Argonaut Data Query Implementation Guide Version 1.0.0

This page is part of the Argonaut Data Query Implementation Guide (v1.0.0: Release) based on FHIR R2. This is the current published version in it's permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

D.4.1 StructureDefinition-argo-observationresults

Laboratory results are grouped and summarized using the DiagnosticReport resource which reference Observation resources. Each Observation resource represents an individual laboratory test and result value, a “nested” panel (such as a microbial susceptibility panel) which references other observations, or rarely a laboratory test with component result values. This profile sets minimum expectations for the Observation resource resource to record, search and fetch laboratory test results associated with a patient. It identifies which core elements, extensions, vocabularies and value sets SHALL be present in the resource when using this profile.

Example Usage Scenarios:

The following are example usage scenarios for the Argonaut Results profile:

  • Query for lab results belonging to a Patient
  • Record lab results belonging to a Patient
Mandatory Data Elements and Terminology

The following data-elements are mandatory (i.e data MUST be present). These are presented below in a simple human-readable explanation. Profile specific guidance and examples are provided as well. The Formal Profile Definition below provides the formal summary, definitions, and terminology requirements.

Each Observation must have:

  1. a status
  2. a category code of ‘laboratory’
  3. a LOINC code, if available, which tells you what is being measured
  4. a patient
  5. a result value and, if the result value is a numeric quantity, a standard UCUM unit

Each Observation SHOULD have:

  1. a time indicating when the measurement was taken
  2. a reference range if available

Profile specific implementation guidance:

  • Additional codes that translate or map to the Observation code or category codes are allowed. For example:
    • providing both a local system codes and a LOINC code that it map to
    • providing a more specific category codes such as “chemistry’, SNOMED CT concepts, or system specific codes in addition to the “laboratory” category code.
  • If there is no result then you have to supply a reason unless Observation is being used to group other results then there is no value. Instead, it includes composite values or references to other Observations
  • See the General Guidance Section for further guidance on using UCUM

Examples

D.4.1.1 Formal Views of Profile Content

The official URL for this profile is: 

http://fhir.org/guides/argonaut/StructureDefinition/argo-observationresults

This profile builds on Observation.

This profile was published on Tue Oct 18 00:00:00 AEDT 2016 as a draft by Argonaut Project.

Description of Profiles, Differentials, Snapshots, and how the XML and JSON presentations work.

Complete Summary of the Mandatory Requirements

  1. One status in Observation.status which has an required binding to ObservationStatus
  2. A category in Observation.category which must have:
  3. One code in Observation.code which has an extensible binding to LOINC Observation Codes
    • Other additional codes are allowed - e.g. system specific codes. All codes SHALL have a code system value
  4. One patient in Observation.subject
  5. Either one Observation.value[x] or one code in Observation.DataAbsentReason (unless the Observation.code is a panel code)

Each Observation SHOULD have:

  1. A date and time in effectiveDateTime or effectivePeriod
  2. A reference range if applicable in Observation.referenceRange
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Argonaut Observation Results Profile
arg-2: If there is no component or related element then either a value[x] or a data absent reason must be present
... status S1..1codeBinding: ObservationStatus (required)
... category S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]}
... code S1..1CodeableConceptLab Test Name
Binding: LOINC Codes (extensible)
... subject S1..1Reference(Argonaut Patient Profile)
... effective[x] SI0..1dateTime, Periodarg-1: Datetime must be at least to day.
... value[x] SI0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, Periodarg-3: SHALL use UCUM for coded quantity units.
arg-4: SHOULD use Snomed CT for coded Results
... dataAbsentReason SI0..1CodeableConceptBinding: Observation Value Absent Reason (extensible)

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Argonaut Observation Results Profile
obs-6: SHALL only be present if Observation.value[x] is not present
obs-7: Component code SHALL not be same as observation code
arg-2: If there is no component or related element then either a value[x] or a data absent reason must be present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: IETF BCP-47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional Content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier 0..*IdentifierUnique Id for this particular observation
... status ?!S1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category S1..1CodeableConceptClassification of type of observation
Binding: Observation Category Codes (example)
Required Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]}
... code S1..1CodeableConceptLab Test Name
Binding: LOINC Codes (extensible)
... subject S1..1Reference(Argonaut Patient Profile)Who and/or what this is about
... encounter 0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SI0..1dateTime, PeriodClinically relevant time/time-period for observation
arg-1: Datetime must be at least to day.
... issued Σ0..1instantDate/Time this was made available
... performer Σ0..*Reference(Practitioner), Reference(Organization), Reference(Patient), Reference(RelatedPerson)Who is responsible for the observation
... value[x] SI0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual result
arg-3: SHALL use UCUM for coded quantity units.
arg-4: SHOULD use Snomed CT for coded Results
... dataAbsentReason SI0..1CodeableConceptWhy the result is missing
Binding: Observation Value Absent Reason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comments 0..1stringComments about result
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMED CT Body Structures (example)
... method 0..1CodeableConceptHow it was done
Binding: Observation Methods (example)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device), Reference(DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... meaning 0..1CodeableConceptIndicates the meaning/use of this range of this range
Binding: Observation Reference Range Meaning Codes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related Σ0..*BackboneElementResource related to this observation
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required)
.... target 1..1Reference(Observation), Reference(QuestionnaireResponse)Resource that is related to this one
... component Σ0..*BackboneElementComponent results
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINC Codes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: Observation Value Absent Reason (extensible)
.... referenceRange 0..*Unknown reference to #Observation:argoprofile.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

Complete Summary of the Mandatory Requirements

  1. One status in Observation.status which has an required binding to ObservationStatus
  2. A category in Observation.category which must have:
  3. One code in Observation.code which has an extensible binding to LOINC Observation Codes
    • Other additional codes are allowed - e.g. system specific codes. All codes SHALL have a code system value
  4. One patient in Observation.subject
  5. Either one Observation.value[x] or one code in Observation.DataAbsentReason (unless the Observation.code is a panel code)

Each Observation SHOULD have:

  1. A date and time in effectiveDateTime or effectivePeriod
  2. A reference range if applicable in Observation.referenceRange

Differential View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Argonaut Observation Results Profile
arg-2: If there is no component or related element then either a value[x] or a data absent reason must be present
... status S1..1codeBinding: ObservationStatus (required)
... category S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]}
... code S1..1CodeableConceptLab Test Name
Binding: LOINC Codes (extensible)
... subject S1..1Reference(Argonaut Patient Profile)
... effective[x] SI0..1dateTime, Periodarg-1: Datetime must be at least to day.
... value[x] SI0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, Periodarg-3: SHALL use UCUM for coded quantity units.
arg-4: SHOULD use Snomed CT for coded Results
... dataAbsentReason SI0..1CodeableConceptBinding: Observation Value Absent Reason (extensible)

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Argonaut Observation Results Profile
obs-6: SHALL only be present if Observation.value[x] is not present
obs-7: Component code SHALL not be same as observation code
arg-2: If there is no component or related element then either a value[x] or a data absent reason must be present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: IETF BCP-47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional Content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier 0..*IdentifierUnique Id for this particular observation
... status ?!S1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category S1..1CodeableConceptClassification of type of observation
Binding: Observation Category Codes (example)
Required Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]}
... code S1..1CodeableConceptLab Test Name
Binding: LOINC Codes (extensible)
... subject S1..1Reference(Argonaut Patient Profile)Who and/or what this is about
... encounter 0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SI0..1dateTime, PeriodClinically relevant time/time-period for observation
arg-1: Datetime must be at least to day.
... issued Σ0..1instantDate/Time this was made available
... performer Σ0..*Reference(Practitioner), Reference(Organization), Reference(Patient), Reference(RelatedPerson)Who is responsible for the observation
... value[x] SI0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual result
arg-3: SHALL use UCUM for coded quantity units.
arg-4: SHOULD use Snomed CT for coded Results
... dataAbsentReason SI0..1CodeableConceptWhy the result is missing
Binding: Observation Value Absent Reason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comments 0..1stringComments about result
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMED CT Body Structures (example)
... method 0..1CodeableConceptHow it was done
Binding: Observation Methods (example)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device), Reference(DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... meaning 0..1CodeableConceptIndicates the meaning/use of this range of this range
Binding: Observation Reference Range Meaning Codes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related Σ0..*BackboneElementResource related to this observation
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required)
.... target 1..1Reference(Observation), Reference(QuestionnaireResponse)Resource that is related to this one
... component Σ0..*BackboneElementComponent results
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINC Codes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: Observation Value Absent Reason (extensible)
.... referenceRange 0..*Unknown reference to #Observation:argoprofile.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

Downloads: StructureDefinition: (XML, JSON, CSV), Schema: XML Schematron

 

D.4.1.2 Quick Start

Below is an overview of the required search and read operations for this profile. See the Conformance requirements for the Argonaut Data Query implementation guide server for a complete list of supported RESTful operations and search parameters for this IG.

GET [base]/Observation?patient=[id]&category=laboratory

Example:

GET https://fhir-open-api-dstu2.smarthealthit.org/Observation?patient=1134281&category=laboratory

Support: Mandatory to support search by patient and category code = ‘laboratory’.

Implementation Notes: Search based on laboratory category code = “laboratory”. This fetches a bundle of all Observation resources with laboratory categories for the specified patient [(how to search by reference)] and [(how to search by token)].

Response Class:

  • (Status 200): successful operation
  • (Status 400): invalid parameter
  • (Status 401/4xx): unauthorized request
  • (Status 403): insufficient scope

GET [base]/Observation?patient=[id]&code=[LOINC{,LOINC2,LOINC3,...}]

Example: Search for all blood glucose lab results (LOINC = 2339-0 Glucose [Mass/volume] in Blood) for a patient:

GET https://fhir-open-api-dstu2.smarthealthit.org/Observation?patient=1134281&code=2339-0

Example: Search for all blood glucose, urine glucose (LOINC = 25428-4 Glucose [Presence] in Urine by Test strip) and urine ketones (LOINC = 2339-0 Ketones [Presence] in Urine by Test strip) for a patient

GET https://fhir-open-api-dstu2.smarthealthit.org/Observation?patient=1134281&code=2339-0,25428-4,2514-8

Support: Mandatory support search by a laboratory LOINC code. SHOULD support search by multiple LOINC codes.

Implementation Notes: 1) Search based on laboratory LOINC code(s). This fetches a bundle of all Observation resources for a specific observation LOINC code(s) for the specified patient [(how to search by reference)] and [(how to search by token)]. 2) The Argonaut Observation “code” parameter has been defined to search both in both Observation.code and Observation.component.code.

Response Class:

  • (Status 200): successful operation
  • (Status 400): invalid parameter
  • (Status 401/4xx): unauthorized request
  • (Status 403): insufficient scope

GET [base]/Observation?patient=[id]&category=laboratory&date=[date]{&date=[date]}

Example: Find all the laboratory results after 2013-03-14

GET http://fhir2.healthintersections.com.au/open/Observation?patient=555580&category=laboratory&date=ge2015-01-14

Support: Mandatory support search by category code =”laboratory” and date or period

Implementation Notes: Search based on laboratory category code and date. This fetches a bundle of all Observation resources with category ‘laboratory’ for the specified patient for a specified time period [(how to search by reference)], [(how to search by token)] amd [(how to search by date)].

Response Class:

  • (Status 200): successful operation
  • (Status 400): invalid parameter
  • (Status 401/4xx): unauthorized request
  • (Status 403): insufficient scope [(how to search by reference)]: http://hl7.org/fhir/DSTU2/search.html#reference [(how to search by token)]: http://hl7.org/fhir/DSTU2/search.html#token [Composite Search Parameters]: http://hl7.org/fhir/search.html#combining [(how to search by date)]: http://hl7.org/fhir/DSTU2/search.html#date