SEEK Documents

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SEEK Publications

• Journal and Refereed Publications
• Books Or Other One-time Publications
• Research Abstracts and Conference Papers and Posters
• Teaching Aids
• Software Tools
• White Papers and Reports

Journal and Refereed Publications

• Altintas, I., A. Birnbaum, K. Baldridge, W. Sudholt, M. Miller, C. Amoreira, Y. Potier, and B. Ludäscher. 2005. A Framework for the Design and Reuse of Grid Workflows, Intl. Workshop on Scientific Applications on Grid Computing (SAG'04), LNCS 3458, Springer, 2005
• Altintas, I., C. Berkley, E. Jaeger, M. Jones, B. Ludäscher, S. Mock. 2004. Kepler: An Extensible System for Design and Execution of Scientific Workflows. 16th International Conference on Scientific and Statistical Database Management. IEEE publication number P2146.
• Altintas, I., S. Bhagwanani, D. Buttler, S. Chandra, Z. Cheng, M. Coleman, T. Critchlow, A. Gupta, W. Han, L. Liu, B. Ludäscher, C. Pu, R. Moore,A. Shoshani, and M. Vouk, "A Modeling and Execution Environment for Distributed Scientific Workflows", 15th Intl. Conference on Scientific and Statistical Database Management (SSDBM), Boston, Massachusetts, vol. , (2003), p. . Accepted.
• Anderson, R. P., D. Lew, and A. T. Peterson. 2003. Evaluating predictive models of species' distributions: Criteria for selecting optimal models. Ecological Modelling, 162:211232.
• Balmin. A, Y. Papakonstantinou, V. Vianu: "Incremental Validation of XML Documents." Invited to special issue of ACM Transactions on Database Systems (TODS), to appear. Journal Article.
• Berkley, C., S. Bowers, M. Jones, B. Ludäscher, M. Schildhauer, and J. Tao. 2005. Incorporating Semantics in Scientific Workflow Authoring. 17th International Conference on Scientific and Statistical Database Management. IEEE Computer Society. Accepted.
• Boucelma, O., S. Castano, C. A. Goble, V. Josifovski, Z. Lacroix, and B. Ludäscher, "Report on the EDBT'2002 Panel on Scientific Data Integration", SIGMOD Record, vol. 31(4), (2002), p. 107. Published.
• Bowers S and Delcambre L. 2004. Incremental navigation: Providing simple and generic access to heterogeneous structures. In Proceedings of the 23rd International Conference on Conceptual Modeling (ER),Springer, LNCS, to appear. Research Article.
• Bowers S and Delcambre L. Using the Uni-Level Description (ULD) to Support Data-Model Interoperability. Data and Knowledge Engineering. In press.
• Bowers S and Ludäscher B. 2005. Actor-Oriented Design of Scientific Workflows. In Proceedings of the International Conference on Conceptual Modeling (ER'2005), LNCS, volume 3716, pp. 369-384.
• Bowers S and Ludäscher B. (2004). An ontology-driven framework for data transformation in scientific workflows. In Proceedings of the International Workshop on Data Integration in the Life Sciences (DILS), Springer, LNCS, volume 2994.
• Bowers S and Ludäscher B. 2005. Towards Automatic Generation of Semantic Types in Scientific Workflows. In Proceedings of the International Workshop on Scalable Semantic Web Knowledge Base Systems (SSWS), WISE 2005 Workshop Proceedings, LNCS, volume 3807, pp. 207-216.
• Bowers S, B Ludäscher, AHH Ngu, T Critchlow. Enabling Scientific Workflow Reuse through Structured Composition of Dataflow and Control-Flow. In IEEE Workshop on Workflow and Data Flow for Scientific Applications (SciFlow), 2006, accepted.
• Bowers S, B Ludäscher. A Calculus for Propagating Semantic Annotations through Scientific Workflow Queries. In Query Languages and Query Processing (QLQP), 2006, accepted.
• Bowers S, Lin K, and Ludäscher B. (2004). On integrating scientific resources through semantic registration. In Proceedings of the 16th International Conference on Scientific and Statistical Database Management (SSDBM), IEEE Computer Society.
• Bowers, S and Ludäscher B. (2003). Towards a generic framework for semantic registration of scientific data. In Proceedings of the Workshop on Semantic Web Technologies for Searching and Retrieving Scientific Data, CEUR Workshop Proceedings, volume 83, ISSN 16130073.
• Bowers, S, Thau D, Williams R, and Ludäscher B. (2004). Data procurement for enabling scientific workflows: On exploring interant parasitism. In Proceedings of the 2nd International Workshop on Semantic Web and Databases (SWDB), co-located with VLDB04, Springer, LNCS, to appear.
• Brambilla M, Deutsch A, Sui L, Vianu V. 2005. The Role of Visual Tools in a Web Application Design and Verification Framework: A Visual Notation for LTL Formulae. 5th International Conference on Web Engineering (ICWE), 557-568.
• Cushing, J., K. Vanderbilt, J. Brunt, M. Jones, A. Gupta, P. McCartney. 2005. NSF Long Term Ecological Research Sites Praxis et Theoria – LTER Information Management & CS Research. 17th International Conference on Scientific and Statistical Database Management. IEEE Computer Society. Accepted.
• Day, T and DRB Stockwell, (in press). A dynamic surrogate model of global landslide distribution. Earth Surface Processes.
• Deutsch Alin, Liying Sui, Victor Vianu, Dayou Zhou. 2006. A System for Specification and Verification of Interactive, Data-driven Web Applications. Demo at SIGMOD Conference 2006.
• Deutsch Alin, Liying Sui, Victor Vianu, Dayou Zhou. 2006. Verification of communicating, data-driven web services. Proceedings of the Twenty-fifth ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems (PODS).
• Deutsch Alin, Liying Sui, Victor Vianu. 2004. Specification and Verification of Data-driven Web Services. Proceedings of the Twenty-third ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems (PODS) 2004: 71-82. Journal version invited to special issue of the Journal of Computer and Systems Science (JCSS), accepted.
• Deutsch Alin, Monica Marcus, Liying Sui, Victor Vianu, Dayou Zhou. 2005. A Verifier for Interactive, Data-Driven Web Applications. Proceedings of the ACM SIGMOD International Conference on Management of Data, 2005: 539-550.
• Deutsch, A., B. Ludäscher, and A. Nash. 2005. Rewriting Queries Using Views with Access Patterns Under Integrity Constraints. Intl. Conference on Database Theory (ICDT'05), Edinburgh, Scotland, January 2005.
• Deutsch, A., L. Sui, V. Vianu. Specification and Verification of Data-Driven Web Services. Invited to special issue of J. of Computer and Systems Science (JCSS) (submitted, under review).
• Frank, E., Altintas, I., Zhang, J., Ludaescher, B., Pennington, D., and Michener, W., 2005, A scientific workflow approach to distributed geospatial data processing using web services. Proceedings of the 17th International Scientific and Statistical Database Management Conference (SSDBM 2005), June 27-29, 2005, University of California, Santa Barbara, pp. 87-90.
• Franz, N. M. 2005. On the lack of good scientific reasons for the growing phylogeny/classification gap. Cladistics 21: 495-500.
• Franz, N. M., R. K. Peet & A. S. Weakley. 2006. On the use of taxonomic concepts in support of biodiversity research and taxonomy. To appear in the Proceedings of the New Taxonomy Symposium. (in press).
• Gauch S and Chandramouli A. Semi-Automatic Update of Existing Taxonomy using Text Mining. 5th International Conference on Ecological Informatics ISEI5, December 4-7, 2006, Santa Barbara, USA, (accepted).
• Gauch S, Ranganathan S, Chandramouli A. Training a Hierarchical Classifier using Inter-Document Relationships. ACM Trans. on Information Systems, (under review).
• Gauch, S. and J. Trajkova. 2004. Improving Ontology-Based User Profiles. RIAO 2004, University of Avignon (Vaucluse), France, April 26-28, pp. 380-389.
• Gauch, Susan, Jason Chaffee, and Alexander Pretschner. 2003. "Ontology-Based User Profiles for Search and Browsing", User Modeling and User-Adapted Interaction: The Journal of Personalization Research, Special Issue on User Modeling for Web and Hypermedia Information Retrieval. Submitted.
• Goguen, J. 2004. Three Perspectives on Information Integration. In Proceedings, Seminar 04391, Semantic Interoperability and Integration, Schloss Dagstuhl, Germany, September 2024, 2004. Published.
• Goguen, J. 2005. What is a Concept? In Proceedings, 13th International Conference on Conceptual Structures (ICCS '05), edited by Frithjof Dau and MarieLaure Mungier, Springer Lecture Notes in Artificial Intelligence, Volume 3596, pages 5277. Published.
• Graham, M. and Kennedy, J. 2005. Extending Taxonomic Visualisation to Incorporate Synonymy and Structural Markers. Information Visualization, 4(3), 206-223.
• Graham, M., Kennedy, J. and Downey L. 2006. Visual Comparison and Exploration of Natural History Collections. To appear in, Advanced Visual Interfaces (AVI) 2006. Venice, Italy: ACM Press.
• Iguchi, K., K. Matsuura, K. McNyset, A. T. Peterson, R. Scachetti Pereira, K. A. Powers, D. A. Vieglais, E. O. Wiley, and T. Yodo. 2005. Predicting invasions of North American basses in Japan using native range data and a genetic algorithm. Transactions of the American Fisheries Society. In press.
• Illoldi, P., V. Sanchez-Cordero, and A. T. Peterson. 2005. Predicting distributions of Mexican mammals using ecological niche modeling. Journal of Mammalogy, in press.
• Jones, M.B., M. Schildhauer, O.J. Reichman, and S. Bowers. 2006 (In press) The new bioinformatics: integrating ecological data from the gene to the biosphere. Annual Review of Ecology, Evolution, and Systematics.
• Kennedy, J., Hyam, R., Kukla, R. and Paterson, T. 2006. A Standard Data Model Representation for Taxonomic Information. To appear in OMICS: A Journal of Integrative Biology.
• Kennedy, J., Kukla, R. and Paterson, T. 2005. Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration. in Proceedings of the 2nd International Workshop on Data Integration in the Life Sciences. San Diego, USA: Lecture Notes in Computer Science, Volume 3615, Aug 2005, Pages 80 – 95.
• Krivov S., F. Villa, Action Ontologies, Natural Actions and Interactions ; submitted to Journal of Logic and Computation http://www.uvm.edu/~skrivov/ic.pdf
• Krivov S., R. Williams, F. Villa, X.Wu, A Visualization Model for the Languages of Semantic Web ; submitted to Information Visualization http://www.uvm.edu/~skrivov/SWVL.pdf
• Krivov S., R. Williams, F. Villa. 2006. GrOWL, visual browser and editor for OWL ontologies. Journal of Web Semantics: Science, Services and Agents on the World Wide Web. In press.
• Krivov, S., 2005. Villa, F. Towards the paradigm of an ontology-based user interface: from simple knowledge maps to graphical query languages. 2nd International Workshop on Data Integration in the Life Sciences, University of California, San Diego, July 20-22, 2005.
• Krivov, S., Villa, F. 2005. Towards an ontology-based query system. In: Ludascher, B., Raschid, L., (Eds) Data Integration in Life Sciences, Lecture Notes in Computer Science, 3615: 313-316, Springer.
• Levine, R. S., A. T. Peterson, and M. Q. Benedict. 2004b. Geographic and ecologic distributions of the Anopheles gambiae complex predicted using a genetic algorithm. American Journal of Tropical Medicine & Hygiene, 70:105109.
• Levine, R. S., M. Q. Benedict, and A. T. Peterson. 2004a. Distribution of Anopheles quadrimaculatus Say s.l. and implications for its role in malaria transmission in the US. Journal of Medical Entomology, 41:607613.
• Linke, S., Norris, R.H., Faith, D.P. and Stockwell, D. 2005. ANNA: A new prediction method for bioassessment programs. Freshwater Biology 50:1, 147.
• Ludäscher B, K Lin, S Bowers, E Jaeger-Frank, B Brodaric, C Baru. Managing Scientific Data: From Data Integration to Scientific Workflows In GSA Today, Special Issue on Geoinformatics, 2006.
• Ludäscher, B., I. Altintas, A. Gupta, "Compiling Abstract Scientific Workflows into Web Service Workflows", 15th Intl. Conference on Scientific and Statistical Database Management (SSDBM), Boston, Massachussets, vol. , (2003), p. . Accepted
• Ludäscher, B., I. Altintas, C. Berkley, D. Higgins, E. Jaeger-Frank, M. Jones, E. Lee, J. Tao, Y. Zhao. 2005. Scientific Workflow Management and the Kepler System, In Concurrency and Computation: Practice & Experience, Special Issue on Scientific Workflows, to appear, 2005.
• Ludäscher, B., K. Lin, S. Bowers, E. Jaeger-Frank, B. Brodaric, and C. Baru. 2005. Managing Scientific Data: From Data Integration to Scientific Workflows. In GSA Today, Special Issue on Geoinformatics, 2005.
• Martínez-Meyer, E., A. T. Peterson, and A. G. Navarro-Sigenza. 2004b. Evolution of seasonal ecological niches in the Passerina buntings (Aves: Cardinalidae). Proceedings of the Royal Society B, 271:11511157.
• Martínez-Meyer, E., A. T. Peterson, and W. W. Hargrove. 2004a. Ecological niches as stable distributional constraints on mammal species, with implications for Pleistocene extinctions and climate change projections for biodiversity. Global Ecology and Biogeography, 13:305314.
• McPhillips TM and Bowers S. 2005. An Approach for Pipelining Nested Collections in Scientific Workflows. SIGMOD Record, 34(3):12—17.
• McPhillips TM, S Bowers, B Ludaescher, S Cohen, SB Davidson. A Model for User-Oriented Data Provenance in Pipelined Scientific Workflows. In International Provenance and Annotation Workshop (IPAW) 2006, accepted.
• Michener W, J Beach, S Bowers, L Downey, M Jones, B Ludaescher, D Pennington, A Rajasekar, S Romanello, M Schildhauer, D Vieglais, J Zhang. 2005. SEEK: Data Integration and Workflow Solutions for Ecology. In Proceedings of the Workshop on Data Integration in the Life Sciences (DILS'2005), LNCS, volume 3615, pp. 321-324.
• Michener, W. 2006. Meta-information concepts for ecological data management. Ecological Informatics 1:3-7.
• Michener, W., J. Beach, M. Jones, B. Ludäscher, D. Pennington, R. Pereira, A. Rajasekar, and M. Schildhauer. 2004. A Knowledge Environment for the Biodiversity and Ecological Sciences, Journal of Intelligent Information Systems. In press.
• Michener, W., J. Beach, S. Bowers, L. Downey, M. Jones, B. Ludäscher, D. Pennington, A. Rajasekar, S. Romanello, M. Schildhauer, D. Vieglais, and J. Zhang. 2005. Data Integration and Workflow Solutions for Ecology. 2nd International Workshop on Data Integration in the Life Sciences, 2005, LNCS, to appear.
• Michener, W., OJ Reichman, J. Beach, M. Jones, B. Ludäscher, A. Rajasekar, M. Schildhauer, S. Bowers, D. Pennington, S. Romanello. 2005. Creating and Providing Data Management Services for the Biological and Ecological Sciences: Science Environment for Ecological Knowledge. 17th International Conference on Scientific and Statistical Database Management. IEEE Computer Society. Accepted.
• Nakazawa, Y., A. T. Peterson, E. Martinez-Meyer, and A. G. Navarro-Sigenza. 2004. Seasonal niches of NearcticNeotropical migratory birds: Implications for the evolution of migration. Auk, 121:610618.
• Nash. A and B. Ludäscher. Processing First-Order Queries with Limited Access Patterns. In ACM Symposium on Principles of Database Systems (PODS), Paris, France, June 2004. Research Article.
• Nash. A and B. Ludäscher. Processing Unions of Conjunctive Queries with Negation under Limited Access Patterns. In Intl. Conference on Extending Database Technology (EDBT), 2004. Research Article
• Oberhauser, K. S., and A. T. Peterson. 2004. Modeling current and future potential wintering distributions of eastern North American monarch butterflies. Proceedings of the National Academy of Sciences USA, 100:1406314068.
• Ortega-Huerta, M. A., and A. T. Peterson. 2005. Effects of geographic scale on analyzing associations between regional habitats and distribution patterns of Mexican birds. Anales del Instituto de Biologia, U.N.A.M. In press.
• Papes, M., and A. T. Peterson. 2003. Predicting the potential invasive distribution for Eupatorium adenophorum Spreng. in China. Journal of Wuhan Botanical Research, 21:137142.
• Pennington D, D Higgins, AT Peterson, MB Jones, B Ludaescher, S Bowers. Ecological Niche Modeling Using the Kepler Workflow System. Workflows for eScience: Scientific Workflows for Grids, Chapter 8, Springer, to appear.
• Pennington, D. and Michener, W.K. in press?, The EcoGrid and the Kepler Workflow System: a new platform for conducting ecological analyses. ESA Bulletin (Emerging Technologies).
• Pennington, D., Zhang, J., Altintas, I., et al. submitted?, Grid-enabled scientific analysis and modeling using the Kepler Workflow System. International Journal of Geographic Information Science.
• Peterson, A. T. 2003a. Predicting the geography of species' invasions via ecological niche modeling. Quarterly Review of Biology, 78:419433.
• Peterson, A. T. 2003b. Projected climate change effects on Rocky Mountain and Great Plains birds: Generalities of biodiversity consequences. Global Change Biology, 9:647655.
• Peterson, A. T. 2004a. Climate change effects on species and biodiversity. In R. Ragaini (ed.), International Seminar on Nuclear War and Planetary Emergencies, 30th Session, pp. 5968. World Scientific, New Jersey.
• Peterson, A. T. 2005c. Kansas Gap Analysis: The importance of validating distributional models before using them. Southwestern Naturalist. In press.
• Peterson, A. T., A. G. Navarro-Sigenza, and R. S. Pereira. 2004c. Detecting errors in biodiversity data based on collectors' itineraries. Bulletin of the British Ornithologists' Club, 124:143151.
• Peterson, A. T., and C. R. Robins. 2003. Using ecological-niche modeling to predict Barred Owl invasions with implications for Spotted Owl conservation. Conservation Biology, 17:11611165.
• Peterson, A. T., and D. A. Kluza. 2003. New distributional modeling approaches for Gap Analysis. Animal Conservation, 6:4754.
• Peterson, A. T., and J. J. Shaw. 2003. Lutzomyia vectors for cutaneous leishmaniasis in southern Brazil: Ecological niche models, predicted geographic distributions, and climate change effects. International Journal of Parasitology, 33:919931.
• Peterson, A. T., and R. D. Holt. 2003. Niche differentiation in Mexican birds: Using point occurrences to detect ecological innovation. Ecology Letters, 6:774782.
• Peterson, A. T., D. A. Vieglais, A. G. Navarro-Sigenza, and M. Silva. 2003g. A global distributed biodiversity information network: Building the world museum. Bulletin of the British Ornithologists' Club, 123A:186196.
• Peterson, A. T., D. A. Vieglais, and J. Andreasen. 2003f. Migratory birds as critical transport vectors for West Nile Virus in North America. Vector Borne and Zoonotic Diseases, 3:3950.
• Peterson, A. T., E. Martinez-Meyer, and C. GonzlezSalazar. 2004b. Reconstructing the Pleistocene geography of the Aphelocoma jays (Corvidae). Diversity and Distributions, 10:237246.
• Peterson, A. T., E. Martinez-Meyer, C. Gonzlez-Salazar, and P. Hall. 2005d. Modeled climate change effects on distributions of Canadian butterfly species. Canadian Journal of Zoology. In press.
• Peterson, A. T., J. T. Bauer, and J. N. Mills. 2004a. Ecological and geographic distribution of filovirus disease. Emerging Infectious Diseases, 10:4047.
• Peterson, A. T., M. Papes, and D. A. Kluza. 2003d. Predicting the potential invasive distributions of four alien plant species in North America. Weed Science, 51:863 868.
• Peterson, A. T., N. Komar, O. Komar, A. G. Navarro-Sigenza, M. B. Robbins, and E. Martinez-Meyer. 2005c. West Nile Virus in the New World: Potential impacts on bird species. Bird Conservation International. In press.
• Peterson, A. T., R. S. Pereira, and V. L. Fonseca de Camargo-Neves. 2004d. Using epidemiological survey data to infer geographic distributions of leishmania vector species. Revista da Sociedade Brasileira de Medicina Tropical, 37:1014.
• Peterson, A. T., R. S. Pereira, and D. A. Kluza. 2003e. Assessment of invasive potential of Homalodisca coagulata in western North America and South America. Biota Neotropica, 3:Online journal: http://www.biotaneotropica.org.br/v3n1/pt/abstract?article+BN00703012003.
• Peterson, A. T., R. S. Pereira, and W. W. Hargrove. 2004e. Potential geographic distribution of Anoplophora glabripennis (Coleoptera: Cerambycidae) in North America. American Midland Naturalist, 151:170178.
• Rajasekar, Arcot, Michael Wan and Reagan Moore, Arun Jagatheesan, and George Kremenek, "Real-life Experiences with Data Grids: Case Studies in using the SRB", The 6th International Conference on High Performance Computing (HPCAsia2002) Bangalore, India, December 1619, 2002, vol. , (2002), p. . Published
• Rajasekar, Arcot, Michael Wan, Reagan Moore, George Kremenek,and Tom Guptill, "Data Grids, Collections and Grid Bricks", 20th IEEE/ 11th NASA Goddard Conference on Mass Storage Systems & Technologies (MSST2003) San Diego, California, April 710, 2003, vol. , (2003), p. . Published
• Rajasekar, Arcot, Michael Wan, Reagan Moore, Wayne Schroeder, George Kremenek, Arun Jagatheesan, Charles Cowart, Bing Zhu, SheauYen Chen, Roman Olschanowsky. 2003. Storage Resource Broker Managing Distributed Data in a Grid. Computer Society of India Journal, Special Issue on SAN, Vol. 33, No. 4, pp. 4254.
• Raxworthy, C. J., E. Martinez-Meyer, N. Horning, R. A. Nussbaum, G. E. Schneider, M. A. Ortega-Huerta, and A. T. Peterson. 2003. Predicting distributions of known and unknown reptile species in Madagascar. Nature, 426:837841.
• Rice, N. H., E. Martinez-Meyer, and A. T. Peterson. 2003. Ecological niche differentiation in the Aphelocoma jays: A phylogenetic perspective. Biological Journal of the Linnaean Society, 80:369383.
• Romanello, S. 2005. Natural and Social Scientist Perceptions of Uncertainty: A Study Informed by Sense-Making Methodology. Paper presented at a non-divisional workshop held at the meeting of the International Communication Association, New York City.
• Romanello, S., Dervin, B., Fortner, F. and Heimlich, J. Submitted. Differences in natural and social scientists’ assessments of the philosophic nature of uncertainty and the implications for the communication of global climate change. Climatic Change.
• Romanello, S., Dervin, B., Fortner, F. and Heimlich, J. Submitted. The nature of disagreements between natural and social scientists during discussions of global climate change. Global Environmental Change.
• Siqueira, M. F. d., and A. T. Peterson. 2003. Global climate change consequences for cerrado tree species. Biota Neotropica, In press.
• Soberon, J., and A. T. Peterson. 2004. Biodiversity informatics: Managing and applying primary biodiversity data. Philosophical Transactions of the Royal Society of London B, 359:689698.
• Stockwell D.R.B. (in review) Sources and sizes of biases in estimated extinctions from models of species' ranges shifted by warming.
• Stockwell, D. R. B., and A. T. Peterson. 2003. Comparison of resolution of methods used in mapping biodiversity patterns from point occurrence data. Ecological Indicators, 3:213-221.
• Stockwell, D.R.B. 2006. Reconstruction of past climate using series with red noise. Australian Institute of Geologists News, 83: pp14.
• Stockwell, D.R.B. and Wang J.T.L., Biomonitoring, Phylogenetics and Anomaly Aggregation Systems, Lecture Notes in Computer Science, Volume 3495, Apr 2005, Pages 523-529.
• Stockwell, David R.B. 2006. Improving ecological niche models by data mining large environmental datasets. Ecological Modelling 192: 188–196.
• Stockwell, David R.B., James H. Beach, Aimee Stewart, Gregory Vorontsov, David Vieglais, Ricardo Scachetti Pereira, "Lifemapper an Internet computing application for biodiversity science", Ecological Modelling, In press.
• Stockwell, David, Oliver Ryder, and Philippe Youkharibac, "Informatics Issues in Integrated Biodiversity Resource Archives: problems and solutions", Environmental Informatics, vol. , (), p. . Submitted
• Thomas, C. D., A. Cameron, R. E. Green, M. Bakkenes, L. J. Beaumont, Y. C. Collingham, B. F. N. Erasmus, M. Ferreira de Siqueira, A. Grainger, L. Hannah,L. Hughes, B. Huntley, A. S. Van Jaarsveld, G. E. Midgely, L. Miles, M. A. Ortega-Huerta, A. T. Peterson, O. L. Phillips, and S. E. Williams. 2004a.Extinction risk from climate change. Nature, 427:145148.
• Thomas, C. D., S. E. Williams, A. Cameron, R. E. Green, M. Bakkenes, L. J. Beaumont,Y. C. Collingham, B. F. N. Erasmus, M. Ferreira de Siqueira, A. Grainger, L.Hannah, L. Hughes, B. Huntley, A. S. Van Jaarsveld, G. F. Midgely, L. Miles, M.A. Ortega-Huerta, A. T. Peterson, and O. L. Phillips. 2004b. Thomas et al. reply. Nature, 430:12.
• Vanderbilt, K. and W. K. Michener. In press. Information management standards and strategies for net primary production data. Pages - in Fahey, T. and A. Knapp (eds.) Standard Net Primary Production Research Methods. Oxford University Press.
• Vianu. V, XML: From Practice to Theory. SBBD 2003, 1125. Research Article.
• Villa, F. 2004. A semantic framework and software design to enable the transparent integration, reorganization and discovery of natural systems knowledge. Journal of Intelligent Information Systems. In press.
• Villa, F. 2005. Book review: H.G. Natke, Introduction to Multi-Disciplinary Model Building. Ecological Economics 53 (3): 431-432.
• Villa, F. Creating the enabling infrastructure for Integrated Digital Collaboratories: technologies and case studies. Being submitted to Environmental Modelling and Software.
• Villa, F. Semantically-driven ecological modelling and knowledge discovery: previewing the Ecoinformatics innovation. Ecological Modelling.
• Villa, F., Ceroni, M., Krivov, S. Intelligent databases enable transparent and sound economic valuation of ecosystem services. Environmental Management.
• Villa, F., Krivov, S. Semantically-driven databases: towards machine-assisted knowledge discovery. Environmental Modelling and Software.
• Wiley, E. O., K. M. McNyset, A. T. Peterson, C. R. Robins, and A. M. Stewart. 2003. Niche modeling and geographic range predictions in the marine environment using a machine-learning algorithm. Oceanography, 16:120127.
• YoungKwang Nam, Joseph Goguen, and Guilian Wang, "A Metadata IntegrationAssistant Generator for Heterogeneous Distributed Databases", Proceedings, 16th Conference on Ontologies, DataBases, and Applications of Semantics for Large Scale Information Systems, Springer, Lecture Notes in Computer Science, vol. 2519, (2002), p. 1332. Published
• YoungKwang Nam, Joseph Goguen, and Guilian Wang., "A Metadata Tool for Retrievalfrom Heterogeneous Distributed XML Documents", Proceedings, InternationalConference on Computational Science, Springer, Lecture Notes in Computer Science, vol. , (2003), p. . Accepted.
• Zhang Sen, Katherine G. Herberty Jason T. L. Wangz William H. Pielx, David R. B. Stockwell, (accepted) PhyloMiner: A Tool for Evolutionary Data Analysis, 18th International Conference on Scientific and Statistical Database Management, July 3-5, 2006, Vienna, Austria.

Books Or Other One-time Publications

• Gauch, Susan, "Biodiversity Information Organization using Taxonomy (BIOT)" , bibl. Los Angeles, CA, May 20 � 28, 2002, pp. 169174, (2002). Proceedings Published of Collection: , "Proc. Of the National Conference on Digital Government Research".
• Goguen Joseph. Data, Schema and Ontology Integration. In Proceedings, CombLog'04 Workshop. Lisbon, 2830 July 2004. http://www.cs.ucsd.edu/~goguen/pps/lisbon04.pdf
• Goguen, J. 2004. Ontology, Society, and Ontotheology. In Formal Ontology in Information Systems, edited by Achille Varzi and Laure Vieu, IOS Press, pages 95103, 2004. Proceedings of Conference on Formal Ontology in Information Systems (FOIS'04). Published.
• Goguen, J. 2005. Data, Schema, Ontology, and Logic Integration. In "Combining Logics", book edited by Walter Carnielli, Miguel Dionisio, and Paulo Mateus. Springer Verlag. Accepted.
• Goguen, J.. 2005. Information Integration in Institutions. Jon Barwise Memorial Volume, edited by Larry Moss. Indiana University Press. Accepted.
• Ludäscher, B., A. Gupta, and M. E. Martone, "A ModelBased Mediator System for Scientific Data Management" , bibl. Morgan Kaufmann, (2003). Book Accepted of Collection: T. Critchlow and Z. Lacroix, "Bioinformatics: Managing Scientific Data".
• Peterson, A. T., H. Tian, E. Martinez-Meyer, B. Huntley, J. Sober�n, and V. S�nchez Cordero. 2005f. Modeling distributional shifts of individual species and biomes. In T. E. Lovejoy and L. Hannah (eds.), Biodiversity and Climate Change. Yale University Press, New Haven, Conn.
• Rizzoli, A.E., M. Donatelli, R. Muetzelfeldt, T. Otjens, M.G.E. Svensson, F. van Evert, F. Villa, J. Bolte. 2004. SEAMFRAME: a proposal for an integrated modelling framework for agricultural systems. In: SEJacobsen, C.R. Jensen, J.R. Porter, Proceedings of the VII ESA Congress European Agriculture in a Global Context. KVL Copenhagen, Denmark, 1115 July 2004. ISBN 8776110621, pp 331332.
• Villa, F., Voinov, A. Fitz, C. Costanza, R. 2004. Performance and goodness of fit of complex simulation models: a multi-criteria approach to model calibration using the Model Performance Index (MPI) framework. Pp. 77-118 in: Costanza, R., Voinov, A. (eds): Landscape Simulation Modelling: a Spatially Explicit, Dynamic Approach.. Springer-Verlag, New York, 330pp.
• Wang Guilian, Joseph Goguen, YoungKwang Nam, and Kai Lin. Critical Points for Interactive Schema Matching. In Advanced Web Technologies and Applications, edited by Jeffrey Xu Yu, Xuemin Lin, Hongjun Lu and YanChun Zhang, Springer Lecture Notes in Computer Science, volume 3007, 2004, pages 654664. Proceedings of Sixth Asia Pacific Web Conference, Hangzhou, China, 1417 April 2004.
• Wiley, E. O., and A. T. Peterson. 2004. Biodiversity and the Internet: Building and using the virtual world museum. In A. Scharl (ed.), Environmental Online Communication, pp. 9199. SpringerVerlag, London.
• Zhang, J., Pennington, D., and Michener, W.K., 2006, Automatic Transformation from Geospatial Conceptual Workflow to Executable Workflow Using GRASS GIS Command Line Modules in Kepler, 1st International Workshop on Workflow systems in e-Science (WSES), Reading, UK, May 2006, to appear in Lecture Notes in Computer Science (), Springer, pp. ()
• Zhang, J., Pennington, D., Michener, W.K., 2005. Using web services and scientific workflow for species distribution prediction modeling, 6th International Conference on Web-Age Information Management (WAIM), Hangzhou, China, October 2005, Lecture Notes in Computer Science 3739, Springer, pp. 610-617. ISBN: 3-540-29227-6.

Research Abstracts and Conference Papers and Posters

• Altintas I, C. Berkley, E. Jaeger, M. Jones, B. Ludäscher, and S. Mock. Kepler: Towards a Grid Enabled System for Scientific Workflows. In Workshop on Workflow in Grid Systems, GlobalGrid Forum (GGF10), Berlin, Germany, March 2004. Research Abstract.
• Altintas. I, E. Jaeger, K. Lin, B. Ludäscher, and A. Memon. A Web Service Composition and Deployment Framework for Scientific Workflows. In 2nd Intl. Conference on Web Services (ICWS), San Diego, California, July 2004. Research Abstract.
• Downey, L. 2005. "Making Technology Work for Scientists". LTER Network News, Vol 18, No 1, Spring 2005.
• Jones, M.B., "SEEK EcoGrid: integrating data and computational resources for ecology", DataBits: An electronic newsletter for Information Managers, vol. Spring, (2003), p. . Published
• Lin. K and B. Ludäscher. A System for Semantic Integration of Geologic Maps via Ontologies. In Semantic Web Technologies for Searching and Retrieving Scientific Data (SCISW), Sanibel Island, Florida, 2003. Research Abstract.
• Ludäscher. B and A. Nash. Web Service Composition Through Declarative Queries: The Case of Conjunctive Queries with Union and Negation. In 20th Intl. Conf. on Data Engineering (ICDE), 2004. Research Abstract.
• Michener, William K., "Building SEEK: the Science Environment for Ecological Knowledge ", DataBits: An electronic newsletter for Information Managers, vol. Spring, (2003), p. . Published
• Pennington, D., 2005, Cyberinfrastructure for grassland biodiversity studies. The Network News, a publication of the Long Term Ecological Research (LTER) Network, Spring 2005.
• Rizzoli, A.E., Villa, F., Semantic Links in Model Components for Integrated Modelling Frameworks. 2005. Proceedings MODSIM 05, Melbourne, Australia, December 2005.
• Romanello, S 2005. A coming of age. LTER Network News, Winter, 2005. http://www.lternet.edu/news/Article57.html
• Romanello, S. 2005. Informatics training lab opens at LNO. LTER Network News, Spring 2005. http://www.lternet.edu/news/Article17.html
• Romanello, S. 2005. KNB data management tools workshop. LTER Databits: Information Management Newsletter of Long-Term Ecological Research, Spring 2005. http://intranet.lternet.edu/archives/documents/Newsletters/DataBits/05spring/
• VanEvert, F., Rizzoli, A.E, Svensson, M., Villa, F. 2005. Convergence among integrated modeling frameworks. Proceedings MODSIM 05, Melbourne, Australia, December 2005.
• Villa, F. 2005. A semantic model of computation for natural system modelling. Proceedings MODSIM 05, Melbourne, Australia, December 2005.
• Villa, F., Donatelli, M., Rizzoli, A.E., Krause. P. 2006. Declarative modelling for architecture independence and data/model integration: a case study. Accepted for IEMSS06 Summit on Environmental Modelling, Burlington, VT, July 2006.
• Zhang, J., Pennington, D., and Michener, W.K., 2005, Validating Compositions of Geospatial Processing Web Services in a Scientific Workflow Environment, the 3rd IEEE International Conference on Web Services (ICWS), Orlando, FL, July 2005, pp. 821-822. ISBN 0-7695-2409-5.

Teaching aids

• Ludäscher, B., I. Altintas, A. Gupta, and K. Lin, Scientific Data Integration and Mediation . Tutorial at the NPACI All Hands Meeting, San Diego, 2003. Available at: http://www.sdsc.edu/~ludaesch/Paper/ahm03datamediation.ppt
• Ludäscher, B. CSE291: Ontologies in Data Integration, graduate class, Department of Computer Science & Engineering, University of California, San Diego, Spring 2003. Available at: http://www.sdsc.edu/~ludaesch/CSE291Spring03/

Software tools

• Altintas, I., C. Berkley, S. Bowers, M. Brooke, C. Brooks, Z. Cheng, T. Fricke, D. Higgins, E. Jaeger, M. Jones, E. Lee, B. Ludäscher, T. McPhillips, W. Sudholt, J. Tao, M. Vouk, X. Xin, and Y. Zhao. Kepler: a system for scientific workflows. Release 1.0.0alpha1 through 1.0.0alpha9, and 1.0.0beta1. Available at "http://kepler-project.org/". Kepler is SEEK's multi-platform, open-source scientific workflow editing and execution system and Grid access (data and compute services) application. Kepler is a multi-institutional, multidisciplinary development effort.
• Gales, R. L. and A. M. Stewart, 2004. Software?. Taxonomic Object Service Version 1.0. Includes a taxonomic concept resolution interface that is publicly accessible from the web and a variety of clients (perl, python, java). This is an integrated product of the SEEK/taxon working group. The software is available from the SEEK CVS server and is distributed under an open source license. The service is accessible as a web service: http://seek.ittc.ku.edu:9080/TaxObjServ/services/TaxonomicObjectService?wsdl
• Krivov S., F. Villa, and R. Williams. 2004. GrOWL. An open source, extensible Java framework for graphical browsing and editing of OWLDL knowledge bases. Among its applications, it will constitute the ontology interface for SEEK's analysis and modeling environment (Kepler). Available in the SEEK Concurrent Version System (http://cvs.ecoinformatics.org under "seek/projects/kr sms/ontobrowser").
• Kukla, R. and J. Kennedy. 2004. Software?. SEEK Taxonomic Concept Schema. Kukla, R. and J. Kennedy. 2004. SEEK Taxonomic Schema. Being submitted for consideration as a standard by the Taxonomic Data Working Group (TDWG). http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/seek/projects/taxon/schemas/seek_napier.xs d?only_with_tag=EdinburghMeeting and http://www.soc.napier.ac.uk/tdwg/index.php?pagename=TheSchema
• Liu X., R. K. Peet, N.M. Franz, and L.L. Downey. 2006. ConceptMapper. ConceptMapper is a desktop tool to assist taxonomists to relate taxonomic concepts from one classification to another and to manage taxonomic concept metadata that precisely define taxonomic concepts. Database schema has been developed to hold taxonomic concept data, including scientific names, concept references, character and specimen circumscription information, parent-child relationships and third-party assertions that relate concepts between different classifications. Concept data stored in the database can be retrieved, visualized and changed through the ConceptMapper user interface. Main functions include importing , exporting, querying and viewing concept data, adding and editing relationships, concepts, references and specimens. Some other features include relationship expression validation, redo/undo support and preference settings. A help document is also developed and embedded with the tool to offer background information and usage guidance. ConceptMapper can be used by taxonomists to manage their data, especially in creating mappings across multiple classifications. It can also be used by those who need to know more about taxa in data interpretation and analysis as a convenient concept exploring tool. The ConceptMapper installation program can be downloaded from: http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/seek/projects/taxon/conceptmapper/setup.zip
• Villa, F. 2004. Integrating Modelling Architecture (IMA). An ontology-driven modeling architecture that provides separation between the declaration of data and models and their visualization and execution, allowing enough semantic richness to enable arbitrary composition of models with automatic enforcement of semantic integrity and automated mediation between different representations and scales. It provides a base of concepts and algorithms for translation of formally specified conceptual descriptions of natural entities and their spatiotemporal contexts into generic executable workflows. IMA is an open source project (Integrating Modelling Toolkit) hosted at the Sourceforge community portal: http://sf.net/projects/imt.
• Villa, F. ThinkCap: a collaborative knowledge portal toolkit. 2006. Web page: http://ecoinformatics.uvm.edu/technologies/thinkcap.html

White Papers and Reports

• Rizzoli, A., Athanasiadis, I., Donatelli, M. Huber, D., Muetzelfeldt, R., van Evert, F., van de Broek M., van der Wal, T., Villa. F. Overall architectural design of SeamFrame. Refereed European Union report 7, Ref.: D5.3.1,December 2005.
• Rizzoli, A., Svensson, M., Rowe, E., Donatelli, M., Muetzelfeldt, R., van der Wal, T., van Evert, F., Villa, F. Modelling Framework (SeamFrame) requirements. . Refereed European Union report Report 6, Ref.: PD5.2.2,December 2005
• Villa, F. 2005. Design of the Domain Manager component of SEAMFRAME. Refereed European Union report SEAMLESS PD5.3.2. 54pp.
• Villa, F., Athanasiadis, I. 2005.Guidelines for populating the SEAMLESS knowledge base. Refereed European Union report SEAMLESS PD4.2.1. 20pp.
• Villa, F., Ceroni, M., DeGroot, R. 2005. Setting the basis for a worldwide coordination for the economic valuation of Ecosystem Services. Ecoinformatics Collaboratory White paper.
• Villa, F., Wilson M., Ceroni, M., and Boumans, R. 2004. Developing and applying new ecological and economic tools for the valuation of ecosystem goods and services. Ecoinformatics Collaboratory white paper.