refs/refs/fhir-to-omop-demo/data/convert/mapping/009-DiagnosticReport-measurement.sh

142 lines · sh
  1#!/bin/bash
  2#
  3# Converts FHIR DiagnosticReport resources to OMOPCDM measurement records.
  4#
  5source _common.sh
  6
  7REPO="https://github.com/barabo/fhir-to-omop-demo"
  8FILE="data/convert/mapping/009-DiagnosticReport-measurement.sh"
  9
 10simple_map '
 11#--------------------------#-------------------------------#-----------------#
 12# FHIR DiagnosticReport    # OMOP measurement              # Notes           #
 13#--------------------------#-------------------------------#-----------------#
 14  null,                    # measurement_id                # REQUIRED        #
 15  null,                    # person_id                     # REQUIRED        #
 16  null,                    # measurement_concept_id        # REQUIRED        #
 17  null,                    # measurement_date              # REQUIRED        #
 18  null,                    # measurement_datetime          #
 19  null,                    # measurement_time              #
 20  null,                    # measurement_type_concept_id   # REQUIRED        #
 21  null,                    # operator_concept_id           #
 22  null,                    # value_as_number               #
 23  null,                    # value_as_concept_id           #
 24  null,                    # unit_concept_id               #
 25  null,                    # range_low                     #
 26  null,                    # range_high                    #
 27  null,                    # provider_id                   #
 28  null,                    # visit_occurrence_id           #
 29  null,                    # visit_detail_id               #
 30  null,                    # measurement_source_value      #
 31  null,                    # measurement_source_concept_id #
 32  null,                    # unit_source_value             #
 33  null,                    # unit_source_concept_id        #
 34  null,                    # value_source_value            #
 35  null,                    # measurement_event_id          #
 36  null,                    # meas_event_field_concept_id   #
 37#--------------------------#-------------------------------#-----------------#
 38'
 39
 40exit 0
 41
 42cat <<NOTES  # Everything below is notes.
 43
 44# Terminology search:
 45https://athena.ohdsi.org/search-terms/terms
 46
 47# OMOP CDM 5.4 measurement TABLE
 48https://ohdsi.github.io/CommonDataModel/cdm54.html#measurement
 49CREATE TABLE measurement (
 50  measurement_id integer NOT NULL PRIMARY KEY,
 51  person_id integer NOT NULL REFERENCES PERSON (PERSON_ID),
 52  measurement_concept_id integer NOT NULL REFERENCES CONCEPT (CONCEPT_ID),
 53  measurement_date date NOT NULL,
 54  measurement_datetime datetime NULL,
 55  measurement_time TEXT NULL,
 56  measurement_type_concept_id integer NOT NULL REFERENCES CONCEPT (CONCEPT_ID),
 57  operator_concept_id integer NULL REFERENCES CONCEPT (CONCEPT_ID),
 58  value_as_number REAL NULL,
 59  value_as_concept_id integer NULL REFERENCES CONCEPT (CONCEPT_ID),
 60  unit_concept_id integer NULL REFERENCES CONCEPT (CONCEPT_ID),
 61  range_low REAL NULL,
 62  range_high REAL NULL,
 63  provider_id integer NULL REFERENCES PROVIDER (PROVIDER_ID),
 64  visit_occurrence_id integer NULL REFERENCES VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID),
 65  visit_detail_id integer NULL REFERENCES VISIT_DETAIL (VISIT_DETAIL_ID),
 66  measurement_source_value TEXT NULL,
 67  measurement_source_concept_id integer NULL REFERENCES CONCEPT (CONCEPT_ID),
 68  unit_source_value TEXT NULL,
 69  unit_source_concept_id integer NULL REFERENCES CONCEPT (CONCEPT_ID),
 70  value_source_value TEXT NULL,
 71  measurement_event_id integer NULL,
 72  meas_event_field_concept_id integer NULL REFERENCES CONCEPT (CONCEPT_ID)
 73);
 74
 75# FHIR R4 Example DiagnosticReport Resource
 76https://www.hl7.org/fhir/R4B/DiagnosticReport.html
 77{
 78  "resourceType": "DiagnosticReport",
 79  "id": "4220",
 80  "meta": {
 81    "versionId": "1",
 82    "lastUpdated": "2024-06-01T20:19:17.304+00:00",
 83    "source": "#8IRCgpLiSxJLv3VD",
 84    "profile": [
 85      "http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note"
 86    ]
 87  },
 88  "status": "final",
 89  "category": [
 90    {
 91      "coding": [
 92        {
 93          "system": "http://loinc.org",
 94          "code": "34117-2",
 95          "display": "History and physical note"
 96        },
 97        {
 98          "system": "http://loinc.org",
 99          "code": "51847-2",
100          "display": "Evaluation+Plan note"
101        }
102      ]
103    }
104  ],
105  "code": {
106    "coding": [
107      {
108        "system": "http://loinc.org",
109        "code": "34117-2",
110        "display": "History and physical note"
111      },
112      {
113        "system": "http://loinc.org",
114        "code": "51847-2",
115        "display": "Evaluation+Plan note"
116      }
117    ]
118  },
119  "subject": {
120    "reference": "Patient/4217"
121  },
122  "encounter": {
123    "reference": "Encounter/4218"
124  },
125  "effectiveDateTime": "1959-02-22T06:37:53-05:00",
126  "issued": "1959-02-22T06:37:53.630-05:00",
127  "performer": [
128    {
129      "reference": "Practitioner/2187",
130      "display": "Dr. Douglass930 Windler79"
131    }
132  ],
133  "presentedForm": [
134    {
135      "contentType": "text/plain",
136      "data": "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"
137    }
138  ]
139}
140
141NOTES
142