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svittoz committed Feb 13, 2024
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118 changes: 118 additions & 0 deletions docs/functionalities/biology/concepts_sets.md
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# 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 However new codes may appear or become outdated.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'] |
1 change: 1 addition & 0 deletions docs/functionalities/biology/index.md
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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
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