Snomed: The IG specifies a different version (http://snomed.info/sct/900000000000207008/version/20240201) to the US edition of SNOMED CT version in the parameters (http://snomed.info/sct/731000124108)
Error from http://tx.fhir.org/r4: Error parsing HGVS response: HTTP/1.1 500 Internal Server Error
Editor's Comment: Known HGVS validation error, https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Validation.20issue.20for.20HGVS.2FHGNC.20code. These error messages sometimes show 0 use, but when I remove them here, they appear again.
None of the codings provided are in the value set 'Human Genome Variation Society (HGVS) Nomenclature' (http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs|2.0.0), and a coding from this value set is required) (codes = http://varnomen.hgvs.org#NG_005905.2:g.126148_126152del)
Editor's Comment: Known HGVS validation error, https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Validation.20issue.20for.20HGVS.2FHGNC.20code. These error messages sometimes show 0 use, but when I remove them here, they appear again.Terminology_TX_NoValid_1_CC
A PR has been created to add this code to the Codesystem Fragment
INFORMATION: ValueSet/mcode-cancer-staging-method-vs: ValueSet.compose.include[1].concept[0]: Unknown Code 'C15432' in the CodeSystem 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl' version '' - note that the code system is labeled as a fragment, so the code may be valid in some other fragment (1 uses)
All Slices have been validated
INFORMATION: Observation/ecog-performance-status-fully-active: Observation.category[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-ecog-performance-status|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
All slices have been validated
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[18].resource/*Observation/ecog-performance-status-jenny-m*/.category[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-ecog-performance-status|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Observation/ecog-performance-status-jenny-m: Observation.category[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-ecog-performance-status|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Observation/karnofsky-performance-status-normal-activity: Observation.category[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-karnofsky-performance-status|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Observation/lansky-performance-status-brian-l: Observation.category[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-lansky-play-performance-status|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
Known HGVS validation error, https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Validation.20issue.20for.20HGVS.2FHGNC.20code. These error messages sometimes show 0 use, but when I remove them here, they appear again.
ERROR: Observation/genomic-variant-germline-deletion: Observation.component[1].value.ofType(CodeableConcept).coding[0]: Error from http://tx.fhir.org/r4: Error parsing HGVS response: HTTP/1.1 500 Internal Server Error (1 uses)
ERROR: Observation/genomic-variant-germline-deletion: Observation.component[1].value.ofType(CodeableConcept): None of the codings provided are in the value set 'Human Genome Variation Society (HGVS) Nomenclature' (http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs|2.0.0), and a coding from this value set is required) (codes = http://varnomen.hgvs.org#NG_005905.2:g.126148_126152del) (1 uses)
Noted. SNOMED is the target code system.
Target Code System http://snomed.info/sct is only supported on the terminology server, so the target codes are not validated for performance reasons (1 uses)
Reference to condition-category, observation-category, medicationrequest-category code system is inherited from US Core and we can't change that
Reference to draft CodeSystem http://terminology.hl7.org/CodeSystem/medicationrequest-category|1.0.0 (12 uses)
Reference to deprecated extension included for backwards compatibility.
The extension http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-treatment-termination-reason|4.0.0 is retired (1 uses)
SNOMEDCT Code is included intentionally since uly 2024 Release -- https://browser.ihtsdotools.org/?perspective=full&conceptId1=1342413004&edition=MAIN/2024-07-01&release=&languages=en
WARNING: ValueSet/mcode-cancer-stage-type-vs: ValueSet.compose.include[0].concept[36]: The code '1342413004' is not valid in the system http://snomed.info/sct (Unknown code '1342413004' in the CodeSystem 'http://snomed.info/sct' version 'http://snomed.info/sct/900000000000207008/version/20240201') (1 uses)
SUPPRESS 'The discriminator type 'pattern' has been deprecated' WARNINGS that are in US Core 6.1.0. See Grahame Grieve's comment in https://chat.fhir.org/#narrow/channel/179252-IG-creation/topic/deprecated.20pattern.20slicing/near/482196925
INFORMATION: StructureDefinition/mcode-ALL-risk-assessment: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-cancer-related-medication-request: StructureDefinition.snapshot.element[15].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-cancer-risk-assessment: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-cancer-stage: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-comorbidities: StructureDefinition.snapshot.element[15].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-deauville-scale: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-ecog-performance-status: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-genomic-region-studied: StructureDefinition.snapshot.element[49].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-genomic-variant: StructureDefinition.snapshot.element[50].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-genomics-report: StructureDefinition.snapshot.element[18].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-histologic-behavior-and-type: StructureDefinition.snapshot.element[14].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-histologic-grade: StructureDefinition.snapshot.element[14].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-history-of-metastatic-cancer: StructureDefinition.snapshot.element[14].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-karnofsky-performance-status: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-lansky-play-performance-status: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-lymphoma-stage: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-primary-cancer-condition: StructureDefinition.snapshot.element[14].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-rhabdomyosarcoma-risk-assessment: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-secondary-cancer-condition: StructureDefinition.snapshot.element[19].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-tnm-category: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-tnm-distant-metastases-category: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-tnm-primary-tumor-category: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-tnm-regional-nodes-category: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-tnm-stage-group: StructureDefinition.snapshot.element[13].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-tumor-marker-test: StructureDefinition.snapshot.element[14].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
INFORMATION: StructureDefinition/mcode-tumor-morphology: StructureDefinition.snapshot.element[14].slicing.discriminator[0]: The discriminator type 'pattern' is deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing) (1 uses)
SUPPRESS US CORE COMPLIANCE WARNINGS. For STU4, exceptions to US Core parent profiles was approved by Cross-Group Projects Work Group on 03/21/2024. See https://jira.hl7.org/browse/FHIR-44928
WARNING: StructureDefinition.where(url = 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-disease-status').baseDefinition: US FHIR Usage rules require that all profiles on Observation derive from one of the base US profiles. See https://confluence.hl7.org/display/CGP/US+Core+Variance+Request+Process (1 uses)
WARNING: StructureDefinition.where(url = 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-region-studied').baseDefinition: US FHIR Usage rules require that all profiles on Observation derive from one of the base US profiles. See https://confluence.hl7.org/display/CGP/US+Core+Variance+Request+Process (1 uses)
WARNING: StructureDefinition.where(url = 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant').baseDefinition: US FHIR Usage rules require that all profiles on Observation derive from one of the base US profiles. See https://confluence.hl7.org/display/CGP/US+Core+Variance+Request+Process (1 uses)
WARNING: StructureDefinition.where(url = 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report').baseDefinition: US FHIR Usage rules require that all profiles on DiagnosticReport derive from one of the base US profiles. See https://confluence.hl7.org/display/CGP/US+Core+Variance+Request+Process (1 uses)
WARNING: StructureDefinition.where(url = 'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tumor-size').baseDefinition: US FHIR Usage rules require that all profiles on Observation derive from one of the base US profiles. See https://confluence.hl7.org/display/CGP/US+Core+Variance+Request+Process (1 uses)
TG263 codesystem and valueset are placeholder only. There is no terminology resource that will support validity checking
WARNING: ConceptMap/TG263CM: ConceptMap.group[0].source: Source Code System http://hl7.org/fhir/us/mcode/CodeSystem/tg263-cs doesn't have all content (content = not-present), so the source codes cannot be checked (1 uses)
WARNING: ValueSet.where(id = 'tg263-vs'): Error from http://tx.fhir.org/r4: Unable to provide support for code system http://hl7.org/fhir/us/mcode/CodeSystem/tg263-cs (1 uses)
TG263 concept map is indeed large by intent
INFORMATION: ConceptMap/TG263CM: ConceptMap: The concept map has too many codes to validate (1,346) (1 uses)
TG263 is a terminology managed by the AAPM. Mapping is included here for documentation purposes.
INFORMATION: CodeSystem/tg263-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
The following code system are not discoverable because they are code systems in THO, but THO doesn't define the codes. They have been checked and the identifiers are correct
A definition for CodeSystem 'http://www.genenames.org' could not be found, so the code cannot be validated (47 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/clinvar' could not be found, so the code cannot be validated (3 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/gtr' could not be found, so the code cannot be validated (3 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/refseq' could not be found, so the code cannot be validated (6 uses)
A definition for CodeSystem 'http://www.sequenceontology.org/' could not be found, so the code cannot be validated (23 uses)
A definition for CodeSystem 'https://www.gensop.com' could not be found, so the code cannot be validated (2 uses)
A definition for CodeSystem 'https://www.ncbi.nlm.nih.gov/gene' could not be found, so the code cannot be validated (22 uses)
Error from http://tx.fhir.org/r4: Unable to provide support for code system http://cancerstaging.org (4 uses)
The definition for the Code System with URI 'urn:oid:2.16.840.1.113883.6.238' doesn't provide any codes so the code cannot be validated (14 uses)
These codes are valid. A PR has been created to add them to the Code System Fragment
WARNING: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[2].resource/*ServiceRequest/gx-order-tumornormal-gensop-inc*/.reasonCode[0].coding[1].code: Unknown Code '8140/3' in the CodeSystem 'http://terminology.hl7.org/CodeSystem/icd-o-3' version '2000' - note that the code system is labeled as a fragment, so the code may be valid in some other fragment (1 uses)
WARNING: Observation/histologic-behavior-and-type-non-small-cell: Observation.value.ofType(CodeableConcept).coding[0].code: Unknown Code '80463/3' in the CodeSystem 'http://terminology.hl7.org/CodeSystem/icd-o-3' version '2000' - note that the code system is labeled as a fragment, so the code may be valid in some other fragment (1 uses)
WARNING: ServiceRequest/gx-order-tumornormal-gensop-inc: ServiceRequest.reasonCode[0].coding[1].code: Unknown Code '8140/3' in the CodeSystem 'http://terminology.hl7.org/CodeSystem/icd-o-3' version '2000' - note that the code system is labeled as a fragment, so the code may be valid in some other fragment (1 uses)
This is intentional. These are instances of resources from other IGs (US Core, Genomics IG) that are relevant to care of a cancer patient.
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[1].resource/*DiagnosticReport/gx-genomics-report-adam-anyperson*/.result[13]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Bundle/gx-genomic-bundle-adam-anyperson: Bundle.entry[1].resource/*DiagnosticReport/gx-genomics-report-adam-anyperson*/.result[14]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[27]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[30]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[31]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[38]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: Bundle/mcode-patient-bundle-jenny-m: Bundle.entry[39]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-patient-bundle|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: DiagnosticReport/gx-genomics-report-adam-anyperson: DiagnosticReport.result[13]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
INFORMATION: DiagnosticReport/gx-genomics-report-adam-anyperson: DiagnosticReport.result[14]: This element does not match any known slice defined in the profile http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report|4.0.0 (this may not be a problem, but you should check that it's not intended to match a slice) (1 uses)
This issue is a commentary on SNOMEDCT, rather than on the valueset. ALl values have been checked.
INFORMATION: ValueSet/mcode-radiotherapy-treatment-location-vs: ValueSet.compose.include[0]: This SNOMED-CT based include has some concepts with semantic tags (FSN terms) and some without (preferred terms) - check that this is what is intended (examples for FSN: [Aortic structure (body structure), Ascending aorta structure (body structure), Branch of brachiocephalic artery (body structure), Carotid artery structure (body structure), Structure of celiac artery (body structure)] and examples for no FSN: [Tumor bed (morphologic abnormality), Scar (morphologic abnormality), Vaginal cuff (morphologic abnormality)]) (1 uses)
This valueset is known to be quite large, so inability to validate is not a problem.
INFORMATION: ValueSet/mcode-primary-malignant-neoplasm-disorder-vs: ValueSet.compose.include[1]: The value set include has too many codes to validate (1,046), so each individual code has not been checked (1 uses)
Use of UCUM inherited from Genomics IG (nothing we can do about it)
UCUM Codes that contain human readable annotations like {Base} can be misleading (e.g. they are ignored when comparing units). Best Practice is not to depend on annotations in the UCUM code, so this usage should be checked, and the Quantity.unit SHOULD contain the annotation (1 uses)
WARNING: Observation/gx-genomic-tmb: Observation.value.ofType(Quantity): UCUM Codes that contain human readable annotations like {Base} can be misleading (e.g. they are ignored when comparing units). Best Practice is not to depend on annotations in the UCUM code, so this usage should be checked, and the Quantity.unit SHOULD contain the annotation (1 uses)
None of the codings provided are in the value set 'Human Genome Variation Society (HGVS) Nomenclature' (http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs|2.0.0), and a coding from this value set is required) (codes = http://varnomen.hgvs.org#NG_005905.2:g.126148_126152del)