BioNames: linking taxonomy, texts, and trees

Abstract

BioNames is a web database of taxonomic names for animals, linked to the primary literature and, wherever possible, to phylogenetic trees. It aims to provide a taxonomic “dashboard” where at a glance we can see a summary of the taxonomic and phylogenetic information we have for a given taxon and hence provide a quick answer to the basic question “what is this taxon?” BioNames combines classifications from the Global Biodiversity Information Facility (GBIF) and GenBank, images from the Encyclopedia of Life (EOL), animal names from the Index of Organism Names (ION), and bibliographic data from multiple sources including the Biodiversity Heritage Library (BHL) and CrossRef. The user interface includes display of full text articles, interactive timelines of taxonomic publications, and zoomable phylogenies. It is available at .

Ozymandias: A biodiversity knowledge graph

“…The general structure of the knowledge graph is based on (Page, 2013(Page, , 2016a. The core enti-107 ties are taxa, taxonomic names, publications, journals, and people.…”

“…The knowledge graph in Ozymandias features only a subset of the entities depicted in earlier 541 work sketching the "biodiversity knowledge graph" (Page, 2013(Page, , 2016a. There are several 542 entities that are obvious candidates to be added to Ozymandias, such as specimens and nu-543 cleotide sequences.…”

Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature

“…One option for publication is to create a custom interface to the links, to make them both discoverable and interesting. Examples include links between the NCBI taxonomy [Federhen 2011] and Wikipedia [Page 2011], or BioNames [Page 2013], which comprises links between animal names and the primary literature. These may be user friendly, but they provide limited functionality, especially if a user wants programmatic access to the underlying data.…”

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

“…Thus, in spite of the central role of Code-compliant names in interconnecting biodiversity data [69,70,78], these names have shortcomings as identifiers of granular differences between taxonomic perspectives that biodiversity data communities create and apply at any given time. Sound knowledge representation in the biodiversity data realm requires recognition of, and compensation for, these systemic insufficiencies [32,34,58].…”

“…To some degree the inadequacies are manageable through social processes, including conservative re-/naming practices or 'standardized' taxonomies [6,44,55,79,91]. In practice, the long-term drawbacks of using taxonomic names as concept identifiers are frequently mitigated by the ability of well-trained human scientists to contextualize name usages and thereby infer the intended meanings [30,32,69]. However, no counteracting human practice can alter the insight that taxonomic names and nomenclatural relationships are fundamentally not designed to track granular similarities and differences in taxonomic meaning of the sort exemplified in the Andro-UC.…”