Validation Results for GenomicsReporting

Generated Tue Nov 19 22:06:11 UTC 2024, FHIR version 4.0.1 for hl7.fhir.uv.genomics-reporting#3.0.0 (canonical = http://hl7.org/fhir/uv/genomics-reporting (history)). See Full QA Report

Quality Checks

Publisher Version:

IG Publisher Version: v1.7.3

Publication Code:

genomics-reporting . PackageId = hl7.fhir.uv.genomics-reporting, Canonical = http://hl7.org/fhir/uv/genomics-reporting

Realm Check for UV:

Publication Request:

package-id

hl7.fhir.uv.genomics-reporting

version

3.0.0

path

http://hl7.org/fhir/uv/genomics-reporting/STU3

Pub-Mode

working release

status

trial-use

Release-Label

release

sequence

STU 3

desc

STU3 update of Genomics Reporting IG

descmd

STU3 update of Genomics Reporting IG

Proposed path for this publication should usually be the canonical with the version or sequence appended and then some kind of label (typically '-snapshot')
This release is not labelled as a milestone or technical correction, so should have a patch version (3.0.0)
This release is labelled as a working release in the sequence 'STU 3'. This is an unexpected workflow - check that the sequence really is correct.

Supressed Messages:

91 Suppressed Issues

Dependency Checks:

Package	Version	FHIR	Canonical	Web Base
hl7.fhir.uv.genomics-reporting	3.0.0	R4	http://hl7.org/fhir/uv/genomics-reporting
hl7.terminology.r4	6.1.0 M	R4	http://terminology.hl7.org	http://terminology.hl7.org/6.1.0
hl7.fhir.uv.extensions.r4	5.1.0 M	R4	http://hl7.org/fhir/extensions	http://hl7.org/fhir/extensions/5.1.0

Templates: hl7.fhir.template#0.10.1 -> hl7.base.template#0.10.1 -> fhir.base.template#0.8.1. Tools: 0.3.0

Dependent IGs:

1 guide

Global Profiles:

(none declared)

Terminology Server(s):

http://tx.fhir.org/r4 (details)

HTA Analysis:

All OK

R5 Dependencies:

(none)

Draft Dependencies:

hl7.fhir.r4.core#4.0.1: GuideParameterCode (15 uses), allele-database (3 uses), glstring (3 uses), EventStatus (3 uses), EventStatus (1 uses), Practitioner (33 uses), RelatedPerson (23 uses), Organization (28 uses), CommonLanguages (17 uses), CarePlan (15 uses), DeviceRequest (11 uses), ImmunizationRecommendation (12 uses), MedicationRequest (12 uses), NutritionOrder (12 uses), ServiceRequest (15 uses), MedicationAdministration (14 uses), MedicationDispense (12 uses), MedicationStatement (14 uses), Procedure (19 uses), Immunization (12 uses), ImagingStudy (24 uses), ObservationCategoryCodes (34 uses), LOINCCodes (98 uses), Group (17 uses), Device (38 uses), Location (16 uses), Encounter (17 uses), PractitionerRole (31 uses), CareTeam (15 uses), SNOMEDCTBodyStructures (13 uses), ObservationMethods (8 uses), Specimen (14 uses), DeviceMetric (11 uses), ObservationReferenceRangeMeaningCodes (11 uses), ObservationReferenceRangeAppliesToCodes (11 uses), QuestionnaireResponse (22 uses), MolecularSequence (26 uses), DocumentReference (16 uses), Media (12 uses), Task (8 uses), ActivityDefinition (4 uses), TaskStatus (2 uses), TaskIntent (2 uses), RequestPriority (2 uses), ProcedurePerformerRoleCodes (4 uses), HealthcareService (2 uses), Coverage (2 uses), ClaimResponse (2 uses), Provenance (2 uses), DocumentReferenceStatus (1 uses), CompositionStatus (1 uses), DocumentRelationshipType (1 uses), EpisodeOfCare (1 uses), DiagnosticReport (4 uses), DiagnosticReportStatus (1 uses), DiagnosticServiceSectionCodes (2 uses), LOINCDiagnosticReportCodes (1 uses), SNOMEDCTClinicalFindings (1 uses), RiskAssessment (2 uses), PlanDefinition (6 uses), ProcedureCategoryCodes(SNOMEDCT) (2 uses), ProcedureCodes(SNOMEDCT) (1 uses), ProcedureReasonCodes (2 uses), Condition (5 uses), ProcedureOutcomeCodes(SNOMEDCT) (2 uses), Composition (2 uses), Condition/Problem/DiagnosisCodes (2 uses), ProcedureFollowUpCodes(SNOMEDCT) (2 uses), ProcedureDeviceActionCodes (2 uses), Medication (4 uses), Substance (2 uses), FHIRDeviceTypes (2 uses), MedicationKnowledge (2 uses), ResearchStudy (2 uses)
hl7.fhir.uv.tools.r4#0.3.0: ResourceSortExt (296 uses)

Modifier Extensions:

(none)

Previous Version Comparison:

Comparison with version 3.0.0-ballot

IPA Comparison:

n/a

IPS Comparison:

n/a

Validation Flags:

On: autoLoad; Off: hintAboutNonMustSupport, anyExtensionsAllowed, checkAggregation, showReferenceMessages, noExperimentalContent, displayWarnings

Summary:

errors = 0, warn = 0, info = 0, broken links = 0

Filename

Errors

Warnings

Hints

Build Errors

n/a Show Validation Information

Suppressed Messages (Warnings, hints, broken links)

An example of DiagnosticImplication<Observation>.derivedFrom() that we slice to only allow our profiles. In this example, we did not define specific Variant instances and just refer to some variants by identifier (rather than a full resource), so ignoring these warnings

INFORMATION: Observation/PolyGenicDiagnosticImpExample: Observation.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication% (1 uses)
INFORMATION: Observation/PolyGenicDiagnosticImpExample: Observation.derivedFrom[1]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication% (1 uses)

CG has reviewed these CodeSystems and have decided to keep this in our IG

INFORMATION: CodeSystem/clinvar-evidence-level-custom-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/coded-annotation-types-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-change-type-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-data-format-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-method-type-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-status-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-type-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/molecular-biomarker-ontology-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/pharmgkb-evidence-level-custom-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/sequence-phase-relationship-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (0 uses)
INFORMATION: CodeSystem/tbd-codes-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/variant-confidence-status-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (0 uses)

Code Systems for diseases - MONDO - https://terminology.hl7.org/CodeSystem-MONDO.html

A definition for CodeSystem 'http://purl.obolibrary.org/obo/mondo.owl' could not be found, so the code cannot be validated (3 uses)

CodeSystem and ValueSets - dbSNP - https://terminology.hl7.org/CodeSystem-v3-dbSNP.html

A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/projects/SNP' could not be found, so the code cannot be validated (3 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/projects/SNP' version '137' could not be found, so the code cannot be validated. Valid versions: [] (1 uses)

CodeSystem and ValueSets - gtr - https://terminology.hl7.org/CodeSystem-GTR.html

A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/gtr' could not be found, so the code cannot be validated (15 uses)

CodeSystem and ValueSets - refseq - https://terminology.hl7.org/CodeSystem-v3-refSeq.html

A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/refseq' could not be found, so the code cannot be validated (152 uses)

CodeSystems and ValueSets - ISCN - https://terminology.hl7.org/CodeSystem-ISCN.html

A definition for CodeSystem 'https://iscn.karger.com' could not be found, so the code cannot be validated (2 uses)

CodeSystems and ValueSets - imgt HLA alleles - https://jira.hl7.org/browse/HTA-127.

A definition for CodeSystem 'http://www.ebi.ac.uk/ipd/imgt/hla' could not be found, so the code cannot be validated (8 uses)
A definition for CodeSystem 'http://www.ebi.ac.uk/ipd/imgt/hla' version '3.23' could not be found, so the code cannot be validated. Valid versions: [] (19 uses)
A definition for CodeSystem 'http://www.ebi.ac.uk/ipd/imgt/hla' version '3.31.0' could not be found, so the code cannot be validated. Valid versions: [] (1 uses)

CodeSystems and ValueSets not supported yet - clinvar - https://terminology.hl7.org/CodeSystem-ClinVarV.html

A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/clinvar' could not be found, so the code cannot be validated (15 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/clinvar' version '???' could not be found, so the code cannot be validated. Valid versions: [] (1 uses)

CodeSystems and ValueSets not supported yet -- clinicaltrials - https://jira.hl7.org/browse/HTA-126

A definition for CodeSystem 'http://clinicaltrials.gov' could not be found, so the code cannot be validated (3 uses)

CodeSystems and ValueSets not supported yet -- genenames -- https://terminology.hl7.org/CodeSystem-v3-hgnc.html

%Unable to provide support for code system http://www.genenames.org (1 uses)
%because the code system http://www.genenames.org was not found (188 uses)
A definition for CodeSystem 'http://www.genenames.org' could not be found, so the code cannot be validated% (99 uses)

CodeSystems and ValueSets not supported yet -- glstring - https://jira.hl7.org/browse/HTA-84

A definition for CodeSystem 'http://glstring.org' version '1.0' could not be found, so the code cannot be validated. Valid versions: [] (5 uses)

CodeSystems and ValueSets not supported yet -- human-phenotype-ontology - https://terminology.hl7.org/CodeSystem-HPO.html

%Unable to provide support for code system http://human-phenotype-ontology.org (1 uses)
%because the code system http://human-phenotype-ontology.org was not found (2 uses)
A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (1 uses)

CodeSystems and ValueSets not supported yet -- pharmvar - https://jira.hl7.org/browse/HTA-85

A definition for CodeSystem 'http://www.pharmvar.org' could not be found, so the code cannot be validated (11 uses)

CodeSystems and ValueSets not supported yet -- sequenceontology - https://terminology.hl7.org/CodeSystem-SO.html

%Unable to provide support for code system http://www.sequenceontology.org (4 uses)
%because the code system http://www.sequenceontology.org was not found (130 uses)
%because the code system http://www.sequenceontology.org, http://www.sequenceontology.org was not found (4 uses)
A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the code cannot be validated (73 uses)

Each of these codes have been validated (as of Jul 5 2024), so suppressing these warnings until HPO becomes a supported code system.

INFORMATION: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[0]: Unable to evaluate based on code system with status = not-present (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[0].target[0].code: The code 'SO:0002073' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[1].target[0].code: The code 'SO:0000159' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[2].target[0].code: The code 'SO:1000035' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[3].target[0].code: The code 'SO:0000667' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[4].target[0].code: The code 'SO:1000032' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[5].target[0].code: The code 'SO:1000036' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[6].target[0].code: The code 'SO:1000002' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].target: Target Code System http://www.sequenceontology.org doesn't have all content (content = not-present), so the target codes cannot be checked (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[0]: The code 'HP:0000006' is not valid in the system http://human-phenotype-ontology.org (Unable to evaluate based on code system with status = not-present) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[10]: The code 'HP:0003743' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[11]: The code 'HP:0003745' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[12]: The code 'HP:0010983' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[13]: The code 'HP:0012274' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[14]: The code 'HP:0012275' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[15]: The code 'HP:0025352' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[16]: The code 'HP:0032113' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[1]: The code 'HP:0000007' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[2]: The code 'HP:0001417' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[3]: The code 'HP:0001419' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[4]: The code 'HP:0001423' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[5]: The code 'HP:0001426' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[6]: The code 'HP:0001427' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[7]: The code 'HP:0001442' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[8]: The code 'HP:0001450' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)
WARNING: ValueSet/condition-inheritance-mode-vs: ValueSet.compose.include[0].concept[9]: The code 'HP:0001470' is not valid in the system http://human-phenotype-ontology.org (A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated) (1 uses)

GenomicReport<DiagnosticReport>.result referencing Observation instances. We have defined our report profile to slice .result with our Observation profiles. We allow slicing, so can ignore informational message

INFORMATION: Bundle/bundle-cgexample-withGrouping: Bundle.entry[0].resource/*DiagnosticReport/report-withGrouping*/.result[4]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: Bundle/bundle-oncologyexamples-r4-withGrouping: Bundle.entry[14].resource/*DiagnosticReport/Inline-Instance-for-oncologyexamples-r4-withGrouping-15*/.result[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: Bundle/bundle-oncologyexamples-r4-withGrouping: Bundle.entry[14].resource/*DiagnosticReport/Inline-Instance-for-oncologyexamples-r4-withGrouping-15*/.result[6]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: DiagnosticReport/PGxGenomicReportEMERGE-withGrouping: DiagnosticReport.result[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: DiagnosticReport/PGxGenomicReportEMERGE-withGrouping: DiagnosticReport.result[1]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: DiagnosticReport/PGxGenomicReportEMERGE-withGrouping: DiagnosticReport.result[2]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)

In several places we use experimental ValueSets with experimental bindings. The elements are marked as experimental. So we suppress the warning. See https://chat.fhir.org/#narrow/channel/179252-IG-creation/topic/consent-content-code.20warning

%which is experimental, but this structure is not labeled as experimental (9 uses)

Observation.component instances that do not match our slices, but is OK (and this is ok since we use open slicing)

INFORMATION: Bundle/bundle-cgexample: Bundle.entry[5].resource/*Observation/discrete-variant*/.component[18]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant% (1 uses)
INFORMATION: Bundle/bundle-cgexample: Bundle.entry[5].resource/*Observation/discrete-variant*/.component[19]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant% (1 uses)
INFORMATION: Observation/variant-with-molec-consequences: Observation.component[9]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant% (1 uses)

Our Observation profiles require a code from the Observation Category value set (LAB), but in some cases require additional codes from other value sets. Since this binding is "Preferred" the resources are still conformant, so we are Suppressing these messages.

None of the codings provided are in the value set 'Observation Category Codes' (http://hl7.org/fhir/ValueSet/observation-category|4.0.1), and a coding is recommended to come from this value set (codes = http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs#biomarker-category) (5 uses)
None of the codings provided are in the value set 'Observation Category Codes' (http://hl7.org/fhir/ValueSet/observation-category|4.0.1), and a coding is recommended to come from this value set (codes = http://terminology.hl7.org/CodeSystem/v2-0074#GE) (179 uses)

Suppress all references to example CodeSystems

A definition for CodeSystem 'http://example.org/% (11 uses)

These slice messages have been reviewed, and our StructureDefinition apporpriately defines the slices of extension, and examples look valid. Have asked for feedback here: https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/slicing.20in.20Observation.2Ecomponent.2Eextension.20information.20help.3F

INFORMATION: Bundle/bundle-oncologyexamples-r4-withGrouping: Bundle.entry[8].resource/*Observation/Inline-Instance-for-oncologyexamples-r4-withGrouping-9*/.component[3].extension[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication% (1 uses)
INFORMATION: Bundle/bundle-oncologyexamples-r4: Bundle.entry[12].resource/*Observation/Inline-Instance-for-oncologyexamples-r4-14*/.component[0].extension[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication% (1 uses)

These slice messages that have been reviewed. Each of these refer to (via derivedFrom) a Variant, and are a valid Variant instance. They are similar to ones mentioned on https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/slicing.20in.20Observation.2Ecomponent.2Eextension.20information.20help.3F

INFORMATION: Parameters/FindSubjectMolecConseqOutput: Parameters.parameter[0].resource/*Observation/MC1*/.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence% (1 uses)
INFORMATION: Parameters/FindSubjectMolecConseqOutput: Parameters.parameter[1].resource/*Observation/MC2*/.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence% (1 uses)
INFORMATION: Parameters/FindSubjectMolecConseqOutput: Parameters.parameter[2].resource/*Observation/MC3*/.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence% (1 uses)
INFORMATION: Parameters/FindSubjectMolecConseqOutput: Parameters.parameter[3].resource/*Observation/MC4*/.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence% (1 uses)

We define several experimental CodeSystems that we use, so OK to suppress this for all IG defined CSs

Reference to experimental CodeSystem http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/% (263 uses)
Reference to experimental CodeSystem http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs% (11 uses)

the IG Validator returns different warnings on this error: https://github.com/HL7/fhir-ig-publisher/issues/420 - in short, the validator returns the "among choices" profiles in a different order different times.

Found multiple matching profiles for Task/med-usage-impact-task-pgx-example among choices: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation, http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation (1 uses)
Found multiple matching profiles for Task/med-usage-impact-task-pgx-example among choices: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation, http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation (0 uses)
Found multiple matching profiles for Task/usage-1a among choices: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation, http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation (1 uses)
Found multiple matching profiles for Task/usage-1a among choices: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation, http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation (0 uses)

the mappings in this concept map have been human reviewed and is correct

INFORMATION: ConceptMap/dna-change-type-map: ConceptMap.group[0].source: Source Code System http://loinc.org is only supported on the terminology server, so the source codes are not validated for performance reasons (1 uses)

this code has been human reviewed and is correct

INFORMATION: ValueSet/molecular-biomarker-code-vs: ValueSet.compose.include[1].concept[0]: Unknown Code 'C120465' in the system 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl' version '' - note that the code system is labeled as a fragment, so the code may be valid in some other fragment (1 uses)

Errors sorted by type