HCPCS

Vocabulary_ID=5

The following describes the procedure to update the HCPCS 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/HCPCS).

Script Name	Description
05_create_schema.sql	Create prestage-stage schema with tables and indexes
05_transform_row_maps.sql	Convert and store in stage table SOURCE_TO_CONCEPT_MAP_STAGE
05_load_to_prestage_concepts.ctl	Concepts control file
05_load_concepts.sql	Load only new concepts into concept table, add invalid code information
05_load_maps.sql	Load only new maps into SOURCE_TO_CONCEPT_MAP table, add invalid code information
05_transform_row_concepts.sql	Convert and store in stage table concept_stage

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/HCPCSReleaseCodeSets/Alpha-Numeric-HCPCS-Items/CMS1253559.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.12anweb.zip (2012 Alpha-Numeric HCPCS File [ZIP, 808KB] ) )
Transfer downloaded zip file to /data/HCPCS 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/HCPCS 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.

1.3 Build Database Schema

All tables will be located in the schema HCPCS_<DateOfSourceFile> as following: HCPCS_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: MRCONSO as well as staging tables:

CONCEPT_STAGE, CONCEPT_ANCESTOR_STAGE,

CONCEPT_RELATIONSHIP_STAGE,
SOURCE_TO_CONCEPT_MAP_STAGE

$ sqlplus System/<SystemPass>@DEV_VOCAB @05_create_schema.sql < HCPCS_Schema> <Pass_HCPCS_Schema>

Format of HCPCS_Schema should be HCPCS_YYYYMMDD (e.g. HCPCS_20120507)

1.4 Raw data load into Oracle tables

1.4.1 Extract files from the zip archive into the current directory

$ unzip -u 12anweb.zip

1.4.2 Verify that the following file(s) have been created:

12anweb.txt (Latest file size ~1MB)

1.4.3 Create consistent file names that are not release dependent.

$ mv 12anweb.txt tXXanweb_V3.txt

1.4.4 Load CMS raw data into Oracle.

Each sqlldr process will run for about 1min.

$ sqlldr HCPCS_20120507/myPass@DEV_VOCAB control=05_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 HCPCS_20120507/myPass@DEV_VOCAB

Execute the following SQL commands:

SELECT count(*) FROM txxanweb_V3;

Current production row count is: 9,439 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 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/HCPCS/*.zip /data/backup_area ; cp -Ru /data/HCPCS/*.log /data/backup_area

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

$ sqlplus HCPCS_20120507/myPass@DEV_VOCAB

Execute the following SQL commands:

SELECT count(*) FROM MRCONSO;

Current production row count is: 10,810,680 Rows

1.5 Loading Staging Tables from raw

1.5.1 Convert and store in staging table concepts

Loaded from raw staged data RXNCONSO into the staged data CONCEPT_STAGE

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

$ sqlplus HCPCS_20120507/myPass@DEV_VOCAB @05_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 HCPCS_20120507/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 = 05
UNION ALL
SELECT '- Num Rec in DEV not deleted' AS scr, COUNT (8) cnt
FROM DEV.CONCEPT d
WHERE d.VOCABULARY_ID = 05 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 = 05
       AND NOT EXISTS
              (SELECT 1
                 FROM DEV.CONCEPT d
                WHERE d.VOCABULARY_ID = 05 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 = 05
       AND NVL (d.INVALID_REASON, 'X') <> 'D'
       AND NOT EXISTS
              (SELECT 1
                 FROM CONCEPT_STAGE c
                WHERE c.VOCABULARY_ID = 05 AND c.CONCEPT_CODE = D.CONCEPT_CODE);

Current Result:

- Num Rec in stage            5952

- Num Rec in DEV not deleted             5819

- How many records would be new in DEV added        209

- How many DEV active will be marked for deletion 78

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 HCPCS_20120507/myPass@DEV_VOCAB @05_load_concepts.sql

1.5.4 Convert and store in staging table maps

Loaded from raw staged data RXNCONSO into the staged data SOURCE_TO_CONCEPT_MAP_STAGE

$ sqlplus HCPCS_20120507/myPass@DEV_VOCAB @05_transform_row_maps.sql

1.5.5 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

$ sqlplus HCPCS_20120507/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 (05)
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 (05)
       AND D.TARGET_VOCABULARY_ID IN (05)
       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 (05) AND c.TARGET_VOCABULARY_ID IN (05)
       AND NOT EXISTS
                  (SELECT 1
                     FROM DEV.SOURCE_TO_CONCEPT_MAP d
                    WHERE     d.SOURCE_VOCABULARY_ID IN (05)
                          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 (05)
       AND D.TARGET_VOCABULARY_ID IN (05)
       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 (05)
                          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            6533

- Num Rec in DEV not deleted             6752

- How many records would be new in DEV added        209

- How many DEV active will be marked for deletion 0

    1.5.6 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 HCPCS_20120507/myPass@DEV_VOCAB @05_load_maps.sql