1. the Government Semantic Interoperability Community of Practice (SICoP)
To:
the Government Semantic Interoperability Community of Practice (SICoP)
Pilot and Preview on “CODS” – a Collaborative Ontology Development Service & Infrastructure by
Peter Yim (CIM3) & Mark Musen (SMI)
September 14, 2005 – MITRE, McLean, VA
( v 1.23 )

2. Introduction Stanford Medical Informatics- developer of Protégé
An open-source ontology tool platform
Comprehensive OWL / RDF / Reasoning support
Active community with thousands of users (33,000+ registrations)
Has been used to edit ontologies with tens of thousands of concepts
CIM3 – the ISP for CWEs (Collaborative Work Environments)
Mission: to enable more effective distributed collaboration and virtual enterprise through bootstrapping collective intelligence over the Internet
Products/Services: providing a robust CWE infrastructure that enables high performance distributed project teams, virtual enterprise partners and communities of practice to work
Host to the Ontolog-Forum – an international CoP focusing on the practical issues of both formal and informal ontologies, and their adoption into mainstream application through standardization
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

3. The Team Up
SMI & CIM3 – to develop and host an open Collaborative Ontology Development Service (CODS) and Ontology Repository for all
the initial CODS team:
Mark Musen, Ray Fergerson, Natasha Noy, Jonathan Cheyer and Peter Yim; with the support of their colleagues at Stanford Medical Informatics (SMI) and CIM Engineering, Inc. (CIM3)
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

4. Protégé – Ontology & Knowledgebase Editor
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

5. Software Featured in CODS
Protégé Multiuser Server
RDBMS backend (Oracle or MySql)
PomptTAB (Protégé plugin)
Subversion server & client (TortoiseSVN client for Windows)
Apache web server & WebDAV server
Linux platform
Augmentation of the team collaboration with the CWE suite of open source collaboration tools (for portal, archived discussion, wiki & file-sharing workspace)
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

6. Hosted Infrastructure
Product features:
CWE – “open”, “community-only” & “secured”
Robust, scalable, enterprise performance
Secured and Fault Tolerant
Platform neutral (PC’s, Mac’s, Linux, Unix, …)
Infrastructure:
Tier-1 hosting facility
100Mbps bandwidth into the Internet backbone
Backbone: multiple OC48 & Gige self-healing fiber-ring
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

7. Our Hosting Facility
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

8. An Augmented Approach
We combine the strengths of both the Protégé ontology tools platform, and CIM3’s infrastructure to provide a collaborative ontology development environment for both humans and machines, optimizing between (sometimes conflicting) objectives like:
Human expressiveness vs. machine rigor
Average user vs. power user expectation
Secured system vs. open system
Transaction system vs. groupware system behavior
Our intent is to foster shared understanding and learning
We are trying to spur innovation, as well as organic or emergent behavior in the user communities and teams
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

9. Software Featured in CODS
Protégé Multiuser Server
RDBMS backend (Oracle or MySql)
PomptTAB (Protégé plugin)
Subversion server & client (TortoiseSVN client for Windows)
Apache web server & WebDAV server
Linux platform
Augmentation of the team collaboration with the CWE suite of open source collaboration tools (for portal, archived discussion, wiki & file-sharing workspace)
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

10. Protégé Multiuser Server Login
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

11. Select Project
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

12. Metaproject Instances
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

13. Software Featured in CODS
Protégé Multiuser Server
RDBMS backend (Oracle or MySql)
PomptTAB (Protégé plugin)
Subversion server & client (TortoiseSVN client for Windows)
Apache web server & WebDAV server
Linux platform
Augmentation of the team collaboration with the CWE suite of open source collaboration tools (for portal, archived discussion, wiki & file-sharing workspace)
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

14. Protégé – convert to format
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

15. Connecting to the Oracle backend
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

16. Connecting to the MySql backend
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

17. Software Featured in CODS
Protégé Multiuser Server
RDBMS backend (Oracle or MySql)
PomptTAB (Protégé plugin)
Subversion server & client (TortoiseSVN client for Windows)
Apache web server & WebDAV server
Linux platform
Augmentation of the team collaboration with the CWE suite of open source collaboration tools (for portal, archived discussion, wiki & file-sharing workspace)
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

18. Configure PromptTAB (1)
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

19. PromptTAB (2)
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

20. Prompt: Comparing versions
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

21. Examine class changes Prompt displays: Properties that were
Added
Deleted
Changed
Old and new values for properties
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

22. Accept and Reject Changes
The lead editor can accept or reject changes
For each property
For a class as a whole
For a subtree
All changes by a specific user
All changes to classes with no conflicts
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

23. Software Featured in CODS
Protégé Multiuser Server
RDBMS backend (Oracle or MySql)
PomptTAB (Protégé plugin)
Linux server platform
Augmentation of the team collaboration with the CWE suite of open source collaboration tools (for portal, archived discussion, wiki & file-sharing workspace)
Apache web server & WebDAV server
Subversion server & client (TortoiseSVN client for Windows)
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

24. CODS – file structure (v1.45)
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

25. Subversion Repository Access
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

26. Subversion Checkout
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

27. Use case Scenarios Small/medium size ontology development project
user/team registers project with CODS-Admin and uploads seed ontology
CODS-Admin opens collaborative project on Protégé multiuser server
user/team collaboratively develops ontology and commits it to the subversion repository
Publishes /releases ontology (via CODS-Admin)
Large scale ontology project (similar to above, but…)
dedicated review/accept process (through a lead editor)
probably also a full-time project manager or project administrator who will also be responsible for version and release control
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

28. A use case NCI Thesaurus: Collaborative editing
New baseline version produced every month
Multiple editors start with the baseline and edit it in Protégé in multiuser mode
Prompt compares the current baseline to the new version produced by editors
Lead editor accepts or rejects changes
New baseline is produced
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

29. What Next? Pilot projects welcome Further refinement of process
Funding solicited to support the development of both the open source tools and the infrastructure
Skills & expertise in software engineering welcome
Skills & expertise in ontological engineering welcome
Formation and participation of a community to carry this project forward
Please Peter Yim or Mark Musen
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005

30. Questions ?
ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep-2005