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Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

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Page 1: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Bibliometric Analysis with Sci2:Choose Your Own Adventure

Laura RidenourSchool of Library and Information

Science, Indiana University

Page 2: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Overview

• Paper citation network using Sci2• Gathering data• Examining and understanding file format• Adjusting program parameters for speed• Using the Network Analysis Toolkit• Visualizing a network• Exporting data for use in other programs

Page 3: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Gathering Data

• ISI file format– Text file with special formatting– Downloadable from Web of Science

• 500 records at a time from WoS

– Other sources include the Scholarly Database (http://sdb.cns.iu.edu/search/), but data from this source works slightly differently than shown in this tutorial

• Can also use any data with nodes and edges, as long as it’s a clean data set

Page 4: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Required tools

• Sci2 - https://sci2.cns.iu.edu/user/welcome.php– Must create an account in order to download

• A text editor

• Helpful:– Oxygen, Gephi

Page 5: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Allocating Additional Memory

• In the Sci2 directory, open the .ini file for Sci2 and change the settings to the following:– -vmargs– -Xms30m– -Xmx1028m

• Save and close the file, re-open Sci2• Note: you may need to adjust the memory

parameters slightly depending on system capabilities and settings

Page 6: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

http://www.libraries.iub.edu

Page 7: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Web of Knowledge

Page 8: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Download Settings

Page 9: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

What an ISI File Looks Like

Page 10: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Using Multiple ISI Files

• Strip out all headers but the beginning and end tag – can do this manually, or with a script

Page 11: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Sci2

• File > Load > (select your file and click ‘Open’) > choose ‘ISI flat format’ > click ‘Select’

Page 12: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

In the Data Manager• Right-click the loaded file, select “view” to check and/or modify the file• If you modify the file, be sure to save the file to a permanent location and

reload it into the data manager

Page 13: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Extracting the Network

Page 14: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Data Manager

Page 15: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Using the Network Analysis Toolkit (NAT)

• Choose “Network Analysis Toolkit”

Page 16: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

NAT Analysis is Displayed in the Console

Page 17: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Examining the Output

• Checking the NAT results can save time. If the network is particularly densely connected, using a faster system may save time

Page 18: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Visualization

• Select the extracted network to visualize from the Data Manager

Page 19: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Visualization (cont’d)

• Visualization > Networks > GUESS

Page 20: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Visualization (GUESS)

Page 21: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Choosing a layout (GUESS)

• Layout > GEM (or whichever layout you would like to use)

Page 22: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Initial GEM Layout (GUESS)

Page 23: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Graph Modifier Dashboard in GUESS

Page 24: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Play!!

• Take some time to play with different properties in the network. Feel free to use the interpreter, it uses jython (examples on next slide, from CNS wiki)

Page 25: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Jython Examples

Page 26: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Exporting Data

• From the Data Manager, right click the appropriate graph file and select “Save”

Page 27: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Exporting Data (cont’d)

• Choose GraphML for importing a graph into Gephi– After saving, change the file extension from .XML

to .graphml to make the file usable by Gephi• Choose .net for Pajek

Page 28: Bibliometric Analysis with Sci2: Choose Your Own Adventure Laura Ridenour School of Library and Information Science, Indiana University

Additional Resources

• http://wiki.cns.iu.edu/• http://gephi.org/