This profile defines the patient's genomic variant.

This profile defines the patient's genomic variant.

Used for simple observations such as device measurements, laboratory atomic results, vital signs, height, weight, smoking status, comments, etc. Other resources are used to provide context for observations such as laboratory reports, etc.

The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.

The only time that a resource does not have an id is when it is being submitted to the server using a create operation.

The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.

A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.

Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.

The base language in which the resource is written.

Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).

A human language.

A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.

Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later.

These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.

This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.

An Extension

Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.

For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings.

Record details about the anatomical location of a specimen or body part. This resource may be used when a coded concept does not provide the necessary detail needed for the use case.

An Extension

A unique identifier assigned to this observation.

Allows observations to be distinguished and referenced.

A plan, proposal or order that is fulfilled in whole or in part by this event. For example, a MedicationRequest may require a patient to have laboratory test performed before it is dispensed.

Allows tracing of authorization for the event and tracking whether proposals/recommendations were acted upon.

A larger event of which this particular Observation is a component or step. For example, an observation as part of a procedure.

To link an Observation to an Encounter use encounter. See the Notes below for guidance on referencing another Observation.

The status of the result value.

This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.

Codes providing the status of an observation.

Need to track the status of individual results. Some results are finalized before the whole report is finalized.

A code that classifies the general type of observation being made.

In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.

Codes for high level observation categories.

Used for filtering what observations are retrieved and displayed.

A code that classifies the general type of observation being made.

In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.

Codes for high level observation categories.

Used for filtering what observations are retrieved and displayed.

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

An Extension

A reference to a code defined by a terminology system.

Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.

Allows for alternative encodings within a code system, and translations to other code systems.

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

An Extension

The identification of the code system that defines the meaning of the symbol in the code.

The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously.

Need to be unambiguous about the source of the definition of the symbol.

The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.

Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date.

A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination).

Need to refer to a particular code in the system.

A representation of the meaning of the code in the system, following the rules of the system.

Need to be able to carry a human-readable meaning of the code for readers that do not know the system.

Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays).

Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely.

This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing.

Describes what was observed. Sometimes this is called the observation "name".

All code-value and, if present, component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Codes identifying names of simple observations.

Knowing what kind of observation is being made is essential to understanding the observation.

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

An Extension

A reference to a code defined by a terminology system.

Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.

Allows for alternative encodings within a code system, and translations to other code systems.

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

An Extension

The identification of the code system that defines the meaning of the symbol in the code.

The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously.

Need to be unambiguous about the source of the definition of the symbol.

The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.

Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date.

A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination).

Need to refer to a particular code in the system.

A representation of the meaning of the code in the system, following the rules of the system.

Need to be able to carry a human-readable meaning of the code for readers that do not know the system.

Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays).

Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely.

This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing.

The patient, or group of patients, location, or device this observation is about and into whose record the observation is placed. If the actual focus of the observation is different from the subject (or a sample of, part, or region of the subject), the focus element or the code itself specifies the actual focus of the observation.

One would expect this element to be a cardinality of 1..1. The only circumstance in which the subject can be missing is when the observation is made by a device that does not know the patient. In this case, the observation SHALL be matched to a patient through some context/channel matching technique, and at this point, the observation should be updated.

Observations have no value if you don't know who or what they're about.

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

An Extension

A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.

Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure "/[type]/[id]" then it should be assumed that the reference is to a FHIR RESTful server.

The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.

The type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. "Patient" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).

This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.

Aa resource (or, for logical models, the URI of the logical model).

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy.

When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference

Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.

Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).

Plain text narrative that identifies the resource in addition to the resource reference.

This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.

The actual focus of an observation when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, fetus, or donor. For example, fetus observations in a mother's record. The focus of an observation could also be an existing condition, an intervention, the subject's diet, another observation of the subject, or a body structure such as tumor or implanted device. An example use case would be using the Observation resource to capture whether the mother is trained to change her child's tracheostomy tube. In this example, the child is the patient of record and the mother is the focus.

Typically, an observation is made about the subject - a patient, or group of patients, location, or device - and the distinction between the subject and what is directly measured for an observation is specified in the observation code itself ( e.g., "Blood Glucose") and does not need to be represented separately using this element. Use specimen if a reference to a specimen is required. If a code is required instead of a resource use either bodysite for bodysites or the standard extension focusCode.

The healthcare event (e.g. a patient and healthcare provider interaction) during which this observation is made.

This will typically be the encounter the event occurred within, but some events may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter (e.g. pre-admission laboratory tests).

For some observations it may be important to know the link between an observation and a particular encounter.

The time or time-period the observed value is asserted as being true. For biological subjects - e.g. human patients - this is usually called the "physiologically relevant time". This is usually either the time of the procedure or of specimen collection, but very often the source of the date/time is not known, only the date/time itself.

At least a date should be present unless this observation is a historical report. For recording imprecise or "fuzzy" times (For example, a blood glucose measurement taken "after breakfast") use the Timing datatype which allow the measurement to be tied to regular life events.

Knowing when an observation was deemed true is important to its relevance as well as determining trends.

The date and time this version of the observation was made available to providers, typically after the results have been reviewed and verified.

For Observations that don’t require review and verification, it may be the same as the lastUpdated time of the resource itself. For Observations that do require review and verification for certain updates, it might not be the same as the lastUpdated time of the resource itself due to a non-clinically significant update that doesn’t require the new version to be reviewed and verified again.

Who was responsible for asserting the observed value as "true".

May give a degree of confidence in the observation and also indicates where follow-up questions should be directed.

The information determined as a result of making the observation, if the information has a simple value.

An observation may have; 1) a single value here, 2) both a value and a set of related or component values, or 3) only a set of related or component values. If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

The presence or absence of the variant described in the components. If not searching for specific variations and merely reporting what's found, the profile's value should be set to 'Present'.

An observation may have; 1) a single value here, 2) both a value and a set of related or component values, or 3) only a set of related or component values. If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Provides a reason why the expected value in the element Observation.value[x] is missing.

Null or exceptional values can be represented two ways in FHIR Observations. One way is to simply include them in the value set and represent the exceptions in the value. For example, measurement values for a serology test could be "detected", "not detected", "inconclusive", or "specimen unsatisfactory".

The alternate way is to use the value element for actual observations and use the explicit dataAbsentReason element to record exceptional values. For example, the dataAbsentReason code "error" could be used when the measurement was not completed. Note that an observation may only be reported if there are values to report. For example differential cell counts values may be reported only when > 0. Because of these options, use-case agreements are required to interpret general observations for null or exceptional values.

Codes specifying why the result (Observation.value[x]) is missing.

For many results it is necessary to handle exceptional values in measurements.