openhie/covid19-casereporting

covid19-casereporting's Issues

IG Content - Consider ‘Background’ section Technical (will need to wait as well)

IG Content - Introduction

• Purpose
• In/out of scope
• Audience/ stakeholders
• Type of IG
• IP considerations
• Credits, acknowledgements, authors

CARES FHIR IG Issues

Details logged here: https://docs.google.com/spreadsheets/d/1U98hCXskavTp_G1TN5smbzi3Q4hOmN1Lj7IyQ1SjQEk/edit#gid=0

Add logical transaction bundles

Refer to https://github.com/jembi/vlsms-lab-integration-poc/tree/master/input/fsh

To facilitate the creation of a postman collection similar to: https://www.notion.so/gicsandbox/VLSMS-Lab-integration-POC-6efc06ad596643eea95a83b9033e1836#288ea1728d714122aa64b8ab46ec2133

This should also simplify the IG.

"Other (please specify) fields

Adapt best practise conistent pattern for capuring "Other (please specify) details across related elements.
Check all elements related to "Other"

Lab Order Management section

Align this section with the standard for Lab info exchange:

Eleme

statusReason in Covid19 Lab Order Cancellation profile is linked to the wrong value set, "Test Types" instead of "Cancellation Reasons". Value set URL says "Cancellation Reason" (https://openhie.github.io/cares-covid-ig/ValueSet-vs-cancellation-reason.html) but Value Set is Test Types. Additionally, the values listed for this value set aren't clear, as they say they are codes from ICD, but the values appear to be SNOMED_CT codes, though without any display names.

localtest-updates

Issues resolved during comparison of the Cares Bundle with the Cares IG:

• Covid19AssessmentEncounterExaaple:
  Add: reasonCode.coding.system = "http://openhie.org/fhir/covid19-casereporting/CodeSystem/cs-other"
  Remove: diagnosis.condition = Reference(Covid19PresentationExample) --> creates circular referencing

• Covid19AssessmentVaccinationExample:
  reportOrigin --> "system": "http://openhie.org/fhir/covid19-casereporting/CodeSystem/cs-source-of-info",

• Covid19SymptomExample:
  Add--> * investigation.code = $SCT#21522001
  Removed code (Binding for path ClinicalImpression.code has no source, so can't be checked)

• Patient:
  Add: contact[0].telecom.value = "[phone]" (aligned with the Cares Bundle)

• Covid19Diagnosis
  Add system--> ExampleverificationStatus = $SCT#410605003

• Covid19VaccinationExample
  Add: ReportOrigin, and EncounterReference

• service request:
  add system for: reasonCode = **$SCT#**Surveillance

• Covid19TestResultExample
  Add subject = Reference(Covid19PatientExample)

Estimated age doesn't make sense as, as time passes this changes

https://github.com/openhie/cares-covid-ig/blob/36521e0e0f13772cab03acb94bf964d8a777a458/input/fsh/profiles.fsh#L115

birthDate is allowed to have missing values so I think we can capture and estimated date by just providing a year for example - https://hl7.org/fhir/patient-definitions.html#Patient.birthDate

Update Index.html page

Introduction on the home page

Add an introduction on the home page - focused on Covid case reporting.“This IG is a content specification IG… (look at medmorph linked above table)”

Introduction

• Purpose
• In/out of scope
• Audience/ stakeholders
• Type of IG
• IP considerations
• Credits, acknowledgements, authors

IG Content - Title

Consider if title ‘Covid-19 Case Reporting and Lab Management’ needs updating

Bind VaccineSeries to correct field/extension

Currently located here: Covid19Vaccination.protocolApplied.series

The series must bind with VSDoseNumber (Primary/Secondary/Booster)

@rcrichton No suitable field identified for this on immunization, I think this should be an extension?

IG Content - FHIR Maturity

Reason test not performed

Value set name and values are "COVID-19 Specimen Type" instead of covid19-reason-test-not-performed

IG Content - Personas

IG Content - Deployment Guidance

Cardinality changes

details: https://docs.google.com/spreadsheets/d/1i7UX0MV-VIHgNFu4qdKhIrK6-qLiwvOH/edit#gid=1487123901

Changes required:

• Patient.identifier slice should only be 0..1 (just s single instance at most)
• Patient.managingOrganization should be changed to mandatory (1..1)
• Reasons for assessment must be 1..*
• Presentation must be 1..1

Fix field otherSpecimenType

I don't think the description for "otherSpecimenType" should be "Other-reason for Assessment". This "other" is to describe a type of sample other than "Nasopharyngeal Swab" or "
Anterior nasal swab".

Covid19PatientOutcome Extensions

Reconsider use of extensions. The reasons for a lot of the extension was to group elements logically as part of an resource.
Should we then create an additional section rather in the composition for grouping patient Outcome observations ?

Add terminologies to value-sets

Details:
Address the elements which affect the COVID indicators first:
Refer to Gap Analysis: https://docs.google.com/spreadsheets/d/1vRnQ80COcKrKbYD9bLsxxBUmHegA7z3u/edit#gid=1627898364

Resolve what should happen when "unspecified" is checked for the vaccine administered

What happens "unspecified" is checked for the vaccine administered? Also, "other"?

IG Content - Simple architecture (CRSubmitter, Transformer, Repository)

Middle names are usually listed as part of the name.given array. I don't think we need a new extension for this.

https://github.com/openhie/cares-covid-ig/blob/36521e0e0f13772cab03acb94bf964d8a777a458/input/fsh/profiles.fsh#L85-L89

Lab Management Results - issues

Refer also to https://docs.google.com/spreadsheets/d/1i7UX0MV-VIHgNFu4qdKhIrK6-qLiwvOH/edit#gid=1487123901

identify and implement conditional validations

-If value is Other, then notes/text must be provided

Diagnostic Report Specimen

COVID Lab Management - Lab Results

I see Extension: Covid19 Specimen Type profile, but can't track what profile it's referenced from. Also, the value set for specimen types doesn't match the options available in OHRI, which are only: Anterior nasal swab, Nasopharyngeal swab, Other (Specify)

IG Content - Transactions

Codeableconcept system element

All CodeableConcept instances must have a system url value
Check all elements and align according to this standard

Value set 3.56.1 is misnamed as "Test Types"

COVID Lab Management - Order cancellation:
(task.statusreason)
Value set 3.56.1 is misnamed as "Test Types" (there's another value set with the same name). it should be something like "Test Cancellation Reasons"

ServiceRequest Status

Section: COVID Lab Management (lab order)

Should this only allow "status" = active in order to indicate that it must be active when OHRI value is "yes"?

IG Content - How to read this IG - Technical with BA input to ensure understandable (but need the rest of the content done)

IG Content - Security and privacy

IG Content - References to downstream (and upstream?) IGs - Technical (but not ready to do this yet)

IG Content - Expected Actions

Immunization element alignment: Assessment vaccination info vs Vaccination event info

Check that the fields are aligned, update profiles where required

IG Content - Content Profiles

These should be observations

https://github.com/openhie/cares-covid-ig/blob/36521e0e0f13772cab03acb94bf964d8a777a458/input/fsh/profiles.fsh#L149-L187

https://github.com/openhie/cares-covid-ig/blob/36521e0e0f13772cab03acb94bf964d8a777a458/input/fsh/profiles.fsh#L211-L215

To me these ones sounds like observations that are linked to the encounter. We should use extensions as a last resort as they create very custom ways in which the resources should be processed.

Convert remaining Extensions to Observations where possible

Details: https://docs.google.com/spreadsheets/d/1i7UX0MV-VIHgNFu4qdKhIrK6-qLiwvOH/edit#gid=1487123901

The following fields to be converted to observations:

• Client Middle Name
• Comorbidity present
• Conditions or Comorbidity
• Test Requested
• Other Reasons for testing

IG Content - Reference Implementations

IG Content - Usage Workflows

IG Content - Functional requirements

Obs effectivedatetime is probably better for this

https://github.com/openhie/cares-covid-ig/blob/36521e0e0f13772cab03acb94bf964d8a777a458/input/fsh/profiles.fsh#L224

IG Content - Credits, acknowledgements, authors (at the very end)

IG Content - Use Cases / Application

IG Content - Actors

Add: "Treatment dispensed or prescribed"

Add: "Treatment dispensed or prescribed"
Check also that all fields are included even if "Needed for Covid Case Reporting" is not Yes. (where where possible, because some fields like Estimated age is only for the EMR

https://docs.google.com/spreadsheets/d/1cIMIsqOZYt7NSSblTIQoUvRVx1PSzH-QyOdrJBZel2Q/edit#gid=1730088127

IG Content - External references

Recommend removal of "other" from value sets

I believe best practice for other, specify concept is not to include "Other" as an acceptable value in the value set. The text provided in the "specify" free text field should be mapped to the Code[CodeableConcept].text (which I believe has already been updated where needed), but it is not necessary to also represent "Other" in the Code[CodeableConcept].coding. See Comorbidity Value Set https://openhie.github.io/cares-covid-ig/ValueSet-vs-conditions-comorbidity.html#root as example; but this should apply to all value sets where "Other" has been added.

composition and bundle example updates

Bundle fullUrl should start by / e.g: "Patient/Covid19PatientExample"