![Page 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/1.jpg)
The CODS Protégé Server
![Page 2: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/2.jpg)
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.
![Page 3: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/3.jpg)
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
![Page 4: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/4.jpg)
BioPortal
![Page 5: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/5.jpg)
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
![Page 6: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/6.jpg)
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)
![Page 7: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/7.jpg)
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
![Page 8: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/8.jpg)
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.
![Page 9: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/9.jpg)
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
![Page 10: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/10.jpg)
10
Running Protégé
Obtain Protégé 3.4 Beta http://protégé.stanford.edu
Install and run
![Page 11: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/11.jpg)
11
Running Protégé
Select Open Other
Opening Screen
![Page 12: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/12.jpg)
12
Running ProtégéRegistering
1. Select “Server”
3. Create New Account2. Server Address
![Page 13: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/13.jpg)
13
Setting Up the Account
ClickClick
Don’t Choose a greatPassword.
![Page 14: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/14.jpg)
14
Choose the Project
Hungry?
![Page 15: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/15.jpg)
15
Reward
![Page 16: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/16.jpg)
16
Server Stats Plugin
Project -> Configure
![Page 17: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/17.jpg)
17
Server Stats Plugin
![Page 18: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/18.jpg)
18
Protégé Plugins
Editting Query, Navigation, Forms
Alignment (PROMPT) Collaboration
Collaboration Tab, Chat, Changes Scripting Visualization
Jambalaya, OWLViz, OntoViz Inference
DL, PAL, SWRL, Jess
![Page 19: 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](https://reader036.vdocuments.us/reader036/viewer/2022062223/55149a7e55034640138b4610/html5/thumbnails/19.jpg)
19
Future (BioPortal & Protégé)
BioPortal Browsing Web-based visualization Versions & Downloads
Protégé Collaborative Editing environment