A new technique and software to optimize compression and data retrieval in the Material Examined section of taxonomic publications

  • Alexandre P. Aguiar Federal University of Espírito Santo, Dept of Biological Sciences, Zoology, Av. Fernando Ferrari 514, Goiabeiras, Vitória, ES, 29075−010, Brazil
  • Gavin R. Broad Natural History Museum, Cromwell Road, London SW7 5BD, UK
Keywords: biodiversity, distribution, metadata, meta-analysis, time series

Abstract

Elusive flaws are identified in techniques widely adopted to organize the Material Examined sections in taxonomic publications, mostly regarding the usage of the term ibidem and the nesting of information such as country and states. Logical errors are identified that prevent objective retrieval of the original information and can hinder or block its interpretation, even in case-by-case analyses. It is demonstrated that the free usage of ibidem in the sense of “same as previous except as follows” compromises the interpretation of data, characterizing bad practice. Solutions are proposed for the precise usage of both the term ibidem and the nesting technique. A new technique for organizing, compressing, and presenting information, called grid-setting, is described and evaluated. Its most notable practical effect is that the Material Examined section becomes literally a coded data sheet, which can be accurately converted back to spreadsheet format. In addition, the grid-setting technique was able to generate texts up to 30% shorter than those edited with the best-known traditional techniques. The new ideas and fixes are incorporated into a new software, flexible enough to process varied and unlimited data into largely user-defined texts, which remain nevertheless universal in their format and logical interpretation.

References

Aguiar A.P. 1998. Revision of the genus Hemistephanus Enderlein, 1906 (Hymenoptera, Stephanidae), with methodological considerations. Brazilian Journal of Entomology 41: 343–429.

Aguiar A.P. 2013. Publishing large DNA sequence data in reduced spaces and lasting formats, in paper or PDF. Zootaxa 3609 (6): 593–600. https://doi.org/10.11646/zootaxa.3609.6.5

Aguiar A.P. & Ramos A.C.B. 2011. Revision of Digonocryptus Viereck (Hymenoptera: Ichneumonidae: Cryptinae), with twenty six new taxa and cladistic interpretation of two species complexes. Zootaxa 2846 (1): 1–98. https://doi.org/10.11646/zootaxa.2846.1.1

Anderson N.R., Tarczy-Hornoch P. & Bumgarner R.E. 2006. On the persistence of supplementary resources in biomedical publications. BMC Bioinformatics 7: 260. https://doi.org/10.1186/1471-2105-7-260

BDJ – Biodiversity Data Journal. 2022. Instructions for Authors. Available from https://bdj.pensoft.net/about#For-authors [accessed 30 Jun. 2022].

Brown B.V. 2013. Automating the “Material examined” section of taxonomic papers to speed up species descriptions. Zootaxa 3683 (3): 297–299. https://doi.org/10.11646/zootaxa.3683.3.8

Brown B.V. 2021. Automatex – Automated Material Examined. Available from http://phorid.net/automatex/auto.php [accessed 20 Feb. 2022].

Chester C., Agosti D., Sautter G., Catapano T., Martens K., Gérard I. & Bénichou L. 2019. EJT editorial standard for the semantic enhancement of specimen data in taxonomy literature. European Journal of Taxonomy 586: 1–22. https://doi.org/10.5852/ejt.2019.586

Darwin Core Maintenance Group. 2021. Darwin Core text guide. Biodiversity Information Standards (TDWG). Available from http://rs.tdwg.org/dwc/terms/guides/text/2021-07-15 [accessed 30 Jun. 2022].

Güntsch A., Hyam R., Hagedorn G., Chagnoux S., Röpert D., Casino A., Droege G., Glöckler F., Gödderz K., Groom Q., Hoffmann J., Holleman A., Kempa M., Koivula H., Marhold K., Nicolson N., Smith V.S. & Triebel D. 2017. Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects. Database 2017: 1–9. https://doi.org/10.1093/database/bax003

Kenyon J. & Sprague N.R. 2014. Trends in the use of supplementary materials in environmental science journals. Issues in Science and Technology Librarianship 75. https://doi.org/10.5062/F40Z717Z

Pop M. & Salzberg S.L. 2015. Use and mis-use of supplementary material in science publications. BMC Bioinformatics 16 (237): 1–4. https://doi.org/10.1186/s12859-015-0668-z

Seeber F. 2008. Citations in supplementary information are invisible. Nature 451: 887. https://doi.org/10.1038/451887d

Supeleto F.A., Santos B.F. & Aguiar A.P. 2019. Revision of Distictus Townes, 1966 (Hymenoptera, Ichneumonidae, Cryptinae), with descriptions of ten new species. European Journal of Taxonomy 542: 1–64. https://doi.org/10.5852/ejt.2019.542

Telnov D. 2020. A revision of the Maechidiini Burmeister, 1855 (Coleoptera: Scarabaeidae: Melolonthinae) from the Indo-Australian transition zone, and the first record of the tribe west of Wallace’s Line. European Journal of Taxonomy 721: 1–210. https://doi.org/10.5852/ejt.2020.721.1127

Zanella F.C.V., Oliveira M.L. & Gaglianone M.C. 2000. Standardizing lists of locality data for examined specimens in systematic and biogeography studies of new world taxa. Biogeographica 76: 145–160.

Published
2022-12-15
How to Cite
Aguiar, A. P. ., & Broad, G. R. (2022). A new technique and software to optimize compression and data retrieval in the Material Examined section of taxonomic publications. European Journal of Taxonomy, 852(1), 43-56. https://doi.org/10.5852/ejt.2022.852.2007
Section
Opinion Paper