MINE Databases

The MINE Database contains code for generating (through Pickaxe) and storing and retrieving compounds from a database. Pickaxe applies reaction rules, representing reaction transformation patterns, to a list of user-specified compounds in order to predict reactions.

Documentation

For general information on MINE Databases, please consult JJeffryes et al. 2015..

Documentation is hosted at https://mine-database.readthedocs.io/en/latest/. It gives more detailed descriptions and example uses of the software.

Installation (current)

You need the uv package manager. If you don't have it, install it with the following command:

# On macOS and Linux.
curl -LsSf https://astral.sh/uv/install.sh | sh

# On Windows.
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Also be sure to install MongoDB (https://docs.mongodb.com/manual/installation/) if you are using the write_db = True option in Pickaxe. Installation information on Ubuntu system https://www.mongodb.com/docs/manual/tutorial/install-mongodb-on-ubuntu/

Running Pickaxe

Example Running Pickaxe through the CLI

Using MetaCyc rules and coreactants.

uv run mine_database/pickaxe_commons.py -C ./mine_database/data/metacyc_rules/metacyc_coreactants.tsv -r ./mine_database/data/metacyc_rules/metacyc_generalized_rules.tsv  -g 1 -c ./example_data/lotus_10.csv -o ./data/

Using original rules and coreactants (Enzymatic)

uv run mine_database/pickaxe_commons.py \
    --coreactant_list ./mine_database/data/original_rules/EnzymaticCoreactants.tsv \
    --rule_list ./mine_database/data/original_rules/EnzymaticReactionRules.tsv \
    --generations 1 \
    --compound_file ./example_data/Solanum_1000.csv \
    --output_dir ./data/ \
    --processes 8 \
    --explicit_h \
    --database testing-mine

or

uv run mine_database/pickaxe_commons.py -C ./mine_database/data/original_rules/EnzymaticCoreactants.tsv -r ./mine_database/data/original_rules/EnzymaticReactionRules.tsv  -g 1 -c ./example_data/lotus_1000.csv -o ./data/ -m 60

Complete command (writing to database):

uv run mine_database/pickaxe_commons.py --coreactant_list ./mine_database/data/original_rules/EnzymaticCoreactants.tsv --rule_list ./mine_database/data/original_rules/EnzymaticReactionRules.tsv --generations 1 --compound_file ./example_data/230106_frozen_metadata_for_mines.csv --output_dir ./data/ --processes 60 --verbose --explicit_h --database lotus_mines

Command without writing to database:

uv run mine_database/pickaxe_commons.py --coreactant_list ./mine_database/data/original_rules/EnzymaticCoreactants.tsv --rule_list ./mine_database/data/original_rules/EnzymaticReactionRules.tsv --generations 1 --compound_file ./example_data/lotus_10.csv --output_dir ./data/ --processes 60 --verbose --explicit_h

Command with generalized rules and full LOTUS dataset without writing to database:

uv run mine_database/pickaxe_commons.py --coreactant_list ./mine_database/data/metacyc_rules/metacyc_coreactants.tsv --rule_list ./mine_database/data/metacyc_rules/metacyc_generalized_rules.tsv --generations 1 --compound_file ./data/LOTUS_inputfiles/230106_frozen_metadata_inchy_smiles.csv --output_dir ./data/ --processes 60 --verbose --explicit_h

Accessing the mongodb database

To access the mongodb database, you can use the following command:

mongosh

Then, you can use the following commands to access the database:

use example_db
db.compounds.find()

Optionally the DB can be observed using MongoDB Compass. See https://www.mongodb.com/docs/compass/current/install/