Appendix: Vocabularies
Vocabulary used comes from the FinOMOP vocabularies v1.0.0.
https://github.com/FinOMOP/FinOMOP_OMOP_vocabulary/releases/tag/v1.0.0
This contains the vocabularies downloaded from Athena v5.0 23-JAN-23 and the vocabularies created by FinOMOP. Within the FinOMOP vocabularies, vocabulary FGVisitType was created by FinnGen to code the visit as they appear in the source data.
List of vocabularies from Athena
| VOCABULARY ID | VOCABULARY NAME |
|---|---|
| SNOMED | Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO) |
| ICD9CM | International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) |
| ICD9Proc | International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS) |
| CPT4 | Current Procedural Terminology version 4 (AMA) |
| HCPCS | Healthcare Common Procedure Coding System (CMS) |
| LOINC | Logical Observation Identifiers Names and Codes (Regenstrief Institute) |
| RxNorm | RxNorm (NLM) |
| NDC | National Drug Code (FDA and manufacturers) |
| Gender | OMOP Gender |
| Race | Race and Ethnicity Code Set (USBC) |
| CMS Place of Service | Place of Service Codes for Professional Claims (CMS) |
| ATC | WHO Anatomic Therapeutic Chemical Classification |
| ICD10 | International Classification of Diseases, Tenth Revision (WHO) |
| ICD10PCS | ICD-10 Procedure Coding System (CMS) |
| Revenue Code | UB04/CMS1450 Revenue Codes (CMS) |
| Ethnicity | OMOP Ethnicity |
| NUCC | National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC) |
| Medicare Specialty | Medicare provider/supplier specialty codes (CMS) |
| SPL | Structured Product Labeling (FDA) |
| OPCS4 | OPCS Classification of Interventions and Procedures version 4 (NHS) |
| HES Specialty | Hospital Episode Statistics Specialty (NHS) |
| Currency | International Currency Symbol (ISO 4217) |
| ABMS | Provider Specialty (American Board of Medical Specialties) |
| RxNorm Extension | RxNorm Extension (OHDSI) |
| ICDO3 | International Classification of Diseases for Oncology, 3rd Edition |
| Episode Type | OMOP Episode Type |
| HemOnc | HemOnc |
| NAACCR | Data Standards & Data Dictionary Volume II (NAACCR) |
| Nebraska Lexicon | Nebraska Lexicon |
| OMOP Extension | OMOP Extension (OHDSI) |
| Cancer Modifier | Diagnostic Modifiers of Cancer (OMOP) |
| OMOP Genomic | OMOP Genomic vocabulary |
| UCUM | Unified Code for Units of Measure (Regenstrief Institute) |
List of vocabularies from FinOMOP
For more information on the mapping status see the status dashboard
| VOCABULARY ID | VOCABULARY NAME |
|---|---|
| FHL | Finnish Hospital League |
| ICD8fi | International Classification of Diseases, Eight Revision (Finland) |
| HPN | Heart Patients Codes (New) |
| ICD9fi | International Classification of Diseases, Ninth Revision (Finland) |
| ICD10fi | International Classification of Diseases, Tenth Revision (Finland) |
| LABfi_ALL | Laboratory Codes FinnGen Specific along with all the codes in Finland |
| MEDSPECfi | Medical Specialty Finland |
| MICROBEfi | Microbial Codes Finland |
| MICROBEfi_TKU | Microbial Codes Finland, Turku Hospital Extension |
| NCSPfi | NOMESCO Classification of Surgical Procedures (Finland) |
| SNOMED2fi | Systematic Nomenclature of Medicine, Second Edition (Finland) |
| ProcedureModifier | Procedure Modifier |
| REIMB | Kela Reimbursement Codes |
| SPAT | SPAT Procedure Codes For Primary Care |
| UNITfi_ALL | Units for FinnGen specific along with all units from Finland |
| VNRfi | Nordic Article Number (Finland) |
| ICPC | International Classification of Primary Care |
| HPO | Heart Patients Codes (Old) |
| ProfessionalCode | Professional Code |
| FGVisitType | FinnGen Visit Type |