Scientific Names Are Ambiguous as Identifiers for Biological Taxa: Their Context and Definition Are Required for Accurate Data Integration

Abstract

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.

Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity

“…What the BIEN team seeks for plant science is not simply a new data network and cyberinfrastructure, but a new paradigm with respect to how data are recorded and integrated. The need for this paradigm switch is well documented [33][34][35], but making it happen has proven difficult. With support from the National Center for Ecological Analysis and Synthesis (NCEAS 3 ), the BIEN grand challenge team held a planning meeting in December 2008.…”

Names are not good enough: Reasoning over taxonomic change in the Andropogon complex1

“…We adopt the view that taxonomic names and nomenclatural relationships are necessary but not sufficient for integrating biodiversity data for semantic information environments Web [5,35,58,73]. The reasons for this insufficiency are systemic and well known to taxonomy contributors and users [3,10,66,74].…”

Biological Taxonomy and Ontology Development: Scope and Limitations

“…Often these meanings are revised, expanded, or contracted in complex ways. As taxonomic revisions accumulate and supersede each other over time, they tend to create a network of many-to-many relationships among valid names, invalid synonyms, and past and present meanings (Koperski et al, 2000;Geoffroy and Berendsohn, 2003;Franz, 2005a;Kennedy et al, 2005;Franz et al, 2008). The situation is compounded by the fact that nomenclatural and full-blown taxonomic relationships are established in different and frequently non-congruent ways; the former being determined strictly on the basis of the identity of type specim ens, whereas the latter involve comparison of diagnostic features and other kinds of phylogenetic information.…”

“…The situation is compounded by the fact that nomenclatural and full-blown taxonomic relationships are established in different and frequently non-congruent ways; the former being determined strictly on the basis of the identity of type specim ens, whereas the latter involve comparison of diagnostic features and other kinds of phylogenetic information. The trajectories of nomenclatural and taxonomic relationships among names are therefore semi-independent and must be modeled separately to record partial name/meaning disjunctions over time (Koperski et al, 2000;Kennedy et al, 2005;Franz and Peet, 2009).…”

“…For instance, taxonomic experts might have great use for an ontology of strictly nomenclatural relationships (homonymy, synonymy, typification, etc.) among accepted and rejected Linnaean names (Scoble, 2004;Kennedy et al, 2005;Page, 2006;Franz and Peet, 2009;Huber and Klump, 2009). Such nomenclatural entities and relationships have a tractable history, and representations of this history in an ontological network are useful -up to a point -for identifying and integrating taxonomic legacy information .…”