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https://github.com/cthoyt/ontoportal-client

🎡 Unified access to OntoPortal instances like BioPortal, AgroPortal, and EcoPortal

https://github.com/cthoyt/ontoportal-client

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.2%) to scientific vocabulary

Keywords

agroportal bioportal cookiecutter-snekpack ecoportal obo obofoundry ontologies ontoportal python

Keywords from Contributors

uri owl rdf semantic-web linkml monarchinitiative linked-data knowledge-graphs large-language-models information-extraction
Last synced: 6 months ago · JSON representation

Repository

🎡 Unified access to OntoPortal instances like BioPortal, AgroPortal, and EcoPortal

Basic Info
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Topics
agroportal bioportal cookiecutter-snekpack ecoportal obo obofoundry ontologies ontoportal python
Created over 3 years ago · Last pushed over 3 years ago
Metadata Files
Readme Contributing License Code of conduct

README.md

OntoPortal Client

Tests PyPI PyPI - Python Version PyPI - License Documentation Status Codecov status Cookiecutter template from @cthoyt Code style: black Contributor Covenant

A client to BioPortal and other OntoPortal instances.

💪 Getting Started

One of several OntoPortal clients can be instantiated and accessed with the same API:

```python from ontoportal_client import BioPortalClient

bioportalclient = BioPortalClient() ontologies = bioportalclient.get_ontologies() ```

Complete documentation can be found on ontoportal-client.readthedocs.io

🚀 Installation

shell $ pip install ontoportal_client

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

shell $ pip install git+https://github.com/cthoyt/ontoportal-client.git

⚙️ Configuration

Configuration of the API tokens for for each of the clients is mediated by pystow. Using BioPortal as an example, you can either:

  1. Pass the API key in the construtor of the client class
  2. Set the BIOPORTAL_API_KEY environment variable
  3. Create a file ~/.config/bioportal.ini and set the api_key value under the [bioportal] section.

👐 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.

🍪 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: ```bash $ git clone git+https://github.com/cthoyt/ontoportal-client.git $ cd ontoportal-client $ pip install -e . ``` ### 🥼 Testing After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be run reproducibly with: ```shell $ tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/cthoyt/ontoportal-client/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell $ git clone git+https://github.com/cthoyt/ontoportal-client.git $ cd ontoportal-client $ tox -e docs $ open docs/build/html/index.html ``` The documentation automatically installs the package as well as the `docs` extra specified in the [`setup.cfg`](setup.cfg). `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). ### 📦 Making a Release After installing the package in development mode and installing `tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment in `tox.ini`. Run the following from the shell: ```shell $ tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/ontoportal_client/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 [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid the need for manual input at this step 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.

Owner

  • Name: Charles Tapley Hoyt
  • Login: cthoyt
  • Kind: user
  • Location: Bonn, Germany
  • Company: RWTH Aachen University

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 24
  • Total Committers: 3
  • Avg Commits per committer: 8.0
  • Development Distribution Score (DDS): 0.083
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Charles Tapley Hoyt c****t@g****m 22
Chris Mungall c****m@b****g 1
Patrick Kalita p****a@l****v 1
Committer Domains (Top 20 + Academic)
lbl.gov: 1 berkeleybop.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 5
  • Average time to close issues: about 15 hours
  • Average time to close pull requests: about 6 hours
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.75
  • Average comments per pull request: 1.4
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cmungall (2)
  • cthoyt (1)
  • pkalita-lbl (1)
Pull Request Authors
  • cthoyt (3)
  • cmungall (1)
  • pkalita-lbl (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 24,707 last-month
  • Total docker downloads: 147
  • Total dependent packages: 1
  • Total dependent repositories: 8
  • Total versions: 4
  • Total maintainers: 1
pypi.org: ontoportal-client

A client to BioPortal and other OntoPortal instances.

  • Versions: 4
  • Dependent Packages: 1
  • Dependent Repositories: 8
  • Downloads: 24,707 Last month
  • Docker Downloads: 147
Rankings
Dependent packages count: 3.2%
Downloads: 3.9%
Dependent repos count: 5.3%
Average: 12.0%
Forks count: 22.8%
Stargazers count: 25.1%
Maintainers (1)
cthoyt
Last synced: 6 months ago