AllergyIntolerance resource group

An AllergyIntolerance resource records a patient’s risk of a harmful reaction to a substance: a drug, a food, something in the environment, or a biologic product. The endpoint codes each allergy with SNOMED CT. The resource follows the FHIR R4 AllergyIntolerance specification, and each field name below links to its R4 definition. Allergies get their own resource instead of a Condition, because decision support needs to know the category, the criticality, and the reaction. A prescribing system can then warn before it orders penicillin.

If your EHR already keeps a structured allergy list, treat it as the source of truth. Use extracted allergies to suggest additions for a clinician to review, or turn the group off. See Reduce extraction errors.

What becomes an AllergyIntolerance

Note says	`code`	`type`	`category`
”Penicillin causes hives”	`91936005` Allergy to penicillin	`allergy`	`medication`
”Peanut allergy, carries an EpiPen”	`91935009` Allergy to peanut	`allergy`	`food`
”Lactose intolerant”	`782415009` Intolerance to lactose	`intolerance`	`food`
”Hay fever from grass pollen”	`418689008` Allergy to grass pollen	`allergy`	`environment`

No known allergies

The code names the allergy in positive form. “NKDA” (no known drug allergies) does not become 409137002 No known drug allergy. It becomes an AllergyIntolerance with code 416098002 Allergy to drug and verificationStatus: refuted.

Note says	`code`	`verificationStatus`
”Penicillin allergy”	`91936005` Allergy to penicillin	`confirmed`
”NKDA”	`416098002` Allergy to drug	`refuted`
”Not allergic to penicillin after all, tolerated amoxicillin”	`91936005` Allergy to penicillin	`refuted`

A refuted AllergyIntolerance tells you that someone checked, and found no allergy. That is different from no AllergyIntolerance at all, which only means the note did not mention allergies.

Fields

Field	Type	What it holds	Example from a note
`code`	CodeableConcept	The allergy or intolerance, in SNOMED CT	”penicillin allergy” → `91936005`
`clinicalStatus`	CodeableConcept	`active`, `inactive`, or `resolved`. Defaults to `active`. Left out when `verificationStatus` is `entered-in-error`, as R4 requires. See the R4 value set.	”outgrew egg allergy” → `resolved`
`verificationStatus`	CodeableConcept	`unconfirmed`, `confirmed`, `refuted`, or `entered-in-error`. See the R4 value set.	”possible sulfa allergy” → `unconfirmed`
`type`	code	`allergy` or `intolerance`. See the R4 value set.
`category`	list of code	`food`, `medication`, `environment`, or `biologic`. See the R4 value set.
`criticality`	code	`low`, `high`, or `unable-to-assess`. See the R4 value set.	”anaphylaxis” → `high`
`onsetDateTime` or `onsetString`	dateTime or string	When it started	”since childhood” → `onsetString: "childhood"`
`patient`	Reference	The Patient of the Bundle	Always set
`lastOccurrence`	dateTime	The last known reaction. Free text such as “last month” is left out, because the field only accepts dates.	”last reaction in 2024” → `2024`
`reaction`	list	The reaction, with `manifestation`, `substance`, and `exposureRoute` as text, `description` as a string, `onset` as a dateTime when the note states a date, and `severity` as `mild`, `moderate`, or `severe`. R4 requires `manifestation`: when the note names no manifestation, it is marked unknown with the data-absent-reason extension.	”hives” → `manifestation[0].text: "hives"`
`note`	list of Annotation	Extra context
`extension`	list of Extension	Mentions and alternatives

The endpoint does not fill the optional R4 encounter reference, because an allergy outlasts the visit where someone wrote it down. If you want to record the visit where the allergy was asserted, add the reference yourself. AllergyIntolerance also has no bodySite, because FHIR R4 does not define one.

Category is a plain code

FHIR R4 defines category as a list of plain codes, so each category is a string: food, medication, environment, or biologic. It carries no SNOMED CT equivalent, because a plain code has room for only one value.

Codes the endpoint can assign

The endpoint only searches a fixed part of each coding system for each field. A code outside that part never appears, and a filter can only narrow the part further, never widen it. Codes come from a fixed scope explains why.

Field	Coding system	Allowed codes	Example
`code`	SNOMED CT	Semantic tag `finding`	`91936005` Allergy to penicillin
`category`	FHIR value set	A fixed list, shown in Category is a plain code
`clinicalStatus`, `verificationStatus`	HL7 code systems	The FHIR value sets listed under Fields

The code is the allergy finding, such as “Allergy to penicillin”, not the substance “Penicillin”. Substances have the semantic tag substance, which is outside the allowed set. The reaction fields hold text, so the endpoint assigns no codes there.

Example

Penicillin causes hives and throat swelling. Confirmed by allergist.

Simplified
JSON

Field	Value
`code`	`91936005` Allergy to penicillin
`clinicalStatus`	`active`
`verificationStatus`	`confirmed`
`type`	`allergy`
`category`	`medication`
`criticality`	`high`
`reaction`	”hives and throat swelling”, severity `severe`

{
  "resourceType": "AllergyIntolerance",
  "id": "e1153f83-e4c1-5aed-8237-5bbe5c0f4ed8",
  "clinicalStatus": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical",
        "code": "active",
        "display": "Active"
      }
    ],
    "text": "Active"
  },
  "verificationStatus": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/allergyintolerance-verification",
        "code": "confirmed",
        "display": "Confirmed"
      }
    ],
    "text": "Confirmed"
  },
  "type": "allergy",
  "category": ["medication"],
  "criticality": "high",
  "code": {
    "coding": [
      {
        "system": "http://snomed.info/sct",
        "code": "91936005",
        "display": "Allergy to penicillin"
      }
    ],
    "text": "Allergy to penicillin"
  },
  "patient": { "reference": "urn:uuid:b49ecda5-92db-5325-a7a9-f82c71500bad", "type": "Patient" },
  "reaction": [
    {
      "manifestation": [{ "text": "hives and throat swelling" }],
      "severity": "severe"
    }
  ]
}

Clinical Text Generation

Medical Coding

FHIR Extraction

Clinical Assistant

What becomes an AllergyIntolerance

No known allergies

Fields

Category is a plain code

Codes the endpoint can assign

Example

Next steps

FamilyMemberHistory resource group

Condition resource group

​What becomes an AllergyIntolerance

​No known allergies

​Fields

​Category is a plain code

​Codes the endpoint can assign

​Example

​Next steps

FamilyMemberHistory resource group

Condition resource group

What becomes an AllergyIntolerance

No known allergies

Fields

Category is a plain code

Codes the endpoint can assign

Example

Next steps