A relation extraction toolkit for biomedical text mining
Project description
Kindred is a package for relation extraction in biomedical texts. Given some training data, it can build a model to identify relations between entities (e.g. drugs, genes, etc) in a sentence.
Installation
You can install “kindred” via pip from PyPI:
$ pip install kindred
Kindred relies on the Stanford CoreNLP toolkit for parsing. By default it will attempt to connect to a local server (localhost:9000). If you want Kindred to download the CoreNLP files and run it as a subprocess when a server can’t be found, use the following command:
>>> import kindred >>> kindred.downloadCoreNLP()
Usage
Full documentation can be found at readthedocs.
PubAnnotation Example
>>> corpus = kindred.pubannotation.load('bionlp-st-gro-2013-development')
PubTator Example
>>> corpus = kindred.pubtator.load([19894120,19894121])
Contributing
Contributions are very welcome.
License
Distributed under the terms of the MIT license, “kindred” is free and open source software
Issues
If you encounter any problems, please file an issue along with a detailed description.
Project details
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