A framework for keeping biomedical text mining result up-to-date
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use subJournal and subJournalISO in subArticle
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README.rst

PubRunner

PyPI Release Travis CI status Coverage status Documentation status MIT license

PubRunner is a framework to keep text mining tools running on the latest publications.

Installation

PubRunner uses Python3 and can be installed via pip from 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 to see a small number of projects that use PubRunner on Pubmed.

Documentation

Documentation including a tutorial can be found at the readthedocs page.

Contributing

Contributions are very welcome.

License

Distributed under the terms of the MIT license, "pubrunner" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.