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Laboratory Results

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Introduction

The Argonaut Laboratory Results guide provides the API documentation for searching and fetching Laboratory Results. It is based on the Data Access Framework (DAF) Laboratory Results and draws requirements from Argonaut Sprint 6. 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).

Argonaut Success Criteria

Clients

  • A client has connected to a server and fetched all of a patient's laboratory diagnostic reports using GET [base]/DiagnosticReport?patient=[id]&category=LAB.
  • A client has connected to a server and fetched all of a patient's laboratory results listed in the table below using GET [base]/Observation?patient=[id]&category=laboratory.

Servers

  • A server is capable of returning all of a patient's laboratory diagnostic reports using GET [base]/DiagnosticReport?patient=[id].
  • A server is capable of returning all of a patient's laboratory results using GET [base]/Observation?patient=[id].
  • 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.

Mandatory Data Elements

The following data-elements in the Observation resource 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 table for additional quidance and examples for the various laboratory tests.

Each DiagnosticReport must have:

(big issue is do we support both DR and Obs do we create separate IGs)

  • 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. method specific LOINC Codes, SNOMED CT concepts, system specific codes
  • at least one result (an Observation reference)
    • note: if there is no numeric result then you have to supply a reason
  • 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), SNOMED CT concepts, system specific codes
  • a time indicating when the measurement was taken
  • a time indicating when the measurement was reported
  • who issues the report


Each Observation must have:

  • a patient
  • a LOINC code which tells you what is being measured
    • note: additional codes that translate or map to these are allowed - e.g. method specific LOINC Codes, SNOMED CT concepts, system specific codes
  • a result value and if the result value is a numeric quantity, a standard UCUM unit
    • note: if there is no numeric result then you have to supply a reason
  • 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

Laboratory Results Table

The attached table is derived from the LOINC Top 2000+ Lab Observations and lists the LOINC observation code, and corresponding UCUM units of measure codes for qualitative tests. This Argonaut profile does not make the presence or absence of any of these mandatory and is provided for guidance only.

LOINC TOP 2000 (CLICK on the title for the complete listings)

Rank LOINC # Long Common Name UCUM Comment
1 2160-0 Creatinine [Mass/volume] in Serum or Plasma mg/dL
2 718-7 Hemoglobin [Mass/volume] in Blood g/dL 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
3 2823-3 Potassium [Moles/volume] in Serum or Plasma mmol/L
4 2345-7 Glucose [Mass/volume] in Serum or Plasma mg/dL
5 2951-2 Sodium [Moles/volume] in Serum or Plasma mmol/L
6 3094-0 Urea nitrogen [Mass/volume] in Serum or Plasma mg/dL Usually called BUN
7 2028-9 Carbon dioxide, total [Moles/volume] in Serum or Plasma mmol/L
8 2075-0 Chloride [Moles/volume] in Serum or Plasma mmol/L
9 789-8 Erythrocytes [#/volume] in Blood by Automated count 10*6/uL
10 786-4 Erythrocyte mean corpuscular hemoglobin concentration [Mass/volume] by Automated count g/dL
11 785-6 Erythrocyte mean corpuscular hemoglobin [Entitic mass] by Automated count pg
12 17861-6 Calcium [Mass/volume] in Serum or Plasma mg/dL
13 2339-0 Glucose [Mass/volume] in Blood mg/dL
14 4544-3 Hematocrit [Volume Fraction] of Blood by Automated count % Most Hematocrits delivered by referral and hospital laboratories will be produced by automated count- and will be delivered with this code
15 6690-2 Leukocytes[#/volume] in Blood by Automated count 10*3/uL
16 1742-6 Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma U/L
17 787-2 Erythrocyte mean corpuscular volume [Entitic volume] by Automated count fL 99% of these values will be done by automated method
18 777-3 Platelets [#/volume] in Blood by Automated count 10*3/uL 99% of all blood count will be automated so this is usually the right choice
19 1920-8 Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma U/L
20 1751-7 Albumin [Mass/volume] in Serum or Plasma g/dL
21 1975-2 Bilirubin.total [Mass/volume] in Serum or Plasma mg/dL Total bilirubin = direct + indirect.
22 2885-2 Protein [Mass/volume] in Serum or Plasma g/dL
23 6768-6 Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma U/L
24 788-0 Erythrocyte distribution width [Ratio] by Automated count % This it the version of the RDW reported with units of % Do not confuse with the term that reports the same test name with units of fL (LOINC 21000-5)
25 770-8 Neutrophils/100 leukocytes in Blood by Automated count % 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.
... ... ... ... ...

Complete Summary of the Mandatory Requirements

todo

Quick Start

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

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 DiagnosticReports 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]/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)

Support: Mandatory to support search by category code.

Implementation Notes: Search based on laboratory category codes. 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=1186747&category=vital-signs]

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 to support search DiagnosticReport by laboratory order LOINCs listed above.

Implementation Notes: Search based on Diagnostic report LOINC code. This fetches a bundle of all DiagnosticReport resources for a specific diagnostic order code listed in the table above 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 heart rate observations for a patient:
[GET https://fhir-open-api-dstu2.smarthealthit.org/Observation?patient=1186747&code=8867-4]

GET [base]/Observation?patient=[id]&code=[Laboratory order LOINC]

( do we want an _include here to get all the associated obs - not covered in sprint)

Support: Mandatory to support search Observation by laboratory LOINCs.

Implementation Notes: Search based on Observation LOINC code. This fetches a bundle of all DiagnosticReport resources for a specific diagnostic order code listed in the table above 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 heart rate observations for a patient:
[GET https://fhir-open-api-dstu2.smarthealthit.org/Observation?patient=1186747&code=8867-4]

GET [base]/Observation?patient=[id]&code=[lab1 LOINC, lab2 LOINC, etc]

(repeat for DR)

Support: Mandatory to support Observation search by multiple LOINCs. .

Implementation Notes: Search based on multiple vital sign LOINC codes. This fetches a bundle of all Observation resources for specific laboratory results listed in the table above for the specified patient (how to search by reference) and (how to search by token) and (how to search for multiple values)

Response Class:

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

Example:

Search for all heart rate, respiratory rate and blood pressure observations for a patient
[GET https://fhir-open-api-dstu2.smarthealthit.org/Observation?patient=1186747&code=8867-4,9279-1,55284-4]

GET [base]/Observation?patient=[id]&category=laboratory=[eq|ne|lt|gt|geyyyy-mm-dd]

(repeat for DR)

Support: Should support search by category code and date

Implementation Notes: Search based on vital sign category code and date. This fetches a bundle of all Observation resources with category 'vital-signs' 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=vital-signs&date=ge2015-01-14]

Open Issues

The following issues have been identified:

  1. What is a consistent pattern for grouping Observations into panels?
    • Whether to use DiagnosticReport and Observation or just Observation or both
  2. Should scope success criteria should be just fetching all labs or also fetching specific labs based on codes as well?
  3. Are there other way to select only labs vs other observations rather than the suggested approach proposed above?
  4. (several of the same issues as in Vitals)
  5. Should a DiagnosticOrder reference be mandatory element for DiagnosticReport as it is in the DAF profile?


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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