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feat: add MIMIC-IV OMOP test support (closes #13) #24

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Merged
tompollard merged 1 commit into from
Nov 23, 2025
Merged

feat: add MIMIC-IV OMOP test support (closes #13) #24

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3,886 changes: 3,886 additions & 0 deletions ...miciv_demo_omop/physionet.org/files/mimic-iv-demo-omop/0.9/1_omop_data_csv/2b_concept.csv
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7,717 changes: 7,717 additions & 0 deletions ...op/physionet.org/files/mimic-iv-demo-omop/0.9/1_omop_data_csv/2b_concept_relationship.csv
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28 changes: 28 additions & 0 deletions ...iv_demo_omop/physionet.org/files/mimic-iv-demo-omop/0.9/1_omop_data_csv/2b_vocabulary.csv
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vocabulary_id,vocabulary_name,vocabulary_reference,vocabulary_version,vocabulary_concept_id
mimiciv_micro_organism,mimiciv_micro_organism,Odysseus generated,,2110000014
mimiciv_drug_route,mimiciv_drug_route,Odysseus generated,,2110000005
mimiciv_obs_insurance,mimiciv_obs_insurance,Odysseus generated,,2110000019
mimiciv_cond_chartevents_value,mimiciv_cond_chartevents_value,Odysseus generated,,2110000002
mimiciv_vis_admission_location,mimiciv_vis_admission_location,Odysseus generated,,2110000025
mimiciv_meas_wf_unit,mimiciv_meas_wf_unit,Odysseus generated,,2110000011
mimiciv_vis_discharge_location,mimiciv_vis_discharge_location,Odysseus generated,,2110000027
mimiciv_vis_admission_type,mimiciv_vis_admission_type,Odysseus generated,,2110000026
mimiciv_meas_wf,mimiciv_meas_wf,Odysseus generated,,2110000010
mimiciv_meas_chartevents_value,mimiciv_meas_chartevents_value,Odysseus generated,,2110000007
mimiciv_micro_resistance,mimiciv_micro_resistance,Odysseus generated,,2110000015
mimiciv_cs_place_of_service,mimiciv_cs_place_of_service,Odysseus generated,,2110000003
mimiciv_proc_itemid,mimiciv_proc_itemid,Odysseus generated,,2110000024
mimiciv_micro_antibiotic,mimiciv_micro_antibiotic,Odysseus generated,,2110000012
mimiciv_obs_drgcodes,mimiciv_obs_drgcodes,Odysseus generated,,2110000018
mimiciv_mimic_generated,mimiciv_mimic_generated,Odysseus generated,,2110000017
mimiciv_proc_datetimeevents,mimiciv_proc_datetimeevents,Odysseus generated,,2110000023
mimiciv_vis_service,mimiciv_vis_service,Odysseus generated,,2110000028
mimiciv_obs_marital,mimiciv_obs_marital,Odysseus generated,,2110000021
mimiciv_meas_lab_loinc,mimiciv_meas_lab_loinc,Odysseus generated,,2110000008
mimiciv_drug_ndc,mimiciv_drug_ndc,Odysseus generated,,2110000004
mimiciv_micro_microtest,mimiciv_micro_microtest,Odysseus generated,,2110000013
mimiciv_per_ethnicity,mimiciv_per_ethnicity,Odysseus generated,,2110000022
mimiciv_obs_language,mimiciv_obs_language,Odysseus generated,,2110000020
mimiciv_micro_specimen,mimiciv_micro_specimen,Odysseus generated,,2110000016
mimiciv_meas_unit,mimiciv_meas_unit,Odysseus generated,,2110000009
mimiciv_meas_chart,mimiciv_meas_chart,Odysseus generated,,2110000006
1 change: 1 addition & 0 deletions ..._omop/physionet.org/files/mimic-iv-demo-omop/0.9/1_omop_data_csv/attribute_definition.csv
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attribute_definition_id,attribute_name,attribute_description,attribute_type_concept_id,attribute_syntax
32 changes: 32 additions & 0 deletions ...imiciv_demo_omop/physionet.org/files/mimic-iv-demo-omop/0.9/1_omop_data_csv/care_site.csv
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care_site_id,care_site_name,place_of_service_concept_id,location_id,care_site_source_value,place_of_service_source_value
7482024270134467590,Med/Surg/GYN,,1,Med/Surg/GYN,Med/Surg/GYN
6872771148744744676,Trauma SICU (TSICU),,1,Trauma SICU (TSICU),Trauma SICU (TSICU)
4662258935512879919,Unknown,,1,Unknown,Unknown
-2501038380264497908,Med/Surg,,1,Med/Surg,Med/Surg
8603684584038321926,Observation,,1,Observation,Observation
-4921759089326952807,Surgical Intensive Care Unit (SICU),,1,Surgical Intensive Care Unit (SICU),Surgical Intensive Care Unit (SICU)
-1391555203687435837,Psychiatry,,1,Psychiatry,Psychiatry
4992481836892397716,Cardiology Surgery Intermediate,,1,Cardiology Surgery Intermediate,Cardiology Surgery Intermediate
1017962119019862949,Vascular,,1,Vascular,Vascular
6301497417699858963,Medicine/Cardiology Intermediate,,1,Medicine/Cardiology Intermediate,Medicine/Cardiology Intermediate
5795622005232202614,Hematology/Oncology Intermediate,,1,Hematology/Oncology Intermediate,Hematology/Oncology Intermediate
-9001082880759516720,Surgery/Trauma,,1,Surgery/Trauma,Surgery/Trauma
8893574135069298541,Neuro Intermediate,,1,Neuro Intermediate,Neuro Intermediate
4260571064587438420,Medical Intensive Care Unit (MICU),,1,Medical Intensive Care Unit (MICU),Medical Intensive Care Unit (MICU)
-1994974909868859633,Neuro Stepdown,,1,Neuro Stepdown,Neuro Stepdown
1236875180544517908,PACU,,1,PACU,PACU
9163527066039634598,Neuro Surgical Intensive Care Unit (Neuro SICU),,1,Neuro Surgical Intensive Care Unit (Neuro SICU),Neuro Surgical Intensive Care Unit (Neuro SICU)
2622982412586685824,Cardiac Surgery,,1,Cardiac Surgery,Cardiac Surgery
7883369686195988084,Medical/Surgical Intensive Care Unit (MICU/SICU),,1,Medical/Surgical Intensive Care Unit (MICU/SICU),Medical/Surgical Intensive Care Unit (MICU/SICU)
-4595469263819475121,Cardiac Vascular Intensive Care Unit (CVICU),,1,Cardiac Vascular Intensive Care Unit (CVICU),Cardiac Vascular Intensive Care Unit (CVICU)
-4692107866841310865,Transplant,,1,Transplant,Transplant
2567623729868189377,Cardiology,,1,Cardiology,Cardiology
-1687181949124712268,Coronary Care Unit (CCU),,1,Coronary Care Unit (CCU),Coronary Care Unit (CCU)
-6388176138378808864,Neurology,,1,Neurology,Neurology
-1961798000198430351,Hematology/Oncology,,1,Hematology/Oncology,Hematology/Oncology
-428473802128370025,Med/Surg/Trauma,,1,Med/Surg/Trauma,Med/Surg/Trauma
6624301826366063357,Surgery/Vascular/Intermediate,,1,Surgery/Vascular/Intermediate,Surgery/Vascular/Intermediate
3867689376711056927,Medicine/Cardiology,581383,1,Medicine/Cardiology,Medicine/Cardiology
-539367094141958574,Medicine,38004515,1,Medicine,Medicine
-3633440072147213200,Emergency Department Observation,8870,1,Emergency Department Observation,Emergency Department Observation
6888076371289519343,Emergency Department,8870,1,Emergency Department,Emergency Department
2 changes: 2 additions & 0 deletions ...miciv_demo_omop/physionet.org/files/mimic-iv-demo-omop/0.9/1_omop_data_csv/cdm_source.csv
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cdm_source_name,cdm_source_abbreviation,cdm_holder,source_description,source_documentation_reference,cdm_etl_reference,source_release_date,cdm_release_date,cdm_version,vocabulary_version
MIMIC IV,mimiciv,PhysioNet,"MIMIC-IV is a publicly available database of patients admitted to the Beth Israel Deaconess Medical Center in Boston, MA, USA.",https://mimic-iv.mit.edu/docs/,https://github.com/OHDSI/MIMIC/,2020-09-01,2021-05-03,5.3.1,v5.0 10-SEP-20
1 change: 1 addition & 0 deletions ...t/mimiciv_demo_omop/physionet.org/files/mimic-iv-demo-omop/0.9/1_omop_data_csv/cohort.csv
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cohort_definition_id,subject_id,cohort_start_date,cohort_end_date
1 change: 1 addition & 0 deletions ...demo_omop/physionet.org/files/mimic-iv-demo-omop/0.9/1_omop_data_csv/cohort_attribute.csv
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cohort_definition_id,subject_id,cohort_start_date,cohort_end_date,attribute_definition_id,value_as_number,value_as_concept_id
1 change: 1 addition & 0 deletions ...emo_omop/physionet.org/files/mimic-iv-demo-omop/0.9/1_omop_data_csv/cohort_definition.csv
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cohort_definition_id,cohort_definition_name,cohort_definition_description,definition_type_concept_id,cohort_definition_syntax,subject_concept_id,cohort_initiation_date
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