refs/refs/fhir-to-omop-demo/data/convert/mapping/010-DiagnosticReport-note.sh

lines 14–29 128 lines · sh
  1#!/bin/bash
  2#
  3# Converts FHIR DiagnosticReport resources to OMOPCDM note records.
  4#
  5source _common.sh
  6
  7REPO="https://github.com/barabo/fhir-to-omop-demo"
  8FILE="data/convert/mapping/010-DiagnosticReport-note.sh"
  9
 10simple_map '
 11#--------------------------#-----------------------------#-------------------#
 12# FHIR DiagnosticReport    # OMOP note                   # Notes             #
 13#--------------------------#-----------------------------#-------------------#
 14  null,                    # note_id                     # REQUIRED          #
 15  null,                    # person_id                   # REQUIRED          #
 16  null,                    # note_date                   # REQUIRED          #
 17  null,                    # note_datetime               # set the time to midnight if not given
 18  null,                    # note_type_concept_id        # REQUIRED          #
 19  null,                    # note_class_concept_id       # REQUIRED          #
 20  null,                    # note_title                  #
 21  null,                    # note_text                   # REQUIRED          #
 22  null,                    # encoding_concept_id         # REQUIRED          #
 23  null,                    # language_concept_id         # REQUIRED          #
 24  null,                    # provider_id                 #
 25  null,                    # visit_occurrence_id         #
 26  null,                    # visit_detail_id             #
 27  null,                    # note_source_value           #
 28  null,                    # note_event_id               #
 29  null,                    # note_event_field_concept_id #
 30#--------------------------#-----------------------------#-------------------#
 31'
 32
 33exit 0
 34
 35cat <<NOTES  # Everything below is notes.
 36
 37# Terminology search:
 38https://athena.ohdsi.org/search-terms/terms
 39
 40# OMOP CDM 5.4 note TABLE
 41https://ohdsi.github.io/CommonDataModel/cdm54.html#note
 42CREATE TABLE note (
 43  note_id integer NOT NULL PRIMARY KEY,
 44  person_id integer NOT NULL REFERENCES PERSON (PERSON_ID),
 45  note_date date NOT NULL,
 46  note_datetime datetime NULL,
 47  note_type_concept_id integer NOT NULL REFERENCES CONCEPT (CONCEPT_ID),
 48  note_class_concept_id integer NOT NULL REFERENCES CONCEPT (CONCEPT_ID),
 49  note_title TEXT NULL,
 50  note_text TEXT NOT NULL,
 51  encoding_concept_id integer NOT NULL REFERENCES CONCEPT (CONCEPT_ID),
 52  language_concept_id integer NOT NULL REFERENCES CONCEPT (CONCEPT_ID),
 53  provider_id integer NULL REFERENCES PROVIDER (PROVIDER_ID),
 54  visit_occurrence_id integer NULL REFERENCES VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID),
 55  visit_detail_id integer NULL REFERENCES VISIT_DETAIL (VISIT_DETAIL_ID),
 56  note_source_value TEXT NULL,
 57  note_event_id integer NULL,
 58  note_event_field_concept_id integer NULL REFERENCES CONCEPT (CONCEPT_ID)
 59);
 60
 61# FHIR R4 Example DiagnosticReport Resource
 62https://www.hl7.org/fhir/R4B/DiagnosticReport.html
 63{
 64  "resourceType": "DiagnosticReport",
 65  "id": "4220",
 66  "meta": {
 67    "versionId": "1",
 68    "lastUpdated": "2024-06-01T20:19:17.304+00:00",
 69    "source": "#8IRCgpLiSxJLv3VD",
 70    "profile": [
 71      "http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note"
 72    ]
 73  },
 74  "status": "final",
 75  "category": [
 76    {
 77      "coding": [
 78        {
 79          "system": "http://loinc.org",
 80          "code": "34117-2",
 81          "display": "History and physical note"
 82        },
 83        {
 84          "system": "http://loinc.org",
 85          "code": "51847-2",
 86          "display": "Evaluation+Plan note"
 87        }
 88      ]
 89    }
 90  ],
 91  "code": {
 92    "coding": [
 93      {
 94        "system": "http://loinc.org",
 95        "code": "34117-2",
 96        "display": "History and physical note"
 97      },
 98      {
 99        "system": "http://loinc.org",
100        "code": "51847-2",
101        "display": "Evaluation+Plan note"
102      }
103    ]
104  },
105  "subject": {
106    "reference": "Patient/4217"
107  },
108  "encounter": {
109    "reference": "Encounter/4218"
110  },
111  "effectiveDateTime": "1959-02-22T06:37:53-05:00",
112  "issued": "1959-02-22T06:37:53.630-05:00",
113  "performer": [
114    {
115      "reference": "Practitioner/2187",
116      "display": "Dr. Douglass930 Windler79"
117    }
118  ],
119  "presentedForm": [
120    {
121      "contentType": "text/plain",
122      "data": "CjE5NTktMDItMjIKCiMgQ2hpZWYgQ29tcGxhaW50Ck5vIGNvbXBsYWludHMuCgojIEhpc3Rvcnkgb2YgUHJlc2VudCBJbGxuZXNzCkh1bWJlcnRvNDgyCiBpcyBhIDM1IHllYXItb2xkIG5vbi1oaXNwYW5pYyB3aGl0ZSBtYWxlLgoKIyBTb2NpYWwgSGlzdG9yeQpQYXRpZW50IGlzIG1hcnJpZWQuIFBhdGllbnQgaXMgYW4gYWN0aXZlIHNtb2tlciBhbmQgaXMgYW4gYWxjb2hvbGljLgogUGF0aWVudCBpZGVudGlmaWVzIGFzIGhldGVyb3NleHVhbC4KClBhdGllbnQgY29tZXMgZnJvbSBhIGhpZ2ggc29jaW9lY29ub21pYyBiYWNrZ3JvdW5kLgogUGF0aWVudCBoYXMgY29tcGxldGVkIHNvbWUgY29sbGVnZSBjb3Vyc2VzLgpQYXRpZW50IGN1cnJlbnRseSBoYXMgSHVtYW5hLgoKIyBBbGxlcmdpZXMKTm8gS25vd24gQWxsZXJnaWVzLgoKIyBNZWRpY2F0aW9ucwpObyBBY3RpdmUgTWVkaWNhdGlvbnMuCgojIEFzc2Vzc21lbnQgYW5kIFBsYW4KUGF0aWVudCBpcyBwcmVzZW50aW5nIHdpdGggYm9keSBtYXNzIGluZGV4IDMwKyAtIG9iZXNpdHkgKGZpbmRpbmcpLiAKCiMjIFBsYW4KCg=="
123    }
124  ]
125}
126
127NOTES
128