metaspace2020/sm-molecular-db

Unified REST API for molecular database data

This project has been migrated into https://github.com/metaspace2020/metaspace

Molecular Database RESTful Web API

HMDB, ChEBI and other molecular databases.

Molecular attributes: InChI, InChI key, sum formula, name, database id

Installation (Ubuntu)

Install and setup PostgreSQL (LINK)

Create a user and database

sudo -u postgres psql
CREATE ROLE mol_db LOGIN CREATEDB NOSUPERUSER PASSWORD 'simple_pass';
CREATE DATABASE mol_db WITH OWNER sm;
\q  # exit

Install OpenBabel

sudo apt-get install openbabel

Python of at least 3.4 version is required

sudo pip install -U pip
sudo pip install -r requirements.txt

Running

python3 app/main.py

Funding

This project is funded from the European Horizon2020 project METASPACE (no. 634402), NIH NIDDK project KPMP and internal funds of the European Molecular Biology Laboratory.

License

This project is licensed under the Apache 2.0 license.