Journal of Intelligent Information Systems

, Volume 29, Issue 1, pp 111–126 | Cite as

A knowledge environment for the biodiversity and ecological sciences

  • William K. Michener
  • James H. Beach
  • Matthew B. Jones
  • Bertram Ludäscher
  • Deana D. Pennington
  • Ricardo S. Pereira
  • Arcot Rajasekar
  • Mark Schildhauer
Article

Abstract

The Science Environment for Ecological Knowledge (SEEK) is a knowledge environment that is being developed to address many of the current challenges associated with data accessibility and integration in the biodiversity and ecological sciences. The SEEK information technology infrastructure encompasses three integrated systems: (1) EcoGrid—an open architecture for data access; (2) a Semantic Mediation System based on domain-specific ontologies; and (3) an Analysis and Modeling System that supports semantically integrated analytical workflows. Multidisciplinary scientists and programmers from multiple institutions comprise the core development team. SEEK design and development are informed by three multidisciplinary teams of scientists organized in Working Groups. The Biodiversity and Ecological Analysis and Modeling Working Group informs development through evaluation of SEEK efficacy in addressing biodiversity and ecological questions. The Knowledge Representation Working Group provides knowledge representation requirements from the domain sciences and develops the corresponding knowledge representations (ontologies) to support the assembly of analytical workflows in the Analysis and Modeling System, and the intelligent data and service discovery in the EcoGrid. A Biological Classification and Nomenclature Working Group investigates solutions to mediating among multiple taxonomies for naming organisms. A multifaceted education, outreach and training program ensures that the SEEK research products, software, and information technology infrastructure optimally benefit the target communities.

Keywords

Analytical workflow Data grid Ecoinformatics Ecological niche model Knowledge environment Semantic mediation Metadata 

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References

  1. Altintas, I., Berkley, C., Jaeger, E., Jones, M., Ludäscher, B., & Mock, S. (2004). Kepler: An extensible system for design and execution of scientific workflows. I. In 16th International Conference on Scientific and Statistical Database Management (SSDBM’04), Santorini Island, Greece (pp. 21–23).Google Scholar
  2. Baru, C., Gupta, A., Ludäscher, B., Marciano, R., Papakonstantinou, Y., Velikhov, P., et al. (1999). XML-based information mediation with MIX. In ACM Intl. Conference on Management of Data (SIGMOD), Philadelphia, PA (pp. 597–599).Google Scholar
  3. Beach, J. H., Pramanik, S., & Beaman, J. H. (1993). Hierarchic taxonomic databases. In R. Fortuner (Ed.), Advances in computer methods for systematic biology (pp. 241–256). Baltimore, MD: The Johns Hopkins University Press.Google Scholar
  4. Berkley, C. (2003). Monarch: Metadata-driven analytical processing. LTER DataBits. Retrieved Spring 2003, from http://intranet.lternet.edu/archives/documents/Newsletters/DataBits/03spring/.
  5. Biron, P., & Malhotra, A. (2001). XML schema part 2: Datatypes. W3C Recommendation. Retrieved May 02, 2001, from http://www.w3.org/TR/xmlschema-2/.
  6. Boucelma, O., Castano, S., Goble, C. A., Josifovski, V., Lacroix, Z., & Ludäscher, B. (2002). Scientific data integration—Report on the EDBT’02 panel. SIGMOD Record, 31(4), 107–112.CrossRefGoogle Scholar
  7. Bowers, S., Lin, K., & Ludäscher, B. (2004). On integrating scientific resources through semantic registration. In 16th International Conference on Scientific and Statistical Database Management (SSDBM’04), Santorini Island, Greece (pp. 21–23).Google Scholar
  8. Bowers, S., & Ludäscher, B. (2004). An ontology-driven framework for data transformation in scientific workflows. In Intl. Workshop on Data Integration in the Life Sciences (DILS’04), Leipzig, Germany.Google Scholar
  9. Brilhante, V., & Robertson, D. S. (2001). Metadata-supported automated ecological modelling. In C. Rautenstrauch & S. Patig (Eds.), Environmental information systems in industry and public administration. Hershey, PA: Idea Group Publishing (http://www.dai.ed.ac.uk/groups/ssp/psfiles/virginia/EnvIS_chap.aw.ps).
  10. Brodaric, B., & Gahegan, M. (2002). Distinguishing instances and evidence of geographical concepts for geospatial database design. In M. J. Egenhofer & D. M. Mark (Eds.), Geographic Information Science, 2nd Intl. Conference (GIScience), number 2478 in LNCS. Boulder, CO: Springer (September). Retrieved from http://link.springer-ny.com/link/service/series/0558/tocs/t2478.htm.
  11. Center for Environmental Studies. (2002). Xanthoria: A distributed query system for XML encoded data. Arizona State University. Retrieved from http://ces.asu.edu/bdi/Subjects/Xanthoria/.
  12. Chaffee, J., & Gauch, S. (2000). Personal ontologies for web navigation. In Ninth International Conference on Information and Knowledge Management (CIKM 2000) (pp. 227–234).Google Scholar
  13. Fonseca, F., Martin, J., & Rodreguez, M. A. (2002). From geo- to eco-ontologies. In M. J. Egenhofer & D. M. Mark (Eds.), Geographic Information Science, 2nd Intl. Conference (GIScience), number 2478 in LNCS. Boulder, CO: Springer (http://link.springer-ny.com/link/service/series/0558/tocs/t2478.htm).
  14. Garcia-Molina, H., Papakonstantinou, Y., Quass, D., Rajaraman, A., Sagiv, Y., Ullman, J., et al. (1997). The TSIMMIS approach to mediation: Data models and languages. Journal of Intelligent Information Systems, 8(2), 117–132.CrossRefGoogle Scholar
  15. Gauch, S. (2002). Biodiversity Information Organization using Taxonomy (BIOT). In Proc. of the National Conference on Digital Government Research, Los Angeles, CA (pp. 169–174).Google Scholar
  16. Graham, M., Watson, M., & Kennedy, J. (2002). Novel visualisation techniques for working with multiple, overlapping classification hierarchies. Taxon, 51(2), 351–358.CrossRefGoogle Scholar
  17. Gupta, A., Ludäscher, B., & Martone, M. E. (2002). Registering scientific information sources for semantic mediation. In 21st Intl. Conference on Conceptual Modeling (ER), LNCS 2503, Tampere, Finland (pp. 182–198). Berlin Heidelberg New York: Springer.Google Scholar
  18. Halevy, A. (2001). Answering queries using views: A survey. VLDB Journal, 10(4), 270–294 (http://link.springer.de/link/service/journals/00778/bibs/1010004/10100270.htm).Google Scholar
  19. Jones, M. B., Berkley, C., Bojilova, J., & Schildhauer, M. (2001). Managing scientific metadata. IEEE Internet Computing, 5(5), 59–68.CrossRefGoogle Scholar
  20. Khoral. (2002). Khoros Pro 2001 integrated development environment. Retrieved from http://www.khoral.com/.
  21. Knowledge Network for Biocomplexity. (2003). Retrieved from http://knb.ecoinformatics.org/.
  22. Lee, E. A. (2001). Overview of the Ptolemy project. Technical memorandum UCB/ERL M01/11. University of California, Berkeley, CA.Google Scholar
  23. Levy, A. Y. (1999). Logic-based techniques in data integration. In J. Minker (Ed.), Workshop on logic-based artificial intelligence. Washington, DC, College Park, MD.Google Scholar
  24. London e-Science Centre (2003). Discovery net. Imperial College of London. Retrieved from http://www.lesc.ic.ac.uk/projects/dnet.html.
  25. Long Term Ecological Research Network (2003). The U.S. long term ecological research network. Retrieved from http://www.lternet.edu/.
  26. Ludäscher, B., Altintas, I., & Gupta, A. (2003). Compiling abstract scientific workflows into web service workflows. In 15th Intl. Conference on Scientific and Statistical Database Management (SSDBM), Boston, MA.Google Scholar
  27. Ludäscher, B., Gupta, A., & Martone, M. E. (2001). Model-based mediation with domain maps. In 17th Intl. Conf. on Data Engineering (ICDE), Heidelberg, Germany.Google Scholar
  28. Ludäscher, B., Gupta, A., & Martone, M. E. (2003). A model-based mediator system for scientific data management. In T. Critchlow & Z. Lacroix (Eds.), Bioinformatics: Managing scientific data. San Mateo, CA: Morgan Kaufmann.Google Scholar
  29. Ludäscher, B., Papakonstantinou, Y., & Velikhov, P. (2000). Navigation-driven evaluation of virtual mediated views. In Intl. Conference on Extending Database Technology (EDBT), LNCS 1777, Konstanz, Germany (pp. 150–165). Berlin Heidelberg New York: Springer.Google Scholar
  30. Manola, F., & Miller, E. (2003). RDF primer, W3C working draft. Retrieved from http://www.w3.org/TR/rdf-primer/.
  31. MDL Information Systems, Inc. (2003). Pipeline pilot. Retrieved from http://www.mdli.com/products/pipelinepilot.html.
  32. Michener, W. K., Brunt, J. W., Helly, J. J., Kirchner, T. B., & Stafford, S. G. (1997). Nongeospatial metadata for the ecological sciences. Ecological Applications, 7(1), 330–342.CrossRefGoogle Scholar
  33. Natural Resource and Ecology Lab. (2003). CENTURY soil organic matter model v. 5. Colorado State University. Retrieved from http://www.nrel.colostate.edu/projects/century5/.
  34. Open Source Development Network. (2003). Distributed Generic Info Retrieval (DiGIR). Retrieved from http://sourceforge.net/projects/digir/.
  35. Open Source Initiative. (2003). Retrieved from http://www.opensource.org/.
  36. Organization of Biological Field Stations. (2003). Retrieved from http://www.obfs.org/.
  37. Partnership for Interdisciplinary Studies of Coastal Oceans. (2002). Retrieved from http://www.piscoweb.org/.
  38. Paton, N. W., Khan, S. A., Hayes, A., Moussouni, F., Brass, A., Eilbeck, K., et al. (2000). Conceptual modelling of genomic information. Bioinformatics, 16(6), 548–557.CrossRefGoogle Scholar
  39. Peet, R. K. (2002). The VegBank taxonomic datamodel. NBII All-Node Meeting. Davis, CA. Retrieved from http://www.bio.unc.edu/faculty/peet/pubs/NBII_Taxa.ppt.
  40. Peim, M., Franconi, E., Paton, N. W., & Goble, C. A. (2002). Query processing with description logic ontologies over object-wrapped databases. In 14th Intl. Conference on Scientific and Statistical Database Management (SSDBM), Edinburgh, Scotland. Retrieved from http://www.computer.org/proceedings/ssdbm/1632/16320027abs.htm.
  41. Peterson, A. T., Sanchez-Cordero, V., Soberon, J., Bartley, J., Buddemeier, R. H., & Navarro-Siguenza, A. G. (2001). Effects of global climate change on geographic distributions of Mexican Cracidae. Ecological Modelling, 144, 21–30.CrossRefGoogle Scholar
  42. Peterson, A. T., & Vieglais, D. A. (2001). Predicting species invasions using ecological niche modeling: New approaches from bioinformatics attack a pressing problem. BioScience, 51(5), 363–371.CrossRefGoogle Scholar
  43. Pretschner, A., & Gauch, S. (1999). Ontology-based personalized search. In Proceedings of the Eleventh IEEE International Conference on Tools with Artificial Intelligence (ICTAI ’99), Chicago IL (pp. 391–398).Google Scholar
  44. Pullan, M. R., Watson, M., Kennedy, J., Raguenaud, C., & Hyam, R. (2000). The Prometheus taxonomic model: A practical approach to representing multiple classifications. Taxon, 49, 55–75.CrossRefGoogle Scholar
  45. Pundt, H., & Bishir, Y. (2002). Domain ontologies for data sharing—An example from environmental monitoring using field GIS. Computers & Geosciences, 28(1), 95–102 (http://dx.doi.org/10.1016/S0098-3004(01)00018-8).
  46. Raguenaud, D., Graham, M., & Kennedy, J. (2001). Two approaches to representing multiple overlapping classifications: A comparison, 13th international conference on scientific and statistical database management -SSDBM 2001 (pp. 239–244). Fairfax, Virginia: George Mason University.Google Scholar
  47. Raguenaud, C., & Kennedy, J. (2002). Multiple overlapping classifications: Issues and solutions. In J. Kennedy (Ed.), 14th International conference on scientific and statistical database management—SSDBM 2002, Edinburgh, Scotland (pp. 77–86).Google Scholar
  48. Raguenaud, D., Kennedy, J., & Barclay, P. (2000). The Prometheus database for taxonomy. In O. Gunther & J. Lenz-H. (Eds.), 12th International Conference on Scientific and Statistical Database Management, SSDBM 2000, Berlin, Germany (pp. 250–252).Google Scholar
  49. Raguenaud, C., Pullan, M. R., Watson, M., Kennedy, J., Newman, M., & Barclay, P. (2002). Implementation of the Prometheus taxonomic model: A comparison of database systems. Taxon, 51(1), 131–142.CrossRefGoogle Scholar
  50. San Diego Supercomputer Center. (2002). Storage resource broker. Retrieved from http://www.npaci.edu/dice/srb/.
  51. Sheth, A. (1998). Changing focus on interoperability in information systems: From system, syntax, structure to semantics. In M. Goodchild, M. Egenhofer, R. Fegeas, & C. Kottman (Eds.), Interoperating geographic information systems (pp. 5–30). Kluwer (http://lsdis.cs.uga.edu/lib/1998.html.
  52. Stockwell, D. R. B., & Noble, I. R. (1992). Induction of sets of rules from animal distribution data: A robust and informative method of data analysis. Math and Computers in Simulation, 33, 385–390.CrossRefGoogle Scholar
  53. Stockwell, D. R. B., & Peters, D. (1999). The GARP modeling system: Problems and solutions to automated spatial prediction. International Journal of Geographic Information Science, 13, 143–158.CrossRefGoogle Scholar
  54. University of California Natural Reserve System. (2003). Retrieved from http://nrs.ucop.edu/default.htm.
  55. University of Kansas Center for Research. (2002). Desktop GARP (Genetic Algorithm for Ruleset Production). Retrieved from http://www.lifemapper.org/desktopgarp/.
  56. Uschold, M., & Gruninger, M. (1996). Ontologies: Principles, methods, and applications. Knowledge Engineering Review, 11(2), 93–155 (http://citeseer.nj.nec.com/uschold96ontologie.html).
  57. van Harmelen, F., Hendler, J., Horrocks, I., McGuinness, D. L., Patel-Schneider, P. F., & Stein, L. A. (2003). OWL web ontology language reference W3C working draft. Retrieved March 31, 2003, from http://www.w3.org/TR/owl-ref/.
  58. Wiederhold, G. (1992). Mediators in the architecture of future information systems. IEEE Computer, 25(3), 38–49.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • William K. Michener
    • 1
  • James H. Beach
    • 2
  • Matthew B. Jones
    • 3
  • Bertram Ludäscher
    • 4
  • Deana D. Pennington
    • 1
  • Ricardo S. Pereira
    • 5
  • Arcot Rajasekar
    • 4
  • Mark Schildhauer
    • 3
  1. 1.Biology Department, LTER Network OfficeUniversity of New MexicoAlbuquerqueUSA
  2. 2.Biodiversity Research CenterUniversity of KansasLawrenceUSA
  3. 3.National Center for Ecological Analysis and SynthesisSanta BarbaraUSA
  4. 4.San Diego Supercomputer CenterUniversity of California, San DiegoSan DiegoUSA
  5. 5.Natural History Museum and Biodiversity Research CenterUniversity of KansasLawrenceUSA

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