This page is part of the MII Implementation Guide Molecular Tumor Board (v2027.0.0-ballot.1: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions

DNPM Transformation

This page describes the transformation of DNPM DIP MTB patient records into MII-CDS-conformant FHIR bundles using FHIR StructureMaps and the Matchbox FHIR server.

• Logical data model (DNPM)
• Mapping table: DNPM to MII FHIR
• StructureMaps (FML)
• Transformation with Matchbox

Logical data model (DNPM)

The DNPM source data model represents the JSON structure of the DNPM DIP MTB API as a FHIR logical model. Source: DAM data model V2.1 incl. MVGenomSeq adjustments

Mapping table: DNPM to MII FHIR

The mapping table shows the element assignment between the DNPM source data model and the MII FHIR profiles from various MII modules (Person, MTB, Oncology, MolGen report, Pathology).

StructureMaps (FML)

The transformation is split modularly into individual StructureMaps:

The FML files live under input/maps/ in the repository and can be executed directly with Matchbox.

Example: patient demographics

The following StructureMap exemplifies the transformation of DNPM patient data into an MII-CDS-conformant FHIR Patient:

group MapPatient(source src : BackboneElement, target tgt : Patient) {

  src.id as srcId -> tgt.id = cast(srcId, "id") "patientId";
  src.birthDate as birthDateDt -> tgt.birthDate = cast(birthDateDt, 'date') "birthDate";

  // Profile meta - MII KDS Person Patient
  src -> tgt.meta as m then {
    src -> m.profile = 'https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient' "patientProfile";
  } "patientMeta";

  // Gender: DNPM codes -> FHIR administrative-gender
  src.gender as g where g.code = 'female'  -> tgt.gender = 'female'  "genderFemale";
  src.gender as g where g.code = 'male'    -> tgt.gender = 'male'    "genderMale";
  src.gender as g where g.code = 'other'   -> tgt.gender = 'other'   "genderOther";
  src.gender as g where g.code = 'unknown' -> tgt.gender = 'unknown' "genderUnknown";

  // Vital status
  src.vitalStatus as vs where vs.code = 'deceased' -> tgt.deceased = true  "deceasedTrue";
  src.vitalStatus as vs where vs.code = 'alive'    -> tgt.deceased = false "deceasedFalse";

  // Address: municipalityCode -> AGS extension
  src.address as srcAddr -> tgt.address as tgtAddr then MapAddress(srcAddr, tgtAddr) "address";
}

Transformation with Matchbox

Matchbox is a FHIR server based on HAPI FHIR that supports StructureMap-based transformations ($transform).

1. Start Matchbox

docker compose -f scripts/docker-compose.matchbox.yaml up -d

The server is reachable at http://localhost:8080/matchbox/fhir. Readiness can be checked with:

curl -sf http://localhost:8080/matchbox/fhir/metadata

2. Load StructureMaps

FML files are sent as text/fhir-mapping to the StructureMap endpoint. Matchbox automatically compiles the FML syntax into a StructureMap resource:

curl -X POST \
  -H "Content-Type: text/fhir-mapping" \
  -H "Accept: application/fhir+json" \
  --data-binary @input/maps/sm-patient-demographics.fml \
  http://localhost:8080/matchbox/fhir/StructureMap

3. Run the transformation

A DNPM patient record is transformed into an MII MTB FHIR bundle via $transform:

curl -X POST \
  -H "Content-Type: application/fhir+json" \
  -H "Accept: application/fhir+json" \
  -d @dnpm-patient-record.json \
  "http://localhost:8080/matchbox/fhir/StructureMap/\$transform?source=https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureMap/dnpm-to-mii-mtb"

4. Automated

The script scripts/fetch-and-transform.sh runs all steps automatically:

1. fetch a DNPM test record from the API
2. load all FML StructureMaps into Matchbox
3. run the transformation
4. store the resulting bundle at scripts/output/mii-mtb-bundle.json

./scripts/fetch-and-transform.sh

The result can then be validated against the MII MTB profiles with scripts/validate-output.sh.