Standard and non-standard codes

Atlas uses the Observational Medical Outcomes Partnership (OMOP) common data model (OMOP-CDM). Atlas cohorts can be created using both standard and non-standard codes.

Medical codes from OHDSI standardized vocabularies are called standard codes. Other medical codes are called non-standard codes. We recommend using the standard codes except in specific circumstances (e.g. FGVisitType).

Advantages of standard codes

• Phenotype data can be combined across multiple sources using standard codes (e.g. FinnGen and UKBB).

• Standard codes are organized into hierarchies and allow cohorts to be created at different levels of these hierarchies.

• Some standard codes (e.g. drug ATC codes) are grouped into alternative hierarchies using classification codes.

• Standard codes are divided into domains (e.g. condition, drug, procedure, observation).

Advantages of non-standard codes

• Some non-standard codes are more specific than the standard codes they have been mapped to

• Some non-standard codes may not have a mapping to standard codes

• Some non-standard codes are organized into hierarchies

Mapping non-standard codes to standard codes

FinnGen contains medical codes from several national registers. In addition to standard OHDSI vocabularies, FinnGen uses Finnish national vocabularies from FinOMOP and FinnGen-specific vocabularies. All these vocabularies are loaded into FinnGen Atlas to allow cohorts to be created using both standard and non-standard codes.

The mapping of non-standard codes to standard codes is explained in detail in FinnGen ETL to OMOP CDM. FinOMOP maintains a report that shows the percentage of codes in non-standard vocabularies mapped to standard OHDSI vocabularies.

Standard vocabularies

Standard OHDSI vocabularies used in FinnGen are explained in FinnGen ETL to OMOP CDM and listed in the table below:

Vocabulary	Description
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)
NAACCR	Data Standards & Data Dictionary Volume II (NAACCR)
Nebraska Lexicon	Nebraska Lexicon
OMOP Extension	OMOP Extension (OHDSI)
CAP	CAP electronic Cancer Checklists (College of American Pathologists)
CIM10	International Classification of Diseases, Tenth Revision, French Edition
NCCD	Normalized Chinese Clinical Drug
OMOP Genomic	OMOP Genomic vocabulary
UCUM	Unified Code for Units of Measure (Regenstrief Institute)
ICDO3	International Classification of Diseases for Oncology, 3rd Edition

Non-standard vocabularies

Non-standard vocabularies used in FinnGen are explained in FinnGen ETL to OMOP CDM and listed in the table below:

Vocabulary	Description
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)
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
VNRfi	Nordic Article Number (Finland)
ICPC	International Classification of Primary Care
HPO	Heart Patients Codes (Old)
ProfessionalCode	Professional Code
FGVisitType	FinnGen Visit Type
LABfi_ALL	Laboratory Codes Finland. Improved by combining codes LABfi, LABfi_TMP, LABfi_TKU and LABfi_HUS vocabularies.
UNITfi_ALL	Units Finland. Taken from UNITfi vocabulary and improved for FinnGen Kanta data registry.
KantaServiceProvider	Service provider extracted from CODING_SYSTEM_OID column within FinnGen Kanta registry

Atlas Search

In Atlas, three types of codes are displayed using different colours:

• non-standard codes are in red

• standard codes are in blue

• classification codes are in purple

From DF11 onwards drug codes in Atlas are VNR codes. To use ATC codes user can select to include descendants in the Concept Set to allow translation from ATC to VNR codes.

Atlas Cohort Definitions

In Atlas, a cohort definition starts by creating a Concept Set of medical codes of interest. The Concept Set is then used to create cohorts using additional criteria defined in Cohort Definitions.

Do not mix both standard and non-standard codes in the same Concept Set (see common mistakes below for more information).

Standard codes are given as "condition/procedure/observation" values while non-standard codes are given as "Source Concept" values.

Detailed instructions on how to define standard and non-standard codes in different circumstances are available here.

For example, when defining Inclusion Criteria in the example below:

• standard codes are defined in the "condition occurrence of" box

• non-standard codes are defined in the "Condition Source Concept" box

When defining Cohort Entry Events in the example below:

• standard codes are defined in the "procedure occurrence of" box

• non-standard codes are defined in the "Procedure Source Concept" box

Mixing standard and non-standard codes

To use both standard and non-standard codes at the same time, separate criteria must be defined for the standard and non-standard codes.

In the example below, we have created two Inclusion Criteria; the first for standard and the second for non-standard codes:

Common mistakes

A common mistake is to define both standard and non-standard codes using the same criteria. This will select patients that have both standard and non-standard codes instead of patients with either standard or non-standard codes.

If you define both standard and non-standard codes using the same criteria then the search will first create a group of patients that have the standard codes and then from this group select only those patients that also have the non-standard codes. As a result, we have patients with both standard and non-standard codes instead of patients with standard or non-standard codes.

Do not define both standard and non-standard codes using the same criteria:

Another common mistake is to create a Concept Set with both standard and non-standard codes.

Another common mistake is to create a Concept Set with mixed standard and non-standard codes and then use this Concept Set in the "condition/procedure/observation" or the "Source Concept" box. This search will result in patients with either standard or non-standard codes depending on which box was used.