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Technical Projects

Ecoinformatics International Technical Collaboration

Seattle, Washington, USAJanuary 26, 2010

Bruce BargmeyerLawrence Berkeley National LaboratoryandBerkeley Water CenterUniversity of California, BerkeleyTel: +1 510-495-2905bebargmeyer@lbl.gov

EITC Technical ProjectsWork Group

WG pursues information exchange, collaborative R&D, & collaborative activities under umbrella of EITC

Met as part of the EITC Strategic Planning meeting in Copenhagen, March 2009

Met after the Ecoterm meeting in Rome in October 2009 Holds telecons monthly (more or less) during the year. Individuals hold more frequent telecons on specific

activities

Some Tech. Proj. WG Activities

Ecoterm GEMET Terminology Standards Array Abu Dhabi initiative Collaborative R&D Metadata Registry and Semantics Management Web deployment SciScope, Eye on Earth Standards

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ECOTERM V WORKSHOP

Ecoterm started meeting in 2004 with the focus on the identification and implementation of best practices related to environmental terminologies and knowledge organization systems on the Web.

This meeting was held at U.N. Food and Agriculture Organization, Rome, Italy, 5-6 October 2009 attended by approximately 30 people from 18 organizations and 8

countries both in-person and virtually. Presentations are on the Ecoinformatics web site

Agreement: Ecoterm product/service to be developed is a federated approach to accessing terminology and knowledge organization systems in the area of the environment that would allow them to be accessed, interchanged, and used in traditional indexing and search approaches, as well as semantic web applications.

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Ecoterm V Workshop

In order to achieve this, there are several requirements which must be addressed. A common way to find these resources Common descriptions (metadata) for these resources so that others (especially systems) can

know how to use them Common Web services to provide external access and consistent functionality Unique IDs at the system and concept/term level to clearly and uniquely establish the links An approach that will work globally An approach that is based on open standards An approach that can be implemented by organizations somewhat independent of one

another, since the Ecoinformatics International Technical Collaboration, while based on an international agreement, does not have an extensive governance structure or funding support

An approach that can begin as a prototype but is robust enough to grow into a useful product/service

Technologies that are being used by other communities so that this effort can link to initiatives in other disciplines that may eventually be relevant to the environment

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Ecoterm V Workshop

Technical approach SKOS (Simple Knowledge Organization System) would be used

to publish the thesauri and other terminology systems The SKOS files would also be published as linked data Complement this with voiD files which are used to describe RDF

resources in a linked data environment. A simple umbrella web page would be created to aid in the

management, promotion, and access to this network of linked data

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GEneral Multilingual Environmental Thesaurus (GEMET)

Created by EEA A thesaurus of 5,000+ concepts with expression in 23 languages INSPIRE initiative gives new impetus, GEMET is included in

legislation. Extend GEMET –

Ecoterm action EPA update? EEA invests in the translations and some to advance to SKOS. EPA and UNEP have written letters of support to China MEP to

encourage development of Chinese translation (with help of Wuhan University)

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Technical Projects WG Activities

Terminology Work underway by EPA, USGS, EEA

Standards Array Initiated at EITC Strategic Directions meeting

in Copenhagen, March 2009 Scope described during this meeting Work Underway, Technical Projects WG will

spend a half day (Thursday) on this.

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Technical Projects WG Activities

Abu Dhabi initiative Introduced in this meeting. We will pursue it

further in the Tech. Proj. WG meeting on Tuesday afternoon, Wednesday and, Thursday

Collaborative R&D Have developed a proposal outline, looking for

funding possibilities

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SciScope

Developed in collaborative effort between Microsoft Research, Berkeley Water Center (UCB), Lawrence Berkeley National Laboratory

EITC leadership wanted demo of how semantics management – terminology, ontologies, and metadata – could be used to help prepare indicators and assessments.

SciScope demonstrates capabilities that help users to discover, evaluate, and access water data for analysis, presentation, indicators, assessment, ….

SciScope shows the use of a water ontology, linked to water “variables” (data elements), with metadata descriptions, and an easy to use geographic interface.

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Broad Use Case: Semantics Management - Linking Ontologies, Models, Metadata and Data

ID Date Temp Hg

A 06-09-13 4.4 4

B 06-09-13 9.3 2

X 06-09-13 6.7 78

Name Datatype Definition Units

ID textMonitoring Station Identifier

not applicable

Date date Date yy-mm-dd

Temp numberTemperature (to 0.1 degree C)

degrees Celcius

Hg numberMercury contamination

micrograms per liter

Register, curate, interrelate and manageSemantics.

Data

Metadata

Biological Radioactive

Contamination

lead cadmiummercury

Chemical

Ontology

Model

Data sources…

USGS

EPA

CIMS

TCEQ

NADP

Source: Bora Beran

What are we after?

A search engine that creates a unified view over multiple heterogeneous data repositories allowing scientists to discover and retrieve data in a simple and intuitive way. In technical terms: A searchable metadata repository/aggregator An ontology based interface for data discovery Links to metadata describing the available data A mediator (semantics/syntax/structure) A light-weight web GIS

Adapted from: Bora Beran

Data retrieval

SciScope currently hosts only metadata.Data are requested on the fly from the

original publisher using web service wrappers written specifically for each data source.

Data are reformatted to provide a unified view over the repositories.

What is behind SciScope?

Source: Bora Beran

Knowledge Base

Relationships are stored as RDF triples in a relational database

Supports transitive, symmetric and inverse properties

Inferred statements are pre-computed

What is behind SciScope?

‘Escherichia coli’ same-as ‘E. coli’‘E. coli’ is-a ‘Indicator Organism’

‘Nitrogen’ is-a ‘Macronutrient’‘Macronutrient’ is-a ‘Nutrient’‘Hypoxia’ isMeasuredUsing ‘DissolvedOxygen’‘Hypoxia’ isRelatedTo ‘Eutrophication’

Source: Bora Beran

Inference

Transitive‘Nitrogen’ is-a ‘Macronutrient’‘Macronutrient’ is-a ‘Nutrient’

Inference: ‘Nitrogen’ is-a ‘Nutrient’ Symmetric‘Hypoxia’ isRelatedTo ‘Eutrophication’

Inference: ‘Eutrophication’ isRelatedTo ‘Hypoxia’

Inverse‘Macronutrient’ is-a ‘Nutrient’

Inference: ‘Nutrient’ isBroaderThan ‘Macronutrient’

Source: Bora Beran

Geographical Features Catalog

Collection of features such as dams, aquifers, geologic formations, watersheds, sensors

Based on data and maps from USGS, EPA, National Atlas

What is behind SciScope?

Source: Bora Beran

SciScope.org

SciScope provides access to observations from approximately 1.65 million sensors in the US adding up to 358 million observations.

Tutorials1. Managing map layers2. Setting layer transparency3. Browsing geographical features4. Drawing polygons5. Search and data retrieval

Code available for download at: http://sciscope.codeplex.com

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SciScope

Demos given to EITC in December 2008 & March 2009 EPA Office of Environmental Information Computational Methods for Water Resources (Conference) Japan Construction Information Center (JACIC) Japan Life Cycle Data Management (LCDM ) Forum Open Forum on Metadata Registries, Seoul Korea June, 2009 Ecoterm V, Rome, Italy, October, 2009 Earth Sciences Information Partners, Winter Meeting, January, 2010 Many online accesses at SciScope.org …

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SciScope & Eye on Earth

Usability for end usersDemonstrates utility of the underlying

technologies and standardsAlready descried at this meetingQuestion: how can Eye on Earth and

SciScope play together?Topic of Technical Project WG meeting this

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Technical Projects Activities

Metadata Registry and Semantics Management ISO/IEC 11179-3 is in Final Committee draft Considerable work on Ontology: ISO/IEC 19763

Metamodel Framework for Interoperability Wuhan University leading work on several standards.

We will hear from Rong PENG in the Technical Projects WG

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Acknowledgement

This material is based upon work supported by the National Science Foundation, under Grant No. 0637122 and by USEPA. 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 or USEPA .

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