RxNorm

https://www.nlm.nih.gov/research/umls/rxnorm/docs/
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RxNorm is a standardized nomenclature for clinical drugs produced by the National Library of...
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### Configure populate_mysql_rxn.sh parameters

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Example configuration block for the load script parameters.

```bash
MYSQL_HOME= /usr   
user=myuser   
password=p4ssw0rd   
db_name=RxNormPrescribe   
dbserver=ServerName
```

--------------------------------

### Configure Populate_mysql_rxn.bat Parameters

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Example configuration for the batch script parameters required to connect to the MySQL database.

```batch
Set MYSQL_HOME= “C:\Program Files\MySQL\MySQL Server 5.0"
Set user=myuser
Set password=p4ssword
Set host_name=localhost
Set db_name =RxNorm
```

--------------------------------

### Configure MySQL Batch Parameters

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Example configuration for the Populate_mysql_rxn.bat script parameters.

```batch
Set MYSQL_HOME= “C:\Program Files\MySQL\MySQL Server 5.0"
Set user=myuser
Set password=p4ssword
Set host_name=localhost
Set db_name =RxNormPrescribe
```

--------------------------------

### Get drug name and schedule for a specific RxCUI

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Joins rxnconso and rxnsat to retrieve the SBD drug name and MTHSPL drug schedule.

```SQL
SELECT distinct a.rxcui, b.atv as schedule, a.str   
FROM rxnconso a, rxnsat b   
WHERE a.rxcui = '1049565'   
AND a.tty = 'SBD'   
AND a.rxcui = b.rxcui   
AND b.sab = 'MTHSPL'   
AND b.atn = 'DCSA';
```

--------------------------------

### Create MySQL indexes

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Commands to set permissions and execute the index creation script.

```bash
chmod +x Indexes_mysql_rxn.sql   
mysql -umyuser –pmypass -hmyhost RxNorm < Indexes_mysql_rxn.sql
```

--------------------------------

### Create a New MySQL Database

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Command to initialize a new database with UTF-8 character encoding.

```sql
CREATE DATABASE IF NOT EXISTS [database name] CHARACTER SET utf8;
```

--------------------------------

### Execute Indexing Script

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Commands to select the database and run the index creation script.

```sql
USE <DATABASENAME>
\. C:\RXNORM\MySQL\Indexes_mysql_rxn.sql
```

--------------------------------

### Execute Indexing Script

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Commands to select the database and run the index creation script.

```sql
USE <DATABASENAME>

\. C:\RXNORM\MySQL\Indexes_mysql_rxn.sql
```

--------------------------------

### Configure MySQL population script parameters

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Set these variables at the top of populate_mysql_rxn.sh to match your local database environment.

```bash
MYSQL_HOME= /usr   
user=myuser   
password=p4ssw0rd   
db_name=RxNorm   
dbserver=ServerName
```

--------------------------------

### Execute MySQL population script

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Commands to set file permissions and run the population script.

```bash
chmod 775 populate_mysql_rxn.sh
```

```bash
populate_mysql_rxn.sh
```

--------------------------------

### Configure MySQL Indexing for RXNSAT

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Workaround for MySQL index limitation issues by enabling large prefixes and defining specific index and key sizes.

```sql
Set innodb_large_prefix to ON
Create index rxnsat_idx on RXNSAT (RXAUI, RXCUI, SAB, ATN(250),ATV(700))
Alter table RXNSAT add primary key (RXAUI, RXCUI, SAB, ATN(250),ATV(700))
```

--------------------------------

### Monitor MySQL Load Process

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Command to check the status of the database load process within the MySQL shell.

```sql
mysql>show processlist;
```

--------------------------------

### Modify MySQL Load Command for Password-less Connections

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Adjust the execution line in the batch script when the database does not require a password.

```batch
%MYSQL_HOME%\bin\mysql –u %user% -p%password% -h%hostname% --local-infile=1 %db_name% <Table_scripts_mysql_rxn.sql >>mysql.log 2 >&1
```

```batch
%MYSQL_HOME%\bin\mysql –u %user% -h%hostname% --local-infile=1 %db_name% <Table_scripts_mysql_rxn.sql >>mysql.log 2 >&1
```

--------------------------------

### Find quantified form drug data for a given RxCUI

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Retrieves quantified form drug data by querying rxnconso and filtering via rxnrel relationships.

```SQL
SELECT rxcui, sab, tty, suppress, str   
FROM rxnconso   
WHERE tty in ('SCD', 'SBD')   
AND rxcui in (SELECT rxcui1 FROM rxnrel WHERE rxcui2='1359714' AND rela='has_quantified_form');
```

--------------------------------

### Find CODE for a given RxCUI

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Retrieves the CODE associated with a specific RxCUI from the rxnconso table.

```SQL
SELECT code   
FROM rxnconso   
WHERE rxcui='243670';
```

--------------------------------

### Find current RxCUI for a retired RxCUI

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Retrieves the current RxCUI mapping for a retired RxCUI from the rxncui table.

```SQL
SELECT cui2   
FROM rxncui   
WHERE cui1='102889';
```

--------------------------------

### Find normalized NDCs for a given RxCUI

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Retrieves only the RxNorm normalized NDC codes for a specific RxCUI.

```SQL
SELECT atv   
FROM rxnsat   
WHERE atn = 'NDC'   
AND rxcui = '313820'   
AND sab = 'RXNORM';
```

--------------------------------

### Find RxCUI for a given NDDF GCN_SEQ_NO

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Retrieves the RxCUI for a drug using the NDDF GCN_SEQ_NO code.

```SQL
SELECT rxcui   
FROM rxnconso   
WHERE code='023855'   
AND sab='NDDF';
```

--------------------------------

### Find all NDCs for a given RxCUI

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Retrieves all NDC codes associated with a specific RxCUI from the rxnsat table.

```SQL
SELECT atv   
FROM rxnsat   
WHERE atn = 'NDC'   
AND rxcui = '313820';
```

--------------------------------

### Find RxCUI for a given NDC

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Retrieves the RxCUI associated with a specific NDC code from the rxnsat table.

```SQL
SELECT rxcui   
FROM rxnsat   
WHERE atv = '00093075301';
```

--------------------------------

### Modify MySQL command for passwordless access

Source: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html

Adjust the mysql execution line when no password is required for the database connection.

```bash
$MYSQL_HOME/bin/mysql –u $user –p$password $db_name <Table_scripts_mysql_rxn.sql >>mysql.log 2>&1
```

```bash
$MYSQL_HOME/bin/mysql –u$user $db_name <Table_scripts_mysql_rxn.sql >>mysql.log 2>&1
```
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