1. 1 CODS - a Collaborative Ontology Development Service Infrastructure to the Protégé Project Team Stanford Medical Informatics by Peter P. Yim Peter P. Yim peter.yim@cim3.com April 21, 2006 ( v 1.01 )

2. ppy/Protege-CIM3_presentation_20060421/Apr-20062 of 19 Introducing CIM CIM Engineering, Inc. - San Mateo, CACIM Engineering, Inc. - San Mateo, CA Incorporated in California – Jan. 1989Incorporated in California – Jan. 1989 CIM: Computer Integrated Manufacturing (with our origin in manufacturing and manufacturing systems)CIM: Computer Integrated Manufacturing (with our origin in manufacturing and manufacturing systems) CIM3:CIM3:  originally, “Computer Integrated-Man-Machine Manufacturing”  now, “Collaboration In huMan-Machine-Methodology”  Effectively, we are about optimizing systems of: People, Tools and Process

3. ppy/Protege-CIM3_presentation_20060421/Apr-20063 of 19 What Does CIM3 Do? 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 Doing business as:Doing business as:  “cim3.com”, “cim3.net” and “cim3.org”  cim3.com – the business arm of the company  cim3.net – the collaborative work environments where client Communities of Practice and distributed team workspaces are hosted  cim3.org – the research arm, and holder of the company’s open technology, content and other intellectual properties 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.

4. ppy/Protege-CIM3_presentation_20060421/Apr-20064 of 19 Our Focus: Communities & Distributed Teams People as an integral part of the systemPeople as an integral part of the system The Community Spectrum [Kaplan/iCohere]The Community Spectrum [Kaplan/iCohere]  Affinity Networks  Learning Communities  Communities of Practice (CoP’s)  Project Teams We optimize our infrastructure, tools and process for CoP’s and Distributed Project TeamsWe optimize our infrastructure, tools and process for CoP’s and Distributed Project Teams

5. ppy/Protege-CIM3_presentation_20060421/Apr-20065 of 19 Our Hosting Facility

6. ppy/Protege-CIM3_presentation_20060421/Apr-20066 of 19 CIM3 – CWE Hosting CWE product Line-up:CWE product Line-up:  “Open” CWE  “Community CWE”  “Secured CWE” – soliciting project & funding Infrastructure:Infrastructure:  Tier-1 hosting facility  100Mbps bandwidth into the Internet backbone  Backbone: multiple OC192 & Gige self-healing fiber-ring (among the top 10 networks in the world as measured by connectivity to the rest of the Internet.) Linux / SELinux Servers (on IBM 1u boxes)Linux / SELinux Servers (on IBM 1u boxes)  Triple redundant storage (in 2 locations)

7. ppy/Protege-CIM3_presentation_20060421/Apr-20067 of 19 CIM3's Approach Augmentation - human-machine interaction - collaboration - communitiesAugmentation - human-machine interaction - collaboration - communities Openness - we use open-source software & comply with open standards as much as we can; we open-source our technology and content, and participate in open standards developmentOpenness - we use open-source software & comply with open standards as much as we can; we open-source our technology and content, and participate in open standards development Capitalizing on the Internet technology: taking itCapitalizing on the Internet technology: taking it  from the research and academic network  to the current form as publishing media  to Transactions and Web Services  onto being its future as knowledge media in the Semantic Web Providing Enterprise performance, quality, robustness, security & fault toleranceProviding Enterprise performance, quality, robustness, security & fault tolerance Providing platform neutrality: supporting machines on PC’s, Mac’s, Linux, Unix, …Providing platform neutrality: supporting machines on PC’s, Mac’s, Linux, Unix, … System built upon a knowledge architecture optimized for distributed teamworkSystem built upon a knowledge architecture optimized for distributed teamwork Emphasis on effectiveness and strategic value - not technologyEmphasis on effectiveness and strategic value - not technology Supporting entire user spectrum: from the everyday users to the power usersSupporting entire user spectrum: from the everyday users to the power users While we do open-source work, we believe in properly remunerating our contributors, and in helping create a viable economic model for open workWhile we do open-source work, we believe in properly remunerating our contributors, and in helping create a viable economic model for open work

8. 8 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, Upper Ontology Summit, event podcast, Ontologizing the Ontolog Content...   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/ What are we?

9. ppy/Protege-CIM3_presentation_20060421/Apr-20069 of 19 Ontolog – an open CoP Caption: John McCarthy having a dialog with Doug Engelbart at a tavern … with ‘the fishnet’ on the wall

10. ppy/Protege-CIM3_presentation_20060421/Apr-200610 of 19 An Organizational Form that the CWE aims at Supporting Source: Institute for the Future: Johansen, R., Swigart, R. Upsizing the Individual in the Downsized OrganizationUpsizing the Individual in the Downsized Organization The Fishnet Organization

11. ppy/Protege-CIM3_presentation_20060421/Apr-200611 of 19 Ontolog’s key Differentiation Activities are community driven; we are neutral, open, and we are not answerable to any authority or institutional structure, except for (explicitly) our charter & IPR policy, and (implicitly) our professional integrity. We are adamant about collaboration, sharing and open knowledge … and are trying to spur organic or emergent behaviour in the community and our project teams

12. ppy/Protege-CIM3_presentation_20060421/Apr-2006 Case Examples of Communities on the CIM3.NET Collaborative Work Environments (CWE’s) Ontolog CWE-dev Bootstrap Protégé eGov: COLAB eGov: DRM project work & public forum NIST IMS-US Millennium Project (AC/UNU) Digital Art Ontology Hosting of: SUMO, CODS, … (more)

13. ppy/Protege-CIM3_presentation_20060421/Apr-200613 of 19 The CODS 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)

14. ppy/Protege-CIM3_presentation_20060421/Apr-200614 of 19 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)

15. ppy/Protege-CIM3_presentation_20060421/Apr-200615 of 19 Connecting to the MySql backend

16. ppy/Protege-CIM3_presentation_20060421/Apr-200616 of 19 CODS – file structure (v1.45)

17. ppy/Protege-CIM3_presentation_20060421/Apr-200617 of 19 Subversion Repository Access

18. ppy/Protege-CIM3_presentation_20060421/Apr-200618 of 19 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

19. ppy/Protege-CIM3_presentation_20060421/Apr-200619 of 19 References Doug Engelbart's Bootstrap Vision and MissionDoug Engelbart's Bootstrap Vision and MissionDoug EngelbartVision and MissionDoug EngelbartVision and Mission [ontolog-forum]: http://ontolog.cim3.net/wiki/[ontolog-forum]: http://ontolog.cim3.net/wiki/http://ontolog.cim3.net/wiki/ CWE Community: http://community.cim3.netCWE Community: http://community.cim3.nethttp://community.cim3.net CIM3 ISP/ASP Product & Pricing: Collaborative Work Environment HostingCIM3 ISP/ASP Product & Pricing: Collaborative Work Environment HostingCollaborative Work Environment HostingCollaborative Work Environment Hosting More Information:More Information:  CIM Engineering, Inc. CIM Engineering, Inc. CIM Engineering, Inc.  Peter P. Yim (bio) (cv) biocvbiocv