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

Observations are a key aspect of healthcare. This resource is used to capture those that do not require more sophisticated mechanisms.

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 resoure. 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.

An Extension

• 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 - values should be 1-23, X, Y, mitochondrial, viral, bacterial.

The genomic reference sequence identifier is included, to support testing using alternative reference sequences.

Nucleotide location for start of genomic finding on the positive (+) genomics strand.

Nucleotide location 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. Use '-' for insertions.

Oserved nucleotides from genomic start to genomic stop on the positive (+) genomic strand. Use '-' for delections.

HGNC gene symbol and identifier from HUGO Gene Nomenclature Committee at: http://www.genenames.org/.

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

cDNA variant following HGVS nomenclature on the given TranscriptReferenceSequenceId.

Identifier for variant. If a germline variant, ClinVar or dbSNP identifier should be used. If ClinVar is used, the identifier should be prefixed with 'ClinVar:' (e.g. ClinVar:17661). dbSNP ids are start with 'rs' (rs28897672) and COSMIC id's start with 'COSM' (e.g. COSM12979). Note, dbSNP id's are not unique to a variant but a location, so nucleotide change and germline/somatic classification are needed to resolve. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used.

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

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.

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

Protein variant following HGVS nomenclature on the given ProteinReferenceSequenceId.

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

Common name for variant or gene allele.

The genomic class of the variant: Germline for inherited genome, somatic for cancer genome (e.g. DNA from tumor cells), and prenatal for fetal genome. Associated with LOINC answer list: 48002-0.

The level of occurrence of a DNA Sequence Variation. Heterozygous: present in one of the two genes of homologous chromosomes, while Homozygous means it's present in both genes. Hemizygous: Variation in the only single copy of a gene in a non-homologous chromosome (i.e. male X and Y chromosome). Homoplasmic: Variation is present in all of the copies of mitochondrial DNA while Hemiplasmic is present in only some copies. LOINC Answer List values 53034-5.

supports testing of human, viruses, and bacteria.

A sequence of of base lengths and the associated operation, used to indicate which bases align (either a match/mismatch) with the reference, are deleted from the reference, and are insertions that are not in the reference. string of observed nucleotides. Observed nucleotides matching the reference are in capital letters. Observed nucleotides not matching the reference are in lower case letters. Use '-' a dash for deleted/missing nucleotides in the observed sequence. Allowable characters are A,T,C,G, a,t,c,g and -.

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.

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.

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 store) may have both a value and related observations (for apgar, 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/v2/vs/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.

The assessment made based on the result of the observation.

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.

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.

Updated when the result is updated.

The status of the result value.

Need to track the status of individual results - some results are finalised before the whole report is finalised.

An estimate of the degree to which quality issues have impacted on the value reported.

Not all results are completely reliable, and some are still reported anyway.

Note that in most contexts, unreliable results are not recorded, deleted, or otherwise excluded, but it's not always possible to exclude them from the record. If the reliability indicator is present, interpreters of a result, whether human or machine, should always either be aware of the status or prevented from using the observation without being unaware that the reliability is not "ok".

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.

Indicates the mechanism used to perform the observation.

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

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

A unique identifier for the simple observation.

Allows observations to be distinguished and referenced.

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, 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 (http://hl7.org/fhir/StructureDefinition/indirectTarget) can be used.

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 are often used in contexts that track the specimen explicitly (e.g. Diagnostic Report).

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 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.

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.

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. If this element is omitted, the low bound of the reference range is assumed to be meaningless. (e.g. reference range is <2.3) If the low.comparator element is missing, it is assumed to be '>'.

The value of the high bound of the reference range. If this element is omitted, the high bound of the reference range is assumed to be meaningless. (e.g. reference range is > 5) If the low.comparator element is missing , it is assumed to be '<'.

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'.

Related observations - either components, or previous observations, or statements of derivation.

Some observations have important relationships to other observations (e.g Blood Pressure = systolic + diastolic), or are derived from other observations (e.g. calculated apgar score).

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

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 observation.

May need to indicate whether this observation is composed of others, or merely derived from them.

A relationship type SHOULD be provided. If the relationship type is "COMP" (composed), then the observation should not be displayed/interpreted in the absence of the related observations.

A reference to the observation that is related to this observation.