Troubleshooting

• I updated Knowtator to the latest version and now I am having troubles opening my annotation project.
• Knowtator/Protégé runs out of memory
• Something goes wrong on my Mac installation of Knowtator/Protégé.
• Knowtator is getting cluttered with a bunch of annotations that I no longer want.

I updated Knowtator to the latest version and now I am having troubles opening my annotation project. If you are having difficulty loading your annotation project after you have upgraded Knowtator to the latest version, here are some possible reasons and their workarounds:

• The included project "knowtator.pprj" is referenced by an absolute file name. Knowtator annotation projects require a Protégé project called knowtator.pprj to be included with a relative path name. The directory that contains your annotation project files (e.g. my-annotations.pprj, my-annotations.pont, and my-annotations.pins) should also contain the files knowtator.pprj, knowtator.pont, and knowtator.pins. These are copied into the directory when your annotation project is first created. Your annotation project (e.g. my-annotations.pprj) should reference knowtator.pprj with a relative path name. However, there are cases when Protégé will insert an absolute path such as when you use the "Save Project as..." menu option to copy your annotation project somewhere else. To diagnose this as the problem (and fix it) do the following:
  • Open your annotation project in a text editor (e.g. my-annotations.pprj).
  • Search for the string "knowtator.pprj" to find the statement that includes the Knowtator project files.
  • The statement should appear as (included_projects "knowtator.pprj"). If instead the statement includes an absolute path name, then this will create problems for upgrading Knowtator.
  • Replace (included_projects "/my/absolute/directory/path/knowtator.pprj") with (included_projects "knowtator.pprj").
  • Save your edited annotation project file
  • Make sure the latest copy of the knowtator project files are in the same directory where your annotation project files are located. These files can be located at /plugins/edu.uchsc.ccp.knowtator. Copy knowtator.pprj, knowtator.pont, and knowtator.pins to your annotation project directory.
• You are using a version of Protégé that is out of date. Please verify that you are using version 3.2.1 (build 243) or later. This can be done by selecting Menu->Help->About Protégé.

Knowtator/Protégé runs out of memory. Protégé has a default maximum heap size set to 100MB. If the virtual machine exceeds this amount, then a message such as "java.lang.OutOfMemoryError" is displayed in the system output window. When Protégé is launched there are two windows that are created - one of which is a system output window. To increase the maximum heap size you must do one of the following:

1. Edit the file 'Protege.lax' if there is one in your Protégé installation (typically Windows users)
   1. If there is a file in your Protege installation directory called 'Protege.lax', then find this file. On windows it is usually located at: C:\Program Files\Protege\Protege.lax.
   2. Open this file for edit. Somewhere in the file there is a property that looks like this:

      			#   LAX.NL.JAVA.OPTION.JAVA.HEAP.SIZE.MAX
      			#   -------------------------------------
      			#   maximum heap size
      		
      			lax.nl.java.option.java.heap.size.max=800000000
      			

   3. Set the number to a value that you think your system can handle such as 500000000, 750000000, or 1000000000 depending on how much RAM you have.
2. Edit the Protégé startup script (typically Mac users)
   1. Open the startup script for edit (e.g. "run_protege.sh")
   2. There is a parameter under JVM Options called MAXIMUM_MEMORY. The parameter looks like -Xmx100m by default. Change the parameter to some larger value such as -Xmx512m or -Xmx1024m depending on how much RAM you have.

Something goes wrong on my Mac installation of Knowtator/Protégé. When Protégé is launched on a Mac, there is no console window for system output to display (Windows users will see two windows appear when Protégé is started - one is the application window and the other is a console for system output.) If things are going poorly on your Mac installation of Knowtator/Protégé and you haven't a clue what it might be, then try launching Protégé from the command line. This can be done by opening a shell and changing your directory to e.g. /Applications/Protege-3.3.1 and running the file run_protege.sh. You may have to type ./run_protege.sh.

Knowtator is getting cluttered with a bunch of annotations that I no longer want. If you have merged several annotation projects together, done several rounds of annotation, and/or created a consensus set. It may be that you have large numbers of annotations that you no longer want in your Knowtator project. A menu item labeled 'Annotation removal' provides a way to remove large numbers of unwanted annotations. This option allows you to choose an annotation filter that defines the set of annotations to keep. All other annotations are deleted. It is a good idea to archive your project using the Protégé 'Project -> Archive Current Project' option prior to to using this option. Also, if you are unhappy with the results, simply close the project without saving the changes that have been made.