CodeSystem

Overview

The CodeSystem resource specifies a set of Concepts included in this code system.

Aidbox assumes a separate creation of the CodeSystem resource and a set of Concepts composing it. This means that the CodeSystem resource describes only meta information of the code system: url, name, publisher, etc. Whereas Concept resources describe the content of the code system and are associated with the code system by the Concept.system attribute with the same value as the CodeSystem.url element.

For FHIR conformance, we allow to create the CodeSystem resource with a list of included concepts. If it contains listed Concepts at the moment of saving a CodeSystem, then Aidbox saves submitted Concepts as separate resources. The CodeSystem resource itself is saved without the concept attribute. This method of the CodeSystem creation may be used for small dictionaries (generally, not more than 100 concepts). In the case when your code system is big, Aidbox strongly recommends to create the CodeSystem resource separately and upload Concepts in parts.

CRUD

Create

CodeSystem resource can be created as a FHIR resource with embedded concepts itself. This approach is applicable for those cases when your code system contains a small number of concepts, usually no more than 100.

For example, we will create a CodeSystem for eye color containing Brown, Blue, Green, Hazel, Heterochromia coded concepts.

Request

POST [base]/CodeSystem

{
	"resourceType" : "CodeSystem",
	"id": "custom-eye-color",
	"status": "draft",
	"url": "http://code.system/eyes.color",
	"content": "example",
	"concept" : [     
		{
			"code": "ec-bn",
			"display": "Brown"
		},
		{
			"code": "ec-be",
			"display": "Blue"
		},
		{
			"code": "ec-gn",
			"display": "Green"
		},
		{
			"code": "ec-hl",
			"display": "Hazel"
		},
		{
			"code": "ec-h",
			"display": "Heterochromia"
		}
	]	
}

Response

STATUS: 201

{
    "resourceType": "CodeSystem",
    "id": "custom-eye-color"
    "url": "http://code.system/eyes.color",
    "status": "draft",
    "content": "example"
}

As you can see, the request returns only CodeSystem meta information (url, status, content....), and does not return concept listed in that request. It is because Aidbox divides CodeSystem to CodeSystem body and contained concepts list, and creates all concepts as independent Concept resources.

And if we get Concept with system = http://code.system/eyes.color, we will receive all concepts for this CodeSystem.

Request

GET [base]/CodeSystem?system=http://code.system/eyes.color

Response

STATUS: 200

{
    "resourceType": "Bundle",
    "type": "searchset",
    "entry": [
        {
            "resource": {
                "id": "custom-eye-color-ec-bn",
                "code": "ec-bn",
                "system": "http://code.system/eyes.color",
                "display": "Brown",
                "resourceType": "Concept"
            }
        },
        {
            "resource": {
                "id": "custom-eye-color-ec-be",
                "code": "ec-be",
                "system": "http://code.system/eyes.color",
                "display": "Blue",
                "resourceType": "Concept"
            }
        },
        {
            "resource": {
                "id": "custom-eye-color-ec-gn",
                "code": "ec-gn",
                "system": "http://code.system/eyes.color",
                "display": "Green",
                "resourceType": "Concept"
            }
        },
        {
            "resource": {
                "id": "custom-eye-color-ec-hl",
                "code": "ec-hl",
                "system": "http://code.system/eyes.color",
                "display": "Hazel",
                "resourceType": "Concept"
            }
        },
        {
            "resource": {
                "id": "custom-eye-color-ec-h",
                "code": "ec-h",
                "system": "http://code.system/eyes.color",
                "display": "Heterochromia",
                "resourceType": "Concept"
            }
        }
    ],
    "total": 5,
    ......
}

Another way to create CodeSystem is a separate creation of the CodeSystem body and Concepts.

For example, lets create a CodeSystem with a custom subset of Units of measurement (aka UCUM). We will compose this CodeSystem from the most common healthcare units of measure.

Code	Descriptive Name	Display
%	Persent	%
/uL	PerMicroLiter	/uL
[iU]/L	InternationalUnitsPerLiter	IU/L
kPa	KiloPascal	kPa
ng/mL	NanoGramsPerMilliLiter	ng/mL
U/L	UnitsPerLiter	U/L
u[iU]/mL	MicroInternationalUnitsPerMilliLiter	uIU/mL
ug/dL	MicroGramsPerDeciLiter	ug/dL
ug/L	MicroGramsPerLiter	ug/L
ug/mL	MicroGramsPerMilliLiter	ug/mL
umol/L	MicroMolesPerLiter	umol/L

For this subset, let's create the CodeSystem resource.

Request

POST [base]/CodeSystem

{
    "resourceType": "CodeSystem",
    "id": "custom-ucum-subset",
    "url": "http://code.system/ucum.subset",
    "status": "active",
    "content": "complete"
}

Response

STATUS: 201

{
    "id": "custom-ucum-subset",
    "resourceType": "CodeSystem"
    "url": "http://code.system/ucum.subset",
    "status": "active",
    "content": "complete"
}

And then, create all listed concepts. We can create a set of concepts via multiple POST requests or via one Transaction request.

Multiple requests

POST [base]/Concept

{
 "resourceType": "Concept",
 "system": "http://code.system/ucum.subset",
 "code": "%",
 "display": "%",
 "definition": "Persent"
}

POST [base]/Concept

{
 "resourceType": "Concept",
 "system": "http://code.system/ucum.subset",
 "code": "/uL",
 "display": "/uL",
 "definition": "PerMicroLiter"
}

POST [base]/Concept

{
 "resourceType": "Concept",
 "system": "http://code.system/ucum.subset",
 "code": "[iU]/L",
 "display": "IU/L",
 "definition": "InternationalUnitsPerLiter"
}

......

POST [base]/Concept

{
 "resourceType": "Concept",
 "system": "http://code.system/ucum.subset",
 "code": "umol/L",
 "display": "umol/L",
 "definition": "MicroMolesPerLiter"
}

Transaction request

POST [base]

{
  "type": "transaction",
  "entry": [
    {
      "request": {
        "method": "POST",
        "url": "/Concept"
      },
      "resource": {
        "resourceType": "Concept",
        "system": "http://code.system/ucum.subset",
        "code": "%",
        "display": "%",
        "definition": "Persent"
      }
    },
    {
      "request": {
        "method": "POST",
        "url": "/Concept"
      },
      "resource": {
        "resourceType": "Concept",
        "system": "http://code.system/ucum.subset",
        "code": "/uL",
        "display": "/uL",
        "definition": "PerMicroLiter"
      }
    },
    {
      "request": {
        "method": "POST",
        "url": "/Concept"
      },
      "resource": {
        "resourceType": "Concept",
        "system": "http://code.system/ucum.subset",
        "code": "umol/L",
        "display": "umol/L",
        "definition": "MicroMolesPerLiter"
      }
    }
  ]
}

Read

The read operation works same as the FHIR read interaction.

Request

GET [base]/CodeSystem/custom-eye-color

Response

STATUS: 201

{
    "resourceType": "CodeSystem",
    "id": "custom-eye-color"
    "url": "http://code.system/eyes.color",
    "status": "draft",
    "content": "example"
}

Update

Aidbox does not support update for the CodeSystem resource.

In the terminology, it is a good practice not to update existing Coded Systems. Aidbox follows this principle. If you need to update any existing CodeSystem resource, you will have to explicitly delete this CodeSystem and re-create it again with your changes.

Delete

On delete CodeSystem, Aidbox deletes CodeSystem resource, and marks each Concept with the deprecated = true.

Request

DELETE [base]/CodeSystem/custom-eye-color

Response

STATUS: 201

{
    "url": "http://code.system/eyes.color",
    "status": "draft",
    "content": "example",
    "id": "custom-eye-color",
    "resourceType": "CodeSystem"
}

Let's check all concepts of the system.

Request

GET [base]/Concept/?system=http://code.system/eyes.color

Response

STATUS: 200

{
    "resourceType": "Bundle",
    "type": "searchset",
    "entry": [
        {
            "resource": {
                "id": "custom-eye-color-ec-bn",
                "deprecated": true,
                "code": "ec-bn",
                "system": "http://code.system/eyes.color",
                "display": "Brown",
                "resourceType": "Concept"
            }
        },
        {
            "resource": {
                "id": "custom-eye-color-ec-be",
                "deprecated": true,
                "code": "ec-be",
                "system": "http://code.system/eyes.color",
                "display": "Blue",
                "resourceType": "Concept"
            }
        },
        {
            "resource": {
                "id": "custom-eye-color-ec-gn",
                "deprecated": true,
                "code": "ec-gn",
                "system": "http://code.system/eyes.color",
                "display": "Green",
                "resourceType": "Concept"
            }
        },
        {
            "resource": {
                "id": "custom-eye-color-ec-hl",
                "deprecated": true,
                "code": "ec-hl",
                "system": "http://code.system/eyes.color",
                "display": "Hazel",
                "resourceType": "Concept"
            }
        },
        {
            "resource": {
                "id": "custom-eye-color-ec-h",
                "deprecated": true,
                "code": "ec-h",
                "system": "http://code.system/eyes.color",
                "display": "Heterochromia",
                "resourceType": "Concept"
            }
        }
    ],
    "total": 5,
    ......
}

Operations

Aidbox supports all standard FHIR terminology CodeSystem operations.

FHIR specification	Status	Documentation and samples
$lookup	supported	CodeSystem Concept Lookup
$subsumes	supported	CodeSystem Subsumption testing
$compose	supported	CodeSystem Code composition