{"id":15014159,"url":"https://github.com/baderlab/saber","last_synced_at":"2025-04-12T06:05:10.822Z","repository":{"id":46104660,"uuid":"121638656","full_name":"BaderLab/saber","owner":"BaderLab","description":"Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. 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align=\"center\"\u003e\n  \u003cimg src=\"docs/img/saber_logo.png\", style=\"height:150px\"\u003e\n\u003c/p\u003e\n\n\u003ch1 align=\"center\"\u003e\n  Saber\n\u003c/h1\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://travis-ci.org/BaderLab/saber\"\u003e\n    \u003cimg src=\"https://travis-ci.org/BaderLab/saber.svg?branch=master\"\n         alt=\"Travis CI\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://www.codacy.com/app/JohnGiorgi/Saber?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=BaderLab/saber\u0026amp;utm_campaign=Badge_Grade\"\u003e\n    \u003cimg src=\"https://api.codacy.com/project/badge/Grade/d122e87152d84f959ee6d97b71d616cb\" alt='Codacy Status'/\u003e\n  \u003c/a\u003e\n  \u003ca href='https://coveralls.io/github/BaderLab/saber?branch=master'\u003e\n    \u003cimg src='https://coveralls.io/repos/github/BaderLab/saber/badge.svg?branch=master' alt='Coverage Status'/\u003e\n  \u003c/a\u003e\n  \u003ca href='http://makeapullrequest.com'\u003e\n    \u003cimg src='https://img.shields.io/badge/PRs-welcome-blue.svg?style=shields' alt='PRs Welcome'/\u003e\n  \u003c/a\u003e\n  \u003ca href='https://opensource.org/licenses/MIT'\u003e\n    \u003cimg src='https://img.shields.io/badge/License-MIT-blue.svg' alt='License'/\u003e\n  \u003c/a\u003e\n    \u003ca href='https://colab.research.google.com/drive/1WD7oruVuTo6p_908MQWXRBdLF3Vw2MPo'\u003e\n    \u003cimg src='https://img.shields.io/badge/launch-Google%20Colab-orange.svg' alt='Colab'/\u003e\n  \u003c/a\u003e\n  \u003c/a\u003e\n    \u003ca href='https://join.slack.com/t/saber-nlp/shared_invite/enQtNzE0MzY5ODM3MTc0LWZmY2VjMTY5MjllMmIzNDhkM2VhZjk5ODE1MDYyZjE5OGFjYWVhY2I2NDk5Yjk1N2Q3NTI4YTdhMTI5MjRiOGY'\u003e\n    \u003cimg src='https://img.shields.io/badge/slack-@saber--nlp-blueviolet.svg?logo=slack' alt='Slack'/\u003e\n  \u003c/a\u003e\n  \n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\u003cb\u003eSaber\u003c/b\u003e (\u003cb\u003eS\u003c/b\u003eequence \u003cb\u003eA\u003c/b\u003ennotator for \u003cb\u003eB\u003c/b\u003eiomedical \u003cb\u003eE\u003c/b\u003entities and \u003cb\u003eR\u003c/b\u003eelations) is a deep-learning based tool for \u003cb\u003einformation extraction\u003c/b\u003e in the biomedical domain.\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"#installation\"\u003eInstallation\u003c/a\u003e •\n  \u003ca href=\"#quickstart\"\u003eQuickstart\u003c/a\u003e •\n  \u003ca href=\"#documentation\"\u003eDocumentation\u003c/a\u003e\n\u003c/p\u003e\n\n## Installation\n\n_Note! This is a work in progress. Many things are broken, and the codebase is not stable._\n\nTo install Saber, you will need `python3.6`.\n\n### Latest PyPI stable release\n\n[![PyPI-Status](https://img.shields.io/pypi/v/saber.svg?colorB=blue)](https://pypi.org/project/saber/)\n[![PyPI-Downloads](https://img.shields.io/pypi/dm/saber.svg?colorB=blue\u0026logo=python\u0026logoColor=white)](https://pypi.org/project/saber)\n[![Libraries-Dependents](https://img.shields.io/librariesio/dependent-repos/pypi/saber.svg?colorB=blue\u0026logo=koding\u0026logoColor=white)](https://github.com/baderlab/saber/network/dependents)\n\n```sh\n(saber) $ pip install saber\n```\n\n\u003e The install from PyPI is currently broken, please install using the instructions below.\n\n### Latest development release on GitHub\n\n[![GitHub-Status](https://img.shields.io/github/tag-date/baderlab/saber.svg?logo=github)](https://github.com/baderlab/saber/releases)\n[![GitHub-Stars](https://img.shields.io/github/stars/baderlab/saber.svg?logo=github\u0026label=stars)](https://github.com/baderlab/saber/stargazers)\n[![GitHub-Forks](https://img.shields.io/github/forks/baderlab/saber.svg?colorB=blue\u0026logo=github\u0026logoColor=white)](https://github.com/BaderLab/saber/network/members)\n[![GitHub-Commits](https://img.shields.io/github/commit-activity/y/baderlab/saber.svg?logo=git\u0026logoColor=white)](https://github.com/baderlab/saber/graphs/commit-activity)\n[![GitHub-Updated](https://img.shields.io/github/last-commit/baderlab/saber.svg?colorB=blue\u0026logo=github)](https://github.com/baderlab/saber/pulse)\n\nPull and install straight from GitHub\n\n```sh\n(saber) $ pip install git+https://github.com/BaderLab/saber.git\n```\n\nor install by cloning the repository\n\n```sh\n(saber) $ git clone https://github.com/BaderLab/saber.git\n(saber) $ cd saber\n```\n\nand then using either `pip`\n\n```sh\n(saber) $ pip install -e .\n```\nor `setuptools`\n\n```sh\n(saber) $ python setup.py install\n```\n\nSee the [documentation](https://baderlab.github.io/saber/installation/) for more detailed installation instructions.\n\n## Quickstart\n\nIf your goal is to use Saber to annotate biomedical text, then you can either use the [web-service](#web-service) or a [pre-trained model](#pre-trained-models). If you simply want to check Saber out, without installing anything locally, try the [Google Colaboratory](#google-colaboratory) notebook.\n\n### Google Colaboratory\n\nThe fastest way to check out Saber is by following along with the Google Colaboratory notebook ([![Colab](https://img.shields.io/badge/launch-Google%20Colab-orange.svg)](https://colab.research.google.com/drive/1WD7oruVuTo6p_908MQWXRBdLF3Vw2MPo)). In order to be able to run the cells, select \"Open in Playground\" or, alternatively, save a copy to your own Google Drive account (File \u003e Save a copy in Drive).\n\n### Web-service\n\nTo use Saber as a **local** web-service, run\n\n```\n(saber) $ python -m saber.cli.app\n```\n\nor, if you prefer, you can pull \u0026 run the Saber image from **Docker Hub**\n\n```sh\n# Pull Saber image from Docker Hub\n$ docker pull pathwaycommons/saber\n# Run docker (use `-dt` instead of `-it` to run container in background)\n$ docker run -it --rm -p 5000:5000 --name saber pathwaycommons/saber\n```\n\nThere are currently two endpoints, `/annotate/text` and `/annotate/pmid`. Both expect a `POST` request with a JSON payload, e.g.,\n\n```json\n{\n  \"text\": \"The phosphorylation of Hdm2 by MK2 promotes the ubiquitination of p53.\"\n}\n```\n\nor\n\n```json\n{\n  \"pmid\": 11835401\n}\n```\n\nFor example, running the web-service locally and using `cURL`\n\n```sh\n$ curl -X POST 'http://localhost:5000/annotate/text' \\\n--data '{\"text\": \"The phosphorylation of Hdm2 by MK2 promotes the ubiquitination of p53.\"}'\n```\n\nDocumentation for the Saber web-service API can be found [here](https://baderlab.github.io/saber-api-docs/).\n\n### Pre-trained models\n\nFirst, import the `Saber` class. This is the interface to Saber\n\n```python\nfrom saber.saber import Saber\n```\n\nthen create a `Saber` object\n\n```python\nsaber = Saber()\n```\n\nand then load the model of our choice\n\n```python\nsaber.load('PRGE')\n```\n\nTo annotate text with the model, just call the `Saber.annotate()` method\n\n```python\nsaber.annotate(\"The phosphorylation of Hdm2 by MK2 promotes the ubiquitination of p53.\")\n```\nSee the [documentation](https://baderlab.github.io/saber/quick_start/#pre-trained-models) for more details on using pre-trained models.\n\n## Documentation\n\nDocumentation for the Saber package can be found [here](https://baderlab.github.io/saber/). The web-service API has its own documentation [here](https://baderlab.github.io/saber-api-docs/#introduction). \n\nYou can also call `help()` on any Saber method for more information\n\n```python\nfrom saber import Saber\n\nsaber = Saber()\n\nhelp(saber.annotate)\n```\n\nor pass the `--help` flag to any of the command-line interfaces\n\n```\npython -m src.cli.train --help\n```\n\nFeel free to open an issue or reach out to us on our slack channel ([![Slack](https://img.shields.io/badge/slack-@saber--nlp-blueviolet.svg?logo=slack)](https://join.slack.com/t/saber-nlp/shared_invite/enQtNzE0MzY5ODM3MTc0LWZmY2VjMTY5MjllMmIzNDhkM2VhZjk5ODE1MDYyZjE5OGFjYWVhY2I2NDk5Yjk1N2Q3NTI4YTdhMTI5MjRiOGY)) for more help.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbaderlab%2Fsaber","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbaderlab%2Fsaber","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbaderlab%2Fsaber/lists"}