This repo contains a series of Jupiter Notebooks to download the Tox21 data from PubChem (via the PUG API and reformat it for visualisation in DataWarrior.
DataWarrior is an open source tool similar to Spotfire and Vortex; for those new to DataWarrior, a comprehensive manual is available here.
The notebooks are intended to be run in sequence; intermediate data structures are stored as pickle files in the directory data/ and the final output file, tox21_data_for_eu-toxrisk.csv, is also written to this directory. This CSV file may be loaded into DataWarrior and the template tox21_data_for_eu-toxrisk.dwat (found the directory files/) applied to set up the desired visualization.
Briefly...
0_Tox21_assays.ipynb: determines set of Tox21 Summary assays in PubChem1_Tox21_compounds.ipynb: retrieves set of substances and compounds tested in Tox21 assays from PubChem2_Case_study_compounds.ipynb: pre-processes list of EU-ToxRisk case study compounds3_Tox21_compounds_vs_case_study_compounds.ipynb: determines overlap of Tox21 compounds in PubChem and the case study compounds4_Tox21_get_data.ipynb: retrieves Summary assay data from PubChem5_Tox21_reformat_data.ipynb: reformats assay data for visualization in DataWarrior
Information on the EU-ToxRisk case strudy compounds is stored in the file case_study_compounds_141216.txt (found the directory files/); as the project progresses, this file may require updating. If this is the case, or if new Tox21 data is released, the visualization will be regenerated and the fact noted here.
The notebook 3_Tox21_compounds_vs_case_study_compounds.ipynb requires a connection to a local instance of the ChEMBL database. If this is not available, the portion of the code using the connection should be commented out. If this is a problem, please let me know and I will modify the notebook to remove the need for database access by default.
Some of the notebooks can take a while to run, so, for convenience, the complete DataWarrior visualization file tox21_data_for_eu-toxrisk.dwar is available via DropBox.
Note that this is a work in progress, so things may change. For example, it has been suggested taht some Tox21 assays may be of lesser utility than others and could thus be excluded or hidden by default. I have not yet looked into this, but will do so as time allows.
This project is based on preliminary work by Patricia Bento (patricia@ebi.ac.uk); the case study compound information was compiled by Anne Hersey (ahersey@ebi.ac.uk). Please address any comments or suggestions to me (francis@ebi.ac.uk).