Open Reaction Database: Schema (ord-schema)

This repository contains the schema for the Open Reaction Database initiative, based in part on survey of importance (summary). For more details on the database, please see the documentation at http://open-reaction-database.org.

This repository does not contain the database itself. Rather, ord-schema is designed to store the database schema and tools for creating, validating, and submitting data to the database.

We are currently in the process of formalizing the schema and creating examples for both low-level and high-level use. Consider joining the mailing list to stay up to date with announcements and opportunities for providing feedback.

Examples

The examples/ directory contains examples of dataset creation and use.

Click here to run the examples with Binder:

Local installation

Many of the schema validators require RDKit, so we recommend that you install ord-schema in a conda environment.

1. Clone the ord-schema repository to your local machine. If you are planning to contribute changes, you should fork the repository first (see Contributing).

2. Install Anaconda or Miniconda (instructions).

3. Run the following commands to install ord-schema:

   $ pip install -r requirements.txt
   $ conda install -c rdkit rdkit
   $ python setup.py install

4. After installation, you can run the tests by executing

   $ ./run_tests.sh

   Note that if you have made changes to the code or .proto files, you should run python setup.py install to pick up the new changes. If you are only editing Python code (or you are willing to run protoc yourself), you may wish to use python setup.py develop to avoid having to reinstall the package each time.