Notice
- Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
- This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.
Terminologies
SNOMED CT Mappings
Below is a list of all the MDS elements (except for those to be removed in MDSv1.05) which are expected to be populated using SNOMED CT concepts. These have been pulled out into a separate list, with links to SNOMED CT, FHIR ValueSets or Genomics ConceptMaps to aid implementation.
Mapping
| Source Data item | Target FHIR Element | Binding |
|---|---|---|
| P-013 | Observation.code | 160475008 |
| P-021 | Observation.code | ConceptMap Genomic Observation Chromosomal Sex |
| F-003 | Observation.code | ConceptMap Genomic Observation Chromosomal Sex |
| F-006 | Patient.extension:fetalStatus/Observation.code | ConceptMap Genomic Patient Born Status |
| TR-012 | ServiceRequest.extension:priorityReason | Any code under 64572001 |
| PS-011 | Specimen.type | ConceptMap Genomic Primary Sample |
| PS-025 | Specimen.container.additiveCodeableConcept | ConceptMap Genomic Specimen Container |
| PS-031 | Specimen.processing.additiveCodeableConcept | ConceptMap Genomic Specimen Container |
| PS-034 | Specimen.processing | ConceptMap Genomic Specimen Tumour Enrichment Method |
| PS-013 | Observation.code | 405921002 |
| PS-014 | Observation.code | 1022461000000100 |
| PS-015 | Observation.code | 371510003 |
| PS-026 | Observation.code | No mapping identified |
| PS-017 | BodyStructure.morphology | SNOMED CT Morphologic Abnormalities |
| PS-018 | BodyStructure.location | SNOMED CT Body Structures |
| PS-036 | Observation.valueCodeableConcept | mCODE Cancer Stage |
| PS-037 | Observation.valueCodeableConcept | mCODE Histologic Grade |
| PS-039 | Specimen.collection.method | Spcimen Collection Method |
| PS-019 | Specimen.collection.bodySite | SNOMED CT Body Structures |
| PS-021 | Observation.valueQuantity | 726741007 TBC |
| PS-021 | Observation.valueQuantity | No mapping identified |
| PS-023 | Observation.code | 1015521000000107 |
| PS-24 | Specimen.collection.extension:specimen-specialHandling.valueCoding.code | ConceptMap Genomic Specimen Special Handling |
| PS-035 | BodyStructure.morhoplogy | ConceptMap Genomic Condition Solid Tumour Type |
| PCI-001 | Observation.code | 723621000000103 |
| PCI-011 | Condition.bodySite | SNOMED CT Body Structures |
| PCI-017 | Condition.code | ConceptMap Genomic Condition Laterality of Hearing Loss |
| PCI-018 | Observation.code | ConceptMap Fetal Maternal Screening Genotype |
| PCI-022 | Observation.code | ConceptMap Fetal Maternal Screening Genotype |
| PCI-028 | Condition.code | Code under 15188001 |
| PCI-029 | Condition.code | Code under 95695004 |
| PCI-031 | Condition.code | Code under 86095007 |
| PCI-032 | TBC Condition.bodySite | SNOMED CT Body Structures |
| PCI-033 | TBC Condition.bodySite | SNOMED CT Body Structures |
| PCI-034 | TBC Procedure.code | 698802001 |
| PCI-036 | Observation.code | 77386006-Pregnant, 60001007-Not Pregnant |
| PCI-037 | Observation.component.code | ConceptMap Genomic Patient Pregnancy Type |
| PCI-038 | Observation.component.valueDuration | 226081000000107 |
| PCI-039 | Observation.component.valueDuration | 57036006 |
| PCI-040 | Observation.component.code | 161714006 |
| PCI-041 | Observation.code | 433475001 |
| PCI-042 | Procedure.code, Observation.code, Observation.valueCodeableConcept | Procedure with code under 77465005 - Transplantation, alternatively, Observation with code 416128008 with valueCodeableConcept 263903005 for no history of transplant |
| PCI-043 | Procedure.code | ConceptMap Genomic Type of Transplant Procedure |
| PCI-045 | Procedure.code, Observation.code, Observation.codeableConcept | code under 5447007, alternatively,Observation with code 416128008 with valueCodeableConcept 303955003 for no history of transfusion |
| PCI-046 | Procedure.code | ConceptMap Genomic Procedure Transfusion Type |
| PCI-048 | Observation.valueQuantity | 54871000237100 |
HPO Terms
This page is a placeholder for HPO term mappings from the MDS. Currently only 'PCI-6 - Phenotypic details' has been identified as requiring HPO terms, recorded as Observations with codes from the Human Phenotype Ontology. Guidance regarding use of HPO as opposed to SNOMED CT concepts is pending Terminology input.
HPO terms are recorded as being either Absent or Present, this is represented within FHIR by the HPO term being recorded in Observation.code.coding.code, with the Absent/Present status being recorded as Observation.valueBoolean set as false or true respectively.
For any Observations using HPO codes, the Observation.code.coding.system SHALL be fixed to http://human-phenotype-ontology.org