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
PS-11 - Primary Sample - Primary sample Specimen.type ConceptMap Genomic Primary Sample
PS-17 - Primary Sample - Solid tumour morphology BodyStructure.morphology SNOMED CT Morphologic Abnormalities
PS-18 - Primary Sample - Solid tumour topography BodyStructure.location SNOMED CT Body Structures
PS-19 - Primary Sample - Biopsy Site Specimen.collection.bodySite SNOMED CT Body Structures
PC-23 - Primary Sample - Blasts % Observation.code 1015521000000107
P-21 -Patient - Chromosomal sex Observation.code ConceptMap Genomic Observation Chromosomal Sex
PCI-8 - Disease penetrance Observation.code 86426007 for complete penetrance or 87006007 for incomplete penetrance
F3 -Fetus - Chromosomal sex Observation.code 734840008
F6 -Fetus - Life status at time of request Patient.extension:fetalStatus ConceptMap Genomic Patient Born Status
PS-13 - Primary Sample - Necrosis Observation.code 405921002
PS-14 -Patient - Primary Sample - Nucleated cell count Observation.code 1022461000000100
PS-15 - Primary Sample - Tumour nuclear content in whole section Observation.code 371510003
PS-21 - Primary Sample - Observed maternal cell contamination (MCC) Observation.valueBoolean 726741007 TBC
PS-24 - Primary Sample - High infection risk reason Specimen.collection.extension:specimen-specialHandling.valueCoding.code ConceptMap Genomic Specimen Special Handling
PCI-1 -Patient clinical information - Genomic ethnicity Observation.code 723621000000103
PCI-7 - Patient clinical information - Symptoms Observation.code SNOMED CT Clinical Findings
PCI-11 - Patient clinical information - Site of tumour BodyStructure.location SNOMED CT Body Structures
PCI-12 - Patient clinical information - Solid tumour type Condition.code ConceptMap Genomic Condition Solid Tumour Type
PCI-17 - Patient clinical information - Laterality of hearing loss Condition.code ConceptMap Genomic Condition Laterality of Hearing Loss
PCI-18 - Patient clinical information - Fetal haemoglobinopathy maternal screening genotype Observation.code ConceptMap Fetal Maternal Screening Genotype
PCI-22 - Patient clinical information - Fetal haemoglobinopathy paternal screening genotype Observation.code ConceptMap Fetal Maternal Screening Genotype
PCI-28 - Patient clinical information - Severity of hearing loss Condition.code Code under 15188001
PCI-29 - Patient clinical information - Retinal degeneration Condition.code Code under 95695004
PCI-31 - Patient clinical information - Suspected inborn error type(s) Condition.code Code under 86095007
PCI-32 - Patient clinical information - Abnormal infection history site TBC Condition.bodySite SNOMED CT Body Structures
PCI-33 - Patient clinical information - Abnormal infection history site organism TBC Condition.bodySite SNOMED CT Body Structures
PCI-34 - Patient clinical information - Is on ig replacement TBC Procedure.code 698802001
PCI-42 Patient clinical information - Had transplant 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-43 -Patient clinical information - Type of transplant Procedure.code ConceptMap Genomic Type of Transplant Procedure
PCI-45 -Patient clinical information - Had transfusion in the last 6 weeks Procedure.code, Observation.code, Observation.codeableConcept code under 5447007, alternatively,Observation with code 416128008 with valueCodeableConcept 303955003 for no history of transfusion
P-13 -Patient - Is from consanguineous union Observation.code 160475008
PCI-35 -Patient clinical information - Being treated for cancer Procedure.reasonCode Code under 363346000
PCI-36 -Patient clinical information - Pregnancy status Observation.code 77386006-Pregnant, 60001007-Not Pregnant
PCI-37 -Patient clinical information - Pregnancy type Observation.component.code ConceptMap Genomic Patient Pregnancy Type
PCI-38 -Patient clinical information - Pregnancy gestation period Observation.component.valueDuration 226081000000107
PCI-39 -Patient clinical information - Fetal gestation Observation.component.valueDuration 57036006
PCI-40 -Patient clinical information - Estimated delivery date (EDD) Observation.component.code 161714006
PCI-41 -Patient clinical information - IVF age of egg donor Observation.code 433475001
PCI-46 -Patient clinical information - Type of transfusion Procedure.code ConceptMap Genomic Procedure Transfusion Type
PCI-48 -Patient clinical information - Height (m) Observation.valueQuantity 54871000237100
PCI-12 -Patient clinical information - Solid tumour type Condition.code ConceptMap Genomic Condition Solid Tumour Type
PCI-39 -Patient clinical information - Fetal gestation Observation.code 598151000005105
TR-12 - Test request - Urgency reason ServiceRequest.extension:priorityReason Any code under 64572001
SP-8 - Sample Preparation - Sample preparation Specimen.processing.procedure ConceptMap Genomic Specimen Sample Preparation
FS-9 - Final Sample - Final sample Specimen.type ConceptMap Genomic Specimen Final Sample
PGR-17 - Previous genomic report - Result of genetic analysis DiagnosticReport.conclusionCode, DiagnosticReport.result SNOMED CT Clinical Findings

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.