diff --git a/.gitattributes b/.gitattributes index bed0738c7eeb449bca98b5d2f33c89a1ee56349a..fd4812f9ea1ddf18bf42df1bad3d2f85c5b89625 100644 --- a/.gitattributes +++ b/.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 diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000000000000000000000000000000000000..d1ba2bc046f57329090278c0dbe615d68e539ab0 --- /dev/null +++ b/.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. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000000000000000000000000000000000000..11fc491ef1dae316f2b06bbb40eaba9c757fdfd1 --- /dev/null +++ b/.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. diff --git a/.github/PULL_REQUEST_TEMPLATE/submission.md b/.github/PULL_REQUEST_TEMPLATE/submission.md new file mode 100644 index 0000000000000000000000000000000000000000..e57e65ebd3c5344aaa4afbf3a2813e624359453d --- /dev/null +++ b/.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) diff --git a/.github/workflows/submission.yml b/.github/workflows/submission.yml new file mode 100644 index 0000000000000000000000000000000000000000..73ab62a8e14b97007a43684894bdda0156002704 --- /dev/null +++ b/.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 diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml new file mode 100644 index 0000000000000000000000000000000000000000..3513cdfdcc72e8b754fa49c8f48f8224c706996f --- /dev/null +++ b/.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="${FILTER}" \ + --n_jobs=4 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..6c2e3e685cca1afff37258d3f7e0a0218616b569 --- /dev/null +++ b/.gitignore @@ -0,0 +1,131 @@ +.idea/ + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$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/ diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000000000000000000000000000000000000..994aacd63d39e0f3c8aa7837072fb525bb2ff3b5 --- /dev/null +++ b/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 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000000000000000000000000000000000000..98a8facdbb7c33faac74648c00ec90e38e16815c --- /dev/null +++ b/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. + +
Open Reaction Database Project License Agreement
+ +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. diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md new file mode 100644 index 0000000000000000000000000000000000000000..fe1e8b467689946a00fc7714840eee39eb44ae6c --- /dev/null +++ b/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 | diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..cc3e2459dc5c46f1936b6e3b54137099063818e0 --- /dev/null +++ b/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. 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For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. diff --git a/README.md b/README.md index 340a31bb5f9b74dc06138cb27c713a0410017851..e157c50cd57b491dbe41a295f8b69dcb8c3c532c 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,68 @@ ---- -license: cc-by-sa-4.0 ---- +# ord-data + + + +[](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). diff --git a/badges/reactions.svg b/badges/reactions.svg new file mode 100644 index 0000000000000000000000000000000000000000..2051ac489546a5d29e11a85bb0b06ba6f68e2365 --- /dev/null +++ b/badges/reactions.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/data/00/ord_dataset-00005539a1e04c809a9a78647bea649c.pb.gz b/data/00/ord_dataset-00005539a1e04c809a9a78647bea649c.pb.gz new file mode 100644 index 0000000000000000000000000000000000000000..5e206e74ff4ca40078e934e4d95cf8cd91d5e61c --- /dev/null +++ b/data/00/ord_dataset-00005539a1e04c809a9a78647bea649c.pb.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:491531891f31ad2bbfdfccf347e265fa82b7e2bd7fda5813d6473dd309c29d4a +size 261136 diff --git 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Chemistry informer libraries: a chemoinformatics enabled approach to evaluate and advance synthetic methods. Chem. Sci., 2016,7, 2604-2613; https://doi.org/10.1039/C5SC04751J" +reactions { + inputs { + key: "Amine" + value { + components { + identifiers { + type: SMILES + value: "C1CCNCC1" + } + amount { + moles { + value: 3.75 + units: MICROMOLE + } + } + reaction_role: REACTANT + is_limiting: false + } + components { + identifiers { + type: SMILES + value: "[O-]P(=O)([O-])[O-].[K+].[K+].[K+]" + } + amount { + moles { + value: 7.5 + units: MICROMOLE + } + } + reaction_role: REAGENT + } + components { + identifiers { + type: SMILES + value: "[Cu]I" + } + amount { + moles { + value: 0.25 + units: MICROMOLE + } + } + reaction_role: CATALYST + } + components { + identifiers { + type: SMILES + value: "CS(=O)C" + } + amount { + volume { + value: 12.5 + units: MICROLITER + } + volume_includes_solutes: true + } + reaction_role: SOLVENT + } + addition_order: 2 + } + } + inputs { + key: "Aryl Halide" + value { + components { + identifiers { + type: SMILES + value: 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Bar" + } + } + workups { + type: ADDITION + details: "The reaction vials were then cooled to r.t.\nand diluted with 100 \316\274L of 5% AcOH in DMSO, containing 1,3,5-trimethoxybenzene (0.005M) and were\nshaken vigorously." + input { + components { + identifiers { + type: SMILES + details: "NAME resolved by the PubChem API" + value: "CS(C)=O" + } + amount { + volume { + value: 95.0 + units: MICROLITER + } + } + reaction_role: WORKUP + } + components { + identifiers { + type: SMILES + details: "NAME resolved by the PubChem API" + value: "CC(=O)O" + } + amount { + volume { + value: 5.0 + units: MICROLITER + } + } + reaction_role: WORKUP + } + components { + identifiers { + type: NAME + value: "1,3,5-trimethoxybenzene" + } + identifiers { + type: SMILES + details: "NAME resolved by the PubChem API" + value: "COc1cc(OC)cc(OC)c1" + } + amount { + moles { + value: 0.5 + units: MICROMOLE + } + } + reaction_role: INTERNAL_STANDARD + } + } + } + workups { + type: ALIQUOT + details: "25 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