biomadeira / citation-network-explorer

Tool for exploring local citation networks.

Welcome to Gecko!

This is a tool that uses the citation relations between scientific papers to help researchers find interesting and relevant papers.

The user specifies several 'seed' papers which define the specific area of the scientific landscape they are interested in.

The tool then searches several databases to find the papers that cite or are cited-by the seed papers.

Papers that are cited by a lot of the seed papers are likely to be important foundational papers in the field (or certainly worth being aware of at least).

Papers that cite a lot of the seed papers are likely to be more recent papers in the same area that might be worth reading.

The tool allows the user to view these highly connected papers either in a table or in the context of the network.

Setting up Gecko to run locally

1. Clone the repo (or just download as a zip)

git clone https://github.com/bjw49/citation-network-explorer.git

2. To be able to use the Microsoft Academic Graph you'll need an API key for the Microsoft Academic Knowledge API from here. You can use the tool without one but the title search functionality won't work and the coverage of the Open Citation Corpus isn't as good yet (though it is growing every day).

3. If you have an API key, open the file microsoft.js in a text editor and paste the API key into the line below (making the obvious substitution):

MICROSFT_API_KEY = "YOUR API KEY GOES HERE"

Instructions for use

1. Open GeckoApp.html (in the /public folder) or go to http://citationgecko.com
2. To get started add some seed papers by clicking the 'add more seed papers' button in the left-hand panel.
3. There are three ways of choosing seed papers to start with:
   1. Add directly by DOI
   2. Upload a bibTex file (NOTE: currently only entries with a DOI will be added)
      • There is an example BibTex in the repository (exampleBibTex.bib) which you can try importing as a test case.
   3. Search for seed papers by title
      • Papers with titles containing the query words are displayed in a table.
      • Choose which papers to add as seeds by clicking the Add buttons at the end of each row.
4. The seed papers added are listed in the left-hand panel and connections between them shown graphically in the right hand panel.
5. For a list of the papers connected to these seed papers click the 'Connected' tab in the left-hand panel. Papers can sorted by "Seeds Cited" or "Seeds Cited-By" in order to find highly connected papers.
6. In order to hide less well connected papers from the Network View use the Threshold Slide to select the minimum number of connections to be displayed.
7. You can switch between viewing a graph showing only references of the seed papers and a graph showing only the papers that cite the seed papers by clicking the toggle between 'Papers Cited-By Seed Papers' and 'Papers Citing Seed Papers' that also acts as a key.
8. If one of the connected papers seems highly relevant you can add it as a seed paper either from the list view or network view, expanding the network in order to uncover more papers.