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Ecoinformatics International Technical Collaboration

Technical Projects Workgroup Update

October 5, 2009

Bruce BargmeyerLawrence Berkeley National LaboratoryTel: +1 510-495-2905bebargmeyer@lbl.gov

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Topics

Introduction Current Activities

Uses of terminology and Ontology

Ecoinformatics CooperationBackground

Initiated about 1994 Leverage resources of agencies with major health and

environmental programs in their missions EEA (and DG Environment, Research, Information Society) US Government--EPA, USGS, NSF, DOD, … Intergovernmental organizations (IGOs)--UNEP Scientific research organizations—LBNL, JRC

Cooperate on standards and technology development, demonstration, deployment.

EPA and EEA play leadership role Evolving name: Initiated the use of term “ecoinformatics” for the

participants: Interagency/International Cooperation on Ecoinformatics, Ecoinformatics International Technical Collaboration (EITC)

Ecoterm group was created under umbrella of this group

Ecoinformatics International Technical Collaboration

Purpose The following are major purposes for the projects and

activities of the EITC Share experiences and results Establish and foster an ecoinformatics marketplace and the pillars

that will support it: common vision, standards, sharable designs and practices.

Cooperate on emerging technologies Cooperate on key elements for interoperability Cooperate on developing and deploying interagency/international

environmental information systems Share the costs and benefits of key elements for interoperation Demonstrate results Publicity

Two levels: Principals (top-level government) and technical-level workgroups Primary organizers William Sonntag (EPA) David Stanners (EEA)

EcoinformaticsActivities & Research

Two kinds of activities:Advances/activities as part of current operations

with internal agency resources Ecoinformatics result: primarily technology transfer

by sharing ideas.Activities requiring additional resources

(contracts, research grants, …) Ecoinformatics result: technology transfer of ideas,

research results, and tools/infrastructure.

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Coordinate R&D in Ecoinformatics

Share cost and benefits through coordination of US & EU (& Asia?) ecoinformatics R&D

Identify key advances needed at the core of ecoinformatics Semantics management, semantics services, semantic computing Terminology web services IT support for indicators, … Demonstrate in ecoinformatics “Test Bed” Develop an “architecture” of advanced ecoinformatics

technologies? Research, Development and Demonstration projects ranging from

improvements in operations to strategic breakthroughs

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Ecoinformatics Technologies

Identify existing and emerging technologies useful for ecoinformatics, e.g., Environmental data grids and computer grids Semantic Web Metadata registries XML registries and XML data exchange Terminology systems Ontology Address earlier stages of technology adoption

Stages of adoption are, e.g.: examine technology that is interesting, determine that technology is potentially useful, develop a prototype, implement a pilot, develop for broad deployment, deploy, operate as mature technology

Share costs and increase benefits of early stages

Ecoterm I

Nee:1st Environmental Terminology Meeting 15-16 April 2004 in Geneva Hosted by UNEP with programming support by EPA,

EEA, JRC and USGS > 30 participants Participants included terminology developers, IT

professionals, and those interested in multilingual issues from governments, intergovernmental organizations (especially UN agencies), scientific institutions, corporations and vendors

This is the fifth meeting of the Ecoterm group. USGS support has done much to advance this group

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Ecoinformatics CollaborationCurrent Activities

Ecoterm activities (as updated at this meeting)EPA, EEA, UNEP collaboration with

Microsoft EEA – Microsoft Partnership Agreement

Eye on Earth UNEP – Microsoft MOU EPA, LBNL, Berkeley Water Center, Microsoft

Research – R&D collaboration SciScope

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Ecoinformatics CollaborationCurrent Activities

Global Standards Array for Interoperability Initiated at the March 2009 EITC meeting in Copenhagen Challenge is to develop an interoperability solution for global environmental

assessment, reporting and observations networks Using the talent and expertise of the EITC as the forum and primary resource.  

EITC discussions resulted in an understanding that an array of global standards for the environmental information domain would do the most to further interoperability.  

This recommended array would be based on the best of current standards and approaches now adopted by the Ecoinformatics partners and standards currently in use by national, regional, global networks, communities of practice of portions of the environmental information domain and consensus processes like GEO.

Draft scoping document under preparation  Participants agreed to provide their initial thoughts on the starting list of standards that

they believe would be potential constituent parts in the potential standards array. Next Telecon October 7, 2009

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Ecoinformatics CollaborationCurrent Activities

GEMET - GEneral Multilingual Environmental Thesaurus Developed as an indexing, retrieval and control tool. The basic idea for the development of GEMET was to use the best

of the available multilingual thesauri. GEMET was conceived as a “general” thesaurus, aimed to define a common general language, a core of general terminology for the environment.

Use widened to include INSPIRE and other new applications Discussion beginning about how to extend GEMET Update tomorrow from Stefan Jensen

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Ecoinformatics CollaborationCurrent Activities

Cooperation with Earth Science Information Partners (ESIP) and GEOSS ESIP Water Cluster Activities EPA Office of Water - Water Quality Exchange (WQX) CAUHSI Activities – Water ontology development related to Hydroseek

(Bora Beran) and potentially SciScope Potential for use of EPA OEI Substance Registry System (SRS) chemicals

and other terminology related to water GEOSS Related activities (in consultation with EPA/EEA/NASA/NOAA)

Metadata registry and ontology standards ISO/IEC 11179 and 19763 families of standards

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Current Activities

Water Information System for Europe, Shared Environmental Information System

SPIRE - Semantic Eco-blogging; Aquatic Invasive Prediction, linked data USGS initiatives, NBII Metadata Catalog, Gap Analysis EPA terminology and registry advancements

Office of Research and Development + Office of Environmental Information

Ecoinformatics Implementing Arrangement under US – EU Science and Technology Agreement- coordinated research

Co-operation and coordination with GMES, GEOSS, GEO - strengthening data integration and data exchange

Work with EEA and EPA to explore possible interaction with National Cancer Institute relating to caBIG approaches to interoperability of dispersed data.

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Concept

Concept Concept ）

ConceptConcept Concept

Term

Term

Ontology

Employee

Model

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Modeling, Ontology, Terminology

Terminology

“person”

“Employee”

Source: Hajime Horiuchi, Tokyo International University

Areas of Interoperability

There are four areas of compatibility—an application must meet the guidelines in all four areas to be considered "caBIG Compatible:”

• Syntactic Interoperability

1. Programming and Messaging Interfaces• Semantic Interoperability

2. Information Models

3. Common Data Elements

4. Vocabularies and Ontologies

Vocabularies Information Models

APIs

CDEs

caBIG: NCI cancer Biomedical Informatics Grid

Semantics for Data Management & Semantics Services – ISO/IEC 11179 (E3)

Object ClassChemopreventive

Agent

PropertyNSCNumber

Conceptual DomainAgent

Data Element ConceptChemopreventive Agent

NSC Number

Data ElementChemopreventive Agent Name

Value DomainNSC Code

ContextcaCORE

RepresentationCode

Cla

ssif

icat

ion

Sch

emes

caD

SR

Tra

inin

g

Valid ValuesCyclooxygenase Inhibitor

DoxercalciferolEflornithine

…Ursodiol

Source: Denise Warzel, National Cancer Institute

Enterprise Vocabulary Services (EVS) Concepts Unite NCI MDR

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Ontologies for Role, Goal, Process, Service (ISO/IEC 19763)

G

S

Service

Composite ServiceAtomic Service

realizes

Goal

Nonfunctional Goal Functional Goal

Role GoalPersonal Goal

Process

Composite ProcessAtomic Process

P

achievescontributes

prefers takesChargeR

Role OrganizationActorplays consistsOf

Entity Ontology

Operation Ontology

Context Ontology

ObjecthasObject

InputhasInput

OutputhasOutput

Message

hasMessage

Semantic Annotation

Operation

hasOperation

Dynamic Context Profile

Contextual Depend

Contextual Expectation

Contextual Property

Domain Ontologies

Functional Goal:

Sort Order

Acknowledgements

Thanks to: Yangfan HE, Wuhan University Gail Hodge, IIA/USGS Harold Solbrig, Mayo Clinic Denise Warzel, NCI

This material is based upon work supported by the National Science Foundation, under Grant No. 0637122, by USEPA, and by NCI. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, NCI, or USEPA.

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