Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
Mappings for the genomic-data-file resource profile.
| GenomicDataFile |
| DocumentReference | Entity. Role, or Act, Document[classCode="DOC" and moodCode="EVN"] |
| text | Act.text? |
| contained | N/A |
| extension | N/A |
| modifierExtension | N/A |
| masterIdentifier | .id |
| identifier | .id / .setId |
| status | interim: .completionCode="IN" & ./statusCode[isNormalDatatype()]="active"; final: .completionCode="AU" && ./statusCode[isNormalDatatype()]="complete" and not(./inboundRelationship[typeCode="SUBJ" and isNormalActRelationship()]/source[subsumesCode("ActClass#CACT") and moodCode="EVN" and domainMember("ReviseDocument", code) and isNormalAct()]); amended: .completionCode="AU" && ./statusCode[isNormalDatatype()]="complete" and ./inboundRelationship[typeCode="SUBJ" and isNormalActRelationship()]/source[subsumesCode("ActClass#CACT") and moodCode="EVN" and domainMember("ReviseDocument", code) and isNormalAct() and statusCode="completed"]; withdrawn : .completionCode=NI && ./statusCode[isNormalDatatype()]="obsolete" |
| docStatus | .statusCode |
| type | ./code |
| category | .outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code |
| subject | .participation[typeCode="SBJ"].role[typeCode="PAT"] |
| date | .availabilityTime[type="TS"] |
| author | .participation[typeCode="AUT"].role[classCode="ASSIGNED"] |
| authenticator | .participation[typeCode="AUTHEN"].role[classCode="ASSIGNED"] |
| custodian | .participation[typeCode="RCV"].role[classCode="CUST"].scoper[classCode="ORG" and determinerCode="INST"] |
| relatesTo | .outboundRelationship |
| id | n/a |
| extension | n/a |
| modifierExtension | N/A |
| code | .outboundRelationship.typeCode |
| target | .target[classCode="DOC", moodCode="EVN"].id |
| description | .outboundRelationship[typeCode="SUBJ"].target.text |
| securityLabel | .confidentialityCode |
| content | document.text |
| id | n/a |
| extension | n/a |
| modifierExtension | N/A |
| attachment | document.text |
| format | document.text |
| context | outboundRelationship[typeCode="SUBJ"].target[classCode<'ACT'] |
| id | n/a |
| extension | n/a |
| modifierExtension | N/A |
| encounter | unique(highest(./outboundRelationship[typeCode="SUBJ" and isNormalActRelationship()], priorityNumber)/target[moodCode="EVN" and classCode=("ENC", "PCPR") and isNormalAct]) |
| event | .code |
| period | .effectiveTime |
| facilityType | .participation[typeCode="LOC"].role[classCode="DSDLOC"].code |
| practiceSetting | .participation[typeCode="LOC"].role[classCode="DSDLOC"].code |
| sourcePatientInfo | .participation[typeCode="SBJ"].role[typeCode="PAT"] |
| related | ./outboundRelationship[typeCode="PERT" and isNormalActRelationship()] / target[isNormalAct] |
| GenomicDataFile |
| DocumentReference | when describing a CDA |
| masterIdentifier | ClinicalDocument/id |
| type | ClinicalDocument/code/@code
The typeCode should be mapped from the ClinicalDocument/code element to a set of document type codes configured in the affinity domain. One suggested coding system to use for typeCode is LOINC, in which case the mapping step can be omitted. |
| category | Derived from a mapping of /ClinicalDocument/code/@code to an Affinity Domain specified coded value to use and coding system. Affinity Domains are encouraged to use the appropriate value for Type of Service, based on the LOINC Type of Service (see Page 53 of the LOINC User's Manual). Must be consistent with /ClinicalDocument/code/@code |
| subject | ClinicalDocument/recordTarget/ |
| author | ClinicalDocument/author |
| authenticator | ClinicalDocument/legalAuthenticator |
| securityLabel | ClinicalDocument/confidentialityCode/@code |
| content | |
| attachment | ClinicalDocument/languageCode, ClinicalDocument/title, ClinicalDocument/date |
| format | derived from the IHE Profile or Implementation Guide templateID |
| context | |
| period | ClinicalDocument/documentationOf/
serviceEvent/effectiveTime/low/
@value --> ClinicalDocument/documentationOf/
serviceEvent/effectiveTime/high/
@value |
| facilityType | usually a mapping to a local ValueSet. Must be consistent with /clinicalDocument/code |
| practiceSetting | usually from a mapping to a local ValueSet |
| sourcePatientInfo | ClinicalDocument/recordTarget/ |
| related | ClinicalDocument/relatedDocument |
| GenomicDataFile |
| DocumentReference | |
| masterIdentifier | DocumentEntry.uniqueId |
| identifier | DocumentEntry.entryUUID |
| status | DocumentEntry.availabilityStatus |
| type | DocumentEntry.type |
| category | DocumentEntry.class |
| subject | DocumentEntry.patientId |
| author | DocumentEntry.author |
| authenticator | DocumentEntry.legalAuthenticator |
| relatesTo | DocumentEntry Associations |
| code | DocumentEntry Associations type |
| target | DocumentEntry Associations reference |
| description | DocumentEntry.comments |
| securityLabel | DocumentEntry.confidentialityCode |
| content | |
| attachment | DocumentEntry.mimeType, DocumentEntry.languageCode, DocumentEntry.URI, DocumentEntry.size, DocumentEntry.hash, DocumentEntry.title, DocumentEntry.creationTime |
| format | DocumentEntry.formatCode |
| context | |
| event | DocumentEntry.eventCodeList |
| period | DocumentEntry.serviceStartTime, DocumentEntry.serviceStopTime |
| facilityType | DocumentEntry.healthcareFacilityTypeCode |
| practiceSetting | DocumentEntry.practiceSettingCode |
| sourcePatientInfo | DocumentEntry.sourcePatientInfo, DocumentEntry.sourcePatientId |
| related | DocumentEntry.referenceIdList |
|
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