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Genomic study resource #1

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HL7 FHIR Pull Request

Note: No pull requests will be accepted against ./source unless logged in the HL7 Jira issue tracker.

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yunwwang and others added 30 commits April 3, 2022 20:24
* Updated bundle-ImagingSelection-search-params.xml to match oid to id update
Remove Immunization.recorded
FHIR-29673 - Fixed display names for SNOMED codes in gender identity value set
Add ServiceRequest to Immunization.basedOn
Added Patient and RelatedPerson to Immunization.performer.actor
Updated wording of the search description to include "individuals"
Related to already applied FHIR-33021
Moved offset from EvidenceVariable.characteristic.offset to EvidenceVariable.characteristic.definitionByTypeAndValue.offset
J# 37660 EvidenceVariable element change
MolecularSequence.relative.ordinalPosition and *.sequenceRange
MolecularSequence.relative.reference and others
Increase cardinality of EvidenceVariable.characteristic.method from 0..1 to 0..*
MolecularSequence.relative.reference and others
riksmithies and others added 28 commits July 18, 2022 12:51
Further modeling suggests method 0..* CodeableConcept is functionally a modifier of the type element in definitionByTypeAndValue.type[x] and allows simplification to definitionByTypeAndValue.type 1..1 CodeableConcept because method can express necessary modifiers of how the type is determined.  This leads to an overall simplification of the Resource (typeReference and typeId are no longer needed) and the proposed disposition is now to:

Delete EvidenceVariable.characteristic.method
Add EvidenceVariable.characteristic.definitionByTypeAndValue.method 0..* CodeableConcept
Change EvidenceVariiable.characteristic.definitionByTypeAndValue.type[x] to simply type 1..1 CodeableConcept

Further modeling was done with an example of "Coagulopathy as serious adverse event" modeled in 5 variations.  The set of examples can be found at https://fevir.net/resources/Project/52195 and the preferred/optimal version is at https://fevir.net/resources/EvidenceVariable/52198

There are further changes that can simplify the EvidenceVariable Resource (in addition to the prior comment) including (1) moving the device element from EvidenceVariable.characteristic to EvidenceVariable.characteristic.definitionByTypeAndValue and (2) deleting the EvidenceVariable.characteristic.groupMeasure element as it can be handled as a method by include the value set in the CharacteristicMethod value set.

This leads to an even better overall simplification of the Resource and the proposed disposition is now to:

Delete EvidenceVariable.characteristic.method
Delete EvidenceVariable.characteristic.device
Delete EvidenceVariable.characteristic.groupMeasure
Change EvidenceVariable.characteristic.definitionByTypeAndValue.type[x] to simply type 1..1 CodeableConcept
Add EvidenceVariable.characteristic.definitionByTypeAndValue.method 0..* CodeableConcept with Preferred binding to DefinitionMethod value set
Add EvidenceVariable.characteristic.definitionByTypeAndValue.device 0..1 Reference(Device | DeviceMetric)
Create a DefinitionMethod value set by combining:
2 terms from the CharacteristicMethod value set http://build.fhir.org/valueset-characteristic-method.html
6 terms from the GroupMeasure value set http://build.fhir.org/valueset-group-measure.html
additional terms for commonly used source vocabularies for adverse event definitions (e.g. MedDRA (23.0))
J# 37715 preapplied as amended in the comments
Update text on ICD, NDF-RT and MED-RT pages
FHIR-35800 and 31601 Update text on ICD, NDF-RT and MED-RT pages
Corrected reference to DocRef that should have been DiagRpt
@sirkyp sirkyp deleted the branch khalifa-aly:genomicStudyResource July 21, 2022 22:36
@sirkyp sirkyp deleted the genomicStudyResource branch July 21, 2022 22:36
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