…tions

This creates the covid19 labarotory result questionnaire profile

DSC19-84

This adds the covid19 lab result questionnaire response example

DSC19-84

DSC19-84

DSC19-86

DSC19-84

DSC19-84

DSC19-84

Some syntax is not supported in the old version

DSC1-85

This is the diagnostic profile for the covid19 lab result

DSC19-85

The cardinality for the fields should be 1..1 and this has been changed

DSC19-85

This will add the organization profiles for the ordering clinic and the test lab

DSC19-87 DSC19-88

Incorrect instances were being used in the examples resulting in the meta information not being added to the resources by sushi

DSC19-66

This is used in the example bundle for a lab result

DSC19-86

The encounter is a required field for the diagnostic report

DSC19-87

This is a bundle that will collect all the resources that represent the lab result

DSC19-89

These fields indicate the information needed to be given by the user.
The existing questionnaire and questionnaireResponse examples end these
fields with colons. For consistency these fields should as well.

DSC19-84

This field is a questionnaire section divider - no information comes
from this field directly

DSC19-84

Group related data within the questionnaire to make it a more readable

DSC19-84

The loinc code is specific to the clinical relevance of this field. The
field display name alone does not hold the relevenat medical context for
interpretation

DSC19-84

The previous code was incorrect - it was a copied from the clinic code

DSC19-84

In the case report there are two separate country loinc codes:
96546-7 - Country where diagnosed
77983-5 - Country of usual residence [Location]

There meanings are quite different - in three places the loinc codes
appear to have been switched

DSC19-84
https://loinc.org/77983-5/
https://loinc.org/96546-7/

The previous code was for a case identifier and used multiple times.
This new loinc code is specific to lab results.
Another option could be 19146-0 which relates to reference lab test
results - I did not use this one however as it does not specify that it
is an identifier field - which 30896-5 does.

https://loinc.org/30896-5/
https://loinc.org/19146-0/
https://jembiprojects.jira.com/browse/DSC19-84

The previous loinc code referenced the case report.
This is specific to the performing lab.

https://loinc.org/91562-9/
https://jembiprojects.jira.com/browse/DSC19-84

The previous loinc code referenced states and districts as defined by
the US postal service - since this is an international project
referencing counties and provinces - a different loinc code was needed.

https://loinc.org/96547-5/

The previous loinc code referenced results of a very specific nucleic
acid assay that could confirm presence of covid.
This is too specific. We do not know what test method was used for
presence confirmation - since the accuracy of different test methods is
so variable it is important that the loinc code not give an innaccurate
reading of accuracy.

https://loinc.org/19146-0/
https://jembiprojects.jira.com/browse/DSC19-84

FHIR shorthand has concise syntax for coding definitions which makes
fields easier to write and maintain

https://jembiprojects.jira.com/browse/DSC19-85

The purpose of the FHIR transaction Bundle containing the resources is
to give clinical context of an event. In the lab report event the result
of the report was listed. Previously this value was displayed as an
observation that was not referenced in any of the other resources in the
transation Bundle - this piece of information would be missing its
clinical relevance if the entire Bundle wasn't read (since it is a
transaction Bundle it wouldn\t be read in this manner - this would need
to be a document Bundle to function in that way)
Therefore, to ensure the lab report date context was kept, the date will
be added to the diagnortic report effectiveDateTime. This field aims to
document the "time of the procedure" in this case the reporting.

https://jembiprojects.jira.com/browse/DSC19-85

The previous fields defined as "must support" were object fields
containing nested fields. These nested fields are also required
therefore they need "must support" specified as well

https://jembiprojects.jira.com/browse/DSC19-85

from the questionnaire response we only receive one name field that is
optional. This field will then be mapped to the humanName text field as
this is a very vague field coming in

https://jembiprojects.jira.com/browse/DSC19-89

The field requires a county - counties match to Provinces in South
Africa. Cape Town is not a province

https://jembiprojects.jira.com/browse/DSC19-89

The two profiles were included in one file that did not link the two by
name therfore they need to be in separate files

https://jembiprojects.jira.com/browse/DSC19-87

The FHIR resource uses the american version of the word

https://jembiprojects.jira.com/browse/DSC19-87

To hava a consistent naming convention within the project

https://jembiprojects.jira.com/browse/DSC19-77

The type of specimen used for the covid testing is captured in the
questionnaire and is recorded in the Specimen reource type which in tur
is referenced by the diagnostic report

https://jembiprojects.jira.com/browse/DSC19-77

The lab report data flow happens separately from the initial case
report flow and therefore it is helpful to keep their profile definitions
separate.

https://jembiprojects.jira.com/browse/DSC19-77

The Patient profile definitions of the two flows are different therefore
two separate files will be easier to manage

https://jembiprojects.jira.com/browse/DSC19-77

Using a consistent naming convention makes it easier to navigate around
the project and encourages collaboration

https://jembiprojects.jira.com/browse/DSC19-77

We assume that the Organization already exist. We will do a lookup to
confirm but it is out of our scope to manage the Facility Registry

We will however keep a profile for the Organization resource as we have
requirements of what data the resources must contain

https://jembiprojects.jira.com/browse/DSC19-88

The code used there did not make sense. It described the possible
presence of covid via a nucleotide test.
This conclusion code is more general on whether the patient has covid or
not independent of test method

https://jembiprojects.jira.com/browse/DSC19-88

The Patient should already exist in the FHIR store the details received
in the Lab Report will be used to update that resource not to create
another

https://jembiprojects.jira.com/browse/DSC19-89

We currently only have one possible response listed "Covid PCR test"
We don't have a source system controlling this yet - for now we can use
the value we receive here as the coding text.
We can use the defined diagnostic service with the general code of
virology for the actual coding - this should cover all covid test bases

https://jembiprojects.jira.com/browse/DSC19-85

During the refactor some sample resources had name changes that weren't
updated everywhere

https://jembiprojects.jira.com/browse/DSC19-85

This commit will remove the Practitioner and Location resources
from the WHO Cr Bundle Example. These resources will not be new to the
server so they should not be sent as part of the bundle.

Related Tickets:
 - DSC19-37
 - DSC19-105

Related Tickets:
 - https://jembiprojects.jira.com/browse/DSC19-105
 - https://jembiprojects.jira.com/browse/DSC19-37

…ctitioner

DSC19-37: Remove Location and Practitioner from Cr Bundle

This resource had no other place to be recorded in context

The Patient resource must be created in this bundle request as it would
not exist before this request

DSC19-35

Related Tickets:
 - https://jembiprojects.jira.com/browse/DSC19-59
 - https://jembiprojects.jira.com/browse/DSC19-78

This adds profiles for observation, encounter and condition resources that represent properties of the case report. Profiles have been created for the properties - report_test_reason, report_country, report_date, comcond, patcourse_admit, patcourse_presHCF, patcourse_icu, patcourse_vent, patcourse_ecmo, patcourse_iso, patcourse_dateiso, patinfo_occhcw, expo_travel_country1, expo_travel_city, expo_travel_date1, expo_visit_healthcare, expo_contact_case, expo_ID1, expo_case_date_first, expo_case_date_last and expo_cse_location

DSC19-127

This adds example observations, encounters and conditions which are constrained by the new profiles

DSC19-127

The questionnaire response has been updated with other fields that describe a covid19 case report

DCS19-71

This adds the other properties of the case report that have been added to the IG

DSC19-71

The valueset that was being used for the countries was incorrect and has been corrected. Some observation profiles have been changed to use the valuestring, valueDatetime or valueCodeablecConcept, and not the component field. This is for consistency as all other observation profiles do not use the component which would result in us having to add the observation code twice.

DSC19-71

Some of the fields had been incorrectly nested

DSC19-71

The profile has been changed to use the effectiveDateTime field and not the valueDateTime

DSC19-71

…c19-78-case-outcome

DSC19-78

DSC19-78

DSC19-78

The encounter was previously based on the base Encounter
profile. When applied, this commit will base the encounter
on the Case Report hospitalization encounter profile.

DSC19-78

DSC19-78

DSC19-78

DSC19-78

DSC19-130

DSC19-130

DSC19-130

This commit will add an example Observation resource for an unknown
Outcome Contacts Followed value

DSC19-130

When applied, this commit will remove the Outcome Asymp Date
observation profile and add it as an effective date for Outcome Asymp
Observation.

DSC19-130

This profile is no longer required according to the spec

DSC19-130

When applied, this commit will remove the Outcome Lab Date
Observation profile and add it as an effective date for Outcome Lab
result Observation profile.

DSC19-130

DSC19-130

This commit will remove Encounter examples from the
Observations fsh file

DSC19-130

DSC19-130

Co-authored-by: Matt <matthew.dickie@jembi.org>

Co-authored-by: Matt <matthew.dickie@jembi.org>

The one observation was the date on which the admission happened. This
refers to the effective DateTime of the observation - not an independant
Observation.

DSC19-78

This commit will remove the cardinality definition of note from
Outcome Contacts Followed observation profile. The base FHIR profile
already has a 1..1 cardinality defined

DSC19-130

DSC19-78: Case Outcome

The resource example was not resolving

DSC19-111

Some cardinalities were incorrect and the case isolation date and case isolation profile has been merged into one

DSC-163

One profile is now used for the country and city travelled to and the date of travel

DSC19-163

These are no longer used

DSC19-163

The details about contacting a case has been merged into one profile. This is the date of cantact the setting and the case id

DSC19-78

The condition profile is no longer used as it requiers a patient reference which cannot be provided in this case. The comorbidities are now in the comorbidities profile

DSC19-68

Dsc19 78 case report update

touch file to trigger build