PT  - JOURNAL ARTICLE
AU  - Nico M. Franz
AU  - Beckett W. Sterner
TI  - Taxonomy - for Computers
AID  - 10.1101/022145
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 022145
4099  - http://biorxiv.org/content/early/2015/07/08/022145.short
4100  - http://biorxiv.org/content/early/2015/07/08/022145.full
AB  - We explore solutions for identifying and reconciling taxonomic concepts that take advantage of the powers of computational representation and reasoning without compromising the suitability of the Linnaean system of nomenclature for human communication. Using the model of the semiotic triangle, we show that taxonomic names must variously achieve reference to nomenclatural types, taxonomic concepts (human-created theories of taxonomic identities), and taxa (evolutionary entities in nature). Expansion of the reference models into temporally transitioning systems shows that the elements of each triangle, and provenance among elements across triangles, are only identifiable if taxonomic names and concepts are precisely contextualized. The Codes of nomenclature, by mandating identifier (name) reuse but not requiring concept-specific identifier granularity, leave the challenge of framing and aligning the symbol/reference instances to human communicators who have superior cognitive abilities in this regard. Computers, in turn, can process greater volumes of narrowly framed and logically aligned data. Comparative, taxonomically referenced biological data are becoming increasingly networked and reutilized in analyses that expand their original context of generation. If we expect our virtual comparative information environments to provide logically mediated taxonomic concept provenance services, then we must improve the syntax and semantics of human taxonomy making – for computers.