refs/refs/tofhir-mappings/mappings/omop/specimen-mapping.json

 1{
 2  "id": "specimen-mapping",
 3  "url": "https://aiccelerate.eu/fhir/mappings/omop/specimen-mapping",
 4  "name": "specimen-mapping",
 5  "title": "Mapping of omop specimen to AIC-Specimen FHIR profile",
 6  "source": [
 7    {
 8      "alias": "source",
 9      "url": "https://some-url-for-metadata-purposes"
10    }
11  ],
12  "mapping": [
13    {
14      "expression": {
15        "name": "result",
16        "language": "application/fhir-template+json",
17        "value": {
18          "resourceType": "Specimen",
19          "id": "{{mpp:getHashedId('Specimen', specimen_id.toString())}}",
20          "meta": {
21            "profile": [
22              "https://aiccelerate.eu/fhir/StructureDefinition/AIC-Specimen"
23            ],
24            "source": "{{%sourceSystem.sourceUri}}"
25          },
26          "identifier": [
27            {
28              "use": "official",
29              "system": "{{%sourceSystem.sourceUri}}",
30              "value": "{{specimen_id.toString()}}"
31            }
32          ],
33          "subject": "{{? mpp:createFhirReferenceWithHashedId('Patient', person_id.toString())}}",
34          "type":
35            {
36              "coding": [
37                {
38                  "code": "{{concept_code}}",
39                  "system": "{{vocabulary_id}}",
40                  "display": "{{concept_name}}"
41                }
42              ]
43            },
44          "collection":
45          {
46            "collectedDateTime": "{{? specimen_date.utl:toFhirDate('yyyy-MM-dd')}}",
47            "quantity": {
48              "value": "{{? quantity}}",
49              "unit": "{{? unit_code}}",
50              "system": "{{? unit_system}}"
51            },
52            "bodySite": {
53              "coding": [
54                {
55                  "code": "{{? body_site_code}}",
56                  "system": "{{? body_site_vocab_id}}",
57                  "display": "{{? body_site_name}}"
58                }
59              ]
60            }
61          }
62
63        }
64      }
65    }
66  ]
67}
68