expowo: An R package for mining global plant diversity and distribution data
Abstract Premise Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity...
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| Format: | Article |
| Language: | English |
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Wiley
2024-11-01
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| Series: | Applications in Plant Sciences |
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| Online Access: | https://doi.org/10.1002/aps3.11609 |
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| author | Débora C. Zuanny Bruno Vilela Peter W. Moonlight Tiina E. Särkinen Domingos Cardoso |
| author_facet | Débora C. Zuanny Bruno Vilela Peter W. Moonlight Tiina E. Särkinen Domingos Cardoso |
| author_sort | Débora C. Zuanny |
| collection | DOAJ |
| description | Abstract Premise Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open‐source package that facilitates extracting and using botanical data from POWO. Methods and Results The expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species‐discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy‐to‐handle outputs, we also show empirical examples from a set of biodiverse countries and representative species‐rich and ecologically important angiosperm families. Conclusions By harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns. |
| format | Article |
| id | doaj-art-a8730eb2a88342bc9e706a11fb535e41 |
| institution | Kabale University |
| issn | 2168-0450 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj-art-a8730eb2a88342bc9e706a11fb535e412024-12-02T15:08:29ZengWileyApplications in Plant Sciences2168-04502024-11-01126n/an/a10.1002/aps3.11609expowo: An R package for mining global plant diversity and distribution dataDébora C. Zuanny0Bruno Vilela1Peter W. Moonlight2Tiina E. Särkinen3Domingos Cardoso4Instituto de Biologia Universidade Federal da Bahia, Rua Barão de Jeremoabo s.n., Ondina Salvador 40170‐115 Bahia BrazilInstituto de Biologia Universidade Federal da Bahia, Rua Barão de Jeremoabo s.n., Ondina Salvador 40170‐115 Bahia BrazilSchool of Botany Trinity College Dublin 1 College Green, Dublin 2 IrelandRoyal Botanic Garden Edinburgh, 20a Inverleith Row Edinburgh EH3 5LR Scotland United KingdomInstituto de Biologia Universidade Federal da Bahia, Rua Barão de Jeremoabo s.n., Ondina Salvador 40170‐115 Bahia BrazilAbstract Premise Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open‐source package that facilitates extracting and using botanical data from POWO. Methods and Results The expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species‐discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy‐to‐handle outputs, we also show empirical examples from a set of biodiverse countries and representative species‐rich and ecologically important angiosperm families. Conclusions By harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns.https://doi.org/10.1002/aps3.11609biodiversitydata miningnatural history collectionsvascular plants |
| spellingShingle | Débora C. Zuanny Bruno Vilela Peter W. Moonlight Tiina E. Särkinen Domingos Cardoso expowo: An R package for mining global plant diversity and distribution data Applications in Plant Sciences biodiversity data mining natural history collections vascular plants |
| title | expowo: An R package for mining global plant diversity and distribution data |
| title_full | expowo: An R package for mining global plant diversity and distribution data |
| title_fullStr | expowo: An R package for mining global plant diversity and distribution data |
| title_full_unstemmed | expowo: An R package for mining global plant diversity and distribution data |
| title_short | expowo: An R package for mining global plant diversity and distribution data |
| title_sort | expowo an r package for mining global plant diversity and distribution data |
| topic | biodiversity data mining natural history collections vascular plants |
| url | https://doi.org/10.1002/aps3.11609 |
| work_keys_str_mv | AT deboraczuanny expowoanrpackageforminingglobalplantdiversityanddistributiondata AT brunovilela expowoanrpackageforminingglobalplantdiversityanddistributiondata AT peterwmoonlight expowoanrpackageforminingglobalplantdiversityanddistributiondata AT tiinaesarkinen expowoanrpackageforminingglobalplantdiversityanddistributiondata AT domingoscardoso expowoanrpackageforminingglobalplantdiversityanddistributiondata |