NCEAS Working Groups
Science Environment for Ecological Knowledge (SEEK) (Hosted by NCEAS)
Project Description
The goals of the Science Environment for Ecological Knowledge (SEEK) are to make fundamental improvements in how researchers can 1) gain global access to ecological data and information, 2) rapidly locate and utilize distributed computational services, and 3) exercise powerful new methods for capturing, reproducing, and extending the analysis process itself. The project involves a multidisciplinary team of computer scientists, ecologists and technologists from the Partnership for Biodiversity Informatics (PBI), a consortium comprising the National Center for Ecological Analysis and Synthesis (NCEAS); the San Diego Supercomputer Center (SDSC); the University of Kansas (KU); and the University of New Mexico (UNM) and partnering institutions (Arizona State University, University of North Carolina, University of Vermont, and Napier University in Scotland).
Principal Investigator(s)
Matthew B. Jones, James H. Beach, Bertram Ludaescher, William K. Michener, Mark P. Schildhauer
Project Dates
Start: October 1, 2002
End: September 30, 2007
completed
Participants
- Ilkay Altintas
- University of California, San Diego
- P. Mark Anderson
- University of California, Santa Barbara
- James H. Beach
- University of Kansas
- Chad Berkley
- University of California, Santa Barbara
- Shawn Bowers
- University of California, San Diego
- James W. Brunt
- University of New Mexico
- David R. Chalcraft
- East Carolina University
- Christopher M. Clark
- Unknown
- Elsa E. Cleland
- Stanford University
- Stephen B. Cox
- Texas Tech University
- Paul Craig
- Napier University
- Laura Downey
- University of New Mexico
- Nico M. Franz
- University of California, Santa Barbara
- Robert Gales
- University of Kansas
- Susan Gauch
- University of Kansas
- Lucas Gilbert
- Daniel Graf
- Academy of Natural Sciences
- Martin Graham
- Napier University
- Corinna Gries
- Arizona State University
- Dan Higgins
- University of California, Santa Barbara
- Efrat Jaeger-Frank
- University of California, San Diego
- Matthew B. Jones
- University of California, Santa Barbara
- Manu Juyal
- Arizona State University
- Samantha Katz
- University of New Mexico
- Jessie Kennedy
- Napier University
- Serguei Krivov
- University of Vermont
- Robert Kukla
- Napier University
- Michael T. Lee
- University of North Carolina
- Xianhua Liu
- University of North Carolina, Chapel Hill
- Bertram Ludaescher
- University of California, San Diego
- Joshua S. Madin
- University of California, Santa Barbara
- Peter McCartney
- Arizona State University
- Timothy McPhillips
- University of California, Davis
- William K. Michener
- University of New Mexico
- Trevor Patterson
- Unknown
- Robert K. Peet
- University of North Carolina, Chapel Hill
- Deana D. Pennington
- University of New Mexico
- Richard L. Pyle
- Arcot Rajasekar
- University of California, San Diego
- Omar J. Reichman
- University of California, Santa Barbara
- Mark P. Schildhauer
- University of California, Santa Barbara
- David Sledge
- University of New Mexico
- Rod Spears
- University of Kansas
- Aimee Stewart
- University of Kansas
- David Stockwell
- University of California, San Diego
- Katharine N. Suding
- University of California, Irvine
- Amy Sundermier
- Arizona State University
- Jing Tao
- University of California, Santa Barbara
- Dave Thau
- University of California, Davis
- Joana Trajkova
- University of Kansas
- Srinivas Vadrevu
- Arizona State University
- Paul Valentich-Scott
- Santa Barbara Museum of Natural History
- David A. Vieglais
- University of Kansas
- Ferdinando Villa
- University of Vermont
- Jenny Wang
- University of California, San Diego
- Evan Weiher
- University of Wisconsin, Eau Claire
- Richard J. Williams
- University of California, Santa Barbara
- Jianting Zhang
- University of New Mexico
- Bing Zhu
- University of California, San Diego
- Daniel Zinn
- University of California, Davis
Products
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Journal Article / 2003
A modeling and execution environment for distributed scientific workflows
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Journal Article / 2004
A web service composition and deployment framework for scientific workflows [abstract]
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Journal Article / 2004
Kepler: An extensible system for design and execution of scientific workflows
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Journal Article / 2004
Kepler: Towards a grid enabled system for scientific workflows
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Book Chapter / 2005
A framework for the design and reuse of grid workflows
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Journal Article / 2003
Evaluating predictive models of species' distributions: Criteria for selecting optimal models
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Journal Article / 2007
Enabling knowledge-based software engineering through semantic object-relational mappings
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Journal Article / 2007
Ontologies, javabeans and relational databases for enabling semantic linking
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Journal Article / 2004
Incremental validation of xml documents
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Journal Article / 2008
Accessing and using sensor data within the Kepler scientific workflow system
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Journal Article / 2005
Incorporating semantics in scientific workflow authoring
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Journal Article / 2009
Improving data discovery in metadata repositories through semantic search
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Journal Article / 2002
Report on the EDBT'2002 panel on scientific data integration
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Journal Article / 2003
Towards a generic framework for semantic registration of scientific data
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Journal Article / 2004
An ontology-driven framework for data transformation in scientific workflows
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Journal Article / 2004
Incremental navigation: Providing simple and generic access to heterogeneous structures
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Journal Article / 2004
On integrating scientific resources through semantic registration
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Journal Article / 2005
Actor-oriented design of scientific workflows
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Journal Article / 2005
Data procurement for enabling scientific workflows: On exploring inter-ant parasitism
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Journal Article / 2005
Towards automatic generation of semantic types in scientific workflows
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Journal Article / 2006
A calculus for propagating semantic annotations through scientific workflow queries
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Presentations / 2006
A model for user-oriented data provenance in pipelined scientific workflows
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Presentations / 2006
Enabling scientific workflow reuse through structured composition of dataflow and control-flow
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Journal Article / 2006
Using the uni-level description (uld) to support data-model interoperability
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Journal Article / 2007
Project histories: Managing data provenance across collection-oriented scientific workflow runs
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Journal Article / 2008
A conceptual modeling framework for expressing observational data semantics
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Journal Article / 2008
Kepler/ppod: Scientific workflow and provenance support for assembling the tree of life
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Journal Article / 2008
Provenance in collection-oriented workflows
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Journal Article / 2005
The role of visual tools in a web application design and verification framework: A visual notation for LTL formulae
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Journal Article / 2007
CyberInfrastructure for the analysis of ecological acoustic sensor data: A use case study in grid deployment
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Journal Article / 2008
Scale-dependent responses of plant biodiversity to nitrogen enrichment
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Journal Article / 2008
Concept relationship editor: A visual interface to support the assertion of synonymy relationships between taxonomic classifications
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Journal Article / 2005
NSF long term ecological research sites praxis et theoria - LTER information management and CS research
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Journal Article / 2007
Provenance in scientific workflow systems
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Journal Article / In Press
A dynamic surrogate model of global landslide distribution
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Journal Article / 2004
Specification and verification of data-driven web services
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Journal Article / 2005
A verifier for interactive, data-driven web applications
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Journal Article / 2005
Rewriting queries using views with access patterns under integrity constraints
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Journal Article / 2006
Verification of communicating, data-driven web services
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Journal Article / 2007
Rewriting queries using views with access patterns under integrity constraints
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Journal Article / 2005
Making technology work for scientists
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Journal Article / 2006
Designing annotation mechanisms with users in mind: A paper prototyping case study from the scientific environment for ecological knowledge (SEEK)
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Journal Article / 2007
Group usability testing: Evolution in usability techniques
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Journal Article / 2009
Bridging the gap between technology and science with examples from ecology and biodiversity
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Journal Article / 2004
Network structure and robustness of marine food webs
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Journal Article / 2005
On the lack of good scientific reasons for the growing phylogeny/classification gap
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Journal Article / 2007
On the use of taxonomic concepts in support of biodiversity research and taxonomy
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Journal Article / 2009
Towards a language for mapping relationships among taxonomic concepts
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Journal Article / 2002
Biodiversity information organization using taxonomy (BIOT)
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Journal Article / 2003
Ontology-based user profiles for search and browsing
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Journal Article / 2004
Improving ontology-based user profiles
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Journal Article / 2006
Semi-automatic update of existing taxonomy using text mining
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Journal Article / 2009
Training a hierarchical classifier using inter document relationships
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Journal Article / 2004
Data, schema and ontology integration
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Book Chapter / 2004
Data, schema, ontology, and logic integration
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Journal Article / 2004
Ontology, society, and ontotheology
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Journal Article / 2004
Three perspectives on information integration
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Journal Article / 2005
Data, schema, ontology, and logic integration
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Journal Article / 2005
Information integration in institutions
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Journal Article / 2005
What is a concept?
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Journal Article / 2005
Extending taxonomic visualisation to incorporate synonymy and structural markers
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Journal Article / 2006
Visual comparison and exploration of natural history collections
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Journal Article / 2007
Exploring multiple trees through DAG representations
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Journal Article / 2007
Visual exploration of alternative taxonomies through concepts
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Journal Article / 2008
Visualisation to aid biodiversity studies through accurate taxonomic reconciliation
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Journal Article / 2004
Predicting invasions of North American basses in Japan using native range data and a genetic algorithm
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Journal Article / 2004
Predicting distributions of Mexican mammals using ecological niche modeling
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Journal Article / 2005
A scientific workflow approach to distributed geospatial data processing using web services
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Journal Article / 2007
A metadata-driven framework for generating field data entry interfaces in ecology
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Journal Article / 2001
Managing scientific metadata
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Journal Article / 2006
The new bioinformatics: Integrating ecological data from the gene to the biosphere
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Journal Article / 2007
Meta-information systems and ontologies: A special feature from ISEI'06
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Journal Article / 2005
Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration
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Journal Article / 2006
A standard data model representation for taxonomic information
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Journal Article / 2005
Towards an ontology-based visual query system
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Book Chapter / 2005
Towards the paradigm of an ontology-based user interface: From simple knowledge maps to graphical query languages
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Book Chapter / 2006
On visualization of OWL ontologies
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Journal Article / 2007
GrOWL: A tool for visualization and editing of OWL ontologies
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Journal Article /
Action ontologies, natural actions and interactions
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Journal Article / 2008
Using metadata for loading and querying heterogeneous scientific data
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Journal Article / 2010
A metadata-driven approach to loading and querying heterogeneous scientific data
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Journal Article / 2004
Distribution of members of Anopheles quadrimaculatus Say s.l. (Diptera: Culicidae) and implications for their roles in malaria transmission in the United States
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Journal Article / 2004
Geographic and ecologic distributions of the anopheles gambiae complex predicted using a genetic algorithm
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Journal Article / 2003
A system for semantic integration of geologic maps via ontologies [abstract]
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Journal Article / 2005
ANNA: A new prediction method for bioassessment programs
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Book Chapter / 2003
A model-based mediator system for scientific data management
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Journal Article / 2003
Compiling abstract scientific workflows into web service workflows
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Journal Article / 2004
Web service composition through declarative queries: The case of conjunctive queries with union and negation [abstract]
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Journal Article / 2006
Managing scientific data: from data integration to scientific workflows
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Journal Article / 2006
Scientific workflow management and the kepler system
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Journal Article / 2006
Scientific workflows: More e-science mileage from cyberinfrastructure
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Journal Article / 2006
Scientific workflows: Towards a new synthesis for information integration
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Journal Article / 2008
From computation models to models of provenance: The RWS approach
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Book Chapter / 2009
Scientific workflows
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Journal Article / 2007
An ontology for describing and synthesizing ecological observation data
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Journal Article / 2008
Advancing ecological research with ontologies
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Journal Article / 2006
Long-term preservation of large-scale multimedia collections: A digital workflow approach
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Journal Article / 2004
Ecological niches as stable distributional constraints on mammal species, with implications for Pleistocene extinctions and climate change projections for biodiversity
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Journal Article / 2004
Evolution of seasonal ecological niches in the Passerina buntings (aves: cardinalidae)
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Journal Article / 2005
An approach for pipelining nested collections in scientific workflows
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Journal Article / 2006
Collection-oriented scientific workflows for integrating and analyzing biological data
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Journal Article / 2008
Scientific workflow design for mere mortals
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Journal Article / 2005
Data integration and workflow solutions for ecology
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Journal Article / 2005
SEEK: Data integration and workflow solutions for ecology
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Journal Article / 2006
Meta-information concepts for ecological data management
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Journal Article / 2007
A knowledge environment for the biodiversity and ecological sciences
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Journal Article / 2006
Storage resource broker global data grids
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Journal Article / 2004
Seasonal niches of nearctic-neotropical migratory birds: Implications for the evolution of migration
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Journal Article / 2002
A metadata integration assistant generator for heterogeneous distributed databases
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Journal Article / 2003
A metadata tool for retrievalfrom heterogeneous distributed XML documents
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Journal Article / 2004
Processing first-order queries with limited access patterns
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Journal Article / 2004
Processing unions of conjunctive queries with negation under limited access patterns
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Journal Article / 2008
Flexible scientific workflow modeling using frames, templates, and dynamic embedding
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Journal Article / 2004
Modeling current and future potential wintering distributions of eastern North American monarch butterflies
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Journal Article / 2003
Geographic scale effects on ecological distributions of Mexican birds
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Journal Article / 2003
Predicting the potential invasive distribution for Eupatorium adenophorum Spreng. in China
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Journal Article / 2005
Cyberinfrastructure for grassland biodiversity studies
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Journal Article / 2005
The EcoGrid and the Kepler workflow system: a new platform for conducting ecological analyses
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Journal Article / 2006
Representing the dimensions of an ecological niche
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Journal Article / 2007
Computer-supported collaborative knowledge modeling in ecology
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Book Chapter / 2007
Ecological niche modeling using the kepler workflow system
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Journal Article / 2007
Exploratory modeling of forest disturbance scenarios in central Oregon using computational experiments in GIS
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Journal Article / 2007
Supporting large-scale science with workflows
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Journal Article / 2008
Cross-disciplinary collaboration and learning
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Journal Article / 2008
Indirectly driven knowledge modeling in ecology
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Journal Article / 2008
Transforming scientists through technical education - a view from the trenches
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Journal Article /
Collaborative research teams as dynamic distributed cognitive systems
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Journal Article / 2003
A global distributed biodiversity information network: Building the world museum
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Journal Article / 2003
Assessment of invasive potential of Homalodisca coagulata in western North America and South America
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Journal Article / 2003
Lutzomyia vectors for cutaneous leishmaniasis in southern Brazil: Ecological niche models, predicted geographic distributions, and climate change effects
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Journal Article / 2003
Migratory birds modeled as critical transport agents for west nile virus in North America
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Journal Article / 2003
New distributional modeling approaches for gap analysis
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Journal Article / 2003
Niche differentiation in Mexican birds: Using point occurrences to detect ecological innovation
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Journal Article / 2003
Predicting the geography of species' invasions via ecological niche modeling
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Journal Article / 2003
Predicting the potential invasive distributions of four alien plant species in North America
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Journal Article / 2003
Projected climate change effects on Rocky Mountain and Great Plains birds: Generalities of biodiversity consequences
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Journal Article / 2003
Using ecological-niche modeling to predict barred owl invasions with implications for spotted owl conservation
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Book Chapter / 2004
Climate change effects on species and biodiversity
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Journal Article / 2004
Detecting errors in biodiversity data based on collectors' itineraries
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Journal Article / 2004
Ecological and geographic distribution of filovirus disease
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Journal Article / 2004
Modeled climate change effects on distributions of Canadian butterfly species
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Journal Article / 2004
Potential geographic distribution of Anoplophora glabripennis (Coleoptera: Cerambycidae) in North America
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Journal Article / 2004
Using epidemiological survey data to infer geographic distributions of leishmania vector species
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Journal Article / 2004
West nile virus in the new world: Potential impacts on bird species
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Journal Article / 2005
Kansas gap analysis: The importance of validating distributional models before using them
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Book Chapter / 2005
Modeling distributional shifts of individual species and biomes
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Journal Article / 2007
Workflow automation for processing plasma fusion simulation data
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Journal Article / 2003
Data grids, collections and grid bricks
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Journal Article / 2003
Storage resource broker managing distributed data in a grid
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Journal Article / 2004
Data grid federation
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Journal Article / 2005
Accessing sensor data using meta data: A virtual object ring buffer framework
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Journal Article / 2005
Digital preservation lifecycle management for multi-media collections
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Journal Article / 2006
Building a demonstration prototype for the preservation of large-scale multimedia collections
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Journal Article / 2003
Predicting distributions of known and unknown reptile species in Madagascar
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Journal Article / 2003
Ecological niche differentiation in the Aphelocoma jays: A phylogenetic perspective
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Journal Article / 2004
SEAMFRAME: a proposal for an integrated modelling framework for agricultural systems
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Journal Article / 2005
Modelling Framework (SeamFrame) requirements
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Journal Article / 2005
Overall architectural design of SeamFrame
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Journal Article / 2005
Semantic links in integrated modelling frameworks
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Journal Article / 2008
Integrated modelling frameworks for environmental assessment and decision support
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Journal Article / 2005
A coming of age
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Journal Article / 2005
Creating and providing data management services for the biological and ecological sciences: Science environment for ecological knowledge
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Journal Article / 2005
Informatics training lab opens at LNO
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Journal Article /
Differences in natural and social scientists assessments of the philosophic nature of uncertainty and the implications for the communication of global climate change
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Journal Article /
The nature of disagreements between natural and social scientists during discussions of global climate change
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Journal Article / 2003
Consequences of global climate change for geographic distributions of Cerrado Tree species
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Journal Article / 2004
Biodiversity informatics: Managing and applying primary biodiversity data
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Journal Article / 2003
Comparison of resolution of methods used in mapping biodiversity patterns from point occurrence data
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Journal Article / 2003
Informatics issues in integrated biodiversity resource archives: Problems and solutions
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Journal Article / 2005
Biomonitoring, phylogenetics and anomaly aggregation systems
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Journal Article / 2006
Improving ecological niche models by data mining large environmental datasets
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Journal Article / 2006
Reconstruction of past climate using series with red noise
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Journal Article / 2006
The use of the GARP genetic algorithm and Internet grid computing in the Lifemapper world atlas of species biodiversity
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Journal Article / 2007
Reasoning about taxonomies in first-order logic
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Journal Article / 2008
Merging taxonomies under RCC-5 algebraic articulations
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Journal Article / 2008
Reasoning about taxonomies and articulations
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Journal Article / 2004
Biodiversity conservation: Uncertainty in predictions of extinction risk/Effects of changes in climate and land use/Climate change and extinction risk (reply)
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Journal Article / 2004
Extinction risk from climate change
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Book Chapter / 2007
Information management standards and strategies for net primary production data
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Journal Article / 2005
Convergence among integrated modeling frameworks
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Journal Article / 2006
ROADNET: A Real-time Data Aware System for Earth, Oceanographic, and Environmental Applications
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Book Chapter / 2004
Performance and goodness of fit of complex simulation models: A multi-criteria approach to model calibration using the Model Performance Index (MPI) framework
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Journal Article / 2005
A semantic model of computation for natural system modelling
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Journal Article / 2005
Book review: H.G. Natke, introduction to multi-disciplinary model building
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Journal Article / 2005
Design of the domain manager component of SEAMFRAME
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Journal Article / 2005
Guidelines for populating the SEAMLESS knowledge base
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Journal Article / 2005
Setting the basis for a worldwide coordination for the economic valuation of ecosystem services
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Journal Article / 2006
Declarative modelling for architecture independence and data/model integration: A case study
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Journal Article / 2007
An ontology for the semantic modelling of natural systems
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Journal Article / 2007
A semantic framework and software design to enable the transparent integration, reorganization and discovery of natural systems knowledge
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Journal Article / 2007
The SEAMLESS knowledge manager
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Journal Article / 2009
Modelling with knowledge: A review of emerging semantic approaches to environmental modelling
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Journal Article /
Semantically-driven databases: Towards machine-assisted knowledge discovery
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Journal Article /
Thinklab: An infrastructure for semantic decision support systems
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Journal Article /
Towards a coordinated strategy to facilitate and oversee a transparent practice of ecosystem services valuation
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Journal Article / 2003
A simple mass storage system for the SRB data grid
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Journal Article / 2004
Critical points for interactive schema matching
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Journal Article / 2008
A high-level distributed execution framework for scientific workflows
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Journal Article / 2003
Niche modeling and geographic range predictions in the marine environment using a machine-learning algorithm
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Book Chapter / 2004
Biodiversity and the Internet: Building and using the virtual world museum
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Journal Article / 2005
Using web services and scientific workflow for species distribution prediction modeling
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Journal Article / 2005
Validating compositions of geospatial processing web services in a scientific workflow environment
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Journal Article / 2006
Ontology-driven composition and validation of scientific grid workflows in Kepler: A case study of hyperspectral image processing
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Journal Article / 2006
Opening the black box of feature extraction: Incorporating visualization into high-dimensional data mining processes
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Journal Article / 2006
PhyloMiner: A tool for evolutionary data analysis
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Journal Article / 2006
Tracking dynamics of geospatial phenomena in distributed and heterogeneous environments using scientific workflow and web services technologies
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Journal Article / 2007
GBD-Explorer: Extending open source java GIS for exploring ecoregion-based biodiversity data
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Journal Article / 2007
Performance evaluations of geospatial web services composition and invocation
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Journal Article / 2008
X-CSR: Dataflow optimization for XML processing pipelines