ICD-9-CM

Vocabulary_ID=2

The following describes the procedure to update the ICD-9-CM vocabulary 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.

1.1 Scripts Transfer

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

Script Name	Description
02_create_schema.sql	Create prestage-stage schema with tables and indexes
02_transform_row_maps.sql	Convert and store in stage table SOURCE_TO_CONCEPT_MAP_STAGE
02_load_to_prestage_concepts.ctl	Concepts control file
02_load_maps.sql	Load only new maps into SOURCE_TO_CONCEPT_MAP table, add invalid code information
02_load_to_prestage_FDB_NDC.ctl	ICD9CM_SEARCH control file
02_load_to_prestage_FDB_IND.ctl	FDB Concept Indications control file

1.2 Download data from source

1.2.1 Download data from CMS source

The most current international release is located at the following URL: http://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.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. cmsv30_master_descriptions.zip)
Transfer downloaded zip file to /data/ICD directory.

Latest production zip file is ~1MB in size

1.2.2 Download data from UMLS source

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

Download the latest release file (e.g. )

2012AA UMLS Files
May 7 2012 11:00:00 ET
2012AA.CHK
2012AA.MD5
2012AA-1-meta.nlm
2012AA-2-meta.nlm
2012AA-otherks.nlm
mmsys.zip
Copyright_Notice.txt
README.txt

Transfer downloaded zip file to /data/ICD directory.

Latest production zip file is ~4GB in size

Download and extract all UMLS data and zip files to the same directory.

Read the README file before downloading, which includes information on installing the UMLS Knowledge Sources and highlights changes for this release.

Additional documentation is available at http://www.nlm.nih.gov/research/umls.

At 1M bits/second, it will take approximately 4 hours to download the complete UMLS release. Downloading is advised only if you have a very fast Internet connection.

1.2.3 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/ICD directory.

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

Note: For the rest of the document we will be referring to current schema as ICD9CM_20120831 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 as following: ICD9CM_20120831
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: CMS_DESC_LONG_DX as well as staging tables:

CONCEPT_STAGE, CONCEPT_ANCESTOR_STAGE,

CONCEPT_RELATIONSHIP_STAGE,
SOURCE_TO_CONCEPT_MAP_STAGE

$ sqlplus System/<SystemPass>@DEV_VOCAB @02_create_schema.sql < ICD9CM _Schema> <Pass_ ICD9CM _Schema>

Format of ICD9CM _Schema should be ICD9CM _YYYYMMDD (e.g. ICD9CM _20120831)

1.4 Raw data load into Oracle tables

1.4.1 Extract files from the zip archive into the current directory

$ unzip -u cmsv30_master_descriptions.zip

1.4.2 Verify that the following 2 files have been created:

CMS_DESC_LONG_DX.txt (Latest file size ~1MB)

CMS_DESC_LONG_SG.txt (Latest file size ~0.1MB)

1.4.3 Create consistent file names that are not release dependent.

$ mv CMS30_DESC_LONG_DX.txt CMS_DESC_LONG_DX.txt

1.4.4 Load CMS raw data into Oracle.

      Each sqlldr process will run for about 1min.
          $ sqlldr  ICD9CM_20120831/myPass@DEV_VOCAB control=02_load_to_prestage_concepts.ctl

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

1.4.6 Verify that number of records loaded is equivalent to prior production load
                     $ sqlplus  ICD9CM_20120831/myPass@DEV_VOCAB
           Execute the following SQL commands:
    SELECT count(*) FROM CMS_DESC_LONG_DX;
Current production row count is:     14,567 Rows

1.4.7 Load UMLS raw data into Oracle.

INSTALLING FROM DVD OR HARD DISK
- For best results the DVD drive should be 6X or higher.
- Insert DVD and start MetamorphoSys:
- Windows: The DVD should autorun. If not, or if installing from hard disk, go to the DVD root directory and click on "run.bat."

Click on "Install UMLS" button.
Each UMLS release includes MetamorphoSys, required to install Knowledge Sources files, and to create, search and browse customized Metathesaurus subsets. MetamorphoSys requires a minimum of 30 GB of free hard disk and takes 2-10 hours to run on a range of platforms tested. The actual time will depend on your configuration, hardware and operating system platforms.

MetamorphoSys can generate custom load scripts for Oracle when creating a Metathesaurus subset or installing the Semantic Network. Instructions for loading a subset of the UMLS Metathesaurus or Semantic Network into a database, by using the scripts and files created by MetamorphoSys, are provided below. Some modification of the scripts created by MetamorphoSys might be needed under special circumstances.

Create a schema specifically for this data.

Set tablespace at unlimited, or high enough to ensure the amount of space available is what is needed by the data. Granting UNLIMITED TABLESPACE is acceptable as long as "AUTOEXTEND" is turned on to allow for unlimited table space growth.

Create synonyms for tables or only access tables using the same login used to create them.

Do not use the SYS/SYSTEM account to load data into the database since the default table space is SYSTEM, which is reserved for the data dictionary.

Use MTH or another account to insert data into the database; do not use "AS SYSDBA" to see the tables. Setting the proper grants from the beginning will solve this problem.

The loader script must be changed to SCHEMA.TABLE format to insert data into the proper tables if the SYS/SYSTEM account is used.

The database must use the UTF-8 character set.

Go to the top-level UMLS directory and click on "populate_oracle_db.bat"

1.4.8 Verify that number of records loaded is equivalent to prior production load
                     $ sqlplus  ICD9CM_20120831/myPass@DEV_VOCAB
           Execute the following SQL commands:
    SELECT count(*) FROM MRCONSO;
Current production row count is:         11,254,051 Rows

1.4.9 Load FDB raw data into Oracle.

Each sqlldr process will run for about 1min.

$ sqlldr ICD9CM_20120831/myPass@DEV_VOCAB control=02_load_to_prestage_FDB_NDC.ctl

$ sqlldr ICD9CM_20120831/myPass@DEV_VOCAB control=02_load_to_prestage_FDB_IND.ctl

1.4.10 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/ICD/*.zip /data/backup_area ; cp -Ru /data/ICD/*.log /data/backup_area

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

$ sqlplus ICD9CM_20120831/myPass@DEV_VOCAB

Execute the following SQL commands:

SELECT count(*) FROM RFMLISR0_ICD9CM_SEARCH;

Current production row count is: 172,276 Rows

SELECT count(*) FROM RFMLDX0_DXID;

Current production row count is: 4,544 Rows

1.5 Loading Staging Tables from raw

1.5.1 Convert and store in staging table maps
Loaded from raw staged data CMS_DESC_LONG_DX into the staged data SOURCE_TO_CONCEPT_MAP_STAGE

$  sqlplus ICD9CM_20120831/myPass@DEV_VOCAB @02_transform_row_maps.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 ICD9CM_20120831/myPass@DEV_VOCAB

Execute the following SQL commands:

SELECT '- Num Rec in stage' AS scr, COUNT (8) cnt
FROM SOURCE_TO_CONCEPT_MAP_STAGE c
WHERE c.SOURCE_VOCABULARY_ID IN (02)
UNION ALL
SELECT '- Num Rec in DEV not deleted' AS scr, COUNT (8) cnt
FROM DEV.SOURCE_TO_CONCEPT_MAP d
WHERE     d.SOURCE_VOCABULARY_ID IN (02)
       AND D.TARGET_VOCABULARY_ID IN (01, 19)
       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 SOURCE_TO_CONCEPT_MAP_STAGE c
WHERE c.SOURCE_VOCABULARY_ID IN (02) AND c.TARGET_VOCABULARY_ID IN (01, 19)
       AND NOT EXISTS
                  (SELECT 1
                     FROM DEV.SOURCE_TO_CONCEPT_MAP d
                    WHERE     d.SOURCE_VOCABULARY_ID IN (02)
                          AND c.SOURCE_CODE = D.SOURCE_CODE
                          AND d.SOURCE_VOCABULARY_ID = c.SOURCE_VOCABULARY_ID
                          AND d.MAPPING_TYPE = c.MAPPING_TYPE
                          AND d.TARGET_CONCEPT_ID = c.TARGET_CONCEPT_ID
                          AND d.TARGET_VOCABULARY_ID = c.TARGET_VOCABULARY_ID)
UNION ALL
SELECT '- How many DEV active will be marked for deletion' AS scr,
       COUNT (8) cnt
FROM DEV.SOURCE_TO_CONCEPT_MAP d
WHERE     d.SOURCE_VOCABULARY_ID IN (02)
       AND D.TARGET_VOCABULARY_ID IN (01, 19)
       AND NVL (d.INVALID_REASON, 'X') <> 'D'
       AND d.VALID_START_DATE <
              TO_DATE (
                 SUBSTR (USER, REGEXP_INSTR (USER, '_[[:digit:]]') + 1, 256),
                 'YYYYMMDD')
       AND NOT EXISTS
                  (SELECT 1
                     FROM SOURCE_TO_CONCEPT_MAP_STAGE c
                    WHERE     c.SOURCE_VOCABULARY_ID IN (02)
                          AND c.SOURCE_CODE = D.SOURCE_CODE
                          AND d.SOURCE_VOCABULARY_ID = c.SOURCE_VOCABULARY_ID
                          AND d.MAPPING_TYPE = c.MAPPING_TYPE
                          AND d.TARGET_CONCEPT_ID = c.TARGET_CONCEPT_ID
                          AND d.TARGET_VOCABULARY_ID = c.TARGET_VOCABULARY_ID)
       AND EXISTS
              (SELECT 1
                 FROM SOURCE_TO_CONCEPT_MAP_STAGE c
                WHERE     d.SOURCE_CODE = c.SOURCE_CODE
                      AND d.SOURCE_VOCABULARY_ID = c.SOURCE_VOCABULARY_ID
                      AND d.MAPPING_TYPE = c.MAPPING_TYPE
                      AND d.TARGET_VOCABULARY_ID = c.TARGET_VOCABULARY_ID);

Current Result:

- Num Rec in stage 14266
- Num Rec in DEV not deleted         32948
- How many records would be new in DEV added          1359
- How many DEV active will be marked for deletion    2105

  1.5.3   Load new maps 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 SOURCE_TO_CONCEPT_MAP_STAGE to DEV.SOURCE_TO_CONCEPT_MAP table

   $  sqlplus ICD9CM_20120831/myPass@DEV_VOCAB @02_load_maps.sql