the Government Semantic Interoperability Community of Practice (SICoP) To: the Government Semantic Interoperability Community of Practice (SICoP) Pilot and Preview on “CODS” – a Collaborative Ontology Development Service & Infrastructure by Peter Yim (CIM3) & Mark Musen (SMI) September 14, 2005 – MITRE, McLean, VA ( v 1.23 )

Introduction Stanford 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) 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_20050914.ppt/Sep-2005

The Team Up SMI & CIM3 – to develop and host an open Collaborative Ontology Development Service (CODS) and Ontology Repository for all the initial CODS team: 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) ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Protégé – Ontology & Knowledgebase Editor ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Software Featured in CODS Protégé 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_20050914.ppt/Sep-2005

Hosted Infrastructure Product features: CWE – “open”, “community-only” & “secured” Robust, scalable, enterprise performance Secured and Fault Tolerant Platform neutral (PC’s, Mac’s, Linux, Unix, …) Infrastructure: Tier-1 hosting facility 100Mbps bandwidth into the Internet backbone Backbone: multiple OC48 & Gige self-healing fiber-ring ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Our Hosting Facility ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

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: Human expressiveness vs. machine rigor Average user vs. power user expectation Secured system vs. open system Transaction system vs. groupware system behavior Our 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 teams ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Software Featured in CODS Protégé 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_20050914.ppt/Sep-2005

Protégé Multiuser Server Login ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Select Project ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Metaproject Instances ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Software Featured in CODS Protégé 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_20050914.ppt/Sep-2005

Protégé – convert to format ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Connecting to the Oracle backend ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Connecting to the MySql backend ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Software Featured in CODS Protégé 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_20050914.ppt/Sep-2005

Configure PromptTAB (1) ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

PromptTAB (2) ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Prompt: Comparing versions ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Examine class changes Prompt displays: Properties that were Added Deleted Changed Old and new values for properties ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

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_20050914.ppt/Sep-2005

Software Featured in CODS Protégé Multiuser Server RDBMS backend (Oracle or MySql) PomptTAB (Protégé plugin) Linux server platform 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 server Subversion server & client (TortoiseSVN client for Windows) ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

CODS – file structure (v1.45) ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Subversion Repository Access ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Subversion Checkout ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Use case Scenarios Small/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…) 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_20050914.ppt/Sep-2005

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_20050914.ppt/Sep-2005

What Next? Pilot projects welcome Further refinement of process Funding solicited to support the development of both the open source tools and the infrastructure Skills & expertise in software engineering welcome Skills & expertise in ontological engineering welcome Formation and participation of a community to carry this project forward Please email: Peter Yim peter.yim@cim3.com or Mark Musen <musen@smi.stanford.edu> ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005

Questions ? ppy-mm/CIM3-SMI_CODS-presentation_20050914.ppt/Sep-2005