Validation Results for GenomicsReporting

Generated Mon Dec 18 22:55:10 UTC 2023, FHIR version 4.0.1 for hl7.fhir.uv.genomics-reporting#3.0.0-ballot (canonical = http://hl7.org/fhir/uv/genomics-reporting (history)). See Full QA Report

Quality Checks

Publisher Version: IG Publisher Version: v1.5.8

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-ballot

path

http://hl7.org/fhir/uv/genomics-reporting/2024Jan

Pub-Mode

working release

status

ballot

sequence

STU 3

desc

Ballot version for STU3 update of Genomics Reporting IG

descmd

Ballot version for 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')

Supressed Messages: 51 Suppressed Issues

Dependency Checks:

Package	Version	FHIR	Canonical	Web Base	Comment
hl7.fhir.uv.genomics-reporting	3.0.0-ballot	R4	http://hl7.org/fhir/uv/genomics-reporting
hl7.terminology.r4	5.3.0 O	R4	http://terminology.hl7.org	http://terminology.hl7.org/5.3.0	Latest Release is 5.4.0
hl7.fhir.uv.extensions.r4	1.0.0 M	R4	http://hl7.org/fhir/extensions	http://hl7.org/fhir/extensions/1.0.0

Templates: hl7.fhir.template#0.8.0 -> hl7.base.template#0.8.0 -> fhir.base.template#0.6.0. Tools: current

Dependent IGs: no references

Global Profiles: (none declared)

HTA Analysis: All OK

R5 Dependencies: (none)

Draft Dependencies:

hl7.fhir.r4.core#4.0.1: wg (94 uses), GuideParameterCode (15 uses), allele-database (3 uses), glstring (3 uses), relatedArtifact (15 uses), EventStatus (3 uses), EventStatus (1 uses), profile (17 uses), fhir-type (231 uses), Practitioner (34 uses), RelatedPerson (24 uses), Organization (29 uses), bestpractice (18 uses), bestpractice-explanation (18 uses), maxValueSet (18 uses), bindingName (453 uses), CommonLanguages (18 uses), secondaryFinding (12 uses), BodyStructure Reference (12 uses), CarePlan (16 uses), DeviceRequest (12 uses), ImmunizationRecommendation (13 uses), MedicationRequest (13 uses), NutritionOrder (13 uses), ServiceRequest (16 uses), MedicationAdministration (15 uses), MedicationDispense (13 uses), MedicationStatement (15 uses), Procedure (20 uses), Immunization (13 uses), ImagingStudy (26 uses), display-hint (12 uses), ObservationCategoryCodes (37 uses), translatable (29 uses), LOINCCodes (94 uses), Group (18 uses), Device (40 uses), Location (17 uses), Encounter (18 uses), PractitionerRole (32 uses), CareTeam (16 uses), SNOMEDCTBodyStructures (14 uses), ObservationMethods (9 uses), Specimen (15 uses), DeviceMetric (12 uses), ObservationReferenceRangeMeaningCodes (12 uses), ObservationReferenceRangeAppliesToCodes (12 uses), QuestionnaireResponse (24 uses), MolecularSequence (28 uses), DocumentReference (17 uses), Media (13 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), supportingInfo (2 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#1.0.0-candidate: ResourceSortExt (294 uses)
hl7.terminology.r4#5.3.0: ObservationCategoryCodes (309 uses), RiskProbability (2 uses)

Modifier Extensions: (none)

Previous Version Comparison: Comparison with version 2.0.0

IPA Comparison: n/a

IPS Comparison: n/a

Summary: errors = 0, warn = 1, info = 2, broken links = 0

Filename	Errors	Warnings	Hints
Build Errors	0	0	0
C:\temp\hl7.fhir.uv.genomics-reporting#3.0.0-ballot\fsh-generated\resources\ValueSet-condition-inheritance-mode-vs	0	1	0

n/a Show Validation Information

C:\temp\hl7.fhir.uv.genomics-reporting#3.0.0-ballot\fsh-generated\resources\ValueSet-condition-inheritance-mode-vs.json Show Validation Information (1)

Path

Severity

Message

ValueSet.compose.include[0]

warning

Unknown System 'http://human-phenotype-ontology.org' specified, so Concepts and Filters can't be checked (Details: Resolved system http://human-phenotype-ontology.org (v1.0.0), but the definition doesn't include any codes, so the code has not been validated)

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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)

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

The definition for the Code System with URI 'http://purl.obolibrary.org/obo/mondo.owl' doesnt provide any codes so the code cannot be validated (3 uses)

Code has been checked and are correct

%The system http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl was found but did not contain enough information to properly validate the code "C43359" ("Group") (mode = fragment) (from Tx-Server)% (6 uses)

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

The definition for the Code System with URI 'http://www.ncbi.nlm.nih.gov/projects/SNP' doesnt provide any codes so the code cannot be validated (6 uses)

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

Code System URI 'http://www.ncbi.nlm.nih.gov/gtr' could not be found so the code cannot be validated (9 uses)

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

The definition for the Code System with URI 'http://www.ncbi.nlm.nih.gov/refseq' doesnt provide any codes so the code cannot be validated (151 uses)

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

The definition for the Code System with URI 'https://iscn.karger.com' doesnt provide any codes so the code cannot be validated (2 uses)

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

Code System URI 'http://www.ebi.ac.uk/ipd/imgt/hla' could not be found so the code cannot be validated (28 uses)

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

The definition for the Code System with URI 'http://www.ncbi.nlm.nih.gov/clinvar' doesnt provide any codes so the code cannot be validated (16 uses)

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

Code System URI 'http://clinicaltrials.gov' could not be found so the code cannot be validated (3 uses)

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

Code System URI 'http://glstring.org' could not be found so the code cannot be validated (5 uses)

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

Code System URI 'http://www.genenames.org' could not be found so the code cannot be validated (89 uses)
Code System URI 'http://www.genenames.org' could not be found so the code cannot be validated; Unable to check whether the code is in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs|3.0.0-BALLOT (89 uses)
Error from http://tx.fhir.org/r4: Unable to provide support for code system http://www.genenames.org (1 uses)
The definition for the Code System with URI 'http://www.genenames.org' doesnt provide any codes so the code cannot be validated (92 uses)
Unable to check whether the code is in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs|3.0.0-BALLOT (89 uses)

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

Code System URI 'http://human-phenotype-ontology.org' could not be found so the code cannot be validated (1 uses)
Error from http://tx.fhir.org/r4: Unable to provide support for code system http://human-phenotype-ontology.org (1 uses)
The definition for the Code System with URI 'http://human-phenotype-ontology.org' doesnt provide any codes so the code cannot be validated (1 uses)
Unknown System 'http://human-phenotype-ontology.org' specified, so Concepts and Filters can't be checked (Details: Resolved system http://human-phenotype-ontology.org (v1.0.0), but the definition is not complete) (0 uses)

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

Code System URI 'http://www.pharmvar.org' could not be found so the code cannot be validated (13 uses)

CodeSystems and ValueSets not supported yet -- sequenceontology - https://jira.hl7.org/browse/HTA-37 (should be in THO soon)

Code System URI 'http://sequenceontology.org' could not be found so the code cannot be validated (126 uses)
Code System URI 'http://sequenceontology.org' could not be found so the code cannot be validated; Code System URI 'http://sequenceontology.org' could not be found so the code cannot be validated; Unable to check whether the code is in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-consequence-vs|3.0.0-BALLOT (2 uses)
Code System URI 'http://sequenceontology.org' could not be found so the code cannot be validated; Unable to check whether the code is in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs|3.0.0-BALLOT (36 uses)
Code System URI 'http://sequenceontology.org' could not be found so the code cannot be validated; Unable to check whether the code is in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-effect-vs|3.0.0-BALLOT (4 uses)
Code System URI 'http://sequenceontology.org' could not be found so the code cannot be validated; Unable to check whether the code is in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-consequence-vs|3.0.0-BALLOT (13 uses)
Error from http://tx.fhir.org/r4: Unable to provide support for code system http://sequenceontology.org (3 uses)
Unable to check whether the code is in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs|3.0.0-BALLOT (36 uses)
Unable to check whether the code is in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-effect-vs|3.0.0-BALLOT (4 uses)
Unable to check whether the code is in the value set http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-consequence-vs|3.0.0-BALLOT (15 uses)

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

INFORMATION: Bundle/bundle-cgexample-withGrouping: Bundle.entry[0].resource/*DiagnosticReport/report-withGrouping*/.result[5]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: DiagnosticReport/PGxGenomicReportEMERGE-withGrouping: DiagnosticReport.result[3]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (1 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[6].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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Bundle/bundle-cgexample: Bundle.entry[6].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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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 supressing 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) (186 uses)

These slice messages that have been reviewed. Each of these refer to (via derivedFrom) a Variant, and it seems it is a valid Variant instance. So, not clear why it does not match a known slice:

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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (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|3.0.0-BALLOT (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)

This is a publisher induced issue. The extension in question is introduced by the publisher. See https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/New.20ConceptMap.20Warning.20--.20induced.20by.20IG.20Publisher

The modifier extension http://hl7.org/fhir/1.0/StructureDefinition/extension-ConceptMap.element.target.equivalence from FHIR version {3} is not allowed to be used at this point (allowed = e:ConceptMap.element.target; this element is [[BackboneElement, ConceptMap.group.element.target]; this is a warning since contexts may be renamed between FHIR versions) (15 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)

Errors sorted by type