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Retrieve and process PubTator annotations

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PubTator: tagged PubMed abstracts for literature mining

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PubTator and its 2.0 version (PubTator Central) uses text mining to tag PubMed abstracts/artciles with standardized concepts. This repository retrieves and processes PubTator annotations for use in greenelab/snorkeling and elsewhere.

Get Started

Set-up Environment

Conda

  1. Install the conda environment.
  2. Create the pubtator environmenmt by running:
conda create --name pubtator python=3.8
  1. Install packages via pip by running the following:
pip install -r requirements.txt
  1. Activate with conda activate pubtator.

Pip

  1. Make sure you have python version 3.8 installed.
  2. Install packages by running the following:
pip install -r requirements.txt

Execution

To start processing Pubtator/Pubtator Central run the following command:

python execute.py --config config_files/pubtator_central_config.json

If the original Pubtator is desired replace pubtator_central_config.json with pubtator_config.json. The json file contains all the necessary parameters needed to run. More information for the json file can be found here.

License

This repository is dual licensed as BSD 3-Clause and CC0 1.0, meaning any repository content can be used under either license. This licensing arrangement ensures source code is available under an OSI-approved License, while non-code content — such as figures, data, and documentation — is maximally reusable under a public domain dedication.

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Retrieve and process PubTator annotations

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