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The CODS Protégé Server

The CODS Protégé Server. 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

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The CODS Protégé Server

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  1. The CODS Protégé Server

  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.cim3.net/cgi-bin/wiki.pl?CODS has all the links. 2

  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 3

  4. BioPortal

  5. Browsing and Editing • Semantic Wiki’s (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 5

  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) 6

  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 7

  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. 8

  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 9

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

  11. Running Protégé Opening Screen Select Open Other 11

  12. Running Protégé Registering 2. Server Address 3. Create New Account 1. Select “Server” 12

  13. Setting Up the Account Click Click Don’t Choose a great Password. 13

  14. Choose the Project Hungry? 14

  15. Reward 15

  16. Server Stats Plugin Project -> Configure 16

  17. Server Stats Plugin 17

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

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

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