Ecoinformatics International Technical Collaboration Technical Projects Workgroup Update October 5, 2009 Bruce Bargmeyer Lawrence Berkeley National Laboratory Tel: +1 510-495-2905 bebargmeyer@lbl.gov

Topics Introduction Current Activities Uses of terminology and Ontology

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

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)

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.

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

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

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

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

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

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 11179 and 19763 families of standards

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.

Modeling, Ontology, Terminology Concept Concept） “person” “Employee” Employee Terminology Term 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) 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 11179 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

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

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.