// RareLink Diagnostic Implication Observation { "resourceType" : "Observation", "id" : "<id>", // Logical id of this artifact "meta" : {Meta}, // C? Metadata about the resource "implicitRules" : "<uri>", // C? A set of rules under which this content was created "language" : "<code>", // C? Language of the resource content "text" : {Narrative}, // C? Text summary of the resource, for human interpretation "contained" : [{Resource}], // Contained, inline Resources "extension": [ { // C? Only One! 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 "url": "http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding", "valueCodeableConcept" : {CodeableConcept} // C? R! Value of extension }, { // C? Only One! Target anatomic location or structure "url": "http://hl7.org/fhir/StructureDefinition/bodySite", "valueReference" : {Reference(BodyStructure)} // C? R! Value of extension }, { // C?Documentation relevant to the 'parent' resource "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", "valueRelatedArtifact" : {RelatedArtifact} // C? R! Value of extension }, { // C?Genomic Risk Assessment "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment", "valueReference" : {Reference(RiskAssessment)} // C? Value of extension } ], "identifier" : [{Identifier}], // C? Business Identifier for observation "basedOn" : [{Reference(CarePlan)}], // C? Fulfills plan, proposal or order "partOf" : [{Reference(MedicationAdministration)}], // C? Part of referenced event "status" : "final", // C? R! "category" : [ // sliced by value:coding in the specified order Open { // Classification of type of observation C? R! Only One! "extension" : [ // sliced by value:url in the specified order Open ], "coding" : [{Coding}], // C? R! Only One! Code defined by a terminology system "text" : "<string>" // C? Plain text representation of the concept }, { // Classification of type of observation C? R! Only One! "extension" : [ // sliced by value:url in the specified order Open ], "coding" : [{Coding}], // C? R! Only One! Code defined by a terminology system "text" : "<string>" // C? Plain text representation of the concept } ], "code" : { // C? R! diagnostic-implication "extension": [ ], "coding" : [{ // C? Code defined by a terminology system "extension": [ ], "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", // C? "version" : "<string>", // C? Version of the system - if relevant "code" : "diagnostic-implication", // C? "display" : "<string>", // C? Representation defined by the system "userSelected" : <boolean> // C? If this coding was chosen directly by the user }], "text" : "<string>" // C? Plain text representation of the concept }, "subject" : {Reference(Patient)}, // C? Who and/or what the observation is about "focus" : [{Reference(Resource)}], // C? What the observation is about, when it is not about the subject of record "encounter" : {Reference(Encounter)}, // C? Healthcare event during which this observation is made // effective[x]: Clinically relevant time/time-period for observation. One of these 4: "effectiveDateTime" : "<dateTime>", // C? Clinically relevant time/time-period for observation "effectivePeriod" : {Period}, // C? Clinically relevant time/time-period for observation "effectiveTiming" : {Timing}, // C? Clinically relevant time/time-period for observation "effectiveInstant" : "<instant>", // C? Clinically relevant time/time-period for observation "issued" : "<instant>", // C? Date/Time this version was made available "performer" : [{Reference(Practitioner)}], // C? Who is responsible for the observation "dataAbsentReason" : {CodeableConcept}, // C? Why the result is missing "interpretation" : [{CodeableConcept}], // C? High, low, normal, etc. "note" : [{Annotation (as CodedAnnotation)}], // C? Comments about the Observation that also contain a coded type "bodySite" : {CodeableConcept}, // C? Observed body part "method" : {CodeableConcept}, // C? How it was done "specimen" : {Reference(Specimen)}, // C? Specimen used for this observation "device" : {Reference(Device)}, // C? (Measurement) Device "referenceRange" : [{ // C? Provides guide for interpretation "extension": [ ], "low" : {Quantity (as SimpleQuantity)}, // C? Low Range, if relevant "high" : {Quantity (as SimpleQuantity)}, // C? High Range, if relevant "type" : {CodeableConcept}, // C? Reference range qualifier "appliesTo" : [{CodeableConcept}], // C? Reference range population "age" : {Range}, // C? Applicable age range, if relevant "text" : "<string>", // C? Text based reference range in an observation }], "hasMember" : [{Reference(Observation)}], // C? Related resource that belongs to the Observation group "derivedFrom" : [ // sliced by profile:resolve() in the specified order Open { // Variant the implication is derived from C? // from Element: extension }, { // Genotype the implication is derived from C? // from Element: extension }, { // Haplotype the implication is derived from C? // from Element: extension }, { // MolecularBiomarker the implication is derived from C? // from Element: extension }, { // Related measurements the observation is made from C? R! Only One! "extension" : [ // sliced by value:url in the specified order Open ], "reference" : "<string>", // C? R! Literal reference, Relative, internal or absolute URL "type" : "<uri>", // C? Type the reference refers to (e.g. "Patient") "identifier" : {Identifier}, // C? Logical reference, when literal reference is not known "display" : "<string>" // C? Text alternative for the resource } ], "component" : [ // sliced by value:code in the specified order Open { // Clinical Conclusion C? Only One! "modifierExtension" : [{Extension}], // C? Extensions that cannot be ignored even if unrecognized "code" : {CodeableConcept}, // C? R! conclusion-string "valueString" : "<string>", // C? Summary conclusion (interpretation/impression) "dataAbsentReason" : {CodeableConcept}, // C? Why the component result is missing "interpretation" : [{CodeableConcept}], // C? High, low, normal, etc. "referenceRange" : [<n/a>] // C? Provides guide for interpretation of component result }, { // Level of Evidence C? "modifierExtension" : [{Extension}], // C? Extensions that cannot be ignored even if unrecognized "code" : {CodeableConcept}, // C? R! 93044-6 "valueCodeableConcept" : {CodeableConcept}, // C? R! 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star "dataAbsentReason" : {CodeableConcept}, // C? Why the component result is missing "interpretation" : [{CodeableConcept}], // C? High, low, normal, etc. "referenceRange" : [<n/a>] // C? Provides guide for interpretation of component result }, { // Clinical significance C? Only One! "extension" : [ // sliced by value:url in the specified order Open ], "modifierExtension" : [{Extension}], // C? Extensions that cannot be ignored even if unrecognized "code" : {CodeableConcept}, // C? R! 53037-8 "valueCodeableConcept" : {CodeableConcept}, // C? R! Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign "dataAbsentReason" : {CodeableConcept}, // C? Why the component result is missing "interpretation" : [{CodeableConcept}], // C? High, low, normal, etc. "referenceRange" : [<n/a>] // C? Provides guide for interpretation of component result }, { // Predicted phenotype C? "extension" : [ // sliced by value:url in the specified order Open ], "modifierExtension" : [{Extension}], // C? Extensions that cannot be ignored even if unrecognized "code" : {CodeableConcept}, // C? R! 81259-4 "valueCodeableConcept" : {CodeableConcept}, // C? R! Phenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO "dataAbsentReason" : {CodeableConcept}, // C? Why the component result is missing "interpretation" : [{CodeableConcept}], // C? High, low, normal, etc. "referenceRange" : [<n/a>] // C? Provides guide for interpretation of component result }, { // Mode of Inheritance C? Only One! "extension" : [ // sliced by value:url in the specified order Open ], "modifierExtension" : [{Extension}], // C? Extensions that cannot be ignored even if unrecognized "code" : {CodeableConcept}, // C? R! condition-inheritance "valueCodeableConcept" : {CodeableConcept}, // C? R! Autosomal dominant | Autosomal recessive | X-linked | ... (more) "dataAbsentReason" : {CodeableConcept}, // C? Why the component result is missing "interpretation" : [{CodeableConcept}], // C? High, low, normal, etc. "referenceRange" : [<n/a>] // C? Provides guide for interpretation of component result }, { // Component results C? Only One! "extension" : [ // sliced by value:url in the specified order Open ], "modifierExtension" : [{Extension}], // C? Extensions that cannot be ignored even if unrecognized "code" : { // C? R! Type of component observation (code / type) "extension": [ ], "coding" : [{ // C? Code defined by a terminology system "extension": [ ], "system" : "http://loinc.org", // C? "version" : "<string>", // C? Version of the system - if relevant "code" : "<code>", // C? Symbol in syntax defined by the system "display" : "<string>", // C? Representation defined by the system "userSelected" : <boolean> // C? If this coding was chosen directly by the user }], "text" : "<string>" // C? Plain text representation of the concept }, "valueCodeableConcept" : {CodeableConcept}, // C? Actual component result "dataAbsentReason" : {CodeableConcept}, // C? Why the component result is missing "interpretation" : [{CodeableConcept}], // C? High, low, normal, etc. "referenceRange" : [<n/a>] // C? Provides guide for interpretation of component result }, { // Component results C? Only One! "extension" : [ // sliced by value:url in the specified order Open ], "modifierExtension" : [{Extension}], // C? Extensions that cannot be ignored even if unrecognized "code" : { // C? R! Type of component observation (code / type) "extension": [ ], "coding" : [{ // C? Code defined by a terminology system "extension": [ ], "system" : "http://loinc.org", // C? "version" : "<string>", // C? Version of the system - if relevant "code" : "<code>", // C? Symbol in syntax defined by the system "display" : "<string>", // C? Representation defined by the system "userSelected" : <boolean> // C? If this coding was chosen directly by the user }], "text" : "<string>" // C? Plain text representation of the concept }, "valueCodeableConcept" : {CodeableConcept}, // C? Actual component result "dataAbsentReason" : {CodeableConcept}, // C? Why the component result is missing "interpretation" : [{CodeableConcept}], // C? High, low, normal, etc. "referenceRange" : [<n/a>] // C? Provides guide for interpretation of component result }, { // Component results C? Only One! "extension" : [ // sliced by value:url in the specified order Open ], "modifierExtension" : [{Extension}], // C? Extensions that cannot be ignored even if unrecognized "code" : { // C? R! Type of component observation (code / type) "extension": [ ], "coding" : [{ // C? Code defined by a terminology system "extension": [ ], "system" : "http://loinc.org", // C? "version" : "<string>", // C? Version of the system - if relevant "code" : "<code>", // C? Symbol in syntax defined by the system "display" : "<string>", // C? Representation defined by the system "userSelected" : <boolean> // C? If this coding was chosen directly by the user }], "text" : "<string>" // C? Plain text representation of the concept }, "valueCodeableConcept" : { // C? Actual component result "extension": [ ], "coding" : [ { // Code defined by a terminology system C? "extension" : [ // sliced by value:url in the specified order Open ], "system" : "http://purl.obolibrary.org/obo/mondo.owl", // C? R! "version" : "<string>", // C? Version of the system - if relevant "code" : "<code>", // C? Symbol in syntax defined by the system "display" : "<string>", // C? Representation defined by the system "userSelected" : <boolean> // C? If this coding was chosen directly by the user }, { // Code defined by a terminology system C? "extension" : [ // sliced by value:url in the specified order Open ], "system" : "http://omim.org", // C? R! "version" : "<string>", // C? Version of the system - if relevant "code" : "<code>", // C? Symbol in syntax defined by the system "display" : "<string>", // C? Representation defined by the system "userSelected" : <boolean> // C? If this coding was chosen directly by the user } ], "text" : "<string>", // C? Plain text representation of the concept }, "dataAbsentReason" : {CodeableConcept}, // C? Why the component result is missing "interpretation" : [{CodeableConcept}], // C? High, low, normal, etc. "referenceRange" : [<n/a>] // C? Provides guide for interpretation of component result } ], }