Taxonomic Names Resolution Service

Brian Maitner

2021-03-28

About the Taxonomic Name Resolution Service

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The TNRS corrects spelling errors and alternative spellings to a standard list of names, and converts out of date names (synonyms) to the current accepted name.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.

Using the TNRS

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^sA‰A¬Aºll. 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
## 1                 1         1960517                         Mauritia
## 2                 1          511364                 Solanum bipatens
## 3           0.93028          567775 Hypopterygium incrassatolimbatum
## 4  0.59957384396743           55516         Diplothrix juniperifolia
## 5                 1           37359              Leopoldinia pulchra
## 6                 1          305732                Leandra schenckii
## 7                 1         1284586           Hydnocarpus macrocarpa
## 8  0.67965907517394          540191         Warnstorfia trichophylla
## 9                 1          363887                   Piper arboreum
## 10                1          387911  Pseudochaetochloa australiensis
##          Name_score Name_matched_rank              Author_submitted
## 1                 1             Genus                              
## 2                 1           species                         Dunal
## 3                 1           species               Ma^sAAAll. Hal.
## 4  0.59957384396743           species                              
## 5                 1           species                         Mart.
## 6                 1           species                              
## 7                 1           species                              
## 8  0.59957384396743           species (Warnst. ) Tuom. & T. J. Kop.
## 9                 1           species                         Aubl.
## 10                1           species                       Hitchc.
##                 Author_matched Author_score            Canonical_author
## 1                                                                      
## 2                        Dunal            1                       Dunal
## 3                   Müll. Hal.       0.6514                  Müll. Hal.
## 4                                                                   DC.
## 5                        Mart.            1                       Mart.
## 6                                                                 Cogn.
## 7                                                                 Warb.
## 8  (Warnst.) Tuom. & T.J. Kop.            1 (Warnst.) Tuom. & T.J. Kop.
## 9                        Aubl.            1                       Aubl.
## 10                     Hitchc.            1                     Hitchc.
##    Name_matched_accepted_family   Genus_submitted     Genus_matched Genus_score
## 1                     Arecaceae          Mauritia          Mauritia           1
## 2                    Solanaceae           Solanum           Solanum           1
## 3              Hypopterygiaceae     Hypopterygium     Hypopterygium           1
## 4                    Asteraceae        Diplothrix        Diplothrix           1
## 5                     Arecaceae       Leopoldinia       Leopoldinia           1
## 6               Melastomataceae           Leandra           Leandra           1
## 7                   Achariaceae       Hydnocarpus       Hydnocarpus           1
## 8               Amblystegiaceae       Warnstorfia       Warnstorfia           1
## 9                    Piperaceae             Piper             Piper           1
## 10                      Poaceae Pseudochaetochloa Pseudochaetochloa           1
##    Specific_epithet_submitted Specific_epithet_matched Specific_epithet_score
## 1                                                                            
## 2                    bipatens                 bipatens                      1
## 3          incrassatolimbatum       incrassatolimbatum                      1
## 4               juniperifolia            juniperifolia                      1
## 5                     pulchra                  pulchra                      1
## 6                   schenckii                schenckii                      1
## 7                  macrocarpa               macrocarpa                      1
## 8                trichophylla             trichophylla                      1
## 9                    arboreum                 arboreum                      1
## 10              australiensis            australiensis                      1
##    Family_submitted   Family_matched Family_score Infraspecific_rank
## 1         Arecaceae        Arecaceae            1                   
## 2        Solanaceae       Solanaceae            1                   
## 3  Hypopterygiaceae Hypopterygiaceae            1                   
## 4       Helotiaceae                                                 
## 5         Arecaceae        Arecaceae            1                   
## 6   Melastomataceae  Melastomataceae            1                   
## 7                                                                   
## 8      Campyliaceae                                                 
## 9                                                                   
## 10          Poaceae          Poaceae            1                   
##    Infraspecific_epithet_matched Infraspecific_epithet_score
## 1                                                           
## 2                                                           
## 3                                                           
## 4                                                           
## 5                                                           
## 6                                                           
## 7                                                           
## 8                                                           
## 9                                                           
## 10                                                          
##    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                                                           
## 2                                                           
## 3                                                           
## 4                                                Helotiaceae
## 5                                                           
## 6                                                           
## 7                                                           
## 8                                               Campyliaceae
## 9                                                           
## 10                                                          
##                                                                Name_matched_url
## 1                                                                              
## 2                  http://www.theplantlist.org/tpl1.1/search?q=Solanum+bipatens
## 3  http://www.theplantlist.org/tpl1.1/search?q=Hypopterygium+incrassatolimbatum
## 4          http://www.theplantlist.org/tpl1.1/search?q=Diplothrix+juniperifolia
## 5               http://www.theplantlist.org/tpl1.1/search?q=Leopoldinia+pulchra
## 6                 http://www.theplantlist.org/tpl1.1/search?q=Leandra+schenckii
## 7                                        http://www.tropicos.org/Name/100431320
## 8          http://www.theplantlist.org/tpl1.1/search?q=Warnstorfia+trichophylla
## 9                    http://www.theplantlist.org/tpl1.1/search?q=Piper+arboreum
## 10                                        http://www.tropicos.org/Name/25520644
##    Name_matched_lsid Phonetic Taxonomic_status                   Accepted_name
## 1                           Y         Accepted                        Mauritia
## 2                           Y       No opinion                                
## 3                           Y          Synonym         Hypopterygium tamarisci
## 4                           Y          Synonym            Zinnia juniperifolia
## 5                           Y         Accepted             Leopoldinia pulchra
## 6                           Y          Synonym               Leandra regnellii
## 7                           Y         Accepted          Hydnocarpus macrocarpa
## 8                           Y         Accepted        Warnstorfia trichophylla
## 9                           Y         Accepted                  Piper arboreum
## 10                          Y         Accepted Pseudochaetochloa australiensis
##                   Accepted_species        Accepted_name_author Accepted_name_id
## 1                                                                       1960517
## 2                                                                              
## 3          Hypopterygium tamarisci   (Sw.) Brid. ex Müll. Hal.           567887
## 4             Zinnia juniperifolia                (DC.) A.Gray          1941999
## 5              Leopoldinia pulchra                       Mart.            37359
## 6                Leandra regnellii              (Triana) Cogn.           305723
## 7           Hydnocarpus macrocarpa                       Warb.          1284586
## 8         Warnstorfia trichophylla (Warnst.) Tuom. & T.J. Kop.           540191
## 9                   Piper arboreum                       Aubl.           363887
## 10 Pseudochaetochloa australiensis                     Hitchc.           387911
##    Accepted_name_rank
## 1               Genus
## 2                    
## 3             species
## 4             species
## 5             species
## 6             species
## 7             species
## 8             species
## 9             species
## 10            species
##                                                       Accepted_name_url
## 1                                                                      
## 2                                                                      
## 3   http://www.theplantlist.org/tpl1.1/search?q=Hypopterygium+tamarisci
## 4      http://www.theplantlist.org/tpl1.1/search?q=Zinnia+juniperifolia
## 5       http://www.theplantlist.org/tpl1.1/search?q=Leopoldinia+pulchra
## 6         http://www.theplantlist.org/tpl1.1/search?q=Leandra+regnellii
## 7                                http://www.tropicos.org/Name/100431320
## 8  http://www.theplantlist.org/tpl1.1/search?q=Warnstorfia+trichophylla
## 9            http://www.theplantlist.org/tpl1.1/search?q=Piper+arboreum
## 10                                http://www.tropicos.org/Name/25520644
##    Accepted_name_lsid  Accepted_family Overall_score_order
## 1                            Arecaceae                   1
## 2                                                        1
## 3                     Hypopterygiaceae                   1
## 4                           Asteraceae                   1
## 5                            Arecaceae                   1
## 6                      Melastomataceae                   1
## 7                          Achariaceae                   1
## 8                      Amblystegiaceae                   1
## 9                           Piperaceae                   1
## 10                             Poaceae                   1
##    Highertaxa_score_order   Source Warnings
## 1                       1      tpl        2
## 2                       1      tpl        0
## 3                       1      tpl        0
## 4                       7      tpl        4
## 5                       1      tpl        0
## 6                       1      tpl        0
## 7                       1 tropicos        0
## 8                       3      tpl        4
## 9                       1      tpl        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.

TNRS metadata

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:

  1. Bibtex-formatted citation information. This information can be optionally be written to a file specified by the “bibtex_file” argument.
  2. Information about TNRS data sources
  3. TNRS version information
metadata <- TNRS_metadata()

#If you want to see the TNRS version information (e.g. to report in an manuscript):

metadata$version
##   sourceID sourceName                               sourceNameFull
## 1        1   tropicos Missouri Botanical Gardens Tropicos database
## 2        2        tpl                    The Plant List (ver. 1.1)
## 3        3       usda                                  USDA Plants
##                               sourceUrl
## 1             https://www.tropicos.org/
## 2          http://www.theplantlist.org/
## 3 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 Plant List (TPL) was a working list of all known plant species produced by the botanical community in response to Target 1 of the 2002-2010 Global Strategy for Plant Conservation (GSPC). TPL has been static since 2013, but was used as the starting point for the Taxonomic Backbone of the World Flora Online (WFO), and updated information can be found at www.worldfloraonline.org
## 3                                                                                                                                                                                                                                   The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories.
##                                  dataUrl           logo_path version
## 1          http://services.tropicos.org/ images/tropicos.png    <NA>
## 2                                             images/tpl.png     1.1
## 3 http://plants.usda.gov/adv_search.html     images/usda.png    <NA>
##   sourceReleaseDate tnrsDateAccessed
## 1              <NA>       2020-05-30
## 2        2013-09-01       2020-06-25
## 3              <NA>       2020-07-03
#To see the sources that are used by the TNRS:

metadata$sources
##   db_version build_date code_version api_version
## 1      4.1.3 2020-10-01        5.0.2       1.1.2
#To get the citation information to paste into a reference manager (e.g. paperpile, zotero):

 # writeLines(text = metadata$citations$citation)