Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions
| Active as of 2024-12-12 |
JSON representation of the genomic-study-analysis-metrics extension.
{
"resourceType" : "StructureDefinition",
"id" : "genomic-study-analysis-metrics",
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: StructureDefinition genomic-study-analysis-metrics</b></p><a name=\"genomic-study-analysis-metrics\"> </a><a name=\"hcgenomic-study-analysis-metrics\"> </a><a name=\"genomic-study-analysis-metrics-en-US\"> </a><table border=\"0\" cellpadding=\"0\" cellspacing=\"0\" style=\"border: 0px #F0F0F0 solid; font-size: 11px; font-family: verdana; vertical-align: top;\"><tr style=\"border: 1px #F0F0F0 solid; font-size: 11px; font-family: verdana; vertical-align: top\"><th style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a href=\"https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views\" title=\"The logical name of the element\">Name</a></th><th style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a href=\"https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views\" title=\"Information about the use of the element\">Flags</a></th><th style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a href=\"https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views\" title=\"Minimum and Maximum # of times the element can appear in the instance\">Card.</a></th><th style=\"width: 100px\" class=\"hierarchy\"><a href=\"https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views\" title=\"Reference to the type of the element\">Type</a></th><th style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a href=\"https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views\" title=\"Additional information about the element\">Description & Constraints</a><span style=\"float: right\"><a href=\"https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views\" title=\"Legend for this format\"><img src=\"data:image/png;base64,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\" alt=\"doco\" style=\"background-color: inherit\"/></a></span></th></tr><tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white\"><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_element.gif\" alt=\".\" style=\"background-color: white; background-color: inherit\" title=\"Element\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension\" title=\"Metrics about the sequencing analysis that was performed\">Extension</a><a name=\"Extension\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"opacity: 0.5\">0</span><span style=\"opacity: 0.5\">..</span><span style=\"opacity: 0.5\">*</span></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a href=\"http://hl7.org/fhir/R4/extensibility.html#Extension\">Extension</a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">Genomic Study Analysis Metrics</td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7\"><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck13.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_slice.png\" alt=\".\" style=\"background-color: #F7F7F7; background-color: inherit\" title=\"Slice Definition\" class=\"hierarchy\"/> Slices for extension<a name=\"Extension.extension\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">Content/Rules for all slices</td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white\"><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck135.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_slicer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_slice_item.png\" alt=\".\" style=\"background-color: white; background-color: inherit\" title=\"Slice Item\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:read-depth\" title=\"Slice read-depth: The average read depth (number of reads for a position) for the sequencing test\">extension:read-depth</a><a name=\"Extension.extension.2\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">0..1</td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a style=\"opacity: 0.5\" href=\"http://hl7.org/fhir/R4/extensibility.html#Extension\">Extension</a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">Read Depth</td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7\"><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1350.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline_slicer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_slice.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_extension_simple.png\" alt=\".\" style=\"background-color: #F7F7F7; background-color: inherit\" title=\"Simple Extension\" class=\"hierarchy\"/> <span style=\"text-decoration:line-through\">extension</span><a name=\"Extension.extension.extension\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"text-decoration:line-through\"/><span style=\"text-decoration:line-through\">0</span><span style=\"text-decoration:line-through\">..</span><span style=\"text-decoration:line-through\">0</span></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white\"><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1350.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline_slicer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_slice.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_element.gif\" alt=\".\" style=\"background-color: white; background-color: inherit\" title=\"Element\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:read-depth.url\">url</a><a name=\"Extension.extension.url\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"opacity: 0.5\">1</span><span style=\"opacity: 0.5\">..</span><span style=\"opacity: 0.5\">1</span></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a style=\"opacity: 0.5\" href=\"http://hl7.org/fhir/R4/datatypes.html#uri\">uri</a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"color: darkgreen\">"read-depth"</span></td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7\"><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1340.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline_slicer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_end_slice.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_datatype.gif\" alt=\".\" style=\"background-color: #F7F7F7; background-color: inherit\" title=\"Data Type\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:read-depth.value[x]\">value[x]</a><a name=\"Extension.extension.value_x_\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"opacity: 0.5\">0</span><span style=\"opacity: 0.5\">..</span><span style=\"opacity: 0.5\">1</span></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a href=\"http://hl7.org/fhir/R4/datatypes.html#SimpleQuantity\" title=\"Quantity\">SimpleQuantity</a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">30, 100</td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white\"><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck135.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_slicer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_slice_item.png\" alt=\".\" style=\"background-color: white; background-color: inherit\" title=\"Slice Item\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:sequencing-coverage\" title=\"Slice sequencing-coverage: The percentage of the studied regions that were sequenced\">extension:sequencing-coverage</a><a name=\"Extension.extension.3\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">0..1</td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a style=\"opacity: 0.5\" href=\"http://hl7.org/fhir/R4/extensibility.html#Extension\">Extension</a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">Sequencing Coverage</td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7\"><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1350.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline_slicer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_slice.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_extension_simple.png\" alt=\".\" style=\"background-color: #F7F7F7; background-color: inherit\" title=\"Simple Extension\" class=\"hierarchy\"/> <span style=\"text-decoration:line-through\">extension</span><a name=\"Extension.extension.extension.2\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"text-decoration:line-through\"/><span style=\"text-decoration:line-through\">0</span><span style=\"text-decoration:line-through\">..</span><span style=\"text-decoration:line-through\">0</span></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white\"><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1350.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline_slicer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_slice.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_element.gif\" alt=\".\" style=\"background-color: white; background-color: inherit\" title=\"Element\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:sequencing-coverage.url\">url</a><a name=\"Extension.extension.url.2\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"opacity: 0.5\">1</span><span style=\"opacity: 0.5\">..</span><span style=\"opacity: 0.5\">1</span></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a style=\"opacity: 0.5\" href=\"http://hl7.org/fhir/R4/datatypes.html#uri\">uri</a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"color: darkgreen\">"sequencing-coverage"</span></td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7\"><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1340.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline_slicer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_end_slice.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_datatype.gif\" alt=\".\" style=\"background-color: #F7F7F7; background-color: inherit\" title=\"Data Type\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:sequencing-coverage.value[x]\">value[x]</a><a name=\"Extension.extension.value_x_.2\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"opacity: 0.5\">0</span><span style=\"opacity: 0.5\">..</span><span style=\"opacity: 0.5\">1</span></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a href=\"http://hl7.org/fhir/R4/datatypes.html#SimpleQuantity\" title=\"Quantity\">SimpleQuantity</a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">95, 100</td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white\"><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck125.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_end_slicer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_slice_item.png\" alt=\".\" style=\"background-color: white; background-color: inherit\" title=\"Slice Item\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:metrics-description\" title=\"Slice metrics-description: Freetext description of the coverage metrics for the sequencing test\">extension:metrics-description</a><a name=\"Extension.extension.4\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">0..1</td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a style=\"opacity: 0.5\" href=\"http://hl7.org/fhir/R4/extensibility.html#Extension\">Extension</a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\">Metrics Description</td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7\"><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1250.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_blank.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_slice.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_extension_simple.png\" alt=\".\" style=\"background-color: #F7F7F7; background-color: inherit\" title=\"Simple Extension\" class=\"hierarchy\"/> <span style=\"text-decoration:line-through\">extension</span><a name=\"Extension.extension.extension.3\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"text-decoration:line-through\"/><span style=\"text-decoration:line-through\">0</span><span style=\"text-decoration:line-through\">..</span><span style=\"text-decoration:line-through\">0</span></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white\"><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1250.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_blank.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_slice.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_element.gif\" alt=\".\" style=\"background-color: white; background-color: inherit\" title=\"Element\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:metrics-description.url\">url</a><a name=\"Extension.extension.url.3\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"opacity: 0.5\">1</span><span style=\"opacity: 0.5\">..</span><span style=\"opacity: 0.5\">1</span></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a style=\"opacity: 0.5\" href=\"http://hl7.org/fhir/R4/datatypes.html#uri\">uri</a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"color: darkgreen\">"metrics-description"</span></td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7\"><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1240.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vline.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_blank.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_end_slice.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_primitive.png\" alt=\".\" style=\"background-color: #F7F7F7; background-color: inherit\" title=\"Primitive Data Type\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:metrics-description.value[x]\">value[x]</a><a name=\"Extension.extension.value_x_.3\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"opacity: 0.5\">0</span><span style=\"opacity: 0.5\">..</span><span style=\"opacity: 0.5\">1</span></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"opacity: 0.5\">Value of extension</span></td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white\"><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck10.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_element.gif\" alt=\".\" style=\"background-color: white; background-color: inherit\" title=\"Element\" class=\"hierarchy\"/> <a href=\"StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.url\">url</a><a name=\"Extension.url\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"opacity: 0.5\">1</span><span style=\"opacity: 0.5\">..</span><span style=\"opacity: 0.5\">1</span></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><a style=\"opacity: 0.5\" href=\"http://hl7.org/fhir/R4/datatypes.html#uri\">uri</a></td><td style=\"vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"color: darkgreen\">"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"</span></td></tr>\r\n<tr style=\"border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7\"><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck00.png)\" class=\"hierarchy\"><img src=\"tbl_spacer.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"tbl_vjoin_end.png\" alt=\".\" style=\"background-color: inherit\" class=\"hierarchy\"/><img src=\"icon_element.gif\" alt=\".\" style=\"background-color: #F7F7F7; background-color: inherit\" title=\"Element\" class=\"hierarchy\"/> <span style=\"text-decoration:line-through\">value[x]</span><a name=\"Extension.value_x_\"> </a></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"><span style=\"text-decoration:line-through\"/><span style=\"text-decoration:line-through\">0</span><span style=\"text-decoration:line-through\">..</span><span style=\"text-decoration:line-through\">0</span></td><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/><td style=\"vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px\" class=\"hierarchy\"/></tr>\r\n<tr><td colspan=\"5\" class=\"hierarchy\"><br/><a href=\"https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views\" title=\"Legend for this format\"><img src=\"data:image/png;base64,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\" alt=\"doco\" style=\"background-color: inherit\"/> Documentation for this format</a></td></tr></table></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "cg"
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics",
"version" : "3.0.0",
"name" : "GenomicStudyAnalysisMetrics",
"title" : "Genomic Study Analysis Metrics",
"status" : "active",
"date" : "2024-12-12T20:43:36+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" : "Metrics about the sequencing analysis that was performed",
"jurisdiction" : [
{
"coding" : [
{
"system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001",
"display" : "World"
}
]
}
],
"fhirVersion" : "4.0.1",
"mapping" : [
{
"identity" : "rim",
"uri" : "http://hl7.org/v3",
"name" : "RIM Mapping"
}
],
"kind" : "complex-type",
"abstract" : false,
"context" : [
{
"type" : "element",
"expression" : "Procedure"
}
],
"type" : "Extension",
"baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Extension",
"derivation" : "constraint",
"snapshot" : {
"element" : [
{
"id" : "Extension",
"path" : "Extension",
"short" : "Genomic Study Analysis Metrics",
"definition" : "Metrics about the sequencing analysis that was performed",
"min" : 0,
"max" : "*",
"base" : {
"path" : "Extension",
"min" : 0,
"max" : "*"
},
"condition" : [
"ele-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false
},
{
"id" : "Extension.id",
"path" : "Extension.id",
"representation" : [
"xmlAttr"
],
"short" : "Unique id for inter-element referencing",
"definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.id",
"min" : 0,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "string"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension",
"path" : "Extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"description" : "Extensions are always sliced by (at least) url",
"rules" : "open"
},
"short" : "Additional content defined by implementations",
"definition" : "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment" : "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias" : [
"extensions",
"user content"
],
"min" : 0,
"max" : "*",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:read-depth",
"path" : "Extension.extension",
"sliceName" : "read-depth",
"short" : "Read Depth",
"definition" : "The average read depth (number of reads for a position) for the sequencing test",
"requirements" : "This value is typically represented with an 'x' after the number (30x). Simply share the quantity here.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false
},
{
"id" : "Extension.extension:read-depth.id",
"path" : "Extension.extension.id",
"representation" : [
"xmlAttr"
],
"short" : "Unique id for inter-element referencing",
"definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.id",
"min" : 0,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "string"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:read-depth.extension",
"path" : "Extension.extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"description" : "Extensions are always sliced by (at least) url",
"rules" : "open"
},
"short" : "Extension",
"definition" : "An Extension",
"min" : 0,
"max" : "0",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false
},
{
"id" : "Extension.extension:read-depth.url",
"path" : "Extension.extension.url",
"representation" : [
"xmlAttr"
],
"short" : "identifies the meaning of the extension",
"definition" : "Source of the definition for the extension code - a logical name or a URL.",
"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
"base" : {
"path" : "Extension.url",
"min" : 1,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "uri"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri" : "read-depth",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:read-depth.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "30, 100",
"definition" : "The comparator is not used on a SimpleQuantity",
"comment" : "The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "Quantity",
"profile" : [
🔗 "http://hl7.org/fhir/StructureDefinition/SimpleQuantity"
]
}
],
"condition" : [
"ele-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "qty-3",
"severity" : "error",
"human" : "If a code for the unit is present, the system SHALL also be present",
"expression" : "code.empty() or system.exists()",
"xpath" : "not(exists(f:code)) or exists(f:system)",
"source" : "http://hl7.org/fhir/StructureDefinition/Quantity"
},
{
"key" : "sqty-1",
"severity" : "error",
"human" : "The comparator is not used on a SimpleQuantity",
"expression" : "comparator.empty()",
"xpath" : "not(exists(f:comparator))",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
},
{
"identity" : "v2",
"map" : "SN (see also Range) or CQ"
},
{
"identity" : "rim",
"map" : "PQ, IVL<PQ>, MO, CO, depending on the values"
}
]
},
{
"id" : "Extension.extension:sequencing-coverage",
"path" : "Extension.extension",
"sliceName" : "sequencing-coverage",
"short" : "Sequencing Coverage",
"definition" : "The percentage of the studied regions that were sequenced",
"requirements" : "This value is typically represented with an '%' after the number (95%). Simply share the quantity here.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false
},
{
"id" : "Extension.extension:sequencing-coverage.id",
"path" : "Extension.extension.id",
"representation" : [
"xmlAttr"
],
"short" : "Unique id for inter-element referencing",
"definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.id",
"min" : 0,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "string"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:sequencing-coverage.extension",
"path" : "Extension.extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"description" : "Extensions are always sliced by (at least) url",
"rules" : "open"
},
"short" : "Extension",
"definition" : "An Extension",
"min" : 0,
"max" : "0",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false
},
{
"id" : "Extension.extension:sequencing-coverage.url",
"path" : "Extension.extension.url",
"representation" : [
"xmlAttr"
],
"short" : "identifies the meaning of the extension",
"definition" : "Source of the definition for the extension code - a logical name or a URL.",
"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
"base" : {
"path" : "Extension.url",
"min" : 1,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "uri"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri" : "sequencing-coverage",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:sequencing-coverage.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "95, 100",
"definition" : "The comparator is not used on a SimpleQuantity",
"comment" : "The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "Quantity",
"profile" : [
🔗 "http://hl7.org/fhir/StructureDefinition/SimpleQuantity"
]
}
],
"condition" : [
"ele-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "qty-3",
"severity" : "error",
"human" : "If a code for the unit is present, the system SHALL also be present",
"expression" : "code.empty() or system.exists()",
"xpath" : "not(exists(f:code)) or exists(f:system)",
"source" : "http://hl7.org/fhir/StructureDefinition/Quantity"
},
{
"key" : "sqty-1",
"severity" : "error",
"human" : "The comparator is not used on a SimpleQuantity",
"expression" : "comparator.empty()",
"xpath" : "not(exists(f:comparator))",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
},
{
"identity" : "v2",
"map" : "SN (see also Range) or CQ"
},
{
"identity" : "rim",
"map" : "PQ, IVL<PQ>, MO, CO, depending on the values"
}
]
},
{
"id" : "Extension.extension:metrics-description",
"path" : "Extension.extension",
"sliceName" : "metrics-description",
"short" : "Metrics Description",
"definition" : "Freetext description of the coverage metrics for the sequencing test",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false
},
{
"id" : "Extension.extension:metrics-description.id",
"path" : "Extension.extension.id",
"representation" : [
"xmlAttr"
],
"short" : "Unique id for inter-element referencing",
"definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.id",
"min" : 0,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "string"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:metrics-description.extension",
"path" : "Extension.extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"description" : "Extensions are always sliced by (at least) url",
"rules" : "open"
},
"short" : "Extension",
"definition" : "An Extension",
"min" : 0,
"max" : "0",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false
},
{
"id" : "Extension.extension:metrics-description.url",
"path" : "Extension.extension.url",
"representation" : [
"xmlAttr"
],
"short" : "identifies the meaning of the extension",
"definition" : "Source of the definition for the extension code - a logical name or a URL.",
"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
"base" : {
"path" : "Extension.url",
"min" : 1,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "uri"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri" : "metrics-description",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:metrics-description.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Value of extension",
"definition" : "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "string"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.url",
"path" : "Extension.url",
"representation" : [
"xmlAttr"
],
"short" : "identifies the meaning of the extension",
"definition" : "Source of the definition for the extension code - a logical name or a URL.",
"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
"base" : {
"path" : "Extension.url",
"min" : 1,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "uri"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.value[x]",
"path" : "Extension.value[x]",
"short" : "Value of extension",
"definition" : "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).",
"min" : 0,
"max" : "0",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "base64Binary"
},
{
"code" : "boolean"
},
{
"code" : "canonical"
},
{
"code" : "code"
},
{
"code" : "date"
},
{
"code" : "dateTime"
},
{
"code" : "decimal"
},
{
"code" : "id"
},
{
"code" : "instant"
},
{
"code" : "integer"
},
{
"code" : "markdown"
},
{
"code" : "oid"
},
{
"code" : "positiveInt"
},
{
"code" : "string"
},
{
"code" : "time"
},
{
"code" : "unsignedInt"
},
{
"code" : "uri"
},
{
"code" : "url"
},
{
"code" : "uuid"
},
{
"code" : "Address"
},
{
"code" : "Age"
},
{
"code" : "Annotation"
},
{
"code" : "Attachment"
},
{
"code" : "CodeableConcept"
},
{
"code" : "Coding"
},
{
"code" : "ContactPoint"
},
{
"code" : "Count"
},
{
"code" : "Distance"
},
{
"code" : "Duration"
},
{
"code" : "HumanName"
},
{
"code" : "Identifier"
},
{
"code" : "Money"
},
{
"code" : "Period"
},
{
"code" : "Quantity"
},
{
"code" : "Range"
},
{
"code" : "Ratio"
},
{
"code" : "Reference"
},
{
"code" : "SampledData"
},
{
"code" : "Signature"
},
{
"code" : "Timing"
},
{
"code" : "ContactDetail"
},
{
"code" : "Contributor"
},
{
"code" : "DataRequirement"
},
{
"code" : "Expression"
},
{
"code" : "ParameterDefinition"
},
{
"code" : "RelatedArtifact"
},
{
"code" : "TriggerDefinition"
},
{
"code" : "UsageContext"
},
{
"code" : "Dosage"
},
{
"code" : "Meta"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"xpath" : "@value|f:*|h:div",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
}
]
},
"differential" : {
"element" : [
{
"id" : "Extension",
"path" : "Extension",
"short" : "Genomic Study Analysis Metrics",
"definition" : "Metrics about the sequencing analysis that was performed"
},
{
"id" : "Extension.extension:read-depth",
"path" : "Extension.extension",
"sliceName" : "read-depth",
"short" : "Read Depth",
"definition" : "The average read depth (number of reads for a position) for the sequencing test",
"requirements" : "This value is typically represented with an 'x' after the number (30x). Simply share the quantity here.",
"min" : 0,
"max" : "1"
},
{
"id" : "Extension.extension:read-depth.extension",
"path" : "Extension.extension.extension",
"max" : "0"
},
{
"id" : "Extension.extension:read-depth.url",
"path" : "Extension.extension.url",
"fixedUri" : "read-depth"
},
{
"id" : "Extension.extension:read-depth.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "30, 100",
"type" : [
{
"code" : "Quantity",
"profile" : [
🔗 "http://hl7.org/fhir/StructureDefinition/SimpleQuantity"
]
}
]
},
{
"id" : "Extension.extension:sequencing-coverage",
"path" : "Extension.extension",
"sliceName" : "sequencing-coverage",
"short" : "Sequencing Coverage",
"definition" : "The percentage of the studied regions that were sequenced",
"requirements" : "This value is typically represented with an '%' after the number (95%). Simply share the quantity here.",
"min" : 0,
"max" : "1"
},
{
"id" : "Extension.extension:sequencing-coverage.extension",
"path" : "Extension.extension.extension",
"max" : "0"
},
{
"id" : "Extension.extension:sequencing-coverage.url",
"path" : "Extension.extension.url",
"fixedUri" : "sequencing-coverage"
},
{
"id" : "Extension.extension:sequencing-coverage.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "95, 100",
"type" : [
{
"code" : "Quantity",
"profile" : [
🔗 "http://hl7.org/fhir/StructureDefinition/SimpleQuantity"
]
}
]
},
{
"id" : "Extension.extension:metrics-description",
"path" : "Extension.extension",
"sliceName" : "metrics-description",
"short" : "Metrics Description",
"definition" : "Freetext description of the coverage metrics for the sequencing test",
"min" : 0,
"max" : "1"
},
{
"id" : "Extension.extension:metrics-description.extension",
"path" : "Extension.extension.extension",
"max" : "0"
},
{
"id" : "Extension.extension:metrics-description.url",
"path" : "Extension.extension.url",
"fixedUri" : "metrics-description"
},
{
"id" : "Extension.extension:metrics-description.value[x]",
"path" : "Extension.extension.value[x]",
"type" : [
{
"code" : "string"
}
]
},
{
"id" : "Extension.url",
"path" : "Extension.url",
"fixedUri" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"
},
{
"id" : "Extension.value[x]",
"path" : "Extension.value[x]",
"max" : "0"
}
]
}
}
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change