Biological Names and Taxonomies on the Semantic Web – Managing the Change in Scientific Conception 

Abstract

Abstract. Biodiversity management requires the usage of heterogeneous biological information from multiple sources. Indexing, aggregating, and finding such information is based on names and taxonomic knowledge of organisms. However, taxonomies change in time due to new scientific findings, opinions of authorities, and changes in our conception about life forms. Furthermore, organism names and their meaning change in time, different authorities use different scientific names for the same taxon in different times, and various vernacular names are in use in different languages. This makes data integration and information retrieval difficult without detailed biological information. This paper introduces a meta-ontology for managing the names and taxonomies of organisms, and presents three applications for it: 1) publishing biological species lists as ontology services (ca. 20 taxonomies including more than 80,000 names), 2) collaborative management of the vernacular names of vascular plants (ca. 26,000 taxa), and 3) management of individual scientific name changes based on research results, covering a group of beetles. The applications are based on the databases of the Finnish Museum of Natural History and are used in a living lab environment on the web.

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

“…They permit the assembly of multiple alternative, internally coherent hierarchies where all concepts derived from one hierarchy can be connected via parent/child (is_a) relationships [35,84,87]. In a subsequent step, the hierarchies' entities can be aligned in reference to a variety of similarity indicators; including nomenclatural relationships, member composition, or diagnostic features [16,22,34,43,88].…”

“…Other taxonomically focused integration projects that do not utilize RCC-5 include [10,13,66,73,88]. The degree to which the RCC-5 alignment approach is relevant to 3 A MIR is the unique node in a given R 32 lattice that implies all other true articulations in the lattice.…”

ENVIROFI - Bringing Biodiversity to the Future Internet

“…In order to overcome this problem, various projects such as ALTER-Net [10] or SEEK [11] and SONet [12] have proposed the use of ontologies for structuring environmental data. Within ENVIROFI, it was proposed to utilize the power the TaxMeOn Species Ontology [13] developed of ontologies for the following purposes:…”

The Birds of the World Ontology AVIO

“…Modeling and managing scientific and common names is not trivial [2,3] because names change over time. For example, a species may be shifted into another genus, which is reflected in the scientific name.…”

“…The ontology is an application of our earlier work, the meta-ontology model TaxMeOn for biological names and classifications [3]. The aim of the AVIO ontology is to provide a reference to the species names of the birds, e.g., for indexing bird related information.…”