README.md

In gdancik/pmc2nc: PubMed Central Citation Network Construction

Overview

The R package pmc2nc is a PubMed Central citation network construction tool for facilitating citation network analyses for articles in PMC. [Eastern Colleges Science Conference Abstract]

DEVELOPMENT OF A PUBMED CENTRAL CITATION COLLECTION TOOL AND NETWORK ANALYSIS OF CANCER-RELATED GENES

Identifying relevant research articles is an inefficient task for researchers due to a steadily increasing number of published articles available across journal databases. Citation analysis tools have previously been utilized to quantify the relative importance of published journals through the application of network science measures to citation networks. This study involved the development of a citation collection tool and subsequent analysis of citation networks for articles available within PubMed Central that mention cancer genes, such as BRCA2. The citation collection tool, called pmc2nc, allows users to quickly generate edge lists for articles of interest. The edge list can then be imported into network visualization and analysis tools. The pmc2nc tool, developed in the R programming language, uses the rentrez package to extract citation information, and is available as an R package and as a Shiny application. The Gephi graphing software was used to construct and analyze the networks. Specifically, we used the PageRank and HITS algorithms to identify "important" articles based on the authority, hub, and PageRank weights. The interpretation and utility of these measures for identifying important articles will be discussed.

Availability

Download the R package

# Install the R package from Github using the _devtools_ package:
devtools::install_github('gdancik/pmc2nc')

# generate an edge list for multiple articles
res <- get_pmc_cited_in(c(21876761,29463753))
e <- generateEdgeList(res2)

# get article information (title, authors, etc)
info <- get_article_info(c(21876726,21876761))

Run the Shiny app

A shiny web application, the shiny citation collection tool (shinycct) is available and can be downloaded from https://github.com/anaxisa/anaxisa.github.io.

Run the Shiny app from a docker container (recommended for non-programmers).

1. Download docker from https://www.docker.com/get-started
2. Run the application by typing the following at your docker command prompt:

docker run -it -p 3838:3838 gdancik/shinycct

1. Point your browser to localhost:3838

gdancik/pmc2nc documentation built on May 5, 2019, 7:09 a.m.