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Updates for release
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TomDonoghue committed Aug 16, 2019
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# Ignore tutorial & example db
**/lisc_db/**

# Ignore disribution files
build/*
dist/*
lisc.egg-info/*
61 changes: 34 additions & 27 deletions README.md
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# LISC - Literature Scanner

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LISC is a package for collecting and analyzing the scientific literature.

LISC is a package for performing automated meta-analyses of scientific papers, built on top of the Pubmed E-Utils API.
## Overview

NOTE: the current version is still a development version (0.1.0-dev) and may not be totally stable.
LISC acts as a wrapper and connector between available APIs, allowing users to collect data from and about scientific articles, and to do analyses on this data, such as performing automated meta-analyses.

## Overview
A curated list of some projects enabled by LISC is available on the [projects](https://github.com/lisc-tools/Projects) page.

LISC is a python module for collecting and analzying scientific literature.
#### Supported APIs

#### Data Collection
Supported APIs through LISC includes:
- the NCBI [EUtils](https://www.ncbi.nlm.nih.gov/books/NBK25497/). EUtils provides programmatic access to the National Center for Biotechnology Information (NCBI), including the Pubmed database.
- the [OpenCitations](https://opencitations.net) API. OpenCitations provides access to citation data.

For data collection, LISC currently offers support for using the Pubmed E-Utilities.
#### Data Collection

LISC provides for two different 'types' of literature data collection:
- 'Counts': popularity and co-occurence analysis of specified search terms.
- 'Words': collects text data and meta-data from papers identified by specified search terms.
For data collection, LISC currently offers support for the following 'types' of literature data collection:
- 'Counts': collects counts and co-occurrences of specified search terms in the literature.
- 'Words': collects text data and meta-data from articles identified by specified search terms.
- 'Citations': collect citation and reference data for articles, based on DOIs.

#### Data Analysis
#### Analysis & Other Functionality

LISC provides support and utities for:
- Custom data objects for managing and operating on returned data.
- Save and load utilties for storing collected data.
- Support and tools for analyzing and plotting returned data.
- Data visualization utilities.
In addition to connecting to external APIs, LISC also provides:
- custom data objects for managing collected data
- a database structure, and save and load utilties for storing collected data
- functions and utilities to analyze collected data
- Data visualization functions for plotting collected data and analysis outputs

## Documentation

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LISC is written in Python 3, and requires Python 3.5 or greater to run.

Requirements:
- numpy
- requests
- lxml
- beautifulsoup4
- nltk

Optional dependencies, used for plots & analysis:
- matplotlib
- seaborn
- scipy
- wordcloud
- [numpy](https://pypi.org/project/numpy/)
- [requests](https://pypi.org/project/requests/)
- [lxml](https://pypi.org/project/lxml/)
- [beautifulsoup4](https://pypi.org/project/beautifulsoup4/)
- [nltk](https://pypi.org/project/nltk/)

Optional dependencies, used for plots, 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

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22 changes: 21 additions & 1 deletion setup.py
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long_description = \
"""
Literature Scanner.
LISC, or 'literature scanner' is a package for collecting and analyzing scientific literature.
LISC acts as a wrapper and connector between available APIs, allowing users to collect data from
and about scientific articles, and to do analyses on this data, such as performing automated meta-analyses.
Supported APIs available through LISC include the NCBI EUtils which provides programmatic access to the
National Center for Biotechnology Information (NCBI), including the Pubmed database, and the
OpenCitations API, which provides access to citation data.
For data collection, LISC currently offers support for the following 'types' of literature data collection:
- 'Counts': collects counts and co-occurrences of specified search terms in the literature.
- 'Words': collects text data and meta-data from articles identified by specified search terms.
- 'Citations': collect citation and reference data for articles, based on DOIs.
In addition to connecting to external APIs, LISC also provides:
- custom data objects for managing collected data
- a database structure, and save and load utilties for storing collected data
- functions and utilities to analyze collected data
- data visualization functions for plotting collected data and analysis outputs
"""

setup(
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