Validation Results for PhenomicsExchange

Generated Tue Jun 18 22:13:17 UTC 2024, FHIR version 4.0.1 for hl7.fhir.uv.phenomics-exchange#0.1.0 (canonical = http://hl7.org/fhir/uv/phenomics-exchange (history)). See Full QA Report

Quality Checks
Publisher Version:IG Publisher Version: v1.6.11
Publication Code:phenomics-exchange . PackageId = hl7.fhir.uv.phenomics-exchange, Canonical = http://hl7.org/fhir/uv/phenomics-exchange
Realm Check for UV:
  • n/a
Publication Request:
  • Error fetching package-list from http://hl7.org/fhir/uv/phenomics-exchange: Not Found
  • No publication request found
Supressed Messages:No Suppressed Issues
Dependency Checks:
PackageVersionFHIRCanonicalWeb BaseComment
.. hl7.fhir.uv.phenomics-exchange0.1.0R4http://hl7.org/fhir/uv/phenomics-exchange
... hl7.terminology.r45.5.0 MR4http://terminology.hl7.orghttp://terminology.hl7.org/5.5.0
... hl7.fhir.uv.genomics-reporting2.0.0 MR4http://hl7.org/fhir/uv/genomics-reportinghttp://hl7.org/fhir/uv/genomics-reporting/STU2
... hl7.fhir.uv.extensions5.1.0-cibuild VR5http://hl7.org/fhir/extensionshttps://build.fhir.org/ig/HL7/fhir-extensions/FHIR Version Mismatch
.... hl7.terminology.r55.5.0 MR5http://terminology.hl7.orghttp://terminology.hl7.org/5.5.0FHIR Version Mismatch
Templates: hl7.fhir.template#current -> hl7.base.template#current -> fhir.base.template#current. Tools: 0.1.0
Dependent IGs:no references
Global Profiles:(none declared)
Terminology Server(s):http://tx.fhir.org/r4 (details)
HTA Analysis:All OK
R5 Dependencies:(none)
Draft Dependencies:
Modifier Extensions:
Previous Version Comparison: Unable to compare with previous version: Unable to find version history at http://hl7.org/fhir/uv/phenomics-exchange (Problem #1 with package-list.json at http://hl7.org/fhir/uv/phenomics-exchange: Not Found)
IPA Comparison: n/a
IPS Comparison: n/a
Summary: errors = 18, warn = 139, info = 124, broken links = 0
FilenameErrorsWarningsHints
Build Errors100
/scratch/repo/fsh-generated/resources/Bundle-PhenopacketsBundleExample0132118
/scratch/repo/fsh-generated/resources/Condition-intellectualDisabilityDisease011
/scratch/repo/fsh-generated/resources/DiagnosticReport-PhenopacketsGenomicInterpretationExample01211
/scratch/repo/fsh-generated/resources/DiagnosticReport-PhenopacketsGenomicInterpretationExample02211
/scratch/repo/fsh-generated/resources/MedicationAdministration-losartan011
/scratch/repo/fsh-generated/resources/Observation-CHF-with-severity042
/scratch/repo/fsh-generated/resources/Observation-MVP-with-onset011
/scratch/repo/fsh-generated/resources/Observation-PhenopacketsVariantExample01030
/scratch/repo/fsh-generated/resources/Observation-Polydactyly-with-modifier042
/scratch/repo/fsh-generated/resources/Observation-amyotrophy021
/scratch/repo/fsh-generated/resources/Observation-arachnodactyly021
/scratch/repo/fsh-generated/resources/Observation-globalDevelopmentalDelay021
/scratch/repo/fsh-generated/resources/Observation-hp.0003557031
/scratch/repo/fsh-generated/resources/Observation-hypotonia021
/scratch/repo/fsh-generated/resources/Observation-karyotypic-sex-invalid-1032
/scratch/repo/fsh-generated/resources/Observation-karyotypic-sex-valid-1032
/scratch/repo/fsh-generated/resources/Observation-longPhiltrum021
/scratch/repo/fsh-generated/resources/Observation-lowSetEars021
/scratch/repo/fsh-generated/resources/Observation-lvdysfunction-excluded021
/scratch/repo/fsh-generated/resources/Observation-microphthalmia021
/scratch/repo/fsh-generated/resources/Observation-muscleWeakness021
/scratch/repo/fsh-generated/resources/Observation-phenotypic-abnormality-invalid-10317
/scratch/repo/fsh-generated/resources/Observation-phenotypic-abnormality-valid-10311
/scratch/repo/fsh-generated/resources/Observation-reducedVisualAcuity021
/scratch/repo/fsh-generated/resources/Observation-retinalDetachment021
/scratch/repo/fsh-generated/resources/Observation-tga021
/scratch/repo/fsh-generated/resources/Observation-thrombocytopenia020
/scratch/repo/fsh-generated/resources/SearchParameter-service-request-supporting-info300
/scratch/repo/fsh-generated/resources/Specimen-biosample.specimen.id.2012
/scratch/repo/fsh-generated/resources/Specimen-bladderCarcinoma063
/scratch/repo/fsh-generated/resources/StructureDefinition-CodedOnset010
/scratch/repo/fsh-generated/resources/StructureDefinition-DiagnosticMarker010
/scratch/repo/fsh-generated/resources/StructureDefinition-KaryotypicSex010
/scratch/repo/fsh-generated/resources/StructureDefinition-MeasurementExt010
/scratch/repo/fsh-generated/resources/StructureDefinition-Onset010
/scratch/repo/fsh-generated/resources/StructureDefinition-PhenotypicFeatureExt010
/scratch/repo/fsh-generated/resources/StructureDefinition-Taxonomy010
/scratch/repo/fsh-generated/resources/StructureDefinition-acmg-pathogenicity-classification020
/scratch/repo/fsh-generated/resources/StructureDefinition-additional-variant-identifier020
/scratch/repo/fsh-generated/resources/StructureDefinition-filter-status020
/scratch/repo/fsh-generated/resources/StructureDefinition-interpretation-status010
/scratch/repo/fsh-generated/resources/StructureDefinition-molecule-context020
/scratch/repo/fsh-generated/resources/StructureDefinition-phenopackets-genomic-interpretation045
/scratch/repo/fsh-generated/resources/StructureDefinition-phred-quality-score020
/scratch/repo/fsh-generated/resources/StructureDefinition-related-concept-id020
/scratch/repo/fsh-generated/resources/StructureDefinition-therapeutic-actionability020
/scratch/repo/fsh-generated/resources/StructureDefinition-vcf-info020
/scratch/repo/fsh-generated/resources/StructureDefinition-vrs-object020
/scratch/repo/fsh-generated/resources/ValueSet-DiagnosticMarker100
/scratch/repo/fsh-generated/resources/ValueSet-HistologicalDiagnosis100
/scratch/repo/fsh-generated/resources/ValueSet-HpoSeverity061
/scratch/repo/fsh-generated/resources/ValueSet-Onset010
/scratch/repo/fsh-generated/resources/ValueSet-PhenotypicModifierValueSet021
/scratch/repo/fsh-generated/resources/ValueSet-Taxonomy010
/scratch/repo/fsh-generated/resources/ValueSet-TumorGrade100
/scratch/repo/fsh-generated/resources/ValueSet-TumorStage100
/scratch/repo/fsh-generated/resources/ValueSet-acmgPathogenicityClassification-vs020
/scratch/repo/fsh-generated/resources/ValueSet-geno-ontology-allelic-state-vs110
/scratch/repo/fsh-generated/resources/ValueSet-interpretationStatus-vs020
/scratch/repo/fsh-generated/resources/ValueSet-moleculeContext-vs020
/scratch/repo/fsh-generated/resources/ValueSet-phenotypic-abnormality100
/scratch/repo/fsh-generated/resources/ValueSet-phenotypic-component041
/scratch/repo/fsh-generated/resources/ValueSet-sequence-ontology-structural-variant-vs110
/scratch/repo/fsh-generated/resources/ValueSet-therapeuticActionability-vs020

n/a Show Validation Information

errorThere is no jira specification file defined with the expected name of FHIR-phenomics-exchange in the xml folder of the https://github.com/HL7/Jira-Spec-Artifacts project. This must exist before ballot or publication.

fsh-generated/resources/Bundle-PhenopacketsBundleExample01.json Show Validation Information (32)

PathSeverityMessage
Bundle​.entry[0]​.resource​/*Composition​/PhenopacketCompositionExample01*​/​.section[0]​.code (l26​/c14)informationReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
Bundle​.entry[0]​.resource​/*Composition​/PhenopacketCompositionExample01*​/​.section[1]​.code (l42​/c14)informationReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
Bundle​.entry[0]​.resource​/*Composition​/PhenopacketCompositionExample01*​/​.section[2]​.code (l58​/c14)informationReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
Bundle​.entry[0]​.resource​/*Composition​/PhenopacketCompositionExample01*​/​.section[3]​.code (l74​/c14)informationReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
Bundle​.entry[0]​.resource​/*Composition​/PhenopacketCompositionExample01*​/​.section[4]​.code (l90​/c14)informationReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
Bundle​.entry[0]​.resource​/*Composition​/PhenopacketCompositionExample01*​/​.section[3]​.entry[0] (l83​/c16)errorUnable to find a match for profile DiagnosticReport/PhenopacketsGenomicInterpretationExample02 among choices: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-genomic-interpretation
Bundle​.entry[0]​.resource​/*Composition​/PhenopacketCompositionExample01*​/​.section[3]​.entry[0] (l83​/c16)Slicing InformationDetails for DiagnosticReport/PhenopacketsGenomicInterpretationExample02 matching against profile http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-genomic-interpretation|0.1.0 Show Reasoning
Bundle​.entry[3]​.resource​/*Observation​/CHF-with-severity*​/ (l236​/c8)warningBest Practice Recommendation: In general, all observations should have a performer
Bundle​.entry[3]​.resource​/*Observation​/CHF-with-severity*​/​.code​.coding[0]​.system (l248​/c10)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Bundle​.entry[3]​.resource​/*Observation​/CHF-with-severity*​/​.component[0]​.code​.coding[0]​.system (l269​/c14)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Bundle​.entry[3]​.resource​/*Observation​/CHF-with-severity*​/​.component[0]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l278​/c14)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Bundle​.entry[3]​.resource​/*Observation​/CHF-with-severity*​/​.component[0]​.value​.ofType(CodeableConcept) (l278​/c14)warningUnable to check whether the code is in the value set 'http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/HpoSeverity|0.1.0' because the code system http://human-phenotype-ontology.org was not found
Bundle​.entry[3]​.resource​/*Observation​/CHF-with-severity*​/​.component[0]​.value​.ofType(CodeableConcept) (l278​/c14)warningA definition for CodeSystem 'http://human-phenotype-ontology.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/phenomics-exchange/ValueSet/HpoSeverity|0.1.0' because the code system http://human-phenotype-ontology.org was not found
Bundle​.entry[4]​.resource​/*Observation​/thrombocytopenia*​/ (l293​/c8)warningBest Practice Recommendation: In general, all observations should have a subject
Bundle​.entry[4]​.resource​/*Observation​/thrombocytopenia*​/ (l293​/c8)warningBest Practice Recommendation: In general, all observations should have a performer
Bundle​.entry[5]​.resource​/*Condition​/CHF-stageIII*​/​.code​.coding[0]​.system (l352​/c10)informationA definition for CodeSystem 'http://purl.obolibrary.org/obo/mondo.owl' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Bundle​.entry[5]​.resource​/*Condition​/CHF-stageIII*​/​.stage[0]​.summary​.coding[0] (l366​/c14)informationA definition for CodeSystem 'http://github.com/EBISPOT/efo' could not be found, so the code cannot be validated
Bundle​.entry[6]​.resource​/*Specimen​/bladderCarcinoma*​/​.extension[0]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l401​/c14)warningUnknown Code 'NCIT_C39853' 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 (from http://tx.fhir.org/r4)
Bundle​.entry[6]​.resource​/*Specimen​/bladderCarcinoma*​/​.extension[1]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l413​/c14)warningUnknown Code 'NCIT_C84509' 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 (from http://tx.fhir.org/r4)
Bundle​.entry[6]​.resource​/*Specimen​/bladderCarcinoma*​/​.extension[2]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l425​/c14)warningUnknown Code 'NCIT_C36136' 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 (from http://tx.fhir.org/r4)
Bundle​.entry[6]​.resource​/*Specimen​/bladderCarcinoma*​/​.extension[3]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l437​/c14)warningUnknown Code 'NCIT_C28054' 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 (from http://tx.fhir.org/r4)
Bundle​.entry[6]​.resource​/*Specimen​/bladderCarcinoma*​/​.extension[4]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l449​/c14)warningUnknown Code 'NCIT_C48699' 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 (from http://tx.fhir.org/r4)
Bundle​.entry[6]​.resource​/*Specimen​/bladderCarcinoma*​/​.extension[5]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l461​/c14)informationA definition for CodeSystem 'http://github.com/EBISPOT/efo' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Bundle​.entry[6]​.resource​/*Specimen​/bladderCarcinoma*​/​.type​.coding[0] (l484​/c10)informationA definition for CodeSystem 'http://github.com/EBISPOT/efo' could not be found, so the code cannot be validated
Bundle​.entry[6]​.resource​/*Specimen​/bladderCarcinoma*​/​.collection​.bodySite​.coding[0]​.system (l473​/c12)informationA definition for CodeSystem 'http://github.com/obophenotype/uberon' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Bundle​.entry[6]​.resource​/*Specimen​/bladderCarcinoma*​/​.processing[0]​.procedure​.coding[0]​.code (l503​/c14)warningUnknown Code 'NCIT_C5189' 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 (from http://tx.fhir.org/r4)
Bundle​.entry[7]​.resource​/*DiagnosticReport​/PhenopacketsGenomicInterpretationExample02*​/​.modifierExtension[0]​.value​.ofType(CodeableConcept)​.coding[0] (l530​/c14)errorA definition for CodeSystem 'http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus' could not be found, so the code cannot be validated
Bundle​.entry[7]​.resource​/*DiagnosticReport​/PhenopacketsGenomicInterpretationExample02*​/​.modifierExtension[0]​.value​.ofType(CodeableConcept) (l530​/c14)warningUnable to check whether the code is in the value set 'http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/interpretationStatus-vs|0.1.0' because the code system http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus was not found
Bundle​.entry[7]​.resource​/*DiagnosticReport​/PhenopacketsGenomicInterpretationExample02*​/​.modifierExtension[0]​.value​.ofType(CodeableConcept) (l530​/c14)errorNone of the codings provided are in the value set 'Interpretation Status Value Set' (http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/interpretationStatus-vs|0.1.0), and a coding from this value set is required) (codes = http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus#0)
Bundle​.entry[7]​.resource​/*DiagnosticReport​/PhenopacketsGenomicInterpretationExample02*​/​.code​.coding[0]​.system (l582​/c10)informationA definition for CodeSystem 'http://loinc' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Bundle​.entry[7]​.resource​/*DiagnosticReport​/PhenopacketsGenomicInterpretationExample02*​/​.code (l582​/c10)informationNone of the codings provided are in the value set 'LOINC Diagnostic Report Codes' (http://hl7.org/fhir/ValueSet/report-codes|4.0.1), and a coding is recommended to come from this value set (codes = http://loinc#123)
Bundle​.entry[8]​.resource​/*Observation​/PhenopacketsVariantExample01*​/ (l595​/c8)warningBest Practice Recommendation: In general, all observations should have a subject
Bundle​.entry[8]​.resource​/*Observation​/PhenopacketsVariantExample01*​/ (l595​/c8)warningBest Practice Recommendation: In general, all observations should have a performer
Bundle​.entry[8]​.resource​/*Observation​/PhenopacketsVariantExample01*​/ (l595​/c8)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()
Bundle (l1/c2)informationCan't find 'Patient/phenopacketPatientExample01' in the bundle (Bundle.entry[7].resource.subject)
Bundle (l1/c2)informationCan't find 'Specimen/phenopacketSpecimenExample01' in the bundle (Bundle.entry[7].resource.specimen[0])
Bundle.entry[3].resource (l236/c8)warningBest Practice Recommendation: In general, all observations should have a performer
Bundle.entry[4].resource (l293/c8)warningBest Practice Recommendation: In general, all observations should have a subject
Bundle.entry[4].resource (l293/c8)warningBest Practice Recommendation: In general, all observations should have a performer
Bundle.entry[8].resource (l595/c8)warningBest Practice Recommendation: In general, all observations should have a subject
Bundle.entry[8].resource (l595/c8)warningBest Practice Recommendation: In general, all observations should have a performer
Bundle.entry[8].resource (l595/c8)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Condition-intellectualDisabilityDisease.json Show Validation Information (1)

PathSeverityMessage
Condition.code.coding[0].system (l9/c4)informationA definition for CodeSystem 'http://purl.obolibrary.org/obo/mondo.owl' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Condition (l1/c2)warningConstraint failed: con-3: 'Condition.clinicalStatus SHALL be present if verificationStatus is not entered-in-error and category is problem-list-item' (defined in http://hl7.org/fhir/StructureDefinition/Condition) (Best Practice Recommendation)

fsh-generated/resources/DiagnosticReport-PhenopacketsGenomicInterpretationExample01.json Show Validation Information (1)

PathSeverityMessage
DiagnosticReport​.modifierExtension[0]​.value​.ofType(CodeableConcept)​.coding[0] (l13​/c8)errorA definition for CodeSystem 'http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus' could not be found, so the code cannot be validated
DiagnosticReport​.modifierExtension[0]​.value​.ofType(CodeableConcept) (l13​/c8)warningUnable to check whether the code is in the value set 'http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/interpretationStatus-vs|0.1.0' because the code system http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus was not found
DiagnosticReport​.modifierExtension[0]​.value​.ofType(CodeableConcept) (l13​/c8)errorNone of the codings provided are in the value set 'Interpretation Status Value Set' (http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/interpretationStatus-vs|0.1.0), and a coding from this value set is required) (codes = http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus#0)
DiagnosticReport​.code​.coding[0]​.system (l60​/c4)informationA definition for CodeSystem 'http://loinc' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)

fsh-generated/resources/DiagnosticReport-PhenopacketsGenomicInterpretationExample02.json Show Validation Information (1)

PathSeverityMessage
DiagnosticReport​.modifierExtension[0]​.value​.ofType(CodeableConcept)​.coding[0] (l13​/c8)errorA definition for CodeSystem 'http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus' could not be found, so the code cannot be validated
DiagnosticReport​.modifierExtension[0]​.value​.ofType(CodeableConcept) (l13​/c8)warningUnable to check whether the code is in the value set 'http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/interpretationStatus-vs|0.1.0' because the code system http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus was not found
DiagnosticReport​.modifierExtension[0]​.value​.ofType(CodeableConcept) (l13​/c8)errorNone of the codings provided are in the value set 'Interpretation Status Value Set' (http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/interpretationStatus-vs|0.1.0), and a coding from this value set is required) (codes = http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus#0)
DiagnosticReport​.code​.coding[0]​.system (l65​/c4)informationA definition for CodeSystem 'http://loinc' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)

fsh-generated/resources/MedicationAdministration-losartan.json Show Validation Information (1)

PathSeverityMessage
MedicationAdministration​.medication​.ofType(CodeableConcept)​.coding[0]​.system (l21​/c4)informationA definition for CodeSystem 'http://drugcentral.org/' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
MedicationAdministration​.dosage​.route​.coding[0]​.code (l41​/c6)warningUnknown Code 'NCIT_C38288' 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 (from http://tx.fhir.org/r4)

fsh-generated/resources/Observation-CHF-with-severity.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.code​.coding[0]​.system (l34​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l43​/c8)warningA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.value​.ofType(CodeableConcept) (l43​/c8)warningUnable to check whether the code is in the value set 'http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/HpoSeverity|0.1.0' because the code system http://human-phenotype-ontology.org was not found
Observation​.component[0]​.value​.ofType(CodeableConcept) (l43​/c8)warningA definition for CodeSystem 'http://human-phenotype-ontology.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/phenomics-exchange/ValueSet/HpoSeverity|0.1.0' because the code system http://human-phenotype-ontology.org was not found
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer

fsh-generated/resources/Observation-MVP-with-onset.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer

fsh-generated/resources/Observation-PhenopacketsVariantExample01.json Show Validation Information (9)

PathSeverityMessage
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a subject
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-Polydactyly-with-modifier.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.code​.coding[0]​.system (l34​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l43​/c8)warningA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.value​.ofType(CodeableConcept) (l43​/c8)warningUnable to check whether the code is in the value set 'http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/PhenotypicModifierValueSet|0.1.0' because the code system http://human-phenotype-ontology.org was not found
Observation​.component[0]​.value​.ofType(CodeableConcept) (l43​/c8)warningA definition for CodeSystem 'http://human-phenotype-ontology.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/phenomics-exchange/ValueSet/PhenotypicModifierValueSet|0.1.0' because the code system http://human-phenotype-ontology.org was not found
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer

fsh-generated/resources/Observation-amyotrophy.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-arachnodactyly.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-globalDevelopmentalDelay.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-hp.0003557.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l15​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a subject
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-hypotonia.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-karyotypic-sex-invalid-1.json Show Validation Information (1)

PathSeverityMessage
Observation.code.coding[0] (l5/c4)informationA definition for CodeSystem 'http://purl.obolibrary.org/obo/GSSO' could not be found, so the code cannot be validated
Observation​.value​.ofType(CodeableConcept)​.coding[0] (l13​/c4)informationA definition for CodeSystem 'http://github.com/phenopackets/core-ig/CodeSystem/observation-karyotypic-sex' could not be found, so the code cannot be validated
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a subject
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-karyotypic-sex-valid-1.json Show Validation Information (1)

PathSeverityMessage
Observation.code.coding[0] (l5/c4)informationA definition for CodeSystem 'http://purl.obolibrary.org/obo/GSSO' could not be found, so the code cannot be validated
Observation​.value​.ofType(CodeableConcept)​.coding[0] (l13​/c4)informationA definition for CodeSystem 'http://github.com/phenopackets/core-ig/CodeSystem/observation-karyotypic-sex' could not be found, so the code cannot be validated
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a subject
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-longPhiltrum.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-lowSetEars.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-lvdysfunction-excluded.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-microphthalmia.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-muscleWeakness.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-phenotypic-abnormality-invalid-1.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l5​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.code​.coding[0]​.system (l18​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l27​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[1]​.code​.coding[0]​.system (l38​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[1]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l47​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[2]​.code​.coding[0]​.system (l58​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[2]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l67​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[3]​.code​.coding[0]​.system (l78​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[3]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l87​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[4]​.code​.coding[0]​.system (l98​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[4]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l107​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[5]​.code​.coding[0]​.system (l118​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[5]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l127​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[6]​.code​.coding[0]​.system (l138​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[6]​.value​.ofType(Quantity) (l147​/c8)informationA definition for CodeSystem 'http://some/unit/system' could not be found, so the code cannot be validated
Observation​.component[7]​.code​.coding[0]​.system (l155​/c8)informationA definition for CodeSystem 'http://github.com/phenopackets/core-ig/CodeSystem/OTHER' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[7]​.value​.ofType(CodeableConcept)​.coding[0] (l164​/c8)informationA definition for CodeSystem 'http://github.com/phenopackets/core-ig/CodeSystem/OTHER' could not be found, so the code cannot be validated
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a subject
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-phenotypic-abnormality-valid-1.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l5​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.code​.coding[0]​.system (l18​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[0]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l27​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[1]​.code​.coding[0]​.system (l38​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[1]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l47​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[2]​.code​.coding[0]​.system (l58​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[2]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l67​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[3]​.code​.coding[0]​.system (l78​/c8)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[3]​.value​.ofType(Quantity) (l87​/c8)informationA definition for CodeSystem 'http://some/unit/system' could not be found, so the code cannot be validated
Observation​.component[4]​.code​.coding[0]​.system (l95​/c8)informationA definition for CodeSystem 'http://github.com/phenopackets/core-ig/CodeSystem/OTHER' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation​.component[4]​.value​.ofType(CodeableConcept)​.coding[0] (l104​/c8)informationA definition for CodeSystem 'http://github.com/phenopackets/core-ig/CodeSystem/OTHER' could not be found, so the code cannot be validated
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a subject
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-reducedVisualAcuity.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-retinalDetachment.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-tga.json Show Validation Information (1)

PathSeverityMessage
Observation​.code​.coding[0]​.system (l13​/c4)informationA definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have an effective[x] ()

fsh-generated/resources/Observation-thrombocytopenia.json Show Validation Information (1)

PathSeverityMessage
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a subject
Observation (l1/c2)warningBest Practice Recommendation: In general, all observations should have a performer

fsh-generated/resources/SearchParameter-service-request-supporting-info.json Show Validation Information (1)

PathSeverityMessage
SearchParameter​.where(url = 'http:​/​/github​.com​/phenopackets​/core-ig​/SearchParameter​/service-request-supporting-info')errorConformance resource /scratch/repo/fsh-generated/resources/SearchParameter-service-request-supporting-info.json - the canonical URL (http://hl7.org/fhir/uv/phenomics-exchange/SearchParameter/service-request-supporting-info) does not match the URL (http://github.com/phenopackets/core-ig/SearchParameter/service-request-supporting-info)
SearchParameter​.where(url = 'http:​/​/github​.com​/phenopackets​/core-ig​/SearchParameter​/service-request-supporting-info')errorConformance resource /scratch/repo/fsh-generated/resources/SearchParameter-service-request-supporting-info.json - the canonical URL (http://hl7.org/fhir/uv/phenomics-exchange/SearchParameter/service-request-supporting-info) does not match the URL (http://github.com/phenopackets/core-ig/SearchParameter/service-request-supporting-info)
fsh-generated​/resources​/SearchParameter-service-request-supporting-infoerrorURL Mismatch http://hl7.org/fhir/uv/phenomics-exchange/SearchParameter/service-request-supporting-info vs http://github.com/phenopackets/core-ig/SearchParameter/service-request-supporting-info

fsh-generated/resources/Specimen-biosample.specimen.id.2.json Show Validation Information (1)

PathSeverityMessage
Specimen​.extension[0]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l12​/c8)informationA definition for CodeSystem 'http://github.com/EBISPOT/efo' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Specimen​.collection​.bodySite​.coding[0] (l24​/c6)informationA definition for CodeSystem 'http://github.com/obophenotype/uberon' could not be found, so the code cannot be validated
Specimen​.processing[0]​.procedure​.coding[0]​.code (l45​/c8)warningUnknown Code 'NCIT_C51895' 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 (from http://tx.fhir.org/r4)

fsh-generated/resources/Specimen-bladderCarcinoma.json Show Validation Information (1)

PathSeverityMessage
Specimen​.extension[0]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l12​/c8)warningUnknown Code 'NCIT_C39853' 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 (from http://tx.fhir.org/r4)
Specimen​.extension[1]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l24​/c8)warningUnknown Code 'NCIT_C84509' 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 (from http://tx.fhir.org/r4)
Specimen​.extension[2]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l36​/c8)warningUnknown Code 'NCIT_C36136' 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 (from http://tx.fhir.org/r4)
Specimen​.extension[3]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l48​/c8)warningUnknown Code 'NCIT_C28054' 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 (from http://tx.fhir.org/r4)
Specimen​.extension[4]​.value​.ofType(CodeableConcept)​.coding[0]​.code (l60​/c8)warningUnknown Code 'NCIT_C48699' 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 (from http://tx.fhir.org/r4)
Specimen​.extension[5]​.value​.ofType(CodeableConcept)​.coding[0]​.system (l72​/c8)informationA definition for CodeSystem 'http://github.com/EBISPOT/efo' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Specimen.type.coding[0] (l95/c4)informationA definition for CodeSystem 'http://github.com/EBISPOT/efo' could not be found, so the code cannot be validated
Specimen​.collection​.bodySite​.coding[0]​.system (l84​/c6)informationA definition for CodeSystem 'http://github.com/obophenotype/uberon' could not be found, so the code cannot be validated (from http://tx.fhir.org/r4)
Specimen​.processing[0]​.procedure​.coding[0]​.code (l114​/c8)warningUnknown Code 'NCIT_C5189' 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 (from http://tx.fhir.org/r4)

fsh-generated/resources/StructureDefinition-CodedOnset.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/CodedOnset')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-DiagnosticMarker.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/DiagnosticMarker')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-KaryotypicSex.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/KaryotypicSex')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-MeasurementExt.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/MeasurementExt')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-Onset.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/Onset')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-PhenotypicFeatureExt.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/PhenotypicFeatureExt')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-Taxonomy.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/Taxonomy')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-acmg-pathogenicity-classification.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for acmg-pathogenicity-classification: extensions should not have a context of Element unless it's really intended that they can be used anywhere
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/acmg-pathogenicity-classification')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-additional-variant-identifier.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for additional-variant-identifier: extensions should not have a context of Element unless it's really intended that they can be used anywhere
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/additional-variant-identifier')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-filter-status.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for filter-status: extensions should not have a context of Element unless it's really intended that they can be used anywhere
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/filter-status')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-interpretation-status.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for interpretation-status: extensions should not have a context of Element unless it's really intended that they can be used anywhere

fsh-generated/resources/StructureDefinition-molecule-context.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for molecule-context: extensions should not have a context of Element unless it's really intended that they can be used anywhere
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/molecule-context')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-phenopackets-genomic-interpretation.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition​.snapshot​.element[26]​.constraint[1] (l1​/c59685)warningConstraint failed: eld-21: 'Constraints should have an expression or else validators will not be able to enforce them'
StructureDefinition​.snapshot​.element[32]​.constraint[1] (l1​/c68295)warningConstraint failed: eld-21: 'Constraints should have an expression or else validators will not be able to enforce them'
StructureDefinition​.differential​.element[3]​.constraint[0] (l1​/c92489)warningConstraint failed: eld-21: 'Constraints should have an expression or else validators will not be able to enforce them'
StructureDefinition​.differential​.element[4]​.constraint[0] (l1​/c93044)warningConstraint failed: eld-21: 'Constraints should have an expression or else validators will not be able to enforce them'
StructureDefinition​.differential​.element[3]​.constraint[0] (l1​/c92489)informationThe constraint 'phenopackets-subject-or-specimen-id' has no computable expression, so validators will not be able to check it
StructureDefinition​.differential​.element[4]​.constraint[0] (l1​/c93044)informationThe constraint 'phenopackets-subject-or-specimen-id' has no computable expression, so validators will not be able to check it
StructureDefinition​.snapshot​.element[23]​.pattern​.ofType(Coding)informationThe repeating element has a pattern. The pattern will apply to all the repeats (this has not been clear to all users)
StructureDefinition​.snapshot​.element[26]​.constraint[1] (l1​/c59685)informationThe constraint 'phenopackets-subject-or-specimen-id' has no computable expression, so validators will not be able to check it
StructureDefinition​.snapshot​.element[32]​.constraint[1] (l1​/c68295)informationThe constraint 'phenopackets-subject-or-specimen-id' has no computable expression, so validators will not be able to check it

fsh-generated/resources/StructureDefinition-phred-quality-score.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for phred-quality-score: extensions should not have a context of Element unless it's really intended that they can be used anywhere
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/phred-quality-score')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-related-concept-id.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for related-concept-id: extensions should not have a context of Element unless it's really intended that they can be used anywhere
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/related-concept-id')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-therapeutic-actionability.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for therapeutic-actionability: extensions should not have a context of Element unless it's really intended that they can be used anywhere
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/therapeutic-actionability')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-vcf-info.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for vcf-info: extensions should not have a context of Element unless it's really intended that they can be used anywhere
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/vcf-info')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/StructureDefinition-vrs-object.json Show Validation Information (1)

PathSeverityMessage
StructureDefinition.context[0]warningReview the extension type for vrs-object: extensions should not have a context of Element unless it's really intended that they can be used anywhere
StructureDefinition​.where(url = 'http:​/​/hl7​.org​/fhir​/uv​/phenomics-exchange​/StructureDefinition​/vrs-object')warningThe Implementation Guide contains no examples for this extension

fsh-generated/resources/ValueSet-DiagnosticMarker.json Show Validation Information (1)

PathSeverityMessage
ValueSet.where(id = 'DiagnosticMarker')errorError from http://tx.fhir.org/r4: Unable to locate code NCIT:C36292 (from , see log)

fsh-generated/resources/ValueSet-HistologicalDiagnosis.json Show Validation Information (1)

PathSeverityMessage
ValueSet​.where(id = 'HistologicalDiagnosis')errorError from http://tx.fhir.org/r4: Unable to locate code NCIT:C28101 (from , see log)

fsh-generated/resources/ValueSet-HpoSeverity.json Show Validation Information (1)

PathSeverityMessage
ValueSet​.compose​.include[0]​.concept[0] (l1​/c1697)warningThe code 'HP:0012828' is not valid in the system http://human-phenotype-ontology.org (Unable to evaluate based on code system with status = not-present)
ValueSet​.compose​.include[0]​.concept[0] (l1​/c1697)informationUnable to evaluate based on code system with status = not-present
ValueSet.compose.include[0].concept[1]warningThe code 'HP:0012826' 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)
ValueSet.compose.include[0].concept[2]warningThe code 'HP:0012825' 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)
ValueSet.compose.include[0].concept[3]warningThe code 'HP:0012827' 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)
ValueSet.compose.include[0].concept[4]warningThe code 'HP:0012829' 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)
ValueSet.where(id = 'HpoSeverity')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://human-phenotype-ontology.org (from , see log)

fsh-generated/resources/ValueSet-Onset.json Show Validation Information (1)

PathSeverityMessage
ValueSet.where(id = 'Onset')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://human-phenotype-ontology.org (from , see log)

fsh-generated/resources/ValueSet-PhenotypicModifierValueSet.json Show Validation Information (1)

PathSeverityMessage
ValueSet​.compose​.include[0]​.concept[0] (l1​/c1789)warningThe code 'HP:0012823' is not valid in the system http://human-phenotype-ontology.org (Unable to evaluate based on code system with status = not-present)
ValueSet​.compose​.include[0]​.concept[0] (l1​/c1789)informationUnable to evaluate based on code system with status = not-present
ValueSet​.where(id = 'PhenotypicModifierValueSet')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://human-phenotype-ontology.org (from , see log)

fsh-generated/resources/ValueSet-Taxonomy.json Show Validation Information (1)

PathSeverityMessage
ValueSet.where(id = 'Taxonomy')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://purl.obolibrary.org/obo/ncbitaxon.owl (from , see log)

fsh-generated/resources/ValueSet-TumorGrade.json Show Validation Information (1)

PathSeverityMessage
ValueSet.where(id = 'TumorGrade')errorError from http://tx.fhir.org/r4: Unable to locate code NCIT:C28076 (from , see log)

fsh-generated/resources/ValueSet-TumorStage.json Show Validation Information (1)

PathSeverityMessage
ValueSet.where(id = 'TumorStage')errorError from http://tx.fhir.org/r4: Unable to locate code NCIT:C48232 (from , see log)

fsh-generated/resources/ValueSet-acmgPathogenicityClassification-vs.json Show Validation Information (1)

PathSeverityMessage
ValueSet.compose.include[0]warningUnknown System 'http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#acmgpathogenicityclassification' specified, so Concepts and Filters can't be checked (Details: A definition for CodeSystem 'http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#acmgpathogenicityclassification' could not be found, so the code cannot be validated)
ValueSet​.where(id = 'acmgPathogenicityClassification-vs')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#acmgpathogenicityclassification (from , see log)

fsh-generated/resources/ValueSet-geno-ontology-allelic-state-vs.json Show Validation Information (1)

PathSeverityMessage
ValueSet.compose.include[0].filter[0]errorThe value for a filter based on property 'concept' must be a valid code from the system 'http://www.ebi.ac.uk/ols/ontologies/geno', and 'GENO_0000875' is not (A definition for CodeSystem 'http://www.ebi.ac.uk/ols/ontologies/geno' could not be found, so the code cannot be validated)
ValueSet​.where(id = 'geno-ontology-allelic-state-vs')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://www.ebi.ac.uk/ols/ontologies/geno (from , see log)

fsh-generated/resources/ValueSet-interpretationStatus-vs.json Show Validation Information (1)

PathSeverityMessage
ValueSet.compose.include[0]warningUnknown System 'http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus' specified, so Concepts and Filters can't be checked (Details: A definition for CodeSystem 'http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus' could not be found, so the code cannot be validated)
ValueSet​.where(id = 'interpretationStatus-vs')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus (from , see log)

fsh-generated/resources/ValueSet-moleculeContext-vs.json Show Validation Information (1)

PathSeverityMessage
ValueSet.compose.include[0]warningUnknown System 'http://phenopacket-schema.readthedocs.io/en/v2/variant.html#rstmoleculecontext' specified, so Concepts and Filters can't be checked (Details: A definition for CodeSystem 'http://phenopacket-schema.readthedocs.io/en/v2/variant.html#rstmoleculecontext' could not be found, so the code cannot be validated)
ValueSet​.where(id = 'moleculeContext-vs')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://phenopacket-schema.readthedocs.io/en/v2/variant.html#rstmoleculecontext (from , see log)

fsh-generated/resources/ValueSet-phenotypic-abnormality.json Show Validation Information (1)

PathSeverityMessage
ValueSet​.where(id = 'phenotypic-abnormality')errorError from http://tx.fhir.org/r4: Unable to locate code HP:0000118 (from , see log)

fsh-generated/resources/ValueSet-phenotypic-component.json Show Validation Information (1)

PathSeverityMessage
ValueSet​.compose​.include[0]​.concept[0] (l1​/c1575)warningThe code 'HP:0012823' is not valid in the system http://human-phenotype-ontology.org (Unable to evaluate based on code system with status = not-present)
ValueSet​.compose​.include[0]​.concept[0] (l1​/c1575)informationUnable to evaluate based on code system with status = not-present
ValueSet.compose.include[0].concept[1]warningThe code 'HP:0012824' 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)
ValueSet.compose.include[0].concept[2]warningThe code 'HP:0003674' 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)
ValueSet​.where(id = 'phenotypic-component')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://human-phenotype-ontology.org (from , see log)

fsh-generated/resources/ValueSet-sequence-ontology-structural-variant-vs.json Show Validation Information (1)

PathSeverityMessage
ValueSet.compose.include[0].filter[0]errorThe value for a filter based on property 'concept' must be a valid code from the system 'http://www.sequenceontology.org/', and 'SO:0001537' is not (A definition for CodeSystem 'http://www.sequenceontology.org/' could not be found, so the code cannot be validated)
ValueSet​.where(id = 'sequence-ontology-structural-variant-vs')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://www.sequenceontology.org/ (from , see log)

fsh-generated/resources/ValueSet-therapeuticActionability-vs.json Show Validation Information (1)

PathSeverityMessage
ValueSet.compose.include[0]warningUnknown System 'http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#therapeuticactionability' specified, so Concepts and Filters can't be checked (Details: A definition for CodeSystem 'http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#therapeuticactionability' could not be found, so the code cannot be validated)
ValueSet​.where(id = 'therapeuticActionability-vs')warningError from http://tx.fhir.org/r4: Unable to provide support for code system http://phenopacket-schema.readthedocs.io/en/v2/variant-interpretation.html#therapeuticactionability (from , see log)

Suppressed Messages (Warnings, hints, broken links)

No suppressed messsages

Errors sorted by type


All_observations_should_have_a_performer

fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-CHF-with-severity.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-MVP-with-onset.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-PhenopacketsVariantExample01.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-Polydactyly-with-modifier.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-amyotrophy.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-arachnodactyly.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-globalDevelopmentalDelay.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-hp.0003557.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-hypotonia.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-karyotypic-sex-invalid-1.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-karyotypic-sex-valid-1.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-longPhiltrum.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-lowSetEars.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-lvdysfunction-excluded.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-microphthalmia.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-muscleWeakness.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-phenotypic-abnormality-invalid-1.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-phenotypic-abnormality-valid-1.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-reducedVisualAcuity.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-retinalDetachment.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-tga.jsonBest Practice Recommendation: In general, all observations should have a performer
fsh-generated/resources/Observation-thrombocytopenia.jsonBest Practice Recommendation: In general, all observations should have a performer

All_observations_should_have_a_subject

fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Observation-PhenopacketsVariantExample01.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Observation-hp.0003557.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Observation-karyotypic-sex-invalid-1.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Observation-karyotypic-sex-valid-1.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Observation-phenotypic-abnormality-invalid-1.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Observation-phenotypic-abnormality-valid-1.jsonBest Practice Recommendation: In general, all observations should have a subject
fsh-generated/resources/Observation-thrombocytopenia.jsonBest Practice Recommendation: In general, all observations should have a subject

All_observations_should_have_an_effectiveDateTime_or_an_effectivePeriod

fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-PhenopacketsVariantExample01.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-amyotrophy.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-arachnodactyly.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-globalDevelopmentalDelay.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-hp.0003557.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-hypotonia.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-karyotypic-sex-invalid-1.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-karyotypic-sex-valid-1.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-longPhiltrum.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-lowSetEars.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-lvdysfunction-excluded.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-microphthalmia.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-muscleWeakness.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-phenotypic-abnormality-invalid-1.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-phenotypic-abnormality-valid-1.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-reducedVisualAcuity.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-retinalDetachment.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()
fsh-generated/resources/Observation-tga.jsonBest Practice Recommendation: In general, all observations should have an effective[x] ()

Bundle_BUNDLE_Entry_NotFound

fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonCan't find 'Patient/phenopacketPatientExample01' in the bundle (Bundle.entry[7].resource.subject)
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonCan't find 'Specimen/phenopacketSpecimenExample01' in the bundle (Bundle.entry[7].resource.specimen[0])

CODESYSTEM_THO_CHECK

fsh-generated/resources/CodeSystem-HtsFormat.jsonMost 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)
fsh-generated/resources/CodeSystem-KaryotypicSex.jsonMost 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)
fsh-generated/resources/CodeSystem-categories.jsonMost 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)
fsh-generated/resources/CodeSystem-phenotypicFeatureStatusCS.jsonMost 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)
fsh-generated/resources/CodeSystem-section-type.jsonMost 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)

ED_INVARIANT_NO_EXPRESSION

fsh-generated/resources/StructureDefinition-phenopackets-genomic-interpretation.jsonThe constraint 'phenopackets-subject-or-specimen-id' has no computable expression, so validators will not be able to check it
fsh-generated/resources/StructureDefinition-phenopackets-genomic-interpretation.jsonThe constraint 'phenopackets-subject-or-specimen-id' has no computable expression, so validators will not be able to check it
fsh-generated/resources/StructureDefinition-phenopackets-genomic-interpretation.jsonThe constraint 'phenopackets-subject-or-specimen-id' has no computable expression, so validators will not be able to check it
fsh-generated/resources/StructureDefinition-phenopackets-genomic-interpretation.jsonThe constraint 'phenopackets-subject-or-specimen-id' has no computable expression, so validators will not be able to check it

MSG_DRAFT

fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Composition-DevelopmentalDelay.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Composition-DevelopmentalDelay.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Composition-DevelopmentalDelay.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Composition-PhenopacketCompositionExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Composition-PhenopacketCompositionExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Composition-PhenopacketCompositionExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Composition-PhenopacketCompositionExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Composition-PhenopacketCompositionExample01.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/Practitioner-PeterGeneticist.jsonReference to draft CodeSystem http://terminology.hl7.org/CodeSystem/v2-0360|2.7|0360
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-Phenopacket.jsonReference to draft CodeSystem http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type|0.1.0
fsh-generated/resources/StructureDefinition-phenopackets-variant.jsonReference to draft CodeSystem http://terminology.hl7.org/CodeSystem/observation-category|1.0.0

RESOURCE_CANONICAL_MISMATCH

fsh-generated/resources/SearchParameter-service-request-supporting-info.jsonConformance resource /scratch/repo/fsh-generated/resources/SearchParameter-service-request-supporting-info.json - the canonical URL (http://hl7.org/fhir/uv/phenomics-exchange/SearchParameter/service-request-supporting-info) does not match the URL (http://github.com/phenopackets/core-ig/SearchParameter/service-request-supporting-info)
fsh-generated/resources/SearchParameter-service-request-supporting-info.jsonConformance resource /scratch/repo/fsh-generated/resources/SearchParameter-service-request-supporting-info.json - the canonical URL (http://hl7.org/fhir/uv/phenomics-exchange/SearchParameter/service-request-supporting-info) does not match the URL (http://github.com/phenopackets/core-ig/SearchParameter/service-request-supporting-info)

Reference_REF_CantMatchChoice

fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonUnable to find a match for profile DiagnosticReport/PhenopacketsGenomicInterpretationExample02 among choices: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-genomic-interpretation

TERMINOLOGY_TX_SYSTEM_NOT_USABLE

fsh-generated/resources/StructureDefinition-PhenotypicFeature.jsonThe definition for the Code System with URI 'http://human-phenotype-ontology.org' doesn't provide any codes so the code cannot be validated
fsh-generated/resources/StructureDefinition-PhenotypicFeature.jsonThe definition for the Code System with URI 'http://human-phenotype-ontology.org' doesn't provide any codes so the code cannot be validated
fsh-generated/resources/StructureDefinition-PhenotypicFeature.jsonThe definition for the Code System with URI 'http://human-phenotype-ontology.org' doesn't provide any codes so the code cannot be validated
fsh-generated/resources/StructureDefinition-PhenotypicFeature.jsonThe definition for the Code System with URI 'http://human-phenotype-ontology.org' doesn't provide any codes so the code cannot be validated

Terminology_TX_NoValid_1_CC

fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonNone of the codings provided are in the value set 'Interpretation Status Value Set' (http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/interpretationStatus-vs|0.1.0), and a coding from this value set is required) (codes = http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus#0)
fsh-generated/resources/DiagnosticReport-PhenopacketsGenomicInterpretationExample01.jsonNone of the codings provided are in the value set 'Interpretation Status Value Set' (http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/interpretationStatus-vs|0.1.0), and a coding from this value set is required) (codes = http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus#0)
fsh-generated/resources/DiagnosticReport-PhenopacketsGenomicInterpretationExample02.jsonNone of the codings provided are in the value set 'Interpretation Status Value Set' (http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/interpretationStatus-vs|0.1.0), and a coding from this value set is required) (codes = http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus#0)

Terminology_TX_NoValid_3_CC

fsh-generated/resources/Bundle-PhenopacketsBundleExample01.jsonNone of the codings provided are in the value set 'LOINC Diagnostic Report Codes' (http://hl7.org/fhir/ValueSet/report-codes|4.0.1), and a coding is recommended to come from this value set (codes = http://loinc#123)

UNKNOWN_CODESYSTEM

fsh-generated/resources/Observation-phenotypic-abnormality-invalid-1.jsonA definition for CodeSystem 'http://some/unit/system' could not be found, so the code cannot be validated
fsh-generated/resources/Observation-phenotypic-abnormality-valid-1.jsonA definition for CodeSystem 'http://some/unit/system' could not be found, so the code cannot be validated

VALUESET_BAD_FILTER_VALUE_VALID_CODE

fsh-generated/resources/ValueSet-geno-ontology-allelic-state-vs.jsonThe value for a filter based on property 'concept' must be a valid code from the system 'http://www.ebi.ac.uk/ols/ontologies/geno', and 'GENO_0000875' is not (A definition for CodeSystem 'http://www.ebi.ac.uk/ols/ontologies/geno' could not be found, so the code cannot be validated)
fsh-generated/resources/ValueSet-sequence-ontology-structural-variant-vs.jsonThe value for a filter based on property 'concept' must be a valid code from the system 'http://www.sequenceontology.org/', and 'SO:0001537' is not (A definition for CodeSystem 'http://www.sequenceontology.org/' could not be found, so the code cannot be validated)