Population cdm_source table

SQL/create_CDMv5_tables.sql

@@ -207,7 +207,20 @@ CREATE TABLE IF NOT EXISTS cdm_source
     )
 ;
 
-
+INSERT INTO cdm_source (
+       cdm_source_name,
+       cdm_source_abbreviation,
+       source_description,
+       cdm_release_date,
+       cdm_version) VALUES (
+       'Medicare Claims Synthetic Public Use Files (SynPUFs)',
+       'synPuf',
+       'Medicare Claims Synthetic Public Use Files (SynPUFs) were created to allow interested parties to gain familiarity using Medicare claims data while protecting beneficiary privacy. These files are intended to promote development of software and applications that utilize files in this format, train researchers on the use and complexities of Centers for Medicare and Medicaid Services (CMS) claims, and support safe data mining innovations. The SynPUFs were created by combining randomized information from multiple unique beneficiaries and changing variable values. This randomization and combining of beneficiary information ensures privacy of health information.',
+       CURRENT_DATE,
+       '5.2.2'
+       );
+
+
 
 
 

python_etl/CMS_SynPuf_ETL_CDM_v5.py

@@ -474,7 +474,7 @@ def build_maps():
 									status = "No self map from OMOP (HCPCS/CPT4) to OMOP (HCPCS/CPT4) or code invalid for " + concept_id
 									recs_skipped += 1
 								if( vocabulary_id == OMOP_CONSTANTS.NDC_VOCABULARY_ID):
-									status = "No map from OMOP (NCD) to OMOP (RxNorm) or code invalid for " + concept_id
+									status = "No map from OMOP (NDC) to OMOP (RxNorm) or code invalid for " + concept_id
 									recs_skipped += 1
 								source_code_concept_dict[vocabulary_id,concept_code] = [SourceCodeConcept(concept_code, concept_id, "0", destination_file)]
                         else:

python_etl/README.md

@@ -281,7 +281,7 @@ c) Only two ethnicity concepts (38003563, 38003564) are available.  38003563: Hi
 d) When a concept id has no mapping in the CONCEPT_RELATIONSHIP table:
 - If there is no mapping from OMOP (ICD9) to OMOP (SNOMED) for an ICD9 concept id, target_concept_id for such ICD9 concept id is populated with '0' .
 - If there is no self-mapping from OMOP (HCPCS/CPT4) to OMOP (HCPCS/CPT4) for an HCPCS/CPT4 concept id, target_concept_id for such HCPCS/CPT4 concept id is populated with '0' .
-- If there is no mapping from OMOP (NCD) to OMOP (RxNorm) for an NCD concept id, target_concept_id for such NCD concept id is populated with '0'.
+- If there is no mapping from OMOP (NDC) to OMOP (RxNorm) for an NDC concept id, target_concept_id for such NDC concept id is populated with '0'.
 
 e) The source data contains concepts that appear in the CONCEPT.csv file but do not have relationship mappings to target vocabularies. For these, we create records with concept_id 0 and include the source_concept_id in the record. Achilles Heel will give warnings about these concepts for the Condition, Observation, Procedure, and Drug tables as follows. If condition_concept_id or observation_concept_id or procedure_concept_id or drug_concept_id is '0' respectively:
 - WARNING: 400-Number of persons with at least one condition occurrence, by condition_concept_id; data with unmapped concepts

python_etl/constants.py

@@ -63,7 +63,7 @@ class OMOP_CONSTANTS(object):
 
 # --------------------
 # Record layout for the CONCEPT_RELATIONSHIP.csv file
-# It is used to map: OMOP (NCD) -> OMOP (RXNORM)
+# It is used to map: OMOP (NDC) -> OMOP (RXNORM)
 # It is used to map: OMOP (ICD9) -> OMOP (SNOMED)
 # It is used to map: OMOP (HCPCS) -> OMOP (CPT4)
 # --------------------