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WHO ATC

Vocabulary_ID=21

The following describes the procedure to update the WHO ATC vocabulary (concepts, synonyms, relationships, ancestry) with the latest release of the source.

The load process is a complete refresh of data. All new vocabulary entieties will be added. All vocabulary entities that do not exist in the latest files set will be marked as deprecated.

The concept hierarchy is defined in OMOP for WHO ATC concepts that are part of the following:

    - Anatomical Therapeutic Chemical Classification


1.1 Scripts Transfer

All scripts and files listed at the bottom of this page should be transferred to specially created directory (eg /data/WHO_ATC).


 Script Name  Description
21_create_schema.sql  Create prestage-stage schema with tables and indexes
21_load_to_prestage.sh 
 Load RxNorm row-data
21_transform_row_concepts.sql 
 Convert and store in stage table concept_stage
21_transform_row_relations.sql   Convert and store in stage table concept_relationship_stage
21_load_concepts.sql   Load only new concepts into concept table, add invalid code information
21_load_relations.sql    Load only new relationships into relationship table, add invalid code information.
21_load_to_prestage_ATC_DESC.ctl  Concept Descriptons control file
21_load_to_prestage_ATC_SEQ.ctl Concept SEQNO control file


1.2 Download data from source

            1.2.1 Download data from FDB source

                    The most current international release is located at the following URL: http://www.fdbhealth.com/


    
               
Download the latest release file (e.g.FDB_20120815.zip)

                     Transfer downloaded zip file to /data/WHO_ATC directory.

                    Zip file suffix contains release date (e.g. 07022012=02-Jul-2012)
                     Latest production zip file is ~2MB in size


            1.2.2 Download data from RxNorm source

                    The most current international release is located at the following URL: http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html

                    Historical archives located at: http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormarchive.html

                    Note: Make sure you perform updates in chronological order. So, if you want to process a January and April release, execute the below steps for January, and after successful completion, for April.

                    Download the latest release file (e.g. RxNorm_full_07022012.zip)
                     Transfer downloaded zip file to /data/WHO_ATC directory.

                    Zip file suffix contains release date (e.g. 07022012=02-Jul-2012)
                     Latest production zip file is ~136MB in size

                    Note: For the rest of the document we will be referring to current schema as WHO_ATC_20120702 you would have to adjust this entry to correspond to current release date file

1.3 Build Database Schema

All tables will be located in the schema WHO_ATC_<DateOfSourceFile> as following: WHO_ATC_20120131
The following steps will create a schema and will grant to a schema owner appropriate permissions. 


In addition to the schema, it will create tables to load raw data: RXNCONSO, RETCTBL0_ETC_ID and RETCGC0_ETC_GCNSEQNO as well as staging tables: 

CONCEPT_STAGE, CONCEPT_ANCESTOR_STAGE, 

CONCEPT_RELATIONSHIP_STAGE, 

SOURCE_TO_CONCEPT_MAP_STAGE



$ sqlplus System/<SystemPass>@DEV_VOCAB @21_create_schema.sql <WHO_ATC_Schema> <Pass_WHO_ATC_Schema>

Format of WHO_ATC_Schema should be WHO_ATC_YYYYMMDD (e.g. WHO_ATC_20120815)

1.4 Raw data load into Oracle tables

1.4.1 Extract files from the zip archive into the current directory

        $ unzip -u RxNorm_full_07022012.zip -d rxnorm_20120702


1.4.2 Verify that the following 3 files have been created:

1.4.2.1 RxNorm raw data

     RXNCONSO.RRF    (Latest file size ~96MB)

1.4.2.2 FDB raw data


                RATCD0_ATC_DESC.rrf  ( Search it in FDB source )
                RATCGC0_ATC_GCNSEQNO_LINK.rrf

   

          1.4.3.    Load raw data into Oracle. 

      

1.4.3.1   Load RxNorm raw data into Oracle. 

            This sqlldr process will run for about 2min.

        $ ./21_load_to_prestage.sh /data/WHO_ATC/rxnorm_20120702 <WHO_ATC_Schema>/<Pass_ WHO_ATC_Schema>


        1.4.3.2    Load FDB raw data into Oracle. 

                Each sqlldr process will run for about 1min.

              sqlldr  WHO_ATC_20120815/myPass@DEV_VOCAB control=21_load_to_prestage_ATC_DESC.ctl

              $  sqlldr  WHO_ATC_20120815/myPass@DEV_VOCAB control=21_load_to_prestage_ATC_SEQ.ctl

1.4.3.3 Verify that files with extension .bad are empty, no records have been rejected.


1.4.3.4 Copy data and intermediate files to backup area In this step, downloaded files will be archived to preserve source of the data. Discuss a location of backup area with your system administrator.         

        $ cp -Ru /data/WHO_ATC/*.zip /data/backup_area ; cp -Ru /data/WHO_ATC/*.log /data/backup_area

1.4.3.5  Verify that number of records loaded is equivalent to prior production load

                     sqlplus  WHO_ATC_20120815 /myPass@DEV_VOCAB

            Execute the following SQL commands:

    SELECT count(*) FROM RXNCONSO;
Current production row count is:     1,036,726 Rows

     SELECT count(*) FROM RATCD0_ATC_DESC;

Current production row count is:     5,837 Rows



     SELECT count(*) FROM RATCGC0_ATC_GCNSEQNO_LINK;

Current production row count is:     22,529 Rows




1.5 Loading Staging Tables from raw


1.5.1 Convert and store in staging table concepts

Loaded from raw staged data RETCTBL0_ETC_ID&RXNCONSO into the staged data CONCEPT_STAGE

In this step we will perform substitute GUID identifiers into numerical format. 

 

$  sqlplus WHO_ATC_20120815/myPass@DEV_VOCAB @21_transform_row_concepts.sql


1.5.2  Verify that number of records loaded is equivalent to prior production load

    In this step we will verify that number of active records in staging tables is valid prior to transfer data to historical DEV schema. 

    a. Number of Records in stage table

    b. Number of records in DEV schema not deleted (active, prior load production)

    c. How many records would be added to DEV schema table

             d. How many active DEV records will be marked for deletion


    In most cases  number of records in stage (a) should be greater than number of active records in production (b) 
    In rare occasion that might not be the case. It is responsibility of the developer running the scripts to verify that that is the the valid.



     $ sqlplus  WHO_ATC_20120815/myPass@DEV_VOCAB




                Execute the following SQL commands:

 SELECT '- Num Rec in stage' AS scr, COUNT (8) cnt
  FROM CONCEPT_STAGE c
 WHERE C.VOCABULARY_ID = 21
UNION ALL
SELECT '- Num Rec in DEV not deleted' AS scr, COUNT (8) cnt
  FROM DEV.CONCEPT d
 WHERE d.VOCABULARY_ID = 21 AND NVL (d.INVALID_REASON, 'X') <> 'D'
UNION ALL
SELECT '- How many records would be new in DEV added' AS scr, COUNT (8) cnt
  FROM CONCEPT_STAGE c
 WHERE C.VOCABULARY_ID = 21
       AND NOT EXISTS
                  (SELECT 1
                     FROM DEV.CONCEPT d
                    WHERE d.VOCABULARY_ID = 21
                          AND c.CONCEPT_CODE = D.CONCEPT_CODE)
UNION ALL
SELECT '- How many DEV active will be marked for deletion' AS scr,
       COUNT (8) cnt
  FROM DEV.CONCEPT d
 WHERE d.VOCABULARY_ID = 21 AND NVL (d.INVALID_REASON, 'X') <> 'D'
       AND NOT EXISTS
                  (SELECT 1
                     FROM CONCEPT_STAGE c
                    WHERE c.VOCABULARY_ID = 21
                          AND c.CONCEPT_CODE = D.CONCEPT_CODE);


Current Result:
- Num Rec in stage                                                     5837
- Num Rec in DEV not deleted                                     5718
- How many records would be new in DEV added          133
- How many DEV active will be marked for deletion         14

     1.5.3    Load new concepts into DEV schema concept table,mark deprecated concepts as deleted. 

              Valid start date, valid end date and invalid reason are left empty for now.
              Transfer records from CONCEPT_STAGE to DEV.CONCEPT table


            $  sqlplus  WHO_ATC_20120815/myPass@DEV_VOCAB @21_load_concepts.sql 


1.5.4    Load new concept relationships stage, identify invalid codes  information 

 Loaded from the raw staged data RXNREL into the staged data CONCEPT_RELATIONSHIP_STAGE
 identify invalid code information    
 

 $  
sqlplus  WHO_ATC_20120815/myPass@DEV_VOCAB @21_transform_row_relations.sql 

1.5.5  Verify that number of records loaded is equivalent to prior production load


 $ sqlplus  WHO_ATC_20120815/myPass@DEV_VOCAB

SELECT '- Num Rec in stage' AS scr, COUNT (8) cnt

  FROM CONCEPT_RELATIONSHIP_STAGE c

UNION ALL

SELECT '- Num Rec in DEV not deleted' AS scr, COUNT (8) cnt

  FROM DEV.CONCEPT_RELATIONSHIP d

 WHERE EXISTS

          (SELECT 1

             FROM DEV.CONCEPT c

            WHERE c.VOCABULARY_ID IN (08, 21) AND c.CONCEPT_ID = CONCEPT_ID_1)

       AND EXISTS

              (SELECT 1

                 FROM DEV.CONCEPT c

                WHERE c.VOCABULARY_ID IN (08, 21)

                      AND c.CONCEPT_ID = CONCEPT_ID_2)

       AND NVL (d.INVALID_REASON, 'X') <> 'D'

       AND D.RELATIONSHIP_ID IN (010, 131, 144, 245)

UNION ALL

SELECT '- How many records would be new in DEV added' AS scr, COUNT (8) cnt

  FROM CONCEPT_RELATIONSHIP_STAGE c

 WHERE NOT EXISTS

              (SELECT 1

                 FROM DEV.CONCEPT_RELATIONSHIP d

                WHERE     c.CONCEPT_ID_1 = d.CONCEPT_ID_1

                      AND c.CONCEPT_ID_2 = d.CONCEPT_ID_2

                      AND c.RELATIONSHIP_ID = d.RELATIONSHIP_ID)

UNION ALL

SELECT '- How many DEV active will be marked for deletion' AS scr,

       COUNT (8) cnt

  FROM DEV.CONCEPT_RELATIONSHIP d

 WHERE EXISTS

          (SELECT 1

             FROM DEV.CONCEPT c

            WHERE c.VOCABULARY_ID IN (08, 21) AND c.CONCEPT_ID = CONCEPT_ID_1)

       AND EXISTS

              (SELECT 1

                 FROM DEV.CONCEPT c

                WHERE c.VOCABULARY_ID IN (08, 21)

                      AND c.CONCEPT_ID = CONCEPT_ID_2)

       AND NVL (d.INVALID_REASON, 'X') <> 'D'

       AND NOT EXISTS

                  (SELECT 1

                     FROM CONCEPT_RELATIONSHIP_STAGE c

                    WHERE     c.CONCEPT_ID_1 = d.CONCEPT_ID_1

                          AND c.CONCEPT_ID_2 = d.CONCEPT_ID_2

                          AND c.RELATIONSHIP_ID = d.RELATIONSHIP_ID)

       AND D.RELATIONSHIP_ID IN (010, 131, 144, 245);   

Current Result:

 - Num Rec in stage

146996

 - Num Rec in DEV not deleted

135784

 - How many records would be new in DEV added

11212

 - How many DEV active will be marked for deletion

2


1.5.6    Load new concept relationships into DEV schema,mark deprecated concept relatuionships as deleted

         Transfer records from CONCEPT_RELATIONSHIP_STAGE to DEV.CONCEPT_RELATIONSHIP table       


     $ 
 sqlplus  WHO_ATC_20120815/myPass@DEV_VOCAB @21_load_relations.sql 




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