SNOMED CT value sets for use in adverse sensitivity documentation generally belong to two types 1) concepts related to the adverse sensitivity per se, i.e. the adverse sensitivity condition/propensity, adverse sensitivity reactions, and products/substances which are claimed to cause adverse sensitivity reactions; and 2) qualifiers or modifiers e.g. clinical status, verification status, criticality, or severity of adverse reaction. Value sets of the first type usually encompass a large number of concepts and are defined intentionally. Value sets of the second type are usually small and enumerated as a list. Different information models have their own definitions and requirements for value sets. In the following discussion, we will focus on the FHIR® AllergyIntolerence base resource

The FHIR AllergyIntolerence base resource is open to various choices of representation for the adverse sensitivity content per se, but often has restricted ways of providing qualifiers and modifiers.

Adverse sensitivity content value sets

The FHIR AllergyIntolerance base resource has example bindings to SNOMED CT for the element AllergyIntolerance.code as well as elements reaction.substance, reaction.manifestation, and reaction.exposureRoute. All example value sets are though very broad and likely not very precise in determining the set of relevant concepts, see table below. For each data element, the number of concepts that are in the Global Patient Set (GPS) is shown here. The GPS is a special SNOMED CT subset that can be used globally with minimal restriction and at no cost.

Since the SNOMED CT value sets in this category usually include a large number of concepts, implementers often ask for lists of most frequently used concepts to facilitate implementation (e.g., building picklists to assist data entry). These frequently-used subsets are sometimes called “starter sets”. Examples of starter sets are:

As a result of a request from HL7 to SNOMED International about the possibility of mapping some of the required HL7® FHIR® Value Sets to SNOMED CT, an analysis of the ability of SNOMED CT to accommodate those needs was performed by the SNOMED CT on FHIR Workgroup. The required value sets of the FHIR AllergyIntolerance resource was included in this analysis.

A particular issue with qualifiers/modifiers is they have a strong dependence on what they qualify or modify, and that linkage is provided specifically by the information model at hand. Taking those concepts out of their information model context, which, debatably, mapping those concepts to SNOMED CT entail, could be a challenge.

In the analysis of the FHIR AllergyIntolerance required value sets, all but two were problematic in at least some way. The two straightforward mappable value sets were for elements AllergyIntolerance.reaction.severity and AllergyIntolerance.type

It was assessed that there was a good match between the HL7 required value set and the SNOMED CT << 272141005 |Severities (qualifier value)| subhierarchy.

The group's suggested approach here is to use concepts taken from <<609433001 |Hypersensitivity disposition (finding)| unless an actual immune mediated hypersensitivity has been proven e.g., by testing. See the section for a further discussion of the rationale behind this approach.

For other required value sets in the FHIR AllergyIntolerance resource there were issues ranging from some concepts in the FHIR value set lacked a corresponding SNOMED CT concept to differences in the underlying ontology making mapping complicated and likely less useful. For more details about mapping FHIR value sets to SNOMED CT, refer to the discussion of the SNOMED on FHIR Workgroup.

FHIR® is an HL7® standard for exchanging healthcare information electronically. The fourth STU release (R4) was published in October 2019, including the first (partial) normative content. FHIR models the classes of information for interoperable use as Resources. The FHIR® Resources relevant to the use cases in the Information Model and Terminology Binding section are AllergyIntolerance, Condition and Observation.

AllergyIntolerance resource

The image below shows the structure of the FHIR AllergyIntolerance resource. The full resource model structure, coded elements and terminology bindings of the AllergyIntolerance resource can be found at http://www.hl7.org/fhir/allergyintolerance.html, with various display options, including UML, XML, JSON, Turtle and the differences it underwent compared to the prior release(s).

The scope of this resource is "A Record of a clinical assessment of an allergy or intolerance; a propensity, or a potential risk to an individual, to have an adverse reaction on future exposure to the specified substance, or class of substance.

Where a propensity is identified, to record information or evidence about a reaction event that is characterized by any harmful or undesirable physiological response that is specific to the individual and triggered by exposure of an individual to the identified substance or class of substance.

Substances include, but are not limited to: a therapeutic substance administered correctly at an appropriate dosage for the individual; food; material derived from plants or animals; or venom from insect stings."

Table: The definition of the main AllergyIntolerance resource elements along with details about their terminology bindings.

It is important to note that

• In the FHIR® AllergyIntolerance resource, some elements (type, category, criticality and severity) have currently a "Code" data type. They thus require the use of the FHIR values provided and no other classification or terminology code can be used as value in these elements, unless one is using a FHIR® extension, while other elements (clinicalStatus, verificationStatus) have a "CodeableConcept" data type and thus allow for simultaneous use of several code systems (ex: both the FHIR values and the SNOMED CT concepts representing the same meaning as those FHIR values).

you will find an example of extension for AllergyIntolerance.type, which allows capturing, in SNOMED CT, more type of reaction values then the two FHIR values of "allergy" and "intolerance".

• When FHIR® R5 is released (expected in late 2022):

  • The reaction.manifestation element should be able to directly reference a FHIR Observation resource representing the manifestation (proposal to be balloted in R5). This will allow the manifestation of an adverse reaction to be recorded only once, not first in an Observation resource and then once again in the AllergyIntolerance resource.

  • The AllergyIntolerance.type element will have a "CodeableConcept" data type and a binding strength of "Preferred", thus allowing the use of SNOMED CT concepts as values without the use of an extension.

The image below shows the structure of the FHIR Observation resource. The full resource model structure, coded elements and terminology bindings of the Observation resource can be found on , with various display options, including UML, XML, JSON, Turtle and the differences it underwent compared to the prior release(s).

Observations in general are a central element in healthcare, used to support diagnosis, monitor progress, determine baselines and patterns and even capture demographic characteristics. Most observations are simple name/value pair assertions with some metadata, but some observations group other observations together logically, or even are multi-component observations. Note that the resource provides a clinical or workflow context for a set of observations and the Observation resource is referenced by DiagnosticReport to represent laboratory, imaging, and other clinical and diagnostic data to form a complete report. In the context of allergies, it can be used to present allergy test results.

Uses for the Observation resource include:

• Vital signs such as , , and

• Laboratory Data like , or an

• Imaging results like or fetal measurements

• Clinical Findings such as

In the context of allergies, the Observation resource can be used to record the manifestation(s) of the allergy (ex: rash on the neck). Note that the boundary between observing a (series of) clinical finding(s) and posing the diagnosis of a disorder isn't always clear cut in medical ontology, and explicit local business rules may be needed to help clinicians record the same clinical situations either as observations or as diagnosis in a consistent way. The Observation resource can also be used to record allergy test results (biological test, like dosage of specific IgE or clinical, like patch and prick tests).

Table: The definition of the main Observation resource elements along with details about their terminology bindings.

The image below shows the structure of the FHIR Condition resource. The resource model structure, coded elements and terminology bindings of the Condition resource can be found on , with various display options, including UML, XML, JSON, Turtle and the differences it underwent compared to the prior release(s).

This resource is used to record detailed information about a condition, problem, diagnosis, or other event, situation, issue, or clinical concept that has risen to a level of concern. The condition could be a point in time diagnosis in the context of an encounter, it could be an item on the practitioner’s Problem List, or it could be an additional concern that does not exist on the practitioner’s Problem List. Often a condition is about a clinician's assessment and assertion of a particular aspect of a patient's state of health. It can be used to record information about a disease/illness identified from application of clinical reasoning over the pathologic and pathophysiologic findings (diagnosis), or identification of health issues/situations that a practitioner considers harmful or potentially harmful and may be investigated and managed (problem), or another health issue/situation that may require ongoing monitoring and/or management (health issue/concern).

While conditions are frequently a result of a clinician's assessment and assertion of a particular aspect of a patient's state of health, conditions can also be expressed by the patient, related person, or any care team member. A clinician may have a concern about a patient condition (e.g. anorexia) that the patient is not concerned about. Likewise, the patient may have a condition (e.g. hair loss) that does not rise to the level of importance such that it belongs on a practitioner’s Problem List.

In the context of allergies, the Condition resource can be used to record the manifestation(s) of the allergy (ex: allergic urticaria).

Table: The definition of the main Condition resource elements along with details about their terminology bindings.

Example of a typical Medication allergy resource from a clinical system (id = "medication") (JSON form

The SNOMED on FHIR group can provide help and direction on how to deal with the specific issues that may arise when using SNOMED CT concepts in FHIR® resources. SNOMED CT implementation in FHIR guidance can be found here: , while proposals of SNOMED CT adapted FHIR resources can be found here: .

You will note that there are two separate FHIR® profiles proposed on this page, based on the general HL7 FHIR AllergyIntolerance resource. One is substance-focused, meaning that the record centers for the AllergyIntolerance.code value on the substance the patient reacts to and captures separately the type of reaction in the AllergyIntolerance.type element. One can say this model captures the allergy/intolerance to X in a post-coordinated way. The second profile is finding-focused, meaning it captures the allergy/intolerance in the AllergyIntolerance.code element using pre-coordinated "allergy/intolerance to X" SNOMED CT concepts and makes no use of the AllergyIntolerance.type element.

Use Case 1: Documentation of Information Related to Allergy, Hypersensitivity, and Intolerance

Scenario 1.1 Documentation of an adverse reaction to a drug substance

Scenario : A physician sees a patient in clinic for routine outpatient care. Recently the patient was prescribed penicillin V 500 mg orally two times daily x 10 days for streptococcal pharyngitis. He tells the physician that he has developed hives the previous week and on examination, the physician confirms the presence of generalized hives. He records this in the patient record as an Observation.

FHIR Observation resource query from patient record (see FHIR representation )

*LOINC codes are the recommended coding system for the FHIR observation.code element but the observation.code being a CodableConcept, one may choose also to use SNOMED CT concepts to represent the value in this field.

A review of systems fails to reveal any other causes and the physician believes that the patient may be having an urticarial reaction to penicillin. He has lingering uncertainty about this and tells the patient to stop the penicillin and employ diphenhydramine for relief. He schedules him back in a week for follow-up and when recording his note for the visit, he adds to his assessment in the problem list: “Moderate urticarial reaction, possible penicillin allergy”.

FHIR Condition resource query from patient record (see FHIR representation )

A week later, the patient returns for follow-up with the itching and rash entirely resolved. He reports that the reaction subsided within days after stopping the penicillin. The physician adds “Penicillin allergy probable: moderate reaction of hives; criticality unable-to-assess” to the allergy list.

FHIR resource query from patient record (see FHIR representation ); EHR using a

Or

FHIR resource query from patient record (see FHIR representation ); EHR using a

*The use of a SNOMED CT concept to represent these values requires the use of a FHIR extension in HL7® FHIR® v4.3.0: R4B - STU (see 2.2.3.1).

Scenario : Several years later, the same patient who has since received an aortic valve replacement is seeing another physician within the organization for consultation on antibiotic prophylaxis for an upcoming dental procedure. The second physician decides that a penicillin class antibiotic is appropriate for the patient.

When the physician creates an order for amoxicillin 2 g orally as a single dose and commits to the electronic prescription, an alert appears which requires a response by the physician warning him of an allergy history to penicillin. The substance-based alert is generated by the EHR drug-disease interactions software, which uses the Allergy list as a reference. As the patient has not received penicillin class antibiotics for several years, the physician decides to refer the patient to an allergy specialist for clarification of current status of penicillin allergy.

The specialist performs skin testing for penicillin allergy, the results of which are positive. The patient is confirmed as penicillin allergic and the results of the testing are documented in the patient’s medical record.

The patient is subsequently prescribed azithromycin for his dental procedure.

FHIR Observation resource for the positive skin test (see FHIR representation )

FHIR resource query from patient record (see FHIR representation ); EHR using a

Or

FHIR resource query from patient record (see FHIR representation ); EHR using a

*The use of a SNOMED CT concept to represent theses values requires the use of a FHIR extension in HL7® FHIR® v4.3.0: R4B - STU (see 2.2.3.1).

Scenario: A 34-year-old female is seen by her primary care provider for complaints of abdominal pain, bloating and change in bowel habits within hours or a few days after ingesting whole wheat bread. In addition, she complains of feeling tired but denies itching rash or wheezing. Those complaints are entered as observations in the EHR.

FHIR Condition resource query from patient record (see FHIR representation )

Due to a family history of celiac disease, tissue transglutaminase IgG and IgA are ordered which are negative. The patient is also referred to a gastroenterologist, who performs an endoscopic biopsy, which is negative for celiac disease. (Both of these examination results can be recorded in the EHR as a FHIR observation using LOINC codes).

The patient is advised to avoid wheat and gluten containing products. An encounter diagnosis of moderate wheat intolerance is documented in the patient’s health record and wheat is entered in the patient’s “allergy” list.

FHIR Condition resource query from patient problem list record (see FHIR representation )

FHIR resource query from patient record (see FHIR representation ); EHR using a

Or

FHIR resource query from patient record (see FHIR representation ); EHR using a

*The use of a SNOMED CT concept to represent theses values requires the use of a FHIR extension in HL7® FHIR® v4.3.0: R4B - STU (see 2.2.3.1).

The causative agent for the realization of an allergic process directed against a living organism (plant or animal) is not the organism itself or a part of the organism such as epithelium but in most cases is a protein derived from the organism. An allergy to an animal should therefore be modeled with a causative agent that is a descendant of 272169002 |Animal protein (substance)| as in the concept below.

Likewise animal related material such as dander, feathers, urine, serum, etc. represent sources where the allergenic proteins are found and should not be used as the causative agents for allergy finding and disorder concepts. Allergen sources should only be used as the active ingredients of products containing these materials such as 411572004 |Cat dander diagnostic allergen extract (product)|.

Scenario : A physician sees a patient for the first time in clinic for routine outpatient care. The patient tells the physician that he has begun to experience asthma symptoms. The physician runs some blood tests and a series of skin tests, which demonstrate an intense reaction to the house dust mite, Dermatophagoides farinae protein with high IgE antibody levels.

FHIR Observation resource for the positive IgE lab test (see FHIR representation )

*LOINC codes are the recommended coding system for the FHIR observation.code element but the observation.code being a CodableConcept, one may choose also to use SNOMED CT concepts to represent the value in this field.

The patient confirms that his wheezing occurs primarily at home, especially while lying in bed at night. The physician opens the allergy record and documents the allergic propensity to Dermatophagoides farinae protein, criticality and severity of low in the EHR allergy list.

FHIR resource query from patient record (see FHIR representation ); EHR using a

Or

FHIR resource query from patient record (see FHIR representation ); EHR using a

*The use of a SNOMED CT concept to represent theses values requires the use of a FHIR extension in HL7® FHIR® v4.3.0: R4B - STU (see 2.2.3.1).

Scenario : A patient’s mother reports to their child’s physician that the child reacts violently to eating peanuts with symptoms that include generalized hives, wheezing and hypotension requiring use of epinephrine for resuscitation. The physician obtains a blood test which documents high levels of IgE antibody against the Arachis h2 peanut protein which is found in unrefined peanut oil (Arachis oil) - the sensitizing agent for clinical peanut allergy. Ara h2 is associated with a risk of severe reactions to peanut. The physician records a peanut allergy in the EHR with anaphylaxis, hives and wheezing as reaction symptoms, records a criticality of high and reaction severity of ‘severe’.

FHIR Observation resource for the positive IgE lab test (see FHIR representation ) Attribute| FHIR code| SNOMED CT concept

*LOINC codes are the recommended coding system for the FHIR observation.code element but the observation.code being a CodableConcept, one may choose also to use SNOMED CT concepts to represent the value in this field.

FHIR resource query from patient record (see FHIR representation ); EHR using a

Or

FHIR resource query from patient record (see FHIR representation ); EHR using a

*The use of a SNOMED CT concept to represent theses values requires the use of a FHIR extension in HL7® FHIR® v4.3.0: R4B - STU (see 2.2.3.1).

Years later, the youngster is seen by a dermatologist for treatment of acne. As part of the plan of care, the physician enters an electronic prescription for Isotretinoin capsules. When the physician commits the order, the EHR software runs allergy cross checking and issues a high priority alert that the capsules contain peanut oil that is not highly refined and therefore may potentially include peanut protein and are contraindicated for the patient. The physician cancels the order and chooses an alternative preparation.

Scenario: A licensed nurse presents to her personal physician for recurring problems of a generalized rash and itching. She works in an intensive care unit and is constantly handing chemicals, disinfectants, assisting in surgical procedures and performing catheter cares for her patients. As a part of the health history, she noticed that she had an eruption on her hands after handling latex catheters. Additionally, she reports a serious allergic reaction to papaya in the past and has been careful in the fruits she eats as a consequence. The clinician suspects a latex allergy cross-reacting with foodstuffs and orders IgE testing for Hevea latex antibody. The serology testing is strongly positive and the clinician advises the nurse of his findings with warnings about other foods, which may cross react. While documenting the clinical encounter, he records a latex allergy in the allergy list.

The EHR software supports selection of foods, chemicals and animal biological products as substances, which may be identified as source substances for an entry onto the allergy list or for recording of an adverse reaction.

FHIR Condition resource query from patient record (see FHIR representation )

FHIR Observation resource for the latex IgE level (see FHIR representation )

*LOINC codes are the recommended coding system for the FHIR observation.code element but the observation.code being a CodableConcept, one may choose also to use SNOMED CT concepts to represent the value in this field.

FHIR resource query from patient record (see FHIR representation ); EHR using a

Or

FHIR resource query from patient record (see FHIR representation ); EHR using a

*The use of a SNOMED CT concept to represent theses values requires the use of a FHIR extension in HL7® FHIR® v4.3.0: R4B - STU (see 2.2.3.1).

Scenario : A nurse is performing an intake examination on a patient that is new to the clinical practice. As part of the clinical interview, he inquires about medication and other allergies. The patient reports that she is not allergic to any medications, foods, chemicals or animals. The nurse opens the ‘allergy list’ in the EHR and documents ‘No known allergies’ which electronically validates that the nurse inquired of the patient and that the history was confirmed negative at the date and time recorded. This satisfies decision support criteria that allergies be documented before medication orders are written and is encoded in the EHR allergy list as confirmed absence of dispositions to adverse reactions.

FHIR resource query from patient record (see FHIR representation ); EHR using a

Alternatively, the EHR could represent no known allergies by using certainty degree of refuted (confirmed absent) to "negate" the recorded substance concept. This method has the advantage of allowing to record the absence of very specific individual allergies that may not exist in SNOMED CT as pre-coordinated Situation with explicit context concepts. Indeed, it might be interesting to record that the physician has asked specifically if the patient has latex allergy, contrast product allergy, iodine disinfectant allergy, etc. before performing a procedure.

FHIR resource query from patient record (see FHIR representation ); EHR using a

*The use of a SNOMED CT concept to represent this value requires the use of a FHIR extension in HL7® FHIR® v4.3.0: R4B - STU (see 2.2.3.1).

Scenario: The patient from Scenario 1.1 is planning a vacation with his family consisting of a cross-country camping trip. In preparation for travels, he speaks to his physician in hospital A and obtains an electronic summary of his healthcare record on a flash drive for himself, his wife and children. His physician informs him that the summary software includes an electronic ‘reader’ as well as a standard format that can be imported into another EHR for patient care. Their vacation unfolds happily until, many miles from home the patient experiences an episode of right ear pain and is taken to a local emergency room in hospital B. He provides the flash drive with his electronic record summary to the emergency room physician whose hospital employs an EHR which can accept FHIR extracted electronic record summaries for integration into the on-site health record system. The emergency room nurse loads the flash drive and accepts the electronic copy of the problem list, allergies and medication list into the on-site record. The software extract manages the differences in information model design between EHR vendors by crosschecking the allergy list with information in the problem list and encounter diagnoses.

After an otoscopic exam, the patient is diagnosed with acute otitis media. The emergency room physician enters an electronic order for “875 mg amoxiliin with clavulanate 125 mg orally twice daily”, the drug of choice for acute otitis in adults. When the physician presses ‘Enter’ to commit the order, a pop-up alert is generated by the EHR with warning that this patient has had an allergic reaction to penicillin and has a high likelihood of cross reacting. While studying the alert, the physician notes that the supporting information was gleaned from the problem list and allergy list. The EHR drug interaction software has cross-referenced the chemical composition of amoxillin/ clavulanate and noted amoxiliin to be a penicillin derivative. The physician decides that the information of penicillin allergy is credible and as the patient has taken cephalosporins in the past without issues, the physician changes his order to Cefuroxime, 500 mg orally twice daily.

The use of SNOMED CT for recording Allergy, Hypersensitivity, and Intolerance requires the definition of an information model and terminology bindings. This will ensure that the information is captured in a consistent and standardized way, which can be used to facilitate better communication and decision-making between healthcare providers. Furthermore, it will enable the sharing of health information between different systems and facilitate better analysis of health data. By defining an information model and terminology bindings, healthcare organizations can ensure that their data is accurately recorded and can be used in a meaningful way.

The use of HL7® FHIR® with SNOMED CT has gained considerable momentum in recent years, and HL7 FHIR has therefore been selected as the preferred information model in this guide. The following pages will discuss recommended approaches for binding SNOMED to HL7 FHIR for documenting Allergies, Hypersensitivity, and Intolerance in the EHR.

• FHIR model

• Terminology Bindings