Generated Mon Dec 18 22:54:57 UTC 2023, FHIR version 4.0.1 for hl7.fhir.uv.genomics-reporting#3.0.0-ballot (canonical = http://hl7.org/fhir/uv/genomics-reporting (history)). See Errors Only
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Publisher Version: | IG Publisher Version: v1.5.8 | ||||||||||||||||||||||||
Publication Code: | genomics-reporting . PackageId = hl7.fhir.uv.genomics-reporting, Canonical = http://hl7.org/fhir/uv/genomics-reporting | ||||||||||||||||||||||||
Realm Check for UV: |
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Publication Request: |
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Supressed Messages: | 51 Suppressed Issues | ||||||||||||||||||||||||
Dependency Checks: |
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Dependent IGs: | no references | ||||||||||||||||||||||||
Global Profiles: | (none declared) | ||||||||||||||||||||||||
HTA Analysis: | All OK | ||||||||||||||||||||||||
R5 Dependencies: | (none) | ||||||||||||||||||||||||
Draft Dependencies: |
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Modifier Extensions: | (none) | ||||||||||||||||||||||||
Previous Version Comparison: | Comparison with version 2.0.0 | ||||||||||||||||||||||||
IPA Comparison: | n/a | ||||||||||||||||||||||||
IPS Comparison: | n/a | ||||||||||||||||||||||||
Summary: | errors = 0, warn = 1, info = 2, broken links = 0 |
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Path | Severity | Message |
Bundle.entry[12].resource/*Observation/Inline-Instance-for-oncologyexamples-r4-14*/.component[0].extension[0] (l1324/c16) | Slicing Information | This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication|3.0.0-ballot (this may not be a problem, but you should check that it's not intended to match a slice) Show Reasoning |
Path | Severity | Message |
Bundle.entry[8].resource/*Observation/Inline-Instance-for-oncologyexamples-r4-withGrouping-9*/.component[3].extension[0] (l823/c16) | Slicing Information | This element does not match any known slice defined in the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication|3.0.0-ballot (this may not be a problem, but you should check that it's not intended to match a slice) Show Reasoning |
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Path | Severity | Message |
ValueSet.compose.include[0] | warning | Unknown System 'http://human-phenotype-ontology.org' specified, so Concepts and Filters can't be checked (Details: Resolved system http://human-phenotype-ontology.org (v1.0.0), but the definition doesn't include any codes, so the code has not been validated) |
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Suppressed Messages (Warnings, hints, broken links)
An example of DiagnosticImplication<Observation>.derivedFrom() that we slice to only allow our profiles. In this example, we did not define specific Variant instances and just refer to some variants by identifier (rather than a full resource), so ignoring these warnings
Code Systems for diseases - MONDO - https://terminology.hl7.org/CodeSystem-MONDO.html
Code has been checked and are correct
CodeSystem and ValueSets - dbSNP - https://terminology.hl7.org/CodeSystem-v3-dbSNP.html
CodeSystem and ValueSets - gtr - https://terminology.hl7.org/CodeSystem-GTR.html
CodeSystem and ValueSets - refseq - https://terminology.hl7.org/CodeSystem-v3-refSeq.html
CodeSystems and ValueSets - ISCN - https://terminology.hl7.org/CodeSystem-ISCN.html
CodeSystems and ValueSets - imgt HLA alleles - https://jira.hl7.org/browse/HTA-127.
CodeSystems and ValueSets not supported yet - clinvar - https://terminology.hl7.org/CodeSystem-ClinVarV.html
CodeSystems and ValueSets not supported yet -- clinicaltrials - https://jira.hl7.org/browse/HTA-126
CodeSystems and ValueSets not supported yet -- glstring - https://jira.hl7.org/browse/HTA-84
CodeSystems and ValueSets not supported yet -- https://terminology.hl7.org/CodeSystem-v3-hgnc.html
CodeSystems and ValueSets not supported yet -- human-phenotype-ontology - https://terminology.hl7.org/CodeSystem-HPO.html
CodeSystems and ValueSets not supported yet -- pharmvar - https://jira.hl7.org/browse/HTA-85
CodeSystems and ValueSets not supported yet -- sequenceontology - https://jira.hl7.org/browse/HTA-37 (should be in THO soon)
GenomicReport<DiagnosticReport>.result referencing Observation instances. We have defined our report profile to slice .result with our Observation profiles. We allow slicing, so we can ignore informational message
Observation.component instances that do not match our slices, but is OK (and this is ok since we use open slicing)
Our Observation profiles require a code from the Observation Category value set (LAB), but in some cases require additional codes from other value sets. Since this binding is "Preferred" the resources are still conformant, so we are supressing these messages.
These slice messages that have been reviewed. Each of these refer to (via derivedFrom) a Variant, and it seems it is a valid Variant instance. So, not clear why it does not match a known slice:
This is a publisher induced issue. The extension in question is introduced by the publisher. See https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/New.20ConceptMap.20Warning.20--.20induced.20by.20IG.20Publisher
the 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.
Errors sorted by type