LISC

LISC: A Python Package for Scientific Literature Collection and Analysis - Published in JOSS (2019)

https://github.com/lisc-tools/lisc

Keywords

Scientific Fields

Repository

Literature Scanner: Automated collection & analyses of the scientific literature.

README.rst

=========================
LISC - Literature Scanner
=========================

|ProjectStatus| |Version| |BuildStatus| |Coverage| |License| |PythonVersions| |Publication|

.. |ProjectStatus| image:: https://www.repostatus.org/badges/latest/active.svg
   :target: https://www.repostatus.org/#active
   :alt: project status

.. |Version| image:: https://img.shields.io/pypi/v/lisc.svg
   :target: https://pypi.org/project/lisc/
   :alt: version

.. |BuildStatus| image:: https://github.com/lisc-tools/lisc/actions/workflows/build.yml/badge.svg
   :target: https://github.com/lisc-tools/lisc/actions/workflows/build.yml
   :alt: build status

.. |Coverage| image:: https://codecov.io/gh/lisc-tools/lisc/branch/main/graph/badge.svg
   :target: https://codecov.io/gh/lisc-tools/lisc
   :alt: coverage

.. |License| image:: https://img.shields.io/pypi/l/lisc.svg
   :target: https://opensource.org/license/apache-2-0
   :alt: license

.. |PythonVersions| image:: https://img.shields.io/pypi/pyversions/lisc.svg
   :target: https://pypi.org/project/lisc/
   :alt: python versions

.. |Publication| image:: https://joss.theoj.org/papers/10.21105/joss.01674/status.svg
   :target: https://doi.org/10.21105/joss.01674
   :alt: publication

LISC is a package for collecting and analyzing scientific literature.

Overview
--------

LISC is a Python module for collection and analyzing the scientific literature. To do so,
LISC wraps and combines existing APIs, allowing users to collect and analyze scientific articles,
allowing for automated meta-analyses.

A curated list of some projects enabled by LISC is available on the
`projects `_ page.

Supported APIs & Collection Approaches
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Supported APIs and data collection approaches include:

- The `EUtils `_ API, which provides access to literature data,
  including the `Pubmed `_ database, from which counts, co-occurrences,
  text, and meta-data from scientific articles can be collected.
- The `OpenCitations `_ 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 `_.

This documentation includes:

- `Tutorials `_:
  with a step-by-step guide through the module and how to use it
- `Examples `_:
  demonstrating example analyses and use cases, and other functionality
- `API list `_:
  which lists and describes all the code and functionality available in the module
- `Reference `_:
  with information for how to reference and report on using the module

For a curated list of projects that use LISC, see the
`projects `_ page.

Dependencies
------------

LISC is written in Python 3, and requires Python >= 3.7 to run.

Requirements:

- `numpy `_
- `requests `_
- `lxml `_
- `beautifulsoup4 `_

Optional dependencies, used for plotting, analyses & testing:

- `matplotlib `_
- `seaborn `_
- `scipy `_
- `wordcloud `_
- `pytest `_

Install
-------

Stable releases of LISC are released on the Github
`release page `_, and on
`PYPI `_.

Descriptions of updates and changes across versions are available in the
`changelog `_.

**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:

.. code-block:: text

    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 `_.

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 `_.

To see and get involved in discussions about the module, check out:

- the `issues board `_
  for topics relating to code updates, bugs, and fixes
- the `development page `_
  for discussion of potential major updates to the module

When interacting with this project, please use the
`contribution guidelines `_
and follow the
`code of conduct `_.

Owner

JOSS Publication

LISC: A Python Package for Scientific Literature Collection and Analysis

Published

September 26, 2019

DOI

10.21105/joss.01674

Volume 4, Issue 41, Page 1674

Authors

Thomas Donoghue
Department of Cognitive Science, University of California, San Diego

Editor

Daniel S. Katz

Tags

python literature analysis text mining web scraping meta science knowledge discovery hypothesis generation automated meta analysis literature based discovery

View PDF Review Thread Software Archive

Citation (CITATION.cff)

cff-version: 1.2.0
message: >-
  If you use this software, please cite it using the metadata from this file.
type: software
title: 'lisc: literature scanner'
authors:
- given-names: 'Thomas'
  family-names: 'Donoghue'
  orcid: 'https://orcid.org/0000-0001-5911-0472'
repository-code: 'https://github.com/lisc-tools/lisc'
url: 'https://lisc-tools.github.io/'
license: Apache-2.0
preferred-citation:
  type: article
  title: 'LISC: A Python Package for Scientific Literature Collection and Analysis'
  authors:
  - given-names: Thomas
    family-names: Donoghue
    orcid: 'https://orcid.org/0000-0001-5911-0472'
  journal: 'Journal of Open Source Software'
  doi: '10.21105/joss.01674'
  issue: 41
  volume: 4
  year: 2019
  start: 1674

GitHub Events

Committers

Last synced: 7 months ago

Issues and Pull Requests

Last synced: 6 months ago

Packages