Literature Scanner
Project description
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 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 text and meta-data from identified articles can be collected, as well as analyses such as counts and co-occurrences of terms.
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 check out the projects page.
Dependencies
LISC is written in Python 3, and requires Python >= 3.7 to run.
Requirements:
Optional dependencies, used for plotting, analyses & testing:
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:
$ pip install liscLISC can also be installed with conda, from the conda-forge channel:
$ conda install -c conda-forge liscDevelopment Version
To get the development version (updates that are not yet published to pip), you can clone this repository.
$ git clone https://github.com/lisc-tools/liscTo install this cloned copy of LISC, move into the directory you just cloned, and run:
$ pip install .Editable Version
If you want to install an editable version, for making contributions, download the development version as above, and run:
$ 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.
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.
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