=========================
LISC - Literature Scanner
=========================
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LISC is a package for collecting and analyzing the scientific literature.
Overview
--------
LISC acts as a wrapper and connector between available APIs, allowing users to collect data from and
about scientific articles, and perform analyses on this data, such as performing automated meta-analyses.
A curated list of some projects enabled by LISC is available on the `projects <https://github.com/lisc-tools/Projects>`_ page.
Supported APIs & Collection Approaches
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Supported APIs and data collection approaches include:
- The `EUtils <https://www.ncbi.nlm.nih.gov/books/NBK25497/>`_ API, which provides access to literature data,
including the `Pubmed <https://pubmed.ncbi.nlm.nih.gov/about/>`_ database, from which text and meta-data from
identified articles can be collected, as well as analyses such as counts and co-occurrences of terms.
- The `OpenCitations <https://opencitations.net>`_ API, which provides access to citation data, from which
citation and reference information can be collected.
Analysis & Other Functionality
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In addition to connecting to external APIs, LISC also provides:
- A database structure, and save and load utilities for storing collected data
- Custom data objects for managing and preprocessing collected data
- Functions and utilities to analyze collected data
- Data visualization functions for plotting collected data and analysis outputs
Documentation
-------------
Documentation is available on the `documentation site <https://lisc-tools.github.io/lisc/>`_.
This documentation includes:
- `Tutorials <https://lisc-tools.github.io/lisc/auto_tutorials/index.html>`_:
with a step-by-step guide through the module and how to use it
- `Examples <https://lisc-tools.github.io/lisc/auto_examples/index.html>`_:
demonstrating example analyses and use cases, and other functionality
- `API list <https://lisc-tools.github.io/lisc/api.html>`_:
which lists and describes all the code and functionality available in the module
- `Reference <https://lisc-tools.github.io/lisc/reference.html>`_:
with information for how to reference and report on using the module
For a curated list of projects that use LISC check out the `projects <https://github.com/lisc-tools/Projects>`_ page.
Dependencies
------------
LISC is written in Python 3, and requires Python >= 3.7 to run.
Requirements:
- `numpy <https://pypi.org/project/numpy/>`_
- `requests <https://pypi.org/project/requests/>`_
- `lxml <https://pypi.org/project/lxml/>`_
- `beautifulsoup4 <https://pypi.org/project/beautifulsoup4/>`_
Optional dependencies, used for plotting, analyses & testing:
- `matplotlib <https://pypi.org/project/matplotlib/>`_
- `seaborn <https://pypi.org/project/seaborn/>`_
- `scipy <https://pypi.org/project/scipy/>`_
- `wordcloud <https://pypi.org/project/wordcloud/>`_
- `pytest <https://pypi.org/project/pytest/>`_
Install
-------
Stable releases of LISC are released on the Github
`release page <https://github.com/lisc-tools/lisc/releases>`_, and on
`PYPI <https://pypi.org/project/lisc/>`_.
Descriptions of updates and changes across versions are available in the
`changelog <https://lisc-tools.github.io/lisc/changelog.html>`_.
**Stable Release Version**
To install the latest stable release, you can install from pip:
.. code-block:: shell
$ pip install lisc
LISC can also be installed with conda, from the conda-forge channel:
.. code-block:: shell
$ conda install -c conda-forge lisc
**Development Version**
To get the development version (updates that are not yet published to pip), you can clone this repository.
.. code-block:: shell
$ git clone https://github.com/lisc-tools/lisc
To install this cloned copy of LISC, move into the directory you just cloned, and run:
.. code-block:: shell
$ pip install .
**Editable Version**
If you want to install an editable version, for making contributions, download the development
version as above, and run:
.. code-block:: shell
$ pip install -e .
Reference
---------
If you use this code in your project, please cite
Donoghue, T. (2018) LISC: A Python Package for Scientific Literature Collection and Analysis.
Journal of Open Source Software, 4(41), 1674. DOI: 10.21105/joss.01674
Direct Link: https://doi.org/10.21105/joss.01674
More information for how to cite this method can be found on the
`reference page <https://lisc-tools.github.io/lisc/reference.html>`_.
Contribute
----------
This project welcomes and encourages contributions from the community!
To file bug reports and/or ask questions about this project, please use the
`Github issue tracker <https://github.com/lisc-tools/lisc/issues>`_.
To see and get involved in discussions about the module, check out:
- the `issues board <https://github.com/lisc-tools/lisc/issues>`_ for topics relating to code updates, bugs, and fixes
- the `development page <https://github.com/lisc-tools/Development>`_ for discussion of potential major updates to the module
When interacting with this project, please use the
`contribution guidelines <https://github.com/lisc-tools/lisc/blob/main/CONTRIBUTING.md>`_
and follow the
`code of conduct <https://github.com/lisc-tools/lisc/blob/main/CODE_OF_CONDUCT.md>`_.
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"description": "=========================\nLISC - Literature Scanner\n=========================\n\n|ProjectStatus|_ |Version|_ |BuildStatus|_ |Coverage|_ |License|_ |PythonVersions|_ |Publication|_\n\n.. |ProjectStatus| image:: https://www.repostatus.org/badges/latest/active.svg\n.. _ProjectStatus: https://www.repostatus.org/#active\n\n.. |Version| image:: https://img.shields.io/pypi/v/lisc.svg\n.. _Version: https://pypi.python.org/pypi/lisc/\n\n.. |BuildStatus| image:: https://github.com/lisc-tools/lisc/actions/workflows/build.yml/badge.svg\n.. _BuildStatus: https://github.com/lisc-tools/lisc/actions/workflows/build.yml\n\n.. |Coverage| image:: https://codecov.io/gh/lisc-tools/lisc/branch/main/graph/badge.svg\n.. _Coverage: https://codecov.io/gh/lisc-tools/lisc\n\n.. |License| image:: https://img.shields.io/pypi/l/lisc.svg\n.. _License: https://opensource.org/licenses/Apache-2.0\n\n.. |PythonVersions| image:: https://img.shields.io/pypi/pyversions/lisc.svg\n.. _PythonVersions: 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