The jira specification file appears to be out of date with the versions, artifacts and pages currently defined in the IG.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 clause: ' This example code systems provides examples on how to properly display the knowledge base version number. Version numbers should always be followed by the letter v and calendar dates are displayed Month Day Year. For clarity the month SHALL be written in full. 'CONFORMANCE_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 clause: 'If there is a possibility of transporting the content of the note in a structured manner the usage of CodedAnnotation is forbidden and the corresponding data structures SHALL be used. For example, if the text to send resembles the interpretation or impression of the Observation, this guide adds Observation.component slice for conclusion-string which is more appropriate than a note. This would include text like interpretative information (typically canned) about a variant identified in the patient. This slice is defined in the Genomic Base profile, which every observation builds upon. Therefore, this component is a defined slice on all observations profiles defined in this Implementation Guide.'CONFORMANCE_STATEMENT_WORD
The link 'StructureDefinition-workflow-supportingInfo.html' for "supportingInfo extension" cannot be resolvedHTML_LINK_CHECK_FAILED
StructureDefinition-genotype.html
information
The html source contains the word 'SHOULD' but it is not in a text phrase marked as a conformance clause: 'For Pharmacogenomics, implementers SHOULD send coded haplotypes, and for genotypes (diplotypes) MAY use a simple, human readable grammar of:'CONFORMANCE_STATEMENT_WORD
StructureDefinition-haplotype.html
information
The html source contains the word 'SHOULD' but it is not in a text phrase marked as a conformance clause: 'For Pharmacogenomics, implementers SHOULD send coded haplotypes. Here is an example using PharmVar:'CONFORMANCE_STATEMENT_WORD
The link 'StructureDefinition-workflow-supportingInfo.html' for "supportingInfo extension" cannot be resolvedHTML_LINK_CHECK_FAILED
StructureDefinition-implication.html
information
The html source contains the word 'SHALL' but it is not in a text phrase marked as a conformance clause: 'Where implications have fields with cardinality > 1, the inclusion of multiple values within a field SHALL indicate an 'AND' condition. An 'OR' condition SHALL be represented by multiple observation instances.'CONFORMANCE_STATEMENT_WORD
The page skips a heading level: <h4> 'evidence-level versus clinical-significance' (id=evidence-level-versus-clinical-significance) follows <h2> 'Resource Profile: Genomic Implication ( Abstract )' (id=root), so it should be <h3>. Heading levels must not skip a level going down (WCAG compliance test)HTML_HEADING_LEVEL_SKIPPED
The link 'StructureDefinition-workflow-supportingInfo.html' for "supportingInfo extension" cannot be resolvedHTML_LINK_CHECK_FAILED
StructureDefinition-therapeutic-implication.html
information
The html source contains the word 'SHALL' but it is not in a text phrase marked as a conformance clause: 'There are two ways to communicate details about a medication whose implication is being described. The profile component medication-assessed is the place to communicate a simple code for the medication. If more detail about the medication is to be shared, use the extension named medication-assessed-reference. The extension can refer to a Medication or MedicationKnowledge resource. This might be used to share specific classification details if they are important as part of the implication being described. It is important to note that since there two ways to do this, implementers SHALL ensure consistent usage. If both the extension and component are used at the same time, they SHALL deliver the same medication. Because this is an international profile, no guidance is provided on drug coding systems.'CONFORMANCE_STATEMENT_WORD
artifacts.html
information
The html source contains the word 'SHALL' but it is not in a text phrase marked as a conformance clause: 'This example code systems provides examples on how to properly display the knowledge base version number. Version numbers should always be followed by the letter v and calendar dates are displayed Month Day Year. For clarity the month SHALL be written in full.'CONFORMANCE_STATEMENT_WORD
general.html
information
The html source contains the word 'SHOULD' but it is not in a text phrase marked as a conformance clause: 'The GenomicStudy instance SHOULD be referenced from a report and CAN be referenced by various observations.'CONFORMANCE_STATEMENT_WORD
pharmacogenomics.html
information
The html source contains the word 'MAY' but it is not in a text phrase marked as a conformance clause: 'Genotype names such as star-alleles can appear in PGx reports either with or without a full description of the underlying coded haplotypes and observed variants. Genotype names MAY be coded, but will oftentimes be textual descriptions only. PGx guidance is often available at the level of these genotypes.'CONFORMANCE_STATEMENT_WORD
output/searchform.html
warning
The html source is not well formed: Found "</a>" expecting "</img>" at line 34 column 177HTML_NOT_WELL_FORMED
output/searchform.html
warning
The html source is not well formed: Found "</div>" expecting "</body>" at line 79 column 10HTML_NOT_WELL_FORMED
output/searchform.html
warning
The html source is not well formed: Found "</div>" expecting "</body>" at line 80 column 9HTML_NOT_WELL_FORMED
output/searchform.html
warning
The html source is not well formed: Found "</div>" expecting "</body>" at line 109 column 8HTML_NOT_WELL_FORMED
output/searchform.html
warning
The html source is not well formed: Found "</div>" expecting "</body>" at line 111 column 12HTML_NOT_WELL_FORMED
output/searchform.html
warning
The html source is not well formed: Found "</div>" expecting "</body>" at line 112 column 20HTML_NOT_WELL_FORMED
output/searchform.html
warning
The html source is not well formed: Found "</div>" expecting "</body>" at line 113 column 16HTML_NOT_WELL_FORMED
output/searchform.html
warning
The html source is not well formed: Found "</div>" expecting "</body>" at line 115 column 12HTML_NOT_WELL_FORMED
sequencing.html
information
The html source contains the word 'MAY' but it is not in a text phrase marked as a conformance clause: 'For each variant reporting pattern, different components MUST be used to properly define the variant where possible. Other components MAY be used to provide additional information for cross referencing external sources or increasing human readability of the instance.'CONFORMANCE_STATEMENT_WORD
The resource CodeSystem/clinvar-evidence-level-custom-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/coded-annotation-types-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/genomic-study-change-type-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/genomic-study-data-format-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/genomic-study-method-type-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/genomic-study-status-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/genomic-study-type-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/knowledge-base-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/molecular-biomarker-ontology-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/pharmgkb-evidence-level-custom-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/sequence-phase-relationship-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/tbd-codes-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource CodeSystem/variant-confidence-status-cs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
A definition for the code system 'http://example.org/hgsc.bcm.edu/lab-test-codes/' could not be found, so this coding was not checked. The CodeableConcept is still valid: another coding is in the value set (from https://tx.fhir.org/r4, see log, or see the servers logic) UNKNOWN_CODESYSTEM_CODING_NOT_CHECKED
0ms tx-op
0ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Analysing http://hl7.org/fhir/ValueSet/report-codes|4.0.1 for validation purposes
0ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Parameters: disp-lang=en-US, generate-narrative, default-to-latest
0ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Prepare include[0]: "(http://loinc.org)"
2ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: CodeSystem found: "http://loinc.org|2.83"
2ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Validate "[http://loinc.org#51969-4 ("undefined"), http://example.org/hgsc.bcm.edu/lab-test-codes/#emerge-seq-ngs-pnl ("undefined")]"
4ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Check "http://loinc.org#51969-4"
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: CodeSystem found: http://loinc.org|2.83 for http://loinc.org
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: check code in (http://loinc.org) at CodeableConcept.coding[0]
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Code "51969-4" found in http://loinc.org|2.83
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Check "http://example.org/hgsc.bcm.edu/lab-test-codes/#emerge-seq-ngs-pnl"
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Include for http://loinc.org not considered for "http://example.org/hgsc.bcm.edu/lab-test-codes/"
A definition for the code system 'http://example.org/hgsc.bcm.edu/lab-test-codes/' could not be found, so this coding was not checked. The CodeableConcept is still valid: another coding is in the value set (from https://tx.fhir.org/r4, see log, or see the servers logic) UNKNOWN_CODESYSTEM_CODING_NOT_CHECKED
0ms tx-op
0ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Analysing http://hl7.org/fhir/ValueSet/report-codes|4.0.1 for validation purposes
0ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Parameters: disp-lang=en-US, generate-narrative, default-to-latest
0ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Prepare include[0]: "(http://loinc.org)"
2ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: CodeSystem found: "http://loinc.org|2.83"
2ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Validate "[http://loinc.org#51969-4 ("undefined"), http://example.org/hgsc.bcm.edu/lab-test-codes/#emerge-seq-ngs-pnl ("undefined")]"
4ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Check "http://loinc.org#51969-4"
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: CodeSystem found: http://loinc.org|2.83 for http://loinc.org
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: check code in (http://loinc.org) at CodeableConcept.coding[0]
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Code "51969-4" found in http://loinc.org|2.83
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Check "http://example.org/hgsc.bcm.edu/lab-test-codes/#emerge-seq-ngs-pnl"
7ms http://hl7.org/fhir/ValueSet/report-codes|4.0.1: Include for http://loinc.org not considered for "http://example.org/hgsc.bcm.edu/lab-test-codes/"
Wrong Display Name 'HER2 [Units/volume] in Tissue by Immunoassay' for http://loinc.org#72382-5. Valid display is one of 3 choices: 'HER2 Ag [Units/volume] in Tissue by Immunoassay' (en-US), 'HER2 Ag [Units/volume] in Tissue by Immunoassay' (en-US) or 'Her2 Ag Tiss IA-aCnc' (en-US) (for the language(s) 'en-US') (from https://tx.fhir.org/r4, see log, or see the servers logic) Display_Name_for__should_be_one_of__instead_of
0ms tx-op
2ms http://loinc.org/vs|2.83: Validate "[http://loinc.org#72382-5 ("HER2 [Units/volume] in Tissue by Immunoassay")]"
4ms http://loinc.org/vs|2.83: Check "http://loinc.org#72382-5"
7ms http://loinc.org/vs|2.83: CodeSystem found: http://loinc.org|2.83 for http://loinc.org|2.83
7ms http://loinc.org/vs|2.83: check code in (http://loinc.org) at CodeableConcept.coding[0]
7ms http://loinc.org/vs|2.83: Code "72382-5" found in http://loinc.org|2.83
The resource ValueSet/coded-annotation-types-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The concepts in the value set include have not been validated because the code system 'http://human-phenotype-ontology.org' is not known, and no terminology service supports itVALUESET_INC_CS_NO_SUPPORT
--
Resource
error
The resource ValueSet/condition-inheritance-mode-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
Error from https://tx.fhir.org/r4: Error: A definition for CodeSystem 'http://human-phenotype-ontology.org' could not be found, so the value set cannot be expanded (from server, see log)
The resource ValueSet/dna-change-type-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
--
ValueSet.where(id = 'dna-change-type-vs')
warning
Error from https://tx.fhir.org/r4: Error: A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the value set cannot be expanded (from server, see log)
The resource ValueSet/evidence-level-example-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/functional-effect-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
--
ValueSet.where(id = 'functional-effect-vs')
warning
Error from https://tx.fhir.org/r4: Error: A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the value set cannot be expanded (from server, see log)
The resource ValueSet/genetic-therapeutic-implications-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/genomic-study-change-type-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
Error from https://tx.fhir.org/r4: Error: A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the value set cannot be expanded (from server, see log)
The resource ValueSet/genomic-study-data-format-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/genomic-study-method-type-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/genomic-study-status-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/genomic-study-type-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/hgnc-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
--
ValueSet.where(id = 'hgnc-vs')
warning
Error from https://tx.fhir.org/r4: Error: A definition for CodeSystem 'http://www.genenames.org' could not be found, so the value set cannot be expanded (from server, see log)
The resource ValueSet/hgvs-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
--
ValueSet.where(id = 'hgvs-vs')
warning
Error from https://tx.fhir.org/r4: Error: The code system 'http://varnomen.hgvs.org' cannot be expanded because its codes cannot be iterated or enumerated in any meaningful sense (from server, see log)
The resource ValueSet/knowledge-base-version-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/molecular-biomarker-category-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
Wrong Display Name 'HER2 [Units/volume] in Tissue by Immunoassay' for http://loinc.org#72382-5. Valid display is one of 3 choices: 'HER2 Ag [Units/volume] in Tissue by Immunoassay' (en-US), 'HER2 Ag [Units/volume] in Tissue by Immunoassay' (en-US) or 'Her2 Ag Tiss IA-aCnc' (en-US) (for the language(s) 'en-US'). Note that the display in the ValueSet does not have to match; this check exists to help check that it's not accidentally the wrong codeVALUESET_CODE_CONCEPT_HINT
--
Resource
error
The resource ValueSet/molecular-biomarker-code-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/molecular-consequence-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
--
ValueSet.where(id = 'molecular-consequence-vs')
warning
Error from https://tx.fhir.org/r4: Error: A definition for CodeSystem 'http://www.sequenceontology.org' could not be found, so the value set cannot be expanded (from server, see log)
The resource ValueSet/sequence-phase-relationship-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/tbd-codes-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
The resource ValueSet/variant-confidence-status-vs must have an OID assigned to cater for possible use with OID based terminology systems e.g. CDA usage (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/ig-guidance/oids.html)
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 (0 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) (12 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) (281 uses)
Pinned versions have been reviewed:
Pinned the version of http://hl7.org/fhir/StructureDefinition/% (44 uses)
Suppress all references to example CodeSystems
A definition for CodeSystem 'http://example.org/% (9 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% (94 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 (9 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 (0 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 (0 uses)
This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication|4.0.0-cibuild (this may not be a problem, but you should check that it's not intended to match a slice)
This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication|4.0.0-cibuild (this may not be a problem, but you should check that it's not intended to match a slice)
This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication|4.0.0-cibuild (this may not be a problem, but you should check that it's not intended to match a slice)
Wrong Display Name 'HER2 [Units/volume] in Tissue by Immunoassay' for http://loinc.org#72382-5. Valid display is one of 3 choices: 'HER2 Ag [Units/volume] in Tissue by Immunoassay' (en-US), 'HER2 Ag [Units/volume] in Tissue by Immunoassay' (en-US) or 'Her2 Ag Tiss IA-aCnc' (en-US) (for the language(s) 'en-US')
The extension http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet|5.4.0 is deprecated with the note: 'Use additionalBinding extension or element instead'
The extension http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding|5.4.0 is deprecated with the note: 'This extension is deprecated - use the [[[http://hl7.org/fhir/StructureDefinition/observation-structure-type]]] instead'
The extension http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database|5.4.0 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|5.4.0 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/)'
A definition for the code system 'http://example.org/hgsc.bcm.edu/lab-test-codes/' could not be found, so this coding was not checked. The CodeableConcept is still valid: another coding is in the value set
A definition for the code system 'http://example.org/hgsc.bcm.edu/lab-test-codes/' could not be found, so this coding was not checked. The CodeableConcept is still valid: another coding is in the value set
Wrong Display Name 'HER2 [Units/volume] in Tissue by Immunoassay' for http://loinc.org#72382-5. Valid display is one of 3 choices: 'HER2 Ag [Units/volume] in Tissue by Immunoassay' (en-US), 'HER2 Ag [Units/volume] in Tissue by Immunoassay' (en-US) or 'Her2 Ag Tiss IA-aCnc' (en-US) (for the language(s) 'en-US'). Note that the display in the ValueSet does not have to match; this check exists to help check that it's not accidentally the wrong code
The concepts in the value set include have not been validated because the code system 'http://human-phenotype-ontology.org' is not known, and no terminology service supports it
hl7.fhir.uv.genomics-reporting
hl7.fhir.uv.tools.r4