From 7d317897035f34550f8c12c95afc4c2ff4365431 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Fri, 30 May 2025 17:43:23 +0100 Subject: [PATCH 1/3] Draft ConceptMap for Chromosomal Sex Need to confirm XX and XY are equivalent to Karyotype 46 --- .../ConceptMap-Genomics-chromosomal-sex.json | 194 ++++++++++++++++++ 1 file changed, 194 insertions(+) create mode 100644 ConceptMap/ConceptMap-Genomics-chromosomal-sex.json diff --git a/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json b/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json new file mode 100644 index 0000000..c166044 --- /dev/null +++ b/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json @@ -0,0 +1,194 @@ +{ + "resourceType": "ConceptMap", + "id": "genomics-chromosomal-sex", + "url": "https://fhir.nhs.uk/ConceptMap/genomics-chromosomal-sex", + "version": "0.1.0", + "name": "GenomicsChromosomalSex", + "title": "Genomics Chromosomal Sex", + "status": "draft", + "date": "2024-08-08T18:15:00.000Z", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net" + } + ] + } + ], + "description": "A ConceptMap used for the translation and recording of concepts from MDS source data(code-options) to equivalent Snomed CT codes, and FHIR spec.", + "purpose": "ConceptMap used for the translation and recording of concepts for fetal maternal screening genotype. This is intended for the element Condition.code. An appropriate SNOMED CT code or free text should be used to record the Genotype.", + "copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "targetUri": "http://snomed.info/sct", + "group": [ + { + "source": "https://future.nhs.uk/NHSgenomics/view?objectId=222250117", + "target": "http://snomed.info/sct", + "element": [ + { + "code": "MALE", + "display": "MALE", + "target": [ + { + "code": "248153007", + "display": "Male", + "equivalence": "equivalent" + } + ] + }, + { + "code": "FEMALE", + "display": "FEMALE", + "target": [ + { + "code": "248152002", + "display": "Female", + "equivalence": "equivalent" + } + ] + }, + { + "code": "INDETERMINATE", + "display": "INDETERMINATE", + "target": [ + { + "code": "32570681000036106", + "display": "Indeterminate sex", + "equivalence": "equivalent" + } + ] + }, + { + "code": "XX", + "display": "XX", + "target": [ + { + "code": "734875008", + "display": "Karyotype 46, XX", + "equivalence": "equivalent" + } + ] + }, + { + "code": "XO", + "display": "XO", + "target": [ + { + "code": "710008008", + "display": "XO syndrome", + "equivalence": "equivalent" + } + ] + }, + { + "code": "XY", + "display": "XY", + "target": [ + { + "code": "734876009", + "display": "Karyotype 46, XY", + "equivalence": "equivalent" + } + ] + }, + { + "code": "XXY", + "display": "XXY", + "target": [ + { + "code": "405769009", + "display": "XXY syndrome", + "equivalence": "equivalent" + } + ] + }, + { + "code": "XYY", + "display": "XYY", + "target": [ + { + "code": "50749006", + "display": "XYY syndrome", + "equivalence": "equivalent" + } + ] + }, + { + "code": "XXX", + "display": "XXX", + "target": [ + { + "code": "35111009", + "display": "XXX syndrome", + "equivalence": "equivalent" + } + ] + }, + { + "code": "XXXX", + "display": "XXXX", + "target": [ + { + "code": "10567003", + "display": "XXXX syndrome", + "equivalence": "equivalent" + } + ] + }, + { + "code": "XXXY", + "display": "XXXY", + "target": [ + { + "code": "78317008", + "display": "XXXY syndrome", + "equivalence": "equivalent" + } + ] + }, + { + "code": "XXYY", + "display": "XXYY", + "target": [ + { + "code": "403760006", + "display": "XXYY syndrome", + "equivalence": "equivalent" + } + ] + }, + { + "code": "UNKNOWN", + "display": "UNKNOWN", + "target": [ + { + "code": "184115007", + "display": "Patient sex unknown", + "equivalence": "equivalent" + } + ] + } + ] + }, + { + "source": "https://future.nhs.uk/NHSgenomics/view?objectId=222250117", + "target": "http://terminology.hl7.org/CodeSystem/sex-parameter-for-clinical-use", + "element": [ + { + "code": "OTHER", + "display": "OTHER", + "target": [ + { + "code": "specified", + "display": "Apply specified setting or reference range", + "equivalence": "equivalent" + } + ] + } + ] + } + ] +} \ No newline at end of file From 035fa3667fdffb61fa4c2a06287f4a3c18db2712 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Fri, 5 Sep 2025 10:35:36 +0100 Subject: [PATCH 2/3] lowercase codes and updated date --- ConceptMap/ConceptMap-Genomics-chromosomal-sex.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json b/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json index c166044..45c4b82 100644 --- a/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json +++ b/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json @@ -6,7 +6,7 @@ "name": "GenomicsChromosomalSex", "title": "Genomics Chromosomal Sex", "status": "draft", - "date": "2024-08-08T18:15:00.000Z", + "date": "2025-09-05T10:33:00.000Z", "publisher": "NHS England", "contact": [ { @@ -29,7 +29,7 @@ "target": "http://snomed.info/sct", "element": [ { - "code": "MALE", + "code": "male", "display": "MALE", "target": [ { @@ -40,7 +40,7 @@ ] }, { - "code": "FEMALE", + "code": "female", "display": "FEMALE", "target": [ { @@ -51,7 +51,7 @@ ] }, { - "code": "INDETERMINATE", + "code": "indeterminate", "display": "INDETERMINATE", "target": [ { @@ -161,7 +161,7 @@ ] }, { - "code": "UNKNOWN", + "code": "unknown", "display": "UNKNOWN", "target": [ { @@ -178,7 +178,7 @@ "target": "http://terminology.hl7.org/CodeSystem/sex-parameter-for-clinical-use", "element": [ { - "code": "OTHER", + "code": "other", "display": "OTHER", "target": [ { From 992a6a32d617eb76ae52eea0825462b1460dec9f Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Fri, 5 Sep 2025 11:07:32 +0100 Subject: [PATCH 3/3] Update to copyright --- ConceptMap/ConceptMap-Genomics-chromosomal-sex.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json b/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json index 45c4b82..f4963d5 100644 --- a/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json +++ b/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json @@ -21,7 +21,7 @@ ], "description": "A ConceptMap used for the translation and recording of concepts from MDS source data(code-options) to equivalent Snomed CT codes, and FHIR spec.", "purpose": "ConceptMap used for the translation and recording of concepts for fetal maternal screening genotype. This is intended for the element Condition.code. An appropriate SNOMED CT code or free text should be used to record the Genotype.", - "copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "copyright": "Copyright © 2025+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", "targetUri": "http://snomed.info/sct", "group": [ {