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https://github.com/biopragmatics/bioontologies

🏷️ Unified access to biomedical ontologies

https://github.com/biopragmatics/bioontologies

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

🏷️ Unified access to biomedical ontologies

Basic Info
Statistics
  • Stars: 10
  • Watchers: 2
  • Forks: 1
  • Open Issues: 5
  • Releases: 23
Created about 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme Contributing License Code of conduct

README.md

Bioontologies

Tests PyPI PyPI - Python Version PyPI - License Documentation Status Codecov status Cookiecutter template from @cthoyt Ruff Contributor Covenant

Tools for biomedical ontologies

💪 Getting Started

This package lets you get OBO Graphs from ontologies based on their OWL files, OBO files, or Bioregistry prefixes. Internally, it uses ROBOT to convert from these formats to OBO Graph JSON.

```python import bioontologies

Get an ontology and convert to OBO Graph object via an OWL IRI

owliri = "http://purl.obolibrary.org/obo/go.owl" parseresults = bioontologies.converttoobograph(owl_iri)

Get an ontology and convert to OBO Graph object via an OBO IRI

oboiri = "http://purl.obolibrary.org/obo/go.obo" parseresults = bioontologies.converttoobograph(obo_iri)

Get an ontology by its Bioregistry prefix

parseresults = bioontologies.getobographbyprefix("go") gographdocument = parseresults.graphdocument ```

🚀 Installation

The most recent release can be installed from PyPI with:

console python3 -m pip install bioontologies

The most recent code and data can be installed directly from GitHub with:

console python3 -m pip install git+https://github.com/biopragmatics/bioontologies.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🎁 Support

The Bioregistry was initially developed by the INDRA Lab, a part of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.

💰 Funding

The development of this package was partially funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions The final section of the README is for if you want to get involved by making a code contribution. ### Development Installation To install in development mode, use the following: ```console git clone git+https://github.com/biopragmatics/bioontologies.git cd bioontologies python3 -m pip install -e . ``` ### Updating Package Boilerplate This project uses `cruft` to keep boilerplate (i.e., configuration, contribution guidelines, documentation configuration) up-to-date with the upstream cookiecutter package. Update with the following: ```console python3 -m pip install cruft cruft update ``` More info on Cruft's update command is available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project). ### 🥼 Testing After cloning the repository and installing `tox` with `python3 -m pip install tox tox-uv`, the unit tests in the `tests/` folder can be run reproducibly with: ```console tox -e py ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/biopragmatics/bioontologies/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```console git clone git+https://github.com/biopragmatics/bioontologies.git cd bioontologies tox -e docs open docs/build/html/index.html ``` The documentation automatically installs the package as well as the `docs` extra specified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins like `texext` can be added there. Additionally, they need to be added to the `extensions` list in [`docs/source/conf.py`](docs/source/conf.py). The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using [this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The [`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration you'll need. You can also set up continuous integration on GitHub to check not only that Sphinx can build the documentation in an isolated environment (i.e., with `tox -e docs-test`) but also that [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html). #### Configuring ReadTheDocs 1. Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/ 2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository 3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters) 4. Click next, and you're good to go! ### 📦 Making a Release #### Configuring Zenodo [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI to each release of your package. 1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click "grant" next to any organizations you want to enable the integration for, then click the big green "approve" button. This step only needs to be done once. 2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make a new repository, you'll have to come back to this After these steps, you're ready to go! After you make "release" on GitHub (steps for this are below), you can navigate to https://zenodo.org/account/settings/github/repository/biopragmatics/bioontologies to see the DOI for the release and link to the Zenodo record for it. #### Registering with the Python Package Index (PyPI) You only have to do the following steps once. 1. Register for an account on the [Python Package Index (PyPI)](https://pypi.org/account/register) 2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email might not have been sent by default, so you might have to click the "options" dropdown next to your address to get to the "re-send verification email" button 3. 2-Factor authentication is required for PyPI since the end of 2023 (see this [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)). This means you have to first issue account recovery codes, then set up 2-factor authentication 4. Issue an API token from https://pypi.org/manage/account/token #### Configuring your machine's connection to PyPI You have to do the following steps once per machine. Create a file in your home directory called `.pypirc` and include the following: ```ini [distutils] index-servers = pypi testpypi [pypi] username = __token__ password = # This block is optional in case you want to be able to make test releases to the Test PyPI server [testpypi] repository = https://test.pypi.org/legacy/ username = __token__ password = ``` Note that since PyPI is requiring token-based authentication, we use `__token__` as the user, verbatim. If you already have a `.pypirc` file with a `[distutils]` section, just make sure that there is an `index-servers` key and that `pypi` is in its associated list. More information on configuring the `.pypirc` file can be found [here](https://packaging.python.org/en/latest/specifications/pypirc). #### Uploading to PyPI After installing the package in development mode and installing `tox` with `python3 -m pip install tox tox-uv`, run the following from the console: ```console tox -e finish ``` This script does the following: 1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to switch the version number in the `pyproject.toml`, `CITATION.cff`, `src/bioontologies/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package) 3. Uploads to PyPI using [`twine upload`](https://github.com/pypa/twine). This will be replaced soon with `uv publish` (see https://github.com/cthoyt/cookiecutter-snekpack/issues/29) 4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped. 5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use `tox -e bumpversion -- minor` after. #### Releasing on GitHub 1. Navigate to https://github.com/biopragmatics/bioontologies/releases/new to draft a new release 2. Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made 3. Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit 4. Click the big green "Publish Release" button This will trigger Zenodo to assign a DOI to your release as well.

Owner

  • Name: Biopragmatics Stack
  • Login: biopragmatics
  • Kind: organization

Software supporting biomedical semantics and pragmatics

GitHub Events

Total
  • Create event: 32
  • Issues event: 1
  • Release event: 6
  • Watch event: 2
  • Delete event: 23
  • Push event: 38
  • Pull request event: 41
Last Year
  • Create event: 32
  • Issues event: 1
  • Release event: 6
  • Watch event: 2
  • Delete event: 23
  • Push event: 38
  • Pull request event: 41

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 137
  • Total Committers: 1
  • Avg Commits per committer: 137.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 48
  • Committers: 1
  • Avg Commits per committer: 48.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Charles Tapley Hoyt c****t@g****m 137

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 5
  • Total pull requests: 54
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 30 days
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 2.2
  • Average comments per pull request: 0.15
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 26
Past Year
  • Issues: 0
  • Pull requests: 44
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 month
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.02
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 26
View more stats
Top Authors
Issue Authors
  • joeflack4 (4)
  • Sulstice (1)
Pull Request Authors
  • cthoyt (27)
  • github-actions[bot] (26)
  • bgyori (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 1,722 last-month
  • Total dependent packages: 4
  • Total dependent repositories: 1
  • Total versions: 28
  • Total maintainers: 1
pypi.org: bioontologies

Tools for biomedical ontologies

  • Homepage: https://github.com/biopragmatics/bioontologies
  • Documentation: https://bioontologies.readthedocs.io
  • License: MIT License Copyright (c) 2024 Charles Tapley Hoyt Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 0.7.3
    published about 1 year ago
  • Versions: 28
  • Dependent Packages: 4
  • Dependent Repositories: 1
  • Downloads: 1,722 Last month
Rankings
Dependent packages count: 2.3%
Downloads: 7.9%
Average: 14.6%
Stargazers count: 18.5%
Dependent repos count: 21.7%
Forks count: 22.6%
Maintainers (1)
cthoyt
Last synced: 11 months ago

Dependencies

.github/workflows/tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v1 composite