OMOP Vocabulary Updates - National-Clinical-Cohort-Collaborative/Data-Ingestion-and-Harmonization GitHub Wiki

OMOP Vocabulary updates are performed monthly or as needed if more frequent update is necessary. OMOP Vocabulary is downloaded from https://athena.ohdsi.org/vocabulary/list.

The following list of standardized vocabularies are included in the update:

  • 12 Gender- OMOP Gender
  • 13 Race- Race and Ethnicity Code Set (USBC)
  • 71 ABMS- Provider Specialty (American Board of Medical Specialties)
  • 55 OPCS4- OPCS Classification of Interventions and Procedures version 4 (NHS)
  • 111 Episode Type- OMOP Episode Type
  • 48 Medicare Specialty- Medicare provider/supplier specialty codes (CMS)
  • 6 LOINC- Logical Observation Identifiers Names and Codes (Regenstrief Institute)
  • 141 Cancer Modifier- Diagnostic Modifiers of Cancer (OMOP)
  • 21 ATC- WHO Anatomic Therapeutic Chemical Classification
  • 2 ICD9CM- International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)
  • 88 CVX- CDC Vaccine Administered CVX (NCIRD)
  • 109 MEDRT- Medication Reference Terminology MED-RT (VA)
  • 82 RxNorm Extension- RxNorm Extension (OHDSI)
  • 14 CMS Place of Service- Place of Service Codes for Professional Claims (CMS)
  • 1 SNOMED- Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)
  • 4 CPT4- Current Procedural Terminology version 4 (AMA)
  • 89 PPI- AllOfUs_PPI (Columbia)
  • 40 DRG- Diagnosis-related group (CMS)
  • 41 MDC- Major Diagnostic Categories (CMS)
  • 43 Revenue Code- UB04/CMS1450 Revenue Codes (CMS)
  • 44 Ethnicity- OMOP Ethnicity
  • 60 PCORNet National Patient-Centered Clinical Research Network (PCORI)
  • 65 Currency- International Currency Symbol (ISO 4217)
  • 72 CIEL- Columbia International eHealth Laboratory (Columbia University)
  • 80 EphMRA ATC- Anatomical Classification of Pharmaceutical Products (EphMRA)
  • 81 NFC- New Form Code (EphMRA)
  • 35 ICD10PCS- ICD-10 Procedure Coding System (CMS)
  • 9 NDC- National Drug Code (FDA and manufacturers)
  • 117 HemOnc- HemOnc
  • 70 ICD10CM- International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)
  • 34 ICD10- International Classification of Diseases, Tenth Revision (WHO)
  • 47 NUCC- National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC)
  • 5 HCPCS- Healthcare Common Procedure Coding System (CMS)
  • 50 SPL- Structured Product Labeling (FDA)
  • 8 RxNorm- RxNorm (NLM)
  • 127 Nebraska Lexicon- Nebraska Lexicon
  • 128 OMOP Extension- OMOP Extension (OHDSI)
  • 3 ICD9Proc- International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS)
  • 138 NCIt- NCI Thesaurus (National Cancer Institute)
  • 7 NDFRT National Drug File - Reference Terminology (VA)
  • 90 ICDO3 - Oncology Extension. Note this is not part of the CDM V.5.3.1 version.
  • 146 OMOP Genomic - OMOP Genomic vocabulary - request to add 7/19/2022
  • 118 NAACCR- Data Standards & Data Dictionary Volume II (NAACCR) - request to add 08/29/2023
  • 46 MeSH Medical Subject Headings (NLM) - requested to add 6/25/2024

The CPT-4 vocabulary is reconstituted to the concept table manually and updated. See below for details.

  1. unpack the zip files.
  2. After unpacking, simply open a command line in the directory you unpacked all the files into and run "java -Dumls-user=xxx -Dumls-password=xxx -jar cpt4.jar 5". Please replace "xxx" with UMLS username and password. (***Note, this step will update the CONCEPT.csv file by merging the CPT4 codes. It is a good practice to create a backup copy of the CONCEPT.csv before running this utility. ) If you have APIKEY then use the APIKEY to connect to UMLS site.
  3. Backup the OMOP vocabulary tables.
  4. Truncate the OMOP vocabulary table.
  5. Load the newly downloaded/ updated *.csv files into the OMOP vocabulary tables.

Important: All vocabularies are fully represented in the downloaded files with the exception of CPT-4: OHDSI does not have a distribution license to ship CPT-4 codes together with the descriptions. Therefore, CPT4 vocabularies are updated manually by logging into the UMLS site. And download the CPT4 codes directly from the UMLS site and merge the update.