1. 1 CODS – a Collaborative Ontology Development Service & Infrastructure “CODS” – a Collaborative Ontology Development Service & Infrastructure Presented at: the 4 th Semantic Interoperability for eGovernment Conference by Peter Yim (CIM3) Mark Musen (SMI) Peter Yim (CIM3) & Mark Musen (SMI) February 10, 2006 – MITRE, McLean, VA ( v 1.00 )

2. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-20052 of 30 Introduction Stanford Medical Informatics- developer of ProtégéStanford 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)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

3. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-20053 of 30 The Team Up SMI & CIM3 – to develop and host an open Collaborative Ontology Development Service (CODS) and Ontology Repository for allSMI & CIM3 – to develop and host an open Collaborative Ontology Development Service (CODS) and Ontology Repository for all the CODS team today:the CODS team today:  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) and Pat Cassidy (SICoP - ONTAC/COSMO)

4. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-20054 of 30 Protégé – Ontology & Knowledgebase Editor

5. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-20055 of 30 Software Featured in CODS Protégé Multiuser ServerProtégé Multiuser Server RDBMS backend (Oracle or MySql)RDBMS backend (Oracle or MySql) PomptTAB (Protégé plugin)PomptTAB (Protégé plugin) Subversion server & client (TortoiseSVN client for Windows)Subversion server & client (TortoiseSVN client for Windows) Apache web server & WebDAV serverApache web server & WebDAV server Linux platformLinux platform Augmentation of the team collaboration with the CWE suite of open source collaboration tools (for portal, archived discussion, wiki & file-sharing workspace)Augmentation of the team collaboration with the CWE suite of open source collaboration tools (for portal, archived discussion, wiki & file-sharing workspace)

6. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-20056 of 30 Hosted Infrastructure Product features:Product features:  CWE – “open”, “community-only” & “secured”  Robust, scalable, enterprise performance  Secured and Fault Tolerant  Platform neutral ( PC’s, Mac’s, Linux, Unix, …) Infrastructure:Infrastructure:  Tier-1 hosting facility  100Mbps bandwidth into the Internet backbone  Backbone: multiple OC48 self-healing fiber-ring

7. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-20057 of 30 Our Hosting Facility

8. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-20058 of 30 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: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 rigorHuman expressiveness vs. machine rigor Average user vs. power user expectationAverage user vs. power user expectation Secured system vs. open systemSecured system vs. open system Transaction system vs. groupware system behaviorTransaction system vs. groupware system behavior Our intent is to foster shared understanding and learningOur 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 teamsWe are trying to spur innovation, as well as organic or emergent behavior in the user communities and teams

9. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-20059 of 30 Software Featured in CODS Protégé Multiuser ServerProtégé 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)

10. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200510 of 30 Protégé Multiuser Server Login

11. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200511 of 30 Select Project

12. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200512 of 30 Metaproject Instances

13. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200513 of 30 Software Featured in CODS Protégé Multiuser Server RDBMS backend (Oracle or MySql)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)

14. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200514 of 30 Protégé – convert to format

15. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200515 of 30 Connecting to the Oracle backend

16. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200516 of 30 Connecting to the MySql backend

17. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200517 of 30 Software Featured in CODS Protégé Multiuser Server RDBMS backend (Oracle or MySql) PomptTAB (Protégé plugin)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)

18. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200518 of 30 Configure PromptTAB (1)

19. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200519 of 30 PromptTAB (2)

20. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200520 of 30 Prompt: Comparing versions

21. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200521 of 30 Examine class changes Prompt displays: –Properties that were Added Deleted Changed –Old and new values for properties

22. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200522 of 30 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

23. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200523 of 30 Software Featured in CODS Protégé Multiuser Server RDBMS backend (Oracle or MySql) PomptTAB (Protégé plugin) Linux server platformLinux server platform Augmentation of the team collaboration with the CWE suite of open source collaboration tools (for portal, archived discussion, wiki & file-sharing workspace)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 serverApache web server & WebDAV server Subversion server & client (TortoiseSVN client for Windows)Subversion server & client (TortoiseSVN client for Windows)

24. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200524 of 30 CODS – file structure (v1.45)

25. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200525 of 30 Subversion Repository Access

26. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200526 of 30 Subversion Checkout

27. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200527 of 30 Use case Scenarios Small/medium size ontology development projectSmall/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…)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

28. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200528 of 30 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

29. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200529 of 30 What Next? COSMO team members to sign-up to get access to CODSCOSMO team members to sign-up to get access to CODS More Pilot projects welcomeMore Pilot projects welcome Further refinement of processFurther refinement of process Funding solicited to support the development of both the open source tools and the infrastructureFunding solicited to support the development of both the open source tools and the infrastructure Skills & expertise in software engineering welcomeSkills & expertise in software engineering welcome Skills & expertise in ontological engineering welcomeSkills & expertise in ontological engineering welcome Formation and participation of a community to carry this project forwardFormation and participation of a community to carry this project forward Please email: Peter Yim peter.yim@cim3.com or Mark Musen peter.yim@cim3.commusen@smi.stanford.edu

30. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-200530 of 30 Questions ?