Protege 5-beta

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This page describes how to get Protege 5 up and running. Note that at the time of writing (Jan 2015) Protege 5 is in beta, so expect some quirks, especially for getting things running. I expect things will become easier before the final version is released. Please check the 'history' button on this page to make sure things aren't too out of date.

Why Upgrade?

  • Direct .obo format support (STILL WAITING ON THIS
    • You can open gene_ontology_write.obo direct from Protege, and save to the same file. No messing with converters!
  • Better (most of us agree?) search
    • the default search widget (box on top right) now searches all annotations, not just rdfs:label
  • direct visibility of axiom annotations
    • this is a big win for GO and OBO library ontologies that use these to state:
      • source of a definition annotation
      • source of a synonym annotation
      • whether a link is tagged-inferred
    • big win for uberon, where individual relationships like develops_from edges are tagged with provenance annotations
  • direct visibility of GCIs under relevant class


  • still a bit fiddly - see below
  • we're using a beta environment plus a nightly build of Elk - a little hair-raising but no problems so far...

Getting started

first, download from - P5 is now the default.

then edit the file Protege_5.0_beta/ and increase the memory. The more the better. Mine says this:


cd `dirname $0`

java -Xmx8G -Xms250M \
     -Dlog4j.configuration=file:log4j.xml \
     -DentityExpansionLimit=100000000 \
     -Dfile.encoding=UTF-8 \
     -classpath bin/felix.jar:bin/ProtegeLauncher.jar \
     $CMD_OPTIONS org.protege.osgi.framework.Launcher

To start Protege:

cd Protege_5.0_beta/



where FOO is the directory where you unpacked the distribution

Running Elk

This is fiddly. We have determined you need Elk 0.5 or higher, this is only available from their nightly builds

  1. Go here:
  2. Select 'Protege Plugin latest build' under Nightly Builds

Now, take the jar file from the zip and place it in the Protege_5.0_beta/plugins

Note: the first time it may complain about not having enough workers. Just ignore and try again.