├── .gitignore ├── 0_prepare_files.py ├── 1_extract_amsterdam.py ├── 1_extract_eicu.py ├── 1_extract_hirid.py ├── 1_extract_mimic3.py ├── 1_extract_mimic4.py ├── 2_harmonize_amsterdam.py ├── 2_harmonize_eicu.py ├── 2_harmonize_hirid.py ├── 2_harmonize_mimic3.py ├── 2_harmonize_mimic4.py ├── 3_harmonize_blendedICU_labels.py ├── 4_write_omop.py ├── LICENSE ├── Readme.md ├── __init__.py ├── amsterdam_preprocessing ├── AmsterdamPreparator.py ├── __init__.py ├── flat_and_labels.py └── timeseries.py ├── auxillary_files ├── OMOP_CDMv5.4_Field_Level.csv ├── diagnoses.json ├── medication_mapping_files │ ├── amsterdam_medications.csv │ ├── drugnames.parquet │ ├── eicu_medications.csv │ ├── hirid_medications.csv │ ├── med_concept_ids.parquet │ ├── medications_v10.json │ ├── medications_v9.json │ ├── mimic3_medications.csv │ ├── mimic4_medications.csv │ └── ohdsi_icu_medications.csv ├── medications_v11.json └── user_input │ ├── admission_origins_v2.json │ ├── discharge_location_v2.json │ ├── manual_icu_meds.csv │ ├── med_administration_routes.json │ ├── medication_ingredients.csv │ ├── timeseries_variables.csv │ └── unit_type_v2.json ├── blended_preprocessing ├── BlendedicuPreparator.py ├── __init__.py ├── diagnoses.py ├── flat_and_labels.py ├── omop_conversion.py └── timeseries.py ├── config.json ├── database_processing ├── __init__.py ├── datapreparator.py ├── dataprocessor.py ├── diagnosesprocessor.py ├── flatandlabelsprocessor.py ├── newmedicationprocessor.py └── timeseriesprocessor.py ├── eicu_preprocessing ├── __init__.py ├── eicupreparator.py ├── flat_and_labels.py └── timeseries.py ├── env.yml ├── figures_and_tables ├── blendedICU_stats.py └── make_appendix.py ├── hirid_preprocessing ├── HiridPreparator.py ├── __init__.py ├── flat_and_labels.py └── timeseries.py ├── mimic3_preprocessing ├── flat_and_labels.py ├── mimic3preparator.py └── timeseries.py ├── mimic4_preprocessing ├── __init__.py ├── diagnoses.py ├── flat_and_labels.py ├── mimic4preparator.py └── timeseries.py ├── omop_cdm ├── OMOP_CDMv5.4_Table_Level.xls ├── __init__.py ├── omop_parquet.py └── tables.py ├── omopize ├── medication_mapping.py ├── omop_diagnoses.py └── omop_medications.py ├── paths.json └── plot ├── Thumbs.db └── kdeplot.png /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/USM-CHU-FGuyon/BlendedICU/HEAD/.gitignore -------------------------------------------------------------------------------- /0_prepare_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/USM-CHU-FGuyon/BlendedICU/HEAD/0_prepare_files.py -------------------------------------------------------------------------------- /1_extract_amsterdam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/USM-CHU-FGuyon/BlendedICU/HEAD/1_extract_amsterdam.py 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