https://github.com/Open-Reaction-Database/ord-schema

Schema for the Open Reaction Database
https://github.com/Open-Reaction-Database/ord-schema

Last synced: 5 days ago
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Schema for the Open Reaction Database

• Host: GitHub
• URL: https://github.com/Open-Reaction-Database/ord-schema
• Owner: open-reaction-database
• License: apache-2.0
• Created: 2020-02-07T01:59:57.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2024-05-03T12:55:06.000Z (about 2 months ago)
• Last Synced: 2024-05-11T10:01:24.793Z (about 2 months ago)
• Language: JavaScript
• Homepage: https://open-reaction-database.org
• Size: 74.6 MB
• Stars: 87
• Watchers: 15
• Forks: 27
• Open Issues: 15
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Authors: AUTHORS

Lists

• awesome-chemical-data - ord-schema - Reaction-Database/ord-schema?style=social)](https://github.com/Open-Reaction-Database/ord-schema)  (Schemas/Ontologies / Organic reactions)

README

        
# Open Reaction Database: Schema (ord-schema)

[![DOI:10.1007/978-3-319-76207-4_15](https://zenodo.org/badge/DOI/10.1021/jacs.1c09820.svg)](https://doi.org/10.1021/jacs.1c09820)

[![PyPI version](https://badge.fury.io/py/ord-schema.svg)](https://badge.fury.io/py/ord-schema)

This repository contains the schema for the Open Reaction Database initiative; please see the documentation

at https://docs.open-reaction-database.org.

This repository does not contain the database itself; that is stored

in [ord-data](https://github.com/open-reaction-database/ord-data). Rather, `ord-schema` is

designed to store the database schema and tools for creating, validating, and submitting data to the database.

## Installation

```shell

$ pip install ord-schema

```

## Examples

The `examples/` directory contains examples of dataset creation and use. To run locally, install with:

```shell

$ pip install "ord-schema[examples]"

```

Click here to run the examples with Binder:

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-reaction-database/ord-schema/HEAD?labpath=examples)

## Development

To install in editable/development mode:

```shell

$ git clone https://github.com/open-reaction-database/ord-schema.git

$ cd ord-schema

$ pip install -e .

```

If you make changes to the protocol buffer definitions, [install](https://grpc.io/docs/protoc-installation/) `protoc`

and run `./compile_proto_wrappers.sh` to rebuild the wrappers.

## Conventions

### 1. convention: compound stoichiometry

##### Created: 2023.07.04

##### Last updated: 2023.07.04

##### Description: 

1. The preferred field for compound stoichiometry is the map `Compound.features` or `ProductCompound.features`.

2. The key should be "stoichiometric_coefficient" or "stoichiometric_ratio".

3. The value should be a `Data` message with its `float_value` representing the compound's stoichiometric 

coefficient or ratio.

##### Related links: 

[#683](https://github.com/open-reaction-database/ord-schema/issues/683) 

[#684](https://github.com/open-reaction-database/ord-schema/pull/684)