amida-tech / cda-fhir

CDA to FHIR converter

cda-fhir

Consolidated CDA (C-CDA) to FHIR converter

Convert C-CDA xml to FHIR bundle

Consolidated CDA (C-CDA)

This library provides the following functionality

• Parse XML document using sax js parser
• Generate set of resources conformant to FHIR DSTU2

Usage example:

'use strict';

var _ = require('lodash');

var bbcms = require('./index');

// Make it transactional bundle
var makeTransactionalBundle = function (bundle, base, patientId) {
    _.each(bundle.entry, function (value) {
        value.request = {
            'method': (value.resource.resourceType === 'Patient') ? 'PUT' : 'POST',
            'url': (value.resource.resourceType === 'Patient') ? 'Patient/' + patientId : value.resource.resourceType
        };
        value.base = base;
    });
    bundle.type = 'transaction';
    return bundle;
};

var request = require('request');

// Get sample file from GitHub
var istream = request.get('https://raw.githubusercontent.com/chb/sample_ccdas/master/Vitera/Vitera_CCDA_SMART_Sample.xml');

istream
    .pipe(new bbcms.CcdaParserStream("test" /* PatientId */))
    .on('data', function (data) {
        var bundle = JSON.stringify(makeTransactionalBundle(data), null, '  ');
		
        console.log(bundle); // Result bundle
		
    })
    .on('error', function (error) {
        console.log(error);
    });

License

Licensed under Apache 2.0

cda-fhir's Issues

Id to Identifier translations are inconsistent between resources

From CCD_1

Patient.identifier:
{"extension": "998991",
"root": "2.16.840.1.113883.19.5.99999.2"} ->
{"system": "urn:oid:2.16.840.1.113883.19.5.99999.2",
"value": "998991"}

Practitioner.identifier:
{"root": "2.16.840.1.113883.19.5.9999.456",
"extension": "2981823"} ->
{ "value": "2.16.840.1.113883.19.5.9999.456"}, extension is lost

race and ethnicity path

According to http://hl7.org/fhir/us-core.html extension paths should end with "us-core-race" and "us-core-ethnicity" not "us-core#race" and "us-core#ethnicity".

id field not mapped correctly

This fragment comes from https://raw.githubusercontent.com/chb/sample_ccdas/master/Allscripts%20Samples/Enterprise%20EHR/b2%20Adam%20Everyman%20ToC.xml

<observation classCode="OBS" moodCode="EVN"> <templateId root="2.16.840.1.113883.10.20.22.4.2" /> <id extension="30011130000073" root="1.3.6.1.4.1.22812.3.9999341.3.4.5" /> <id extension="30011130000077" root="1.3.6.1.4.1.22812.3.9999341.3.4.5" /> <code codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" code="2028-9" displayName="Carbon Dioxide" />

running the script produces:

  "resource": {
    "resourceType": "Observation",
    "id": "Observation/28",
    "subject": {
      "reference": "Patient/test"
    },
    "identifier": [
      {
        "value": "1.3.6.1.4.1.22812.3.9999341.3.4.5"
      },
      {
        "value": "1.3.6.1.4.1.22812.3.9999341.3.4.5"
      }
    ],
    "code": {
      "coding": [
        {
          "system": "http://loinc.org",
          "code": "2028-9",
          "display": "Carbon Dioxide"
        }
      ]
    },

The identifier values seem off - shouldn't "1.3.6.1.4.1.22812.3.9999341.3.4.5" be the 'system' and '30011130000077' be a value?

I'm not a C-CDA expert and maybe the data in sample_ccdas is incorrect - assuming the data is at least somewhat correct.

CCDA Allergy Root Level Severity is Lost

Looks like we only read reaction level severity. Consider capturing it in AllergyIntolerance.criticality.

ProcedureRequest uses "code" instead of "type"

ProcedureRequest lists type correctly only for the first ProcedureRequest, thereafter it uses "code" instead of "type"

Condition.category appears to be wrong

CCD_1.xml Condition Pneumonia has 'Complaint' in source but 'Finding' in translated FHIR.

"completed" is not a valid code for Condition.clinicalStatus

In CCD_1 FHIR translation Pneumonia condition has clinicalStatus as "completed". Valid values appear to be 'active', 'relapse', 'remission', 'resolved' in http://hl7.org/fhir/valueset-condition-clinical.html.

outcome for FamilyMemberHistory not correctly nested

For FamilyMemberHistory outcome needs to be in a coding element

            "outcome": {
                "coding": {
                  "system": "http://snomed.info/sct",
                  "code": "419099009",
                  "display": "Dead"

                }
            }

not

            "outcome": {
                  "system": "http://snomed.info/sct",
              "code": "419099009",
              "display": "Dead"
            }

Conditions codes are not accurate

For CCD_1 example (or bluebutton-01-original) there are two Conditions whose codes are not accurate. The following is the code for the template in a CCDA template not the identification for the problem itself
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.5.6",
"code": "CONC",
"display": "Concern"
}
]
}

Also "Asthma" as a problem in CCDA does not show up as Condition in FHIR. It looks like erroneous Conditions come from ClinicalImpressions.

FamilyMemberHistory.gender, .bornDate should not depend on sdtc:id

In CCDA spec administrativeGenderCode and birthTime does not depend on stdc:id and definitely not to example OID 2.16.840.1.113883.19.5.99999.2. Not sure we have the following code. Due to this code when stdc:id is not there gender and bornDate is not populated

this['sdtc:id'] = function (node) {
    if (node.attributes.root === '2.16.840.1.113883.19.5.99999.2') {
        this._self = {
            administrativeGenderCode: function (node) {
                familyMemberHistory.gender = recodeGender(node.attributes.code);
            },
            birthTime: function (node) {
                familyMemberHistory.bornDate = dateFix(node.attributes.value);
            }
        };
        this._self.prototype = proto;

Observation.code's must be LOINC

http://hl7.org/fhir/observation-definitions.html#Observation.code

From CCD_1.xml a number of them comes up not LOINC, some of them comes up as
"system": "urn:oid:2.16.840.1.113883.5.4",
"code": "ASSERTION"

AllergyIntolerance does not have 'event' property

Looks like it has been changed to 'reaction'

AllergyIntolerance.reaction.severity mapping problems

CCD_1.xml: severity for "PENICILLIN"->"Nausea" reaction shows up as "severe". In the original CCDA file it is "Mild". I think Mild should map to mild, Moderate should map to moderate and Severe should map to severe. Middle severities (Mild to Moderate, Moderate To Severe) should probably go to higher severity.

Practitioner resource is repeated

CCD_1.xml. There are 4 Practitioner resources on "Amanda Assigned" that are identical; Practitioner/16, Practitioner/20, Practitioner/24, and Practitioner/28. Associated organizations (Organization/17, Organization/21, Organization/25, Organization/29) are also repeated.

All Practitioners have the same identifiers as well.

Patient.Contact has no concept of identifier.

Contacts in Patient do not have a concept of identifier, this value is not valid and will not be saved.

ProcedureRequest subject Reference lists "Patient\test"

ProcedureRequest subject Reference does not list a valid PatientID (Hapi accepts this and saves it as sent but I believe we want the value to be the patient ID.)

Condition onset period cannot have same date

Condition onsetPeriod can not have the same start and end date. If the dates match onsetDate must be used. If the dates match and onsetperiod is used Hapi does not save the date at all.

Time zones are not supported

Examples:
CCD_1
social history entry with 'Former Smoker" effectiveTime high
encounter entry effectiveTime high

ClinicalImpression investigations require a code element

For ClinicalImpression, investigations elements must have a code element that is a codeable concept.

Claim.item.type does not have a "coding" child element

For Claim.item.type do not wrap in coding element:

should be like:

             "item": [
          {
            "sequence": 1,
            "type": {
                  "system": "http://snomed.info/sct",
                  "code": "73761001",
                  "display": "Colonoscopy"
                }
          }
        ]

not

        "item": [
          {
            "sequence": 1,
            "type": {
              "coding": [
                {
                  "system": "http://snomed.info/sct",
                  "code": "73761001",
                  "display": "Colonoscopy"
                }
              ]
            }
          }
        ]

Condition.code.coding is sometimes object

CCD_1.xml.

This is inconsistent. Condition.code.coding is sometimes an object and sometimes an array. Same for Condition.category.coding. All the examples I saw on FHIR website coding is always an array.

CCD_1 Plan Of Care Status invalid status, moodCode not considered

CCD_1.xml

'new' is not a valid ProcedureRequest resource status (http://hl7.org/fhir/valueset-procedure-request-status.html). The status looks to be more related to CCDA moodCode not statusCode which is constant.
Since moodCode is not considered all the ProcedureRequest resources generated are identical.

Functional Status entries are missing

CCD_1
Two out of 4 Functional Status entries are missing entirely.

Practitioners managing organization

For Practitioners you have a managing organization at the root level, which is incorrect.

ManagingOrganization is also already in the correct location (practitionerRole.#.managingOrganization) however.

AllergyIntolerance manifestation picks up wrong value

I do not think
"coding": [
{
"system": "http://snomed.info/sct",
"code": "419511003",
"display": "Propensity to adverse reactions to drug"
}

should be in manifestation. It is more related to "AllergyIntolerance.type"

patient identifiers don't go through makeCode translation

A patient with an SSN in a C-CDA ends up looking like this:

      {
        "system": "urn:oid:2.16.840.1.113883.4.1",
        "value": "111-00-1234"
      }

when it probably could look like this (as in the sample HL7 JSON at https://www.hl7.org/fhir/patient-examples-general.json.html):

      {
        "system": "http://hl7.org/fhir/sid/us-ssn",
        "value": "111-00-1234"
      }

now - that translation isn't in makeCode currently, but even if you add it - the code that creates the identifier is:

        _patient.identifier.push({
            'system': 'urn:oid:' + node.attributes.root,
            'value': node.attributes.extension
        });

so the root is just passed through. There is a comment in makeCode that says 'TODO - complete recoding' - so not sure if this is already in the plans or not to generalize a little.

ProcedureRequest is repeated

CCD_1.xml. ProcedureRequest/47, ProcedureRequest/48, ProcedureRequest/49, and ProcedureRequest/50 are identical.