Upload folder using huggingface_hub

.gitattributes

@@ -1,60 +1,3 @@
-*.7z filter=lfs diff=lfs merge=lfs -text
-*.arrow filter=lfs diff=lfs merge=lfs -text
-*.avro filter=lfs diff=lfs merge=lfs -text
-*.bin filter=lfs diff=lfs merge=lfs -text
-*.bz2 filter=lfs diff=lfs merge=lfs -text
-*.ckpt filter=lfs diff=lfs merge=lfs -text
-*.ftz filter=lfs diff=lfs merge=lfs -text
-*.gz filter=lfs diff=lfs merge=lfs -text
-*.h5 filter=lfs diff=lfs merge=lfs -text
-*.joblib filter=lfs diff=lfs merge=lfs -text
-*.lfs.* filter=lfs diff=lfs merge=lfs -text
-*.lz4 filter=lfs diff=lfs merge=lfs -text
-*.mds filter=lfs diff=lfs merge=lfs -text
-*.mlmodel filter=lfs diff=lfs merge=lfs -text
-*.model filter=lfs diff=lfs merge=lfs -text
-*.msgpack filter=lfs diff=lfs merge=lfs -text
-*.npy filter=lfs diff=lfs merge=lfs -text
-*.npz filter=lfs diff=lfs merge=lfs -text
-*.onnx filter=lfs diff=lfs merge=lfs -text
-*.ot filter=lfs diff=lfs merge=lfs -text
-*.parquet filter=lfs diff=lfs merge=lfs -text
+ord_data-* filter=lfs diff=lfs merge=lfs -text
 *.pb filter=lfs diff=lfs merge=lfs -text
-*.pickle filter=lfs diff=lfs merge=lfs -text
-*.pkl filter=lfs diff=lfs merge=lfs -text
-*.pt filter=lfs diff=lfs merge=lfs -text
-*.pth filter=lfs diff=lfs merge=lfs -text
-*.rar filter=lfs diff=lfs merge=lfs -text
-*.safetensors filter=lfs diff=lfs merge=lfs -text
-saved_model/**/* filter=lfs diff=lfs merge=lfs -text
-*.tar.* filter=lfs diff=lfs merge=lfs -text
-*.tar filter=lfs diff=lfs merge=lfs -text
-*.tflite filter=lfs diff=lfs merge=lfs -text
-*.tgz filter=lfs diff=lfs merge=lfs -text
-*.wasm filter=lfs diff=lfs merge=lfs -text
-*.xz filter=lfs diff=lfs merge=lfs -text
-*.zip filter=lfs diff=lfs merge=lfs -text
-*.zst filter=lfs diff=lfs merge=lfs -text
-*tfevents* filter=lfs diff=lfs merge=lfs -text
-# Audio files - uncompressed
-*.pcm filter=lfs diff=lfs merge=lfs -text
-*.sam filter=lfs diff=lfs merge=lfs -text
-*.raw filter=lfs diff=lfs merge=lfs -text
-# Audio files - compressed
-*.aac filter=lfs diff=lfs merge=lfs -text
-*.flac filter=lfs diff=lfs merge=lfs -text
-*.mp3 filter=lfs diff=lfs merge=lfs -text
-*.ogg filter=lfs diff=lfs merge=lfs -text
-*.wav filter=lfs diff=lfs merge=lfs -text
-# Image files - uncompressed
-*.bmp filter=lfs diff=lfs merge=lfs -text
-*.gif filter=lfs diff=lfs merge=lfs -text
-*.png filter=lfs diff=lfs merge=lfs -text
-*.tiff filter=lfs diff=lfs merge=lfs -text
-# Image files - compressed
-*.jpg filter=lfs diff=lfs merge=lfs -text
-*.jpeg filter=lfs diff=lfs merge=lfs -text
-*.webp filter=lfs diff=lfs merge=lfs -text
-# Video files - compressed
-*.mp4 filter=lfs diff=lfs merge=lfs -text
-*.webm filter=lfs diff=lfs merge=lfs -text
+*.pb.gz filter=lfs diff=lfs merge=lfs -text

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE/submission.md

@@ -0,0 +1,23 @@
+---
+name: Submission
+about: Submit data to the Open Reaction Database
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the submission**
+* High-level description of the data
+* Source information (e.g. DOI)
+* Details on how the dataset was created (e.g. web editor, template enumeration, jupyter, etc.)
+* Details about any issues encoding the data (e.g. missing schema fields, ambiguous data, etc.)
+
+**Attach any supporting files**
+
+(Note: they may need to be attached as one or more .zip files)
+* Reaction template and CSV/Excel for enumerated datasets
+* Jupyter notebooks for programmatically defined datasets
+
+---
+[License](https://github.com/open-reaction-database/ord-data/blob/main/LICENSE) • [Terms of Use](https://github.com/open-reaction-database/ord-data/blob/main/CONTRIBUTING.md#terms-of-use) • [Documentation](https://docs.open-reaction-database.org/en/latest/submissions.html)

.github/workflows/submission.yml

@@ -0,0 +1,169 @@
+# Runs process_dataset.py on all new and changed files.
+#
+# Submissions from forks only trigger the "validation" step to validate the new
+# data. After merging into a new branch in the parent repo, the workflow will
+# run again and trigger the "update" step to add reaction IDs, etc. in
+# preparation for merging into the "main" branch.
+
+name: Submission
+
+on: [pull_request, push]
+
+env:
+  ORD_SCHEMA_TAG: v0.3.93
+
+jobs:
+  count_reactions:
+    if: >-
+      github.event_name == 'pull_request' &&
+      ! github.event.pull_request.head.repo.fork
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout ord-data
+      uses: actions/checkout@v2
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+        lfs: true
+      if: github.event_name == 'pull_request'
+    - name: Checkout ord-schema
+      uses: actions/checkout@v2
+      with:
+        repository: Open-Reaction-Database/ord-schema
+        ref: ${{ env.ORD_SCHEMA_TAG }}
+        path: ord-schema
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - name: Install ord_schema
+      run: |
+        cd "${GITHUB_WORKSPACE}/ord-schema"
+        python -m pip install --upgrade pip
+        python -m pip install wheel
+        python -m pip install .
+    - name: Update reactions badge
+      run: |
+        cd "${GITHUB_WORKSPACE}"
+        python ord-schema/badges/reactions.py --root=data --output=badges/reactions.svg
+        git add badges/reactions.svg
+        git config user.name github-actions
+        git config user.email github-actions@github.com
+        # Fail gracefully if there is nothing to commit.
+        git commit -a -m "Update badges" || (( $? == 1 ))
+        git push "https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" "HEAD:${GITHUB_HEAD_REF}"
+
+  check_file_types:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Add upstream for comparisons to HEAD
+      run: |
+        cd "${GITHUB_WORKSPACE}"
+        git remote add upstream \
+          "https://github.com/Open-Reaction-Database/${GITHUB_REPOSITORY##*/}.git"
+        echo "Current branch: $(git rev-parse --abbrev-ref HEAD)"
+        git fetch --no-tags --prune --depth=1 upstream \
+          +refs/heads/*:refs/remotes/upstream/*
+    - name: Check changed files (PR from fork)
+      run: |
+        cd "${GITHUB_WORKSPACE}"
+        git diff --name-only upstream/main > changed_files.txt
+        grep -vE '\.pb(txt)?(.gz)?$' changed_files.txt && \
+          echo "Error: submissions should only contain (gzipped) *.pbtxt or *.pb files" && \
+          exit 1 || true
+      if: >-
+        github.event_name == 'pull_request' &&
+        github.event.pull_request.head.repo.fork
+
+  check_target_branch:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check target branch
+      run: |
+        echo "Target branch: ${GITHUB_BASE_REF}"
+        test "${GITHUB_BASE_REF}" != "main"
+      if: >-
+        github.event_name == 'pull_request' &&
+        github.event.pull_request.head.repo.fork
+
+  process_submission:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout ord-data
+      uses: actions/checkout@v2
+      with:
+        lfs: true
+      if: github.event_name == 'push'
+    - name: Checkout ord-data
+      uses: actions/checkout@v2
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+        lfs: true
+      if: github.event_name == 'pull_request'
+    - name: Add upstream for comparisons to HEAD
+      run: |
+        cd "${GITHUB_WORKSPACE}"
+        git remote add upstream \
+          "https://github.com/Open-Reaction-Database/${GITHUB_REPOSITORY##*/}.git"
+        echo "Current branch: $(git rev-parse --abbrev-ref HEAD)"
+        git fetch --no-tags --prune --depth=1 upstream \
+          +refs/heads/*:refs/remotes/upstream/*
+    - name: Checkout ord-schema
+      uses: actions/checkout@v2
+      with:
+        repository: Open-Reaction-Database/ord-schema
+        ref: ${{ env.ORD_SCHEMA_TAG }}
+        path: ord-schema
+    - name: Identify changed files
+      # NOTE(kearnes): This sets the NUM_CHANGED_FILES variable.
+      run: |
+        cd "${GITHUB_WORKSPACE}"
+        git diff --name-status upstream/main > changed_files.txt
+        echo "Found $(wc -l < changed_files.txt | tr -d ' ') changed files"
+        cat changed_files.txt
+        # Use `|| (( $? == 1 ))` in case no lines match (exit code is nonzero).
+        grep -E "\.pb(txt)?(.gz)?$" changed_files.txt > changed_data_files.txt || (( $? == 1 ))
+        # Use LOCAL_NUM_CHANGED since ::set-env values are not available immediately.
+        LOCAL_NUM_CHANGED="$(wc -l < changed_data_files.txt | tr -d ' ')"
+        echo "NUM_CHANGED_FILES=${LOCAL_NUM_CHANGED}" >> $GITHUB_ENV
+        echo "Found ${LOCAL_NUM_CHANGED} changed dataset files"
+        cat changed_data_files.txt
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+      if: env.NUM_CHANGED_FILES != '0'
+    - name: Install ord_schema
+      run: |
+        cd "${GITHUB_WORKSPACE}/ord-schema"
+        python -m pip install --upgrade pip
+        python -m pip install wheel
+        python -m pip install .
+      if: env.NUM_CHANGED_FILES != '0'
+    - name: Validate submission
+      run: |
+        cd "${GITHUB_WORKSPACE}"
+        python ./ord-schema/ord_schema/scripts/process_dataset.py \
+          --input_file=changed_data_files.txt \
+          --base=upstream/main
+      if: >-
+        env.NUM_CHANGED_FILES != '0' &&
+        ! (github.event_name == 'pull_request' &&
+           ! github.event.pull_request.head.repo.fork)
+    - name: Update submission
+      run: |
+        cd "${GITHUB_WORKSPACE}"
+        python ./ord-schema/ord_schema/scripts/process_dataset.py \
+          --input_file=changed_data_files.txt \
+          --update \
+          --cleanup \
+          --base=upstream/main \
+          --issue=${{ github.event.number }} \
+          --token=${{ secrets.GITHUB_TOKEN }}
+        git config user.name github-actions
+        git config user.email github-actions@github.com
+        # Fail gracefully if there is nothing to commit.
+        git commit -a -m "Update submission" || (( $? == 1 ))
+        git push "https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" "HEAD:${GITHUB_HEAD_REF}"
+      if: >-
+        env.NUM_CHANGED_FILES != '0' &&
+        github.event_name == 'pull_request' &&
+        ! github.event.pull_request.head.repo.fork

.github/workflows/validation.yml

@@ -0,0 +1,61 @@
+# Runs process_dataset.py on all files in the database.
+
+name: Validation
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    paths:
+      # Runs when this file is modified in a PR.
+      - '.github/workflows/validation.yml'
+
+env:
+  ORD_SCHEMA_TAG: v0.3.93
+
+jobs:
+  validate_database:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        filter: [
+          'data/[0-4][0-4]',
+          'data/[0-4][5-9]',
+          'data/[0-4][a-f]',
+          'data/[5-9][0-4]',
+          'data/[5-9][5-9]',
+          'data/[5-9][a-f]',
+          'data/[a-f][0-4]',
+          'data/[a-f][5-9]',
+          'data/[a-f][a-f]',
+        ]
+    steps:
+    - name: Checkout ord-data
+      uses: actions/checkout@v2
+      with:
+        lfs: true
+    - name: Checkout ord-schema
+      uses: actions/checkout@v2
+      with:
+        repository: Open-Reaction-Database/ord-schema
+        ref: ${{ env.ORD_SCHEMA_TAG }}
+        path: ord-schema
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - name: Install ord_schema
+      run: |
+        cd "${GITHUB_WORKSPACE}/ord-schema"
+        python -m pip install --upgrade pip
+        python -m pip install wheel
+        python -m pip install .
+    - name: Validate datasets
+      env:
+        FILTER: ${{ matrix.filter }}
+      run: |
+        cd "${GITHUB_WORKSPACE}"
+        python ./ord-schema/ord_schema/scripts/validate_dataset.py \
+          --input="data/*/*.pb*" \
+          --filter="${FILTER}" \
+          --n_jobs=4

.gitignore

@@ -0,0 +1,131 @@
+.idea/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

CITATION.cff

@@ -0,0 +1,12 @@
+cff-version: 1.2.0
+title: The Open Reaction Database
+message: If you use this dataset, please cite it using the metadata from this file.
+type: dataset
+authors:
+  - name: Open Reaction Database Project
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.4321713
+url: 'https://open-reaction-database.org'
+repository: 'https://github.com/open-reaction-database/ord-data'
+license: CC-BY-SA-4.0

CONTRIBUTING.md

@@ -0,0 +1,91 @@
+# Contributing to the Open Reaction Database
+
+Thanks for helping out! What would you like to do?
+
+* [Report an issue](#report-an-issue)
+* [Suggest an improvement (such as a new dataset)](#suggest-an-improvement)
+* [Submit a new dataset](#submit-a-new-dataset)
+
+## Report an issue
+
+Sorry to hear that you're having trouble! Please [file a bug report](https://github.com/Open-Reaction-Database/ord-data/issues/new?assignees=&labels=bug&template=bug_report.md&title=) to tell us about the problem.
+
+## Suggest an improvement
+
+Great idea! Please [create a feature request](https://github.com/Open-Reaction-Database/ord-data/issues/new?assignees=&labels=enhancement&template=feature_request.md&title=) to let us know what you'd like to see.
+
+## Submit a new dataset
+
+Excellent! Please follow the
+[Submission Workflow](https://ord-schema.readthedocs.io/en/latest/submissions.html)
+in the documentation.
+   
+## Terms of Use
+
+By submitting Contributions (as defined below) to this project, you agree that
+You (as defined below) and your Contributions are bound to the following terms.
+
+<p align="center">Open Reaction Database Project License Agreement</p> 
+
+In order to clarify the intellectual property license granted with Contributions
+to the Open Access Reaction Database from any person or entity, the You must
+indicate agreement to the license terms below.
+
+You accept and agree to the following terms and conditions for Your present and
+future Contributions submitted to ORDP. Except for the license granted herein to
+ORDP and recipients of data distributed by ORDP, You reserve all right, title,
+and interest in and to Your Contributions.
+
+1. Definitions. "You" (or "Your") shall mean the copyright owner or legal entity
+authorized by the copyright owner that is making this Agreement with ORDP. For
+legal entities, the entity making a Contribution and all other entities that
+control, are controlled by, or are under common control with that entity are
+considered to be a single Contributor. For the purposes of this definition,
+"control" means (i) the power, direct or indirect, to cause the direction or
+management of such entity, whether by contract or otherwise, or (ii) ownership
+of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial
+ownership of such entity. "Contribution" shall mean the data, code,
+documentation or any original work of authorship, including any modifications or
+additions to an existing work, that is intentionally submitted by You to ORDP
+for inclusion in the Open Reaction Database managed by ORDP (the "Work"). For
+the purposes of this definition, "submitted" means any form of electronic or
+written communication sent to ORDP or its representatives, including but not
+limited to communication on electronic mailing lists, but excluding
+communication that is conspicuously marked or otherwise designated in writing by
+You as "Not a Contribution."
+
+2. Grant of Copyright License. Subject to the terms and conditions of this
+Agreement, You hereby grant to ORDP and to recipients of the data, software, or
+documentation distributed by ORDP a perpetual, worldwide, non-exclusive,
+no-charge, royalty-free, irrevocable copyright license to reproduce, prepare
+derivative works of, publicly display, publicly perform, sublicense, and
+distribute Your Contributions and such derivative works.
+
+3. Grant of Patent License. Subject to the terms and conditions of this
+Agreement, You hereby grant to ORDP and to recipients of software distributed by
+ORDP a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+(except as stated in this section) patent license to make, have made, use, offer
+to sell, sell, import, and otherwise transfer the Work, where such license
+applies only to those patent claims licensable by You that are necessarily
+infringed by Your Contribution(s) alone or by combination of Your
+Contribution(s) with the Work to which such Contribution(s) was submitted. If
+any entity institutes patent litigation against You or any other entity
+(including a cross-claim or counterclaim in a lawsuit) alleging that your
+Contribution, or the Work to which you have contributed, constitutes direct or
+contributory patent infringement, then any patent licenses granted to that
+entity under this Agreement for that Contribution or Work shall terminate as of
+the date such litigation is filed.
+
+4. You represent that you are legally entitled to grant the above license. If
+your employer(s) has rights to intellectual property that you create that
+includes your Contributions, you represent that you have received permission to
+make Contributions on behalf of that employer, or that your employer has waived
+such rights for your Contributions to ORDP.
+
+5. You are not expected to provide support for Your Contributions, except to the
+extent You desire to provide support. You may provide support for free, for a
+fee, or not at all. Unless required by applicable law or agreed to in writing,
+You provide Your Contributions on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+CONDITIONS OF ANY KIND, either express or implied, including, without
+limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT,
+MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE.

CONTRIBUTORS.md

@@ -0,0 +1,15 @@
+# Contributors to the Open Reaction Database
+
+This list includes both submitters and reviewers.
+Without your contributions, the Open Reaction Database could not exist!
+
+| Name | GitHub Username | Institution |
+| ---- | --------------- | ----------- |
+| Connor Coley | [@connorcoley](https://github.com/connorcoley) | MIT |
+| Steven Kearnes | [@skearnes](https://github.com/skearnes) | Relay |
+| Jun Li | [@jun-li-2020](https://github.com/jun-li-2020) | BMS |
+| Fabio Lima | [@limafabio2](https://github.com/limafabio2) | Novartis |
+| Jesus Martinez Alvarado | [@Jesus00-1](https://github.com/Jesus00-1) | Princeton |
+| Michael Maser | [@michaelmaser](https://github.com/michaelmaser) | Caltech |
+| Jason Wang | [@beef-broccoli](https://github.com/beef-broccoli) | Princeton |
+| Michael Wleklinski | [@mwleklin](https://github.com/mwleklin) | Merck |

LICENSE

@@ -0,0 +1,427 @@
+Attribution-ShareAlike 4.0 International
+
+=======================================================================
+
+Creative Commons Corporation ("Creative Commons") is not a law firm and
+does not provide legal services or legal advice. Distribution of
+Creative Commons public licenses does not create a lawyer-client or
+other relationship. Creative Commons makes its licenses and related
+information available on an "as-is" basis. Creative Commons gives no
+warranties regarding its licenses, any material licensed under their
+terms and conditions, or any related information. Creative Commons
+disclaims all liability for damages resulting from their use to the
+fullest extent possible.
+
+Using Creative Commons Public Licenses
+
+Creative Commons public licenses provide a standard set of terms and
+conditions that creators and other rights holders may use to share
+original works of authorship and other material subject to copyright
+and certain other rights specified in the public license below. The
+following considerations are for informational purposes only, are not
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README.md

@@ -1,3 +1,68 @@
----
-license: cc-by-sa-4.0
----
+# ord-data
+
+![](https://github.com/Open-Reaction-Database/ord-data/workflows/Validation/badge.svg)
+![](https://raw.githubusercontent.com/Open-Reaction-Database/ord-data/main/badges/reactions.svg)
+[![DOI](https://zenodo.org/badge/283813042.svg)](https://zenodo.org/badge/latestdoi/283813042)
+
+## Cloning with Git LFS
+
+We use [Git LFS](https://git-lfs.github.com) to efficiently store
+the Dataset records that make up the ORD. To view these files locally, you'll
+need to install Git LFS before cloning the repository.
+
+## Data Manipulation
+
+The `ord-data` repository contains the Open Reaction Database (ORD) in Google's Protobuf binary
+format, which is stored in the [`data`](data) directory. Currently, all the data are stored in e.g.
+*.pb.gz format (compressed Protobuf binary files) for the sake of efficiency. The user can convert
+the data into human readable text format, *.pb.txt.
+
+```python
+# import requirements
+from ord_schema.message_helpers import load_message, write_message
+from ord_schema.proto import dataset_pb2
+
+# load the binary ord file
+dataset = load_message("input_fname.pb.gz", dataset_pb2.Dataset)
+# save the ord file as human readable text
+write_message(dataset, "output_fname.pbtxt")
+```
+
+We can also convert ORD data into JSON format.
+
+```python
+# import requirements
+import json
+
+from ord_schema.message_helpers import load_message, write_message
+from ord_schema.proto import dataset_pb2
+from google.protobuf.json_format import MessageToJson
+
+input_fname = "sample_file.pb.gz"
+dataset = load_message(
+    input_fname,
+    dataset_pb2.Dataset,
+)
+
+# take one reaction message from the dataset for example
+rxn = dataset.reactions[0]
+rxn_json = json.loads(
+    MessageToJson(
+        message=rxn,
+        including_default_value_fields=False,
+        preserving_proto_field_name=True,
+        indent=2,
+        sort_keys=False,
+        use_integers_for_enums=False,
+        descriptor_pool=None,
+        float_precision=None,
+        ensure_ascii=True,
+    )
+)
+
+print(f"We have converted the {input_fname} to JSON format shown as below, \n{rxn_json}")
+```
+
+## Contributing
+
+Please see the [Submission Workflow](https://docs.open-reaction-database.org/en/latest/submissions.html) documentation. Make sure to review the [license](https://github.com/open-reaction-database/ord-data/blob/main/LICENSE) and [terms of use](https://github.com/open-reaction-database/ord-data/blob/main/CONTRIBUTING.md#terms-of-use).

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