINE
+TRIZANIDINE HCL
+TYZANIDINE
+TYZANIDINE MUSCLE RELAXANT
+TZANIDINE
+XANAFLEX
+XANAFLEX 4MG UNKNOWN
+XANAFLEX MUSCLE RELAXER
+ZAMAFLEX
+ZANAFIEX
+ZANAFLAX
+ZANAFLAX (NOS)
+ZANAFLEX (TIZADNIDINE HYDROCHLORIDE)
+ZANAFLEX (TIZANDIDINE HYDROCHLORIDE)
+ZANAFLEX (TIZANIDFINE HYDROCHLORIDE) (TIZANIDINE HYDROCHLORDIE)
+ZANAFLEX (TYZANIDINE HYDROCHLORIDE)
+ZANAFLEZ
+ZANAFLUX
+ZANALLEX
+ZANAPLEX
+ZANASLEX
+ZANEFLEX
+ZANFLEX
+ZANIFLEX
+ZANNAFLEX
+ZANOFLEX
+ZANTAFLEX
+ZEANAFLEX
+ZENAFLEX
+ZONAFLEX
+
+*/
+
+
+
+
+ -- Query the standardized drug - outcome count tables using the drug concept ids for all reports involving tizanidine and 1 character name variations
+with tizSpecific as (
+   select distinct drug.caseid
+   from faers.drug drug 
+   where drug.drugname ilike '%tizanidine%'
+     or upper(drug.drugname) in ('BIZANIDINE','CANAFLEX','DIZANIDINE','FANAFLEX','LANAFLEX','LIZANIDINE','PIZANIDINE','RIZANIDINE','SANAFLEX','SIDALUD','SIDALUD (SIRDALUD)','SIRADALUD','SIRALUD','SIRALUD 2','SIRDALUD (TIZANDINE HYDROCHLORIDE)','SIRDALUD (TYIZANIDINE HYDROCHLORIDE)','SIRDALUD /00740702/ (SIRDALUD - TIZANADINE HYDROCHLORIDE) 2MG (NOT SPE','SIRDALUD /00740702/ (SIRDALUD - TIZANDINE HYDROCHLORIDE) (NOT SPECIFIE','SIRDALUD/00740702/(SIRDALUD TIZANADINE HYDROCHLORIDE)','SIRDALUL','SIRDALUT','TANAFLEX','TAZANIDINE','TAZANIDINE 4MG 2X/DAY','TAZANIDINE HYDROCHLORIDE (TAZANIDINE HYDROCHLORIDE)','TERNALIN','TERNELIN (TERNELIN - TIZANADINE HYDROCHLORIDE)','TERNELIN (TIAZANIDINE HYDROCHLORIDE)','TERNELLIN','THIZANIDINE HCL','TIANIDINE 4 MG','TIAZANIDINE (TIAZANIDINE)','TICANIDINE','TIDANIDINE','TIDANIDINE HYDROCHLORIDE','TIIZANIDINE','TINZANIDINE','TINZANIDINE HYDROCHLORIDE','TIRANIDINE','TISANIDINE','TITANIDINE','TIVANIDINE','TIVANIDINE HCL','TIXANIDINE','TIZAMIDINE','TIZANADINE 4 MG','TIZANADINE HCL','TIZANADINE HCL (UNKNOWN)','TIZANADINE HYDROCHLORIDE','TIZANDIDINE','TIZANDINE 4MG','TIZANDINE 8MG','TIZANDINE HYDROCHLORIDE','TIZANDINE HYDROCHLORIDE (TIZANDINE HYDROCHLORIDE)','TIZANEDINE','TIZANICINE','TIZANIDANE','TIZANIDENE','TIZANIDIE','TIZANIDIN ACTAVIS','TIZANIDIN EOLAPATADINE','TIZANIDIN TEVA 2MG','TIZANIDINE HYDROCHLORIDE (TIZANADINE HYDROCHLORIDE)','TIZANIDINE HYDROCHLORIDE (TIZANTIDINE HYDROCHLORIDE)','TIZANIDINEM','TIZANIDINI HYDROCLORIDUM','TIZANIDINIE','TIZANINDINE','TIZANISINE','TIZANITINE HCL','TIZANNIDINE (ZARAFLEX)','TIZANOIDINE','TIZANTIDINE','TIZATIDINE','TIZENIDINE','TIZENIDINE (UNKNOWN)','TIZIANIDINE','TIZIANIDINE HCL','TIZINIDINE','TIZNIDINE','TIZONIDINE','TRIZANIDINE','TRIZANIDINE HCL','TYZANIDINE','TYZANIDINE MUSCLE RELAXANT','TZANIDINE','XANAFLEX','XANAFLEX 4MG UNKNOWN','XANAFLEX MUSCLE RELAXER','ZAMAFLEX','ZANAFIEX','ZANAFLAX','ZANAFLAX (NOS)','ZANAFLEX (TIZADNIDINE HYDROCHLORIDE)','ZANAFLEX (TIZANDIDINE HYDROCHLORIDE)','ZANAFLEX (TIZANIDFINE HYDROCHLORIDE) (TIZANIDINE HYDROCHLORDIE)','ZANAFLEX (TYZANIDINE HYDROCHLORIDE)','ZANAFLEZ','ZANAFLUX','ZANALLEX','ZANAPLEX','ZANASLEX','ZANEFLEX','ZANFLEX','ZANIFLEX','ZANNAFLEX','ZANOFLEX','ZANTAFLEX','ZEANAFLEX','ZENAFLEX','ZONAFLEX')
+ ), standardSummary as (
+   select cd.concept_name standard_drug_name,
+          co.concept_name standard_outcome_name,
+          sdod.*           
+   from faers.standard_drug_outcome_drilldown sdod inner join tizSpecific on sdod.caseid = tizSpecific.caseid
+      inner join staging_vocabulary.concept cd on sdod.drug_concept_id = cd.concept_id
+      inner join staging_vocabulary.concept co on sdod.outcome_concept_id = co.concept_id
+)
+select drug.primaryid, drug.caseid, drug.drug_seq, drug.role_cod, drug.drugname, drug.prod_ai, drug.val_vbm, drug.route, drug.dose_vbm, drug.cum_dose_chr, drug.cum_dose_unit, drug.dechal, drug.rechal, drug.lot_num, drug.exp_dt, drug.nda_num, drug.dose_amt, drug.dose_unit, drug.dose_form, drug.dose_freq, drug.filename, 
+       string_agg(distinct standardSummary.drug_concept_id::text, ';') drug_concept_id, string_agg(distinct standardSummary.standard_drug_name, ';') standard_drug_name, 
+       string_agg(distinct standardSummary.standard_outcome_name, ';') standard_outcome_name, string_agg(distinct standardSummary.outcome_concept_id::text, ';') outcome_concept_id, string_agg(distinct standardSummary.snomed_outcome_concept_id::text, ';') snomed_outcome_concept_id, 
+       string_agg(distinct scoc.outc_code, ';') standard_outcome_code, string_agg(distinct scoc.snomed_concept_id::text, ';') standard_outcome_snomed,
+       demo.caseversion, demo.i_f_code, demo.event_dt, demo.mfr_dt, demo.init_fda_dt, demo.fda_dt, demo.rept_cod, demo.auth_num, demo.mfr_num, demo.mfr_sndr, demo.lit_ref, demo.age, demo.age_cod, demo.age_grp, demo.sex, demo.e_sub, demo.wt, demo.wt_cod, demo.rept_dt, demo.to_mfr, demo.occp_cod, demo.reporter_country, demo.occr_country, demo.filename, 
+       indi.indi_drug_seq, indi.indi_pt, indi.filename, 
+       rpsr.rpsr_cod, rpsr.filename 
+from faers.drug drug inner join standardSummary on drug.primaryid = standardSummary.primaryid
+   inner join faers.demo demo on demo.primaryid = standardSummary.primaryid
+   left outer join faers.standard_case_outcome_category scoc on scoc.primaryid = standardSummary.primaryid
+   left outer join faers.indi indi on indi.primaryid = standardSummary.primaryid and indi.indi_drug_seq = drug.drug_seq
+   left outer join faers.rpsr rpsr on rpsr.primaryid = standardSummary.primaryid
+GROUP BY drug.primaryid, drug.caseid, drug.drug_seq, drug.role_cod, drug.drugname, drug.prod_ai, drug.val_vbm, drug.route, drug.dose_vbm, drug.cum_dose_chr, drug.cum_dose_unit, drug.dechal, drug.rechal, drug.lot_num, drug.exp_dt, drug.nda_num, drug.dose_amt, drug.dose_unit, drug.dose_form, drug.dose_freq, drug.filename,         
+         demo.caseversion, demo.i_f_code, demo.event_dt, demo.mfr_dt, demo.init_fda_dt, demo.fda_dt, demo.rept_cod, demo.auth_num, demo.mfr_num, demo.mfr_sndr, demo.lit_ref, demo.age, demo.age_cod, demo.age_grp, demo.sex, demo.e_sub, demo.wt, demo.wt_cod, demo.rept_dt, demo.to_mfr, demo.occp_cod, demo.reporter_country, demo.occr_country, demo.filename, 
+         indi.indi_drug_seq, indi.indi_pt, indi.filename, 
+         rpsr.rpsr_cod, rpsr.filename
+ORDER BY drug.primaryid, drug.drug_seq
+;
+

documentation/example-signal-query.sql

@@ -0,0 +1,12 @@
+set search_path to faers;
+with signals as (
+ select * 
+ from standard_drug_outcome_statistics
+ where case_count >= 10
+  and prr > 3.0
+ limit 100
+ )
+ select c1.concept_name, c2.concept_name, signals.*
+ from staging_vocabulary.concept c1 inner join signals on signals.drug_concept_id = c1.concept_id
+   inner join staging_vocabulary.concept c2 on signals.outcome_concept_id = c2.concept_id
+;