text_selector

A Custom Jupyter Widget for selecting part of text and assingning it one of tags.

Use the widget with the active learning tool:
https://github.com/IINemo/active_learning_toolbox/tree/seq

Usage:

An example of use case can be found in example.ipynb
Note: if you have less than 10 tags you don't need to pass colors, otherwise you have too.

The result is represented via widgets public field res. It can be in 1 of 3 states:

1. Empty: nobody selected anything in widget
2. Containing string of None: text doesn't contain any squences and user checked this widget as "Done"
3. Containing dicts with selected sequences

Installation

To install this extension simply run folowing comands:

$ pip install text_selector
$ jupyter nbextension enable --py --sys-prefix text_selector

To install for jupyterlab

$ jupyter labextension install text_selector

For a development installation (requires npm) run in terminal:

$ git clone https://github.com/randomunrandom/text_selector.git
$ cd text_selector
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix text_selector
$ jupyter nbextension enable --py --sys-prefix text_selector
$ jupyter labextension install js

Docker

To create and start docker container run:

$ git clone https://github.com/randomunrandom/text_selector.git
$ cd text_selector
$ docker build -t text_selector .
$ docker run -p 8888:8888 -it --rm --name text_selector text_selector

if port 8888 is occupied change ${port} to any available port

$ docker run -p ${port}:8888 -it --rm --name text_selector text_selector

Cite

@inproceedings{shelmanov2019bibm,
    title={Active Learning with Deep Pre-trained Models for Sequence Tagging of Clinical and Biomedical Texts},
    author={Artem Shelmanov and Vadim Liventsev and Danil Kireev and Nikita Khromov and Alexander Panchenko and Irina Fedulova and Dmitry V. Dylov},
    booktitle={Proceedings of International Conference on Bioinformatics & Biomedicine (BIBM)},
    year={2019}
}