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https://github.com/jakelever/pubrunner
A framework for keeping biomedical text mining result up-to-date
https://github.com/jakelever/pubrunner
bionlp infrastructure pubmed pubmed-central python snakemake text-mining
Last synced: 2 months ago
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A framework for keeping biomedical text mining result up-to-date
- Host: GitHub
- URL: https://github.com/jakelever/pubrunner
- Owner: jakelever
- License: mit
- Created: 2017-08-30T21:30:51.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2020-07-11T22:13:26.000Z (almost 4 years ago)
- Last Synced: 2024-03-25T01:02:22.088Z (3 months ago)
- Topics: bionlp, infrastructure, pubmed, pubmed-central, python, snakemake, text-mining
- Language: Python
- Homepage:
- Size: 565 KB
- Stars: 41
- Watchers: 7
- Forks: 6
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Lists
- awesome-bioie - Pubrunner - A framework for running text mining tools on the newest set(s) of documents from PubMed. (Tools, Platforms, and Services / Repos for Specific Datasets)
README
# PubRunner
PubRunner is a framework to keep text mining tools running on the latest publications.
## Installation
PubRunner uses Python3 and can be installed via [pip](https://pypi.python.org/pypi/pip/) from [PyPI](https://pypi.python.org/pypi).
```
pip install pubrunner
```
## Usage
To run Pubrunner, you just need to provide it with a path to a biomedical text mining tool (e.g. a Github repo or a local directory). The flag --test tells Pubrunner to execute the test set. Omitting that gets Pubrunner to run the tool on the full corpus (which for Ab3P is PubMed).::
```
pubrunner --test https://github.com/jakelever/Ab3P
```
## Is PubRunner for me?
Are you a biomedical text mining tool developer? Then likely yes. PubRunner makes it easy to run a text mining tool across PubMed and keep it working!
## Examples
Check out the [examples directory](https://github.com/jakelever/pubrunner/tree/master/examples
) to see a small number of projects that use PubRunner on Pubmed.
## Documentation
Documentation including a tutorial can be found at the [readthedocs](http://pubrunner.readthedocs.io/en/stable/) page.
## Contributing
Contributions are very welcome.
## License
Distributed under the terms of the [MIT](http://opensource.org/licenses/MIT) license, "pubrunner" is free and open source software
## Issues
If you encounter any problems, please [file an issue](https://github.com/jakelever/pubrunner/issues) along with a detailed description.