Papyrus dataset postgres dump
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 |