PatientEHRzipper · pipeline
Jackson Shuey
Epic FHIR R4
transaction bundle · .json
legacy HL7v2
ADT / ORU · .hl7
tumor registry
flat export · .csv
parse_fhir
adapters/fhir.py
parse_hl7v2
adapters/hl7.py
parse_csv
adapters/csv_file.py
Claude Haiku
Tier 2 semantic router
zipper
ehrzipper/engine.py
Patient
canonical record
38 properties3 actions5 fx
join_canonical_field
Tier 2 · merge existing
append_canonical_field
Tier 3 · register new
write_zipper_decision
append-only audit
abstract_clinical_facts
stage · ECOG · biomarkers
compute_rwos_km
Kaplan-Meier · real-world OS
lines_of_therapy
lot · drugs · validator
Claude
note abstractor · 94% acc
Cohort Builder
web app · CSV export
Sample data · synthetic NSCLC cohortthree raw feeds in · one canonical table out
{
  "resourceType": "Bundle",
  "type": "transaction",
  "entry": [
    { "resource": {
        "resourceType": "Patient",
        "id": "pat_74b85b9a",
        "name": [{ "family": "Lawrence", "given": ["Daniel"] }],
        "gender": "male",
        "birthDate": "1942-12"
    }},
    { "resource": {
        "resourceType": "Condition",
        "subject": { "reference": "Patient/pat_74b85b9a" },
        "code": { "coding": [
          { "system": "http://hl7.org/fhir/sid/icd-10-cm",
            "code": "C34.10", "display": "Malignant neoplasm of lung" },
          { "system": "http://terminology.hl7.org/CodeSystem/icd-o-3",
            "code": "8140/3", "display": "Adenocarcinoma" }
        ], "text": "NSCLC - Adenocarcinoma" },
        "stage": [{ "summary": { "text": "Stage IVA" } }],
        "onsetDateTime": "2017-10-07T00:00:00Z"
    }},
    { "resource": {
        "resourceType": "Observation",
        "subject": { "reference": "Patient/pat_74b85b9a" },
        "code": { "coding": [
          { "system": "http://loinc.org", "code": "89247-1",
            "display": "ECOG performance status score" } ] },
        "valueInteger": 0
    }}
  ]
}
MSH|^~\&|EHRZIPPER|ONCOLOGY_EMR|EHRZIPPER|CANONICAL_STORE|20241231120000||ADT^A01|EHRZ0000001|P|2.5.1
PID|1||pat_9a049935||Johnson^Mark||194801|M||Black Or African American
DG1|1|I10|C78.02|NSCLC Adenocarcinoma|20141014|F|||||||STAGE_IVB|||||||8140.3

MSH|^~\&|EHRZIPPER|ONCOLOGY_EMR|EHRZIPPER|CANONICAL_STORE|20241231120000||ORU^R01|EHRZ0000002|P|2.5.1
OBR|3|ORD00003|FIL00003|718-7^Hemoglobin [Mass/volume] in Blood^LN||20141016|||||||||F
OBX|1|NM|718-7^Hemoglobin [Mass/volume] in Blood^LN||9.4|g/dL|12.0-17.5|||F
OBX|1|NM|26464-8^Leukocytes [#/volume] in Blood^LN||4.6|10*3/uL|5.0-10.5|||F

MSH|^~\&|EHRZIPPER|ONCOLOGY_EMR|EHRZIPPER|CANONICAL_STORE|20241231120000||ORU^R01|EHRZ0000003|P|2.5.1
OBX|1|ST|53041-0^EGFR gene mutations found [Identifier]^LN||negative|||||F
OBX|1|ST|21704-5^KRAS gene mutations found [Identifier]^LN||negative|||||F
OBX|1|ST|85337-4^PD-L1 (CD274) [Presence] by Immune stain^LN||14%|||||F
biomarker_id,patient_id,biomarker_name,result,result_value,result_date,test_method,specimen_type,lab_vendor,loinc_code
bm_3cd573c2,pat_2ec4ec15,egfr,negative,,2020-03-14,ngs,tissue,Caris Life Sciences,53041-0
bm_db9c1e32,pat_2ec4ec15,alk,negative,,2020-03-12,ngs,tissue,Caris Life Sciences,76042-8
bm_29507a58,pat_2ec4ec15,ros1,negative,,2020-03-12,ngs,tissue,Foundation Medicine,81202-7
bm_d1e6f095,pat_2ec4ec15,kras,positive,KRAS G12C,2020-03-12,ngs,tissue,Caris Life Sciences,21704-5
bm_90e82477,pat_2ec4ec15,braf,negative,,2020-03-12,ngs,tissue,Caris Life Sciences,21702-9
patient_id,practice_id,practice_type,first_name,last_name,date_of_birth,sex,race,ethnicity,state_of_residence,street_address,city,zip_code,smoking_status,pack_years,initial_nsclc_diagnosis_date,advanced_diagnosis_date,advanced_diagnosis_pathway,histology,histology_icdo3_code,icd10_code,stage_at_initial_diagnosis,stage_at_advanced_diagnosis,ajcc_edition,ecog_at_advanced_diagnosis,age_at_advanced_diagnosis,egfr_status,alk_status,ros1_status,kras_status,braf_status,pdl1_status,pdl1_tps_value,vital_status,date_of_death,last_known_alive_date,data_cutoff_date,source_format
pat_cfba510f,prac_0004,community,Jacob,Clark,1951-08,male,white,not_hispanic_or_latino,NC,192 Frank Light Suite 835,East Lydiamouth,53082,former,72,2019-08-20,2019-08-20,de_novo_stage_iiib_plus,adenocarcinoma,8140/3,C34.31,IIIB,IVA,8,1,68,negative,positive,negative,negative,negative,low,1.4,alive,,2024-12-31,2024-12-31,fhir
pat_c2599acf,prac_0007,academic,Mark,Johnson,1941-12,male,white,not_hispanic_or_latino,WI,32181 Johnson Course Apt. 389,New Jamesside,55488,former,63,2018-10-07,2018-10-07,de_novo_stage_iiib_plus,adenocarcinoma,8140/3,C34.30,IVA,IVA,8,2,77,negative,negative,negative,positive,negative,not_tested,,alive,,2024-12-31,2024-12-31,hl7v2
pat_9b7cedbc,prac_0005,community,Katherine,Campos,1958-05,female,white,unknown,MA,26916 Carlson Mountain,Tashatown,89667,former,75,2016-04-12,2016-12-08,progression_from_earlier_stage,squamous_cell_carcinoma,8070/3,C34.10,IIB,IIIC,8,0,58,negative,negative,negative,positive,negative,negative,0.3,alive,,2024-12-31,2024-12-31,csv

All synthetic. The reconciler maps each feed’s native shape (FHIR Condition, HL7 DG1 / OBX, registry rows) into one 38-column schema; the source_format column records where every row came from.

EntityPatient · EHRzipper
OwnerJ. ShueyUpdated2026-05-31
Rows50 patientsRevA