1 CODS - a Collaborative Ontology Development Service Infrastructure to the Protégé Project Team Stanford Medical Informatics by Peter P. Yim Peter P

1

CODS - a Collaborative CODS - a Collaborative Ontology Development Ontology Development Service InfrastructureService Infrastructure

to theto the

Protégé Project TeamProtégé Project TeamStanford Medical InformaticsStanford Medical Informatics

byby

Peter P. YimPeter P. Yim <[email protected]>

April 21, 2006April 21, 2006( v 1.01 )

ppy/Protege-CIM3_presentation_20060421/Apr-2006 2 of 19

Introducing CIMIntroducing CIM

• CIM Engineering, Inc. - San Mateo, CACIM Engineering, Inc. - San Mateo, CA• Incorporated in California – Jan. 1989Incorporated in California – Jan. 1989• CIM: Computer Integrated CIM: Computer Integrated

Manufacturing (with our origin in Manufacturing (with our origin in manufacturing and manufacturing manufacturing and manufacturing systems)systems)

• CIM3: CIM3: originally, “originally, “CComputer omputer IIntegrated-ntegrated-MMan-an-MMachine achine

MManufacturing”anufacturing” now, “now, “CCollaboration ollaboration IIn hun huMMan-an-MMachine-achine-

MMethodology”ethodology” Effectively, we are about optimizing systems of:Effectively, we are about optimizing systems of: PeoplePeople,, Tools Tools

andand Process Process


What Does CIM3 Do?What Does CIM3 Do?• Mission: Mission: to enable more effective to enable more effective

distributed collaboration and virtual distributed collaboration and virtual enterprise through bootstrapping enterprise through bootstrapping collective intelligence over the Internetcollective intelligence over the Internet

• Doing business as:Doing business as: ““cim3.comcim3.com”, “”, “cim3.netcim3.net” and “” and “cim3.orgcim3.org”” cim3.comcim3.com – the business arm of the company – the business arm of the company cim3.netcim3.net – the collaborative work environments – the collaborative work environments

where client Communities of Practice and distributed where client Communities of Practice and distributed team workspaces are hosted team workspaces are hosted

cim3.orgcim3.org – the research arm, and holder of the – the research arm, and holder of the company’s open technology, content and other company’s open technology, content and other intellectual propertiesintellectual properties

• Products/Services: providing an ISP/ASP based Products/Services: providing an ISP/ASP based Collaborative Work Environment (“CWE”)Collaborative Work Environment (“CWE”) infrastructure that enables distributed project teams, infrastructure that enables distributed project teams, virtual enterprise partners and communities of practice virtual enterprise partners and communities of practice to work effectively over the Internet.to work effectively over the Internet.


Our Focus:Our Focus:Communities & Distributed Communities & Distributed

TeamsTeams• People as an integral part of the People as an integral part of the

systemsystem• The Community Spectrum The Community Spectrum

[Kaplan/iCohere][Kaplan/iCohere]

Affinity NetworksAffinity Networks Learning CommunitiesLearning Communities Communities of Practice (CoP’s)Communities of Practice (CoP’s) Project TeamsProject Teams

• We optimize our infrastructure, tools We optimize our infrastructure, tools and process for CoP’s and Distributed and process for CoP’s and Distributed Project TeamsProject Teams


Our Hosting Our Hosting FacilityFacility


CIM3 – CWE HostingCIM3 – CWE Hosting• CWE product Line-up:CWE product Line-up:

““Open” CWEOpen” CWE ““Community CWE”Community CWE” ““Secured CWE” – soliciting project & Secured CWE” – soliciting project &

fundingfunding• Infrastructure:Infrastructure:

Tier-1 hosting facilityTier-1 hosting facility 100Mbps bandwidth into the Internet 100Mbps bandwidth into the Internet

backbonebackbone Backbone: Backbone: multiple OC192 & Gige self-multiple OC192 & Gige self-

healing fiber-ring healing fiber-ring (among the top 10 networks in the world (among the top 10 networks in the world as measured by connectivity to the rest of the Internet.)as measured by connectivity to the rest of the Internet.)

• Linux / SELinux Servers (on IBM 1u Linux / SELinux Servers (on IBM 1u boxes)boxes) Triple redundant storage (in 2 Triple redundant storage (in 2

locations)locations)


CIM3's ApproachCIM3's Approach• Augmentation - human-machine interaction - collaboration - Augmentation - human-machine interaction - collaboration -

communitiescommunities• Openness - we use open-source software & comply with open Openness - we use open-source software & comply with open

standards as much as we can; we open-source our technology standards as much as we can; we open-source our technology and content, and participate in open standards developmentand content, and participate in open standards development

• Capitalizing on the Internet technology: taking it Capitalizing on the Internet technology: taking it from the research and academic networkfrom the research and academic network to the current form as publishing mediato the current form as publishing media to Transactions and Web Services to Transactions and Web Services onto being its future as knowledge media in the Semantic onto being its future as knowledge media in the Semantic

WebWeb• Providing Enterprise performance, quality, robustness, Providing Enterprise performance, quality, robustness,

security & fault tolerancesecurity & fault tolerance• Providing platform neutrality: Providing platform neutrality: supporting machines on PC’s, supporting machines on PC’s,

Mac’s, Linux, Unix, …Mac’s, Linux, Unix, …• System built upon a knowledge architecture optimized for System built upon a knowledge architecture optimized for

distributed teamworkdistributed teamwork• Emphasis on effectiveness and strategic value - not Emphasis on effectiveness and strategic value - not

technologytechnology• Supporting entire user spectrum: from the everyday users to Supporting entire user spectrum: from the everyday users to

the power usersthe power users• While we do open-source work, we believe in properly While we do open-source work, we believe in properly

remunerating our contributors, and in helping create a viable remunerating our contributors, and in helping create a viable economic model for open workeconomic model for open work

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ONTOLOGONTOLOG (aka. (aka. Ontolog ForumOntolog Forum) est. ) est. Apr.2002Apr.2002

• 3 co-conveners 3 co-conveners - PeterYim; LeoObrst & KurtConrad• Hosted Hosted on the CIM3 collaborative work environment

infrastructure• CharterCharter - 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.

• ActivitiesActivities:: 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 participationWe welcome your participation – see: – see: http://ontolog.cim3.net/wiki/http://ontolog.cim3.net/wiki/

What are we?


Ontolog – an Ontolog – an open CoPopen CoP

Caption: John McCarthy having a dialog with Doug Engelbart

at a tavern … with ‘the fishnet’ on the wall


An Organizational Form that An Organizational Form that the CWE aims at Supportingthe CWE aims at Supporting

Source: Institute for the Future: Johansen, R., Swigart, R. Upsizing the Individual in the Downsized Organization

The Fishnet OrganizationThe Fishnet Organization


Ontolog’s key Ontolog’s key DifferentiationDifferentiation

Activities are community driven; we are Activities are community driven; we are neutral, open, and we are not answerable to neutral, open, and we are not answerable to any authority or institutional structure, any authority or institutional structure, except for (explicitly) our charter & IPR except for (explicitly) our charter & IPR policy, and (implicitly) our professional policy, and (implicitly) our professional integrity. 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

ppy/Protege-CIM3_presentation_20060421/Apr-2006

Case Examples of Communities on the CIM3.NET Case Examples of Communities on the CIM3.NET Collaborative Work Environments (CWE’s)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)


The CODS Team UpThe CODS Team Up

• SMI & CIM3 – to develop and host SMI & CIM3 – to develop and host an open Collaborative Ontology an open Collaborative Ontology Development Service (CODS) and Development Service (CODS) and Ontology Repository for allOntology Repository for all

• the CODS team today:the CODS team today: Mark Musen, Ray Fergerson, Natasha Mark Musen, Ray Fergerson, Natasha

Noy, Jonathan Cheyer and Peter Yim; Noy, Jonathan Cheyer and Peter Yim; with the support of their colleagues at with the support of their colleagues at Stanford Medical Informatics (SMI) and Stanford Medical Informatics (SMI) and CIM Engineering, Inc. (CIM3) and Pat CIM Engineering, Inc. (CIM3) and Pat Cassidy Cassidy (SICoP - ONTAC/COSMO)(SICoP - ONTAC/COSMO)


Software Featured in CODSSoftware 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 Subversion server & client (TortoiseSVN

client for Windows)client for Windows)• Apache web server & WebDAV serverApache web server & WebDAV server• Linux platformLinux platform• Augmentation of the team collaboration Augmentation of the team collaboration

with the CWE suite of open source with the CWE suite of open source collaboration tools (for portal, archived collaboration tools (for portal, archived discussion, wiki & file-sharing workspace)discussion, wiki & file-sharing workspace)


Connecting to the MySql Connecting to the MySql backendbackend


CODS – file structureCODS – file structure (v1.45)(v1.45)


Subversion Repository AccessSubversion Repository Access


What Next?What Next?

• COSMO team members to sign-up to get access COSMO team members to sign-up to get access to CODSto CODS

• More Pilot projects welcomeMore Pilot projects welcome• Further refinement of processFurther refinement of process• Funding solicited to support the Funding solicited to support the

development of both the open source tools development of both the open source tools and the infrastructureand the infrastructure

• Skills & expertise in software engineering Skills & expertise in software engineering welcomewelcome

• Skills & expertise in ontological Skills & expertise in ontological engineering welcomeengineering welcome

• Formation and participation of a Formation and participation of a community to carry this project forwardcommunity to carry this project forward

Please email: Peter Yim [email protected] or Mark Musen <[email protected]>


ReferencesReferences

• Doug EngelbartDoug Engelbart's Bootstrap 's Bootstrap Vision and MissionVision and Mission

• [ontolog-forum]: [ontolog-forum]: http://ontolog.cim3.net/wiki/http://ontolog.cim3.net/wiki/

• CWE Community: CWE Community: http://community.cim3.nethttp://community.cim3.net

• CIM3 ISP/ASP Product & Pricing: CIM3 ISP/ASP Product & Pricing: Collaborative Work Environment HostingCollaborative Work Environment Hosting

• More Information:More Information: CIM Engineering, Inc.CIM Engineering, Inc. Peter P. Yim (Peter P. Yim (biobio) () (cvcv))

Documents

1 CODS - a Collaborative Ontology Development Service Infrastructure to the Protégé Project Team Stanford Medical Informatics by Peter P. Yim Peter P