The jira specification file appears to be out of date with the versions, artifacts and pages currently defined in the IG. A proposed revised file to be reviewed and, if appropriate, submitted as a pull request against the XML folder in https://github.com/HL7/JIRA-Spec-Artifacts. To see the differences, perform a file compare on 'template/jira-current.xml' (a normalized view of what is in Github) and 'template/jira-new.xml' (reflects current IG content)
CodeSystem-knowledge-base-cs.html
information
The html source contains the word 'SHALL' but it is not in a text phrase marked as a conformance clauseCONFORMANCE_STATEMENT_WORD
StructureDefinition-coded-annotation.html
information
The html source contains the word 'SHALL' but it is not in a text phrase marked as a conformance clauseCONFORMANCE_STATEMENT_WORD
The extension http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database|5.2.0 is deprecated with the note: 'This extension has been replaced by the profiles and extensions defined in the "Genomics Reporting Guide" (https://hl7.org/fhir/uv/genomics-reporting/)'MSG_DEPENDS_ON_DEPRECATED_NOTE
DiagnosticReport.extension (l1/c140263)
information
The extension http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring|5.2.0 is deprecated with the note: 'This extension has been replaced by the profiles and extensions defined in the "Genomics Reporting Guide" (https://hl7.org/fhir/uv/genomics-reporting/)'MSG_DEPENDS_ON_DEPRECATED_NOTE
The concepts in the value set include have not been validated because the code system is not known, and no terminology service supports itVALUESET_INC_CS_NO_SUPPORT
Error from https://tx.fhir.org/r4: A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the value set cannot be expanded (from server, see log)
Error from https://tx.fhir.org/r4: A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the value set cannot be expanded (from server, see log)
Error from https://tx.fhir.org/r4: A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the value set cannot be expanded (from server, see log)
Error from https://tx.fhir.org/r4: A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the value set cannot be expanded (from server, see log)
Error from https://tx.fhir.org/r4: A definition for CodeSystem 'http://www.genenames.org' could not be found, so the value set cannot be expanded (from server, see log)
Error from https://tx.fhir.org/r4: The code system definition for http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl is a fragment, so this expansion is not permitted unless the expansion parameter "incomplete-ok" has a value of "true" (from server, see log)
Error from https://tx.fhir.org/r4: A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the value set cannot be expanded (from server, see log)
An example of DiagnosticImplication<Observation>.derivedFrom() that we slice to only allow our profiles. In this example, we did not define specific Variant instances and just refer to some variants by identifier (rather than a full resource), so ignoring these warnings
INFORMATION: Observation/PolyGenicDiagnosticImpExample: Observation.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication% (1 uses)
INFORMATION: Observation/PolyGenicDiagnosticImpExample: Observation.derivedFrom[1]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication% (1 uses)
CG has reviewed these CodeSystems and have decided to keep this in our IG
INFORMATION: CodeSystem/clinvar-evidence-level-custom-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/coded-annotation-types-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-change-type-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-data-format-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-method-type-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-status-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/genomic-study-type-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/knowledge-base-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/molecular-biomarker-ontology-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/pharmgkb-evidence-level-custom-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
INFORMATION: CodeSystem/tbd-codes-cs: CodeSystem: Most code systems defined in HL7 IGs will need to move to THO later during the process. Consider giving this code system a THO URL now (See https://confluence.hl7.org/display/TSMG/Terminology+Play+Book, and/or talk to TSMG) (1 uses)
Each of these codes have been validated (as of Jul 5 2024), so suppressing these warnings until HPO becomes a supported code system.
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].target: Target Code System http://www.sequenceontology.org doesn't have all content (content = not-present), so the target codes cannot be checked (1 uses)
GenomicReport<DiagnosticReport>.result referencing Observation instances. We have defined our report profile to slice .result with our Observation profiles. Slicing is open, this informational message can be ignored
INFORMATION: Bundle/bundle-cgexample-withGrouping: Bundle.entry[0].resource/*DiagnosticReport/report-withGrouping*/.result[4]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: Bundle/bundle-oncologyexamples-r4-withGrouping: Bundle.entry[14].resource/*DiagnosticReport/Inline-Instance-for-oncologyexamples-r4-withGrouping-15*/.result[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: Bundle/bundle-oncologyexamples-r4-withGrouping: Bundle.entry[14].resource/*DiagnosticReport/Inline-Instance-for-oncologyexamples-r4-withGrouping-15*/.result[6]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: DiagnosticReport/PGxGenomicReportEMERGE-withGrouping: DiagnosticReport.result[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: DiagnosticReport/PGxGenomicReportEMERGE-withGrouping: DiagnosticReport.result[1]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
INFORMATION: DiagnosticReport/PGxGenomicReportEMERGE-withGrouping: DiagnosticReport.result[2]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report% (1 uses)
OCT 2025 - THE VALUESET IN THE WARNING BECAME 'null'
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[0].target[0].code: The code 'SO:0002073' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'null' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[1].target[0].code: The code 'SO:0000159' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'null' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[2].target[0].code: The code 'SO:1000035' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'null' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[3].target[0].code: The code 'SO:0000667' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'null' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[4].target[0].code: The code 'SO:1000032' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'null' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[5].target[0].code: The code 'SO:1000036' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'null' (1 uses)
WARNING: ConceptMap/dna-change-type-map: ConceptMap.group[0].element[6].target[0].code: The code 'SO:1000002' comes from the system http://www.sequenceontology.org which could not be found, so it's not known whether it's valid in the value set 'null' (1 uses)
Observation.component instances that do not match our slices, but is OK (and this is ok since we use open slicing)
INFORMATION: Bundle/bundle-cgexample: Bundle.entry[5].resource/*Observation/discrete-variant*/.component[18]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant% (1 uses)
INFORMATION: Bundle/bundle-cgexample: Bundle.entry[5].resource/*Observation/discrete-variant*/.component[19]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant% (1 uses)
INFORMATION: Observation/variant-with-molec-consequences: Observation.component[9]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant% (1 uses)
Our Observation profiles require a code from the Observation Category value set (LAB), but in some cases require additional codes from other value sets. Since this binding is "Preferred" the resources are still conformant, so we are Suppressing these messages.
None of the codings provided are in the value set 'Observation Category Codes' (http://hl7.org/fhir/ValueSet/observation-category|4.0.1), and a coding is recommended to come from this value set (codes = http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs#biomarker-category) (5 uses)
None of the codings provided are in the value set 'Observation Category Codes' (http://hl7.org/fhir/ValueSet/observation-category|4.0.1), and a coding is recommended to come from this value set (codes = http://terminology.hl7.org/CodeSystem/v2-0074#GE) (179 uses)
Pinned versions have been reviewed:
Pinned the version of http://hl7.org/fhir/StructureDefinition/% (48 uses)
Suppress all references to example CodeSystems
A definition for CodeSystem 'http://example.org/% (11 uses)
The IG Validator returns different warnings on this error: https://github.com/HL7/fhir-ig-publisher/issues/420 - in short, the validator returns the "among choices" profiles in a different order different times, so suppressing by wildcard
Found multiple matching profiles for Task/med-usage-impact-task-pgx-example among choices% (1 uses)
Found multiple matching profiles for Task/usage-1a among choices:% (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://clinicaltrials.gov' could not be found, so the code cannot be validated (3 uses)
A definition for CodeSystem 'http://glstring.org' version '1.0' could not be found, so the code cannot be validated. No versions of this code system are known (5 uses)
A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the code cannot be validated (1 uses)
A definition for CodeSystem 'http://purl.obolibrary.org/obo/mondo.owl' could not be found, so the code cannot be validated (3 uses)
A definition for CodeSystem 'http://www.ebi.ac.uk/ipd/imgt/hla' could not be found, so the code cannot be validated (8 uses)
A definition for CodeSystem 'http://www.ebi.ac.uk/ipd/imgt/hla' version '3.23' could not be found, so the code cannot be validated. No versions of this code system are known (19 uses)
A definition for CodeSystem 'http://www.ebi.ac.uk/ipd/imgt/hla' version '3.31.0' could not be found, so the code cannot be validated. No versions of this code system are known (0 uses)
A definition for CodeSystem 'http://www.genenames.org' could not be found, so the code cannot be validated% (97 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/clinvar' could not be found, so the code cannot be validated (15 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/clinvar' version '???' could not be found, so the code cannot be validated. No versions of this code system are known (1 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/projects/SNP' could not be found, so the code cannot be validated (3 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/projects/SNP' version '137' could not be found, so the code cannot be validated. No versions of this code system are known (1 uses)
A definition for CodeSystem 'http://www.ncbi.nlm.nih.gov/refseq' could not be found, so the code cannot be validated (152 uses)
A definition for CodeSystem 'http://www.pharmvar.org' could not be found, so the code cannot be validated (11 uses)
A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the code cannot be validated (73 uses)
A definition for CodeSystem 'https://iscn.karger.com' could not be found, so the code cannot be validated (2 uses)
A definition for CodeSystem 'https://www.ncbi.nlm.nih.gov/gtr' could not be found, so the code cannot be validated (9 uses)
The mappings in this concept map have been human reviewed and is correct
INFORMATION: ConceptMap/dna-change-type-map: ConceptMap.group[0].source: Source Code System http://loinc.org is only supported on the terminology server, so the source codes are not validated for performance reasons (1 uses)
These URLs have been validated and are apporpriately used in our examples
No definition could be found for URL value 'http://slk-kliniken.de/fhir/namingSystem/tissueID' (1 uses)
No definition could be found for URL value 'https://civicdb.org/evidence/2994/summary' (2 uses)
No definition could be found for URL value 'https://civicdb.org/evidence/7282/summary' (1 uses)
No definition could be found for URL value 'https://civicdb.org/molecular-profiles/2562/summary' (1 uses)
No definition could be found for URL value 'https://cpicpgx.org/guidelines/guideline-for-clopidogrel-and-cyp2c19' (2 uses)
No definition could be found for URL value 'https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/' (2 uses)
No definition could be found for URL value 'https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/' (1 uses)
No definition could be found for URL value 'https://cpicpgx.org/guidelines/guideline-for-voriconazole-and-cyp2c19/' (1 uses)
No definition could be found for URL value 'https://cpicpgx.org/guidelines/guideline-for-warfarin-and-cyp2c9-and-vkorc1/' (1 uses)
No definition could be found for URL value 'https://gl.nmdp.org/imgt-hla/3.23.0/multilocus-unphased-genotype/ex' (1 uses)
No definition could be found for URL value 'https://pubmed.ncbi.nlm.nih.gov/29614695/' (3 uses)
No definition could be found for URL value 'https://pubmed.ncbi.nlm.nih.gov/33927380/' (3 uses)
No definition could be found for URL value 'https://www.cancer.net/cancer-types/lung-cancer-non-small-cell/types-treatment' (3 uses)
No definition could be found for URL value 'https://www.jmdjournal.org/cms/attachment/ee43a71b-81de-4cb3-ac5e-2fb9a7d41491/gr2.jpg' (4 uses)
No definition could be found for URL value 'https://www.ncbi.nlm.nih.gov/clinvar/variation/53685/#clinical-assertions' (1 uses)
No definition could be found for URL value 'https://www.ncbi.nlm.nih.gov/gene/545#:~:text=ATR%20may%20function%20as%20an,radiation%20when%20ATM%20is%20deficient' (2 uses)
These slice messages have been reviewed, and our StructureDefinition apporpriately defines the slices of extension, and examples look valid. Have asked for feedback here: https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/slicing.20in.20Observation.2Ecomponent.2Eextension.20information.20help.3F
INFORMATION: Bundle/bundle-oncologyexamples-r4-withGrouping: Bundle.entry[8].resource/*Observation/Inline-Instance-for-oncologyexamples-r4-withGrouping-9*/.component[3].extension[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication% (1 uses)
INFORMATION: Bundle/bundle-oncologyexamples-r4: Bundle.entry[12].resource/*Observation/Inline-Instance-for-oncologyexamples-r4-14*/.component[0].extension[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication% (1 uses)
These slice messages that have been reviewed. Each of these refer to (via derivedFrom) a Variant, and are a valid Variant instance. They are similar to ones mentioned on https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/slicing.20in.20Observation.2Ecomponent.2Eextension.20information.20help.3F
INFORMATION: Parameters/FindSubjectMolecConseqOutput: Parameters.parameter[0].resource/*Observation/MC1*/.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence% (1 uses)
INFORMATION: Parameters/FindSubjectMolecConseqOutput: Parameters.parameter[1].resource/*Observation/MC2*/.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence% (1 uses)
INFORMATION: Parameters/FindSubjectMolecConseqOutput: Parameters.parameter[2].resource/*Observation/MC3*/.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence% (1 uses)
INFORMATION: Parameters/FindSubjectMolecConseqOutput: Parameters.parameter[3].resource/*Observation/MC4*/.derivedFrom[0]: This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence% (1 uses)
This version number has been validated
WARNING: Observation/haplotype-hla-a-1-r4: Observation.value.ofType(CodeableConcept).coding[0].system: A definition for CodeSystem 'http://www.ebi.ac.uk/ipd/imgt/hla' version '3.31.0' could not be found, so the code cannot be validated. No versions of this code system are known (1 uses)
We define several experimental CodeSystems that we use, so OK to suppress this for all IG defined CSs, https://chat.fhir.org/#narrow/channel/179202-terminology/topic/Overuse.20of.20the.20Experimental.20flag, https://confluence.hl7.org/x/LKOZCQ
Reference to experimental CodeSystem http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/% (283 uses)
Reference to experimental CodeSystem http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs% (11 uses)
not defined in this IG, so it must be a problem upstream
The extension http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet|5.2.0 is deprecated (1 uses)
The extension http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database|5.2.0 is deprecated with the note: 'This extension has been replaced by the profiles and extensions defined in the "Genomics Reporting Guide" (https://hl7.org/fhir/uv/genomics-reporting/)'
The extension http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring|5.2.0 is deprecated with the note: 'This extension has been replaced by the profiles and extensions defined in the "Genomics Reporting Guide" (https://hl7.org/fhir/uv/genomics-reporting/)'
hl7.fhir.uv.genomics-reporting
hl7.fhir.uv.tools.r4