Published July 20, 2022 | Version 0.1

Papyrus dataset postgres dump

Authors/Creators

  • 1. OMass Therapeutics

Description

The dataset that the database dump was created from is described here: 10.33774/chemrxiv-2021-1rxhk

A dump of the postgres database created from the code in the 'postgres' directory (Papyrus-scripts/src/papyrus_scripts/postgres/) of Rachael Skyner's fork (https://github.com/reskyner/Papyrus-scripts) of Oliver Bequignon's Papyrus-scripts github (https://github.com/OlivierBeq/Papyrus-scripts).  The database was created by:

1. Download the papyrus csv files from Oliver's code using the download functionality

2. Spin up a 'papyrus' container using the docker-compose.yml file in Rachael's fork (running on a machine with access to the postgres instance you want to add the database to)

3. Start a shell in the papyrus container with docker exec -it papyrus /bin/bash

4. Start a jupyter notebook server with jupyter notebook --ip 0.0.0.0 --allow-root --no-browser

5. Run the two notebooks  (1-insert_molecule_data.ipynb and 2-insert_activities.ipynb) in order

6. Create a dump of the database

Files

Files (9.2 GB)

Name Size
md5:ad97f531d12fafc569d5f309cec0efe4
9.2 GB Download