> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/code-sets-in-atlas.md).

# Standard and non-standard codes

Atlas uses the Observational Medical Outcomes Partnership (OMOP) common data model ([OMOP-CDM](https://www.ohdsi.org/data-standardization/the-common-data-model/)). Atlas cohorts can be created using both standard and non-standard codes.

{% hint style="info" %}
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).
{% endhint %}

### 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](/finngen-data-specifics/finnish-health-registers-and-medical-coding/international-and-finnish-health-code-sets.md)) are grouped into alternative hierarchies using classification codes.
* Standard codes are divided into [domains](https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary: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](https://finngen.github.io/ETL). FinOMOP maintains a [report](https://finngen.github.io/FinOMOP_OMOP_vocabulary/StatusReport/dashboard.html#databases-coverage) 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](https://finngen.github.io/ETL/appendix_vocabularies.html) 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](https://finngen.github.io/ETL/appendix_vocabularies.html) 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

![](/files/N0tBPAGEE4ryWhEJ8tUK)

![](/files/ZOehS5oS2fm2dE17tKvp)

From DF11 onwards drug codes in Atlas are VNR codes. To use ATC codes user can select to [include descendants](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/concept-sets/selecting-descendants-for-a-concept-set-in-atlas.md) in the [Concept Set ](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/concept-sets.md)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**.

{% hint style="info" %}
Do not mix both standard and non-standard codes in the same Concept Set (see common mistakes below for more information).
{% endhint %}

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](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/cohort-definitions/mapping-between-atlas-registries-and-medical-codes.md).

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

![](/files/Gk2y9V5MgLMa1w5RGJa0)

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

![](/files/xrSUrPmB8YQCHlLD5vYz)

#### 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:

![](/files/79OZ4GYde9pIY2s1nibt)

#### Common mistakes

{% hint style="info" %}
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.
{% endhint %}

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:

![](/files/MgJneDMXiDxufcH1RNcp)

{% hint style="info" %}
Another common mistake is to create a Concept Set with both standard and non-standard codes.
{% endhint %}

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.