biolexica

📘 Generate and apply coherent biomedical lexical indices for NER and NEN

https://github.com/biopragmatics/biolexica

Keywords

biopragmatics named-entity-linking named-entity-recognition natural-language-processing

Last synced: 10 months ago · JSON representation

Repository

📘 Generate and apply coherent biomedical lexical indices for NER and NEN

Basic Info

Host: GitHub
Owner: biopragmatics
License: mit
Language: Jupyter Notebook
Default Branch: main
Homepage:
Size: 387 MB

Statistics

Stars: 2
Watchers: 2
Forks: 0
Open Issues: 3
Releases: 5

Topics

biopragmatics named-entity-linking named-entity-recognition natural-language-processing

Created over 2 years ago · Last pushed 11 months ago

Metadata Files

Readme Contributing Funding License Code of conduct Citation

Biolexica

biolexica helps generate and apply coherent biomedical lexica. It takes care of the following:

Getting names and synonyms from a diverse set of inputs (ontologies, databases, custom) using pyobo, bioontologies, biosynonyms, and more.
Merging equivalent terms to best take advantage of different synonyms for the same term from different sources using semra.
Generating lexical index and doing NER using a standard interface from SSSLM

Importantly, we pre-define lexica for several entity types that can be readily used with any NLP tools wrapped by SSSLM, such as Gilda. They can be found in the lexica/ folder including:

Getting Started

Load a pre-defined grounder like this:

```python import biolexica

grounder = biolexica.load_grounder("phenotype")

grounder.getbestmatch("Alzheimer's disease") Match(reference=Reference(prefix='doid', identifier='10652'), name="Alzheimer's disease", score=0.7778)

grounder.annotate("Clinical trials for reducing A levels in Alzheimer's disease have been controversial.") [Annotation(text="Alzheimer's disease", start=42, end=61, match=Match(reference=Reference(prefix='doid', identifier='10652'), name="Alzheimer's disease", score=0.7339))] ```

Installation

The most recent release can be installed from PyPI with uv:

console $ uv pip install biolexica

or with pip:

console $ python3 -m pip install biolexica

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

console $ uv --preview pip install git+https://github.com/biopragmatics/biolexica.git

or with pip:

console $ UV_PREVIEW=1 python3 -m pip install git+https://github.com/biopragmatics/biolexica.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.

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/biolexica.git $ cd biolexica $ 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/biolexica/actions?query=workflow%3ATests). ### Building the Documentation The documentation can be built locally using the following: ```console $ git clone git+https://github.com/biopragmatics/biolexica.git $ cd biolexica $ 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/biolexica 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/biolexica/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/biolexica/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

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Last Year

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Last synced: 10 months ago

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Average time to close issues: 8 months
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Average comments per issue: 0.17
Average comments per pull request: 0.79
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 0

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Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 23 minutes
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cthoyt (3)
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Total packages: 1
Total downloads:
- pypi 118 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 7
Total maintainers: 1

pypi.org: biolexica

Generate and apply coherent biomedical lexical indices for NER and NEN

Homepage: https://github.com/biopragmatics/biolexica
Documentation: https://biolexica.readthedocs.io
License: MIT License
Latest release: 0.1.0
published 11 months ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 118 Last month

Rankings

Dependent packages count: 9.9%

Average: 37.7%

Dependent repos count: 65.6%

Maintainers (1)

cthoyt

Funding

https://github.com/sponsors/cthoyt

Last synced: 11 months ago