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[[Implementation Guide|Back to Argonaut Implementation Guide]]
 
[[Implementation Guide|Back to Argonaut Implementation Guide]]
 +
 +
**********************PLEASE NOTE********************************
 +
This guide is no longer being actively maintained and updated.
 +
On January 1st 2017, This guide is being superseded by the online
 +
version of the Argonaut-DSTU2 Implemenation Guide.
 +
hosted at:  http://fhir.org/guides/argonaut
 +
The working CI build is avaible now at :
 +
http://build.fhir.org/ig/Healthedata1/Argo-DSTU2/  
 +
 
==Introduction==
 
==Introduction==
 
The Argonaut Laboratory Results guide provides the API documentation for searching and fetching Laboratory Results. This IG covers two resources -  Observation and DiagnosticReport - because labaratory results are grouped and summarized using reports.  This IG is based on the [http://hl7.org/fhir/daf/observation-daf-results.html Data Access Framework (DAF) Laboratory Results]. The search criteria provided in the [[#Quick_Start | Quick Start]] are intended to support the 2015 Edition ONC Certification criterion Data Category Request 170.315(g)(8).
 
The Argonaut Laboratory Results guide provides the API documentation for searching and fetching Laboratory Results. This IG covers two resources -  Observation and DiagnosticReport - because labaratory results are grouped and summarized using reports.  This IG is based on the [http://hl7.org/fhir/daf/observation-daf-results.html Data Access Framework (DAF) Laboratory Results]. The search criteria provided in the [[#Quick_Start | Quick Start]] are intended to support the 2015 Edition ONC Certification criterion Data Category Request 170.315(g)(8).
  
==Argonaut Success Criteria==
+
==Minimum Requirements==
  
 
===Clients===
 
===Clients===
DiagnosticReport
+
====DiagnosticReport====
 
*A client has connected to a server and fetched all of a patient's laboratory diagnostic reports by searching by category using [[#GET_.5Bbase.5D.2FDiagnosticReport.3Fpatient.3D.5Bid.5D.26category.3DLAB|GET [base]/DiagnosticReport?patient=[id]&category=LAB.]]
 
*A client has connected to a server and fetched all of a patient's laboratory diagnostic reports by searching by category using [[#GET_.5Bbase.5D.2FDiagnosticReport.3Fpatient.3D.5Bid.5D.26category.3DLAB|GET [base]/DiagnosticReport?patient=[id]&category=LAB.]]
*A client has connected to a server and fetched all of a patient's laboratory diagnostic reports searching by category code and date range using GET [base]/DiagnosticReport?patient=[id]&category=LAB&date=[eq|lt|le|gt|geyyyy-mm-dd{&date=[lt|le|gt|geyyyy-mm-dd]}].
 
  
 +
*A client has connected to a server and fetched all of a patient's laboratory diagnostic reports searching by category code and date range using [[#GET_.5Bbase.5D.2FDiagnosticReport.3Fpatient.3D.5Bid.5D.26code.3D.5BLOINC.7B.2CLOINC2.2CLOINC3.2C....7D.5D|GET [base]/DiagnosticReport?patient=[id]&category=LAB&date=[date]{&date=[date]}]].
 +
 +
*A client has connected to a server and fetched all of all of a patient's laboratory diagnostic reports searching by category and code using [[#GET_.5Bbase.5D.2FDiagnosticReport.3Fpatient.3D.5Bid.5D.26code.3D.5BLOINC.7B.2CLOINC2.2CLOINC3.2C....7D.5D|GET [base]/DiagnosticReport?patient=[id]&category=LAB&code=[LOINC]]].
  
*A client '''SHOULD''' be capable of connecting to a server and fetching any of a patient's laboratory diagnostic reports searching by category and code and date range using GET [base]/DiagnosticReport?patient=[id]&category=LAB&code=[LOINC1{,LOINC2,...}]&date=[eq|lt|le|gt|geyyyy-mm-dd{&date=[lt|le|gt|geyyyy-mm-dd]}].
 
  
Observation
+
*A client '''SHOULD''' be capable of connecting to a server and fetching any of a patient's laboratory diagnostic reports searching by category and one or more codes and date range using [[#GET|GET [base]/DiagnosticReport?patient=[id]&category=LAB&code=[LOINC1{,LOINC2,LOINC3,...}]&date=[date]{&date=[date]}]].
*A client has connected to a server and fetched all of a patient's laboratory results by searching by category using[[#GET_.5Bbase.5D.2FObservation.3Fpatient.3D.5Bid.5D.26category.3Dlaboratory|GET [base]/Observation?patient=[id]&category=laboratory.]]
 
*A client has connected to a server and fetched all of a patient's laboratory results by searching by category and date range using GET [base]/Observation?patient=[id]&category=laboratory&date=[eq|lt|le|gt|geyyyy-mm-dd{&date=[lt|le|gt|geyyyy-mm-dd]}].
 
  
 +
====Observation====
 +
*A client has connected to a server and fetched all of a patient's laboratory results by searching by category using [[#GET_.5Bbase.5D.2FObservation.3Fpatient.3D.5Bid.5D.26category.3Dlaboratory|GET [base]/Observation?patient=[id]&category=laboratory.]]
  
 +
*A client has connected to a server and fetched all of a patient's laboratory results searching by category code and date range using [[#GET_.5Bbase.5D.2FObservation.3Fpatient.3D.5Bid.5D.26category.3Dlaboratory.26date.3D.5Bdate.5D.7B.26date.3D.5Bdate.5D.7D|GET [base]/Observation?patient=[id]&category=laboratory&date=[date]{&date=[date]}]].
  
*A client '''SHOULD''' be capable of connecting to a server and fetching any of a patient's laboratory results searching by category and code and date range using GET [base]/Observation?patient=[id]&category=laboratory&code=[LOINC1{,LOINC2,...}]&date=[eq|lt|le|gt|geyyyy-mm-dd{&date=[lt|le|gt|geyyyy-mm-dd]}].
+
*A client has connected to a server and fetched all of all of a patient's laboratory results searching by category and code using [[#GET_.5Bbase.5D.2FObservation.3Fpatient.3D.5Bid.5D.26code.3D.5BLOINC.7B.2CLOINC2.2CLOINC3.2C....7D.5D|GET [base]/Observation?patient=[id]&category=laboratory&code=[LOINC]]].
 +
 
 +
 
 +
*A client '''SHOULD''' be capable of connecting to a server and fetching any of a patient's laboratory results searching by category and one or more codes and date range using [[#GET_.5Bbase.5D.2FObservation.3Fpatient.3D.5Bid.5D.26category.3Dlaboratory.26date.3D.5Bdate.5D.7B.26date.3D.5Bdate.5D.7D|GET [base]/Observation?patient=[id]&category=laboratory&code=[LOINC1{,LOINC2,LOINC3,...}]&date=[date]{&date=[date]}]].
  
 
===Servers===
 
===Servers===
*A server is capable of returning all of a patient's laboratory diagnostic reports queried by category using GET [base]/DiagnosticReport?patient=[id].
+
====DiagnosticReport====
*A server is capable of returning all of a patient's laboratory diagnostic reports queried by category and range using GET [base]/DiagnosticReport?patient=[id]&category=LAB&date=[eq|lt|le|gt|geyyyy-mm-dd{&date=[lt|le|gt|geyyyy-mm-dd]}].
+
*A server is capable of returning all of a patient's laboratory diagnostic reports queried by category using [[#GET_.5Bbase.5D.2FDiagnosticReport.3Fpatient.3D.5Bid.5D.26category.3DLAB|GET [base]/DiagnosticReport?patient=[id]&category=LAB.]]
*A server is capable of returning all of a patient's laboratory results queried by category using GET [base]/Observation?patient=[id].
+
 
*A server is capable of returning all of a patient's laboratory results queried by category and date range using GET [base]/Observation?patient=[id]&category=laboratory&date=[eq|lt|le|gt|geyyyy-mm-dd{&date=[lt|le|gt|geyyyy-mm-dd]}].
+
*A server is capable of returning all of a patient's laboratory diagnostic reports queried by category code and date range using [[#GET_.5Bbase.5D.2FDiagnosticReport.3Fpatient.3D.5Bid.5D.26code.3D.5BLOINC.7B.2CLOINC2.2CLOINC3.2C....7D.5D|GET [base]/DiagnosticReport?patient=[id]&category=LAB&date=[date]{&date=[date]}]].
*A server has ensured that every API request includes a valid Authorization token, supplied via:Authorization: Bearer {server-specific-token-here}
+
 
*A server has rejected any unauthorized requests by returning an HTTP 401 Unauthorized response code.
+
*A server is capable of returning all of a patient's laboratory diagnostic reports queried by category and code using [[#GET_.5Bbase.5D.2FDiagnosticReport.3Fpatient.3D.5Bid.5D.26code.3D.5BLOINC.7B.2CLOINC2.2CLOINC3.2C....7D.5D|GET [base]/DiagnosticReport?patient=[id]&category=LAB&code=[LOINC]]].
 +
 
 +
 
 +
*A server '''SHOULD''' be capable of returning all of a patient's laboratory diagnostic reports queried by category and one or more codes and date range using [[#GET|GET [base]/DiagnosticReport?patient=[id]&category=LAB&code=[LOINC1{,LOINC2,LOINC3,...}]&date=[date]{&date=[date]}]].
 +
 
 +
====Observation====
 +
*A server is capable of returning all of a patient's laboratory results queried by category using [[#GET_.5Bbase.5D.2FObservation.3Fpatient.3D.5Bid.5D.26category.3Dlaboratory|GET [base]/Observation?patient=[id]&category=laboratory.]]
 +
 
 +
*A server is capable of returning all of a patient's laboratory results queried by category code and date range using [[#GET_.5Bbase.5D.2FObservation.3Fpatient.3D.5Bid.5D.26category.3Dlaboratory.26date.3D.5Bdate.5D.7B.26date.3D.5Bdate.5D.7D|GET [base]/Observation?patient=[id]&category=laboratory&date=[date]{&date=[date]}]].
 +
*A server is capable of returning all of a patient's laboratory results queried  by category and code using [[#GET_.5Bbase.5D.2FObservation.3Fpatient.3D.5Bid.5D.26code.3D.5BLOINC.7B.2CLOINC2.2CLOINC3.2C....7D.5D|GET [base]/Observation?patient=[id]&category=laboratory&code=[LOINC]]].
 +
 
 +
 
 +
*A server '''SHOULD''' be capable of returning all of a patient's laboratory results queried by category and one or more codes and date range using [[#GET|GET [base]/Observation?patient=[id]&category=laboratory&code=[LOINC1{,LOINC2,LOINC3,...}]&date=[date]{&date=[date]}]].
  
 
==Mandatory Data Elements==
 
==Mandatory Data Elements==
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The following data-elements in the DiagnosticReport and  Observation resources are mandatory (i.e data MUST be present). These are presented below in simple human-readable explanation and a more thorough summary of the requirements.  Refer to the tables for additional quidance and examples for the various laboratory tests.    Both DiagnosticReport and Observation contain structures to group panels of Observations and both options are presented below.  Both approaches are currently supported in this guide.
 
The following data-elements in the DiagnosticReport and  Observation resources are mandatory (i.e data MUST be present). These are presented below in simple human-readable explanation and a more thorough summary of the requirements.  Refer to the tables for additional quidance and examples for the various laboratory tests.    Both DiagnosticReport and Observation contain structures to group panels of Observations and both options are presented below.  Both approaches are currently supported in this guide.
  
==DiagnosticReport==
+
===DiagnosticReport===
 
When lab test or lab panel, such as CBC, is ordered, a DiagnosticReport represents the order fulfillment and references each of the resulting discrete Observations within that panel.
 
When lab test or lab panel, such as CBC, is ordered, a DiagnosticReport represents the order fulfillment and references each of the resulting discrete Observations within that panel.
  
===Each DiagnosticReport must have:===
+
====Each DiagnosticReport must have:====
  
 
* a patient
 
* a patient
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<!-- * what was requested (a DiagnosticOrder reference) * see issue re DAF-->
 
<!-- * what was requested (a DiagnosticOrder reference) * see issue re DAF-->
  
====Example DiagnosticReports====
+
=====Example DiagnosticReports=====
 
The attached table lists LOINC panels for chemistry, hematology(cbc) and urinalysis results.  This Argonaut profile does not make the presence or absence of any of these mandatory and is provided for guidance only.
 
The attached table lists LOINC panels for chemistry, hematology(cbc) and urinalysis results.  This Argonaut profile does not make the presence or absence of any of these mandatory and is provided for guidance only.
  
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|}
 
|}
  
==== Complete Summary of the Mandatory Requirements ====
+
===== Complete Summary of the Mandatory Requirements =====
  
  
Line 74: Line 100:
 
# One status in '''DiagnosticReport.status'''
 
# One status in '''DiagnosticReport.status'''
 
# One category in '''DiagnosticReport.category''' which must have:  
 
# One category in '''DiagnosticReport.category''' which must have:  
#* a fixed '''DiagnosticReport.category.coding.system="http://hl7.org/fhir/DiagnosticReport-category"'''
+
#* a fixed '''DiagnosticReport.category.coding.system="http://hl7.org/fhir/valueset-diagnostic-service-sections.html"'''
 
#* a fixed '''DiagnosticReport.category.coding.code="LAB"'''
 
#* a fixed '''DiagnosticReport.category.coding.code="LAB"'''
 
# One code in '''DiagnosticReport.code''' which must have if available:
 
# One code in '''DiagnosticReport.code''' which must have if available:
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# A practitioner or organization '''DiagnosticReport.performer'''
 
# A practitioner or organization '''DiagnosticReport.performer'''
  
==Observation==
+
===Observation===
 
Each Observation 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.   
 
Each Observation 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.   
===Each Observation must have:===
+
====Each Observation must have:====
 
* a patient
 
* a patient
 
* a LOINC code, if available, which tells you what is being measured
 
* a LOINC code, if available, which tells you what is being measured
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* a reference range if available
 
* a reference range if available
  
====Example Laboratory tests and results====
+
=====Example Laboratory tests and results=====
 
The attached table is derived from the [https://loinc.org/usage/obs LOINC Top 2000+ Lab Observations] and lists LOINC panel and observation codes for quantitative and qualitative tests for chemistry, hematology(cbc) and urinalysis results.  It also lists the corresponding UCUM units of measure codes for quantitative tests.  The qualitative results include both 'ordinal' and 'nominal' scale.  This Argonaut profile does not make the presence or absence of any of these mandatory and is provided for guidance only.
 
The attached table is derived from the [https://loinc.org/usage/obs LOINC Top 2000+ Lab Observations] and lists LOINC panel and observation codes for quantitative and qualitative tests for chemistry, hematology(cbc) and urinalysis results.  It also lists the corresponding UCUM units of measure codes for quantitative tests.  The qualitative results include both 'ordinal' and 'nominal' scale.  This Argonaut profile does not make the presence or absence of any of these mandatory and is provided for guidance only.
  
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|}
 
|}
  
==== Complete Summary of the Mandatory Requirements ====
+
===== Complete Summary of the Mandatory Requirements =====
 
<!--
 
<!--
 
#One or more Observation identifiers in '''Observation.identifier''' each of which must have:
 
#One or more Observation identifiers in '''Observation.identifier''' each of which must have:
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#*#*[http://snomed.info/sct SNOMED CT] is preferred binding
 
#*#*[http://snomed.info/sct SNOMED CT] is preferred binding
 
#*# OR text in '''Observation.valueCodeableConcept.text'''
 
#*# OR text in '''Observation.valueCodeableConcept.text'''
#*Observation.DataAbsentReason is bound to [http://hl7-fhir.github.io/valueset-observation-valueabsentreason.html Observation Value Absent Reason] Value set (Code set)
+
#*Observation.DataAbsentReason is bound to [http://hl7.org/fhir/valueset-observation-valueabsentreason.html Observation Value Absent Reason] Value set (Code set)
 
# One patient in '''Observation.subject'''
 
# One patient in '''Observation.subject'''
  
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Below is a quick overview of the required search and read operations
 
Below is a quick overview of the required search and read operations
  
==DiagnosticReport==
+
===DiagnosticReport===
===GET [base]/DiagnosticReport?patient=[id]&category=LAB===
+
====GET [base]/DiagnosticReport?patient=[id]&category=LAB====
 
<!--EH need to consider the scope of sprint altrenative is  to list all servive sectors in comma separated list - do we want an _include here to get all the associated obs - not covered in sprint -->
 
<!--EH need to consider the scope of sprint altrenative is  to list all servive sectors in comma separated list - do we want an _include here to get all the associated obs - not covered in sprint -->
  
 
''Support:'' Mandatory to support search by category code = LAB.
 
''Support:'' Mandatory to support search by category code = LAB.
  
''Implementation Notes:'' Search based on diagnostic report category code = 'LAB'. This fetches a bundle of all lab related DiagnosticReports resources for the specified patient [http://hl7.org/fhir/DSTU2/search.html#reference (how to search by reference)] and [http://hl7.org/fhir/DSTU2/search.html#token (how to search by token)].
+
''Implementation Notes:'' Search based on diagnostic report category code = 'LAB'. This fetches a bundle of all lab related DiagnosticReport resources for the specified patient [http://hl7.org/fhir/DSTU2/search.html#reference (how to search by reference)] and [http://hl7.org/fhir/DSTU2/search.html#token (how to search by token)].
  
 
''Response Class:''
 
''Response Class:''
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*(Status 401/4xx): unauthorized request
 
*(Status 401/4xx): unauthorized request
 
*(Status 403): insufficient scope
 
*(Status 403): insufficient scope
====Example:====  
+
=====Example:=====  
 
  [GET http://spark.furore.com/fhir/DiagnosticReport?patient=f201&category=LAB]<!-- need to update to smart server when agree on category -->
 
  [GET http://spark.furore.com/fhir/DiagnosticReport?patient=f201&category=LAB]<!-- need to update to smart server when agree on category -->
  
 
----
 
----
===GET [base]/DiagnosticReport?patient=[id]&code=[Laboratory order LOINC]===
 
<!--do we want an _include here to get all the associated obs - not covered in sprint-->
 
  
''Support:'' Mandatory support search DiagnosticReport by laboratory order codes  <!-- should  we create a table of order too!-->
+
====GET [base]/DiagnosticReport?patient=[id]&code=[LOINC{,LOINC2,LOINC3,...}]====
  
''Implementation Notes:'' Search based on Diagnostic report code. This fetches a bundle of all DiagnosticReport resources for a specific diagnostic order code for the specified patient [http://hl7.org/fhir/DSTU2/search.html#reference (how to search by reference)] and [http://hl7.org/fhir/DSTU2/search.html#token (how to search by token)].
+
''Support:''  Mandatory support search by a laboratory order code. SHOULD support search by multiple order codes.
 +
 
 +
''Implementation Notes:'' Search based on DiagnosticReport code. This fetches a bundle of all DiagnosticReport resources for a specific diagnostic order code for the specified patient [http://hl7.org/fhir/DSTU2/search.html#reference (how to search by reference)] and [http://hl7.org/fhir/DSTU2/search.html#token (how to search by token)].
  
 
''Response Class:''
 
''Response Class:''
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*(Status 401/4xx): unauthorized request
 
*(Status 401/4xx): unauthorized request
 
*(Status 403): insufficient scope
 
*(Status 403): insufficient scope
====Example:)====  
+
=====Example:)=====  
 
Search for all metabolic panel reports for a patient:
 
Search for all metabolic panel reports for a patient:
  
 
  [GET https://fhir-open-api-dstu2.smarthealthit.org/DiagnosticReport?patient=1032702&code=24323-8]
 
  [GET https://fhir-open-api-dstu2.smarthealthit.org/DiagnosticReport?patient=1032702&code=24323-8]
 +
 +
=====Example:=====
 +
Search for all cbc, metabolic panel, and urinalysis panels for a patient
 +
 +
[GET https://fhir-open-api-dstu2.smarthealthit.org/DiagnosticReport?patient=1032702&code=24323-8,58410-2,24356-8]
 +
----
 +
 
----
 
----
  
===GET [base]/DiagnosticReport?patient=[id]&code=[lab1 LOINC, lab2 LOINC, etc]===
+
<!--
 +
====GET [base]/DiagnosticReport?patient=[id]&code=[lab1 LOINC, lab2 LOINC, etc]====
 
(TODO_repeat for DR)
 
(TODO_repeat for DR)
  
''Support:'' SHOULD support Observation search by multiple LOINCs.
+
''Support:'' SHOULD support DiagnosticReport search by multiple LOINCs.
 
.
 
.
  
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*(Status 403): insufficient scope
 
*(Status 403): insufficient scope
  
====Example:====  
+
=====Example:=====  
 
Search for all cbc, metabolic panel, and urinalysis panels for a patient
 
Search for all cbc, metabolic panel, and urinalysis panels for a patient
  
 
  [GET https://fhir-open-api-dstu2.smarthealthit.org/DiagnosticReport?patient=1032702&code=24323-8,58410-2,24356-8]
 
  [GET https://fhir-open-api-dstu2.smarthealthit.org/DiagnosticReport?patient=1032702&code=24323-8,58410-2,24356-8]
 
----
 
----
 +
-->
  
===GET [base]/DiagnosticReport?patient=[id]&category=LAB&[eq|lt|gt|geyyyy-mm-dd{&eq|lt|gt|geyyyy-mm-dd}]===
+
====GET [base]/DiagnosticReport?patient=[id]&category=LAB&date=[date]{&date=[date]}====
  
 
''Support:'' Mandatory support search by category code and date or period
 
''Support:'' Mandatory support search by category code and date or period
  
''Implementation Notes:'' Search based on laboratory category code and date. This fetches a bundle of all Diagnostic Reports resources with category 'LAB' for the specified patient for a specified time period [http://hl7.org/fhir/DSTU2/search.html#reference (how to search by reference)]and [http://hl7.org/fhir/DSTU2/search.html#token (how to search by token)] and [http://hl7.org/fhir/DSTU2/search.html#date (how to search by date)].
+
''Implementation Notes:'' Search based on laboratory category code and date. This fetches a bundle of all DiagnosticReport resources with category 'LAB' for the specified patient for a specified time period [http://hl7.org/fhir/DSTU2/search.html#reference (how to search by reference)]and [http://hl7.org/fhir/DSTU2/search.html#token (how to search by token)] and [http://hl7.org/fhir/DSTU2/search.html#date (how to search by date)].
  
 
''Response Class:''
 
''Response Class:''
Line 288: Line 323:
 
*(Status 401/4xx): unauthorized request
 
*(Status 401/4xx): unauthorized request
 
*(Status 403): insufficient scope
 
*(Status 403): insufficient scope
====Example:====  
+
=====Example:=====  
 
Find all the lab reports issued after 2010-01-14
 
Find all the lab reports issued after 2010-01-14
  
 
  [GET http://spark.furore.com/fhir/DiagnosticReport?patient=f201&category=LAB&date=ge2010-01-14]
 
  [GET http://spark.furore.com/fhir/DiagnosticReport?patient=f201&category=LAB&date=ge2010-01-14]
  
==Observation==
+
===Observation===
===GET [base]/Observation?patient=[id]&category=laboratory===  
+
====GET [base]/Observation?patient=[id]&category=laboratory====  
 
<!-- EH need to consider the scope of sprint and where we want to be also the obs category is heirarchical so would could list heirarcy  = lab or list all servive sectors in comma separated list,  do we want an _include here to get all the associated obs - not covered in sprint -->
 
<!-- EH need to consider the scope of sprint and where we want to be also the obs category is heirarchical so would could list heirarcy  = lab or list all servive sectors in comma separated list,  do we want an _include here to get all the associated obs - not covered in sprint -->
  
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*(Status 401/4xx): unauthorized request
 
*(Status 401/4xx): unauthorized request
 
*(Status 403): insufficient scope
 
*(Status 403): insufficient scope
====Example:====  
+
=====Example:=====  
  
 
  [GET https://fhir-open-api-dstu2.smarthealthit.org/Observation?patient=1134281&category=laboratory]
 
  [GET https://fhir-open-api-dstu2.smarthealthit.org/Observation?patient=1134281&category=laboratory]
Line 313: Line 348:
  
  
===GET [base]/Observation?patient=[id]&code=[LOINC{,LOINC2,LOINC3,...}]===
+
====GET [base]/Observation?patient=[id]&code=[LOINC{,LOINC2,LOINC3,...}]====
<!-- do we want an _include here to get all the associated obs - not covered in sprint-->
 
  
 +
''Support:'' Mandatory support search by a laboratory LOINC code. SHOULD support search by multiple LOINC codes.
  
''Support:'' Mandatory support search Observation by a laboratory LOINC code. SHOULD support Observation 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 [http://hl7.org/fhir/DSTU2/search.html#reference (how to search by reference)] and [http://hl7.org/fhir/DSTU2/search.html#token (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.
 
 
''Implementation Notes:'' 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 [http://hl7.org/fhir/DSTU2/search.html#reference (how to search by reference)] and [http://hl7.org/fhir/DSTU2/search.html#token (how to search by token)].
 
  
 
''Response Class:''
 
''Response Class:''
Line 326: Line 359:
 
*(Status 401/4xx): unauthorized request
 
*(Status 401/4xx): unauthorized request
 
*(Status 403): insufficient scope
 
*(Status 403): insufficient scope
====Example:)====  
+
=====Example:)=====  
 
Search for all blood glucose lab results for a patient:
 
Search for all blood glucose lab results for a patient:
  
Line 337: Line 370:
 
----
 
----
 
<!--
 
<!--
===GET [base]/Observation?patient=[id]&code=[lab1 LOINC, lab2 LOINC, etc]===
+
====GET [base]/Observation?patient=[id]&code=[lab1 LOINC, lab2 LOINC, etc]====
  
 
''Support:'' SHOULD support Observation search by multiple LOINCs.
 
''Support:'' SHOULD support Observation search by multiple LOINCs.
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*(Status 403): insufficient scope
 
*(Status 403): insufficient scope
  
====Example:====  
+
=====Example:=====  
 
Search for all blood glucose, urine glucose and urine ketones for a patient
 
Search for all blood glucose, urine glucose and urine ketones for a patient
  
Line 356: Line 389:
 
----
 
----
 
-->
 
-->
===GET [base]/Observation?patient=[id]&category=laboratory&date=[eq|lt|gt|geyyyy-mm-dd]{&date=[eq|lt|gt|geyyyy-mm-dd]}===
+
 
 +
====GET [base]/Observation?patient=[id]&category=laboratory&date=[date]{&date=[date]}====
  
 
''Support:'' Mandatory support search by category code and date or period
 
''Support:'' Mandatory support search by category code and date or period
Line 367: Line 401:
 
*(Status 401/4xx): unauthorized request
 
*(Status 401/4xx): unauthorized request
 
*(Status 403): insufficient scope
 
*(Status 403): insufficient scope
====Example:====  
+
=====Example:=====  
 
Find all the laboratory results after 2013-03-14
 
Find all the laboratory results after 2013-03-14
  

Latest revision as of 22:02, 22 December 2016

Back to Argonaut Implementation Guide

**********************PLEASE NOTE********************************
This guide is no longer being actively maintained and updated.
On January 1st 2017, This guide is being superseded by the online 
version of the Argonaut-DSTU2 Implemenation Guide.
hosted at:  http://fhir.org/guides/argonaut
The working CI build is avaible now at : 
http://build.fhir.org/ig/Healthedata1/Argo-DSTU2/  

Introduction

The Argonaut Laboratory Results guide provides the API documentation for searching and fetching Laboratory Results. This IG covers two resources - Observation and DiagnosticReport - because labaratory results are grouped and summarized using reports. This IG is based on the Data Access Framework (DAF) Laboratory Results. The search criteria provided in the Quick Start are intended to support the 2015 Edition ONC Certification criterion Data Category Request 170.315(g)(8).

Minimum Requirements

Clients

DiagnosticReport


Observation


Servers

DiagnosticReport


Observation


Mandatory Data Elements

The following data-elements in the DiagnosticReport and Observation resources are mandatory (i.e data MUST be present). These are presented below in simple human-readable explanation and a more thorough summary of the requirements. Refer to the tables for additional quidance and examples for the various laboratory tests. Both DiagnosticReport and Observation contain structures to group panels of Observations and both options are presented below. Both approaches are currently supported in this guide.

DiagnosticReport

When lab test or lab panel, such as CBC, is ordered, a DiagnosticReport represents the order fulfillment and references each of the resulting discrete Observations within that panel.

Each DiagnosticReport must have:

  • a patient
  • a code (preferably a LOINC code) which tells you what is being measured
    • note: additional codes that translate or map to these are allowed - e.g. system specific codes
  • at least one result (an Observation reference)
  • a status
  • a category code of 'LAB'
    • note: additional category codes that translate or map to these are allowed - e.g. more specific category codes such as "CH" (chemistry)
  • a time indicating when the measurement was taken
  • a time indicating when the measurement was reported
  • who issues the report
Example DiagnosticReports

The attached table lists LOINC panels for chemistry, hematology(cbc) and urinalysis results. This Argonaut profile does not make the presence or absence of any of these mandatory and is provided for guidance only.

LOINC # Long Common Name Comment Example
24323-8 Comprehensive metabolic 2000 panel - Serum or Plasma Panel of Common Blood Chemistries Example
58410-2 Complete blood count (hemogram) panel - Blood by Automated count Panel of Common Hematology Tests Example
24356-8 Urinalysis complete panel - Urine Panel of Common Urine Tests Example
Complete Summary of the Mandatory Requirements
  1. One patient in DiagnosticReport.subject
  2. One status in DiagnosticReport.status
  3. One category in DiagnosticReport.category which must have:
  4. One code in DiagnosticReport.code which must have if available:
    • a fixed DiagnosticReport.code.coding.system="http://loinc.org"
    • a LOINC code in DiagnosticReport.code.coding.code
    • Other additional codes are allowed - e.g. system specific codes. All codes SHALL have an system value
  5. One or more DiagnosticReport.result
    • DiagnosticReport.result.reference reference the Observations that are part of this diagnostic report.
  6. A date and time in DiagnosticReport.effectiveDateTime or DiagnosticReport.effectivePeriod
  7. A date and time in DiagnosticReport.issued
  8. A practitioner or organization DiagnosticReport.performer

Observation

Each Observation 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.

Each Observation must have:

  • a patient
  • a LOINC code, if available, which tells you what is being measured
    • note: additional codes that translate or map to these are allowed - e.g. system specific codes
  • a result value and if the result value is a numeric quantity, a standard UCUM unit
    • note: if there is no result then you have to supply a reason unless Observation is being used to group a panel then there is no value. Instead, it just includes composite values or related links
  • a status
  • a category code of 'laboratory'
    • note: additional category codes that translate or map to these are allowed - e.g. more specific category codes such as "chemistry', SNOMED CT concepts, system specific codes

Each Observation should have:

  • a time indicating when the measurement was taken
  • a reference range if available
Example Laboratory tests and results

The attached table is derived from the LOINC Top 2000+ Lab Observations and lists LOINC panel and observation codes for quantitative and qualitative tests for chemistry, hematology(cbc) and urinalysis results. It also lists the corresponding UCUM units of measure codes for quantitative tests. The qualitative results include both 'ordinal' and 'nominal' scale. This Argonaut profile does not make the presence or absence of any of these mandatory and is provided for guidance only.

LOINC # Long Common Name UCUM Comment Example
2160-0 Creatinine [Mass/volume] in Serum or Plasma mg/dL Quantitative Test Example
718-7 Hemoglobin [Mass/volume] in Blood g/dL Quantitative Test, This is the the code included in the CBC auto. It is NOT obtained via the automated counting but uses a chemistry method just like most other hemoglobins Example
2823-3 Potassium [Moles/volume] in Serum or Plasma mmol/L Quantitative Test Example
2951-2 Sodium [Moles/volume] in Serum or Plasma mmol/L Quantitative Test Example
3094-0 Urea nitrogen [Mass/volume] in Serum or Plasma mg/dL Quantitative Test, Usually called BUN Example
2028-9 Carbon dioxide, total [Moles/volume] in Serum or Plasma mmol/L Quantitative Test Example
2075-0 Chloride [Moles/volume] in Serum or Plasma mmol/L Quantitative Test Example
789-8 Erythrocytes [#/volume] in Blood by Automated count 10*6/uL Quantitative Test Example
786-4 Erythrocyte mean corpuscular hemoglobin concentration [Mass/volume] by Automated count g/dL Quantitative Test Example
785-6 Erythrocyte mean corpuscular hemoglobin [Entitic mass] by Automated count pg Quantitative Test Example
17861-6 Calcium [Mass/volume] in Serum or Plasma mg/dL Quantitative Test Example
2339-0 Glucose [Mass/volume] in Blood mg/dL Quantitative Test Example
1975-2 Bilirubin.total [Mass/volume] in Serum or Plasma mg/dL Quantitative Test, Total bilirubin = direct + indirect. Example
770-8 Neutrophils/100 leukocytes in Blood by Automated count % Quantitative Test, This cell type is counted by all modern automated differential machines; so most results will be reported under the LOINC code with method of automated count. Example
5778-6 Color of Urine Qualitative Test (Nominal) Example
32167-9 Clarity of Urine Qualitative Test (Nominal) Example
25428-4 Glucose [Presence] in Urine by Test strip Qualitative Test (Ordinal) Example
5770-3 Bilirubin.total [Presence] in Urine by Test strip Qualitative Test (Ordinal) Example
2514-8 Ketones [Presence] in Urine by Test strip Qualitative Test (Ordinal) Example
5811-5 Specific gravity of Urine by Test strip Quantitative Test Example
5803-2 pH of Urine by Test strip [pH] Quantitative Test Example
20454-5 Protein [Presence] in Urine by Test strip Qualitative Test (Ordinal) Example
20405-7 Urobilinogen [Mass/volume] in Urine by Test strip mg/dL Quantitative Test Example
5802-4 Nitrite [Presence] in Urine by Test strip Qualitative Test (Ordinal) Example
5794-3 Hemoglobin [Presence] in Urine by Test strip Qualitative Test (Ordinal) Example
5799-2 Leukocyte esterase [Presence] in Urine by Test strip Qualitative Test (Ordinal) Example
11279-7 Urine sediment comments by Light microscopy Narrative Narrative Test Example
25145-4 Bacteria [Presence] in Urine sediment by Light microscopy Qualitative Test (Ordinal) Example
5787-7 Epithelial cells [#/area] in Urine sediment by Microscopy high power field /[HPF] Semi-Quantitative Test. Although reported as a range this is probably an ordinal list ( e.g. 1-10, 10-40, 40+) Example
5821-4 Leukocytes [#/area] in Urine sediment by Microscopy high power field /[HPF] Semi-Quantitative Test Although reported as a range this is probably an ordinal list ( e.g. 1-10, 10-40, 40+) Example
13945-1 Erythrocytes [#/area] in Urine sediment by Microscopy high power field /[HPF] Semi-Quantitative Test Although reported as a range this is probably an ordinal list ( e.g. 1-10, 10-40, 40+) Example
... ... ... ... ...
Complete Summary of the Mandatory Requirements
  1. One status in Observation.status
  2. One category in Observation.category which must have:
  3. One code in Observation.code which must have if available:
    • a fixed Observation.code.coding.system="http://loinc.org"
    • a LOINC code in Observation.code.coding.code
    • Other additional codes are allowed - e.g. system specific codes. All codes SHALL have an system value
  4. Either one Observation.value[x] or one code in Observation.DataAbsentReason (unless the Observation.code is a panel code)
    • Each Observation.valueQuantity must have:
      • One numeric value in Observation.valueQuantity.value
      • a fixed Observation.valueQuantity.system="http://unitsofmeasure.org"
      • a UCUM unit code in Observation.valueQuantity.code taken from the "Units" column in the table
    • Each Observation.valueCodeableConcept must have either:
      1. a code in Observation.valueCodeableConcept.coding.code and code system in Observation.valueCodeableConcept.coding.sytem
      2. OR text in Observation.valueCodeableConcept.text
    • Observation.DataAbsentReason is bound to Observation Value Absent Reason Value set (Code set)
  5. One patient in Observation.subject

Each Observation should have:

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

Quick Start

Below is a quick overview of the required search and read operations

DiagnosticReport

GET [base]/DiagnosticReport?patient=[id]&category=LAB

Support: Mandatory to support search by category code = LAB.

Implementation Notes: Search based on diagnostic report category code = 'LAB'. This fetches a bundle of all lab related DiagnosticReport resources 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
Example:
[GET http://spark.furore.com/fhir/DiagnosticReport?patient=f201&category=LAB]

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

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

Implementation Notes: Search based on DiagnosticReport code. This fetches a bundle of all DiagnosticReport resources for a specific diagnostic order code 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
Example:)

Search for all metabolic panel reports for a patient:

[GET https://fhir-open-api-dstu2.smarthealthit.org/DiagnosticReport?patient=1032702&code=24323-8]
Example:

Search for all cbc, metabolic panel, and urinalysis panels for a patient

[GET https://fhir-open-api-dstu2.smarthealthit.org/DiagnosticReport?patient=1032702&code=24323-8,58410-2,24356-8]



GET [base]/DiagnosticReport?patient=[id]&category=LAB&date=[date]{&date=[date]}

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

Implementation Notes: Search based on laboratory category code and date. This fetches a bundle of all DiagnosticReport resources with category 'LAB' for the specified patient for a specified time period (how to search by reference)and (how to search by token) and (how to search by date).

Response Class:

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

Find all the lab reports issued after 2010-01-14

[GET http://spark.furore.com/fhir/DiagnosticReport?patient=f201&category=LAB&date=ge2010-01-14]

Observation

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

Support: Mandatory to support search by 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
Example:
[GET https://fhir-open-api-dstu2.smarthealthit.org/Observation?patient=1134281&category=laboratory]


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

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
Example:)

Search for all blood glucose lab results for a patient:

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

Search for all blood glucose, urine glucose and urine ketones for a patient

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

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

Support: Mandatory support search by category code 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)and (how to search by token) and (how to search by date).

Response Class:

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

Open Issues

Issues for this IG have been identified and tracked HERE

Resources

Formalized testing with test scripts and objective results reporting is available through the participation of AEGIS and MITRE (Crucible). The testscript provided can be used to test servers: [todo]

References



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