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  1. 1. Command line interface
    1. 1.1 Download
    2. 1.2 Sample data
    3. 1.3 How to run VOODOO
    4. 1.4 Output
  2. 2. Voodoo GUI
    1. 2.1 Download
    2. 2.2 Sample data
    3. 2.3 How to run
    4. 2.4 Output
  3. 3. Web interface
    1. 3.1 Sample data
    2. 3.2 How to run
  4. 4. File list

To demonstrate how VOODOO works, we present a tutorial for the 3 interfaces using 3 randomly chosen abstracts from the Biochemical Journal of Pub Med Central.

1.  Command line interface

1.1  Download

  • Download Java code http://onto.eva.mpg.de/voodoo/VoodooConsole.zip .
  • Unzip code files.
  • Hint: Create a separate directory - the unzip procedure will automatically create a lib directory, which probably overlaps with existing lib directories.
Paper clips
Create directory and unpack Java code

1.2  Sample data

The input file contains the abstract from "High membrane potential promotes alkenal-induced mitochondrial uncoupling and influences adenine nucleotide translocase conformation" from Vian Azzu, Nadeene Parker, and Martin D. Brand, published online on June 26, 2008 at http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2474560&rendertype=abstract .

1.3  How to run VOODOO

  • Go to the directory where VOODOO is located.
  • Run on the command line:

java -Xmx2G -jar VoodooConsole.jar -i [text input file] -t [category table file] -o [output file] -l ./englishFactored.ser.gz

Paper clips
How to run VOODOO on the command line - an example

1.4  Output

2.  Voodoo GUI

2.1  Download

  • Download Java code http://onto.eva.mpg.de/voodoo/VoodooConsole.zip .
  • Unzip code files.
  • Hint: Create a separate directory - the unzip procedure will automatically create a lib directory, which probably overlaps with existing lib directories.
Paper clips
Create directory and upack Java code

2.2  Sample data

The input file contains the abstract from "Bcl-2 overexpression prevents calcium overload and subsequent apoptosis in dystrophic myotubes" from Olivier Basset, François-Xavier Boittin, Christian Cognard, Bruno Constantin, and Urs T. Ruegg, published online on March 28, 2006 at http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1422769&rendertype=abstract .

2.3  How to run

  • Go to the directory where VOODOO_GUI is located.
  • Run on the command line:

java -Xmx2G -jar VoodooGUI.jar

Paper clips
How to start the GUI from the command line

2.4  Output

VOODOO_GUI will produce an output in the GUI. The output can also be opened in an html viewer (use "Open output in browser" in the menu of the GUI). A plain text output file like that in the command line version and the html file are saved in ?? .

Paper clips
How to use the GUI

3.  Web interface

You can find the web interface at http://onto.eva.mpg.de/VOODOO/ .

3.1  Sample data

The input file contains the abstract from "Pterin interactions with distinct reductase activities of NO synthase." from M M Pantke, A Reif, J G Valtschanoff, Z Shutenko, A Frey, R J Weinberg, W Pfleiderer, and H H Schmidt, published online on May 15, 2001 at http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1221810 .

3.2  How to run

  • Give the job a name.
  • Browse the category table file.
  • Copy the text you want to analyze in the "Text" box.
  • Submit the job.
Paper clips
Submitting a job in the web interface
  • Go to "list jobs".
  • If job "Finished" is 1, click on the job name.
Paper clips
Finding results of the job
  • Click on "Results" to see the detected categories.
Paper clips
Detected categories in the text

4.  File list