“ cods ” – a collaborative ontology development service & infrastructure

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“CODSCODS” – – a Collaborative Ontology a Collaborative Ontology

Development Development Service & InfrastructureService & Infrastructure

Presented at:Presented at:

the 4the 4thth Semantic Interoperability Semantic Interoperabilityfor eGovernment Conferencefor eGovernment Conference

byby

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

February 10, 2006 – MITRE, McLean, VAFebruary 10, 2006 – MITRE, McLean, VA

( v 1.00 )

ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005 2 of 30

IntroductionIntroduction• Stanford Medical Informatics- Stanford Medical Informatics- developer of developer of

ProtégéProtégé 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+ registrations)Active community with thousands of users (33,000+ registrations) Has been used to edit ontologies with tens of thousands of conceptsHas been used to edit ontologies with tens of thousands of concepts

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

virtual enterprise through bootstrapping collective intelligence over virtual enterprise through bootstrapping collective intelligence over the Internetthe Internet

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

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


The Team UpThe Team Up

• SMI & CIM3 – to develop and host an SMI & CIM3 – to develop and host an open Collaborative Ontology 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 Noy, Mark Musen, Ray Fergerson, Natasha Noy,

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


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 performanceRobust, scalable, enterprise performance 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 self-healing fiber-ringmultiple OC48 self-healing fiber-ring


Our Hosting Our Hosting FacilityFacility


An Augmented ApproachAn Augmented Approach

• We combine the strengths of both the Protégé ontology We combine the strengths of both the Protégé ontology tools platform, and CIM3’s infrastructure to provide a tools platform, and CIM3’s infrastructure to provide a collaborative ontology development environment for collaborative ontology development environment for bothboth humans and machines, optimizing between humans and machines, optimizing between (sometimes conflicting) objectives like:(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 system Secured 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 We are trying to spur innovation, as well as organic or

emergent behavior in the user communities and teamsemergent behavior in the user communities and teams


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 can The lead editor can accept or reject accept or reject changeschanges– For each propertyFor each property– For a class as a wholeFor a class as a whole– For a subtreeFor a subtree– All changes by a All changes by a

specific userspecific user– All changes to classes All changes to classes

with no conflictswith no conflicts


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 projectSmall/medium size ontology development project

user/team registers project with CODS-Admin and user/team registers project with CODS-Admin and uploads seed ontologyuploads seed ontology

CODS-Admin opens collaborative project on Protégé CODS-Admin opens collaborative project on Protégé multiuser servermultiuser 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, but…)(similar to above, but…)

dedicated review/accept process (through a lead editor)dedicated review/accept process (through a lead editor) probably also a full-time project manager or project probably also a full-time project manager or project

administrator who will also be responsible for version administrator who will also be responsible for version and release controland 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 producedNew baseline is produced


What Next?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 Funding solicited to support the development of

both the open source tools and the infrastructureboth the open source tools and the infrastructure• Skills & expertise in software engineering Skills & expertise in software engineering

welcomewelcome• Skills & expertise in ontological engineering Skills & expertise in ontological engineering

welcomewelcome• Formation and participation of a community to Formation and participation of a community to

carry this project forwardcarry this project forwardPlease email: Peter Yim [email protected] or Mark Musen <[email protected]>


QuestionsQuestions

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“ cods ” – a collaborative ontology development service & infrastructure

Documents

cwe open

team collaboration

ontology repository

protg ontology tools

open system transaction

robust cwe infrastructure

allthe cods team

user communities