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The Use and Limits of Scientific Names in Biological Informatics

Real world – Artificial World

All information….

Names as descriptive metadata

All accumulated information of a species is tied to a scientific name, a name that serves as a link between what has been learned in the past and what we today add to the body of knowledge.

- Grimaldi & Engel, 2005, Evolution of the Insects

Nomenclature Taxonomy

Semantic Triangle

Relevance in information retrieval

Syntax and Semantics/Precision and Recall

GRAPHIC HERE (MAYBE)

Change in syntax with no change in semantics

Doryteuthis (Amerigo) pealeiiLoligo pealeiiDoryteuthis pealeii

Impacts on Use and Recall

Doryteuthis pealeii Loligo pealei

Conflation of syntax

Agalinus paupercula borealisAgalinus pauperculum borealisAgalinis paupercula var. BorealisAgalinus pauperculum var. borealisAgalinus paupercula var. borealisAgalinus paupercula var. borealis PennellAgalinus paupercula Britton var. borealis PennellAgalinus paupercula (Gray) Britt. var. borealis PennellAgalinis paupercula (A.Gray) Britton var. borealis PennellAgalinus paupercula (Gray) Britton var. borealis (Pennell) Zenkert 1934

Gerardia paupercula borealisGerardia paupercula var. borealisGerardia paupercula var. borealis (Pennell) DeamGerardia paupercula (Gray) Britt. var. borealis (Pennell) DeamGerardia paupercula (Gray) Britt. var. borealis (Pennell) DeamGerardia paupercula (A. Gray) Britton var. borealis (Pennell) Deam

Gerardia paupercula (A. Gray) Britton subsp. borealis (Pennell) PennellGerardia paupercula (Gray) Britt. ssp. borealis (Pennell) Pennell Gerardia paupercula Britton ssp. borealis Pennell

Change in semantics and no change in syntax

Pneumocystis carinii

Change in semantics and no change in syntax

Pneumocystis carinii

Change in semantics and no change in syntax

Pneumocystis carinii

Polysemy

Change in semantics = change in precision

Three concepts – three identifers

Mint Distinct Taxon Identifiers

Halichondria (Halichondria) panicea (Pallas, 1766)

Spongia panicea Pallas, 1766Alcyonium paniceum (Pallas, 1766) Halina panicea (Pallas, 1766)Amorphina panicea (Pallas, 1766)Halichondria panicea (Pallas, 1766)

Alcyonium medullare Lamarck, 1815

Amorphina appendiculata Schmidt, 1875Eumastia appendiculata (Schmidt, 1875)

Amorphina grisea Fristedt, 1887 Halichondria grisea (Fristedt, 1887)

Amorphina paciscens Schmidt, 1875Halichondria paciscens (Schmidt, 1875)

Clathria (Microciona) seriata (Grant, 1826) Clathria seriata (Grant, 1826)Seriatula seriata (Grant, 1826)Spongia seriata Grant, 1826

Halichondria albescens (Rafinesque, 1818)Spongia albescens Rafinesque, 1818

Hymeniacidon fallaciosus Bowerbank, 1866 Hymeniacidon fragilis Bowerbank, 1866Hymeniacidon lactea Bowerbank, 1866Hymeniacidon membrana Bowerbank, 1866Hymeniacidon parfitti Parfitt, 1868 Hymeniacidon reticulatus Bowerbank, 1866 Hymeniacidon solida Bowerbank, 1874 Hymeniacidon tegeticula Bowerbank, 1874 Hymeniacidon thomasii Bowerbank, 1866 Isodictya crassa Bowerbank, 1882Isodictya perplexa Bowerbank, 1882 Menanetia minchini Topsent, 1896Microciona tumulosa Bowerbank, 1882Pellina bibula Schmidt, 1870 Spongia compacta Sowerby, 1806 Spongia cristata Ellis & Solander, 1786 Spongia tomentosa Linnaeus, 1767 Spongia tubulosa Ellis & Solander, 1786 Spongia urens Ellis & Solander, 1786 Spuma borealis var. convoluta Miklucho-Maclay, 1870 Spuma borealis var. tuberosa Miklucho-Maclay, 1870 Spuma borealis var. velamentosa Miklucho-Maclay, 1870 Trachyopsilla glaberrima Burton, 1931

Halichondria ambigua Bowerbank, 1874Halichondria bibula (Schmidt, 1870)Halichondria caduca Bowerbank, 1866Halichondria coralloides Bowerbank, 1882Halichondria edusa Bowerbank, 1874Hymeniacidon firmus Bowerbank, 1874Halichondria firmus (Bowerbank, 1874)Halichondria glabra Bowerbank, 1866Halichondria incerta Bowerbank, 1866Halichondria lactea (Bowerbank, 1866)Halichondria membrana (Bowerbank, 1866)Halichondria pannosus Verrill, 1874Halichondria papillaris (Linnaeus, 1791)Halichondria reticulata Lieberkühn, 1859Halichondria sevosa Johnston, 1842Halichondria topsenti de Laubenfels, 1936Halichondriella corticata Burton, 1931

Halina papillaris (Pallas, 1766) Halispongia papillaris (Pallas, 1766) Halichondria brettii (Bowerbank, 1866)Hymeniacidon brettii Bowerbank, 1866

Hymeniacidon coccinea (Bowerbank, 1861) Halichondria coccinea Bowerbank, 1861