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Nanoinformatics: Locate, Collaborate, and IntegrateWorkshop on Nanoinformatics Strategies

June 12-13, 2007Westin Arlington Gateway Hotel

Arlington, Virginia

Brand L. Niemann, Senior Enterprise Architect, U.S. EPA,and Co-Chair, CIO Council's Semantic Interoperability

Community of Practice (SICoP)June 4, 2007 DRAFT

Google: Brand NiemannGoogle: SICoP

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Purpose• Nanoinformatics involves the development of effective

mechanisms for collecting, sharing, visualizing and analyzing information relevant to the nanoscale science and engineering community. It also involves the utilization of information and communication technologies that help to launch and support efficient communities of practice. Nanoinformatics is necessary for comparative characterization of nanomaterials, for design and use of nanodevices and nanosystems, for instrumentation development and manufacturing processes.

• The purpose of this workshop is to identify and prioritize nanoinformatics needs, discuss ongoing activities and draw up strategies for the future. Participants include cognizant leaders from national nano networks and centers who are actively engaged in building effective information and communication resources, as well as informatics experts from other research communities who can inform and advise.

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Goals• Identify nanoinformatics needs, challenges and priorities.

Discuss informatics activities currently underway that work to address needs in various research, development and education sectors (NCN, EHS, NNN, NIST, NCLT, nanomaterials, etc).

• Share best practices on cutting edge techniques in data mining, visual analytics, Web 2.0 technologies, literature analysis, data standards, digital clearinghouses, web-based communication tools, and related topics, including those from the other fields (e.g., caBIG, MatML, bioinformatics, high energy physics, computer science) and their connection to bioinformatics, and other informatics areas.

• Discuss interconnecting databases and mechanisms for defining the ontology of terms. Identify and prioritize strategies best suited for catalyzing nanotechnology research, development and education.

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US EPA’s Interest

• Significant environmental, health, and safety issues might arise with development in nanotechnology since some negative effects of nanoparticles in our environment might be overlooked. Such issues include potential occupational safety and health concerns for those involved in the manufacture of nanotechnologies. However nature itself creates all kinds of nanoobjects, so probable dangers are not due to the nanoscale alone, but due to the fact that toxic materials become more harmful when ingested or inhaled as nanoparticles (see nanotoxicology).– Source: Nanotechnology - Societal implications:

• http://www.answers.com/topic/nanotechnology

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Overview

• 1. Introduction

• 2. Locate

• 3. Collaborate

• 4. Integrate

• 5. Next Steps

• 6. Contact Information

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1. Introduction

• 1.1 Semantic Interoperability Community of Practice (SICoP)

• 1.2 Community of Practice

• 1.3 SICoP Co-Chair, Mills Davis

• 1.4 Evolution of the Internet

• 1.5 Data and Information Architecture

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1.1 Semantic Interoperability Community of Practice (SICoP)

• SICoP is chartered to do:– White Papers (3):

• Introducing Semantic Technologies and the Vision of the Semantic Web (2005).

• Semantic Wave 2006 - Executive Guide to the Business Value of Semantic Technologies. Update in 2007.

• Operationalizing the Semantic Web/Semantic Technologies:– A roadmap for agencies on how they can take advantage of

semantic technologies and begin to develop Semantic Web implementations (recently released for public review).

– Conferences (10): 35 Special Recognitions.– Pilots: More than 50.

Google: SICoP

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1.2 Community of Practice• What's the purpose?

– To develop members' capabilities; to build and exchange knowledge.

• Who belongs?– Members who select themselves.

• What holds it together?– Passion, commitment, and identification with the

group's expertise.

• How long does it last?– As long as there is an interest in maintaining the

group.

William Snyder, Building Communities of Practice. Excerpted from the article "Communities of Practice: The Organizational Frontier" in the Harvard Business Review, January-February 2000. http://hbswk.hbs.edu/archive/1317.html

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1.3 SICoP Co-Chair, Mills Davis

Contact: mdavis@project10x.com

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1.4 Internet Evolution to 2020

http://www.semantic-conference.com/2007/handouts/6-UpBW/T8_Davis_Mills_SingleColor.pdf

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1.5 Data and Information Architecture

Tool Program Purpose

Web Search Federal SitemapsGoogle: Federal Sitemaps

LocateMost searches start with Google, Yahoo, and MSN

Wikis COLABGoogle: COLAB Wiki

CollaborateNeed to Share*

Semantic Wikis KnowledgebasesGoogle: DRM 3.0 and Web 3.0

IntegrateResponsibility to Provide*

* Mike McConnell, Director of National Intelligence: Move the intelligence community beyond the "need to share" philosophy toward a "responsibility to provide" model (March 6, 2007).

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2. Locate

• 2.1 Google: Nanotechnology:– June 4, 2007: About 16,000,000

• Wikipedia: http://en.wikipedia.org/wiki/Nanotechnology

• 2.2 Google: Nanoinformatics– June 4, 2007: About 305

• 2.3 Google: Nanoinformatics and Ontology– June 4, 2007: About 8

• http://colab.cim3.net/cgi-bin/wiki.pl?BrandNiemann !

• 2.4 Google: Swoogle (http://swoogle.umbc.edu/):– Nanoinformatics on June 4, 1007: None– Nanotechnology on June 4, 2007: One

• http://www.mindswap.org/2004/multipleOnt/FactoredOntologies/NCI/Ontology19.owl

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2. Locate

• Answers.com: A Mashup of Trusted Reference Knowledge Sources (8)!– A website or application that combines content from more than

one source into an integrated experience (repurposing).• http://www.answers.com/topic/nanotechnology

– Encyclopedia and Handbook (10 Volumes each!)• WordNet Princeton (http://wordnet.princeton.edu/):

– Nanoinformatics: None– Informatics: information science, informatics, information

processing, IP (the sciences concerned with gathering, manipulating, storing, retrieving, and classifying recorded information)

– Nanotechnology: nanotechnology (the branch of engineering that deals with things smaller than 100 nanometers (especially with the manipulation of individual molecules)).

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3. Collaborate

• 3.1 Wiki Knowledge Management

• 3.2 Semantic Web, Meet the Social Web

• 3.3 Service Research & Innovation Initiative

• 3.4 Nanoinformatics Pilot

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3.1 Wiki Knowledge Management

• Technology Can Enable Complex Adaptive Behavior in Human Knowledge Workers:– Capabilities Wikis Bring:

• Because Wikis are real-time, self-authored, hyperlinked bodies of knowledge that are open to everyone on the system, they can adapt as fast as a person can enter information.

• Wikis also provide a space for knowledge evolve as the world changes, without knowledge reengineering.

– Together, Google and the Wikipedia manage more knowledge better and faster and cheaper than any other framework we have yet invented.

Dr. Calvin Andrus, CIA. Closing Keynote, Knowledge Management 2007 Conference, April 3-5.http://events.fcw.com/events/2007/KM/downloads/KM07_Keynote_Andrus_V1.pdf

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3.2 Semantic Web, Meet the Social Web

• Social Web:– Architecture of participation – user data– Emergent, bottom-up value creation– Vital ecosystem of software and data reuse

• Semantic Web:– Architecture of computation – structured data– Value from integration– Ecosystem of service composition

• The Killer Apps of Social + Semantic Web:– Collective Knowledge Systems

Gruber (2007), Grande Challenges for Ontology Design, Ontolog Forum, March 1,2007. Slide 15. http://tomgruber.org/writing/challenges-for-ontology-design.htm

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3.3 Service Research & Innovation Initiative

• Build Knowledgebases for Service Systems:– A semantic model = ontology(s) + the database of

instances built as a social contract between those the know how to build them and those that need them (business partners).

– Dr. James Spohrer, Towards a Science of Service Systems, CIOC Best Practices Committee, March 19, 2007, and Service Research & Innovation Initiative (SRII), Technology Services Research & Innovation Symposium, May 30th, Santa Clara Convention Center, http://www.thesrii.org. (See Slide 18.)

– See Best Practices Committee, April 16, 2007, Pilot with KZO Networks. (See Slide 21.)

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The Challenge: Service Industry Growth

People Business

Products Information

enable develop enable transform

designoperate &maintain

create utilize

Industrial services Information services

Business servicesConsumer services

Non-market services

Source: Dr. Spohrer, Towards a Science of Service Systems, CIOC Best Practices Committee, March 19, 2007.

3.3 Service Research & Innovation Initiative

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The Challenge: CIO Council Silos

People Business

InformationTechnology

Information

Architecture & Infrastructure CommitteeBest Practices Committee

Executive CommitteeIT Workforce Committee

Source: Pages 21-22, Federal Chief Information Officer Council Strategic Plan: FY 2007-2009, 28 pp. http://www.cio.gov/documents/CIOCouncilStrategicPlan2007-2009.pdf

Goal 1(see next slide)

Goal 2Goal 3

Goal 4

3.3 Service Research & Innovation Initiative

The “MediciEffect”

StakeholdersInput and Outreach

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3.3 Service Research & Innovation Initiative

• Goal 1. A cadre of highly capable IT professionals with the mission critical competencies needed to meet agency goals.

• Goal 2. Information securely, rapidly, and reliably delivered to our stakeholders.

• Goal 3. Interoperable IT solutions, identified and used efficiently and effectively across the Federal Government.

• Goal 4. An integrated, accessible Federal infrastructure enabling interoperability across Federal, state, tribal, and local governments, as well as partners in the commercial and academic sectors.

Federal Chief Information Officer Council Strategic Plan (FY 2007-2009) Goals

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3.3 Service Research & Innovation Initiative

People

Information TechnologyBusiness

Information

http://campustechnology.com/articles/46250/

Example of a Service System Application and Interface

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3.3 Service Research & Innovation InitiativeThe Medici Effect

• “The Medicis were a banking family in Florence who funded creators from a wide range of disciplines. Thanks to this family and a few others like it, sculptors, scientists, poets, philosophers, financiers, painters, and architects converged on the city of Florence. There they found each other, learned from one another, and broke down barriers and cultures. Together they forged a new world based on new ideas – what became known as the Renaissance.”– Frans Johansson, The Medici Effect, Harvard

Business School Press, 2006, pages 2-3.• http://hbswk.hbs.edu/archive/4376.html

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3.3 Service Research & Innovation Initiative The Medici Effect

• “When you step into an intersection of fields, disciplines, or cultures, you can combine existing concepts into a large number of extraordinary ideas.”

• “We have met teams and individuals who have searched for, and found, intersections between disciplines, cultures, concepts, and domains. Once there, they have the opportunity to innovate as never before, creating the Medici Effect.”– Frans Johansson, The Medici Effect, Harvard

Business School Press, 2006, page 186.

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3.4 Nanoinformatics Pilot

http://colab.cim3.net/cgi-bin/wiki.pl?NanoinformaticsStrategiesWorkshop_2007_06_1213

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3.4 Nanoinformatics Pilot

• Nanotechnology Characteristics*:– Broad range of topics– Highly multidisciplinary– Diverse lines of inquiry– “Bottom-up” and “Top-down” approaches

• COLAB: An Open Collaborative Work Environment (CWE) to Support Networking Among Communities of Practice:– Includes a wiki, email discussion forum, message archive,

shared file workspace, full text search, and portal.• http://www.gsa.gov/collaborate• http://www.cim3.com/CWE_Hosting_Plan.html

* Wikipedia: http://en.wikipedia.org/wiki/Nanotechnology

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4. Integrate

• 4.1 Table of Contents for Nanotechnology at Wikipedia

• 4.2 DRM 3.0 and Web 3.0 Knowledgebase

• 4.3 Appropriate Applications of the “Spectrum of From Search to Knowing”

• 4.4 Semantic Wikis

• 4.5 Modeling, Simulation, and Visualization

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4.1Table of Contents for Nanotechnology at Wikipedia

• 1 Origins• 2 Fundamental concepts

– 2.1 Larger to smaller: a materials perspective– 2.2 Simple to complex: a molecular perspective– 2.3 Molecular nanotechnology: a long-term view

• 3 Current research– 3.1 Nanomaterials– 3.2 Bottom-up approaches– 3.3 Top-down approaches– 3.4 Functional approaches – 3.5 Speculative

• 4 Tools and techniques• 5 Applications• 6 Implications

– 6.1 Health and environmental issues– 6.2 Broader societal implications and challenges

• 7 References• 8 See also• 9 Further reading• 10 External links

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4.2 DRM 3.0 and Web 3.0 Knowledgebase

• Metadata:– Full text of documents, meeting notes, etc.

• Harmonization– Different ways in which the same words are used.

• Enhanced Search:– Across all documents and showing context (e.g.

words around the term or concepts)

• Mashups:– A website or application that combines content from

more than one source into an integrated experience (repurposing).

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4.3 Appropriate Applications of the “Spectrum of From Search to Knowing”

• Taxonomy:– Categorization, Simple Search & Navigation, Simple Indexing.

• Thesaurus:– Synonyms, Enhanced Search (Improved Recall) & Navigation,

Cross Indexing.

• Data and Object Models:– Enterprise Modeling (system, service, data), Question-

Answering (Improved Precision), Querying, SW Services.

• Logical Theory:– Real World Domain Modeling, Semantic Search (using

concepts, properties, relations, rules), Machine Interpretability (M2M, M2H semantic interoperability), Automated Reasoning, SW Services.

Source: Michael Eschold’s Presentation at SemTech 2007 Based on Leo Obrst.http://colab.cim3.net/file/work/SICoP/2007-05-22/SICoPSTC05222007.ppt

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4.4 Semantic Wikis2007 Semantic Technology Conference Presentations, May 20-24th

• Building Semantic Applications in a Semantic Wiki, Mills Davis, Project10X, and Conor Shankey, Visual Knowledge.

• Semantic Wiki, Michael Lang, Revelytix.– http://www.semantic-conference.com/2007/handouts/2-UpBW/

Lang_Michael_2UpBW.pdf• Policy Wiki for Compliance and Risk, Edgar Rodriguez,

Cogo, Inc., and Conor Shankey, Visual Knowledge.• Five High-Yield Collaborative Applications for Semantic

Wikis, Conor Shankey, Visual Knowledge.• Automatic Generation of Natural Language Reports from

Semantic Research Results, Chuck Rehberg, Semantic Insights.– http://www.semantic-conference.com/2007/handouts/2-UpBW/

Rehberg_Chuck_2UpBW.pdf

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4.4 Semantic WikisNanoinformatics Strategies Pilot

http://www.visualknowledge.com/wiki/Nanoinormatics

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4.4 Semantic WikisVisualKnowledge Semantic Wiki

• What is a semantic wiki?:– Semantic - From the Greek words Greek sEmantikos significant,

from sEmainein to signify, mean - of or having Meaning. – WIKI- A collaborative community web-based environment that

enables prosumers to generate, present, and review content in a peer-reviewed environment.

• A WIKI empowered with an Agent-based ontology authoring, management and reviewing tools. A Semantic WIKI allows users to input data into the system in the same fashion as earlier WIKI and collaborative tools have, however, the Semantic Wiki includes tools for creating a model of that data such that the data entered becomes a network of related concepts, tied into an underlying model of the knowledge domain - in essence a Semantic Wiki is a Wiki that understands its content.

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4.4 Semantic WikisVisualKnowledge Semantic Wiki

• Leveraging the powerful ontology building tools of Visual Knowledge and the OWL/RDF standard representation, the VK Semantic Wiki empowers users to work on three discrete levels. In a VK Semantic Wiki businesses or communities can:

• Allow Subject Matter Experts [SME] to dump knowledge, facts, documents and other unorganized material into an easy to use online interface.

• Allows Content integrators to quickly categorize and instantiate the data entered by the SMEs into the Ontology of the Domain.

• Allows Ontologists (Knowledge Modelers) to create deep OWL ontologies of their corporation utilizing cutting edge web-based visualization tools. Similarly, the Ontologists can also leverage the deeper capacities of Visual Knowledge to build domain specific application functionality.

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4.5 Modeling, Simulation, and Visualization

• New features and capabilities in the VK Semantic Wiki include:– importing table schemas and instances as semantic

models;– modeling/drawing of ontologies; and– wiring semantic behaviors into applications in the

same environment.• BioCAD:

– Integration of Biological Data with Semantic Networks, Michael Hsing,1 and Artem Cherkasov, Current Bioinformatics, 2006, 1, 000-000

• http://colab.cim3.net/file/work/SICoP/2006-10-10/Hsing_CBIO.pdf

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5. Next Steps

• 5.1 Involve NIST Ontology and Manufacturing Capabilities:– http://www.mel.nist.gov/msid/– http://colab.cim3.net/cgi-bin/wiki.pl?

InteroperableManufacturingCommunityofPractice

• 5.2 Form the Nanoinformatics CoP• 5.3 Share Learning and Best Practices• 5.4 Build Knowledgebases to Connect Multiple

Sources of Information Through the Use of Semantic Technologies / Ontologies

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5.2 Form the Nanoinformatics CoP

• Suggested Five Steps:– CoP Mission Statement:

• Slide 2

– CoP Membership List:• Slide 24 - Workshop Attendees

– CoP Strategy:• Slide 3

– Training Conference Call (with items 1-3 entered into the Semantic Wiki space):

• This Workshop

– Commitments to collaboratively publish and edit trusted reference knowledge sources in the Semantic Wiki space.

• This Workshop?

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5.4 Build Knowledgebases

• Recall:– Slide 3: Goal of “interconnecting databases and mechanisms for

defining the ontology of terms.”– 13: Mashup of Trusted Reference Knowledge Sources and

Princeton WordNet.– 17: A semantic model = ontology(s) + the database of instances

built as a social contract between those the know how to build them and those that need them (business partners).

– 27: Table of Contents for Nanotechnology at Wikipedia.– 28: DRM 3.0 and Web 3.0 Knowledgebase (Metadata,

Harmonization, Enhanced Search, and Mashups)– 29: Appropriate Applications of the “Spectrum of From Search to

Knowing” (Taxonomy, Thesaurus, Data and Object Models, and Logical Theory).

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5.4 Build Knowledgebases

• Initial Content Selection:– Nanotechnology at Wikipedia– Nanotehcnology at Answers.com– National Nanotechnlogy Initiative– Final Nanotechnology White Paper, U.S.

Environmental Protection Agency, Washington, DC 20460, February 15, 2007:

• 6.5 Intra-Agency Workgroup. EPA should convene a standing intra-Agency group to foster information sharing regarding risk assessment or regulatory activities for nanomaterials across program offices and regions.

– http://www.epa.gov/osa/nanotech.htm

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5.4 Build Knowledgebases

http://web-services.gov/lpBin22/lpext.dll/Folder21/Infobase13/1?fn=main-j.htm&f=templates&2.0

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6. Contact Information

• Brand Niemann:– Senior Enterprise Architect

• US Environmental Protection Agency• 202-564-9491• Niemann.brand@epa.gov• http://colab.cim3.net/cgi-bin/wiki.pl?BrandNiemann

– Co-Chair, Semantic Interoperability Community of Practice (SICoP):

• http://colab.cim3.net/cgi-bin/wiki.pl?SICoP• http://web-services.gov/