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A user-friendly method for generating overlay maps (2009 update)


(appendix 1 to: Ismael Rafols, Alan L. Porter, and Loet Leydesdorff, “Science overlay maps: a new tool for research policy and library management,” Journal of the American Society for Information Science & Technology 61(9) (2010) 1871-1887; <pdf-version>.)

Manual by Ken Riopelle, May 2010



We follow the method introduced in Rafols & Meyer (forthcoming) 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://idr.gatech.edu/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 Web of Science Category choice produces a list with the number of documents in each Subject Category for Web of Science version 5. (This was called “Subject Category” in version 4, and therefore our abbreviation “SC”.) The resulting list can be downloaded as Analyze.txt. This file is transformed by the mini-programme SC2009.exe (in our tool kit) for upload as SC09.vec into Pajek vector file.


In the next step the analyst can go to our webpage for maps at http://www.idr.gatech.edu/upload.php and upload this data. Or, if one desires more control over the process, one can use a programme Pajek. After opening the programme, press F1 and read the basemap file SC2009-020cut-2D-KK.paj. Then, go to the main menu File>Vector>Read to upload the above prepared file “SC09.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>Size of Vertices in the new draw window. In order to have the standard colour settings, the file SC2008-18Factors-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. (See also here for improving the picture.) 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 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 SC09.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.


Four macro fields (December 2010)

We extended the options with a mapping into four macro-fields: biomedical, environmental, physical, and social sciences (based on a four-factor solution of the citation matrix). The .paj file using these four fields can be retrieved from here, and the .ini file in which the layout and colours correspond with the map in global maps.ppt from here. Note that this attribution of four colours can also be used with the .vec file based on the 222 ISI Subject Categories as described above; one only has to change the .ini file.


Rao-Stirling Diversity

Both procedures (ISI.Exe or SC2009.Exe) also provide a file sc09.dbf. This file can be used as input to the computation of the Stirling-Rao diversity measure using the instruction provided here.


Extension for GEPHI

Clement Levallois < CLevallois@rsm.nl > was so kind to make an excel file with a macro <gephi.xlsm> which allows for generating the corresponding input file for GEPHI (as an alternative to Pajek for the visualization). Save this file under the name gephi.xlsm by right clicking on the hyperlink.


Previous years


2007: One can download the original toolkit for 2007 as a single zip-file from here.

2008: One can find the file SC2008-015cut-2D-KK.paj from here.


The program SC2007.exe (for 221 categories in 2007 and 2008) is available from here. (SC2009.exe operates on 222 ISI Subject Categories.)



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. (forthcoming). Diversity and Network Coherence as indicators of interdisciplinarity: case studies in bionanoscience. Scientometrics, 82(2), 263-287.

Ismael Rafols, Alan L. Porter, and Loet Leydesdorff, “Science overlay maps: a new tool for research policy and library management,” Journal of the American Society for Information Science & Technology 61(9) (2010) 1871-1887.


<click here for downloading this toolkit as a single zip-file>



[1] This file is based on the matrix contained in 221_SCs_2008_Citations&Similarities.xls.