https://github.com/biopragmatics/biolookup
🔍 The Biolookup Service retrieves metadata and ontological information about biomedical entities.
https://github.com/biopragmatics/biolookup
bioinformatics biology biopragmatics cheminformatics chemistry flask metadata obofoundry ontology
Last synced: 3 months ago
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🔍 The Biolookup Service retrieves metadata and ontological information about biomedical entities.
- Host: GitHub
- URL: https://github.com/biopragmatics/biolookup
- Owner: biopragmatics
- License: mit
- Created: 2021-08-29T09:06:03.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2025-03-05T20:36:20.000Z (4 months ago)
- Last Synced: 2025-04-13T00:15:26.369Z (3 months ago)
- Topics: bioinformatics, biology, biopragmatics, cheminformatics, chemistry, flask, metadata, obofoundry, ontology
- Language: Python
- Homepage: http://biolookup.io
- Size: 218 KB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.rst
- License: LICENSE
Awesome Lists containing this project
README
BioLookup
Get metadata and ontological information about biomedical entities.
## 💪 Getting Started
The Biolookup Service has an endpoint `/api/lookup/` 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](https://indralab.github.io) 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`](https://github.com/cthoyt/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](https://pypi.org/project/biolookup/) 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](https://github.com/biopragmatics/biolookup/blob/master/.github/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](https://biopragmatics.github.io)
- [INDRA Lab](https://indralab.github.io), a part of the
[Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/)
and the
[Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu) at
[Harvard Medical School](https://hms.harvard.edu/).
### 💰 Funding
This project has been supported by the following grants:
| Funding Body | Program | Grant |
| ------------ | ----------------------------------------------------------------------------------------------------------------------------- | ------------- |
| DARPA | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009 |
### 🍪 Cookiecutter
This package was created with
[@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using
[@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/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.