WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online taxonomic backbone data

Premise The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (...

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Published inApplications in plant sciences Vol. 8; no. 9; pp. e11388 - n/a
Main Author Kindt, Roeland
Format Journal Article
LanguageEnglish
Published United States John Wiley & Sons, Inc 01.09.2020
John Wiley and Sons Inc
Wiley
Subjects
Algorithms
Biodiversity
biodiversity informatics
Biogeography
computer software
data collection
Datasets
flora
Flowers & plants
Names
online flora
plant name identification
Plant sciences
Plants
Software Note
Software Notes
species name matching
spelling errors
Standardization
taxonomic databases
Taxonomy
Timber
Trees
vegetation
online flora
taxonomic databases
biodiversity informatics
plant name identification
spelling errors
species name matching
Online AccessGet full text
ISSN2168-0450
2168-0450
DOI10.1002/aps3.11388

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Abstract Premise The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort to complete an online flora of all known vascular plants and bryophytes by 2020. Methods and Results Based on direct and fuzzy matching, WorldFlora inserts matching cases from the WFO to a submitted data set containing taxonomic names. The results and success rates for selecting the expected best single matches are presented for four data sets, including two data sets used in recent comparisons of software tools for correcting taxon names. Conclusions WorldFlora offers a straightforward pipeline for semi‐automatic plant name checking. For the four data sets, the success rate of credible matches ranged from 94.7% to 99.9%.
AbstractList Premise The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort to complete an online flora of all known vascular plants and bryophytes by 2020. Methods and Results Based on direct and fuzzy matching, WorldFlora inserts matching cases from the WFO to a submitted data set containing taxonomic names. The results and success rates for selecting the expected best single matches are presented for four data sets, including two data sets used in recent comparisons of software tools for correcting taxon names. Conclusions WorldFlora offers a straightforward pipeline for semi‐automatic plant name checking. For the four data sets, the success rate of credible matches ranged from 94.7% to 99.9%.
PremiseThe standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort to complete an online flora of all known vascular plants and bryophytes by 2020.Methods and ResultsBased on direct and fuzzy matching, WorldFlora inserts matching cases from the WFO to a submitted data set containing taxonomic names. The results and success rates for selecting the expected best single matches are presented for four data sets, including two data sets used in recent comparisons of software tools for correcting taxon names.ConclusionsWorldFlora offers a straightforward pipeline for semi‐automatic plant name checking. For the four data sets, the success rate of credible matches ranged from 94.7% to 99.9%.
The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort to complete an online flora of all known vascular plants and bryophytes by 2020.PREMISEThe standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort to complete an online flora of all known vascular plants and bryophytes by 2020.Based on direct and fuzzy matching, WorldFlora inserts matching cases from the WFO to a submitted data set containing taxonomic names. The results and success rates for selecting the expected best single matches are presented for four data sets, including two data sets used in recent comparisons of software tools for correcting taxon names.METHODS AND RESULTSBased on direct and fuzzy matching, WorldFlora inserts matching cases from the WFO to a submitted data set containing taxonomic names. The results and success rates for selecting the expected best single matches are presented for four data sets, including two data sets used in recent comparisons of software tools for correcting taxon names.WorldFlora offers a straightforward pipeline for semi-automatic plant name checking. For the four data sets, the success rate of credible matches ranged from 94.7% to 99.9%.CONCLUSIONSWorldFlora offers a straightforward pipeline for semi-automatic plant name checking. For the four data sets, the success rate of credible matches ranged from 94.7% to 99.9%.
Premise The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort to complete an online flora of all known vascular plants and bryophytes by 2020. Methods and Results Based on direct and fuzzy matching, WorldFlora inserts matching cases from the WFO to a submitted data set containing taxonomic names. The results and success rates for selecting the expected best single matches are presented for four data sets, including two data sets used in recent comparisons of software tools for correcting taxon names. Conclusions WorldFlora offers a straightforward pipeline for semi‐automatic plant name checking. For the four data sets, the success rate of credible matches ranged from 94.7% to 99.9%.
The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort to complete an online flora of all known vascular plants and bryophytes by 2020. Based on direct and fuzzy matching, WorldFlora inserts matching cases from the WFO to a submitted data set containing taxonomic names. The results and success rates for selecting the expected best single matches are presented for four data sets, including two data sets used in recent comparisons of software tools for correcting taxon names. WorldFlora offers a straightforward pipeline for semi-automatic plant name checking. For the four data sets, the success rate of credible matches ranged from 94.7% to 99.9%.
Author Kindt, Roeland
AuthorAffiliation 1 Tree Productivity and Diversity World Agroforestry P.O. Box 30677‐00100 Nairobi Kenya
AuthorAffiliation_xml – name: 1 Tree Productivity and Diversity World Agroforestry P.O. Box 30677‐00100 Nairobi Kenya
Author_xml – sequence: 1
  givenname: Roeland
  surname: Kindt
  fullname: Kindt, Roeland
  email: R.Kindt@CGIAR.org
  organization: World Agroforestry
BackLink https://www.ncbi.nlm.nih.gov/pubmed/33014632$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Copyright 2020 Kindt. published by Wiley Periodicals LLC on behalf of Botanical Society of America
2020 Kindt. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.
2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Copyright_xml – notice: 2020 Kindt. published by Wiley Periodicals LLC on behalf of Botanical Society of America
– notice: 2020 Kindt. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.
– notice: 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Issue 9
Keywords online flora
taxonomic databases
biodiversity informatics
plant name identification
spelling errors
species name matching
Language English
License Attribution
2020 Kindt. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.
This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Snippet Premise The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The...
The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The...
PremiseThe standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The...
PREMISE: The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The...
Premise The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The...
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StartPage e11388
SubjectTerms Algorithms
Biodiversity
biodiversity informatics
Biogeography
computer software
data collection
Datasets
flora
Flowers & plants
Names
online flora
plant name identification
Plant sciences
Plants
Software Note
Software Notes
species name matching
spelling errors
Standardization
taxonomic databases
Taxonomy
Timber
Trees
vegetation
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Title WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online taxonomic backbone data
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Volume 8
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