Abstract
Biologists use scientific names to label the organisms described in their data; however, these names are not unique identifiers for taxonomic entities. Alternative taxonomic classifications may apply the same name, associated with alternative definition or circumscription. Consequently, labelling data with scientific names alone does not unambiguously distinguish between taxon concepts. Accurate integration and comparison of biological data is required on taxon concepts, as defined in alternative taxonomic classifications. We have derived an abstract, inclusive model for the diverse representations of taxonomic concepts used by taxonomists and in taxonomic databases. This model has been implemented as a proposed standard XML schema for the exchange and comparison of taxonomic concepts between data providers and users. The representation and exchange of taxon definitions conformant with this schema will facilitate the development of taxonomic name/concept resolution services, allowing the meaningful integration and comparison of biological datasets, with greater accuracy than on the basis of name alone.
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
International Union for Conservation of Nature (2004), IUCN Red List of Endangered Species, http://www.iucnredlist.org
Greuter, W., McNeill, J., Barrie, F.R., Burdet, H.M., Demoulin, V., Filgueiras, T.S., Nicolson, D.H., Silva, P.C., Skog, J.E., Trehane, P., Turland, N.J., Hawksworth, D.L. (Editors & Compilers): International Code of Botanical Nomenclature. 16th International Botanical Congress St. Louis, Missouri, 1999. Koeltz Scientific Books, Königstein (2000) (Regnum Vegetabile, 138)
ICZN (International Commission on Zoological Nomenclature), International Code of Zoological Nomenclature. 4th edn. ICZN, London (1999)
ICSP (International Committee on Systematics of Prokaryotes). International Code of Nomenclature of Bacteria. American Society for Microbiology Press, Washington (1990)
ICTV (International Committee on Taxonomy of Viruses). International Code of Virus Classification and Nomenclature (2000), http://www.ncbi.nlm.nih.gov/ICTV/rules.html
http://www.soc.napier.ac.uk/tdwg/index.php?pagename=TCSAndTheLinneanCore
Berendsohn, W.G.: The concept of “potential taxa” in databases. Taxon 22, 207–212 (1995)
Berendsohn, W.G.: A taxonomic information model for botanical databases: the IOPI model. Taxon 46, 283–309 (1997)
Berendsohn, W., Döring, M., Geoffroy, M., Glück, K., Güntsch, A., Hahn, A., Jahn, R., Kusper, W.-H., Li, J., Röpert, D., Specht, F.: MoReTax: Handling factual information linked to taxonomic concepts in biology. Bundesamt für Naturshutz, Bonn (2003) (Schrift. Veget. 39)
Taxonomic Concept Schema Complementary Documentation for Draft Standard, http://tdwg.napier.ac.uk/doc/tdwg_tcs.doc section 2.3
GBIF.The Global Biodiversity Information Facility, http://www.gbif.org
SEEK, The Science Environment for Ecological Knowledge (2004), http://seek.ecoinformatics.org
EML, Ecological Metadata Language (2004), http://knb.ecoinformatics.org/software/eml
CML. Chemical Markup Language (2004), http://wwmm.ch.cam.ac.uk/moin/ChemicalMarkupLanguage
GML. Geography Markup Language (2004), http://opengis.net/gml
DIGIR. Distributed Generic Information Retrieval (2004), http://digir.net
ABCD. Access to Biological Collection Data (2004), http://www.bgbm.org/TDWG/CODATA
Weitzman, A.L., Lyal, C.H.C.: An XML schema for taxonomic literature – taXMLit (2004), available at http://web4.si.edu/sil/bca/status.cfm
MODS. Metadata Object Description Schema (2004), http://www.loc.gov/standards/mods
XOBIS. XML Organic Bibliographic Information Schema (2004), http://laneweb.stanford.edu:2380/wiki/medlane/schema
XMLMARC. XML Machine Readable Cataloging (2004), http://laneweb.stanford.edu:2380/wiki/medlane/xmlmarc
Pyle, R.L.: Taxonomer: a relational data model for managing information relevant to taxonomic research. Phyloinformatics 1(1) (2004)
TDWG Linnean Core Group: http://wiki.cs.umb.edu/twiki/bin/view/UBIF/LinneanCore
Paterson, T., Kennedy, J.B., Pullan, M.R., Cannon, A., Armstrong, K., Watson, M.F., Raguenaud, C., McDonald, S.M., Russell, G.: A universal character model and ontology of defined terms for taxonomic description. In: Rahm, E. (ed.) DILS 2004. LNCS (LNBI), vol. 2994, pp. 63–78. Springer, Berlin (2004)
Zhong, Y., Jung, S., Pramanik, S., Beaman, J.H.: Data model and comparison query methods for interacting classifications in taxonomic databases. Taxon 45, 223–241 (1996)
Zhong, Y., Luo, Y., Pramanik, S., Beaman, J.H.: HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees. Bioinformatics 15(2), 149–156 (1999)
Pullan, M.R., Watson, M.F., Kennedy, J.B., Raguenaud, C., Hyam, R.: The Prometheus taxonomic model: a practical approach to representing multiple taxonomies. Taxon 49(1), 55–75 (2000)
Ytow, N., Morse, D.R., McL Roberts, D.: Nomencurator: a nomenclatural history model to handle multiple taxonomic view. Biological Journal of the Linnaean Society 73, 81–98 (2001)
Koperski, M., Sauer, M., Braun, W., Gradstein, S.R.: Referenzeliste der Moose Deutschlands (Schriftenreihe Vegetationskunde 34). Bundesamt für Naturshutz, Bonn (2000)
DWC. The Darwin Core (2004), http://speciesanalyst.net/docs/dwc
Geoffroy, M., Berendsohn, W.: The concept problem in taxonomy: importance, components, approaches. In: Berendsohn, et al. (eds.), pp. 5–14 (2003) [9]
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kennedy, J.B., Kukla, R., Paterson, T. (2005). Scientific Names Are Ambiguous as Identifiers for Biological Taxa: Their Context and Definition Are Required for Accurate Data Integration. In: Ludäscher, B., Raschid, L. (eds) Data Integration in the Life Sciences. DILS 2005. Lecture Notes in Computer Science(), vol 3615. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11530084_8
Download citation
DOI: https://doi.org/10.1007/11530084_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-27967-9
Online ISBN: 978-3-540-31879-8
eBook Packages: Computer ScienceComputer Science (R0)