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Slide 1 - National Center for Ontological Research


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  • 1. Towards e-Government: The Federal Enterprise Architecture Reference Ontology Presentation at the National Center for Ontological Research Inaugural Meeting, Center for the Arts, University at Buffalo Brand Niemann (US EPA), Chair, Semantic Interoperability Community of Practice (SICoP) Best Practices Committee (BPC), CIO Council and Peter Yim, President & CEO, CIM Engineering, Inc. October 27, 2005 and
  • 2. Bio
    • Dr. Niemann has been with the U.S. EPA for 25 years and currently works in the Office of the Chief Information Officer and Assistant Administrator for Environmental Information as an Enterprise Architect and Semantic Web Services Specialist. He Chairs the Federal CIO Council’s Semantic Interoperability Community of Practice (SICoP). He serves as a member of the XML Conference Planning Committee, the E-Gov Institute Program Planning Committee, the Architecture & Infrastructure Committee, and the Knowledge Management Working Group of the Best Practices Committee.
  • 3. Introduction
    • At the recent Government Computer News “Storage to Knowledge: The Data Lifecycle Management Conference”, I Declared “October as Ontology Month”!
      • I am not an ontologist by training, but consider myself an “evangelist” of ontologies and ontological engineering in support of the Federal Enterprise Architecture and Federal Knowledge Management.
      • This presentation is about the reasons why.
  • 4. October is Ontology Month
    • Start the month:
      • October 5th: First Meeting of the SICoP Ontology and Taxonomy Coordinating Work Group (ONTAC WG, Pat Cassidy, MITRE, Lead):
        • Inventory of Semantic Interoperability Assets and Common Semantic Model Development (COSMO).*
    • End the month:
      • October 27th: Inaugural Event of the National Center for Ontological Research (Barry Smith, Director NCOR-Buffalo and Mark Musen, Director NCOR-Stanford):
        • October 28th: Workshop on Bio-Ontologies co-sponsored by the National Center for Biomedical Ontology ($19M Grant!)
    See and this is remarkably similar to the recent European Commission report – see slide 10.
  • 5. October is Ontology Month
    • And in between the calendar was:
      • October 7th: NIH Forum on Informatics Solutions (An Avian Flu Ontology-Driven Application?):
        • Health Information Technology Ontology Project (HITOP, Marc Wine, GSA, Lead)
      • October 12th: SICoP Public Meeting on the Data Reference Model Ontology and Semantic Technologies Education:
        • In Connection with the GCN “Data to Knowledge: The Data Lifecycle Management” Conference.
      • October 13th: Ontolog Forum – Barry Smith, NCOR Director-Buffalo, "How to Do Things with Paper: The Ontology of Documents and the Technologies of Identification.“
  • 6. October is Ontology Month
    • And in between the calendar was (continued):
      • October 18th and 20th: Data Reference Model 2.0 Delivered to the Federal CIO Council & Architecture & Infrastructure Committee.
        • “ It should be noted that ontologies may also be used for categorization, and also that taxonomies are themselves a lighter form of ontologies. The DRM categorization focus is on taxonomies.”
      • October 20th: SICoP Public Meeting on Semantic Interoperability Architecture/DRM Pilots at a Joint Community of Interest Conference .
        • An Event Ontology for the January 6, 2005, Train Derailment Incident in Granitville, South Carolina.
      • October 20th: Ontolog Forum – Nicolas Rouquette, NASA/JPL, Moderator, “ Semantic Web Services Ontology Standard.”
  • 7. It Took More Than Two Years
    • Milestones:
      • CIO Council’s XML Web Services Working Group Meeting, March 4th, 2003:
        • Ralph Hodgson, "The Promise of Ontology-based Knowledge Technologies for Enabling Citizens: An Exploration with Scenario-based "Capability Cases".”
      • SICoP and the Ontolog Forum Partner, June 23, 2004:
        • Delivered a Response to the National Health Information Network RFI and a Pilot Showing the Use of a Hierarchy of Ontologies.
      • AFCEA International (Bethesda Chapter) and the U.S. Environmental Protection Agency ArchitecturePlus Seminar, January 18, 2005:
        • Richard Murphy, “Semantic Interoperability, Ontology and Their Potential for Federal Information Sharing”:
          • Extracted concepts from paper documents to create the Federal Enterprise Architecture Reference Model Ontology (FEA-RMO) that is a domain specific ontology that turns four FEA Reference Models into their executable representation in OWL-DL with support from TopQuadrant. Also produced four use cases.
  • 8. It Took More Than Two Years
    • Milestones (continued):
      • SICoP “Socializes” the FEA-RMO, March 15, 2005, to the present:
        • Formal Release, Press Coverage, Public Comments Invited, SWOOP (Jim Hendler) - SWANS Conference Demonstration, Promote Use by Agencies and in the FEA-RM Maintenance Process, etc.
        • Executable Integration of the FEA Reference Models in Composite Applications, by Digital Harbor and TopQuadrant.
        • First DRM Public Forum – Six Pilot Demonstrations. Lots More Followed in Our Collaboration Workshops.
      • Acceptance by the Enterprise Architecture Community, July 2005, to the present:
        • Continuity of Communications for the Federal Executive Branch Using Ontological Engineering by Roy Roebuck.
        • Executable Enterprise Models (The FEA Reference Model Ontology) by Irene Polikoff and Robert Coyne Published in the Premier Issue of the Journal of Enterprise Architecture.
          • Also at the 4th International Semantic Web Conference, November 6-10, 2005. Enterprise Architecture Reference Modeling in OWL/RDF.
            • Published by Springer at
  • 9. It Took More Than Two Years
    • Milestones (continued):
      • ONTAC WG, October 5, 2005 (some highlights):
        • Pat Cassidy, “Common Semantic Model (COSMO)”.
        • Richard Murphy, “FEA-RMO Shared Concept Use Case: A Cognitive Perspective on Standardizing the Linkages Between the FEA Reference Models” – Linkages and Execution.
        • Data Reference Model Implementation and the European Commission IDABC Content Interoperability Strategy.
        • Discussion Afterwards: Integrate FEA-RMO and UMLS-SN.
      • SICoP Public Meetings, September 14, 2005, to the present (some highlights):
        • Collaborative Ontology Development Server - Multi-User Protégé, PeterYim, MarkMusen, et al.
        • SICoP Pilot: An OWL-based Schema as an Implementation for the DRM Abstract Model - Eric Peterson, McDonald Bradley.
        • SICoP White Paper: The Business Case for Semantic Technologies and BioCAD/VisualOwl Demo - Mills Davis, SICoP Team Lead and Managing Director, TopQuadrant.
  • 10. Data Reference Model
    • The DRM Implementation Through Iteration and Testing Strategy includes five key activities over the next year:
      • Education and Training in DRM Version 2.0 and use in FEA – DRM-based Information Sharing Pilots (started June 13 th ).
      • Testing of XML Schemas and OWL Ontologies by NIST and the National Center for Ontological Research, respectively, among others (beginning after October 27 th ).
      • Inventory/Repository of Semantic Interoperability Assets and Development of a Common Semantic Model (COSMO) by the new Ontology and Taxonomy Coordinating Work Group (ONTACWG) (started October 5 th ).
      • Continued early implementation of DRM 2.0 concepts and artifacts by industry in “open collaboration with open standards” pilot projects and workshops (started July 19 th ).
      • Fostering champions of DRM Best Practices to improve (1) agency data architectures within agencies and (2) cross-agency data sharing across agencies in funded projects (in process).
  • 11. European Commission IDABC* Content Interoperability Strategy
    • Semantic Interoperability Assets:
      • Dictionaries
      • Thesauri
      • Multilingual thesauri
      • Nomenclatures
      • Cross-references and mapping tables
      • Ontologies
      • Service registries
    • Milestones:
      • Production of a pivot ontology of life & business events connected to administrative activities.
      • Publication of the ontology on the Clearinghouse server.
    * Interoperable Delivery of European eGovernment Services to public Administrations, Business and Citizens.
  • 12. Smart Context Continuum
  • 13. The Tradeoff Between Search and Knowledge Computing How would you really accomplish the seven scenarios in the GSA/OMB RFI? See * See the next slide for the BioCAD/VisualOwl example. Only the content that has been repurposed*. Everything that is electronically accessible. Content Executable Assists Metadata Knowledge Computing Search Purpose
  • 14. BioCAD Source: Knowledge Computing Example in the Business Value of Semantic Technology: Exploiting New Value Paradigms, Mills Davis, Joint CAF, PMCoP, & SICoP Meeting, Reagan Center, September 21, 2005,
  • 15. My Hope Is…
    • Ontologies are Fun by Ed Hovy, December 2004, NSF Eco-Informatics Workshop
    • Ontologies are fun,
    • Ontologies are cool,
    • But when a long day’s done,
    • Doing too much is cruel!
    • So these next four slides,
    • Should go by in a flash.
    • Then in our speedy rides
    • Ramada-ward we’ll dash
    • And drop straight into bed.
    • But ere you fall asleep,
    • Repeat this in your head,
    • And as your mantra keep:
    • Ontologies are fun,
    • Ontologies are cool,
    • Before we are all done,
    • Ontologies will rule!
  • 16. Peter Yim, President & CEO of CIM Engineering, Inc. , and Mark Musen, Stanford Medical Informatics, Stanford University Presented at the 2005 SICoP Annual Meeting, September 14, 2005, at the MITRE Corporation, McLean, VA, by SICoP Chair, Brand Niemann, U.S. EPA. For “Outstanding Contributions” to Providing Critical Infrastructure for Collaborative Ontology Development: The Ontolog Forum, The Collaboration Wiki, Protégé, and The Server for Multi-User Protégé That Support SICoP and Other Federal Communities of Practice, the New National Center for Ontological Research, and a World-Wide Community. Special Recognition Federal CIO Council’s Semantic Interoperability Community of Practice (SICoP)
  • 17. Suggested NCOR Goals and Priorities
    • Ontologies and Ontology Engineering are emerging with a bright future in eGovernment for Enterprise Architecture, Data Architecture, Knowledge Computing, and Electronic Health Information, to mention a few.
    • NCOR provides a critical link in the public-academic-private partnership needed to provide high quality ontologies and ontological engineering applications to eGovernment.
  • 18. Introduction
    • More than 30 years working experience as a manager, entrepreneur, technologist, researcher, strategist, and futurist.
    • President & CEO, CIM Engineering, Inc.
    • Co-convener of the Ontolog Forum.
    • Provider of Collaborative Work Environments to SICoP and Other Federal Communities of Practice.
  • 19. On the Inaugural Event of NCOR
    • I bring our congratulations and best wishes to NCOR and its leadership, on behalf of my CIM3 colleagues, and members of the Ontolog community.
    • I will introduce some of the work we’ve been bringing to the table ... and take the opportunity to pledge my support to the NCOR endeavor.
    • In particular, I take pleasure in announcing the launch of the joint CIM3-SMI Collaborative Ontology Development Infrastructure and Service (CODS).
  • 20. Use-Inspired Basic Research
    • Ontological Research is 'strategic' research that is more appropriately modeled in Donald Stokes' Pasteur's Quadrant (as use-inspired basic research) ... we should no longer treat (and fund) basic-research and applications like opposite poles.
    • With the Internet, virtual communities, and an 'open' paradigm, we have the promises of unprecedented research capabilities in our hands now.
    ttp:// A couple of personal insights I'd like to share:
  • 21. ONTOLOG (aka. Ontolog Forum) est. Apr.2002
    • 3 co-conveners - Peter Yim; Leo Obrst & Kurt Conrad
    • Hosted on the CIM3 collaborative work environment infrastructure
    • Charter - 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.
    • Activities:
      • 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 participation – see:
  • 22. Introduction to the CODS Team
    • 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 internal CoP focusing on the practical issues of both formal and informal ontologies, and their adoption into mainstream application through standardization.
  • 23. The CODS Team
    • SMI & CIM3 – to develop and host an open Collaborative Ontology Development Service (CODS) and Ontology Repository for all.
    • The initial CODS team members:
      • 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).
  • 24. Protégé – Ontology & Knowledgebase Editor
  • 25. 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)
  • 26. 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 data center facility.
      • 100Mbps bandwidth into the Internet backbone.
      • Backbone: multiple OC48 & Gige self-healing fiber-ring.
  • 27. Our Hosting Facility
  • 28. 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.
  • 29. 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.
  • 30. What Next?
    • Pilot projects welcomed.
    • 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.
    For more information, see: To get involved, please email: Peter Yim <> or Mark Musen < musen @s tanford .edu>