Skip to main content

A Universal Character Model and Ontology of Defined Terms for Taxonomic Description

  • Conference paper
Data Integration in the Life Sciences (DILS 2004)

Abstract

Taxonomists classify biological specimens into groups (taxa) on the basis of similarities between their observed features (‘characters’). The description of these ‘characters’ is therefore central to taxonomy, but there is currently no agreed model, defined terminology nor methodology for composing these descriptions. This lack of a common conceptual model, together with the individualistic working practices of taxonomists, means that descriptions are not composed consistently, and are not easy to interpret and re-use, nor are datasets comparable. The purpose of the Prometheus II project is to improve the interpretation and comparison of plant descriptions. To this end we propose a new conceptual model for unambiguously representing character descriptions, and have developed a controlled vocabulary as an ontology of defined terms, which will be used to describe specimens according to our character model.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Wilkinson, M.: A comparison of two methods of character construction. Cladistics 11, 297–308 (1995)

    Article  Google Scholar 

  2. Cannon, A., McDonald, S.M.: Prometheus II - Qualitative Research Case Study: Capturing and relating character concepts in plant taxonomy (2001), www.prometheusdb.org/resources.html

  3. Colless, D. H.: On ’character’ and related terms. Systematic Zoology 34, 229–233(1995); Keogh, J.S.: The importance of systematics in understanding the biodiversity crisis: the role of biological educators. Journal of Biol. Educ. 29 , 293–299 (1995)

    Google Scholar 

  4. Diederich, J., Fortuner, R., Milton, J.: Construction and integration of large character sets for nematode morpho-anatomical data. Fundamental and Applied Nematology 20, 409–424 (1997)

    Google Scholar 

  5. DELTA: Dallwitz, M.J.: A general system for coding taxonomic descriptions. Taxon 29, 41–46 (1980)

    Google Scholar 

  6. NEXUS: Maddison, D.R., Swofford, D.L., Maddison, W.P.: NEXUS: An extensible file format for systematic information. Systematic Biology 46, 590–621 (1997)

    Google Scholar 

  7. LUCID: Developed by Centre for Biological Information Technology: University of Queensland, Australia, www.cpitt.uq.edu.au , www.lucidcentral.com

  8. Davis, P.H., Heywood, V.H.: Principles of Angiosperm Taxonomy. Oliver and Boyd Edinburgh (1963)

    Google Scholar 

  9. TDWG (International Working Group on Taxonomic Databases), www.tdwg.org ; Structure of Descriptive Data.: Subgroup Session Report at the TDWG Meeting in Frankfurt (2000) www.tdwg.org/tdwg2000/sddreport

  10. Prometheus: www.prometheusdb.org

  11. Allkin, R.: Handling Taxonomic Descriptions by Computer. In: Allkin, R., Bisby, F.A. (eds.) Databases in Systematics, Academic Press, London (1984)

    Google Scholar 

  12. The Science Environment for Ecological Knowledge: seek.ecoinformatics.org

  13. Cui, Z., Jones, D.M., O’Brien, P.: Semantic B2B Integration: Issues in Ontology-based Applications. SIGMOD Record 31, 43–48 (2002)

    Article  Google Scholar 

  14. Omelayenko, B.: Syntactic-Level Ontology Integration Rules for E-commerce. In: Proceedings of the Fourteenth International FLAIRS Conference (FLAIRS-2001), Key West, FL, pp. 324–328 (2001)

    Google Scholar 

  15. www.prometheusdb.org/resources.htm

  16. W3C: OWL Web Ontology Language Use Cases and Requirements (2003), http://www.w3.org/TR/webont-req/

  17. Guarino, N.: Formal Ontology and Information Systems. In: Formal Ontologies in Information Systems. Proceedings of FOIS 1998, Trento, Italy, pp. 3–15. IOS Press, Amsterdam (1998)

    Google Scholar 

  18. Sheth, A.: Changing Focus on Interoperability in Information Systems: From System, Syntax, Structure to Semantics. In: Goodchild, M.F., Egenhofer, M.J., Fegeas, R., Kottman, C.A. (eds.) Interoperating Geographic Information Systems, pp. 5–30. Kluwer, Academic Publishers, Dordrecht (1998)

    Google Scholar 

  19. Jaiswal, P., Ware, D., Ni, J., Chang, K., Zhao, W., Schmidt, S., Pan, X., Clark, K., Teytel-man, L., Cartinhour, S., Stein, L., McCouch, S.: Conference Review: Gramene: Development and Integration of Trait and Gene Ontologies for Rice. Comparative and Functional Genomics 3, 132–136 (2002)

    Article  Google Scholar 

  20. The Plant Ontology Consortium: Conference Review: The Plant Ontology Consortium and Plant Ontologies. Comparative and Functional Genomics, vol. 3, pp. 137–142 (2002)

    Google Scholar 

  21. The Plant Ontology Consortium: www.plantontology.org

  22. The Gene Ontology Consortium: www.geneontology.org

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Paterson, T. et al. (2004). A Universal Character Model and Ontology of Defined Terms for Taxonomic Description. In: Rahm, E. (eds) Data Integration in the Life Sciences. DILS 2004. Lecture Notes in Computer Science(), vol 2994. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24745-6_5

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-24745-6_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-21300-0

  • Online ISBN: 978-3-540-24745-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics