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[protege-discussion] collabProtege is fantastic! - trying to convert annotation onto to database

Jens usenet at
Mon Jul 2 08:43:18 PDT 2007

these days I upgraded my server based protege installation from 3.2.1 to 3.3
and include collaborative Protege option.

It's amazing! Natasha, Tania and the rest of the protege group did a great
job. It's the long missing feature for a real multi user environment with
change history. Thank's a lot! 

We build some automated interfaces to populate and modify our ontology. Even
those - as they connect to the remote Protege server - are included in the
change history.

There are a few open questions for me:

- Annotation Database Project is file based. On a protege server installation,
this forces me to use the "saveIntervalSec" option to save the file every 120
seconds. I tried to convert this project to a database project as well, but
it doesn't work when starting the server. Protege allows only conversion to
Frames Database project. Why did you choose RDFS File format in favor of a
Database Annotation Project and is there any way to achieve this?

- How about scalability? Tracking any changes to the main ontology causes
one or more instances in the annotation history. The annotation history could
get very big. What impact does it have? Are there any thoughts on housekeeping
e.g. removing very old changes in the change history


Protege Server side log:
CONFIG: Protege 3.3 Build 411, JVM 1.5.0_11-b03, memory=416M, Linux,
encoding=UTF-8, language=en, country=US
CONFIG: Loaded plugin edu.stanford.smi.protegex.standard_extensions - Graph
Widget, Table Widget
CONFIG: Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF Backend
CONFIG: Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
CONFIG: Loaded plugin edu.stanford.smi.protegex.changes - Changes tab
CONFIG: Loaded plugin edu.stanford.smi.protegex.chatPlugin
CONFIG: Loaded plugin edu.stanford.smi.protege.collab - CollaborativeProtege
CONFIG: Save interval sec=120
INFO: Loading project Onto_Test
INFO: Loaded 5000 instances: onto_ProjectKB_Instance_139
INFO: Set type on 5000 instances: onto_ProjectKB_Instance_40069
INFO: Loaded 6000 instances: cmdb_ProjectKB_Instance_41013
INFO: Set type on 6000 instances: onto_ProjectKB_Instance_70688
INFO: Loading project Onto_Test_Annotations
INFO: Loading project plugins for project Onto_Test
WARNING: There were errors at loading project plugin ChangesProject --
java.lang.ClassCastException: edu.stanford.smi.protege.model.DefaultSimpleInstance
        at edu.stanford.smi.protegex.server_changes.ChangesDb.<init>(Unknown Source)
edu.stanford.smi.protegex.server_changes.ChangesProject.initialize(Unknown Source)
edu.stanford.smi.protegex.server_changes.ChangesProject.afterLoad(Unknown Source)
edu.stanford.smi.protege.plugin.ProjectPluginManager.afterLoad(Unknown Source)
        at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
        at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
        at edu.stanford.smi.protege.server.Server.main(Unknown Source)

INFO: Loading project plugins for project Onto_Test_Annotations
INFO: Protege server ready to accept connections...

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