User's guide to the TNC - Grin

 content
introduction
overview
genus check
      genus names check
      genus spelling check
      genus synonym check
species check
      species names check
      species spelling check
      species synonym check
taxon check
      taxon names check
      taxon spelling check
      taxon synonym check

introduction

The main purpose of this Taxonomic Nomenclature Checker is to allow quick and convenient checking of large numbers of scientific names against other standardized databases. The Taxonomic Nomenclature Checker currently checks lists of scientific names against weekly downloaded taxonomic data from the Germplasm Resources Information Network (GRIN) of the United States Department of Agriculture, Agricultural Research Service. A step-by-step procedure for identifying correctly spelled names, isolating and correcting misspelled names, and determining the acceptance status of names in compared lists is provided.

GRIN TAXONOMY currently contains over 18,000 generic and 65,000 specific or infraspecific records of vascular plants from throughout the world, with a focus on plants important to agriculture or other commerce. While GRIN includes virtually all currently accepted generic names (over 14,000), it does not include all species names, especially of non-agricultural plants; therefore, some of your names may have to be checked elsewhere. A discussion of content, data standards and taxonomic philosophy for GRIN TAXONOMY can be accessed at the preceding link.

overview

Checking is available for lists at three levels: Checking at each of these levels is done in three steps:
  1. names
  2. spelling
  3. synonyms
The initial step should be a check of generic names using the genus check to correct any misspellings before proceeding to check species or taxon names, as the species check and taxon check require the correct spelling of generic names. For lists of genera, generic synonymy can also be evaluated using the genus check. Once generic spellings have been corrected, the species check should be performed on lists composed of binomials, exclusive of hybrid binomials, which along with trinomials must be compared using the taxon check. The taxon check also accepts binomials. The species check or taxon check should proceed in a manner similar to the genus check : 1) an initial check for exact matches, 2) a subsequent check for misspellings of those names which fail to match, 3) spelling corrections to generate additional matches, and finally 4) a synonym check for all matched names to determine their status as accepted names or synonyms.

When lists are compared, the genus check is performed using only the first word and the species check only the first two words in the submitted name string, therefore it is not necessary to extract these from the remaining elements of the string. However, some modifications to submitted names may be desirable before attempting the taxon check (see below). Furthermore, lists need not be in alphabetical order. They may have leading or trailing blank characters or more than one blank character between names. Tab stops instead of blank characters as delimiters between names are also accepted.

If output needs to be saved for later reference, editing or printing, the links in the menu can be opened in new browser pages by using the right mouse button.

At the end of every output list is a summary of checking statistics, with the number of records submitted, the number of records searched, the processing time, etc.

For clarity, the examples in this guide are very short. Lists with several thousand names can be processed in one search. However, as a safeguard against server overload, a time limit of 60 seconds has been set. If this time limit is exceeded, the partial checking results are returned with an error message near the end of the output (error: search timeout).

genus check

This check compares the first word in a submitted string to GRIN generic records. Input lists need not be in alphabetical order and may have leading or trailing blank characters. To facilitate matching to GRIN, intergeneric sexual hybrids should be preceded by "X " and graft chimaeras by "+".

Below is a short list of generic names that is used in the accompanying examples and that can also be tried (using cut and paste) with the checking program.

genus names check

   input:
     Anthocephalus
     Banksia
     Butyrospermum
     Codonopsis
     Actinostropus
     Balsamorrhiza
     Cymbopetallum

   output:

     exact genus matches found:
     Anthocephalus
     Banksia
     Butyrospermum
     Codonopsis

     no genus matches found:
     Actinostropus
     Balsamorrhiza
     Cymbopetallum

The GRIN database contains a complete listing of the ca. 14,000 accepted vascular plant genera in the world with an additional 4,500 synonym genera. The genus names check can therefore be considered a check against a complete database. It produces an output consisting of two sub-lists:

  1. The first sub-list contains those generic names where exact matches were found in the database. The spelling is therefore correct, but the names might be synonyms. If you are interested in determining the acceptance vs. synonymy only for genera in GRIN, this sub-list may be used as input for the genus synonym check. Note that the actual synonymy of species assigned to a genus may differ from that of the genus itself, the latter being based solely on the type species.
  2. The second sub-list contains those generic names where no exact matches were found in the database. This sub-list should be used as input with the genus spelling check.
genus spelling check

   input:
     Actinostropus
     Balsamorrhiza
     Cymbopetallum

   output:
     Actinostropus
         Actinostrobus (1)

     Balsamorrhiza
         Balsamorhiza (1)

     Cymbopetallum
         Cymbopetalum (1)

The input screen of the genus spelling check has two user-adjustable parameters: 1) the maximum number of similar names returned for each genus name to be checked (default=5), and 2) the maximum number of differences between the submitted genus name and the returned similar name (default=2). In the output, the submitted names are left justified and the lists of similar names returned are indented. The similarity value given represents the number of character edits necessary to convert the submitted name into the returned similar name. Insertion, deletion and replacement are counted as a single edit each. This similarity value is given in parentheses, following the returned similar name, and the list of similar names is ordered by this value. If a genus with correct spelling is submitted, the same name is returned with a similarity value of "0" along with any other generic names that meet the specified maximum number of differences.

The returned name appears as a link to the GRIN database report for the particular genus. Additional information in GRIN for that genus, such as its author or family classification, can be used to determine if the similar spelling returned is the intended spelling of your genus. Once generic spelling mistakes have been corrected in your list, proceed to the genus synonym check if your list is comprised only of genera or, alternatively, proceed to the species name check or taxon name check.

genus synonym check

  input:
    Anthocephalus
    Banksia
    Butyrospermum
    Codonopsis

   output:
    Anthocephalus
         Breonia

    Banksia
         Banksia
         Hagenia
         Pimelea

    Butyrospermum
         Vitellaria

Before this check is done generic spellings must first be corrected using the genus spelling check. Generic names with incorrect spelling or lacking entries in GRIN are ignored, so only previously matched genera from the genus names check should be compared. In the output, the submitted names are left justified and the GRIN accepted names returned are indented. Only submitted names that are synonyms in GRIN are output; the remaining names should not be considered as accepted in GRIN unless previously matched.

The returned accepted name appears as a link to the GRIN database report for the particular genus. For genera that have homonyms in GRIN more than one accepted name is returned. For one of these the accepted genus may be identical to the submitted name, as in one example above, indicating that genera matching your spelling are both accepted and synonymized in GRIN. Use the links provided to view additional information in GRIN, such as authorship or family classification, to aid your interpretation of the intended genus.

species check

This check compares the first two words in a submitted string to GRIN species records. Input lists need not be in alphabetical order and may have leading or trailing blank characters or more than one blank character between names. Tab stops instead of blank characters as delimiters between names are also accepted. Correct spelling of generic names should already have been determined using the genus check. Hybrid binomials should not be compared here, but instead use the taxon check.

Below is a short list of species binomials that is used in the accompanying examples and that can also be tried (using cut and paste) with the checking program.

species names check

   input:
    Actea pachypoda
    Agave virginica
    Albizia guachapele
    Bebbia juncea
    Cassia renigera
    Euonymous alatus
    Festuca longifolia
    Pringlea antiescorbutica
    Pyrus betulaefolia
    Ricotia cretica
    Scorpiurus vermicullatus
    Tetracoccus hallii

   output:

    genus and species matches found:
    Agave virginica
    Albizia guachapele
    Cassia renigera
    Festuca longifolia

    genus matches found, no species matches found:
    Pringlea antiescorbutica
    Pyrus betulaefolia
    Scorpiurus vermicullatus

    genus matches found, but no species exist in GRIN for that genus:
    Bebbia juncea
    Ricotia cretica
    Tetracoccus hallii

    incorrect genus names:
    Actea pachypoda
    Euonymous alatus

The GRIN database contains about 53,000 binomials. Almost all agricultural plants are included, but not all vascular plants, therefore the species name check is against an incomplete database. The species name check creates an output consisting of four sub-lists:

  1. The first sub-list contains those binomials where exact matches were found in the database. The spelling is therefore correct, but the names might be synonyms. This sub-list should be used as input for the species synonym check.
  2. The second sub-list contains those binomials where exact matches were found for the genus names, but no exact matches were found for the species epithet in the database. This sub-list should be used as input with the species spelling check.
  3. The third sub-list contains those binomials where the genus names have correct spelling, but there are no species of that genus represented in the database. This sub-list cannot be used further with the GRIN taxonomic database and should be compared to other taxonomic databases.
  4. The fourth sub-list contains those binomials where the genus names have incorrect spelling. The spelling of genus names should be checked using the genus spelling check and corrected before proceeding with the species check.

species spelling check

   input:
    Pringlea antiescorbutica
    Pyrus betulaefolia
    Scorpiurus vermicullatus

   output:
    Pringlea antiescorbutica
         Pringlea antiscorbutica (1)

    Pyrus betulaefolia
         Pyrus betulifolia (2)

    Scorpiurus vermicullatus
         Scorpiurus vermiculatus (1)

The input screen of the species spelling check has two user-adjustable parameters: 1) the maximum number of similar names returned for each genus name to be checked (default=5), and 2) the maximum number of differences between the submitted species name and the returned similar name (default=2). In the output, the submitted names are left justified and the lists of similar names returned are indented. The similarity value given represents the number of character edits necessary to convert the submitted name into the returned similar name. Insertion, deletion and replacement are counted as a single edit each. This similarity value is given in parentheses, following the returned similar name, and the list of similar names is ordered by this value.

Names absent from the output include those submitted with correct spelling, with incorrect generic spelling or with genera not represented among GRIN species records. Generic spelling should first be corrected using the genus spelling check before performing this check. The returned name appears as a link to a GRIN database query that returns a list of all GRIN species data for the particular genus. This list, which will include a link to the GRIN species report on the returned similar name, may be scanned for other binomials in that genus similar to the submitted one. Use the links provided to view additional information in GRIN (such as authorship, distribution, common names, or economic uses) to aid your interpretation of the intended spelling.

Note: Since GRIN taxonomy is not complete with respect to all species of vascular plants, a submitted binomial (e.g. Acacia flavescens) may have correct spelling but be absent from GRIN and the most similar name returned by the species spelling check (Acacia latescens) is that of a different species. Other data in GRIN (such as authorship, distribution, common names, or economic uses) can be used to help determine if this is the case.

species synonym check

   input:
    Agave virginica
    Albizia guachapele
    Cassia renigera
    Festuca longifolia

   output:
    Agave virginica
         Manfreda virginica

    Albizia guachapele
         Pseudosamanea guachapele

    Cassia renigera
         Cassia javanica subsp. renigera

    Festuca longifolia
         Festuca brevipila
         Festuca lemanii
         Festuca longifolia

Before this check is done spellings of binomials must first be corrected using the genus spelling check and/or species spelling check. Binomials submitted with incorrect spelling of any part or belonging to genera not represented in GRIN species records are ignored, so only previously matched binomials from the species names check should be compared. In the output, the submitted names are left justified and the GRIN accepted names returned are indented. Only submitted names that are synonyms in GRIN are output; the remaining names should not be considered as accepted in GRIN unless previously matched.

The returned accepted name appears as a link to the GRIN database report for the particular species. For species that have homonyms in GRIN more than one accepted name is returned. For one of these the accepted binomial may be identical to the submitted one, as in one example above, indicating that binomials matching your spelling are both accepted and synonymized in GRIN. Use the links provided to view additional information in GRIN (such as authorship, distribution, common names, or economic uses) to aid your interpretation of the intended species. Particular caution should be observed in interpreting a name matching to GRIN homonyms when one of these has authorship beginning with "auct. ...". Such names have been mostly or occasionally misapplied, as may be the case in your own data.

Note: Since GRIN taxonomy is not complete with respect to all names of vascular plants, a submitted species name could match, in rare instances, to a homonym present in GRIN that is not the intended species when the desired species is absent from GRIN. If this is suspected other GRIN data (such as authorship, distribution, common names, or economic uses) can be used to help determine if this is indeed the case.

taxon check

This check compares the entire submitted string to GRIN taxon records, therefore name strings of more than two words should be compared here. Input lists need not be in alphabetical order and may have leading or trailing blank characters or more than one blank character between names. Tab stops instead of blank characters as delimiters between names are also accepted. Correct spelling of generic names should already have been determined using the genus check. If they are present, authors should be removed from the submitted string before checking. Quadrinomials are not permitted either and should be converted to trinomials by removing the third epithet and its rank term from the submitted string. To facilitate matching of infraspecific rank designations to GRIN, the following abbreviations should be used: "subsp." (not ssp.) for subspecies, "var." for variety, "f." for forma, an "x" preceding hybrid species epithets, and "notho-" preceding the rank of infraspecific hybrids.

Below is a short list of taxon binomials and trinomials that is used in the accompanying examples and that can also be tried (using cut and paste) with the checking program. Non-hybrid binomials are also acceptable as input for the taxon check.

taxon names check

   input:
    Aesculus x carnea var. planturensis
    Allium flavum var. pulchellum
    Bambusa textilis var. maculatus
    Berberis x emarginata
    Carmichaelia grandiflora var. disaricata
    Linum suffruticosum subsp. salsoloides
    Tetragonolobus conjugatus subsp. requienii
    Jasione blepharodon subsp. penicillata
    Hermannia filifolia var. grandicalyx
    Vella pseudocytisus subsp. glabrata
    Astrogalus argophyllus var. panguicensis
    Ligustum x ibolium

   output:

    taxon matches found:
    Allium flavum var. pulchellum
    Berberis x emarginata
    Linum suffruticosum subsp. salsoloides
    Tetragonolobus conjugatus subsp. requienii

    genus matches found, no taxon matches found:
    Aesculus x carnea var. planturensis
    Bambusa textilis var. maculatus
    Carmichaelia grandiflora var. disaricata

    genus matches found, but no taxa exist in GRIN for that genus:
    Hermannia filifolia var. grandicalyx
    Jasione blepharodon subsp. penicillata
    Vella pseudocytisus subsp. glabrata

    incorrect genus names:
    Astrogalus argophyllus var. panguicensis
    Ligustum x ibolium

The GRIN database contains about 8,200 trinomials. This is only part of those existing for vascular plants, therefore the taxon name check is against an incomplete database. The taxon name check creates an output consisting of four sub-lists:

  1. The first sub-list contains those taxa where exact matches were found in the database. The spelling is therefore correct, but the names might be synonyms. This sub-list should be used as input for the taxon synonym check.
  2. The second sub-list contains those taxa where exact matches were found for the genus names, but no exact matches were found for the names of lower taxonomic rank in the database. This sub-list should be used as input with the taxon spelling check.
  3. The third sub-list contains those taxa where the genus names have correct spelling, but there are no taxa of that genus represented in the database. This sub-list cannot be used further with the GRIN taxonomic database and should be compared to other taxonomic databases.
  4. The fourth sub-list contains those taxa where the genus names have incorrect spelling. The spelling of genus names should be checked using the genus spelling check and corrected first before proceeding with the taxon check.
taxon spelling check

   input:
    Aesculus x carnea var. planturensis
    Bambusa textilis var. maculatus
    Carmichaelia grandiflora var. disaricata

   output:
    Aesculus x carnea var. planturensis
         Aesculus x carnea var. plantierensis (0.96)

    Bambusa textilis var. maculatus
         Bambusa textilis var. maculata (0.95)
         Bambusa textilis var. gracilis (0.85)
         Bambusa textilis var. fusca (0.83)
         Bambusa textilis var. glabra (0.81)
         Bambusa textilis var. albo-striata (0.8)

    Carmichaelia grandiflora var. disaricata
         Carmichaelia grandiflora var. divaricata (0.98)

The input screen of the taxon spelling check has two user-adjustable parameters: 1) the maximum number of similar names returned for each genus name to be checked (default=5), and 2) the minimum similarity between the submitted taxon name and the returned similar name (default=0.8). In the output, the submitted names are left justified and the lists of similar names returned are indented. The similarity is given by a numeric value ranging between 0 (completely different, no character in common) to 1 (exact match). Although the definition of this similarity value is more complex, it can roughly be interpreted as % similarity. This similarity value is given in parentheses following the returned similar name, and the list of similar names is ordered by descending similarity.

Names absent from the output include those submitted with correct spelling, with incorrect generic spelling or with genera not represented among GRIN taxon records. Generic spelling should first be corrected using the genus spelling check before performing this check. The returned name appears as a link to the GRIN database report for the particular taxon. Use the links provided to view additional information in GRIN (such as authorship, distribution, common names, or economic uses) to aid your interpretation of the intended spelling.

Note: Since GRIN taxonomy is not complete with respect to taxa, a submitted taxon name may have correct spelling but be absent from GRIN and the most similar name returned by the taxon spelling check is that of a different taxon. Other data in GRIN (such as authorship, distribution, common names, or economic uses) can be used to help determine if this is the case.

taxon synonym check

   input:
    Allium flavum var. pulchellum
    Berberis x emarginata
    Linum suffruticosum subsp. salsoloides
    Tetragonolobus conjugatus subsp. requienii

   output:
    Allium flavum var. pulchellum
         Allium carinatum subsp. pulchellum

    Linum suffruticosum subsp. salsoloides
         Linum suffruticosum subsp. appressum
         Linum suffruticosum subsp. salsoloides

    Tetragonolobus conjugatus subsp. requienii
         Lotus conjugatus subsp. requienii

Before this check is done spellings of taxa must first be corrected using the genus spelling check, species spelling check, and/or taxon spelling check. Taxa submitted with incorrect spelling of any part or belonging to genera not represented in GRIN species records are ignored, so only previously matched taxa from the taxon names check should be compared. In the output, the submitted names are left justified and the GRIN accepted names returned are indented. Only submitted names that are synonyms in GRIN are output; the remaining names should not be considered as accepted in GRIN unless previously matched.

The returned accepted name appears as a link to the GRIN database report for the particular taxon. For taxa that have homonyms in GRIN more than one accepted name is returned. For one of these the accepted taxon may be identical to the submitted one, as in one example above, indicating that taxa matching your spelling are both accepted and synonymized in GRIN. Use the links provided to view additional information in GRIN (such as authorship, distribution, common names, or economic uses) to aid your interpretation of the intended taxon. Particular caution should be observed in interpreting a name matching to GRIN homonyms when one of these has authorship beginning with "auct. ...". Such names have been mostly or occasionally misapplied, as may be the case in your own data.

Note: Since GRIN taxonomy is not complete with respect to all names of vascular plants, in rare instances a submitted taxon could match to a homonym present in GRIN that is not the intended taxon when the desired taxon is absent from GRIN. If this is suspected other GRIN data (such as authorship, distribution, common names, or economic uses) can be used to help determine if this is indeed the case.

Send your software-related comments to: I. Thormann

Send comments on GRIN data to: Dr. J. H. Wiersema