Human Genome Variation Society (HGVS) nomenclature for a single DNA marker. The use of the nomenclature must be extended to describe non-variations (aka. wild types) see samples for wild type examples.

NCBI's RefSeq ('NM_...'), Ensembl ('ENST...'), and LRG ('LRG...' plus 't1' to indicate transcript)

Multiple bindings acceptable (NCBI or LRG)

Description of the protein (amino acid) sequence change using a valid HGVS-formatted string. The description of the variant is surrounded in parentheses if it is calculated rather than directly observed.

ID of the protein reference sequence, which includes transcribed and non transcribed stretches. It covers the entire protein described.

Multiple bindings acceptable (NCBI or LRG)

A feature consequence categorizes the structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion). NOTE: The bound Molecular Consequence value set is extensible. Variant annotation tools such as snpEff provide a rich assortment of feature consequences (see http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details), some of which are outside the value set.

Concepts in sequence ontology under SO:0001537.

A predicted or observed effect of a variant on the ability of its gene(s) or protein product(s) to function.

Sequence Ontology terms under SO:0001536

Measurements and simple assertions made about a patient, device or other subject.

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.

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.

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.

Documents the 'knowledge artifacts' relevant to the base resource such as citations, supporting evidence, documentation of processes, caveats around testing methodology.

Note that in contrast this extension, the supportingInfo extension references other resources from the patient record that were used in creating the resource.

This SHOULD be used to deliver artifacts that are relevant to the implication.

May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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.

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.

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 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.

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.

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 target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)

This SHOULD be used to deliver artifacts that are specific to the component code and value.

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

Concise and clinically contextualized summary conclusion (interpretation/impression) of the observation

An example would be the interpretative information, typically canned, about a variant identified in the patient.

Need to be able to provide a conclusion that is not lost among the basic result data.

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

The amount of observed support for the association between an implication and a variant / haplotype / genotype / biomarker. There are dozens if not hundreds of evidence-level value sets, generally providing an ordinal range of codes from low evidence (e.g. 'predicted', 'case report', '1-star') to high evidence (e.g. 'professional society guideline', 'expert panel consensus', '1A').

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

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

Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). 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.

PharmGKB or ClinVar

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 clinical impact of an implication on a person's health. There are dozens if not hundreds of clinical-significance value sets, generally providing an ordinal range of codes from low significance (e.g. 'benign') to high significance (e.g. 'pathogenic', 'oncogenic','predictive of drug response').

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)

This SHOULD be used to deliver artifacts that are specific to the component code and value.

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

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

Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). 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.

Human Genome Variation Society (HGVS) nomenclature for a single DNA marker. The use of the nomenclature must be extended to describe non-variations (aka. wild types) see samples for wild type examples.

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

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

Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). 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.

NCBI's RefSeq ('NM_...'), Ensembl ('ENST...'), and LRG ('LRG...' plus 't1' to indicate transcript)

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

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

Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). 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.

Multiple bindings acceptable (NCBI or LRG)

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

Description of the protein (amino acid) sequence change using a valid HGVS-formatted string. The description of the variant is surrounded in parentheses if it is calculated rather than directly observed.

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

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

Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). 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.

ID of the protein reference sequence, which includes transcribed and non transcribed stretches. It covers the entire protein described.

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

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

Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). 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.

Multiple bindings acceptable (NCBI or LRG)

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

A feature consequence categorizes the structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion). NOTE: The bound Molecular Consequence value set is extensible. Variant annotation tools such as snpEff provide a rich assortment of feature consequences (see http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details), some of which are outside the value set.

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

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

Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). 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.

Concepts in sequence ontology under SO:0001537.

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

A predicted or observed effect of a variant on the ability of its gene(s) or protein product(s) to function.

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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

All code-value and 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.

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

Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). 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.

Sequence Ontology terms under SO:0001536

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

Measurements and simple assertions made about a patient, device or other subject.

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.

Documents the 'knowledge artifacts' relevant to the base resource such as citations, supporting evidence, documentation of processes, caveats around testing methodology.

Note that in contrast this extension, the supportingInfo extension references other resources from the patient record that were used in creating the resource.

This SHOULD be used to deliver artifacts that are relevant to the implication.

May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

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.

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

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.

A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.

Very often the text is the same as a displayName of one of the codings.

The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.

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.

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

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.

A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.

Very often the text is the same as a displayName of one of the codings.

The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.

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.

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.

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.

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.

A categorical assessment of an observation value. For example, high, low, normal.

Historically used for laboratory results (known as 'abnormal flag' ), its use extends to other use cases where coded interpretations are relevant. Often reported as one or more simple compact codes this element is often placed adjacent to the result value in reports and flow sheets to signal the meaning/normalcy status of the result.

Codes identifying interpretations of observations.

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

A text note which also contains information about who made the statement and when.

May include general statements about the observation, or statements about significant, unexpected or unreliable results values, or information about its source when relevant to its interpretation. The CodedAnnotation data type, while not allowing for or intending to make the content computable, does allow the author to indicate the type of note. This does not replace the use of interpretation, value, or component values. One important note is that Annotation is a FHIR data type, this is NOT about annotations in the genomic context.

Need to be able to provide free text additional information. Notes SHALL NOT contain information which can be captured in a structured way.

Indicates the site on the subject's body where the observation was made (i.e. the target site).

Only used if not implicit in code found in Observation.code. In many systems, this may be represented as a related observation instead of an inline component.

If the use case requires BodySite to be handled as a separate resource (e.g. to identify and track separately) then use the standard extension bodySite.

Codes describing anatomical locations. May include laterality.

Indicates the mechanism used to perform the observation.

Only used if not implicit in code for Observation.code.

Methods for simple observations.

In some cases, method can impact results and is thus used for determining whether results can be compared or determining significance of results.

The specimen that was used when this observation was made.

Should only be used if not implicit in code found in Observation.code. Observations are not made on specimens themselves; they are made on a subject, but in many cases by the means of a specimen. Note that although specimens are often involved, they are not always tracked and reported explicitly. Also note that observation resources may be used in contexts that track the specimen explicitly (e.g. Diagnostic Report).

The device used to generate the observation data.

Note that this is not meant to represent a device involved in the transmission of the result, e.g., a gateway. Such devices may be documented using the Provenance resource where relevant.

Guidance on how to interpret the value by comparison to a normal or recommended range. Multiple reference ranges are interpreted as an "OR". In other words, to represent two distinct target populations, two referenceRange elements would be used.

Most observations only have one generic reference range. Systems MAY choose to restrict to only supplying the relevant reference range based on knowledge about the patient (e.g., specific to the patient's age, gender, weight and other factors), but this might not be possible or appropriate. Whenever more than one reference range is supplied, the differences between them SHOULD be provided in the reference range and/or age properties.

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

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

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

The value of the low bound of the reference range. The low bound of the reference range endpoint is inclusive of the value (e.g. reference range is >=5 - <=9). If the low bound is omitted, it is assumed to be meaningless (e.g. reference range is <=2.3).

The value of the high bound of the reference range. The high bound of the reference range endpoint is inclusive of the value (e.g. reference range is >=5 - <=9). If the high bound is omitted, it is assumed to be meaningless (e.g. reference range is >= 2.3).

Codes to indicate the what part of the targeted reference population it applies to. For example, the normal or therapeutic range.

This SHOULD be populated if there is more than one range. If this element is not present then the normal range is assumed.

Code for the meaning of a reference range.

Need to be able to say what kind of reference range this is - normal, recommended, therapeutic, etc., - for proper interpretation.

Codes to indicate the target population this reference range applies to. For example, a reference range may be based on the normal population or a particular sex or race. Multiple appliesTo are interpreted as an "AND" of the target populations. For example, to represent a target population of African American females, both a code of female and a code for African American would be used.

This SHOULD be populated if there is more than one range. If this element is not present then the normal population is assumed.

Codes identifying the population the reference range applies to.

Need to be able to identify the target population for proper interpretation.

The age at which this reference range is applicable. This is a neonatal age (e.g. number of weeks at term) if the meaning says so.

Some analytes vary greatly over age.

Text based reference range in an observation which may be used when a quantitative range is not appropriate for an observation. An example would be a reference value of "Negative" or a list or table of "normals".

This observation is a group observation (e.g. a battery, a panel of tests, a set of vital sign measurements) that includes the target as a member of the group.

When using this element, an observation will typically have either a value or a set of related resources, although both may be present in some cases. For a discussion on the ways Observations can assembled in groups together, see Notes below. Note that a system may calculate results from QuestionnaireResponse into a final score and represent the score as an Observation.

The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.