1. The CODS Protégé Server

2. 2 Preliminaries If you want to follow along later Download and install Protégé 3.4 beta (Optional) Download the Server Stats plugin Sites: http://protege.stanford.edu/download/download.html will get Protégé 3.4 beta http://protege.stanford.edu/download/download.html http://protege.cim3.net/cgi-bin/wiki.pl?CODS has all the links. http://protege.cim3.net/cgi-bin/wiki.pl?CODS

3. 3 Collaborative Ontology Development Approaches Browse and Edit (BioPortal, Web Editors) Version Control (analogous to cvs, svn) But should be ontology aware Shared Document Approach (Protégé Server) CODs Protégé Server available protege2.cim3.com:4025

4. BioPortal

5. 5 Browsing and Editing Semantic Wikis (NCI Biomed GT) Protégé Web Client (Vaporware) BioPortal (More browsing oriented) Attributes Simpler Editing Interfaces For people with less experience with ontologies Compelling Display of Ontology Contents Easily shared

6. 6 Version Control Requires an Ontology Versioning System Cvs, svn, etc are not sufficient Somebody needs to make one (NeOn?) Independent updates to ontologies by experts Changes are shared via a commit Simplifies other tools (Editting, inference,…) Performance Distribution of tools on the server-client (inference)

7. 7 Ontology Servers Clients can interact while editting Updates are shared immediately Chat Tab for discussion of changes Collaborative Protégé Access very large ontologies Resource intensive activities can be done on the server

8. 8 Goal To develop all three approaches and to be able to combine them as needed Cim3.net will be a testing ground for the latest technologies.

9. 9 Protégé Server at cim3.net Protégé Server is up and running. Users can create their own accounts. New Ontologies can be added as needed through Peter Yim Snapshots of these ontology projects through svn

10. 10 Running Protégé Obtain Protégé 3.4 Beta http://protégé.stanford.edu Install and run

11. 11 Running Protégé Select Open Other Opening Screen

12. 12 Running Protégé Registering 1. Select Server 3. Create New Account2. Server Address

13. 13 Setting Up the Account Click Dont Choose a great Password.

14. 14 Choose the Project Hungry?

15. 15 Reward

16. 16 Server Stats Plugin Project -> Configure

17. 17 Server Stats Plugin

18. 18 Protégé Plugins Editting Query, Navigation, Forms Alignment (PROMPT) Collaboration Collaboration Tab, Chat, Changes Scripting Visualization Jambalaya, OWLViz, OntoViz Inference DL, PAL, SWRL, Jess

19. 19 Future (BioPortal & Protégé) BioPortal Browsing Web-based visualization Versions & Downloads Protégé Collaborative Editing environment