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

Literature Scanner: Automated collection & analyses of the scientific literature.
https://github.com/lisc-tools/lisc

literature-mining literature-review meta-analysis scientific-publications text-mining web-scraping

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

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README 

          
=========================

LISC - Literature Scanner

=========================



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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 `_.