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Load the NSF data 'yoursci2directory/sampledata/scientometrics/nsf/KatyBorner.nsf' using 'File > Load'. Select NSF csv format from the 'Load' pop-up window. Make sure the loaded dataset in the Data Manager window is highlighted in blue, and run 'Data Preparation > Text Files > Extract Co-Occurrence Network' using these parameters:

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The Sci2 Tool supports the analysis of evolving networks. For this study, load Alessandro Vespignani's publication history from ISI, which can be downloaded from Thomson's Web of Science or loaded from 'using 'File > Load' and following this path: 'yoursci2directory/sampledata/scientometrics/isi/AlessandroVespignani.isi'using 'File > Load' and select 'ISI scholarly format' in the Load window. Slice the data into five year intervals from 1990-2006 using 'Preprocessing > Temporal > Slice Table by Time' and the following parameters:

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To see the evolution of Vespignani's co-authorship network over time, check "cumulative". Then, extract co-authorship networks one at a time for each sliced time table using 'Data Preparation > Text Files > Extract Co-Author Network'', making sure to select "ISI" from the pop-up window during the extraction. Visualize the evolving network using GUESS as shown in Figure 5.4.
 

Figure 5.4: Evolving co-authorship network of Vespignani from 1990-2006

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5.1.4.1 Paper-Paper (Citation) Network

Load the file 'using 'File > Load' and following this path: 'yoursci2directory/sampledata/scientometrics/isi/FourNetSciResearchers.isi' using 'File > Load. ' Choose "ISI scholarly format" in the pop-up 'Load' window. A table of all records and a table of 361 records with unique ISI ids will appear in the Data Manager. In this "clean" file, each original record now has a "Cite Me As" attribute that is constructed from the first author, publication year (PY), journal abbreviation (J9), volume (VL), and beginning page (BP) fields of its ISI record. This "Cite Me As" attribute will be used when matching paper and reference records.

To extract the paper citation network, select the '361 Unique ISI Records' table and run 'Data Preparation > Text Files > Extract Directed Network' using the parameters :

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To produce a co-authorship network in the Sci2 Tool, select the table of all 361 unique ISI records from the 'FourNetSciResearchers' dataset in the Data Manager window. Run 'Data Preparation > Text Files > Extract Co-Author Network' using the parameter:

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The result is two derived files in the Data Manager window: the "Extracted Co-Authorship Network" and an "Author information" table (also known as a "merge table"), which lists unique authors. In order to manually examine and edit the list of unique authors, open the merge table in your default spreadsheet program. In the spreadsheet, select all records, including "label," "timesCited," "numberOfWorks," "uniqueIndex," and "combineValues," and sort by "label." Identify names that refer to the same person. In order to merge two names, first delete the asterisk ('*') in the "combineValues" column of the duplicate node's row. Then, copy the "uniqueIndex" of the name that should be kept and paste it into the cell of the name that should be deleted. Resave the revised table as a .csv file and reload it. Select both the merge table and the network and run 'Data Preparation > Text Files > Update Network by Merging Nodes. ' Table 5.2 shows the result of merging "Albet, R" and "Albert, R": "Albet, R" will be deleted and all of the node linkages and citation counts will be added to "Albert, R".

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A merge table can be automatically generated by applying the Jaro distance metric (Jaro, 1989, 1995) available in the open source Similarity Measure Library (http://sourceforge.net/projects/simmetrics/) to identify potential duplicates. In the Sci2 Tool, simply select the co-author network and run 'Data Preparation > Text Files > Detect Duplicate Nodes' using the parameters:

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To merge identified duplicate nodes, select both the "Extracted Co-Authorship Network" and "Merge Table: based on label" by holding down the 'Ctrl' key. Run 'Data Preparation > Text Files > Update Network by Merging Nodes'. This will produce an updated network as well as a report describing which nodes were merged. To complete this workflow, an aggregation function file must also be selected from the pop-up window:

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In Sci2, a bibliographic coupling network is derived from a directed paper citation network (see section 4.9.1.1. Document-Document (Citation) Network).

Load the file using 'File > Load' and following this path: 'yoursci2directory/sampledata/scientometrics/isi/FourNetSciResearchers.isi' using 'File > Load. ' Choose "ISI scholarly format" in the pop-up 'Load' window. A table of all records and a table of 361 records with unique ISI ids will appear in the Data Manager.

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