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Merge pull request #26 from mcwdsi/update-labels
Update Labels
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| -- Create RxNorm tables in a SQLite database. | ||
| -- Adapted from their scripts/mysql/Table_scripts_mysql_rxn.sql | ||
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| -- DROP TABLE IF EXISTS RXNCONSO; | ||
| CREATE TABLE RXNCONSO | ||
| ( | ||
| RXCUI varchar(8) NOT NULL, | ||
| LAT varchar (3) DEFAULT 'ENG' NOT NULL, | ||
| TS varchar (1), | ||
| LUI varchar(8), | ||
| STT varchar (3), | ||
| SUI varchar (8), | ||
| ISPREF varchar (1), | ||
| RXAUI varchar(8) NOT NULL, | ||
| SAUI varchar (50), | ||
| SCUI varchar (50), | ||
| SDUI varchar (50), | ||
| SAB varchar (20) NOT NULL, | ||
| TTY varchar (20) NOT NULL, | ||
| CODE varchar (50) NOT NULL, | ||
| STR varchar (3000) NOT NULL, | ||
| SRL varchar (10), | ||
| SUPPRESS varchar (1), | ||
| CVF varchar(50) | ||
| ) | ||
| ; | ||
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| -- DROP TABLE IF EXISTS RXNSAT; | ||
| CREATE TABLE RXNSAT | ||
| ( | ||
| RXCUI varchar(8) , | ||
| LUI varchar(8), | ||
| SUI varchar(8), | ||
| RXAUI varchar(9), | ||
| STYPE varchar (50), | ||
| CODE varchar (50), | ||
| ATUI varchar(11), | ||
| SATUI varchar (50), | ||
| ATN varchar (1000) NOT NULL, | ||
| SAB varchar (20) NOT NULL, | ||
| ATV varchar (4000), | ||
| SUPPRESS varchar (1), | ||
| CVF varchar (50) | ||
| ) | ||
| ; | ||
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| -- DROP TABLE IF EXISTS RXNREL; | ||
| CREATE TABLE RXNREL | ||
| ( | ||
| RXCUI1 varchar(8) , | ||
| RXAUI1 varchar(8), | ||
| STYPE1 varchar(50), | ||
| REL varchar(4) , | ||
| RXCUI2 varchar(8) , | ||
| RXAUI2 varchar(8), | ||
| STYPE2 varchar(50), | ||
| RELA varchar(100) , | ||
| RUI varchar(10), | ||
| SRUI varchar(50), | ||
| SAB varchar(20) NOT NULL, | ||
| SL varchar(1000), | ||
| DIR varchar(1), | ||
| RG varchar(10), | ||
| SUPPRESS varchar(1), | ||
| CVF varchar(50) | ||
| ) | ||
| ; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| #!/bin/sh | ||
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| RXNORM=${1:?Please enter an RxNorm_full version: MMDDYYY} | ||
| UMLS_APIKEY=${UMLS_APIKEY:-2} | ||
| UMLS_APIKEY=${UMLS_APIKEY:?Please provide a UMLS API key https://uts.nlm.nih.gov/uts/edit-profile} | ||
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| fail() { | ||
| echo "ERROR: $@" | ||
| exit 1 | ||
| } | ||
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| ROOT=$(git rev-parse --show-toplevel) || fail "Not a git repository" | ||
| DIR="${ROOT}/src/ontology/tmp/rxnorm" | ||
| FILE="${DIR}/RxNorm_full_${RXNORM}.zip" | ||
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| mkdir -p "${DIR}" || fail "Could not create ${DIR}" | ||
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| echo "Downloading RxNorm_full_${RXNORM}" | ||
| curl -L -o "${FILE}" --fail-with-body \ | ||
| "https://uts-ws.nlm.nih.gov/download?url=https://download.nlm.nih.gov/umls/kss/rxnorm/RxNorm_full_${RXNORM}.zip&apiKey=${UMLS_APIKEY}" \ | ||
| || fail "Could not download ${FILE}" | ||
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| echo "Extracting RRF files to ${DIR}/" | ||
| unzip -j -d "${DIR}" "${FILE}" rrf/* \ | ||
| || fail "Could not unzip ${FILE}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| -- Create RxNorm tables in a SQLite database. | ||
| -- Adapted from their scripts/mysql/Table_scripts_mysql_rxn.sql | ||
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| DROP INDEX IF EXISTS IDX_RXNCONSO_RXCUI; | ||
| CREATE INDEX IDX_RXNCONSO_RXCUI ON RXNCONSO(RXCUI); | ||
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| DROP INDEX IF EXISTS IDX_RXNCONSO_RXAUI; | ||
| CREATE INDEX IDX_RXNCONSO_RXAUI ON RXNCONSO(RXAUI); | ||
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| DROP INDEX IF EXISTS IDX_RXNCONSO_SAB; | ||
| CREATE INDEX IDX_RXNCONSO_SAB ON RXNCONSO(SAB); | ||
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| DROP INDEX IF EXISTS IDX_RXNSAT_RXCUI; | ||
| CREATE INDEX IDX_RXNSAT_RXCUI ON RXNSAT(RXCUI); | ||
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| DROP INDEX IF EXISTS IDX_RXNSAT_SAB; | ||
| CREATE INDEX IDX_RXNSAT_SAB ON RXNSAT(SAB); | ||
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| DROP INDEX IF EXISTS IDX_RXNREL_RXCUI1; | ||
| CREATE INDEX IDX_RXNREL_RXCUI1 ON RXNREL(RXCUI1); | ||
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| DROP INDEX IF EXISTS IDX_RXNREL_RXCUI2; | ||
| CREATE INDEX IDX_RXNREL_RXCUI2 ON RXNREL(RXCUI2); | ||
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| DROP INDEX IF EXISTS IDX_RXNREL_RXAUI1; | ||
| CREATE INDEX IDX_RXNREL_RXAUI1 ON RXNREL(RXAUI1); | ||
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| DROP INDEX IF EXISTS IDX_RXNREL_RXAUI2; | ||
| CREATE INDEX IDX_RXNREL_RXAUI2 ON RXNREL(RXAUI2); | ||
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| DROP INDEX IF EXISTS IDX_RXNREL_RELA; | ||
| CREATE INDEX IDX_RXNREL_RELA ON RXNREL(RELA); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| -- Load RxNorm RRF tables into SQLite. | ||
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| PRAGMA foreign_keys = ON; | ||
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| .mode csv | ||
| .separator | | ||
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| .import tmp/rxnorm/RXNCONSO.RRF RXNCONSO | ||
| .import tmp/rxnorm/RXNSAT.RRF RXNSAT | ||
| .import tmp/rxnorm/RXNREL.RRF RXNREL |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| ATTACH 'tmp/dron.db' AS dron; | ||
| ATTACH 'tmp/chebi.db' AS chebi; | ||
| ATTACH 'tmp/rxnorm.db' AS rxnorm; | ||
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| -- Update labels from ChEBI. | ||
| UPDATE dron.ingredient AS d | ||
| SET label = c.object | ||
| FROM chebi.chebi AS c | ||
| WHERE d.curie LIKE 'CHEBI:%' | ||
| AND d.curie = c.subject | ||
| AND c.predicate = 'rdfs:label' | ||
| AND d.label != c.object; | ||
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| -- Update ingredient labels from RxNorm | ||
| UPDATE dron.ingredient AS d | ||
| SET label = r.STR | ||
| FROM rxnorm.RXNCONSO AS r | ||
| WHERE d.curie LIKE 'DRON:%' | ||
| AND d.rxcui = r.RXCUI | ||
| AND r.SAB = 'RXNORM' | ||
| AND r.TTY = 'IN'; | ||
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| -- clinical_drug_form | ||
| CREATE INDEX IF NOT EXISTS dron.clinical_drug_form_rxcui | ||
| ON clinical_drug_form(rxcui); | ||
| UPDATE dron.clinical_drug_form AS d | ||
| SET label = r.STR | ||
| FROM rxnorm.RXNCONSO AS r | ||
| WHERE d.rxcui = r.RXCUI | ||
| AND r.SAB = 'RXNORM' | ||
| AND r.TTY = 'SCDF'; | ||
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| -- clinical_drug | ||
| CREATE INDEX IF NOT EXISTS dron.clinical_drug_rxcui | ||
| ON clinical_drug(rxcui); | ||
| UPDATE dron.clinical_drug AS d | ||
| SET label = r.STR | ||
| FROM rxnorm.RXNCONSO AS r | ||
| WHERE d.rxcui = r.RXCUI | ||
| AND r.SAB = 'RXNORM' | ||
| AND r.TTY = 'SCD'; | ||
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| -- branded_drug | ||
| CREATE INDEX IF NOT EXISTS dron.branded_drug_rxcui | ||
| ON branded_drug(rxcui); | ||
| UPDATE dron.branded_drug AS d | ||
| SET label = r.STR | ||
| FROM rxnorm.RXNCONSO AS r | ||
| WHERE d.rxcui = r.RXCUI | ||
| AND r.SAB = 'RXNORM' | ||
| AND r.TTY = 'SBD'; |
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