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 lab 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. Bundles always have an id, though it is usually a generated UUID.

The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content may 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.

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 as much as possible.

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-readable narrative that contains a summary of the resource, and may 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.

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.

May be used to represent additional information that is not part of the basic definition of the resource. In order 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.

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.

• unordered
• Open
• discriminators: url

The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.

The chromosome containing the genetic finding. The value set binds to NCBI-Gene code system.

Inclusive 0-based nucleotide position for start of genomic finding on the positive (+) genomics strand.

Exclusive 0-based nucleotide position for end of genomic finding on the positive (+) genomic strand.

Nucleotide(s) from genomic start to genomic stop on the positive (+) strand of the genomic reference sequence.

Oserved nucleotides from genomic start to genomic stop on the positive (+) genomic strand.

Reference identifier for cDNA transcript, with version, from NCBI's RefSeq or ENSEMBL.

Reference identifier for protein transcript, with version, from NCBI's RefSeq or ENSEMBL.

Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation here .

cDNA variant following HGVS nomenclature on the given TranscriptReferenceSequenceId.

Identifier for variant. If a germline variant, ClinVar or dbSNP identifier should be used. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC).

Codified type for associated DNA Sequence Variation. DNA Sequence Variations use the HGVS notation which implies the DNA Sequence Variation Type, but the concurrent use of this code will allow a standard and explicit type for technical and display convenience. LOINC Answer List values 48019-4 or Sequence Ontology vaues.

Protein variant following HGVS nomenclature on the given ProteinReferenceSequenceId.

Type of variation expressed using Sequence Ontology or LOINC answer list 48006-1.

Gene region in which the sequence is found. Currently values from HGNC are supported. Other systems or genes not defined in HGNC (e.g. BCR-ABL fusion gene) can be added by using local extension.

Details of exonic location of variant (e.g. Exon 1).

Common name for variant or gene allele.

Genomic source class means category of source of tissue sample used to determine the sequence. Here is the loinc answer List for Allelic state:1. Germline LA6683-2; 2. Somatic LA6684-0; 3. Prenatal LA6685-7; 4. Likely Germline LA18194-3; 5. Likely Somatic LA18195-0; 6. Likely Prenatal LA18196-8; 7. Unknown Genomic Origin LA18197-6.

supports testing of human, viruses, and bacteria.

Results from genetic profile (e.g. One gene mutation with one type variation observed in a patient). It makes genetic profile support various genetic test(e.g. A genetic test reporting a list of gene mutations).

Used to denote condition context for genetic testing, which may influence reported variants and interpretation for large genomic testing panels e.g. lung cancer or familial breast cancer.

The level of occurrence of a single DNA Sequence Variation within a set of chromosomes. Heterozygous indicates the DNA Sequence Variation is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variation is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variation exists in the only single copy of a gene in a non- homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variation is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variation is present in all of the copies of mitochondrial DNA. Here is the loinc answer List for Allelic state:1. Heteroplasmic (LA6703-8); 2. Homoplasmic (LA6704-6); 3. Homozygous (LA6705-3); 4. Heterozygous (LA6706-1); 5. Hemizygous (LA6707-9).

Allele frequencies.

Values: amplificaiton/deletion/LOH.

Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

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. Usually modifier elements provide negation or qualification. In order 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.

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 unique identifier for the simple observation instance.

Allows observations to be distinguished and referenced.

The status of the result value.

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. This is used for searching, sorting and display purposes.

The level of granularity is defined by the category concepts in the value set. More fine-grained filtering can be performed using the metadata and/or terminology hierarchy in Observation.code.

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

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

The patient, or group of patients, location, or device whose characteristics (direct or indirect) are described by the observation and into whose record the observation is placed. Comments: Indirect characteristics may be those of a specimen, fetus, donor, other observer (for example a relative or EMT), or any observation made about the subject.

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

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.

If the target of the observation is different than the subject, the general extension observation-focal-subject. may be used. However, the distinction between the patient's own value for an observation versus that of the fetus, or the donor or blood product unit, etc., are often specified in the observation code.

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

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.

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

At least a date should be present unless this observation is a historical report.

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

Updated when the result is updated.

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

Normally, an observation will have either a value or a set of related observations. A few observations (e.g. Apgar score) may have both a value and related observations (for an Apgar score, the observations from which the measure is derived). If a value is present, the datatype for this element should be determined by Observation.code. This element has a variable name depending on the type as follows: valueQuantity, valueCodeableConcept, valueString, valueRange, valueRatio, valueSampledData, valueAttachment, valueTime, valueDateTime, or valuePeriod. (The name format is "'value' + the type name" with a capital on the first letter of the type).

If the data element is usually coded or if the type associated with the Observation.value defines a coded value, use CodeableConcept instead of string datatype even if the value is uncoded text. A value set is bound to the ValueCodeableConcept element. For boolean values use valueCodeableConcept and select codes from HL7 Version 2 Table 0136. These "yes/no" concepts can be mapped to the display name "true/false" or other mutually exclusive terms that may be needed. For further discussion and examples see the notes section below.

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

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

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. Because of these options, use-case agreements are required to interpret general observations for exceptional values.

The assessment made based on the result of the observation. Intended as a simple compact code often placed adjacent to the result value in reports and flow sheets to signal the meaning/normalcy status of the result. Otherwise known as abnormal flag.

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

May include statements about significant, unexpected or unreliable values, or information about the source of the value where this may be relevant to the interpretation of the result.

Need to be able to provide free text additional information.

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

Knowing where the observation is made is important for tracking if multiple sites are possible.

Only used if not implicit in code found in Observation.code. If the use case requires BodySite to be handled as a separate resource instead of an inline coded element (e.g. to identify and track separately) then use the standard extension body-site-instance.

Indicates the mechanism used to perform the observation.

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

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

The specimen that was used when this observation was made.

Observations are not made on specimens themselves; they are made on a subject, but usually 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.

An extension should be used if further typing of the device is needed. Devices used to support obtaining an observation can be represented using either extension or through the Observation.related element.

Guidance on how to interpret the value by comparison to a normal or recommended range.

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.

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 may 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.

unique id for the element within a resource (for internal references).

May be used to represent additional information that is not part of the basic definition of the element. In order 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.

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 that contains it. Usually modifier elements provide negation or qualification. In order 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.

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.

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).

Code for the meaning of the reference range.

Need to be able to say what kind of reference range this is - normal, recommended, therapeutic, or perhaps what state this reference range applies to (i.e. age, hormonal cycles, etc.).

This SHOULD be populated if there is more than one range.

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'.

A reference to another resource (usually another Observation but could also be a QuestionnaireAnswer) whose relationship is defined by the relationship type code.

Normally, an observation will have either a value or a set of related observations. A few observations (e.g. Apgar score) may have both a value and a set of related observations or sometimes QuestionnaireResponse from which the measure is derived.

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

unique id for the element within a resource (for internal references).

May be used to represent additional information that is not part of the basic definition of the element. In order 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.

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 that contains it. Usually modifier elements provide negation or qualification. In order 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.

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 code specifying the kind of relationship that exists with the target resource.

A relationship type SHOULD be provided.

"derived-from" is only logical choice when referencing QuestionnaireAnswer resource.

A reference to the observation or QuestionnaireResponse resource that is related to this observation.

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.

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.

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

unique id for the element within a resource (for internal references).

May be used to represent additional information that is not part of the basic definition of the element. In order 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.

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 that contains it. Usually modifier elements provide negation or qualification. In order 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.

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.

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

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

Normally, an observation will have either a value or a set of related observations. A few observations (e.g. Apgar score) may have both a value and related observations (for an Apgar score, the observations from which the measure is 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 boolean values use valueCodeableConcept and select codes from <http://hl7.org/fhir/ValueSet/v2-0136> (These "yes/no" concepts can be mapped to the display name "true/false" or other mutually exclusive terms that may be needed"). The element, Observation.value[x], has a variable name depending on the type as follows: valueQuantity, valueCodeableConcept, valueRatio, valueChoice, valuePeriod, valueSampleData, or valueString (The name format is "'value' + the type name" with a capital on the first letter of the type).

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

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

"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 "test not done". 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. Because of these options, use-case agreements are required to interpret general observations for exceptional values.

Guidance on how to interpret the value by comparison to a normal or recommended range.

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.

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 may 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.