Skip to main content

Database-backed decision trees with application to biological informatics


We describe a mechanism for the identification of biological organisms through the use of enhanced taxonomic keys-decision trees with nodes augmented by property lists that can serve as arguments to web or local services that access databases or other resources about species, specimens, and ecosystems. Authors of these identification schemes can use simple spreadsheet tools to structure the identification abstractions, and middleware renders the resulting trees into many different forms, with the databases possibly discovered and queried at the time an identification is proposed.

This is a preview of subscription content, access via your institution.


  • Apache. (2005, accessed 2005). Welcome to WSIF: Web services invocation framework.

  • Apache Jakarta. (2005, accessed 2005). Tomcat.

  • Brickell, C. D., Baum, B. R., Hetterscheid, W. L. A., Leslie, A. C., McNeill, J., & Trehane, P. et al. (2004). International code of nomenclature for cultivated plants. Leuven, Belgium: International Society for Horticultural Science (ISHS).

    Google Scholar 

  • Dallwitz, M. J. (2000, accessed 2005). A comparison of interactive identification programs.

  • Dallwitz, M. J., Paine, T. A., & Zurcher, E. J. (1993, accessed 2005). User’s guide to the DELTA system: A general system for processing taxonomic descriptions (4th ed.).

  • Diva Project. (2005, accessed 2005). Diva home page.

  • EarLab. (2005). EarLab: A digital warehouse of auditory models and data.

  • Ereshefsky, M. (1991). The units of evolution: Essays on the nature of Species. Cambridge, MA: MIT.

    Google Scholar 

  • Ereshefsky, M. (2001). The poverty of the Linnaean hierarchy a philosophical study of biological taxonomy. Cambridge: Cambridge University Press.

    Google Scholar 

  • Exolab. (2005, accessed 2005). The castor project.

  • Gansner, E. R., & North, S. C. (2000). An open graph visualization system and its applications to software engineering. Software Practice and Experience, 30(10), 1203–1233.

    Article  MATH  Google Scholar 

  • ICBN. (2000). International code of botanical nomenclature (St Louis Code). Regnum Vegetabile 138. Königstein: Koeltz Scientific Books.

    Google Scholar 

  • ICZN. (2005, accessed 2005). International code of zoological nomenclature.

  • Maddison, W. P., & Maddison, D. R. (2005, accessed 2005). Mesquite: A modular system for evolutionary analysis.

  • Marenco, L., Tosches, N., Crasto, C., Shepherd, G., Miller, P. L., & Nadkarni, P. M. (2003). Achieving evolvable web-database bioscience applications using the EAV/CR framework: Recent advances. Journal of the American Medical Informatics Association, 10(5), 444–453.

    Google Scholar 

  • Microsoft MSDN. (2005). NET framework.

  • Morris, R. A., Stevenson, R. D. & Haber, W. A. (2007). An Architecture for electronic field guides, Journal of Intelligent Information Systems, this issue, DOI 10.1007/s10844-006-0033-9

  • Pankhurst, R. J. (1991). Practical taxonomic computing. Cambridge: Cambridge University Press.

    Google Scholar 

  • Reaka-Kudla, M. L., Wilson, D. E., Wilson, E. O. (1997). Biodiversity II: Understanding and protecting our biological resources. Washington, D.C.: Joseph Henry.

    Google Scholar 

  • Skonnard, A. (2005). Web services and datasets.

  • Sneath, P. H. A. (1990). International code of nomenclature of bacteria: Bacteriological code, 1990 Revision. Washington, DC: ASM.

  • Stevenson, R. D., Haber, W., & Morris, R. A. (2003). Conservation ecology: Electronic field guides and user communities in the ecoinformatics revolution. Conservation Ecology [online], 7(1), 3. (online) URL:

  • TDWG. (2005a, accessed 2005). CODATA/TDWG Working Group on Access to Biological Collection Data (ABCD).

  • TDWG. (2005b, accessed 2005b). IUBS taxonomic database working group.

  • TDWG. (2005c, accessed 2005c). Taxonomic Database Working Group, Subgroup on the Structure of Descriptive Data (SDD).

  • W3C. (1999, accessed 2005). XSL Transformations (XSLT) version 1.0; W3C recommendation 16 November 1999.

  • W3C. (2004a, accessed 2005a). RDF: Resource description framework.

  • W3C. (2004b, accessed 2005b). XML schema.

  • W3C. (2005, accessed 2005). XSL-FO introduction and overview.

  • Wheeler, Q., & Meier, R. (2000). Species concepts and phylogenetic theory : A debate. New York: Columbia University Press.

    Google Scholar 

  • Wilson, E. O. (1992). The diversity of life. Cambridge, MA: Belknap Press of Harvard University Press.

    Google Scholar 

  • Wilson, E. O., & Peter, F. M. (1988). National forum on bioDiversity: Biodiversity. Washington, D.C.: National Academy.

    Google Scholar 

  • Winston, J. E. (1999). Describing species: Practical taxonomic procedure for biologists. New York: Columbia University Press.

    Google Scholar 

Download references

Author information

Authors and Affiliations


Corresponding author

Correspondence to Robert A. Morris.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Morris, R.A., Asiedu, J.K., Haber, W.A. et al. Database-backed decision trees with application to biological informatics. J Intell Inf Syst 29, 25–38 (2007).

Download citation

  • Published:

  • Issue Date:

  • DOI: