CPDatSSI (V1.x)

This package is mapping any chemicals (from their CASRN) on the CPDAT database and provide a board exposure categorization.
Current Version 1.01 (11/23/2021)

Description

This package developed in python will allow to map any chemicals from their CASRN to an exposure board class using CPDAT database.
Seven classes of board exposure are used:

• Pesticide: include pesticide or derivative chemicals
• Industrial: include produces found in industrial process
• Environemental: include exposure from environment, contaminated water, soil or air exposures
• Diet: include exposure chemicals found in the diet
• Pharmaceuticals: include pharmaceutical chemicals or drugs-like molecules
• Consumer products: include chemicals in consumer products

The mapping uses string terms in the different parts of the database. The all list of search terms is reported in the docs/ folder in the sources.

Installation

Dependancy

• Python >= 3.6 with libraries
  • pip
  • numpy

Installation with pip

$pip install -i https://test.pypi.org/simple/ CPDatSSI

Run CPDatSSI

In Python - example of run

import CPDatSSI
pr_database = "< your path to the database >/CPDatRelease20201216/"
l_CASRN = ["106-50-3", "128-95-0", "2243-62-1", "112-38-9", "82-44-0", "2110-18-1"] # exemple of input
c_CPDAT = CPDatSSI.CPDatSSI(pr_database)
c_CPDAT.loadMapping()
c_CPDAT.listCasToFunct(l_CASRN)
out = c_CPDAT.extractBoardExposure()
print(out)

Script

In the scripts folder in GitHub you can find a script to run CPDat in bash or powershell terminal.

python generateBoardExposure.py -h

Ressources

GitHub

https://github.com/SilentSpringInstitute/CPDatSSI

Package available:

https://test.pypi.org/project/CPDatSSI/

Data input

CPDAT (version="20201216") exposure mapping
Folder: /CPDat/CPDatRelease20201216/"
Download CPDAT:

https://epa.figshare.com/articles/dataset/The_Chemical_and_Products_Database_CPDat_MySQL_Data_File/5352997

 

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Project updates

• 10-12-21: init git
• 11-01-21: transform curent script to package available in pip
• 11-23-21: publish the version 1.0

Version update

• v1.01: match search term "food contact" to Diet and Consumer Product and remove food contact categorie. Correct pharmaceuticals categorie name

TODO list for futur version

• Map on DTXSID

Development command lines

python -m unittest tests/testMapping.py #unit test on Chemical class
python setup.py sdist bdist_wheel
python -m twine upload --repository testpypi dist/* #upload on testpypi and precise the version
pip uninstall CPDatSSI
pip install -i https://test.pypi.org/simple/ CPDatSSI