taxize: Taxonomic Information from Around the Web

種の分類群情報

> library(taxize)

バージョン: 0.6.2

関数名 概略
apg_families Lookup-table for APGIII family names
apg_genera Table of APGIII generic names
apg_lookup Lookup in the APGII taxonomy and replace family names.
apg_orders Lookup-table for APGIII order names
bold_search Search Barcode of Life for taxonomic IDs
children Retrieve immediate children taxa for a given taxon name or ID.
class2tree Convert list of classifications to a tree.
classification Retrieve the taxonomic hierarchy for a given taxon ID.
col_children Search Catalogue of Life for for direct children of a particular taxon.
col_downstream Use Catalogue of Life to get downstream taxa to a given taxonomic level.
col_search Search Catalogue of Life for taxonomic IDs
comm2sci Get scientific names from common names.
downstream Retrieve the downstream taxa for a given taxon name or ID.
eol_dataobjects Given the identifier for a data object, return all metadata about the object.
eol_invasive Search for presence of taxonomic names in EOL invasive species databases.
eol_pages Search for pages in EOL database using a taxonconceptID.
eol_search Search for terms in EOL database.
gbif_name_usage Lookup details for specific names in all taxonomies in GBIF.
gbif_parse Parse taxon names using the GBIF name parser.
genbank2uid Get NCBI taxonomy UID from GenBankID
get_boldid Get the BOLD (Barcode of Life) code for a search term.
get_colid Get the Catalogue of Life ID from taxonomic names.
get_eolid Get the EOL ID from Encyclopedia of Life from taxonomic names.
get_gbifid Get the GBIF backbone taxon ID from taxonomic names.
get_ids Retrieve taxonomic identifiers for a given taxon name.
get_nbnid Get the UK National Biodiversity Network ID from taxonomic names.
get_tpsid Get the NameID codes from Tropicos for taxonomic names.
get_tsn Get the TSN code for a search term.
get_ubioid Get the uBio id for a search term.
get_uid Get the UID codes from NCBI for taxonomic names.
gisd_isinvasive Check invasive species status for a set of species from GISD database
gni_details Search for taxonomic name details using the Global Names Index.
gni_parse Parse scientific names using EOL's name parser.
gni_search Search for taxonomic names using the Global Names Index.
gnr_datasources Get data sources for the Global Names Resolver.
gnr_resolve Resolve names using Global Names Resolver.
iplant_resolve iPlant name resolution
ipni_search Search for names in the International Plant Names Index (IPNI).
itis-api Low level functions for working with the ITIS API.
itis_acceptname Retrieve accepted TSN (with accepted name).
itis_downstream Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
itis_getrecord Get full ITIS record for one or more ITIS TSN's or lsid's.
itis_hierarchy Get hierarchies from TSN values, full, upstream only, or immediate downstream only
itis_kingdomnames Get kingdom names.
itis_lsid Get kingdom names.
itis_name Get taxonomic names for a given taxonomic name query.
itis_native Get jurisdiction data, i.e., native or not native in a region.
itis_refs Get references related to a ITIS TSN.
itis_searchcommon Searches common name and acts as thin wrapper around 'searchbycommonnamebeginswith' and 'searchbycommonnameendswith'
itis_taxrank Retrieve taxonomic rank name from given TSN.
itis_terms Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
iucn_getname Get any matching IUCN species names
iucn_status Extractor functions for 'iucn'-class.
iucn_summary Get a summary from the IUCN Red List.
names_list Get a random vector of species names.
nbn_classifcation Search UK National Biodiversity Network database for taxonomic classification
nbn_search Search UK National Biodiversity Network database
nbn_synonyms Return all synonyms for a taxon name with a given id from NBN
ncbi_children` Search NCBI for children of a taxon
ncbi_get_taxon_summary NCBI taxon information from uids
ncbi_getbyid Retrieve gene sequences from NCBI by accession number.
ncbi_getbyname Retrieve gene sequences from NCBI by taxon name and gene names.
ncbi_search Search for gene sequences available for taxa from NCBI.
phylomatic_format Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
phylomatic_tree Query Phylomatic for a phylogenetic tree.
ping Ping an API used in taxize to see if it's working.
plantGenusNames Vector of 793 genus names of plants
plantNames Vector of 1,182 species names of plants
plantminer Search for taxonomy data from Plantminer.com
rank_ref Lookup-table for IDs of taxonomic ranks
rankagg Aggregate data by given taxonomic rank
resolve Resolve names from many different sources
sci2comm Get common names from scientific names.
scrapenames Resolve names using Global Names Recognition and Discovery.
status_codes Get HTTP status codes
synonyms Retrieve synonyms from various sources given
input taxonomic names or identifiers.
tax_agg Aggregate species data to given taxonomic rank
tax_name Get taxonomic names for a given rank.
tax_rank Get rank for a given taxonomic name.
taxize-defunct Defunct functions in taxize
taxize-deprecated Deprecated functions in taxize
taxize-package Taxonomic information from around the web.
taxize_capwords Capitalize the first letter of a character string.
taxize_cite Get citations and licenses for data sources used in taxize
theplantlist Lookup-table for family, genus, and species names for ThePlantList
tnrs Search the Phylotastic Taxonomic Name Resolution Service.
tnrs_sources Get sources for the Phylotastic Taxonomic Name Resolution Service.
tp_accnames Return all accepted names for a taxon name with a given id.
tp_dist Return all distribution records for for a taxon name with a given id.
tp_refs Return all reference records for for a taxon name with a given id.
tp_search Search Tropicos by scientific name, common name, or Tropicos ID.
tp_summary Return summary data a taxon name with a given id.
tp_synonyms Return all synonyms for a taxon name with a given id.
tpl_families Get The Plant List families.
tpl_get Get The Plant List csv files.
tpl_search A light wrapper around the taxonstand fxn to call Theplantlist.org database.
ubio_classification This function will return all ClassificationBank data pertaining to a particular ClassificationBankID
ubio_classification_search This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID
ubio_id Search uBio by namebank ID.
ubio_search This function will return NameBankIDs that match given search terms
ubio_synonyms Search uBio for taxonomic synonyms by hierarchiesID.
upstream Retrieve the upstream taxa for a given taxon name or ID.
vascan_search Search the CANADENSYS Vascan API.

apg_families

apg_orders

class2tree

classification

comm2sci

gnr_resolve

Global Names Resolverによる学名の不一致の解消

Arguments

  • names
  • data_source_ids
  • resolve_once
  • with_context
  • stripauthority
  • best_match_only
  • preferred_data_sources
  • http
  • callopts
> gnr_resolve(names = c("Helianthus annuus", "Homo sapienss")) %>% head() # Miss spelled to `Homo sapiens`

$results
      submitted_name
1  Helianthus annuus
2  Helianthus annuus
3  Helianthus annuus
4  Helianthus annuus
5  Helianthus annuus
6  Helianthus annuus
7  Helianthus annuus
8  Helianthus annuus
9  Helianthus annuus
10 Helianthus annuus
11 Helianthus annuus
12 Helianthus annuus
13 Helianthus annuus
14 Helianthus annuus
15 Helianthus annuus
16 Helianthus annuus
17 Helianthus annuus
18 Helianthus annuus
19 Helianthus annuus
20 Helianthus annuus
21 Helianthus annuus
22 Helianthus annuus
23 Helianthus annuus
24 Helianthus annuus
25 Helianthus annuus
26 Helianthus annuus
27 Helianthus annuus
28 Helianthus annuus
29 Helianthus annuus
30 Helianthus annuus
31 Helianthus annuus
32     Homo sapienss
33     Homo sapienss
34     Homo sapienss
35     Homo sapienss
36     Homo sapienss
37     Homo sapienss
38     Homo sapienss
39     Homo sapienss
40     Homo sapienss
41     Homo sapienss
42     Homo sapienss
43     Homo sapienss
44     Homo sapienss
45     Homo sapienss
46     Homo sapienss
47     Homo sapienss
48     Homo sapienss
49     Homo sapienss
50     Homo sapienss
51     Homo sapienss
52     Homo sapienss
53     Homo sapienss
54     Homo sapienss
55     Homo sapienss
                                                            matched_name
1                                                      Helianthus annuus
2                                                      Helianthus annuus
3                                                      Helianthus annuus
4                                                      Helianthus annuus
5                                                      Helianthus annuus
6                                                      Helianthus annuus
7                                                      Helianthus annuus
8                                                   Helianthus annuus L.
9                                                   Helianthus annuus L.
10                                                  Helianthus annuus L.
11                                                  Helianthus annuus L.
12                                            Helianthus annuus Linnaeus
13                                                  Helianthus annuus L.
14                                            Helianthus annuus agg. mut
15                                                  Helianthus annuus L.
16                                            Helianthus annuus Linnaeus
17                                           Helianthus annuus L. (1753)
18                                                  Helianthus annuus L.
19                                                  Helianthus annuus L.
20                                            Helianthus annuus Linnaeus
21                                                  Helianthus annuus L.
22                                                  Helianthus annuus L.
23                                                  Helianthus annuus L.
24                                                  Helianthus annuus L.
25                                                  Helianthus annuus L.
26                                                  Helianthus annuus L.
27                                                  Helianthus annuus L.
28 Helianthus annuus [infrasp.unranked] lenticularis (Douglas) Cockerell
29                                                  Helianthus annuus L.
30                                                  Helianthus annuus L.
31                                                  Helianthus annuus L.
32                                           Homo sapiens Linnaeus, 1758
33                                           Homo sapiens Linnaeus, 1758
34                                                          Homo sapiens
35                                           Homo sapiens Linnaeus, 1758
36                                           Homo sapiens Linnaeus, 1758
37                                                          Homo sapiens
38                                           Homo sapiens Linnaeus, 1758
39                                           Homo sapiens Linnaeus, 1758
40                                                       Homo sapiens L.
41                                                          Homo sapiens
42                                                          Homo sapiens
43                                                          Homo sapiens
44                                                          Homo sapiens
45                                           Homo sapiens Linnaeus, 1758
46                                                          Homo sapiens
47                                           Homo sapiens Linnaeus, 1758
48                                           Homo sapiens Linnaeus, 1758
49                                           Homo sapiens Linnaeus, 1758
50                                                          Homo sapiens
51                                           Homo sapiens Linnaeus, 1758
52                                                          Homo sapiens
53                                                          Homo sapiens
54                                            Homo sapiens Linnaeus 1758
55                                            Homo sapiens Linnaeus 1758
                                                        data_source_title
1                                                                    NCBI
2                                                                Freebase
3                                                                     EOL
4                                                    Illinois Wildflowers
5                                                                 CU*STAR
6                                                                   nlbif
7                                                           uBio NameBank
8                                                       Catalogue of Life
9                                                                    ITIS
10                                               GRIN Taxonomy for Plants
11                                                                Union 4
12                        Interim Register of Marine and Nonmarine Genera
13                                                 GBIF Backbone Taxonomy
14                                                 GBIF Backbone Taxonomy
15                                                                    EOL
16                                                                    EOL
17                                                                    EOL
18 Catalogue of Vascular Plant Species of Central and Northeastern Brazil
19                                                       Wikipedia in EOL
20                         Database of Vascular Plants of Canada (VASCAN)
21                                              USDA NRCS PLANTS Database
22                                       The National Checklist of Taiwan
23                                                                  EUNIS
24                                                              BioLib.cz
25                                   Tropicos - Missouri Botanical Garden
26                                                                  nlbif
27                                    The International Plant Names Index
28                                    The International Plant Names Index
29                                                          uBio NameBank
30                                                                 Arctos
31         Checklist da Flora de Portugal (Continental, Açores e Madeira)
32                                                      Catalogue of Life
33                                                                   ITIS
34                                                                   NCBI
35                                                                Union 4
36                        Interim Register of Marine and Nonmarine Genera
37                                                               Freebase
38                                                 GBIF Backbone Taxonomy
39                                                                    EOL
40                                                                    EOL
41                                                                    EOL
42                                                              AskNature
43                                                               BioPedia
44                                                                  AnAge
45                                       The National Checklist of Taiwan
46                                                                CU*STAR
47                                    IUCN Red List of Threatened Species
48                                                              BioLib.cz
49                                                                  nlbif
50                                                Index to Organism Names
51                                                          uBio NameBank
52                                                          uBio NameBank
53                                                                 Arctos
54                                              The Paleobiology Database
55                                        The Mammal Species of The World
   score
1  0.988
2  0.988
3  0.988
4  0.988
5  0.988
6  0.988
7  0.988
8  0.988
9  0.988
10 0.988
11 0.988
12 0.988
13 0.988
14 0.988
15 0.988
16 0.988
17 0.988
18 0.988
19 0.988
20 0.988
21 0.988
22 0.988
23 0.988
24 0.988
25 0.988
26 0.988
27 0.988
28 0.988
29 0.988
30 0.988
31 0.988
32 0.750
33 0.750
34 0.750
35 0.750
36 0.750
37 0.750
38 0.750
39 0.750
40 0.750
41 0.750
42 0.750
43 0.750
44 0.750
45 0.750
46 0.750
47 0.750
48 0.750
49 0.750
50 0.750
51 0.750
52 0.750
53 0.750
54 0.750
55 0.750

$preferred
NULL

$not_known
character(0)

> gnr_resolve(names = c("Helianthus annuus", "Homo sapiens"), best_match_only = TRUE)

$results
     submitted_name      matched_name data_source_title score
1 Helianthus annuus Helianthus annuus              NCBI 0.988
2      Homo sapiens      Homo sapiens              NCBI 0.988

$preferred
NULL

$not_known
character(0)

phylomatic_format

> mynames <- c("Poa annua", "Salix goodingii", "Helianthus annuus")
> phylomatic_format(mynames, format = 'rsubmit')


Retrieving data for taxon 'Poa'


Retrieving data for taxon 'Salix'


Retrieving data for taxon 'Helianthus'

[1] "poaceae%2Fpoa%2Fpoa_annua"                  
[2] "salicaceae%2Fsalix%2Fsalix_goodingii"       
[3] "asteraceae%2Fhelianthus%2Fhelianthus_annuus"

> phylomatic_format(mynames, format = 'isubmit', db = "apg")

[1] "poaceae/poa/poa_annua"                  
[2] "salicaceae/salix/salix_goodingii"       
[3] "asteraceae/helianthus/helianthus_annuus"

phylomatic_tree

参考