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Resource CodeSystem/FHIR Server from package hl7.fhir.uv.genomics-reporting#current (78 ms)

Package hl7.fhir.uv.genomics-reporting
Type CodeSystem
Id Id
FHIR Version R4
Source http://hl7.org/fhir/uv/genomics-reporting/https://build.fhir.org/ig/HL7/genomics-reporting/CodeSystem-tbd-codes-cs.html
Url http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
Version 3.0.1-SNAPSHOT
Status active
Date 2024-10-03T13:33:58+00:00
Name TbdCodesCS
Title To Be Determined Codes
Experimental True
Realm uv
Authority hl7
Description These codes are 'TBD' codes, meaning they are important concepts but codes have not been identifed in available code systems. The CG WG anticpates these codes maturing over time. We may remove some codes as we refine the concepts, or identify suitable replacement codes from other code systems. As we approach normative and these concepts are validated, for codes that remain, we plan to request formal LOINC codes to replace these temporary codes.
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Resources that use this resource

ValueSet
tbd-codes-vs To Be Determined Value Set

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Narrative

Note: links and images are rebased to the (stated) source

Generated Narrative: CodeSystem tbd-codes-cs

This case-sensitive code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs defines the following codes:

CodeDisplayDefinition
associated-therapy Associated TherapyThe non-medication therapy (procedure) associated with this implication.
molecular-consequence Molecular ConsequenceThe calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence.
feature-consequence Feature ConsequenceThe structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion).
diagnostic-implication Diagnostic ImplicationAn observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition.
therapeutic-implication Therapeutic ImplicationAn observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy. Ramifications may include alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time; alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration; alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies.
functional-effect Functional EffectThe effect of a variant on downstream biological products or pathways (from Sequence Ontology).
conclusion-string Conclusion TextClinical conclusion (interpretation) of the observation.
condition-inheritance Condition InheritanceThe transmission pattern of the condition/phenotype in a pedigree.
variant-confidence-status Variant Confidence StatusThe confidence of a true positive variant call.
repeat-motif Repeat Expansion MotifNucleotides of a repeat expansion motif.
repeat-number Number of Repeat ExpansionsNumber of repeats of a repeat expansion.
biomarker-category A characterization of a given biomarker observation.
protein-ref-seq An identifier for the protein reference sequence.

Source

{
  "resourceType" : "CodeSystem",
  "id" : "tbd-codes-cs",
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem tbd-codes-cs</b></p><a name=\"tbd-codes-cs\"> </a><a name=\"hctbd-codes-cs\"> </a><a name=\"tbd-codes-cs-en-US\"> </a><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">associated-therapy<a name=\"tbd-codes-cs-associated-therapy\"> </a></td><td>Associated Therapy</td><td>The non-medication therapy (procedure) associated with this implication.</td></tr><tr><td style=\"white-space:nowrap\">molecular-consequence<a name=\"tbd-codes-cs-molecular-consequence\"> </a></td><td>Molecular Consequence</td><td>The calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence.</td></tr><tr><td style=\"white-space:nowrap\">feature-consequence<a name=\"tbd-codes-cs-feature-consequence\"> </a></td><td>Feature Consequence</td><td>The structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion).</td></tr><tr><td style=\"white-space:nowrap\">diagnostic-implication<a name=\"tbd-codes-cs-diagnostic-implication\"> </a></td><td>Diagnostic Implication</td><td>An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition.</td></tr><tr><td style=\"white-space:nowrap\">therapeutic-implication<a name=\"tbd-codes-cs-therapeutic-implication\"> </a></td><td>Therapeutic Implication</td><td>An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy. Ramifications may include alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time; alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration; alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies.</td></tr><tr><td style=\"white-space:nowrap\">functional-effect<a name=\"tbd-codes-cs-functional-effect\"> </a></td><td>Functional Effect</td><td>The effect of a variant on downstream biological products or pathways (from Sequence Ontology).</td></tr><tr><td style=\"white-space:nowrap\">conclusion-string<a name=\"tbd-codes-cs-conclusion-string\"> </a></td><td>Conclusion Text</td><td>Clinical conclusion (interpretation) of the observation.</td></tr><tr><td style=\"white-space:nowrap\">condition-inheritance<a name=\"tbd-codes-cs-condition-inheritance\"> </a></td><td>Condition Inheritance</td><td>The transmission pattern of the condition/phenotype in a pedigree.</td></tr><tr><td style=\"white-space:nowrap\">variant-confidence-status<a name=\"tbd-codes-cs-variant-confidence-status\"> </a></td><td>Variant Confidence Status</td><td>The confidence of a true positive variant call.</td></tr><tr><td style=\"white-space:nowrap\">repeat-motif<a name=\"tbd-codes-cs-repeat-motif\"> </a></td><td>Repeat Expansion Motif</td><td>Nucleotides of a repeat expansion motif.</td></tr><tr><td style=\"white-space:nowrap\">repeat-number<a name=\"tbd-codes-cs-repeat-number\"> </a></td><td>Number of Repeat Expansions</td><td>Number of repeats of a repeat expansion.</td></tr><tr><td style=\"white-space:nowrap\">biomarker-category<a name=\"tbd-codes-cs-biomarker-category\"> </a></td><td>A characterization of a given biomarker observation.</td><td/></tr><tr><td style=\"white-space:nowrap\">protein-ref-seq<a name=\"tbd-codes-cs-protein-ref-seq\"> </a></td><td>An identifier for the protein reference sequence.</td><td/></tr></table></div>"
  },
  "extension" : [
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
      "valueCode" : "cg"
    }
  ],
  "url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
  "version" : "3.0.1-SNAPSHOT",
  "name" : "TbdCodesCS",
  "title" : "To Be Determined Codes",
  "status" : "active",
  "experimental" : true,
  "date" : "2024-10-03T13:33:58+00:00",
  "publisher" : "HL7 International / Clinical Genomics",
  "contact" : [
    {
      "name" : "HL7 International / Clinical Genomics",
      "telecom" : [
        {
          "system" : "url",
          "value" : "http://www.hl7.org/Special/committees/clingenomics"
        },
        {
          "system" : "email",
          "value" : "cg@lists.HL7.org"
        }
      ]
    }
  ],
  "description" : "These codes are 'TBD' codes, meaning they are important concepts but codes have not been identifed in available code systems. The CG WG anticpates these codes maturing over time. We may remove some codes as we refine the concepts, or identify suitable replacement codes from other code systems. As we approach normative and these concepts are validated, for codes that remain, we plan to request formal LOINC codes to replace these temporary codes.",
  "jurisdiction" : [
    {
      "coding" : [
        {
          "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code" : "001",
          "display" : "World"
        }
      ]
    }
  ],
  "caseSensitive" : true,
  "content" : "complete",
  "count" : 13,
  "concept" : [
    {
      "code" : "associated-therapy",
      "display" : "Associated Therapy",
      "definition" : "The non-medication therapy (procedure) associated with this implication."
    },
    {
      "code" : "molecular-consequence",
      "display" : "Molecular Consequence",
      "definition" : "The calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence."
    },
    {
      "code" : "feature-consequence",
      "display" : "Feature Consequence",
      "definition" : "The structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion)."
    },
    {
      "code" : "diagnostic-implication",
      "display" : "Diagnostic Implication",
      "definition" : "An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition."
    },
    {
      "code" : "therapeutic-implication",
      "display" : "Therapeutic Implication",
      "definition" : "An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy. Ramifications may include alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time; alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration; alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies."
    },
    {
      "code" : "functional-effect",
      "display" : "Functional Effect",
      "definition" : "The effect of a variant on downstream biological products or pathways (from Sequence Ontology)."
    },
    {
      "code" : "conclusion-string",
      "display" : "Conclusion Text",
      "definition" : "Clinical conclusion (interpretation) of the observation."
    },
    {
      "code" : "condition-inheritance",
      "display" : "Condition Inheritance",
      "definition" : "The transmission pattern of the condition/phenotype in a pedigree."
    },
    {
      "code" : "variant-confidence-status",
      "display" : "Variant Confidence Status",
      "definition" : "The confidence of a true positive variant call."
    },
    {
      "code" : "repeat-motif",
      "display" : "Repeat Expansion Motif",
      "definition" : "Nucleotides of a repeat expansion motif."
    },
    {
      "code" : "repeat-number",
      "display" : "Number of Repeat Expansions",
      "definition" : "Number of repeats of a repeat expansion."
    },
    {
      "code" : "biomarker-category",
      "display" : "A characterization of a given biomarker observation."
    },
    {
      "code" : "protein-ref-seq",
      "display" : "An identifier for the protein reference sequence."
    }
  ]
}

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