The Taxonomic Name Resolution Service (TNRS) is a tool for automated standardization of plant scientific names.
The TNRS corrects spelling errors and alternative spellings to a standard list of names, and converts out of date names (synonyms) to the current accepted name. The TNRS can process many names at once, saving hours of tedious and error-prone manual name correction. For names that cannot be resolved automatically, the TNRS present a list of possibilities and provides tools for researching and selecting the preferred name.
The TNRS takes as input either a vector of scientific names, or a data.frame containing two columns: row number and scientific name.
library(TNRS)
# First, we'll grab an example dataset containing two columns: row number and scientific name.
fulldata <- tnrs_testfile
head(fulldata, n = 20)## ID
## 1 1
## 2 2
## 3 3
## 4 4
## 5 5
## 6 6
## 7 7
## 8 8
## 9 9
## 10 10
## 11 11
## 12 12
## 13 13
## 14 14
## 15 15
## 16 16
## 17 17
## 18 18
## 19 19
## 20 20
## taxon
## 1 Arecaceae Mauritia
## 2 Solanaceae Solanum bipatens Dunal
## 3 HYPOPTERYGIACEAE Hypopterygium incrassatolimbatum Ma^sAAAll. Hal.
## 4 Helotiaceae Diplothrix juniperifolia
## 5 Arecaceae Leopoldinia pulchra Mart.
## 6 Melastomataceae Leandra schenckii
## 7 Hydnocarpus macrocarpa
## 8 Campyliaceae Warnstorfia trichophylla (Warnst. ) Tuom. & T. J. Kop.
## 9 Piper arboreum Aubl.
## 10 Poaceae Pseudochaetochloa australiensis Hitchc.
## 11 Juglandaceae Engelhardia spicata var. colebrookeana (Lindl. ex Wall. ) Koord. & Valeton
## 12 Malvaceae Hibiscus 'Old Yella'
## 13 Fabaceae Mimosa vepres Lindm.
## 14 Berberidaceae Epimedium xpurpureum Bailly
## 15 Asteraceae Senecio beguei Humbert
## 16 Coelogyne fragrans
## 17 Cyperaceae Rhynchospora cephalotes (L. ) Vahl
## 18 Pteridophyte Nephrolepis mollis Rosenst.
## 19 Piperaceae Piper crassipeduncullum
## 20 Asteraceae Hieracium billyanum var. parvulum B. de Retz# Note that there are a variety of formats represented here, sometimes including
# scientific name only
# genus only
# family and genus
# family, scientific name, and author
results <- TNRS(taxonomic_names = fulldata)
# Inspect the results
head(results, 10)## ID Name_submitted
## 1 1 Arecaceae Mauritia
## 2 2 Solanaceae Solanum bipatens Dunal
## 3 3 HYPOPTERYGIACEAE Hypopterygium incrassatolimbatum Ma^sAAAll. Hal.
## 4 4 Helotiaceae Diplothrix juniperifolia
## 5 5 Arecaceae Leopoldinia pulchra Mart.
## 6 6 Melastomataceae Leandra schenckii
## 7 7 Hydnocarpus macrocarpa
## 8 8 Campyliaceae Warnstorfia trichophylla (Warnst. ) Tuom. & T. J. Kop.
## 9 9 Piper arboreum Aubl.
## 10 10 Poaceae Pseudochaetochloa australiensis Hitchc.
## Overall_score Name_matched_id Name_matched Name_score
## 1 1.0000000 661203 Mauritia 1.0000000
## 2 1.0000000 511246 Solanum bipatens 1.0000000
## 3 0.9327000 567645 Hypopterygium incrassatolimbatum 1.0000000
## 4 0.5995738 55495 Diplothrix juniperifolia 0.5995738
## 5 1.0000000 37339 Leopoldinia pulchra 1.0000000
## 6 1.0000000 305636 Leandra schenckii 1.0000000
## 7 1.0000000 1284252 Hydnocarpus macrocarpa 1.0000000
## 8 0.6796591 540070 Warnstorfia trichophylla 0.5995738
## 9 1.0000000 363781 Piper arboreum 1.0000000
## 10 1.0000000 387804 Pseudochaetochloa australiensis 1.0000000
## Name_matched_rank Author_submitted Author_matched
## 1 genus
## 2 species Dunal Dunal
## 3 species Ma^sAAAll. Hal. Müll. Hal.
## 4 species
## 5 species Mart. Mart.
## 6 species
## 7 species
## 8 species (Warnst. ) Tuom. & T. J. Kop. (Warnst.) Tuom. & T.J. Kop.
## 9 species Aubl. Aubl.
## 10 species Hitchc. Hitchc.
## Author_score Canonical_author Name_matched_accepted_family
## 1 NA L. f. Arecaceae
## 2 1.0000 Dunal Solanaceae
## 3 0.6635 Müll. Hal. Hypopterygiaceae
## 4 NA DC. Asteraceae
## 5 1.0000 Mart. Arecaceae
## 6 NA Cogn. Melastomataceae
## 7 NA Warb. Achariaceae
## 8 1.0000 (Warnst.) Tuom. & T.J. Kop. Amblystegiaceae
## 9 1.0000 Aubl. Piperaceae
## 10 1.0000 Hitchc. Poaceae
## Genus_submitted Genus_matched Genus_score Specific_epithet_submitted
## 1 Mauritia Mauritia 1
## 2 Solanum Solanum 1 bipatens
## 3 Hypopterygium Hypopterygium 1 incrassatolimbatum
## 4 Diplothrix Diplothrix 1 juniperifolia
## 5 Leopoldinia Leopoldinia 1 pulchra
## 6 Leandra Leandra 1 schenckii
## 7 Hydnocarpus Hydnocarpus 1 macrocarpa
## 8 Warnstorfia Warnstorfia 1 trichophylla
## 9 Piper Piper 1 arboreum
## 10 Pseudochaetochloa Pseudochaetochloa 1 australiensis
## Specific_epithet_matched Specific_epithet_score Family_submitted
## 1 NA Arecaceae
## 2 bipatens 1 Solanaceae
## 3 incrassatolimbatum 1 Hypopterygiaceae
## 4 juniperifolia 1 Helotiaceae
## 5 pulchra 1 Arecaceae
## 6 schenckii 1 Melastomataceae
## 7 macrocarpa 1
## 8 trichophylla 1 Campyliaceae
## 9 arboreum 1
## 10 australiensis 1 Poaceae
## Family_matched Family_score Infraspecific_rank
## 1 Arecaceae 1
## 2 Solanaceae 1
## 3 Hypopterygiaceae 1
## 4 NA
## 5 Arecaceae 1
## 6 Melastomataceae 1
## 7 NA
## 8 NA
## 9 NA
## 10 Poaceae 1
## Infraspecific_epithet_matched Infraspecific_epithet_score
## 1 NA
## 2 NA
## 3 NA
## 4 NA
## 5 NA
## 6 NA
## 7 NA
## 8 NA
## 9 NA
## 10 NA
## Infraspecific_rank_2 Infraspecific_epithet_2_matched
## 1
## 2
## 3
## 4
## 5
## 6
## 7
## 8
## 9
## 10
## Infraspecific_epithet_2_score Annotations Unmatched_terms
## 1 NA
## 2 NA
## 3 NA
## 4 NA Helotiaceae
## 5 NA
## 6 NA
## 7 NA
## 8 NA Campyliaceae
## 9 NA
## 10 NA
## Name_matched_url Name_matched_lsid Phonetic
## 1 http://www.tropicos.org/Name/40015082 Y
## 2 https://wcvp.science.kew.org/taxon/818455-1 Y
## 3 http://www.tropicos.org/Name/35129557 Y
## 4 http://www.tropicos.org/Name/2705463 Y
## 5 http://www.tropicos.org/Name/2400575 Y
## 6 http://www.tropicos.org/Name/20300803 Y
## 7 http://www.tropicos.org/Name/100431320 Y
## 8 http://www.tropicos.org/Name/35100291 Y
## 9 http://www.tropicos.org/Name/25002004 Y
## 10 http://www.tropicos.org/Name/25520644 Y
## Taxonomic_status Accepted_name
## 1 Accepted Mauritia
## 2 Synonym Solanum cordifolium
## 3 Synonym Hypopterygium tamarisci
## 4 Synonym Zinnia juniperifolia
## 5 Accepted Leopoldinia pulchra
## 6 No opinion
## 7 Accepted Hydnocarpus macrocarpa
## 8 Synonym Sarmentypnum trichophyllum
## 9 Accepted Piper arboreum
## 10 Accepted Pseudochaetochloa australiensis
## Accepted_species Accepted_name_author Accepted_name_id
## 1 L. f. 661203
## 2 Solanum cordifolium Dunal 511341
## 3 Hypopterygium tamarisci (Sw.) Brid. ex Müll. Hal. 567757
## 4 Zinnia juniperifolia (DC.) A. Gray 91439
## 5 Leopoldinia pulchra Mart. 37339
## 6
## 7 Hydnocarpus macrocarpa Warb. 1284252
## 8 Sarmentypnum trichophyllum (Warnst.) Hedenäs 644908
## 9 Piper arboreum Aubl. 363781
## 10 Pseudochaetochloa australiensis Hitchc. 387804
## Accepted_name_rank Accepted_name_url
## 1 genus http://www.tropicos.org/Name/40015082
## 2 species https://wcvp.science.kew.org/taxon/818796-1
## 3 species http://www.tropicos.org/Name/35129670
## 4 species http://www.tropicos.org/Name/2743155
## 5 species http://www.tropicos.org/Name/2400575
## 6
## 7 species http://www.tropicos.org/Name/100431320
## 8 species http://www.tropicos.org/Name/35216910
## 9 species http://www.tropicos.org/Name/25002004
## 10 species http://www.tropicos.org/Name/25520644
## Accepted_name_lsid Accepted_family Overall_score_order
## 1 Arecaceae 1
## 2 Solanaceae 1
## 3 Hypopterygiaceae 1
## 4 Asteraceae 1
## 5 Arecaceae 1
## 6 1
## 7 Achariaceae 1
## 8 Amblystegiaceae 1
## 9 Piperaceae 1
## 10 Poaceae 1
## Highertaxa_score_order Source Warnings
## 1 1 tropicos 0
## 2 1 wcvp 0
## 3 1 tropicos 0
## 4 6 tropicos 4
## 5 1 tropicos 0
## 6 1 tropicos 0
## 7 1 tropicos 0
## 8 3 tropicos 4
## 9 1 tropicos 0
## 10 1 tropicos 0# The output includes information on the name submitted, the match score (how close the match is), the name matched, the status of the matched name, and the accepted name.When using the TNRS, we ask that you cite both the TNRS itself and
the data sources that are used by the TNRS. The TNRS couldn’t function
without these data sources, and it is important to recognize the work of
these data providers by citing their work. Users may also want to report
metadata about the version of the TNRS they used in their analyses for
the purposes of reproducibility. The function TNRS_metadata
facilitates citations and version reporting by providing this
information in an easily-used format. This function returns:
metadata <- TNRS_metadata()
# If you want to see the TNRS version information (e.g. to report in an manuscript):
metadata$version## db_version build_date code_version api_version
## 1 4.2 2021-08-02 5.0.3# To see the sources that are used by the TNRS:
metadata$sources## sourceID sourceName sourceNameFull
## 1 1 tropicos Missouri Botanical Gardens Tropicos database
## 2 2 wfo World Flora Online
## 3 3 wcvp World Checklist of Vascular Plants
## 4 4 usda USDA Plants
## sourceUrl
## 1 https://www.tropicos.org/
## 2 http://www.worldfloraonline.org/
## 3 https://wcvp.science.kew.org/
## 4 https://plants.sc.egov.usda.gov/java/
## description
## 1 The Missouri Botanical Garden's Tropicos database links over 1.33M scientific names with over 4.87M specimens and over 685K digital images. The data includes over 150K references from over 52.6K publications offered as a free service to the world's scientific community.
## 2 The World Flora Online will be an open-access, Web-based compendium of the worlds plant species. It will be a collaborative, international project, building upon existing knowledge and published floras, checklists and revisions but will also require the collection and generation of new information on poorly know plant groups and plants in unexplored regions. WFO replaces The Plant List
## 3 The World Checklist of Vascular Plants aims to deliver a sustainable and curated resource. It is based on Kew’s names and taxonomic backbone which has been created by reconciling the names from the International Plant Names Index (IPNI) with the taxonomy from the World Checklist of Selected Plant Families (WCSP). This Beta version therefore only displays names that are in both IPNI and WCVP. It contains both families that have been completed and peer reviewed by both external and internal experts on the relevant families as well as families that are in the process of being edited and reviewed. Some of the original data which WCSP built upon came from our generous collaborators listed in the acknowledgements. WCVP aims to represent a global consensus view of current plant taxonomy by reflecting the latest published taxonomies while incorporating the opinions of taxonomists based around the world
## 4 The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories.
## dataUrl
## 1 http://services.tropicos.org/
## 2 http://104.198.143.165/files/WFO_Backbone/_WFOCompleteBackbone/
## 3 http://sftp.kew.org/pub/data-repositories/WCVP/
## 4 http://plants.usda.gov/adv_search.html
## logo_path
## 1 https://bien.nceas.ucsb.edu/bien/wp-content/uploads/2020/10/TropicosLogo.gif
## 2 https://bien.nceas.ucsb.edu/bien/wp-content/uploads/2021/07/wfo_logo.jpeg
## 3 https://bien.nceas.ucsb.edu/bien/wp-content/uploads/2021/07/kew_logo.png
## 4 https://bien.nceas.ucsb.edu/bien/wp-content/uploads/2020/10/usda-plants-logo.gif
## version sourceReleaseDate tnrsDateAccessed
## 1 <NA> <NA> 2021-07-17
## 2 v.2019.05 2019-05-17 2021-07-07
## 3 v5 2021-06-01 2021-07-12
## 4 <NA> <NA> 2020-04-25# To get the citation information to paste into a reference manager (e.g. paperpile, zotero):
# writeLines(text = metadata$citations$citation)