1. 1 a Collaborative Ontology Development Service & Infrastructure To: SICoP / Ontology & Taxonomy Coordinating (ONTAC) Work Group by Peter P. Yim CIM3, CEO / ONTOLOG, co-convener at the Organization Meeting of ONTAC-WG October 5, 2005 – MITRE, McLean, VA ( v 1.32 ) ppy/Yim_CIM3-Ontolog-CODS_ONTACWG-presentation_20051005.ppt/Oct-2005

2. 2 Coordinating... Working Group on behalf of my colleagues, I bring our congratulations and best wishes to ONTACWG and its missionon behalf of my colleagues, I bring our congratulations and best wishes to ONTACWG and its mission earlier speakers have covered, in considerable depth, on the “ON & TA” - Ontologies and Taxonomiesearlier speakers have covered, in considerable depth, on the “ON & TA” - Ontologies and Taxonomies I will join some of them and focus the next few minutes on the “C & WG” part of thingsI will join some of them and focus the next few minutes on the “C & WG” part of things I will introduce some of the work we’ve been bringing to the table... and take the opportunity to pledge my support to the ONTACWG endeavorI will introduce some of the work we’ve been bringing to the table... and take the opportunity to pledge my support to the ONTACWG endeavor ppy/Yim_CIM3-Ontolog-CODS_ONTACWG-presentation_20051005.ppt/Oct-2005

3. 3 CIM Engineering Inc. (dba. CIM3) est. 1989 Mission: to enable more effective distributed collaboration and virtual enterprise through bootstrapping collective intelligence over the InternetMission: to enable more effective distributed collaboration and virtual enterprise through bootstrapping collective intelligence over the Internet Products/Services: providing an ISP/ASP based Collaborative Work Environment (“CWE”) infrastructure that enables distributed project teams, virtual enterprise partners and communities of practice to work effectively over the Internet.Products/Services: providing an ISP/ASP based Collaborative Work Environment (“CWE”) infrastructure that enables distributed project teams, virtual enterprise partners and communities of practice to work effectively over the Internet. CIM3 - Collaboration In huMan, Methods and Machine, in essence, we are about:CIM3 - Collaboration In huMan, Methods and Machine, in essence, we are about:  People, Process & Tools  Augmented Collaboration Approach-1: People as an integral part of the systemApproach-1: People as an integral part of the system Approach-2: We optimize our infrastructure, tools and process for CoP’s and Distributed Project Teams … we take care of the infrastructure, so that those communities and teams can really focus on their workApproach-2: We optimize our infrastructure, tools and process for CoP’s and Distributed Project Teams … we take care of the infrastructure, so that those communities and teams can really focus on their work Approach-3: We do it because we feel it is important, meaningful, and that we are passionate about it (but then, we still appreciate getting remunerated for the work.)Approach-3: We do it because we feel it is important, meaningful, and that we are passionate about it (but then, we still appreciate getting remunerated for the work.) Introducing: ppy/Yim_CIM3-Ontolog-CODS_ONTACWG-presentation_20051005.ppt/Oct-2005

4. 4 ONTOLOG (aka. Ontolog Forum) est. Apr.2002 3 co-conveners3 co-conveners - PeterYim; LeoObrst & KurtConrad HostedHosted on the CIM3 collaborative work environment infrastructure Charter :Charter - Ontolog is an open, international, virtual community of practice, whose membership will:   Discuss practical issues and strategies associated with the development and application of both formal and informal ontologies.   Identify ontological engineering approaches that might be applied to the UBL effort, as well as to the broader domain of eBusiness standardization efforts.   Strive to advance the field of ontological engineering and semantic technologies, and to help move them into main stream applications. Activities:Activities:   Weekly conference calls of active members   Monthly virtual Invited Speaker events   Scheduled Technical Discussions   Specific Projects: like [CCT-Rep], [Health-Ont], NHIN-RFI response,...   Resides on a virtual collaborative work environment which serves as a dynamic knowledge repository to the community's collective intelligence We welcome your participation – see: http://ontolog.cim3.net/wiki/We welcome your participation – see: http://ontolog.cim3.net/wiki/ Introducing: ppy/Yim_CIM3-Ontolog-CODS_ONTACWG-presentation_20051005.ppt/Oct-2005

5. 5 What Does it Take to do it Effectively?... more than just smart and knowledgeable individuals:... more than just smart and knowledgeable individuals: We need to get organized (even when that ‘organization’ is supposed to be organic) we need to work as distributed nodes in a networked community, and get coordinated we need to arrive at shared understanding we need proper coordination and governance... more than research, experiments and pilots... we need adoption:... we need adoption: we need to apply ontological engineering and semantic technologies to real problems we need to operationalize these applications and deploy them on secured, robust, scalable infrastructures we need to transfer the technology and our learnings to the world at-large... please refer also to:... please refer also to: Yim, P. “Developing Semantic Technologies in a Collaborative Work Environment” presentation at: http://colab.cim3.net/cgi- bin/wiki.pl?ExpeditionWorkshop/SemanticConflictMappingandEnablement_MakingCommitm entsTogether_2005_02_22#nid2IGF ppy/Yim_CIM3-Ontolog-CODS_ONTACWG-presentation_20051005.ppt/Oct-2005

6. 6 An Organizational Form that the CWE aims at Supporting – leading us toward Open Virtual Enterprises Source: Institute for the Future: Johansen, R., Swigart, R. Upsizing the Individual in the Downsized Organization introducing: The Fishnet Organization these are temporary (or semi-permanent) hierarchies, that emerge out of the CoP's, which capitalize on distributed capabilities to achieve specific purposes; when those purposes are achieved (or when the opportunities no longer exist), they disband, and the resources (people, knowledge, skill sets) are returned to the CoP's where they come from. ppy/Yim_CIM3-Ontolog-CODS_ONTACWG-presentation_20051005.ppt/Oct-2005

7. 7 T he real “Key” to success the individual participants hold the key to the communities’ and their project’s success, and it’s all in their “attitude towards sharing and commitment”the individual participants hold the key to the communities’ and their project’s success, and it’s all in their “attitude towards sharing and commitment” ppy/Yim_CIM3-Ontolog-CODS_ONTACWG-presentation_20051005.ppt/Oct-2005

8. 8 Appendix a preview on “CODS” ppy/Yim_CIM3-Ontolog-CODS_ONTACWG-presentation_20051005.ppt/Oct-2005

9. 9 Pilot and Preview on “CODS” – a Collaborative Ontology Development Service & Infrastructure To: the Government Semantic Interoperability Community of Practice (SICoP) by Peter Yim (CIM3) Mark Musen (SMI) Peter Yim (CIM3) & Mark Musen (SMI) September 14, 2005 – MITRE, McLean, VA ( v 1.20 )

10. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 10 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 internal CoP focusing on the practical issues of both formal and informal ontologies, and their adoption into mainstream application through standardization

11. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 11 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 initial CODS team: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)

12. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 12 Protégé – Ontology & Knowledgebase Editor

13. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 13 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)

14. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 14 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 & Gige self-healing fiber-ring

15. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 15 Our Hosting Facility

16. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 16 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

17. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 17 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)

18. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 18 Protégé Multiuser Server Login

19. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 19 Select Project

20. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 20 Metaproject Instances

21. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 21 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)

22. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 22 Protégé – convert to format

23. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 23 Connecting to the Oracle backend

24. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 24 Connecting to the MySQL backend

25. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 25 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)

26. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 26 Configure PromptTAB (1)

27. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 27 PromptTAB (2)

28. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 28 Prompt: Comparing versions

29. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 29 Examine class changes Prompt displays:Prompt displays: –Properties that were AddedAdded DeletedDeleted ChangedChanged –Old and new values for properties

30. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 30 Accept and Reject Changes The lead editor can accept or reject changesThe 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

31. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 31 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)

32. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 32 CODS – file structure (v1.45)

33. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 33 Subversion Repository Access

34. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 34 Subversion Checkout

35. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 35 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

36. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 36 A use case NCI Thesaurus: Collaborative editing New baseline version produced every monthNew baseline version produced every month Multiple editors start with the baseline and edit it in Protégé in multiuser modeMultiple editors start with the baseline and edit it in Protégé in multiuser mode Prompt compares the current baseline to the new version produced by editorsPrompt compares the current baseline to the new version produced by editors Lead editor accepts or rejects changesLead editor accepts or rejects changes New baseline is producedNew baseline is produced

37. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 37 What Next? Pilot projects welcomedPilot projects welcomed 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 or Mark Musen

38. ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 38 Questions ?