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National Center for Ecological Analysis and Synthesis

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).

SEEK Web site

Working Group Participants

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

  1. Journal Article / 2003

    A modeling and execution environment for distributed scientific workflows

  2. Journal Article / 2004

    A web service composition and deployment framework for scientific workflows [abstract]

  3. Journal Article / 2004

    Kepler: An extensible system for design and execution of scientific workflows

  4. Journal Article / 2004

    Kepler: Towards a grid enabled system for scientific workflows

  5. Book Chapter / 2005

    A framework for the design and reuse of grid workflows

  6. Journal Article / 2003

    Evaluating predictive models of species' distributions: Criteria for selecting optimal models

  7. Journal Article / 2007

    Enabling knowledge-based software engineering through semantic object-relational mappings

  8. Journal Article / 2007

    Ontologies, javabeans and relational databases for enabling semantic linking

  9. Journal Article / 2004

    Incremental validation of xml documents

  10. Journal Article / 2008

    Accessing and using sensor data within the Kepler scientific workflow system

  11. Journal Article / 2005

    Incorporating semantics in scientific workflow authoring

  12. Journal Article / 2009

    Improving data discovery in metadata repositories through semantic search

  13. Journal Article / 2002

    Report on the EDBT'2002 panel on scientific data integration

  14. Journal Article / 2003

    Towards a generic framework for semantic registration of scientific data

  15. Journal Article / 2004

    An ontology-driven framework for data transformation in scientific workflows

  16. Journal Article / 2004

    Incremental navigation: Providing simple and generic access to heterogeneous structures

  17. Journal Article / 2004

    On integrating scientific resources through semantic registration

  18. Journal Article / 2005

    Actor-oriented design of scientific workflows

  19. Journal Article / 2005

    Data procurement for enabling scientific workflows: On exploring inter-ant parasitism

  20. Journal Article / 2005

    Towards automatic generation of semantic types in scientific workflows

  21. Journal Article / 2006

    A calculus for propagating semantic annotations through scientific workflow queries

  22. Presentations / 2006

    A model for user-oriented data provenance in pipelined scientific workflows

  23. Presentations / 2006

    Enabling scientific workflow reuse through structured composition of dataflow and control-flow

  24. Journal Article / 2006

    Using the uni-level description (uld) to support data-model interoperability

  25. Journal Article / 2007

    Project histories: Managing data provenance across collection-oriented scientific workflow runs

  26. Journal Article / 2008

    A conceptual modeling framework for expressing observational data semantics

  27. Journal Article / 2008

    Kepler/ppod: Scientific workflow and provenance support for assembling the tree of life

  28. Journal Article / 2008

    Provenance in collection-oriented workflows

  29. Journal Article / 2005

    The role of visual tools in a web application design and verification framework: A visual notation for LTL formulae

  30. Journal Article / 2007

    CyberInfrastructure for the analysis of ecological acoustic sensor data: A use case study in grid deployment

  31. Journal Article / 2008

    Scale-dependent responses of plant biodiversity to nitrogen enrichment

  32. Journal Article / 2008

    Concept relationship editor: A visual interface to support the assertion of synonymy relationships between taxonomic classifications

  33. Journal Article / 2005

    NSF long term ecological research sites praxis et theoria - LTER information management and CS research

  34. Journal Article / 2007

    Provenance in scientific workflow systems

  35. Journal Article / In Press

    A dynamic surrogate model of global landslide distribution

  36. Journal Article / 2004

    Specification and verification of data-driven web services

  37. Journal Article / 2005

    A verifier for interactive, data-driven web applications

  38. Journal Article / 2005

    Rewriting queries using views with access patterns under integrity constraints

  39. Journal Article / 2006

    Verification of communicating, data-driven web services

  40. Journal Article / 2007

    Rewriting queries using views with access patterns under integrity constraints

  41. Journal Article / 2005

    Making technology work for scientists

  42. Journal Article / 2006

    Designing annotation mechanisms with users in mind: A paper prototyping case study from the scientific environment for ecological knowledge (SEEK)

  43. Journal Article / 2007

    Group usability testing: Evolution in usability techniques

  44. Journal Article / 2009

    Bridging the gap between technology and science with examples from ecology and biodiversity

  45. Journal Article / 2004

    Network structure and robustness of marine food webs

  46. Journal Article / 2005

    On the lack of good scientific reasons for the growing phylogeny/classification gap

  47. Journal Article / 2007

    On the use of taxonomic concepts in support of biodiversity research and taxonomy

  48. Journal Article / 2009

    Towards a language for mapping relationships among taxonomic concepts

  49. Journal Article / 2002

    Biodiversity information organization using taxonomy (BIOT)

  50. Journal Article / 2003

    Ontology-based user profiles for search and browsing

  51. Journal Article / 2004

    Improving ontology-based user profiles

  52. Journal Article / 2006

    Semi-automatic update of existing taxonomy using text mining

  53. Journal Article / 2009

    Training a hierarchical classifier using inter document relationships

  54. Journal Article / 2004

    Data, schema and ontology integration

  55. Book Chapter / 2004

    Data, schema, ontology, and logic integration

  56. Journal Article / 2004

    Ontology, society, and ontotheology

  57. Journal Article / 2004

    Three perspectives on information integration

  58. Journal Article / 2005

    Data, schema, ontology, and logic integration

  59. Journal Article / 2005

    Information integration in institutions

  60. Journal Article / 2005

    What is a concept?

  61. Journal Article / 2005

    Extending taxonomic visualisation to incorporate synonymy and structural markers

  62. Journal Article / 2006

    Visual comparison and exploration of natural history collections

  63. Journal Article / 2007

    Exploring multiple trees through DAG representations

  64. Journal Article / 2007

    Visual exploration of alternative taxonomies through concepts

  65. Journal Article / 2008

    Visualisation to aid biodiversity studies through accurate taxonomic reconciliation

  66. Journal Article / 2004

    Predicting invasions of North American basses in Japan using native range data and a genetic algorithm

  67. Journal Article / 2004

    Predicting distributions of Mexican mammals using ecological niche modeling

  68. Journal Article / 2005

    A scientific workflow approach to distributed geospatial data processing using web services

  69. Journal Article / 2007

    A metadata-driven framework for generating field data entry interfaces in ecology

  70. Journal Article / 2001

    Managing scientific metadata

  71. Journal Article / 2006

    The new bioinformatics: Integrating ecological data from the gene to the biosphere

  72. Journal Article / 2007

    Meta-information systems and ontologies: A special feature from ISEI'06

  73. Journal Article / 2005

    Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration

  74. Journal Article / 2006

    A standard data model representation for taxonomic information

  75. Journal Article / 2005

    Towards an ontology-based visual query system

  76. Book Chapter / 2005

    Towards the paradigm of an ontology-based user interface: From simple knowledge maps to graphical query languages

  77. Book Chapter / 2006

    On visualization of OWL ontologies

  78. Journal Article / 2007

    GrOWL: A tool for visualization and editing of OWL ontologies

  79. Journal Article /

    Action ontologies, natural actions and interactions

  80. Journal Article / 2008

    Using metadata for loading and querying heterogeneous scientific data

  81. Journal Article / 2010

    A metadata-driven approach to loading and querying heterogeneous scientific data

  82. 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

  83. Journal Article / 2004

    Geographic and ecologic distributions of the anopheles gambiae complex predicted using a genetic algorithm

  84. Journal Article / 2003

    A system for semantic integration of geologic maps via ontologies [abstract]

  85. Journal Article / 2005

    ANNA: A new prediction method for bioassessment programs

  86. Book Chapter / 2003

    A model-based mediator system for scientific data management

  87. Journal Article / 2003

    Compiling abstract scientific workflows into web service workflows

  88. Journal Article / 2004

    Web service composition through declarative queries: The case of conjunctive queries with union and negation [abstract]

  89. Journal Article / 2006

    Managing scientific data: from data integration to scientific workflows

  90. Journal Article / 2006

    Scientific workflow management and the kepler system

  91. Journal Article / 2006

    Scientific workflows: More e-science mileage from cyberinfrastructure

  92. Journal Article / 2006

    Scientific workflows: Towards a new synthesis for information integration

  93. Journal Article / 2008

    From computation models to models of provenance: The RWS approach

  94. Book Chapter / 2009

    Scientific workflows

  95. Journal Article / 2007

    An ontology for describing and synthesizing ecological observation data

  96. Journal Article / 2008

    Advancing ecological research with ontologies

  97. Journal Article / 2006

    Long-term preservation of large-scale multimedia collections: A digital workflow approach

  98. Journal Article / 2004

    Ecological niches as stable distributional constraints on mammal species, with implications for Pleistocene extinctions and climate change projections for biodiversity

  99. Journal Article / 2004

    Evolution of seasonal ecological niches in the Passerina buntings (aves: cardinalidae)

  100. Journal Article / 2005

    An approach for pipelining nested collections in scientific workflows

  101. Journal Article / 2006

    Collection-oriented scientific workflows for integrating and analyzing biological data

  102. Journal Article / 2008

    Scientific workflow design for mere mortals

  103. Journal Article / 2005

    Data integration and workflow solutions for ecology

  104. Journal Article / 2005

    SEEK: Data integration and workflow solutions for ecology

  105. Journal Article / 2006

    Meta-information concepts for ecological data management

  106. Journal Article / 2007

    A knowledge environment for the biodiversity and ecological sciences

  107. Journal Article / 2006

    Storage resource broker global data grids

  108. Journal Article / 2004

    Seasonal niches of nearctic-neotropical migratory birds: Implications for the evolution of migration

  109. Journal Article / 2002

    A metadata integration assistant generator for heterogeneous distributed databases

  110. Journal Article / 2003

    A metadata tool for retrievalfrom heterogeneous distributed XML documents

  111. Journal Article / 2004

    Processing first-order queries with limited access patterns

  112. Journal Article / 2004

    Processing unions of conjunctive queries with negation under limited access patterns

  113. Journal Article / 2008

    Flexible scientific workflow modeling using frames, templates, and dynamic embedding

  114. Journal Article / 2004

    Modeling current and future potential wintering distributions of eastern North American monarch butterflies

  115. Journal Article / 2003

    Geographic scale effects on ecological distributions of Mexican birds

  116. Journal Article / 2003

    Predicting the potential invasive distribution for Eupatorium adenophorum Spreng. in China

  117. Journal Article / 2005

    Cyberinfrastructure for grassland biodiversity studies

  118. Journal Article / 2005

    The EcoGrid and the Kepler workflow system: a new platform for conducting ecological analyses

  119. Journal Article / 2006

    Representing the dimensions of an ecological niche

  120. Journal Article / 2007

    Computer-supported collaborative knowledge modeling in ecology

  121. Book Chapter / 2007

    Ecological niche modeling using the kepler workflow system

  122. Journal Article / 2007

    Exploratory modeling of forest disturbance scenarios in central Oregon using computational experiments in GIS

  123. Journal Article / 2007

    Supporting large-scale science with workflows

  124. Journal Article / 2008

    Cross-disciplinary collaboration and learning

  125. Journal Article / 2008

    Indirectly driven knowledge modeling in ecology

  126. Journal Article / 2008

    Transforming scientists through technical education - a view from the trenches

  127. Journal Article /

    Collaborative research teams as dynamic distributed cognitive systems

  128. Journal Article / 2003

    A global distributed biodiversity information network: Building the world museum

  129. Journal Article / 2003

    Assessment of invasive potential of Homalodisca coagulata in western North America and South America

  130. Journal Article / 2003

    Lutzomyia vectors for cutaneous leishmaniasis in southern Brazil: Ecological niche models, predicted geographic distributions, and climate change effects

  131. Journal Article / 2003

    Migratory birds modeled as critical transport agents for west nile virus in North America

  132. Journal Article / 2003

    New distributional modeling approaches for gap analysis

  133. Journal Article / 2003

    Niche differentiation in Mexican birds: Using point occurrences to detect ecological innovation

  134. Journal Article / 2003

    Predicting the geography of species' invasions via ecological niche modeling

  135. Journal Article / 2003

    Predicting the potential invasive distributions of four alien plant species in North America

  136. Journal Article / 2003

    Projected climate change effects on Rocky Mountain and Great Plains birds: Generalities of biodiversity consequences

  137. Journal Article / 2003

    Using ecological-niche modeling to predict barred owl invasions with implications for spotted owl conservation

  138. Book Chapter / 2004

    Climate change effects on species and biodiversity

  139. Journal Article / 2004

    Detecting errors in biodiversity data based on collectors' itineraries

  140. Journal Article / 2004

    Ecological and geographic distribution of filovirus disease

  141. Journal Article / 2004

    Modeled climate change effects on distributions of Canadian butterfly species

  142. Journal Article / 2004

    Potential geographic distribution of Anoplophora glabripennis (Coleoptera: Cerambycidae) in North America

  143. Journal Article / 2004

    Using epidemiological survey data to infer geographic distributions of leishmania vector species

  144. Journal Article / 2004

    West nile virus in the new world: Potential impacts on bird species

  145. Journal Article / 2005

    Kansas gap analysis: The importance of validating distributional models before using them

  146. Book Chapter / 2005

    Modeling distributional shifts of individual species and biomes

  147. Journal Article / 2007

    Workflow automation for processing plasma fusion simulation data

  148. Journal Article / 2003

    Data grids, collections and grid bricks

  149. Journal Article / 2003

    Storage resource broker managing distributed data in a grid

  150. Journal Article / 2004

    Data grid federation

  151. Journal Article / 2005

    Accessing sensor data using meta data: A virtual object ring buffer framework

  152. Journal Article / 2005

    Digital preservation lifecycle management for multi-media collections

  153. Journal Article / 2006

    Building a demonstration prototype for the preservation of large-scale multimedia collections

  154. Journal Article / 2003

    Predicting distributions of known and unknown reptile species in Madagascar

  155. Journal Article / 2003

    Ecological niche differentiation in the Aphelocoma jays: A phylogenetic perspective

  156. Journal Article / 2004

    SEAMFRAME: a proposal for an integrated modelling framework for agricultural systems

  157. Journal Article / 2005

    Modelling Framework (SeamFrame) requirements

  158. Journal Article / 2005

    Overall architectural design of SeamFrame

  159. Journal Article / 2005

    Semantic links in integrated modelling frameworks

  160. Journal Article / 2008

    Integrated modelling frameworks for environmental assessment and decision support

  161. Journal Article / 2005

    A coming of age

  162. Journal Article / 2005

    Creating and providing data management services for the biological and ecological sciences: Science environment for ecological knowledge

  163. Journal Article / 2005

    Informatics training lab opens at LNO

  164. 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

  165. Journal Article /

    The nature of disagreements between natural and social scientists during discussions of global climate change

  166. Journal Article / 2003

    Consequences of global climate change for geographic distributions of Cerrado Tree species

  167. Journal Article / 2004

    Biodiversity informatics: Managing and applying primary biodiversity data

  168. Journal Article / 2003

    Comparison of resolution of methods used in mapping biodiversity patterns from point occurrence data

  169. Journal Article / 2003

    Informatics issues in integrated biodiversity resource archives: Problems and solutions

  170. Journal Article / 2005

    Biomonitoring, phylogenetics and anomaly aggregation systems

  171. Journal Article / 2006

    Improving ecological niche models by data mining large environmental datasets

  172. Journal Article / 2006

    Reconstruction of past climate using series with red noise

  173. Journal Article / 2006

    The use of the GARP genetic algorithm and Internet grid computing in the Lifemapper world atlas of species biodiversity

  174. Journal Article / 2007

    Reasoning about taxonomies in first-order logic

  175. Journal Article / 2008

    Merging taxonomies under RCC-5 algebraic articulations

  176. Journal Article / 2008

    Reasoning about taxonomies and articulations

  177. 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)

  178. Journal Article / 2004

    Extinction risk from climate change

  179. Book Chapter / 2007

    Information management standards and strategies for net primary production data

  180. Journal Article / 2005

    Convergence among integrated modeling frameworks

  181. Journal Article / 2006

    ROADNET: A Real-time Data Aware System for Earth, Oceanographic, and Environmental Applications

  182. 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

  183. Journal Article / 2005

    A semantic model of computation for natural system modelling

  184. Journal Article / 2005

    Book review: H.G. Natke, introduction to multi-disciplinary model building

  185. Journal Article / 2005

    Design of the domain manager component of SEAMFRAME

  186. Journal Article / 2005

    Guidelines for populating the SEAMLESS knowledge base

  187. Journal Article / 2005

    Setting the basis for a worldwide coordination for the economic valuation of ecosystem services

  188. Journal Article / 2006

    Declarative modelling for architecture independence and data/model integration: A case study

  189. Journal Article / 2007

    An ontology for the semantic modelling of natural systems

  190. Journal Article / 2007

    A semantic framework and software design to enable the transparent integration, reorganization and discovery of natural systems knowledge

  191. Journal Article / 2007

    The SEAMLESS knowledge manager

  192. Journal Article / 2009

    Modelling with knowledge: A review of emerging semantic approaches to environmental modelling

  193. Journal Article /

    Semantically-driven databases: Towards machine-assisted knowledge discovery

  194. Journal Article /

    Thinklab: An infrastructure for semantic decision support systems

  195. Journal Article /

    Towards a coordinated strategy to facilitate and oversee a transparent practice of ecosystem services valuation

  196. Journal Article / 2003

    A simple mass storage system for the SRB data grid

  197. Journal Article / 2004

    Critical points for interactive schema matching

  198. Journal Article / 2008

    A high-level distributed execution framework for scientific workflows

  199. Journal Article / 2003

    Niche modeling and geographic range predictions in the marine environment using a machine-learning algorithm

  200. Book Chapter / 2004

    Biodiversity and the Internet: Building and using the virtual world museum

  201. Journal Article / 2005

    Using web services and scientific workflow for species distribution prediction modeling

  202. Journal Article / 2005

    Validating compositions of geospatial processing web services in a scientific workflow environment

  203. Journal Article / 2006

    Ontology-driven composition and validation of scientific grid workflows in Kepler: A case study of hyperspectral image processing

  204. Journal Article / 2006

    Opening the black box of feature extraction: Incorporating visualization into high-dimensional data mining processes

  205. Journal Article / 2006

    PhyloMiner: A tool for evolutionary data analysis

  206. Journal Article / 2006

    Tracking dynamics of geospatial phenomena in distributed and heterogeneous environments using scientific workflow and web services technologies

  207. Journal Article / 2007

    GBD-Explorer: Extending open source java GIS for exploring ecoregion-based biodiversity data

  208. Journal Article / 2007

    Performance evaluations of geospatial web services composition and invocation

  209. Journal Article / 2008

    X-CSR: Dataflow optimization for XML processing pipelines

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