Overlay Toolkit

A User-Friendly Method for Generating Overlay Maps

Download this toolkit as a single zip-file Also available at Loet Leydesdorff’s webpage

Appendix 1 to: Ismael Rafols, Alan L. Porter, and Loet Leydesdorff, “Science overlay maps: a new tool for research policy and library management,” in preparation

We follow the method introduced in Rafols & Meyer (2010) to create the overlay map on the basis of a global map of science (Leydesdorff & Rafols, 2009). The steps described below rely on access to the Web of Science and the files available in our mapping kit (also available at http://users.fmg.uva.nl/lleydesdorff/overlaytoolkit/). The objective is to obtain the set of SCs for a given set of articles; provide this to network software (we describe for Pajek); and output as overlay information to add to a suitable basemap.

First, the analyst has to conduct a search in the Thomson Reuters Web of Science (www.isiknowledge.com). Non-expert users should note that this initial step is crucial and should be done carefully: authors may come with different initials, addresses are often inaccurate, and only some types of document ,may be of interest (e.g., only so-called citable items: articles, proceedings papers, reviews, and letters). Once the analyst has chosen a set of documents from searches at Web of Science, one can click the tab, Analyze results. In this new webpage, the selected document set can then be analysed along various criteria (top left hand tab). The Subject Area choice produces a list with the number of documents in each Subject Category. This list can be downloaded as Analyze.txt.  Otherwise, Analyze.txt can be transformed by the mini-programme SC2007.exe (in our tool kit) for upload as SC07.vec into Pajek vector file.

In the next step the analyst can go to our webpage for maps and upload the data. Or, if one desires more control on the process, one can use the programme Pajek. After opening the programme, press F1 and upload the basemap file SC2007-015cut-2D-KK.paj.[1] Then, go to the main menu File>Vector>Read to upload the above prepared file “SC07.vec.” Selecting from the menu Draw>Draw-Partition-Vector (alternatively, pressing Ctrl-Q), the overlay map will be generated. At this stage, the size of nodes will often need adjustment, which can be done by selecting Options>Sizeof Vertices in the new draw window. In order to have the standard colour settings, the file SC2007-18Factors-ColourSettings.txt can be loaded by going to Options>Ini File>Load in the main Pajek window. Crtl-L and Ctrl-D allow visualise and delete, respectively, the labels of each SC. Clickling on nodes allows to move SC to other positions. The image can be exported selecting Export>2D>Bitmap in the menu of the Draw window. A further optional step would be to label the map in terms of factors, by importing this image into powerpoint in order to label groups of clusters, as shown in the file SC2007 Global maps.ppt.

An alternative procedure for more experienced users is to download the records of a document set found in the Web of Science. This can be done by adding the Marked list (bottom bar) the desired documents; second, going to Marked list (top bar) and then downloading the documents in a Tagged Field format after selecting Subject category as one of the fields to download. The downloaded file should be renamed as data.txt and used as input into the program ISI.exe. One of the outputs of the programme ISI.exe is the file SC07.vec that can be used in Pajek as explained above. The advantage of this procedure is that ISI.exe also produces other files with information on fields such as author or journal that may be of interest. Feel free to contact the authors in case of difficulty.

Both procedures (ISI.Exe or SC2007.Exe) also provide a file sc07.dbf. This file can be used as input to the computation of the Stirling-Rao diversity measure.


Leydesdorff, L. & Rafols, I. (2009). A Global Map of Science Based on the ISI Subject Categories. Journal of the American Society for Information Science & Technology, 60(2), 348-362.

Rafols, I. & Meyer, M. (2010). Diversity and Network Coherence as indicators of interdisciplinarity: case studies in bionanoscience. Scientometrics, 82(2), 263-287.

1 – This file is based on the matrix contained in 221_SCs_2007_Citations&Similarities.xls.