Generated Narrative: StructureDefinition mii-pr-mtb-copy-number-variant Name Flags Card. Type Description & Constraints Observation 0..* MII_PR_MolGen_Variante Variant #xD; meta S 0..1 Meta Metadata about the resource #xD; profile S 0..* canonical(StructureDefinition) Profiles this resource claims to conform to #xD; identifier S 0..* Identifier VariantenId im Kontext des NGS-Befundes #xD; focus S 0..* Reference(MII PR Onkologie Diagnose Primärtumor | MII PR MTB Diagnose Primärtumor) What the observation is about, when it is not about the subject of record #xD; Slices for component Content/Rules for all slices #xD; component:gene-studied 0..* BackboneElement Berichtete betroffene Gene #xD; code S 1..1 CodeableConcept 48018-6 #xD; value[x] S 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. #xD; component:chromosome-identifier 0..* BackboneElement Chromosom #xD; component:exact-start-end 0..1 BackboneElement Positionsbereich #xD; code S 1..1 CodeableConcept 81254-5 #xD; value[x] S 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants. #xD; component:copy-number 0..1 BackboneElement Gesamtkopienzahl #xD; code S 1..1 CodeableConcept 82155-3 #xD; Slices for value[x] 0..1 Quantity, Range Actual component result Slice: Unordered, Open by type:$this #xD; value[x]:valueQuantity S 0..1 Quantity Actual component result #xD; component:relative-copy-number S 0..* BackboneElement Relative Kopienzahl #xD; code S 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following #xD; coding 1..* Coding Code defined by a terminology system Fixed Value: (Complex) #xD; system 1..1 uri Identity of the terminology system Fixed Value: https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/CodeSystem/mii-cs-mtb-molekulare-biomarker #xD; code 1..1 code Symbol in syntax defined by the system Fixed Value: relative-copy-number #xD; Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual component result Slice: Unordered, Open by type:$this #xD; value[x]:valueQuantity S 0..1 Quantity Actual component result #xD; component:cna S 0..* BackboneElement CNA #xD; code S 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following #xD; coding 1..* Coding Code defined by a terminology system Fixed Value: (Complex) #xD; system 1..1 uri Identity of the terminology system Fixed Value: https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/CodeSystem/mii-cs-mtb-molekulare-biomarker #xD; code 1..1 code Symbol in syntax defined by the system Fixed Value: copy-number-allele-a #xD; Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual component result Slice: Unordered, Open by type:$this #xD; value[x]:valueQuantity S 0..1 Quantity Actual component result #xD; component:cnb S 0..* BackboneElement CNB #xD; code S 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following #xD; coding 1..* Coding Code defined by a terminology system Fixed Value: (Complex) #xD; system 1..1 uri Identity of the terminology system Fixed Value: https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/CodeSystem/mii-cs-mtb-molekulare-biomarker #xD; code 1..1 code Symbol in syntax defined by the system Fixed Value: copy-number-allele-b #xD; Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual component result Slice: Unordered, Open by type:$this #xD; value[x]:valueQuantity S 0..1 Quantity Actual component result #xD; component:reported-focality S 0..* BackboneElement Berichtete Fokalitaet #xD; code S 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following #xD; coding 1..* Coding Code defined by a terminology system Fixed Value: (Complex) #xD; system 1..1 uri Identity of the terminology system Fixed Value: https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/CodeSystem/mii-cs-mtb-molekulare-biomarker #xD; code 1..1 code Symbol in syntax defined by the system Fixed Value: reported-focality #xD; Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual component result Slice: Unordered, Open by type:$this #xD; value[x]:valueQuantity S 0..1 Quantity Actual component result #xD; component:cnv-type S 0..* BackboneElement CNV-Typ #xD; code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following #xD; coding 1..* Coding Code defined by a terminology system Fixed Value: (Complex) #xD; system 1..1 uri Identity of the terminology system Fixed Value: http://bwhc.de/mtb/genetics-copy-number-variant #xD; code 1..1 code Symbol in syntax defined by the system Fixed Value: type #xD; Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual component result Slice: Unordered, Open by type:$this #xD; value[x]:valueCodeableConcept S 0..1 CodeableConcept Actual component result #xD; component:copy-number-neutral-loh S 0..* BackboneElement Kopienzahlneutraler LoH #xD; code S 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following #xD; coding 1..* Coding Code defined by a terminology system Fixed Value: (Complex) #xD; system 1..1 uri Identity of the terminology system Fixed Value: https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/CodeSystem/mii-cs-mtb-molekulare-biomarker #xD; code 1..1 code Symbol in syntax defined by the system Fixed Value: copy-number-neutral-loh #xD; Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual component result Slice: Unordered, Open by type:$this #xD; value[x]:valueCodeableConcept S 0..1 CodeableConcept Actual component result #xD; Documentation for this format
Measurements and simple assertions made about a patient, device or other subject.
Used for simple observations such as device measurements, laboratory atomic results, vital signs, height, weight, smoking status, comments, etc. Other resources are used to provide context for observations such as laboratory reports, etc.
If the resource is contained in another resource, it SHALL NOT contain nested Resources
not(parent::f:contained and f:contained)
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 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='#'])]))
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
If a resource is contained in another resource, it SHALL NOT have a security label
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]))
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')])))
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())
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
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.
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.
Must have either extensions or value[x], not both
exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
The version specific identifier, as it appears in the version portion of the URL. This value changes when the resource is created, updated, or deleted.
The server assigns this value, and ignores what the client specifies, except in the case that the server is imposing version integrity on updates/deletes.
When the resource last changed - e.g. when the version changed.
This value is always populated except when the resource is first being created. The server / resource manager sets this value; what a client provides is irrelevant. This is equivalent to the HTTP Last-Modified and SHOULD have the same value on a [read](http://hl7.org/fhir/R4/http.html#read) interaction.
Identifies where the resource comes from
A uri that identifies the source system of the resource. This provides a minimal amount of [Provenance](http://hl7.org/fhir/R4/provenance.html#) information that can be used to track or differentiate the source of information in the resource. The source may identify another FHIR server, document, message, database, etc.
In the provenance resource, this corresponds to Provenance.entity.what[x]. The exact use of the source (and the implied Provenance.entity.role) is left to implementer discretion. Only one nominated source is allowed; for additional provenance details, a full Provenance resource should be used. This element can be used to indicate where the current master source of a resource that has a canonical URL if the resource is no longer hosted at the canonical URL.
Profiles this resource claims to conform to
A list of profiles (references to [StructureDefinition](http://hl7.org/fhir/R4/structuredefinition.html#) resources) that this resource claims to conform to. The URL is a reference to [StructureDefinition.url](http://hl7.org/fhir/R4/structuredefinition-definitions.html#StructureDefinition.url).
It is up to the server and/or other infrastructure of policy to determine whether/how these claims are verified and/or updated over time. The list of profile URLs is a set.
Security Labels applied to this resource
Security labels applied to this resource. These tags connect specific resources to the overall security policy and infrastructure.
The security labels can be updated without changing the stated version of the resource. The list of security labels is a set. Uniqueness is based the system/code, and version and display are ignored.
Security Labels from the Healthcare Privacy and Security Classification System.
Tags applied to this resource. Tags are intended to be used to identify and relate resources to process and workflow, and applications are not required to consider the tags when interpreting the meaning of a resource.
The tags can be updated without changing the stated version of the resource. The list of tags is a set. Uniqueness is based the system/code, and version and display are ignored.
Codes that represent various types of tags, commonly workflow-related; e.g. "Needs review by Dr. Jones".
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.
May be used to represent additional information that is not part of the basic definition of the resource. 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.
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
Record details about the anatomical location of a specimen or body part. This resource may be used when a coded concept does not provide the necessary detail needed for the use case.
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).
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](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
Variant ID in the context of the NGS report
Eindeutige ID der Variante im Kontext des NGS-Befundes.
Unique ID of the variant in the context of the NGS report.
Allows observations to be distinguished and referenced.
CX / EI (occasionally, more often EI maps to a resource id or a URL)
II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT]
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.
References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository.
Allows tracing of authorization for the event and tracking whether proposals/recommendations were acted upon.
SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))
not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])
The target of a resource reference is a RIM entry point (Act, Role, or Entity)
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](http://hl7.org/fhir/R4/observation.html#obsgrouping) below for guidance on referencing another Observation.
This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.
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"
Slice based on the category.code pattern
In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.
Used for filtering what observations are retrieved and displayed.
Codes for high level observation categories.
fhir:CodeableConcept rdfs:subClassOf dt:CD
.outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code
A code that classifies the general type of observation being made.
A reference to a code defined by a terminology system.
Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.
Allows for alternative encodings within a code system, and translations to other code systems.
CE/CNE/CWE subset one of the sets of component 1-3 or 4-6
fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding
Plain text representation of the concept
A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.
Very often the text is the same as a displayName of one of the codings.
The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.
C*E.9. But note many systems use C*E.2 for this
fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText
Code zur Identifizierung der Varianten-Beobachtung
*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|
Der Patient oder die Gruppe auf die sich die Variante bezieht
One would expect this element to be a cardinality of 1..1. The only circumstance in which the subject can be missing is when the observation is made by a device that does not know the patient. In this case, the observation SHALL be matched to a patient through some context/channel matching technique, and at this point, the observation should be updated.
Observations have no value if you don't know who or what they're about.
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](http://hl7.org/fhir/R4/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]
Klinisch relevanter Zeitpunkt oder Zeitraum der Beobachtung
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](http://hl7.org/fhir/R4/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)
Datum und Uhrzeit der Freigabe der Beobachtung
For Observations that don’t require review and verification, it may be the same as the [`lastUpdated` ](http://hl7.org/fhir/R4/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'
Das Ergebnis der Variantenanalyse - vorhanden oder abwesend
An observation may have; 1) a single value here, 2) both a value and a set of related or component values, or 3) only a set of related or component values. If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the [Notes section](http://hl7.org/fhir/R4/observation.html#notes) below.
An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.
Indeterminate | No call | Present | Absent.
The presence or absence of the variant described in the components. If not searching for specific variations and merely reporting what's found, the profile's value should be set to 'Present'.
See [here](sequencing.html#variant-assessment) for usage guidance.
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 that also contain a coded type
A text note which also contains information about who made the statement and when.
May include general statements about the observation, or statements about significant, unexpected or unreliable results values, or information about its source when relevant to its interpretation. The CodedAnnotation data type, while not allowing for or intending to make the content computable, does allow the author to indicate the type of note. This does not replace the use of interpretation, value, or component values. One important note is that Annotation is a FHIR data type, this is **NOT** about annotations in the genomic context.
Need to be able to provide free text additional information. Notes SHALL NOT contain information which can be captured in a structured way.
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](http://hl7.org/fhir/R4/extension-bodysite.html).
Codes describing anatomical locations. May include laterality.
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.
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).
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]
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 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.
If a code for the unit is present, the system SHALL also be present
The comparator is not used on a SimpleQuantity
PQ, IVL<PQ>, MO, CO, depending on the values
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.
The stated low and high value are assumed to have arbitrarily high precision when it comes to determining which values are in the range. I.e. 1.99 is not in the range 2 -> 3.
If present, low SHALL have a lower value than high
low.empty() or high.empty() or (low <= high)
not(exists(f:low/f:value/@value)) or not(exists(f:high/f:value/@value)) or (number(f:low/f:value/@value) <= number(f:high/f:value/@value))
NR and also possibly SN (but see also quantity)
IVL<QTY[not(type="TS")]> [lowClosed="true" and highClosed="true"]or URG<QTY[not(type="TS")]>
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".
Note that FHIR strings SHALL NOT exceed 1MB in size
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](http://hl7.org/fhir/R4/observation.html#obsgrouping) below. Note that a system may calculate results from [QuestionnaireResponse](http://hl7.org/fhir/R4/questionnaireresponse.html) into a final score and represent the score as an Observation.
Relationships established by OBX-4 usage
Slice based on the reference profile pattern
Related measurements the observation is made from
The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.
All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see [Notes](http://hl7.org/fhir/R4/observation.html#obsgrouping) below.
Slice based on the component.code pattern
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](http://hl7.org/fhir/R4/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](http://hl7.org/fhir/R4/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.
Textuelle Zusammenfassung oder Schlussfolgerung zur Variante
An example would be the interpretative information, typically canned, about a variant identified in the patient.
Need to be able to provide a conclusion that is not lost among the basic result data.
Summary conclusion (interpretation/impression)
The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Chromosomale Position der Variante in Bandennomenklatur
Die verwendete Referenzgenom-Version wie z.B. GRCh37 oder GRCh38
Chromosome auf dem sich die Variante befindet (chr1 - chr22, chrX, chrY).
Chromosom auf dem sich die Variante befindet - chr1 - chr22 - chrX - chrY
Chromosome on which the variant is located - chr1 - chr22 - chrX - chrY
Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Die cDNA-Änderung in HGVS-Nomenklatur auf Transkriptebene
A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Die genomische DNA-Änderung in HGVS-Nomenklatur
A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Fully describes a variant with a single code. Typically a large variant such as a mosaic, abnormal chromosome numbers, etc.
Die genomische Referenzsequenz-ID wie z.B. NC_000007.14
Versioned genomic reference sequence identifier
Multiple bindings acceptable (NCBI or LRG)
ID of the protein reference sequence, which includes transcribed and non transcribed stretches. It covers the entire protein described.
Versioned protein reference sequence identifier
Die Transkript-Referenzsequenz-ID wie z.B. NM_004333.4
Versioned transcript reference sequence identifier
Positionsbereich der genetischen Variante.
Range in question. 'High' can be omitted for single nucleotide variants.
Der innere Bereich bei strukturellen Varianten
Der äußere Bereich bei strukturellen Varianten
These are different ways of identifying nucleotides or amino acids within a sequence. In the 1-based system, the first unit of the polymer (e.g. the first nucleotide) is counted as number 1. In the 0-based system, the number 0 designates the location before the first nucleotide. Different databases and file types may use different systems.
0-based interval counting | 0-based character counting | 1-based character counting
Die Nukleotidsequenz des Referenz-Allels
Die Nukleotidsequenz des alternativen - mutierten - Allels
Der Typ der DNA-Änderung wie z.B. Substitution oder Deletion
deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Concepts in sequence ontology under SO:0002072
Die Herkunft der Variante wie z.B. somatisch oder Keimbahn
Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Die Häufigkeit des varianten Allels in der untersuchten Probe
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.
see http://en.wikipedia.org/wiki/Uniform_resource_identifier
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
Die Anzahl der Reads die das Allel unterstützen
Der Allelstatus wie z.B. heterozygot oder homozygot
Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Die Vererbungsart der Variante wie z.B. maternal oder paternal
Evidential basis for variant inheritance
The method by which the variant inheritance is determined.
Directly measured | Family DNA | Family history | Inferred from population data
Eindeutiger Identifikator der Variante aus externen Datenbanken wie z.B. ClinVar oder dbSNP
Die Aminosäure-Änderung in HGVS-Nomenklatur auf Proteinebene
A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Copy number variants are often described with a single copy number value. However, due to the nature of assays, such as qPCR and microarray, it can be difficult to assign an exact copy number. Therefore, labs sometimes report a range instead of an exact copy number. They may alternatively choose to report decimal numbers, even if whole numbers are biologically correct. In general, it can be difficult to estimate a copy number from measurements taken on a heterogenous population of cells, such as a tumor. As indicated in the ISCN 2020 specifications, it is appropriate to express the measurements using a range. Furthermore, regardless of cell population, many assays use fluorescent probes to detect copy number. These testing methodologies do not always provide an exact, discrete value for this data point.
There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM.
Der Vertrauensstatus der Variantendetektion
Nucleotides of a repeat expansion motif.
Use to group and order repeat expansion motifs.
If there are multiple repeat expansion pairs, this must be used both to indicate the sequence position of a given repeat-motif and repeat-number pair and to group the related components together. Components with the same extension value describe the same motif.
The value must be a natural number starting from 1 and increasing sequentially
Number of repeats of a repeat expansion.
Ein lesbarer Name für die untersuchte Region. Typischerweise Exon # oder Intron # oder andere.
Details zur Genfusion in Blut oder Gewebe mittels molekulargenetischer Methode
HGNC-Format für Genfusionen GENESYMBOL1::GENESYMBOL2 und Readthrough-Transkripte GENESYMBOL1-GENESYMBOL2
Wird üblicherweise als Prozentsatz angegeben
Copy number neutral Loss of heterozygosity
Kopienzahlneutraler Verlust der Heterozygotie