A knowledge environment for the biodiversity and ecological sciences

Journal of Intelligent Information Systems

Volumn 29, Issue 1, 2007, Pages 111-126

  Michener, William K ^a   Beach, James H ^b   Jones, Matthew B ^c   Ludäscher, Bertram ^d   Pennington, Deana D ^a   Pereira, Ricardo S ^b   Rajasekar, Arcot ^d   Schildhauer, Mark ^c  

^a UNIVERSITY OF NEW MEXICO   (United States)

^b UNIVERSITY OF KANSAS   (United States)

^c NATIONAL CENTER FOR ECOLOGICAL ANALYSIS AND SYNTHESIS   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

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

Indexed keywords

BIODIVERSITY; INFORMATION TECHNOLOGY; METADATA; ONTOLOGY; SEMANTIC WEB;

ANALYTICAL WORKFLOW; DATA GRID; ECOINFORMATICS; ECOLOGICAL NICHE MODEL;

KNOWLEDGE ENGINEERING;

EID: 34547843520     PISSN: 09259902     EISSN: 15737675     Source Type: Journal    
DOI: 10.1007/s10844-006-0034-8     Document Type: Article

References (58)

1. Atentas, 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).
2. Baru, C., Gupta, A., Ludäscher, B., Marciano, R., Papakonstantinou, Y., Velikhov, P., et al. (1999). XMLbased information mediation with MIX. In ACM. Intl. Conference on Management of Data (SIGMOD), Philadelphia, PA (pp. 597-599).
3. Beaeh, J. H., Pramanik, S., & Beaman, J. H. (1993). Hierarchic taxonomie databases. In R. Fortuner (Ed.), Advances in computer methods for systematic biology (pp. 241-256). Baltimore, MD: The Johns Hopkins University Press.
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 schemapart 2: Datatypes. W3CRecommendation. 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.
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).
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.
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).
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://l.ink.springer-ny.com/link/servi.ce/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.
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).
16. Graham, M., Watson, M., & Kennedy, J. (2002). Novel visualisation, techniques for working with multiple, overlapping classification, hierarchies. Taxon, 51(2), 351-358.
17. Gupta, A., Ludäscher, B., & Marione, 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.
18. Halevy, A. (2001). Answering queries using views: A. survey. VLDB Journal, 10(4), 270-294 (http://link. srjringer.de/link/service/journals/ 00778/bibs/1010004/10100270.htm).
19. Jones, M. B., Berkley, C., Bojilova, J., & Schildhauer, M. (2001). Managing scientific metadata. IEEE Internet Computing, 5(5), 59-68.
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.
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.
24. London e-Science Centre (2003). Discovery net. Imperial College of London. Retrieved from http://www. lesc.ic.ac.uk/projects/dnet.html.
25. Lng Term Ecological Research Network (2003). The U.S. long term ecological research network. Retrieved from http://www.lternet.edu/.
26. Ludäscher, B., Atentas, 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.
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.
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.
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.
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.
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.
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 ogic 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.
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.
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).
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.
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/S00983004(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.
47. Raguenaud, C., & Kennedy, J. (2002). Multiple overlapping classifications: Issues and solutions. In J. Kennedy (Ed.), 14th International conference on scientific and statistical database managementSSDBM 2002, Edinburgh, Scotland (pp.' 77-86).
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).
49. Raguenaud, C., Pullan, M. R., Watson, M., Kennedy, J., Newman, M., & Barclay, P. (2002). Implementation of the Prometheus taxonomie model: A comparison of database systems. Taxon, 5/(1), 131-142.
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/rib/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.
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.
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., Horroeks, L., McGuinness, D. L., Patel-Sohneider, 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.