1 CODS – a Collaborative Ontology Development Service & Infrastructure “CODS” – a Collaborative Ontology Development Service & Infrastructure Presented at: the 4 th Semantic Interoperability for eGovernment Conference by Peter Yim (CIM3) Mark Musen (SMI) Peter Yim (CIM3) & Mark Musen (SMI) February 10, 2006 – MITRE, McLean, VA ( v 1.00 )

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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 international CoP focusing on the practical issues of both formal and informal ontologies, and their adoption into mainstream application through standardization

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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 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)

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Protégé – Ontology & Knowledgebase Editor

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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)

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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 self-healing fiber-ring

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Our Hosting Facility

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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)

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Protégé Multiuser Server Login

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Select Project

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Metaproject Instances

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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)

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Protégé – convert to format

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Connecting to the Oracle backend

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Connecting to the MySql backend

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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)

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Configure PromptTAB (1)

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 PromptTAB (2)

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Prompt: Comparing versions

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Examine class changes Prompt displays: –Properties that were Added Deleted Changed –Old and new values for properties

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Accept and Reject Changes The 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

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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)

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 CODS – file structure (v1.45)

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Subversion Repository Access

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Subversion Checkout

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 A use case NCI Thesaurus: Collaborative editing New baseline version produced every month Multiple editors start with the baseline and edit it in Protégé in multiuser mode Prompt compares the current baseline to the new version produced by editors Lead editor accepts or rejects changes New baseline is produced

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 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 Peter Yim or Mark Musen

ppy-mm/CIM3-SMI_CODS-presentation_ ppt/Sep of 30 Questions ?