A Universal Character Model and Ontology of Defined Terms for Taxonomic Description
- 5 Citations
- 342 Downloads
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.
Keywords
State Group Structure Term State Term Structural Context Qualitative StatePreview
Unable to display preview. Download preview PDF.
References
- 1.Wilkinson, M.: A comparison of two methods of character construction. Cladistics 11, 297–308 (1995)CrossRefGoogle 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)CrossRefGoogle 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.
- 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)CrossRefGoogle 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