https://github.com/biopragmatics/biolookup
🔍 The Biolookup Service retrieves metadata and ontological information about biomedical entities.
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.8%) to scientific vocabulary
Keywords
Repository
🔍 The Biolookup Service retrieves metadata and ontological information about biomedical entities.
Basic Info
- Host: GitHub
- Owner: biopragmatics
- License: mit
- Language: Python
- Default Branch: main
- Homepage: http://biolookup.io
- Size: 219 KB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 4
- Releases: 3
Topics
Metadata Files
README.md
BioLookup
Get metadata and ontological information about biomedical entities.
💪 Getting Started
The Biolookup Service has an endpoint /api/lookup/<curie> for retrieving
metadata and ontological information about a biomedical entity via its compact
identifier (CURIE).
```python import requests
res = requests.get("http://localhost:5000/api/lookup/doid:14330").json() assert res["name"] == "Parkinson's disease" assert res["identifier"] == "14330" assert res["prefix"] == "doid" assert res["definition"] is not None # not shown for brevity ```
The INDRA Lab hosts an instance of the Biolookup
Service at http://biolookup.io, so you can alternatively use
http://biolookup.io/api/lookup/doid:14330.
The same can be accomplished using the biolookup package:
```python import biolookup
res = biolookup.lookup("doid:14330") assert res["name"] == "Parkinson's disease"
... same as before
```
If you've configured the BIOLOOKUP_SQLALCHEMY_URI environment variable (or any
other valid way with pystow to point
directly at the database for an instance of the Biolookup Service, it will make
a direct connection to the database instead of using the web-based API.
🕸️ Running the Lookup App
You can run the lookup app in local mode with:
console
$ biolookup web --lazy
This means that the in-memory data from pyobo are used. If you have a large
external database, you can run in remote mode with the --sql flag:
console
$ biolookup web --sql --uri postgresql+psycopg2://postgres:biolookup@localhost:5434/biolookup
If --uri is not given for the web subcommand, it uses
pystow.get_config("biolookup", "sqlalchemy_uri)to look up from
BIOLOOKUP_SQLALCHEMY_URI or in ~/.config/biolookup.ini. If none is given, it
defaults to a SQLite database in ~/.data/biolookup/biolookup.db.
🗂️ Load the Database
shell
$ biolookup load --uri postgresql+psycopg2://postgres:biolookup@localhost:5434/biolookup
If --uri is not given for the load subcommand, it uses
pystow.get_config("biolookup", "sqlalchemy_uri)to look up from
BIOLOOKUP_SQLALCHEMY_URI or in ~/.config/biolookup.ini. If none is given, it
creates a defaults a SQLite database at ~/.data/biolookup/biolookup.db.
🚀 Installation
The most recent release can be installed from PyPI with uv:
console
$ uv pip install biolookup
or with pip:
console
$ python3 -m pip install biolookup
The most recent code and data can be installed directly from GitHub with uv:
console
$ uv --preview pip install git+https://github.com/biopragmatics/biolookup.git
or with pip:
console
$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/biopragmatics/biolookup.git
Note that this requires setting UV_PREVIEW mode enabled until the uv build
backend becomes a stable feature.
👐 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
This project has been supported by the following organizations (in alphabetical order):
- Biopragmatics Lab
- INDRA Lab, a part of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.
💰 Funding
This project has been supported by the following grants:
| Funding Body | Program | Grant | | ------------ | ----------------------------------------------------------------------------------------------------------------------------- | ------------- | | DARPA | Automating Scientific Knowledge Extraction (ASKE) | HR00111990009 |
🍪 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/biolookup.git $ cd biolookup $ uv --preview pip install -e . ``` Alternatively, install using pip: ```console $ UV_PREVIEW=1 python3 -m pip install -e . ``` Note that this requires setting `UV_PREVIEW` mode enabled until the uv build backend becomes a stable feature. ### 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. Install cruft with either `uv tool install cruft` or `python3 -m pip install cruft` then run: ```console $ 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 `uv tool install tox --with tox-uv` or `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/biolookup/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```console $ git clone git+https://github.com/biopragmatics/biolookup.git $ cd biolookup $ 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/biolookup 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. ```console $ uv tool install keyring $ keyring set https://upload.pypi.org/legacy/ __token__ $ keyring set https://test.pypi.org/legacy/ __token__ ``` Note that this deprecates previous workflows using `.pypirc`. #### Uploading to PyPI After installing the package in development mode and installing `tox` with `uv tool install tox --with tox-uv` or `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/biolookup/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 [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package). 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/biolookup/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
- Website: https://biopragmatics.github.io
- Twitter: biopragmatics
- Repositories: 9
- Profile: https://github.com/biopragmatics
Software supporting biomedical semantics and pragmatics
GitHub Events
Total
- Issues event: 1
- Watch event: 1
- Delete event: 1
- Issue comment event: 7
- Push event: 14
- Pull request event: 2
- Create event: 3
Last Year
- Issues event: 1
- Watch event: 1
- Delete event: 1
- Issue comment event: 7
- Push event: 14
- Pull request event: 2
- Create event: 3
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Charles Tapley Hoyt | c****t@g****m | 50 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 6
- Total pull requests: 11
- Average time to close issues: 3 months
- Average time to close pull requests: 22 days
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 1.67
- Average comments per pull request: 0.0
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: about 5 hours
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 3.5
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- cthoyt (3)
- bgyori (2)
- timalamenciak (1)
Pull Request Authors
- cthoyt (13)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 27 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 4
- Total maintainers: 1
pypi.org: biolookup
Get metadata and ontological information about all biomedical entities.
- Homepage: https://github.com/biopragmatics/biolookup
- Documentation: https://biolookup.readthedocs.io/
- License: MIT
-
Latest release: 0.2.0
published over 3 years ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- peter-evans/create-pull-request v4 composite
- actions/checkout v4 composite
- astral-sh/setup-uv v3 composite
- codecov/codecov-action v4 composite
- a2wsgi *
- bioregistry >=0.12.3
- bootstrap-flask *
- click *
- fastapi *
- flask *
- more_click *
- more_itertools *
- psutil *
- psycopg2-binary *
- pydantic *
- pyobo @ git+https://github.com/biopragmatics/pyobo
- pystow *
- sqlalchemy *
- tabulate *
- tqdm *
- typing-extensions *