refs/refs/fhir-omop-ig/input/maps/Observation.fml

 1/// url = 'http://hl7.org/fhir/uv/omop/StructureMap/ObservationMap'
 2/// name = 'ObservationMap'
 3/// title = 'Mapping Observation resource to  Observation OMOP Domain'
 4/// status = 'draft'
 5/// description = "This mapping maps FHIR Observation instances that are NOT considered measurements to OMOP Observation Table objects.  Currently, this is done by considering the category code and mapping 'social-history', 'imaging', 'survey', 'exam', 'therapy', 'activity', and 'procedure' Observations."
 6
 7uses "http://hl7.org/fhir/StructureDefinition/Observation" alias Observation as source
 8uses "http://hl7.org/fhir/uv/omop/StructureDefinition/Observation" alias ObsTable as target
 9
10 group Observe(source src : Observation, target tgt : ObsTable) 
11 {
12    src where ('social-history' | 'imaging' | 'survey' | 'exam' | 'therapy' | 'activity' | 'procedure' ).supersetOf(Observation.category.coding.code)  then {
13    //src.id as id -> tgt.observation_id = cast(id, "integer");
14    src.code as s -> tgt then {
15        s.coding as sc -> tgt then {
16                sc.code as a -> tgt.observation_concept_id = a;
17            };
18        };
19    //    src.subject as s -> tgt then {
20	//	s.identifier as sid -> tgt then {
21	//		sid.value as a-> tgt.person_id = a;
22	//	};
23	//};
24    //    src.encounter as s -> tgt then {
25	//	    s.identifier as sid -> tgt then {
26	//	    	sid.value as b -> tgt.visit_occurrence_id = b;
27	//	};
28	//};
29        src.effective : dateTime as a -> tgt.observation_datetime = a , tgt.observation_date = cast(a, "date");
30        src.effective : instant as einst -> tgt.observation_datetime = cast(einst, "dateTime"), tgt.observation_date = cast(einst, "date");
31        src.effective : Period as s -> tgt then {
32            s.start as ss -> tgt.observation_datetime = cast(ss, "dateTime"), tgt.observation_date = cast(ss, "date");
33        };
34    src.issued  as s  where (s.toDate != src.effectiveDate) -> tgt.observation_source_value = cast(s, "string");    
35    //src.performer as s -> tgt then {
36	//	s.identifier as sid -> tgt then {
37	//		sid.value as b -> tgt.provider_id = b;
38	//	};
39	//};
40    src.value : Quantity as s -> tgt then {
41        s.value as a  -> tgt.value_as_number = a;
42        s.unit as b -> tgt.unit_concept_id = b;
43    };
44    src.value : CodeableConcept as s  -> tgt then {
45            s.coding as sc -> tgt then {
46                sc.code as a -> tgt.value_as_concept_id = a;
47            };
48        };
49    src.value : string as b -> tgt.value_as_string = b;
50    src.note as d -> tgt.observation_source_value = d; 
51    } "OnlyObs";
52};
53