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.

1. Install the conda environment.
2. Create the pubtator environmenmt by running:

conda create --name pubtator python=3.8

3. Install packages via pip by running the following:

pip install -r requirements.txt

4. Activate with conda activate pubtator.

1. Make sure you have python version 3.8 installed.
2. Install packages by running the following:

pip install -r requirements.txt

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.

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.