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Update docs on COVID-19 plugin
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Covid-19
========
.. figure:: https://github.com/asreview/asreview/blob/master/images/intro-covid19-small.png?raw=true
:alt: ASReview against COVID19

.. figure:: ../images/intro-covid19-small.png
:alt: COVID-19 extension
Extension to add publications on COVID-19 to
`ASReview <https://github.com/asreview/asreview>`__.

ASReview against COVID-19
=========================

To help combat the Covid-19 crisis, the ASReview Core Development team has decided to release a package that provides the latest scientific datasets on Covid-19. These are integrated automatically into ASReview once we install the correct packages, so reviewers can start reviewing the latest scientific literature on Covid-19 as soon as possible!
The Active learning for Systematic Reviews software
`ASReview <https://github.com/asreview/asreview>`__ implements learning
algorithms that interactively query the researcher during the title and
abstract reading phase of a systematic search. This way of interactive
training is known as active learning. ASReview offers support for
classical learning algorithms and state-of-the-art learning algorithms
like neural networks. The software can be used for traditional
systematic reviews for which the user uploads a dataset of papers, or
one can make use of the built-in datasets.

Installation
------------
To help combat the COVID-19 crisis, the ASReview team released an
extension that integrates the latest scientific datasets on COVID-19 in
the ASReview software.

To install the Covid-19 package for ASReview, we assume you have installed the main ASReview software. If not, we refer to the :doc:`installation <installation>` page. Once ASReview has been installed, you can go to your terminal again and type "pip install asreview-covid19". This should install the Covid-19 package. We can now run the ASReview software again, by typing "asreview oracle" in the terminal. This should start the ASReview GUI. When we create a new project, the Covid-19 datasets should appear. When we select one of these, we can start reviewing the Covid-19 dataset!
CORD-19 dataset
---------------

The `CORD-19
dataset <https://pages.semanticscholar.org/coronavirus-research>`__ is a
dataset with scientific publications on COVID-19 and coronavirus-related
research (e.g. SARS, MERS, etc.) from PubMed Central, the WHO COVID-19
database of publications, the preprint servers bioRxiv and medRxiv and
papers contributed by specific publishers (currently Elsevier). The
dataset is compiled and maintained by a collaboration of the Allen
Institute for AI, the Chan Zuckerberg Initiative, Georgetown
University’s Center for Security and Emerging Technology, Microsoft
Research, and the National Library of Medicine of the National
Institutes of Health. Version 5 of the dataset
(`csv <https://ai2-semanticscholar-cord-19.s3-us-west-2.amazonaws.com/2020-03-27/metadata.csv>`__,
dated March 27, 2020) contains metadata of 45.8K publications on
COVID-19 and coronavirus-related research. The CORD-19 dataset is
updated weekly.

ASReview plugin
---------------

To help combat the COVID-19 crisis, the ASReview team has decided to
release a package that provides the latest scientific datasets on
COVID-19. These are integrated automatically into ASReview once we
install the correct packages, so reviewers can start reviewing the
latest scientific literature on COVID-19 as soon as possible! Two
versions of the CORD-19 dataset (publications relating to COVID-19) are
made available in ASReview:

- full CORD-19 dataset
- CORD-19 dataset with publications from December 2019 onwards

The datasets are updated in ASReview plugin shortly after the release by
the Allen Institute for AI.

Installation and usage
----------------------

The COVID-19 plug-in requires ASReview 0.8 or higher. Install ASReview
by following the instructions in `Installation of
ASReview <https://asreview.readthedocs.io/en/latest/installation.html>`__.

Install the extension with pip:

.. code:: bash
pip install asreview-covid19
The datasets are immediately available after starting ASReview.

.. code:: bash
asreview oracle
The datasets are selectable in Step 2 of the project initialization. For
more information on the usage of ASReview, please have a look at the
`Quick
Tour <https://asreview.readthedocs.io/en/latest/quicktour.html>`__.

|ASReview CORD19 datasets|

License
-------

The ASReview software and the plugin have an Apache 2.0 LICENSE. For the
datasets, please see the license of the CORD-19 dataset
https://pages.semanticscholar.org/coronavirus-research.


.. |ASReview CORD19 datasets| image:: https://github.com/asreview/asreview/blob/master/images/asrewiew-plugin-cord19-dataset.png?raw=true
:target: https://github.com/asreview/asreview-covid19

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