Generated Narrative: StructureDefinition snp Nom Drapeaux Card. Type Description et contraintes Observation Variant Slices pour extension Content/Rules for all slices extension:strand-bias S 0..1 (Complex) DNA strand bias URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/strand-bias value[x] 0..1 boolean Value of extension subject S 1..1 Reference(Oncology Patient) Who and/or what the observation is about derivedFrom S 1..1 Reference(Sequencing Analysis) Analysis from which come this observation Slices pour component 8..* BackboneElement Component results Slice: Unordered, Open by pattern:code component:cytogenetic-location S 0..1 BackboneElement Cytogenetic map value[x] 1..1 CodeableConcept Actual component result Binding: CytoBand Value Set (required) component:ref-sequence-assembly S 1..1 BackboneElement Reference genome version value[x] 1..1 CodeableConcept Actual component result Binding: GenomeBuild Value Set (extensible) component:dna-chg-type S 1..1 BackboneElement Type value[x] 1..1 CodeableConcept Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type Value Set (extensible) component:genomic-source-class S 1..1 BackboneElement Cellular type value[x] 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo component:allelic-read-depth S 1..1 BackboneElement Depth value[x] 1..1 Quantity Actual component result component:allelic-state S 0..1 BackboneElement Zygotia value[x] 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous component:ref-allele S 1..1 BackboneElement Reference allele value[x] 1..1 string Actual component result component:alt-allele S 1..1 BackboneElement Alternative allele value[x] 1..1 string Actual component result component:exact-start-end 0..1 BackboneElement Exact start-end value[x] low S 1..1 SimpleQuantity Start position high S 1..1 SimpleQuantity End position component:pathogenicity S 0..1 BackboneElement Pathogenicity code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) system 1..1 uri Identity of the terminology system Fixed Value: http://loinc.org code 1..1 code Symbol in syntax defined by the system Fixed Value: 74019-1 value[x] 0..1 CodeableConcept Actual component result Binding: Pathogenicity Value Set (required) component:actionability S 0..1 BackboneElement Impact on patient treatment code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) system 1..1 uri Identity of the terminology system Fixed Value: http://loinc.org code 1..1 code Symbol in syntax defined by the system Fixed Value: 93348-1 value[x] 0..1 boolean Actual component result component:proposed-for-orientation S 0..1 BackboneElement Impact on the choice of therapy code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) system 1..1 uri Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls code 1..1 code Symbol in syntax defined by the system Fixed Value: C0449889 value[x] 0..1 boolean Actual component result component:chromosome S 1..* BackboneElement Chromosome code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) system 1..1 uri Identity of the terminology system Fixed Value: http://loinc.org code 1..1 code Symbol in syntax defined by the system Fixed Value: 48000-4 value[x] S 1..1 CodeableConcept Actual component result Binding: Chromosome Value Set (required) component:variant-read-depth S 1..1 BackboneElement Alternative allele depth code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) system 1..1 uri Identity of the terminology system Fixed Value: http://loinc.org code 1..1 code Symbol in syntax defined by the system Fixed Value: LP232001-0 value[x] S 1..1 Quantity Actual component result Documentation for this format
Observation of a Single Nucleotide Polymorphism (SNP) derived from a Sequencing Analysis.
Details about a set of changes in the tested sample compared to a reference sequence.
This change can be simple/discrete (relatively short), structural (potentially very large), or complex (consisting of multiple independent co-occurring variations).
If the resource is contained in another resource, it SHALL NOT contain nested Resources
not(parent::f:contained and f:contained)
If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))
If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))
If a resource is contained in another resource, it SHALL NOT have a security label
When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time.
A resource should have narrative for robust management
dataAbsentReason SHALL only be present if Observation.value[x] is not present
dataAbsentReason.empty() or value.empty()
not(exists(f:dataAbsentReason)) or (not(exists(*[starts-with(local-name(.), 'value')])))
If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
not(f:*[starts-with(local-name(.), 'value')] and (for $coding in f:code/f:coding return f:component/f:code/f:coding[f:code/@value=$coding/f:code/@value] [f:system/@value=$coding/f:system/@value]))
Observation[classCode=OBS, moodCode=EVN]
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.
All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
A set of rules under which this content was created
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.
This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation
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).
Text summary of the resource, for human interpretation
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.
Must have either extensions or value[x], not both
exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
Allows associating observations to a particular portion of the patient - a fetus, a tumor, a lesion, etc.
exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])
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)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) 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
Allows flagging observations that should be considered secondary findings.
Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Extensions are always sliced by (at least) url
Source of the definition for the extension code - a logical name or a URL.
The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).
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](https://hl7.org/fhir/extensibility.html#modifierExtension).
Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
A unique identifier assigned to this observation.
Allows observations to be distinguished and referenced.
OBX.21 For OBX segments from systems without OBX-21 support a combination of ORC/OBR and OBX must be negotiated between trading partners to uniquely identify the OBX segment. Depending on how V2 has been implemented each of these may be an option: 1) OBR-3 + OBX-3 + OBX-4 or 2) OBR-3 + OBR-4 + OBX-3 + OBX-4 or 2) some other way to uniquely ID the OBR/ORC + OBX-3 + OBX-4.
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](https://hl7.org/fhir/observation.html#obsgrouping) below for guidance on referencing another Observation.
registered | preliminary | final | amended +
… This should generally be 'completed' or 'revised'.
Need to track the status of individual results. Some results are finalized before the whole report is finalized.
This element is labeled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid
Codes providing the status of an observation.
status Amended & Final are differentiated by whether it is the subject of a ControlAct event with a type of "revise"
A code that classifies the general type of observation being made.
Used for filtering what observations are retrieved and displayed.
Codes for high level observation categories.
.outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code
Where testing scenarios are intended to assess the prescence or absence of a known set of DNA variants (e.g. tumor profiling using genotyping technology), then the Genetic Variant Assessment is used in conjunction with answer list supports structured communication of these findings. Of note, 'No Call' is different from 'Absent', because 'No Call' did not result in the determination of the marker's presents or absents. This may be due to test failure or specimen specific context which renders the test ineffective.
*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.
Knowing what kind of observation is being made is essential to understanding the observation.
Codes identifying names of simple observations.
< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
Who and/or what the observation is about
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.
… This must be the same patient as on the DiagnosticReport unless combining data from multiple fetuses or family members in a single report.
Observations have no value if you don't know who or what they're about.
What the observation is about, when it is not about the subject of record
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](https://hl7.org/fhir/extension-observation-focuscode.html).
Healthcare event during which this observation is made
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.
inboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]
Clinically relevant time/time-period for observation
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](https://hl7.org/fhir/datatypes.html#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.
OBX-14, and/or OBX-19 after v2.4 (depends on who observation made)
Date/Time this version was made available
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` ](https://hl7.org/fhir/resource-definitions.html#Meta.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.
OBR.22 (or MSH.7), or perhaps OBX-19 (depends on who observation made)
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.
OBX.15 / (Practitioner) OBX-16, PRT-5:PRT-4='RO' / (Device) OBX-18 , PRT-10:PRT-4='EQUIP' / (Organization) OBX-23, PRT-8:PRT-4='PO'
Indicates whether the indicated variation was found or not.
If not searching for specific variations and merely reporting what's found, this element should be set to "Present".
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.
For many results it is necessary to handle exceptional values in measurements.
Codes specifying why the result (`Observation.value[x]`) is missing.
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.
For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.
Codes identifying interpretations of observations.
Comments about the observation or the results.
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.
Need to be able to provide free text additional information.
NTE.3 (partner NTE to OBX, or sometimes another (child?) OBX)
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](https://hl7.org/fhir/extension-bodysite.html).
Codes describing anatomical locations. May include laterality.
Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Indicates the method of variant analysis.
Only used if not implicit in code for Observation.code.
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 examined to determine genetic information.
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.
Must have at least a low or a high or text
low.exists() or high.exists() or text.exists()
(exists(f:low) or exists(f:high)or exists(f:text))
outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
Additional content defined by implementations
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.
Extensions that cannot be ignored even if unrecognized
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).
Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
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.
Need to be able to say what kind of reference range this is - normal, recommended, therapeutic, etc., - for proper interpretation.
Code for the meaning of a reference range.
< 260245000 |Findings values| OR < 365860008 |General clinical state finding| OR < 250171008 |Clinical history or observation findings| OR < 415229000 |Racial group| OR < 365400002 |Finding of puberty stage| OR < 443938003 |Procedure carried out on subject|
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.
Need to be able to identify the target population for proper interpretation.
Codes identifying the population the reference range applies to.
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.
Text based reference range in an observation
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 resource that belongs to the Observation group
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](https://hl7.org/fhir/observation.html#obsgrouping) below. Note that a system may calculate results from [QuestionnaireResponse](https://hl7.org/fhir/questionnaireresponse.html) into a final score and represent the score as an Observation.
Relationships established by OBX-4 usage
Analysis from which come this observation
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](https://hl7.org/fhir/observation.html#obsgrouping) 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](https://hl7.org/fhir/observation.html#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.
Type of component observation (code / type)
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.
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](https://hl7.org/fhir/observation.html#notes) below.
363714003 |Interprets| < 441742003 |Evaluation finding|
Provides a reason why the expected value in the element Observation.component.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 "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.
Provides guide for interpretation of component result
Guidance on how to interpret the value by comparison to a normal or recommended range.
HUGO Gene Nomenclature Committee (HGNC) identifier for a gene. List the gene(s) examined in full or in part by the study. If the study addresses multiple genes, these can be recorded in multiple gene studied components . The required coding will use the HGNC gene symbol as the display text and HGNC gene ID as the code.
If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
The version of the reference genome used for the reconstruction of the tumor genome.
Human Genome Variation Society (HGVS) nomenclature for a single DNA marker.
HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society
Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)
Annotated changes to sequence features caused by this variant.
Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)
Changes to sequence features caused by this variant.
Functional Annotation (Sequence Ontology)
This term is used to report the unique identifier of the simple variant found in this study.
If this is present, the components can be omitted but they might be included to avoid a need to look up the information in a registry. Typically only one code would be present, though multiple codings expressing the variant in different code systems are possible.
The unique identifier for the variant represented as a small nucleotide polymorphism (SNP). The dbSNP ID is used routinely as the base identifier in pharmacogenomics as well as arrCGH studies. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the dbSNP ID is 368949613. [http://www.ncbi.nlm.nih.gov/clinvar/variation/30880/].
The name of a structural variant reported using HGVS nomenclature.
Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Human Genome Variation Society (HGVS) nomenclature for an amino acid sequence. This value is derivable from the DNA Marker value if available. It is provided for convenience. The use of the nomenclature must be extended to describe non-variations (aka. wild types) see samples for wild type examples.
Codified type for associated Amino Acid Marker. Amino Acid Marker's use the HGVS notation which implies the Amino Acid Marker Type, but the concurrent use of this code will allow a standard and explicit type for technical and display convenience.
Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
This field carries the ID for the transcribed reference sequence, which is the part of the genomic reference sequence that is converted to messenger RNA (i.e., after the introns are removed).
Only needed if the transcript sequence or genomic reference sequence versions don't indicate the version.
This field carries the ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and non transcribed stretches. For this ID use either the NCBI genomic nucleotide RefSeq IDs with their version number (see: NCBI.NLM.NIH.Gov/RefSeq) or use the LRG identifiers, without transcript (t or p) extensions -- when they become available. (See- Report sponsored by GEN2PHEN at the European Bioinformatics Institute at Hinxton UK April 24-25, 2008). The NCI RefSeq genomic IDs are distinguished by a prefix of"NG" for genes from the nuclear chromosomes and prefix of "NC" for genes from mitochondria. The LRG Identifiers have a prefix of "LRG_" Mitochondrial genes are not in the scope of LRG.
The fraction of all reads in a study sample at a given genomic locus that identify the allele (variant) in question.
Numerical value (with implicit precision)
The value of the measured amount. The value includes an implicit precision in the presentation of the value.
The implicit precision in the value should always be honored. Monetary values have their own rules for handling precision (refer to standard accounting text books).
Precision is handled implicitly in almost all cases of measurement.
PQ.value, CO.value, MO.value, IVL.high or IVL.low depending on the value
< | <= | >= | > - how to understand the value
How the value should be understood and represented - whether the actual value is greater or less than the stated value due to measurement issues; e.g. if the comparator is "<" , then the real value is < stated value.
Need a framework for handling measures where the value is <5ug/L or >400mg/L due to the limitations of measuring methodology.
If there is no comparator, then there is no modification of the value
This is labeled as "Is Modifier" because the comparator modifies the interpretation of the value significantly. If there is no comparator, then there is no modification of the value
How the Quantity should be understood and represented.
There are many representations for units of measure and in many contexts, particular representations are fixed and required. I.e. mcg for micrograms.
The identification of the system that provides the coded form of the unit.
Need to know the system that defines the coded form of the unit.
CO.codeSystem, PQ.translation.codeSystem
A computer processable form of the unit in some unit representation system.
The preferred system is UCUM, but SNOMED CT can also be used (for customary units) or ISO 4217 for currency. The context of use may additionally require a code from a particular system.
Need a computable form of the unit that is fixed across all forms. UCUM provides this for quantities, but SNOMED CT provides many units of interest.
PQ.code, MO.currency, PQ.translation.code
Number of 'reads' at the genomic position of the mutation.
Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
The relationship between the alleles found at the same locus on different chromosomes.
The copy number of the large variant. In HGVS, this is the numeric value following the “X”. It is a unit-less value. Note that a copy number of 1 implies a deletion. The copy number can usually be inferred from the HGVS or ISCN fields.
A measured amount (or an amount that can potentially be measured). Note that measured amounts include amounts that are not precisely quantified, including amounts involving arbitrary units and floating currencies.
The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.
There SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.
(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
(f:code or not(f:value)) and (not(exists(f:system)) or (f:system/@value='http://unitsofmeasure.org' and f:code/@value='1')) and not(contains(f:value/@value, '.'))
If a code for the unit is present, the system SHALL also be present
PQ, IVL<PQ>, MO, CO, depending on the values
The allele seen on the forward strand of the reference genome.
This is used in a genotyping test to define the reference and variable nucleotide strings. That is if the sequence variation is an insertion, then Reference Nucleotide will be blank and Variable Nucleotide will contain the inserted nucleotides. In contrast, if the sequence variation is a deletion, then the Reference Nucleotide will contain the deleted nucliotieds, and the Variable Nucleotide will be blank.
The allele resulting from a somatic mutation event during tumorigenesis.
Base number of coordinate system either 0-based, with inclusive start and exclusive end (called interval), or 1-based, with inclusive start and end. However, two versions of 1-based are in common use.These systems are HGVS 1-based (called variant method) and VCF 1-based (called alignment method). In general, HGVS recommends right-justification and VCF recommends left-justification. However, these systems further address questions such as wheather or not to place an insertion before or after the nucleotide, and, if always placed before the nucleotide, how to handle insertion after the end of the sequence. Additionally, the systems deal with handling boundary effects of numbers between features. For more details see the HGVS and VCF guides.
This captures the base numbering used to calculate base positions in the reported sequence information.
0-based interval | 0-based character | 1-based character
Base coordinate systems start and end measurements for variants
This location is the first genomic position in the reference allele that contains a change from the reference allele. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the location is Chr3: 128906220 on Assembly GRCh38.
Starting position of the genetic alteration on the chromosome.
If the low element is missing, the low boundary is not known.
End position of the genetic alteration on the chromosome.
If the high element is missing, the high boundary is not known.
Length of the structural variant, which information may be ascertained in some but not all types of structural variants.
The genomic coordinates of the widest genomic range in which the variant might reside.
The low limit. The boundary is inclusive.
The high limit. The boundary is inclusive.
The genomic coordinates of the narrowest genomic range in which the structural variant might reside.
The type of the chromosome copy number change.
Structural variant reported arrCGH [Ratio]
The comparator is not used on a SimpleQuantity
The type of complex variant, for example, compound heterozygous or haplotype.
When sending a grouping of non-contiguous variants that are meant to be interpreted together but do not signify a named haplotype, one can send the type of complex variant here (determined by where the individual changes are in relation to each other), and use Observation.hasMember to reference the individual variants, which would then be described as normal.
Compound heterozygous | Double heterozygous | Haplotype | Hemizygous
Fully describes a variant with a single code. Typically a large variant such as a mosaic, abnormal chromosome numbers, etc.
ISCN is a syntax for describing cytogenetic findings, from classical karyotypes to details that can be observed with copy number methodologies. Using ISCN nomenclature is highly recommended for reporting structural variants.
Information to indicate the pathogenicity of the genetic alteration.
Can (could) the genetic alteration affect the patient's response to treatment?
Was the genetic alteration used to guide the patient's therapeutic choice?
Number of reads containing the alternative allele at position.
Slice based on the component.code pattern