1. Ecoinformatics International Technical Collaboration
Technical Projects Workgroup
Update
October 5, 2009
Bruce Bargmeyer
Lawrence Berkeley National Laboratory
Tel:

2. Topics Introduction Current Activities
Uses of terminology and Ontology

3. Ecoinformatics Cooperation Background
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

4. 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)

5. Ecoinformatics Activities & 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.

6. 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

7. 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

8. 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

9. Ecoinformatics Collaboration Current 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

10. Ecoinformatics Collaboration Current 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

11. Ecoinformatics Collaboration Current 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

12. Ecoinformatics Collaboration Current 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 and families of standards

13. 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.

14. Modeling, Ontology, Terminology
Concept
Concept）
“person”
“Employee”
Employee
Terminology
Term
Source: Hajime Horiuchi, Tokyo International University

15. 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

16. Semantics for Data Management & Semantics Services – ISO/IEC 11179 (E3)
Conceptual Domain
Agent
Object Class
Chemopreventive
Agent
Valid Values
Cyclooxygenase Inhibitor
Doxercalciferol
Eflornithine …
Ursodiol
Data Element Concept
Chemopreventive Agent
NSC Number
Value Domain
NSC Code
Classification Schemes
caDSRTraining
Property
NSCNumber
Representation
Code
EVS=Enterprise Vocabulary Services. We talked about a Data Element being formed by a concept taking on a specific representation. In ISO terms this translates to the combination of a specific Data Element Concept and a specific Value Domain, you see this denoted in the middle of this chart by the yellow box outlined in red. caDSR administered items are backed by the use of externally defined terminologies and controlled vocabularies. With UMLS as a framework NCI has developed vocabulary services that are accessed via API – application to application interfaces – to provide touch points during creation of content, resulting in administered components that are bound to immutable concept codes. These touchpoints, denoted by the EVS logos, are currently implemented at the Object Class, Property, Representation Term, Value Domain and Valid Value levels of the metadata model.
Data Element
Chemopreventive Agent Name
Context
caCORE
Enterprise Vocabulary Services (EVS) Concepts Unite NCI MDR
Source: Denise Warzel, National Cancer Institute

17. Ontologies for Role, Goal, Process, Service (ISO/IEC 19763)
Functional Goal:
Sort Order
plays
consistsOf
Actor
Role
Organization
Dynamic Context
Profile R
Semantic Annotation
prefers
takesCharge
Personal Goal
Role Goal
Goal
Entity Ontology
Contextual Depend
Object
hasObject
Operation
hasOperation
Nonfunctional Goal
Functional Goal G
Operation Ontology
contributes
achieves
Input
hasInput
Output
hasOutput
Process
Composite Process
Atomic Process P
Context Ontology
Contextual Expectation
Domain Ontologies
realizes
Message
hasMessage
Service
Composite Service
Atomic Service
Contextual Property S

18. 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 , 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.