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Tutorial

This tutorial takes you through the entire workflow of the Biology module.

%reload_ext autoreload
%autoreload 2

import eds_scikit
import pandas as pd

spark, sc, sql = eds_scikit.improve_performances() #

1. Load Data

First, you need to load your data. As detailed in the dedicated section, eds-scikit is expecting to work with Pandas or Koalas DataFrames. We provide various connectors to facilitate data fetching, namely a Hive connector, a Postgres connector and a Pandas connector.

This tutorial uses the Hive connector.

from eds_scikit.io import HiveData

data = HiveData(
    database_name="cse_XXX",
    tables_to_load=[
        "care_site",
        "concept",
        "concept_relationship",
        "measurement",
        "visit_occurrence",
    ],
)

Number of unique patients: 100000

2. Define your concepts-sets

In order to work on the measurements of interest, you can extract a list of concepts-sets by:

  • Selecting default concepts-sets provided in the library.
  • Modifying the codes of a selected default concepts-set.
  • Creating a concepts-set from scratch.

This tutorial uses all the default concepts-set with an additional custom concepts-set.

from eds_scikit.biology import ConceptsSet


protein_blood = ConceptsSet("Protein_Blood_Quantitative")
protein_urine = ConceptsSet("Protein_Urine_Quantitative")
protein = ConceptsSet(
    name="Protein_Quantitative",
    concept_codes=protein_blood.concept_codes + protein_urine.concept_codes,
)

custom_entity = ConceptsSet(
    name="Custom_entity", concept_codes=["G6616", "I2013", "C2102"]
)

concepts_sets = [
    protein,
    custom_entity,
]

3. Define the configuration

The configuration files does 3 things:

  • Remove outliers
  • Remove unwanted codes
  • Normalize units

3.1 The default configuration

A default configuration is available when working on APHP's CDW. You can access it via:

from eds_scikit.resources import registry

biology_config = registry.get("data", "get_biology_config.all_aphp")()

3.2 Create your own configuration (OPTIONAL)

If this default configuration file does not meet your requirements, you can follow this tutorial to create your own configuration file.
As a reminder, a configuration file is a csv table where each row corresponds to a given standard concept_code and a given unit. For each row, it gives a maximum threshold and a minimum threshold to flag outliers and a unit conversion coefficient to normalize units if needed.

3.2.1 Plot statistical summary

The first step is to compute the statistical summary of each concepts-set with the function plot_biology_summary(stats_only=True). 

from eds_scikit.biology import plot_biology_summary

start_date = "2017-01-01"
end_date = "2022-01-01"

plot_biology_summary(
    data,
    concepts_sets=concepts_sets,
    start_date=start_date,
    end_date=end_date,
    stats_only=True,
)

By default, the data will be saved in the Biology_summary folder.

Each ConceptSet will have its own folder. Here, we used, stats_only=True, so

  • No graphical dashboard will be generated
  • Data will not be stratified by care site

Let us display the results for the protein-related ConceptSet:

pd.read_csv("./Biology_summary/Protein_Quantitative/stats_summary.csv")
LOINC_concept_code AnaBio_concept_code LOINC_concept_name AnaBio_concept_name unit_source_value count mean std min 25% 50% 75% max MAD max_threshold min_threshold
0 2885-2 A0249 Prot SerPl-mCnc Protéines_Sérum_g/L g/l 6021 77.286 8.321 24.819 65.504 61.279 85.818 104.826 8.924 103.919 23.073
1 2885-2 A0250 Prot SerPl-mCnc Protéines_Sérum_Electrophorèse_g/L g/l 1176 59.705 7.609 24.735 47.535 84.605 90.445 137.543 7.131 91.838 32.455
2 2885-2 A7347 Prot SerPl-mCnc Protéines_Plasma_g/L g/l 12421 51.113 8.548 22.551 63.876 58.160 77.023 95.262 8.170 86.654 33.378
3 2885-2 B9417 Prot SerPl-mCnc Protéines_Sérum_Colorimétrie_g/L g/l 601 56.906 12.196 32.205 55.820 56.610 69.690 79.671 7.919 121.822 31.160
4 2885-2 C9874 Prot SerPl-mCnc Protéines_Sérum_Electrophorèse 2_g/L g/l 169 54.237 6.402 54.820 51.428 76.413 74.323 84.257 8.145 124.186 34.603
5 2885-2 D0058 Prot SerPl-mCnc Protéines Après dialyse_Sérum/Plasma_g/L g/l 51 64.920 4.699 52.023 71.595 61.444 78.434 76.351 4.502 73.379 39.551
6 2885-2 F2624 Prot SerPl-mCnc Protéines Pédiatrique_Sérum/Plasma_g/L g/l 3 58.934 11.768 45.364 40.882 54.139 59.366 84.880 11.952 77.996 5.854
7 2885-2 F5122 Prot SerPl-mCnc Protéines Duplication A7347_Plasma_g/L g/l 213 80.395 6.134 40.129 69.549 66.730 85.024 110.905 8.824 113.764 38.456
8 2888-6 A1694 Protéines [Masse/Volume] Urine - Numérique Protéines_Urines 24h_g/L g/l 193 2.343 4.262 0.063 0.089 0.257 1.620 52.679 0.162 1.275 0.000
9 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...

3.2.2 Create configuration from statistical summary

Then, you can use the function create_config_from_stats() to pre-fill the configuration file with max_threshold and min_threshold. The thresholds computation is based on the Median Absolute Deviation (MAD) Methodology[@madmethodology].

from eds_scikit.biology.utils.config import create_config_from_stats

config_name = "my_custom_config"

create_config_from_stats(
    concepts_sets=concepts_sets,
    config_name=config_name,
)

3.2.3 Edit units manually

The transformed_unit column is pre-filled with the unit that corresponds to the most measurements. When you notice a unit_source_value different than a transformed_unit, it probably means that the concept's unit needs to be normalized.

  • To normalize the unit of a concept you need to fill in manually the Action column with Transform and the Coefficient column with the unit conversion factor.
  • If you consider the concept irrelevant, you can fill in the Action column with Delete and it will delete the measurements corresponding to the concept.
  • If the unit_source_value matches the transformed_unit you can leave the Action and the Coefficient columns empty.

3.2.4 Use your custom configuration

Once you created your configuration (for instance under the name config_name="my_custom_config"), you can use provide it to the relevant functions (see below).

You can also check the configuration file directly:

from eds_scikit.resources import registry
config = registry.get("data", "biology_config.my_custom_config")()

4. Clean the data

Now you can use the bioclean() function with your custom configuration or the default configuration to:

It will add a bioclean table to your data. For more details, have a look on the dedicated section.

from eds_scikit.biology import bioclean

bioclean(
    data,
    concepts_sets=concepts_sets,
    config_name=config_name, # use config_name="all_aphp" for APHP's default configuration
    start_date=start_date,
    end_date=end_date,
)

See below the columns created by the bioclean() function:

concepts_set LOINC_concept_code LOINC_concept_name AnaBio_concept_code AnaBio_concept_name transformed_unit transformed_value max_threshold min_threshold outlier value_source_value unit_source_value
EntityA_Blood_Quantitative 000-0 EntityA #Bld A0000 EntityA_Blood x10*9/l 115 190 0 False 115 x10*9/l x10*9/l
EntityA_Blood_Quantitative 000-1 EntityA_Blood_Vol A0001 EntityA_Blood_g/l x10*9/l 220 190 0 True 560 g/l g/l
EntityB_Blood_Quantitative 001-0 EntityB_Blood B0000 EntityB_Blood_artery mmol 0.45 8.548 0.542 True 0.45 mmol mmol
EntityB_Blood_Quantitative 001-0 EntityB_Blood B0001 EntityB_Blood_vein mmol 4.52 8.548 0.542 False 4.52 mmol mmol
... ... ... ... ... ... ... ... ... ... ... ...

5. Visualize the statistical summary of clean data

Finally, you can build and save two interactive dashboards and a summary table for each concepts-set. It describes various statistical properties of your clean data.

from eds_scikit.biology import plot_biology_summary

plot_biology_summary(data)

Please see below some examples: