1 a collaborative ontology development service & infrastructure to: sicop / ontology &...

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a Collaborative Ontology a Collaborative Ontology Development Development

Service & InfrastructureService & Infrastructure

To: To:

SICoPSICoP / Ontology & / Ontology & TaxonomyTaxonomy

Coordinating Coordinating (ONTAC)(ONTAC) Work Work GroupGroup

by

Peter P. Yim < [email protected]>

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

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Coordinating . . . Working Coordinating . . . Working GroupGroup

• on behalf of my colleagues, I bring our on behalf of my colleagues, I bring our congratulations and best wishes to congratulations and best wishes to ONTACWG and its missionONTACWG and its mission

• earlier speakers have covered, in earlier speakers have covered, in considerable depth, on the “ON & TA” - considerable depth, on the “ON & TA” - Ontologies and Taxonomies Ontologies and Taxonomies

• I will join some of them and focus the I will join some of them and focus the next few minutes on the “C & WG” part next few minutes on the “C & WG” part of thingsof things

• I will introduce some of the work we’ve I will introduce some of the work we’ve been bringing to the table ... and take been bringing to the table ... and take the opportunity to pledge my support to the opportunity to pledge my support to the ONTACWG endeavor the ONTACWG endeavor


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CIM Engineering Inc.CIM Engineering Inc. (dba. (dba. CIM3CIM3) est. 1989) est. 1989

• Mission: Mission: to enable more effective distributed to enable more effective distributed collaboration and virtual enterprise through collaboration and virtual enterprise through bootstrapping collective intelligence over the Internetbootstrapping collective intelligence over the Internet

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

• CIM3 - Collaboration In huMan, Methods and Machine, in CIM3 - Collaboration In huMan, Methods and Machine, in essence, we are about:essence, we are about: People, Process & ToolsPeople, Process & Tools Augmented CollaborationAugmented 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 Approach-2: We optimize our infrastructure, tools and process for CoP’s and Distributed Project Teams … we process for CoP’s and Distributed Project Teams … we take care of the infrastructure, so that those communities take care of the infrastructure, so that those communities and teams can really focus on their workand teams can really focus on their work

• Approach-3: We do it because we feel it is important, Approach-3: We do it because we feel it is important, meaningful, and that we are passionate about it meaningful, and that we are passionate about it (but then, (but then, we still appreciate getting remunerated for the work.) we still appreciate getting remunerated for the work.)

Introducing:


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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, ... 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/

Introducing:


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What Does it Take to do it What Does it Take to do it Effectively?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 We need to get organized (even when that ‘organization’ is supposed to be organic)organic)

we need to work as distributed nodes in a networked community, and get we need to work as distributed nodes in a networked community, and get coordinatedcoordinated

we need to arrive at shared understandingwe need to arrive at shared understanding

we need proper coordination and governancewe need proper coordination and governance

... more than research, experiments and pilots... more than research, experiments and pilots

• ... we need adoption:... we need adoption:we need to apply ontological engineering and semantic technologies to real we need to apply ontological engineering and semantic technologies to real problemsproblems

we need to operationalize these applications and deploy them on secured, we need to operationalize these applications and deploy them on secured, robust, scalable infrastructuresrobust, scalable infrastructures

we need to transfer the technology and our learnings to the world at-largewe 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 Yim, P. “Developing Semantic Technologies in a Collaborative Work Environment”Environment”

presentation at: http://colab.cim3.net/cgi-bin/wiki.pl?ExpeditionWorkshop/SemanticConflictMappingandEnablement_MakingCommitmentsTogether_2005_02_22#nid2IGF


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An Organizational Form that the CWE aims An Organizational Form that the CWE aims at Supporting – leading us toward Open at Supporting – leading us toward Open

Virtual EnterprisesVirtual Enterprises

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

introducing:introducing: The Fishnet Organization 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.


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TThe real “Key” to successhe real “Key” to success

• the individual participants hold the individual participants hold the key to the communities’ and the key to the communities’ and their project’s success, and their project’s success, and

it’s all in their it’s all in their

““attitude towards attitude towards sharing sharing and commitment and commitment””


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Appendixa preview on “CODS”a preview on “CODS”


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Pilot and Preview on “CODS” – a Collaborative Ontology Development Service & Infrastructure

To: To:

the Government Semantic the Government Semantic InteroperabilityInteroperability

Community of Practice (SICoP)Community of Practice (SICoP)

byby

Peter Yim (CIM3) Peter Yim (CIM3) & Mark Musen (SMI)Mark Musen (SMI)

September 14, 2005 – MITRE, McLean, VASeptember 14, 2005 – MITRE, McLean, VA

( v 1.20 )

ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 10

IntroductionIntroduction• Stanford Medical Informatics- Stanford Medical Informatics-

developer of Protégédeveloper of Protégé An open-source ontology tool platformAn open-source ontology tool platform Comprehensive OWL / RDF / Reasoning supportComprehensive OWL / RDF / Reasoning support Active community with thousands of users (33,000+ Active community with thousands of users (33,000+

registrations)registrations) Has been used to edit ontologies with tens of thousands of Has been used to edit ontologies with tens of thousands of

conceptsconcepts

• CIM3 – CIM3 – the ISP for CWEsthe ISP for CWEs (Collaborative Work (Collaborative Work Environments)Environments) Mission: to enable more effective distributed collaboration Mission: to enable more effective distributed collaboration

and virtual enterprise through bootstrapping collective and virtual enterprise through bootstrapping collective intelligence over the Internetintelligence over the Internet

Products/Services: providing a robust CWE infrastructure Products/Services: providing a robust CWE infrastructure that enables high performance distributed project teams, that enables high performance distributed project teams, virtual enterprise partners and communities of practice to virtual enterprise partners and communities of practice to workwork

Host to the Ontolog-Forum – an internal CoP focusing on Host to the Ontolog-Forum – an internal CoP focusing on the practical issues of both formal and informal the practical issues of both formal and informal ontologies, and their adoption into mainstream application ontologies, and their adoption into mainstream application through standardizationthrough standardization


The Team UpThe 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 initial CODS team:the initial CODS team: 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)CIM Engineering, Inc. (CIM3)


Protégé – Ontology & Knowledgebase Protégé – Ontology & Knowledgebase EditorEditor


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)


Hosted InfrastructureHosted Infrastructure• Product features:Product features:

CWE – “open”, “community-only” & CWE – “open”, “community-only” & “secured”“secured”

Robust, scalable, enterprise Robust, scalable, enterprise performanceperformance

Secured and Fault TolerantSecured and Fault Tolerant Platform neutral (Platform neutral (PC’s, Mac’s, Linux, Unix, …)PC’s, Mac’s, Linux, Unix, …)

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

backbonebackbone Backbone: Backbone: multiple OC48 & Gige self-multiple OC48 & Gige self-

healing fiber-ringhealing fiber-ring


Our Hosting Our Hosting FacilityFacility


An Augmented ApproachAn Augmented Approach

• We combine the strengths of both the Protégé We combine the strengths of both the Protégé ontology tools platform, and CIM3’s infrastructure ontology tools platform, and CIM3’s infrastructure to provide a collaborative ontology development to provide a collaborative ontology development environment for environment for bothboth humans and machines, humans and machines, optimizing between (sometimes conflicting) optimizing between (sometimes conflicting) objectives like: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 system Secured system vs. open system • Transaction system vs. groupware system Transaction system vs. groupware system

behaviorbehavior• Our intent is to foster shared understanding and Our intent is to foster shared understanding and

learninglearning• We are trying to spur innovation, as well as organic We are trying to spur innovation, as well as organic

or emergent behavior in the user communities and or emergent behavior in the user communities and teamsteams


Software Featured in CODSSoftware 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)


Protégé Multiuser Server Protégé Multiuser Server LoginLogin


Select ProjectSelect Project


Metaproject InstancesMetaproject Instances


Software Featured in CODSSoftware Featured in CODS• Protégé Multiuser Server• RDBMS backend (Oracle or MySql)RDBMS backend (Oracle or MySql)• PomptTAB (Protégé plugin)• Subversion server & client (TortoiseSVN




Protégé – convert to formatProtégé – convert to format


Connecting to the Oracle Connecting to the Oracle backendbackend


Connecting to the MySQL Connecting to the MySQL backendbackend


Software Featured in CODSSoftware Featured in CODS• Protégé Multiuser Server• RDBMS backend (Oracle or MySql)• PomptTAB (Protégé plugin)PomptTAB (Protégé plugin)• Subversion server & client (TortoiseSVN




Configure PromptTABConfigure PromptTAB (1)(1)


PromptTAB PromptTAB (2)(2)


Prompt: Comparing versionsPrompt: Comparing versions


Examine class changesExamine class changes

• Prompt Prompt displays:displays:– Properties that Properties that

were were • AddedAdded• DeletedDeleted• ChangedChanged

– Old and new Old and new values for values for propertiesproperties


Accept and Reject Accept and Reject ChangesChanges

• The lead editor The lead editor can accept or can accept or reject changesreject changes– For each propertyFor each property– For a class as a For a class as a

wholewhole– For a subtreeFor a subtree– All changes by a All changes by a

specific userspecific user– All changes to All changes to

classes with no classes with no conflictsconflicts


Software Featured in CODSSoftware Featured in CODS• Protégé Multiuser Server• RDBMS backend (Oracle or MySql)• PomptTAB (Protégé plugin)• Linux server platformLinux server 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)

• Apache web server & WebDAV serverApache web server & WebDAV server• Subversion server & client (TortoiseSVN Subversion server & client (TortoiseSVN

client for Windows)client for Windows)


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


Subversion Repository AccessSubversion Repository Access


Subversion CheckoutSubversion Checkout


Use case ScenariosUse case Scenarios• Small/medium size ontology development Small/medium size ontology development

projectproject user/team registers project with CODS-Admin user/team registers project with CODS-Admin

and uploads seed ontologyand uploads seed ontology CODS-Admin opens collaborative project on CODS-Admin opens collaborative project on

Protégé multiuser serverProtégé multiuser server user/team collaboratively develops ontology and user/team collaboratively develops ontology and

commits it to the subversion repositorycommits it to the subversion repository Publishes /releases ontology (via CODS-Admin) Publishes /releases ontology (via CODS-Admin)

• Large scale ontology project Large scale ontology project (similar to above, (similar to above, but…)but…) dedicated review/accept process (through a lead dedicated review/accept process (through a lead

editor)editor) probably also a full-time project manager or probably also a full-time project manager or

project administrator who will also be responsible project administrator who will also be responsible for version and release controlfor version and release control


A use caseA use caseNCI Thesaurus: Collaborative NCI Thesaurus: Collaborative

editingediting• New baseline version New baseline version

produced every monthproduced every month• Multiple editors start Multiple editors start

with the baseline and with the baseline and edit it in Protégé in edit it in Protégé in multiuser modemultiuser mode

• Prompt compares the Prompt compares the current baseline to the current baseline to the new version produced by new version produced by editorseditors

• Lead editor accepts or Lead editor accepts or rejects changesrejects changes

• New baseline is New baseline is producedproduced


What Next?What Next?• Pilot projects welcomedPilot projects welcomed• 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 < musen @s tanford .edu>


QuestionsQuestions

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1 a collaborative ontology development service & infrastructure to: sicop / ontology &...

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