diff --git a/docs/functionalities/biology/concepts_sets.md b/docs/functionalities/biology/concepts_sets.md new file mode 100644 index 00000000..207c1be3 --- /dev/null +++ b/docs/functionalities/biology/concepts_sets.md @@ -0,0 +1,118 @@ +# Validated Concepts Sets + +Those concept sets can be found in `eds_scikit.datasets.default_concepts_sets`. + +!!! question "How were the code selected ?" + Each concept set codes were selected by coding system expert and validated through statistical analysis. However new codes may appear or become outdated. Feel free to propose new concept sets or concept codes ! + +=== "Blood Count Cell" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:------------------------------------------|:-------------------------------------------------------------------------| + | Hemoglobin_Blood_Count | ['A0163', 'H6738'] | + | Leukocytes_Blood_Count | ['A0174', 'H6740', 'C8824'] | + | Platelets_Blood_Count | ['A0230', 'H6751', 'A1598', 'A1598', 'A2538', 'A2539', 'A2539', 'J4463'] | + | Lymphocytes_Blood_Count | ['A0198', 'H6743'] | + | Monocytes_Blood_Count | ['A0210', 'H6747'] | + | Neutrophil_Polymorphonuclears_Blood_Count | ['A0155', 'H6732'] | + | Eosinophil_Polymorphonuclears_Blood_Count | ['A0150', 'H6730'] | + +=== "Ionogram" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:--------------------------------|:----------------------------------------------------------------------------------| + | Bicarbonate_Blood_Concentration | ['A0422', 'H9622', 'C6408', 'F4161', 'A2136', 'J7371', 'G2031'] | + | Calcium_Blood_Concentration | ['C0543', 'D2359', 'A0038', 'H5041', 'F2625', 'L5047', 'A2512', 'A2512', 'A0607'] | + | Chloride_Blood_Concentration | ['A0079', 'J1179', 'F2619'] | + | Potassium_Blood_Concentration | ['A2380', 'E2073', 'F2618', 'E2337', 'J1178'] | + | Sodium_Blood_Concentration | ['A0262', 'J1177', 'F8162', 'F2617'] | + +=== "Blood Gas" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:--------------------------------|:----------------------------| + | HCO3-_Blood_Concentration | ['A0420', 'L5018'] | + | Lactate_Gaz_Blood_Concentration | ['C8697', 'H7748'] | + | PaCO2_Blood_Concentration | ['A7305', 'A0630'] | + | PaO2_Blood_Concentration | ['A7319', 'H7747'] | + | SaO2_Blood_Concentration | ['A7334', 'L5021'] | + | pH_Blood | ['A0221', 'L5017', 'A0219'] | + +=== "Hepatic Panel" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:------------------------------|:----------------------------------------------| + | ALAT_Activity | ['A0002', 'G1804', 'J7373', 'E2067', 'F2629'] | + | ASAT_Activity | ['A0022', 'G1800', 'E2068', 'F2628'] | + | GGT_Activity | ['A0131', 'F8184', 'E9771', 'J7370', 'K7045'] | + | PAL_Activity | ['A0227', 'F8187', 'E6331', 'F1844'] | + | Total_Bilirubin_Concentration | ['A0029', 'H5264', 'D0189'] | + +=== "Cardiac Biomarkers" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:-------------------------------|:----------------------------------------------------------------------------------| + | BNP_Concentration | ['C8189', 'B5596', 'A2128'] | + | BNP_and_NTProBNP_Concentration | ['C8189', 'B5596', 'A2128', 'A7333', 'J7267', 'J7959'] | + | NTProBNP_Concentration | ['A7333', 'J7267', 'J7959'] | + | Troponine_Concentration | ['A0283', 'C5560', 'F9934', 'E6954', 'L3534', 'G7716', 'J5184', 'A3832', 'E7249'] | + +=== "Inflammatory Panel" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:-----------------------------|:-------------------------------------------------------| + | CRP_Concentration | ['A0248', 'E6332', 'F5581', 'J7381', 'F2631'] | + | Fibrinogen_Concentration | ['A0126'] | + | Proteins_Blood_Concentration | ['A7347', 'F5122', 'F2624', 'B9417', 'A0249', 'B3990'] | + +=== "Martial Panel" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:-----------------------------------|:----------------------------| + | Ferritin_Concentration | ['A0123', 'E9865'] | + | Transferrin_Saturation_Coefficient | ['A0278'] | + +=== "Renal Panel" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:-----------------------------------|:-------------------------------------------------------| + | Glomerular_Filtration_Rate_EPI_CKD | ['G6921', 'F8160', 'F9613', 'F9621', 'F9621'] | + | Glomerular_Filtration_Rate_MDRD | ['F9622', 'G7835', 'B9964', 'A7456', 'A7455', 'H5609'] | + | Urea_Blood_Concentration | ['A0286', 'G3350', 'J7372', 'F2620'] | + +=== "Coagulation" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:--------------------------------------|:----------------------------------------------------------------------------------| + | Activated_Partial_Thromboplastin_Time | ['A1792', 'L7286', 'A7748'] | + | D-Dimers_Concentration | ['C7882', 'C7882', 'I8765', 'A0124', 'C0474', 'C0474', 'C0474', 'B4199', 'F5402'] | + | Quick_INR_Time | ['A0269'] | + | Quick_Prothrombin_Time | ['A1805', 'E9993'] | + +=== "Proteins" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:---------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------| + | Albumine_Blood_Concentration | ['D2358', 'C6841', 'C2102', 'G6616', 'L2260', 'A0006', 'E4799', 'I2013'] | + | EPP_Blood_Concentration | ['A0250', 'C9874', 'A3758', 'A0004', 'F9978', 'A0005', 'H8137', 'C7087', 'A0003', 'C7088', 'B9456', 'B9455', 'A0008', 'H8138', 'C7089', 'A0007'... | + | Phosphates_Blood_Concentration | ['A0226', 'F8186', 'F2626'] | + | Proteins_Urine_24h_Concentration | ['A1695', 'A1694', 'A1696', 'C9990', 'C9991', 'J7268', 'J7269', 'C3941', 'E4745', 'G4187', 'F6060'] | + +=== "Diabete" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:----------------------------|:-------------------------------------------------------------------------------------------------------------| + | B-HCG_Blood_Concentration | ['A7426', 'F2353', 'A0164', 'L2277'] | + | Glucose_Blood_Concentration | ['A0141', 'H7323', 'J7401', 'F2622', 'B9553', 'C7236', 'E7312', 'A7338', 'H7324', 'C0565', 'E9889', 'A8424'] | + | HbA1c_Blood_% | ['B6983', 'A2228', 'A1271', 'E6632', 'I5968'] | + | TSH_Concentration | ['A1831', 'F2150', 'I8385', 'C2666'] | + +=== "Inflammatory Biomarkers" + + | concepts_set_name | GLIMS_ANABIO_concept_code | + |:----------------------------------|:----------------------------------------------------------------------------------------------------| + | IL-1 beta_Blood_Concentration | ['C9351', 'B8921', 'G4800', 'K3662', 'L2217', 'J9193', 'K3665', 'K3687', 'K3661', 'L2197'] | + | IL-10_Blood_Concentration | ['B8922', 'C8763', 'K3478', 'L2210', 'J9187', 'K3481', 'K3472', 'K3475', 'L2198'] | + | IL-6_Blood_Concentration | ['B8929', 'G4799', 'B1910', 'K3467', 'L2205', 'E6992', 'J9190', 'K3456', 'L2193', 'K3435', 'K3460'] | + | Procalcitonin_Blood_Concentration | ['A1661', 'H5267', 'F2632'] | + | TNF alpha_Blood_Concentration | ['B8931', 'G4801', 'C9393', 'K3505', 'L2203', 'E6993', 'J9194', 'K3658', 'K3502', 'K3504', 'L2191'] | diff --git a/docs/functionalities/biology/index.md b/docs/functionalities/biology/index.md index aa32f5ed..a9679a0c 100644 --- a/docs/functionalities/biology/index.md +++ b/docs/functionalities/biology/index.md @@ -3,6 +3,7 @@ The biology module of [eds-scikit](https://github.com/aphp/eds-scikit) supports data scientists working on biological data. Its main objectives are to: +- Provide predefined biology __concept sets__ based on AP-HP coding system - Facilitate __codes mapping__ between different terminologies and referentials - Provide data __visualization tools__ and __statistic summary__ - Allows __automatic units__ conversion from heterogenous units system diff --git a/eds_scikit/datasets/default_concepts_sets.csv b/eds_scikit/datasets/default_concepts_sets.csv index 644306ab..e36767aa 100644 --- a/eds_scikit/datasets/default_concepts_sets.csv +++ b/eds_scikit/datasets/default_concepts_sets.csv @@ -1,73 +1,73 @@ concepts_set_name,GLIMS_ANABIO_concept_code,concepts_set_category -ALAT,"['A0002', 'G1804', 'J7373', 'E2067', 'F2629']",hepatic_panel -ASAT,"['A0022', 'G1800', 'E2068', 'F2628']",hepatic_panel +ALAT_Activity,"['A0002', 'G1804', 'J7373', 'E2067', 'F2629']",hepatic_panel +ASAT_Activity,"['A0022', 'G1800', 'E2068', 'F2628']",hepatic_panel Activated_Partial_Thromboplastin_Time,"['A1792', 'L7286', 'A7748']",coagulation Adenovirus,"['I5915', 'I7952', 'J2229', 'J2988', 'J8817', 'K1527', 'J9968']",virology -Albumin,"['D2358', 'C6841', 'C2102', 'G6616', 'L2260', 'A0006', 'E4799', 'I2013']",proteins -B-HCG,"['A7426', 'F2353', 'A0164', 'L2277']",diabete +Albumine_Blood_Concentration,"['D2358', 'C6841', 'C2102', 'G6616', 'L2260', 'A0006', 'E4799', 'I2013']",proteins +B-HCG_Blood_Concentration,"['A7426', 'F2353', 'A0164', 'L2277']",diabete B.pertussis,"['I7748', 'I7968', 'K1531']",virology -BNP,"['C8189', 'B5596', 'A2128']",cardiac_biomarkers -BNP_and_NT_ProBNP,"['C8189', 'B5596', 'A2128', 'A7333', 'J7267', 'J7959']",cardiac_biomarkers -Bicarbonate_Blood,"['A0422', 'H9622', 'C6408', 'F4161', 'A2136', 'J7371', 'G2031']",ionogram +BNP_Concentration,"['C8189', 'B5596', 'A2128']",cardiac_biomarkers +BNP_and_NTProBNP_Concentration,"['C8189', 'B5596', 'A2128', 'A7333', 'J7267', 'J7959']",cardiac_biomarkers +Bicarbonate_Blood_Concentration,"['A0422', 'H9622', 'C6408', 'F4161', 'A2136', 'J7371', 'G2031']",ionogram C.pneumoniae,"['I5930', 'I7969', 'J2207', 'K1530', 'J9919']",virology -CRP,"['A0248', 'E6332', 'F5581', 'J7381', 'F2631']",inflammatory_panel -Calcium_Blood,"['C0543', 'D2359', 'A0038', 'H5041', 'F2625', 'L5047', 'A2512', 'A2512', 'A0607']",ionogram -Chloride_Blood,"['A0079', 'J1179', 'F2619']",ionogram +CRP_Concentration,"['A0248', 'E6332', 'F5581', 'J7381', 'F2631']",inflammatory_panel +Calcium_Blood_Concentration,"['C0543', 'D2359', 'A0038', 'H5041', 'F2625', 'L5047', 'A2512', 'A2512', 'A0607']",ionogram +Chloride_Blood_Concentration,"['A0079', 'J1179', 'F2619']",ionogram Coronavirus,"['I5916', 'I5917', 'I5918', 'I5919', 'I7953', 'I7954', 'I7955', 'I7956', 'J2199', 'J2996', 'J2994', 'J2993', 'J2992', 'J8829', 'J8828', 'J8823', 'J8822', 'K1525', 'K1524', 'K1522', 'K1523', 'J9969']",virology Creatine Kinase,"['A0090', 'G0171', 'E6330']",other -D-Dimers,"['C7882', 'C7882', 'I8765', 'A0124', 'C0474', 'C0474', 'C0474', 'B4199', 'F5402']",coagulation -EPP,"['A0250', 'C9874', 'A3758', 'A0004', 'F9978', 'A0005', 'H8137', 'C7087', 'A0003', 'C7088', 'B9456', 'B9455', 'A0008', 'H8138', 'C7089', 'A0007', 'C7090', 'A0010', 'H8139', 'C7091', 'A0009', 'C7092', 'C6525', 'C6524', 'A0415', 'C7093', 'A0414', 'C7094', 'B9458', 'B9457', 'A2113', 'H8140', 'E5327', 'A2112', 'E5328', 'C6536', 'C6535', 'E2398', 'E2399', 'A2115', 'H8141', 'E5329', 'A2114', 'E5330', 'C6538', 'C6537', 'E2400', 'E2401', 'A0130', 'H8142', 'C7100', 'A0129', 'C7101', 'G6942', 'G6941', 'B9460', 'B9459', 'C6596', 'C6595', 'C6598', 'C6597', 'E2402', 'E2403', 'K4483', 'A2118', 'A2117', 'E1847', 'B8047', 'A2127', 'I8076', 'A2126', 'I8077', 'X5093', 'X5094', 'X5091', 'X5092', 'A2279', 'L7258', 'A1361', 'L7259', 'C6909', 'B1727', 'B1725', 'C6924', 'I5139', 'X5097', 'X5098', 'X5095', 'X5096', 'A2278', 'L7260', 'A2277', 'L7261', 'D0265', 'B1728', 'B1726', 'D0267', 'I5140', 'X5101', 'X5102', 'X5099', 'X5100', 'H6397', 'L7262', 'H6396', 'L7263', 'D0266', 'C0616', 'D0268', 'I5141', 'A8775', 'A7816', 'A8776', 'A8777', 'A8778', 'A8779', 'A8780', 'A7330', 'F0748', 'F0749', 'H9656', 'H9657', 'H9658', 'H9659', 'H9660']",proteins -Eosinophil_Polymorphonuclears_Blood,"['A0150', 'H6730']",blood_count_cell -Ferritin,"['A0123', 'E9865']",martial_panel -Fibrinogen,['A0126'],inflammatory_panel -GFR (EPI CKD),"['G6921', 'F8160', 'F9613', 'F9621', 'F9621']",renal_panel -GFR (MDRD),"['F9622', 'G7835', 'B9964', 'A7456', 'A7455', 'H5609']",renal_panel -GGT,"['A0131', 'F8184', 'E9771', 'J7370', 'K7045']",hepatic_panel -Glucose_Blood,"['A0141', 'H7323', 'J7401', 'F2622', 'B9553', 'C7236', 'E7312', 'A7338', 'H7324', 'C0565', 'E9889', 'A8424']",diabete -HCO3-_Blood,"['A0420', 'L5018']",blood_gas +D-Dimers_Concentration,"['C7882', 'C7882', 'I8765', 'A0124', 'C0474', 'C0474', 'C0474', 'B4199', 'F5402']",coagulation +EPP_Blood_Concentration,"['A0250', 'C9874', 'A3758', 'A0004', 'F9978', 'A0005', 'H8137', 'C7087', 'A0003', 'C7088', 'B9456', 'B9455', 'A0008', 'H8138', 'C7089', 'A0007', 'C7090', 'A0010', 'H8139', 'C7091', 'A0009', 'C7092', 'C6525', 'C6524', 'A0415', 'C7093', 'A0414', 'C7094', 'B9458', 'B9457', 'A2113', 'H8140', 'E5327', 'A2112', 'E5328', 'C6536', 'C6535', 'E2398', 'E2399', 'A2115', 'H8141', 'E5329', 'A2114', 'E5330', 'C6538', 'C6537', 'E2400', 'E2401', 'A0130', 'H8142', 'C7100', 'A0129', 'C7101', 'G6942', 'G6941', 'B9460', 'B9459', 'C6596', 'C6595', 'C6598', 'C6597', 'E2402', 'E2403', 'K4483', 'A2118', 'A2117', 'E1847', 'B8047', 'A2127', 'I8076', 'A2126', 'I8077', 'X5093', 'X5094', 'X5091', 'X5092', 'A2279', 'L7258', 'A1361', 'L7259', 'C6909', 'B1727', 'B1725', 'C6924', 'I5139', 'X5097', 'X5098', 'X5095', 'X5096', 'A2278', 'L7260', 'A2277', 'L7261', 'D0265', 'B1728', 'B1726', 'D0267', 'I5140', 'X5101', 'X5102', 'X5099', 'X5100', 'H6397', 'L7262', 'H6396', 'L7263', 'D0266', 'C0616', 'D0268', 'I5141', 'A8775', 'A7816', 'A8776', 'A8777', 'A8778', 'A8779', 'A8780', 'A7330', 'F0748', 'F0749', 'H9656', 'H9657', 'H9658', 'H9659', 'H9660']",proteins +Eosinophil_Polymorphonuclears_Blood_Count,"['A0150', 'H6730']",blood_count_cell +Ferritin_Concentration,"['A0123', 'E9865']",martial_panel +Fibrinogen_Concentration,['A0126'],inflammatory_panel +Glomerular_Filtration_Rate_EPI_CKD,"['G6921', 'F8160', 'F9613', 'F9621', 'F9621']",renal_panel +Glomerular_Filtration_Rate_MDRD,"['F9622', 'G7835', 'B9964', 'A7456', 'A7455', 'H5609']",renal_panel +GGT_Activity,"['A0131', 'F8184', 'E9771', 'J7370', 'K7045']",hepatic_panel +Glucose_Blood_Concentration,"['A0141', 'H7323', 'J7401', 'F2622', 'B9553', 'C7236', 'E7312', 'A7338', 'H7324', 'C0565', 'E9889', 'A8424']",diabete +HCO3-_Blood_Concentration,"['A0420', 'L5018']",blood_gas HIV Serology,"['D2865', 'D2867', 'D2845', 'D2864', 'F4252', 'D2866', 'F3257', 'D2869', 'F1705', 'D2846', 'D2847', 'D2844', 'E8605', 'F5401', 'G0175', 'J5891', 'J2672', 'H7667']",serology -HbA1c_Blood,"['B6983', 'A2228', 'A1271', 'E6632', 'I5968']",diabete -Hemoglobin_Blood,"['A0163', 'H6738']",blood_count_cell +HbA1c_Blood_%,"['B6983', 'A2228', 'A1271', 'E6632', 'I5968']",diabete +Hemoglobin_Blood_Count,"['A0163', 'H6738']",blood_count_cell Hepatitis B Serology,"['D2729', 'D2730', 'E1524', 'F2075', 'D2725', 'I1903', 'D2728', 'D2726', 'D2726', 'F5613', 'D2731', 'D2727', 'G1197', 'G1199', 'G1199', 'J5887', 'J5890', 'J2697', 'L6883', 'J2695', 'L7877', 'D2653', 'D2660', 'D2654', 'D2661', 'D2649', 'D2656', 'H9686', 'H9687', 'I6579', 'I6580', 'D2652', 'D2659', 'D2650', 'D2650', 'D2657', 'D2655', 'D2662', 'D2651', 'D2651', 'D2658', 'F5615', 'F5616', 'G1209', 'G1209', 'G1210', 'G1210', 'I2927', 'I2928', 'J5885', 'J5886', 'J2699', 'J2700']",serology Hepatitis C Serology,"['D2780', 'H5078', 'I1846', 'D2777', 'E6503', 'D2778', 'D3088', 'D3088', 'D2774', 'J1518', 'D2776', 'D2771', 'E8372', 'F7465', 'I3151', 'G0173', 'L1237', 'J2678', 'K3833', 'E8373', 'K4228']",serology -IL-1 beta,"['C9351', 'B8921', 'G4800', 'K3662', 'L2217', 'J9193', 'K3665', 'K3687', 'K3661', 'L2197']",inflammatory_biomarkers -IL-10,"['B8922', 'C8763', 'K3478', 'L2210', 'J9187', 'K3481', 'K3472', 'K3475', 'L2198']",inflammatory_biomarkers -IL-6,"['B8929', 'G4799', 'B1910', 'K3467', 'L2205', 'E6992', 'J9190', 'K3456', 'L2193', 'K3435', 'K3460']",inflammatory_biomarkers -INR,['A0269'],coagulation +IL-1 beta_Blood_Concentration,"['C9351', 'B8921', 'G4800', 'K3662', 'L2217', 'J9193', 'K3665', 'K3687', 'K3661', 'L2197']",inflammatory_biomarkers +IL-10_Blood_Concentration,"['B8922', 'C8763', 'K3478', 'L2210', 'J9187', 'K3481', 'K3472', 'K3475', 'L2198']",inflammatory_biomarkers +IL-6_Blood_Concentration,"['B8929', 'G4799', 'B1910', 'K3467', 'L2205', 'E6992', 'J9190', 'K3456', 'L2193', 'K3435', 'K3460']",inflammatory_biomarkers +Quick_INR_Time,['A0269'],coagulation Influenza A,"['I5922', 'I7960', 'J2198', 'J2990', 'J8825', 'K1517']",virology Influenza B,"['I5923', 'I7961', 'J2203', 'J2985', 'J8819', 'K1513']",virology L.pneumophila,"['J2176', 'J3006', 'J8826', 'J9899']",virology LDH,"['A0170', 'H5261', 'J7400', 'C8889', 'J1161']",other -Lactate_Gaz_Blood,"['C8697', 'H7748']",blood_gas +Lactate_Gaz_Blood_Concentration,"['C8697', 'H7748']",blood_gas Legionella Antigenuria,"['D1465', 'H6694', 'J7960']",antigenury -Leukocytes_Blood,"['A0174', 'H6740', 'C8824']",blood_count_cell -Lymphocytes_Blood,"['A0198', 'H6743']",blood_count_cell +Leukocytes_Blood_Count,"['A0174', 'H6740', 'C8824']",blood_count_cell +Lymphocytes_Blood_Count,"['A0198', 'H6743']",blood_count_cell Metapneumovirus,"['I5920', 'I7958', 'J2200', 'J2991', 'J8824', 'K1519', 'J9965']",virology -Monocytes_Blood,"['A0210', 'H6747']",blood_count_cell -NT Pro-BNP,"['A7333', 'J7267', 'J7959']",cardiac_biomarkers -Neutrophil_Polymorphonuclears_Blood,"['A0155', 'H6732']",blood_count_cell -PAL,"['A0227', 'F8187', 'E6331', 'F1844']",hepatic_panel -PaCO2_Blood,"['A7305', 'A0630']",blood_gas -PaO2_Blood,"['A7319', 'H7747']",blood_gas +Monocytes_Blood_Count,"['A0210', 'H6747']",blood_count_cell +NTProBNP_Concentration,"['A7333', 'J7267', 'J7959']",cardiac_biomarkers +Neutrophil_Polymorphonuclears_Blood_Count,"['A0155', 'H6732']",blood_count_cell +PAL_Activity,"['A0227', 'F8187', 'E6331', 'F1844']",hepatic_panel +PaCO2_Blood_Concentration,"['A7305', 'A0630']",blood_gas +PaO2_Blood_Concentration,"['A7319', 'H7747']",blood_gas Parainfluenza,"['I5924', 'I5925', 'I5926', 'I5927', 'I7962', 'I7963', 'I7964', 'I7965', 'J2204', 'J2979', 'J2977', 'J2983', 'J2981', 'J8861', 'J8862', 'J8821', 'J8820', 'K1509', 'K1508', 'K1510', 'K1535', 'J9964']",virology -Phosphates,"['A0226', 'F8186', 'F2626']",proteins -Platelets_Blood,"['A0230', 'H6751', 'A1598', 'A1598', 'A2538', 'A2539', 'A2539', 'J4463']",blood_count_cell +Phosphates_Blood_Concentration,"['A0226', 'F8186', 'F2626']",proteins +Platelets_Blood_Count,"['A0230', 'H6751', 'A1598', 'A1598', 'A2538', 'A2539', 'A2539', 'J4463']",blood_count_cell Pneumococcal Antigenuria,"['D2055', 'J7962', 'A2804']",antigenury -Potassium_Blood,"['A2380', 'E2073', 'F2618', 'E2337', 'J1178']",ionogram -Procalcitonin,"['A1661', 'H5267', 'F2632']",inflammatory_biomarkers -Proteins,"['A1695', 'A1694', 'A1696', 'C9990', 'C9991', 'J7268', 'J7269', 'C3941', 'E4745', 'G4187', 'F6060']",proteins -Proteins_Blood,"['A7347', 'F5122', 'F2624', 'B9417', 'A0249', 'B3990']",inflammatory_panel -Prothrombin_Level,"['A1805', 'E9993']",coagulation +Potassium_Blood_Concentration,"['A2380', 'E2073', 'F2618', 'E2337', 'J1178']",ionogram +Procalcitonin_Blood_Concentration,"['A1661', 'H5267', 'F2632']",inflammatory_biomarkers +Proteins_Urine_24h_Concentration,"['A1695', 'A1694', 'A1696', 'C9990', 'C9991', 'J7268', 'J7269', 'C3941', 'E4745', 'G4187', 'F6060']",proteins +Proteins_Blood_Concentration,"['A7347', 'F5122', 'F2624', 'B9417', 'A0249', 'B3990']",inflammatory_panel +Quick_Prothrombin_Time,"['A1805', 'E9993']",coagulation RSV,"['I5928', 'I7966', 'J2201', 'J2974', 'J8859', 'K1534']",virology Rhino/Enterovirus,"['I5921', 'I7959', 'J2197', 'J2973', 'J8858', 'K1515']",virology SARS-CoV-2,"['K1108', 'J9791', 'J8706', 'J8827', 'K1520']",virology -SaO2_Blood,"['A7334', 'L5021']",blood_gas -Sodium_Blood,"['A0262', 'J1177', 'F8162', 'F2617']",ionogram -TNF alpha,"['B8931', 'G4801', 'C9393', 'K3505', 'L2203', 'E6993', 'J9194', 'K3658', 'K3502', 'K3504', 'L2191']",inflammatory_biomarkers -TSH,"['A1831', 'F2150', 'I8385', 'C2666']",diabete -Total Bilirubin,"['A0029', 'H5264', 'D0189']",hepatic_panel -Transferrin Saturation Coefficient,['A0278'],martial_panel -Troponin,"['A0283', 'C5560', 'F9934', 'E6954', 'L3534', 'G7716', 'J5184', 'A3832', 'E7249']",cardiac_biomarkers -Urea_Blood,"['A0286', 'G3350', 'J7372', 'F2620']",renal_panel +SaO2_Blood_Concentration,"['A7334', 'L5021']",blood_gas +Sodium_Blood_Concentration,"['A0262', 'J1177', 'F8162', 'F2617']",ionogram +TNF alpha_Blood_Concentration,"['B8931', 'G4801', 'C9393', 'K3505', 'L2203', 'E6993', 'J9194', 'K3658', 'K3502', 'K3504', 'L2191']",inflammatory_biomarkers +TSH_Concentration,"['A1831', 'F2150', 'I8385', 'C2666']",diabete +Total_Bilirubin_Concentration,"['A0029', 'H5264', 'D0189']",hepatic_panel +Transferrin_Saturation_Coefficient,['A0278'],martial_panel +Troponine_Concentration,"['A0283', 'C5560', 'F9934', 'E6954', 'L3534', 'G7716', 'J5184', 'A3832', 'E7249']",cardiac_biomarkers +Urea_Blood_Concentration,"['A0286', 'G3350', 'J7372', 'F2620']",renal_panel Venous_Lactate,"['A0173', 'B9146', 'A9995']",other pH_Blood,"['A0221', 'L5017', 'A0219']",blood_gas diff --git a/eds_scikit/datasets/default_concepts_sets_.csv b/eds_scikit/datasets/default_concepts_sets_.csv deleted file mode 100644 index 67f03646..00000000 --- a/eds_scikit/datasets/default_concepts_sets_.csv +++ /dev/null @@ -1,32 +0,0 @@ -concepts_set_name,ITM_LOINC_concept_code,ITM_ANABIO_concept_code -Hemoglobin_Blood_Quantitative,"['30352-9', '718-7', '75928-2', '30350-3', '30313-1', '59260-0', '93846-4']","['E9823', 'C1549', 'J4764', 'C8745', 'J6562', 'Z0363', 'I4392', 'B1947', 'A0163', 'I7893', 'A9882', 'B1946', 'B1945', 'F8179']" -Hemoglobin_Urine_Quantitative,"['726-0', '50559-4', '49137-3']","['F5617', 'Z3115', 'B2320']" -Leukocytes_Blood_Quantitative,"['49498-9', '26464-8', '6690-2', '804-5']","['E6953', 'C9784', 'E4358', 'C9097', 'K3232', 'K6094', 'A0174']" -Neutrophils_Blood_Quantitative,"['751-8', '752-6', '753-4', '26499-4']","['C5022', 'C9109', 'A0155']" -Lymphocytes_Blood_Quantitative,"['30364-4', '731-0', '732-8', '26474-7']","['C5020', 'C3963', 'A0198', 'C9101', 'G3352', 'K3233']" -Platelets_Blood_Quantitative,"['26515-7', '79427-1', '5907-1', '49497-1', '777-3', '778-1', '97995-5']","['I7892', 'G7833', 'A1598', 'A2539', 'J4463', 'H6751', 'G7727', 'G7728', 'A0230', 'B9896', 'K5276', 'A2538']" -Sodium_Blood_Quantitative,"['32717-1', '41657-8', '39791-9', '39792-7', '2947-0', '77139-4', '42570-2', '2951-2']","['H9437', 'J1177', 'K9086', 'A0262', 'H9442', 'H9430', 'D0025', 'H9436', 'H9433', 'C8759', 'B9562', 'J4692', 'F2617', 'I9212', 'H9438', 'H9429', 'H9443', 'H9435', 'H9432', 'H9441', 'C8804', 'F2457', 'H9434', 'J1180', 'H9428', 'H9431', 'H9440', 'A1772', 'C8760', 'F8162', 'H9439', 'H9444']" -Sodium_Urine_Quantitative,['2955-3'],"['D0074', 'H9377', 'H9386', 'A7464', 'H9380', 'H9390', 'H9378', 'H9393', 'F2459', 'H9391', 'H9379', 'D0072', 'H9387', 'H9382', 'H9388', 'H9381', 'H9383', 'H9384', 'H9385', 'D0070', 'H9389', 'H9392', 'A0260']" -Potassium_Blood_Quantitative,"['39790-1', '42569-4', '75940-7', '22760-3', '41656-0', '39789-3', '32713-0', '2823-3', '77142-8', '6298-4']","['H9458', 'C8757', 'H9456', 'H9459', 'E2337', 'J1181', 'H9452', 'H9454', 'C8803', 'H9448', 'H9446', 'H9450', 'C8758', 'D0024', 'H9460', 'F2443', 'H9447', 'H9461', 'H9453', 'J4691', 'A2380', 'A1656', 'B9561', 'E2073', 'H9455', 'F2618', 'H9457', 'H9445', 'H9449', 'H9451', 'J1178']" -Bicarbonate_Blood_Quantitative,"['1959-6', '19232-8', '69964-5', '1963-8', '19229-4', '1962-0', '14627-4', '1961-2', '19230-2', '19231-0', '1960-4', '19233-6']","['F2374', 'F4161', 'C8152', 'H9622', 'A0418', 'A0027', 'A0422', 'E9820', 'A0420', 'H6867', 'A0421', 'C6408']" -Protein_Blood_Quantitative,"['14897-3', '2885-2', '13537-6', '20577-3', '27258-3']","['H9484', 'H9488', 'H9481', 'B9417', 'H9495', 'H9483', 'H9489', 'H9479', 'D0058', 'H9485', 'H9493', 'B3990', 'J4429', 'H9492', 'H9482', 'A0249', 'H9480', 'C9874', 'E3162', 'F2624', 'H9491', 'H9490', 'F5122', 'H9486', 'A0250', 'H9487', 'H9494', 'A7347']" -Protein_Urine_Quantitative,"['5804-0', '27298-9', '50561-0', '2888-6']","['D0060', 'C9990', 'H2200', 'J7268', 'D0064', 'B9512', 'A1695', 'A1694', 'A7463', 'F2453', 'D0062']" -Urea_Blood_Quantitative,"['77136-0', '42571-0', '72926-9', '3091-6', '20977-5', '22664-7', '72927-7', '72903-8']","['F2474', 'H9524', 'J7372', 'H9525', 'H9528', 'H9520', 'H9526', 'J1148', 'H9516', 'H9514', 'G3350', 'H9522', 'H9519', 'H9518', 'H9515', 'H9523', 'J1147', 'J1150', 'J1152', 'H9513', 'H9521', 'H9527', 'J1149', 'H9529', 'F2620', 'H9517', 'A0286', 'J1151']" -Creatinine_Blood_Quantitative,"['35203-9', '38483-4', '2160-0', '14682-9', '77140-2', '59826-8', '21232-4']","['H9419', 'J4687', 'C0697', 'H9416', 'A7813', 'F9409', 'H9418', 'H9420', 'H9412', 'J1002', 'F2621', 'F9410', 'G7834', 'H9414', 'H9426', 'H9421', 'G1974', 'H9423', 'H9424', 'H9413', 'E3180', 'H9422', 'H9411', 'H4038', 'H9417', 'H9425', 'G1975', 'H9415', 'H9427', 'A0094']" -Creatinine_Urine_Quantitative,"['30002-0', '30004-6', '35204-7', '14683-7', '2161-8']","['E9944', 'H9305', 'H9310', 'H9298', 'E7029', 'H9294', 'H9303', 'E9635', 'E9945', 'F9404', 'H9302', 'F9407', 'C8222', 'F9403', 'H9309', 'A0091', 'F9590', 'H9296', 'C0694', 'A7457', 'E4733', 'E9946', 'H9297', 'E4731', 'E7027', 'H9295', 'H9308', 'E7025', 'H9307', 'H9304', 'A0986', 'H9301', 'H9300', 'C0695', 'H9306', 'A9701', 'L1777', 'H9299']" -Alanine-Aminotransferase_Blood_Quantitative,"['77144-4', '1743-4', '76625-3', '1744-2', '1742-6']","['F2629', 'G0162', 'A0002', 'E2067', 'J7373', 'G1804']" -Aspartate-Aminotransferase_Blood_Quantitative,"['30239-8', '88112-8', '1920-8']","['G0163', 'A0022', 'F2628', 'G1800', 'E2068']" -Bilirubin_Blood_Quantitative,"['59827-6', '42719-5', '14631-6', '77137-8', '1975-2', '59828-4', '89872-6', '54363-7', '35194-0', '89871-8']","['E7275', 'J4137', 'C5397', 'D0189', 'C8731', 'I3344', 'E7274', 'I3345', 'Z0017', 'A0029', 'H5264']" -Lactate-Dehydrogenase_Blood_Quantitative,"['14804-9', '2532-0', '14805-6']","['J7400', 'C8889', 'J1161', 'A0170', 'H5261']" -Creatine-Kinase_Blood_Quantitative,"['2157-6', '50756-6']","['A0090', 'G0171', 'E6330']" -Troponin-I_Blood_Quantitative,"['16255-2', '42757-5', '10839-9', '49563-0']","['Z3155', 'E6954', 'J5184', 'L1902', 'F9934', 'A0283', 'C5560', 'K3778', 'G7716']" -Troponin-T_Blood_Quantitative,"['67151-1', '48425-3', '6597-9', '6598-7']","['A3832', 'G6139', 'Z2619', 'E7249']" -Activated-Partial-Thromboplastin-Time_Blood_Quantitative,"['3173-2', '14979-9']","['C2444', 'K9945', 'C2442', 'A3961', 'A0265', 'C2443', 'B9003', 'B8082', 'C2446', 'C2445']" -Prothrombin-Time_Blood_Quantitative,"['5964-2', '5902-2']","['C2478', 'I7481', 'C7895', 'A0275', 'E9992']" -Fibrinogen_Blood_Quantitative,"['48664-7', '55452-7', '3255-7', '42568-6', '30902-1']","['C2430', 'A0127', 'B9989', 'A2667', 'C2432', 'C2433', 'A0126', 'C2431', 'C2428', 'C2429', 'A1114']" -D-Dimer_Blood_Quantitative,"['3246-6', '15129-0', '48067-3', '48058-2', '48065-7', '91556-1', '71427-9', '38898-3', '30240-6', '48066-5', '7799-0']","['I8765', 'A0124', 'B3767', 'B3772', 'B3770', 'B3771', 'B3769', 'B3773', 'F5402', 'C7882', 'B3768', 'H6285', 'C0474', 'B4199']" -C-Reactive-Protein_Blood_Quantitative,"['48421-2', '1988-5', '76485-2']","['E6332', 'J7381', 'A0248', 'B9476', 'F5581', 'F2631', 'F9618']" -Procalcitonin_Blood_Quantitative,"['33959-8', '75241-0']","['A1661', 'F2632', 'G6101', 'F8269', 'H5267', 'B9477', 'K6394']" -Albumin_Blood_Quantitative,"['54347-0', '76631-1', '62234-0', '77148-5', '61151-7', '1751-7', '61152-5', '62235-7']","['G6616', 'I2013', 'C2102', 'D2358', 'E4799', 'A0006', 'C6841', 'C2628']" -Monocytes_Blood_Quantitative,"['26484-6', '743-5', '742-7']","['C9104', 'K3234', 'C5021', 'A0210']" -Glucose_Blood_Quantitative,"['39481-7', '32016-8', '72516-8', '15074-8', '35211-2', '2341-6', '6777-7', '14743-9', '2339-0', '14749-6', '41652-9', '39480-9', '41651-1', '51596-5', '2340-8', '74774-1', '2345-7', '41653-7', '77135-2']","['H9536', 'F2406', 'H9546', 'H9530', 'F2622', 'H7754', 'H9539', 'H9544', 'H9541', 'A1245', 'J7401', 'C8796', 'C9747', 'H9533', 'H9542', 'H9535', 'H9543', 'H9534', 'C7236', 'F9620', 'A8029', 'H9531', 'E7961', 'A0141', 'A9713', 'H9538', 'B9553', 'E7312', 'H9540', 'H9545', 'H7753', 'A8424', 'H9532', 'H7749', 'A7339', 'E4736', 'H9537', 'H7323']" diff --git a/mkdocs.yml b/mkdocs.yml index fd89c9ae..363af5af 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -52,6 +52,7 @@ nav: - functionalities/biology/about_measurement.md - functionalities/biology/prepare_measurement.md - functionalities/biology/visualization.md + - functionalities/biology/concepts_sets.md - Plotting: - Event sequence: functionalities/plotting/event_sequences.md - Generating inclusion/exclusion flowchart: functionalities/plotting/flowchart.ipynb