Biodiversity Science ›› 2016, Vol. 24 ›› Issue (12): 1345-1352.doi: 10.17520/biods.2016231

• Orginal Article • Previous Article     Next Article

Principles behind designing herbarium specimen labels and the R package ‘herblabel’

Jinlong Zhang*(), Huiling Zhu, Jingang Liu, Gunter A. Fischer   

  1. Flora Conservation Department, Kadoorie Farm and Botanic Garden, Hong Kong
  • Received:2016-08-23 Accepted:2016-12-14 Online:2017-01-10
  • Zhang Jinlong E-mail:jinlongzhang01@gmail.com
  • About author:

    # Co-first authors

Voucher specimens are essential for plant taxonomy, ecology, and plant molecular biology. Collection and identification information should be clearly, accurately and formally printed on herbarium labels, without confusion or spelling mistakes. During the preparation of the labels, data entry should be straight-forward and easy to manage. Ideally, the herbarium label printing software should conduct a thorough evaluation to avoid potential errors, and should issue warnings accordingly. By taking these principles into account, we developed the herblabel R package for generating herbarium labels based on Darwin Core and CVH5.0 data exchange standards. During the implementation of herblabel, the spelling and status of scientific names and the family-genera relationship are compared with the embedded databases to determine potential mistakes or incongruence against APG or other new classification systems. As the template is based on Darwin Core exchange standards, the database could not only be used to generate summaries and reports but also could be shared via GBIF or virtual herbaria. This package will increase efficiency and reduce workload for herbarium specimen preparation, management, and data entry, and should play an important role in cataloging plant diversity.

Key words: herbarium, specimens, label, R package, spelling, APG III, Darwin Core

Fig. 1

The workflow of the herblabel R package and its role in a herbarium. herblabel uses data.frame based on the simplified Darwin Core data exchange template, and can check spelling of scientific names, find out the family in new classification systems as well as examine completeness of the collection records. Users need to supply complete scientific names for a species or Chinese names either from Flora Reipublicae Popularis Sinicae or Flora of China. The package will automatically search and find out the corresponding scientific names based on embedded databases, and will fill in the family, genus, specific epithet, authority etc. for the records. Herbarium specimen labels and annotation labels will be in Rich Text Format (RTF), suitable for being viewed and edited in Microsoft Word. The photos of the herbarium specimen, and the examined collection records could then be used in a virtual herbarium."

Fig. 2

An RTF herbarium label generated by herblabel, note the scientific names have been automatically identified and changed to italic. Please note the cutting lines comprised by three dots at the bottom."

Fig. 3

Checking of spelling and the family-genus relationship. Note that a digit was appended to EUPHORBIACEAE, so the family name could not be found among the embedded family name database. Excoreacaria should be in EUPHORBIACEAE, however it could not be matched due to the spelling error and a warning was issued."

Fig. 4

Example of Annotation labels. These labels can be quite flexible in size depending on the text provided. Checking of the spelling and validity could also be implemented. Please note the cutting lines comprised by three dots at the bottom."

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