refs/refs/FhirToCdm/FhirToCdmMappings.cs

  1using Hl7.Fhir.Model;
  2using org.ohdsi.cdm.framework.common.Lookups;
  3using org.ohdsi.cdm.framework.common.Omop;
  4using System;
  5using System.Collections.Generic;
  6using System.Linq;
  7using omop = org.ohdsi.cdm.framework.common.Omop;
  8
  9namespace FHIRtoCDM
 10{
 11    public class FhirToCdmMappings
 12    {
 13        private Vocabulary _vocabulary;
 14
 15        public FhirToCdmMappings(Vocabulary vocabulary)
 16        {
 17            _vocabulary = vocabulary;
 18        }
 19
 20        public IEnumerable<Tuple<omop.Person, List<omop.Location>>> CreatePersonAndLocations(Bundle fhir)
 21        {
 22            //provider_id Patient.generalPractitioner Patient
 23            //care_site_id BodySite.patient BodySite
 24            //birth_datetime Patient.birthDate us-core - patient
 25            //location_id Patient.address Patient
 26
 27            var locations = new HashSet<omop.Location>();
 28            //var pat = fhir.Entry.FirstOrDefault(e => e.Resource.TypeName == "Patient");
 29            foreach (var pat in fhir.Entry.Where(e => e.Resource.TypeName == "Patient"))
 30            {
 31                var patient = (Patient)pat.Resource;
 32                var person = new omop.Person
 33                {
 34                    GenderSourceValue = patient.Gender.ToString(),
 35                    PersonSourceValue = patient.Id,
 36                    YearOfBirth = DateTime.Parse(patient.BirthDate).Year,
 37                    MonthOfBirth = DateTime.Parse(patient.BirthDate).Month,
 38                    DayOfBirth = DateTime.Parse(patient.BirthDate).Day,
 39                    EthnicityConceptId = 0
 40                };
 41
 42                foreach (var ex in patient.Extension)
 43                {
 44                    if (ex.Url.ToLower().Contains("death"))
 45                    {
 46
 47                    }
 48                }
 49
 50                switch (person.GenderSourceValue)
 51                {
 52                    case "Male":
 53                        person.GenderConceptId = 8507;
 54                        break;
 55
 56                    case "Female":
 57                        person.GenderConceptId = 8532;
 58                        break;
 59
 60                    default:
 61                        person.GenderConceptId = 0;
 62                        break;
 63                }
 64
 65                if (patient.GeneralPractitioner.Count > 0)
 66                {
 67
 68                }
 69
 70                foreach (var address in patient.Address)
 71                {
 72                    var location = new omop.Location
 73                    {
 74                        City = address.City,
 75                        State = address.State,
 76                        Zip = address.PostalCode,
 77                        Country = address.Country
 78                    };
 79
 80                    //var line = address.Line.ToList();
 81
 82                    //if (line.Count > 0)
 83                    //    location.Address1 = line[0];
 84
 85                    //if (line.Count > 1)
 86                    //    location.Address2 = line[1];
 87
 88                    locations.Add(location);
 89                }
 90
 91                foreach (var item in patient.Extension)
 92                {
 93                    if (item.Url == "http://hl7.org/fhir/StructureDefinition/us-core-race")
 94                    {
 95                        if (item.Value != null)
 96                        {
 97                            person.RaceSourceValue = ((Hl7.Fhir.Model.Coding)item.Value).Display;
 98                        }
 99                        else if (item.Extension.Count > 0)
100                        {
101                            person.RaceSourceValue = ((Hl7.Fhir.Model.Coding)item.Extension[0].Value).Display;
102                        }
103                        break;
104                    }
105                    else if (item.Url == "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity")
106                    {
107                        if (item.Value != null)
108                        {
109                            person.EthnicitySourceValue = ((Hl7.Fhir.Model.Coding)item.Value).Display;
110                        }
111                        else if (item.Extension.Count > 0)
112                        {
113                            person.RaceSourceValue = ((Hl7.Fhir.Model.Coding)item.Extension[0].Value).Display;
114                        }
115                        break;
116                    }
117                }
118
119                if (!string.IsNullOrEmpty(person.EthnicitySourceValue))
120                {
121                    switch (person.EthnicitySourceValue.ToUpper())
122                    {
123                        case "CENTRAL_AMERICAN":
124                        case "DOMINICAN":
125                        case "MEXICAN":
126                        case "PUERTO_RICAN":
127                        case "SOUTH_AMERICAN":
128                            person.EthnicityConceptId = 38003563;
129                            break;
130
131                        default:
132                            person.EthnicityConceptId = 0;
133                            break;
134                    }
135                }
136
137                if (!string.IsNullOrEmpty(person.RaceSourceValue))
138                {
139                    switch (person.RaceSourceValue.ToUpper())
140                    {
141                        case "ASIAN":
142                            person.RaceConceptId = 8515;
143                            break;
144
145                        case "BLACK":
146                            person.RaceConceptId = 8516;
147                            break;
148
149                        case "OTHER":
150                            person.RaceConceptId = 8522;
151                            break;
152
153                        case "WHITE":
154                            person.RaceConceptId = 8527;
155                            break;
156
157                        case "HISPANIC":
158                            person.RaceConceptId = 0;
159                            person.EthnicityConceptId = 38003563;
160                            break;
161
162                        default:
163                            person.RaceConceptId = 0;
164                            break;
165                    }
166                }
167
168                yield return new Tuple<omop.Person, List<omop.Location>>(person, locations.ToList());
169            }
170        }
171
172
173        public IEnumerable<Tuple<KeyValuePair<string, VisitOccurrence>, Provider>> CreateVisitOccurenceAndProvider(Bundle fhir, Dictionary<string, long> personIds)
174        {
175            //care_site_id Encounter.location.location.identifier us-core - encounter, us - core - location
176            //admitting_source_concept_id Encounter.hospitalization.admitSource or Encounter.hospitalization.origin(location).type    us - core - encounter, us - core - location
177            //discharge_to_concept_id Encounter.location.location.type us-core - encounter,us - core - location
178            //preceding_visit_occurence Encounter.partOf us-core - encounter
179            foreach (var item in fhir.Entry.Where(e => e.Resource.TypeName == "Encounter"))
180            {
181                var encounter = (Encounter)item.Resource;
182
183                var conceptId = 9202;
184
185                if (encounter.Class.Code.ToUpper() == "IMP")
186                    conceptId = 9201;
187                else if (encounter.Class.Code.ToUpper() == "EMER")
188                    conceptId = 9203;
189
190                if (encounter.Diagnosis.Count > 0)
191                {
192
193                }
194
195                if (encounter.ReasonCode.Count > 0)
196                {
197                    foreach (var reasonCode in encounter.ReasonCode)
198                    {
199                        foreach (var code in reasonCode.Coding)
200                        {
201                            if (code.Code == "308646001")
202                            {
203
204                            }
205                        }
206
207                    }
208                }
209
210                if (encounter.Extension.Count > 0)
211                {
212
213                }
214
215                Provider provider = null;
216                if (encounter.ServiceProvider != null)
217                {
218                    provider = new Provider
219                    {
220                        Id = Entity.GetId(encounter.ServiceProvider.Display),
221                        Name = encounter.ServiceProvider.Display,
222                        SourceValue = encounter.ServiceProvider.Display
223                    };
224                }
225
226                var personId = GetPersonId1(encounter.Subject, personIds);
227
228                VisitOccurrence vo = null;
229                if (personId.HasValue)
230                {
231                    vo = new VisitOccurrence(new Entity())
232                    {
233                        PersonId = personId.Value,
234                        SourceValue = encounter.Class.Code,
235                        StartDate = DateTime.Parse(encounter.Period.Start),
236                        EndDate = DateTime.Parse(encounter.Period.End),
237                        TypeConceptId = 32817,
238                        ConceptId = conceptId
239                    };
240
241                    if (provider != null)
242                    {
243                        vo.ProviderId = provider.Id;
244                    }
245                }
246
247                yield return new Tuple<KeyValuePair<string, VisitOccurrence>, Provider>(
248                    new KeyValuePair<string, VisitOccurrence>(encounter.Id, vo), provider);
249            }
250        }
251
252        public IEnumerable<omop.ConditionOccurrence> CreateConditionOccurrence(Bundle fhir, Dictionary<string, long> personIds, Dictionary<string, VisitOccurrence> visits)
253        {
254            //provider_id Condition.asserter us-core - condition
255            //visit_occurrence_id Condition.encounter us-core - condition
256            //condition_status_concept_id Condition.clinicalStatus us-core - condition
257            //stop_reason Condition.Extension(Proposed Name: abatement - reason : CodeableConcept) us - core - condition
258
259            foreach (var item in fhir.Entry.Where(e => e.Resource.TypeName == "Condition"))
260            {
261                var condition = (Condition)item.Resource;
262
263                foreach (var code in condition.Code.Coding)
264                {
265                    var date = DateTime.Parse(((Hl7.Fhir.Model.FhirDateTime)condition.Onset).Value);
266
267                    var personId = GetPersonId1(condition.Subject, personIds);
268                    if (!personId.HasValue)
269                        continue;
270
271                    var co = new ConditionOccurrence(new Entity())
272                    {
273                        PersonId = personId.Value,
274                        TypeConceptId = 32817,
275                        StartDate = date,
276                        SourceValue = code.Code
277                    };
278
279                    if (condition.Abatement != null)
280                    {
281                        co.EndDate = DateTime.Parse(((Hl7.Fhir.Model.FhirDateTime)condition.Abatement).Value);
282                    }
283
284                    var result = LookupCode(code);
285                    if (result.Any())
286                        SetConceptId(co, result[0]);
287
288                    if (co.Domain == "Drug")
289                    {
290                        co.TypeConceptId = 32817;
291                    }
292                    else if (co.Domain == "Observation")
293                    {
294                        co.TypeConceptId = 32817;
295                    }
296
297                    var vo = GetVisitOccurrence(condition.Encounter, visits);
298                    co.VisitOccurrenceId = vo.Id;
299                    co.VisitDetailId = vo.Id;
300
301                    if (!co.EndDate.HasValue)
302                        co.EndDate = vo.EndDate;
303
304                    yield return co;
305                }
306            }
307
308        }
309
310        public IEnumerable<DrugExposure> CreateDrugExposure(Bundle fhir, Dictionary<string, long> personIds, Dictionary<string, VisitOccurrence> visits)
311        {
312            //stop_reason MedicationStatement.statusReason us-core - medicationstatement
313            //refills MedicationStatement.basedOn(MedicationRequest).dispenseRequest.numberOfRepeatsAllowed   us - core - medicationstatement, us - core - medicationrequest
314            //quantity MedicationStatement.basedOn(MedicationRequest).dispenseRequest.quantity us - core - medicationstatement, us - core - medicationrequest
315            //days_supply MedicationStatement.basedOn(MedicationRequest).dispenseRequest.expectedSupplyDuration   us - core - medicationstatement, us - core - medicationrequest
316            //lot_number MedicationStatement.medication.batch.lotNumber us-core - medicationstatement, us - core - medication
317            //route_concept_id MedicationStatement.basedOn(MedicationRequest).dosageInstruction.route  us - core - medicationstatement, us - core - medicationrequest
318            //provider_id MedicationStatement.basedOn(MedicationRequest).requester    us - core - medicationstatement, us - core - medicationrequest
319            //verbatim_end_date MedicationStatement.basedOn(MedicationRequest).validityPeriod   us - core - medicationstatement, us - core - medicationrequest
320
321
322            foreach (var item in fhir.Entry.Where(e => e.Resource.TypeName == "MedicationRequest"))
323            {
324                var medication = (MedicationRequest)item.Resource;
325                var cc = medication.Medication as Hl7.Fhir.Model.CodeableConcept;
326                if (cc == null)
327                    continue;
328
329                foreach (var code in cc.Coding)
330                {
331                    var personId = GetPersonId1(medication.Subject, personIds);
332                    if (!personId.HasValue)
333                        continue;
334
335                    var de = new DrugExposure(new Entity())
336                    {
337                        PersonId = personId.Value,
338                        TypeConceptId = 32817
339                    };
340
341                    if (medication.BasedOn.Count > 0)
342                    {
343
344                    }
345
346                    if (medication.StatusReason != null)
347                    {
348
349                    }
350
351                    if (medication.DosageInstruction != null && medication.DosageInstruction.Count > 0)
352                    {
353                        de.Sig = medication.DosageInstruction[0].Text;
354                    }
355
356                    if (medication.DispenseRequest != null)
357                    {
358
359                    }
360
361                    var result = LookupCode(code);
362                    if (result.Any())
363                        SetConceptId(de, result[0]);
364
365                    var vo = GetVisitOccurrence(medication.Encounter, visits);
366                    de.VisitOccurrenceId = vo.Id;
367                    de.VisitDetailId = vo.Id;
368                    de.StartDate = vo.StartDate;
369                    de.EndDate = vo.EndDate;
370
371                    yield return de;
372                }
373            }
374
375
376            foreach (var item in fhir.Entry.Where(e => e.Resource.TypeName == "Immunization"))
377            {
378                var immunization = (Immunization)item.Resource;
379
380                foreach (var code in ((Hl7.Fhir.Model.CodeableConcept)immunization.VaccineCode).Coding)
381                {
382                    var personId = GetPersonId1(immunization.Patient, personIds);
383                    if (!personId.HasValue)
384                        continue;
385
386                    var de = new omop.DrugExposure(new omop.Entity())
387                    {
388                        PersonId = personId.Value,
389                        TypeConceptId = 32817
390                    };
391
392                    var result = LookupCode(code);
393                    if (result.Any())
394                        SetConceptId(de, result[0]);
395
396                    var vo = GetVisitOccurrence(immunization.Encounter, visits);
397                    de.VisitOccurrenceId = vo.Id;
398                    de.VisitDetailId = vo.Id;
399                    de.StartDate = vo.StartDate;
400                    de.EndDate = vo.EndDate;
401
402                    yield return de;
403                }
404            }
405        }
406
407        public IEnumerable<ProcedureOccurrence> CreateProcedureOccurrence(Bundle fhir, Dictionary<string, long> personIds, Dictionary<string, VisitOccurrence> visits)
408        {
409            //quantity Procedure.Extension(Proposed Name: num - of - procedures : CodeableConcept)    us - core - procedure
410            //provider_id Procedure.performer.actor
411
412            foreach (var item in fhir.Entry.Where(e => e.Resource.TypeName == "Procedure"))
413            {
414                var procedure = (Procedure)item.Resource;
415
416                foreach (var code in ((Hl7.Fhir.Model.CodeableConcept)procedure.Code).Coding)
417                {
418                    var personId = GetPersonId1(procedure.Subject, personIds);
419                    if (!personId.HasValue)
420                        continue;
421
422                    var po = new ProcedureOccurrence(new Entity())
423                    {
424                        PersonId = personId.Value,
425                        TypeConceptId = 32817
426                    };
427
428                    var result = LookupCode(code);
429                    if (result.Any())
430                        SetConceptId(po, result[0]);
431
432                    if (procedure.Extension.Count > 0)
433                    {
434
435                    }
436
437                    if (po.Domain == "Measurement")
438                    {
439                        po.TypeConceptId = 32817;
440                    }
441
442                    var vo = GetVisitOccurrence(procedure.Encounter, visits);
443                    po.VisitOccurrenceId = vo.Id;
444                    po.VisitDetailId = vo.Id;
445                    po.StartDate = DateTime.Parse(((Hl7.Fhir.Model.Period)procedure.Performed).Start);
446                    po.EndDate = DateTime.Parse(((Hl7.Fhir.Model.Period)procedure.Performed).End);
447
448                    yield return po;
449                }
450            }
451        }
452
453        public IEnumerable<omop.Observation> CreateObservation(Bundle fhir, Dictionary<string, long> personIds, Dictionary<string, VisitOccurrence> visits)
454        {
455            foreach (var item in fhir.Entry.Where(e => e.Resource.TypeName == "AllergyIntolerance"))
456            {
457                var allergy = (AllergyIntolerance)item.Resource;
458
459                foreach (var code in ((Hl7.Fhir.Model.CodeableConcept)allergy.Code).Coding)
460                {
461                    var personId = GetPersonId1(allergy.Patient, personIds);
462                    if (!personId.HasValue)
463                        continue;
464
465                    var o = new omop.Observation(new Entity())
466                    {
467                        PersonId = personId.Value,
468                        TypeConceptId = 32817
469                    };
470
471                    var result = LookupCode(code);
472                    if (result.Any())
473                        SetConceptId(o, result[0]);
474
475                    o.StartDate = DateTime.Parse(allergy.RecordedDate);
476
477                    yield return o;
478                }
479            }
480        }
481
482        public IEnumerable<Measurement> CreateMeasurement(Bundle fhir, Dictionary<string, long> personIds, Dictionary<string, VisitOccurrence> visits)
483        {
484            //provider_id Observation.performer(Practitioner)    us - core - observationresults
485            //value_as_concept_id Observation.valueCodeableConcept us-core - observationresults
486
487            foreach (var item in fhir.Entry.Where(e => e.Resource.TypeName == "Observation"))
488            {
489                var observation = (Hl7.Fhir.Model.Observation)item.Resource;
490
491                foreach (var code in ((CodeableConcept)observation.Code).Coding)
492                {
493                    var personId = GetPersonId1(observation.Subject, personIds);
494                    if (!personId.HasValue)
495                        continue;
496
497                    var m = new Measurement(new Entity())
498                    {
499                        PersonId = personId.Value,
500                        TypeConceptId = 32817
501                    };
502
503                    var result = LookupCode(code);
504                    if (result.Any())
505                        SetConceptId(m, result[0]);
506
507                    if (observation.ReferenceRange != null && observation.ReferenceRange.Count > 0)
508                    {
509                        if (observation.ReferenceRange[0].Low != null)
510                            m.RangeLow = observation.ReferenceRange[0].Low.Value;
511
512                        if (observation.ReferenceRange[0].High != null)
513                            m.RangeHigh = observation.ReferenceRange[0].High.Value;
514                    }
515
516                    var vo = GetVisitOccurrence(observation.Encounter, visits);
517                    m.VisitOccurrenceId = vo.Id;
518                    m.VisitDetailId = vo.Id;
519                    m.StartDate = DateTime.Parse(((FhirDateTime)observation.Effective).Value);
520
521                    if (observation.Value != null)
522                    {
523                        var quantity = observation.Value as Quantity;
524                        if (quantity != null)
525                        {
526                            m.UnitSourceValue = quantity.Unit;
527                            var unit = LookupCode(m.UnitSourceValue, "Unit");
528                            if (unit.Any() && unit[0].ConceptId.HasValue)
529                            {
530                                m.UnitConceptId = unit[0].ConceptId.Value;
531                            }
532
533                            m.ValueAsNumber = quantity.Value;
534                            m.ValueSourceValue = m.ValueAsNumber.ToString();
535                        }
536                        else
537                        {
538                            var cc = observation.Value as CodeableConcept;
539
540                            if (cc != null && cc.Coding.Count > 0)
541                            {
542                                m.ValueSourceValue = cc.Coding[0].Display;
543
544                                var conceptId = LookupCode(cc.Coding[0]);
545                                if (conceptId.Any() && conceptId[0].ConceptId.HasValue)
546                                    m.ValueAsConceptId = conceptId[0].ConceptId.Value;
547                            }
548                            else
549                            {
550                                m.ValueSourceValue = observation.Value.ToString();
551                            }
552                        }
553                    }
554
555                    yield return m;
556                }
557            }
558        }
559
560        private long? GetPersonId1(ResourceReference e, Dictionary<string, long> personIds)
561        {
562            var key = e.Reference.Replace("urn:uuid:", "");
563            if (personIds.ContainsKey(key))
564                return personIds[key];
565
566            return null;
567        }
568
569        private VisitOccurrence GetVisitOccurrence(ResourceReference e, Dictionary<string, VisitOccurrence> visits)
570        {
571            return visits[e.Reference.Replace("urn:uuid:", "")];
572        }
573
574        private void SetConceptId(IEntity e, LookupValue value)
575        {
576            if (value.ConceptId.HasValue)
577            {
578                e.ConceptId = value.ConceptId.Value;
579                e.Domain = value.Domain;
580
581                if (value.Ingredients != null)
582                {
583                    e.Ingredients = new List<int>(value.Ingredients.Count);
584                    e.Ingredients.AddRange(value.Ingredients);
585                }
586            }
587
588            e.SourceConceptId = value.SourceConceptId;
589        }
590
591        private List<LookupValue> LookupCode(string code, string vocabularyName)
592        {
593            return _vocabulary.Lookup(code, vocabularyName, DateTime.MinValue);
594        }
595
596        private List<LookupValue> LookupCode(Coding code)
597        {
598            var vocabularyName = "";
599            switch (code.System)
600            {
601                case "http://snomed.info/sct":
602                    vocabularyName = "Snomed";
603                    break;
604
605                case "http://www.nlm.nih.gov/research/umls/rxnorm":
606                    vocabularyName = "Rxnorm";
607                    break;
608
609                case "http://hl7.org/fhir/sid/cvx":
610                    vocabularyName = "Cvx";
611                    break;
612
613                case "http://loinc.org":
614                    vocabularyName = "Loinc";
615                    break;
616
617                default:
618                    throw new Exception("unknown vocabulary " + code.System);
619            }
620
621            return LookupCode(code.Code, vocabularyName);
622        }
623    }
624}
625