https://github.com/unixjunkie/tox21
My copy of the Tox21 dataset
https://github.com/unixjunkie/tox21
Last synced: 6 months ago
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My copy of the Tox21 dataset
- Host: GitHub
- URL: https://github.com/unixjunkie/tox21
- Owner: UnixJunkie
- Created: 2019-11-13T06:33:43.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-11-13T07:43:59.000Z (over 6 years ago)
- Last Synced: 2025-01-31T09:31:08.404Z (over 1 year ago)
- Size: 725 KB
- Stars: 3
- Watchers: 1
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Tox21
My copy of the Tox21 dataset.
# Data source
https://github.com/deepchem/deepchem/tree/master/datasets/tox21.csv
download date: 09/11/2018 at 13:59:05
# Preparation protocol
All smiles strings (molecules) have been standardised using
https://github.com/flatkinson/standardiser
Molecules that did not pass standardisation have been removed.
Cf. standardisation/errors.smi for such molecules.
All molecules tested on a given toxicity endpoint/target were copied
into a specific directory for that target.
All toxic molecules for a given target have had their name prefixed
with the word "active".
Each list of molecules was randomized.
# Directory structure
```
tox21.csv: backup copy of the original data source
targets.txt: list of all toxicity endpoints in the dataset; one per line.
Target names are in the same order than columns
in the tox21.csv file.
TARGET/ligands_std_rand.smi: all toxic molecules for TARGET and all
non toxic molecules; in random order
standardisation/errors.smi: molecules that did not pass standardisation
standardisation/standardised.smi: molecules that passed standardisation
```
# Bibliography
```
@article{Huang2016,
author = {Huang, Ruili and Xia, Menghang and Nguyen, Dac-Trung and Zhao, Tongan and Sakamuru, Srilatha and Zhao, Jinghua and Shahane, Sampada A. and Rossoshek, Anna and Simeonov, Anton},
title = {Tox21Challenge to Build Predictive Models of Nuclear Receptor and Stress Response Pathways as Mediated by Exposure to Environmental Chemicals and Drugs},
journal = {Frontiers in Environmental Science},
volume = {3},
pages = {85},
year = {2016},
doi = {10.3389/fenvs.2015.00085},
}
```