Search network by taxon names and unique taxonomic identifiers.
This function offers the opportunity to retrieve taxon based on (i) known identifier
such as the taxonomic serial number (TSN), GBIF ID etc. or (ii) text search using partial match.
Have a look at the list of arguments to see the complete list of identifiers accessible.
If any unique identifier argument is used (i.e. tsn etc.), then query is ignored. Moreover,
if several taxonomic identifiers are specified, then only the first one is considered.
Usage
search_taxonomy(
query,
tsn = NULL,
gbif = NULL,
eol = NULL,
col = NULL,
bold = NULL,
ncbi = NULL,
verbose = TRUE,
...
)Arguments
- query
a character string including a single keyword. Note that if an empty character string is passed, then all datasets available are returned.
- tsn
a
numeric. Unique taxonomic identifier from Integrated Taxonomic Information System (https://www.itis.gov).- gbif
a
numeric. Unique taxonomic identifier from Global Biodiversity Information Facility (https://www.gbif.org).- eol
a
numeric. Unique taxonomic identifier from Encyclopedia of Life (https://eol.org).- col
a
numeric. Unique taxonomic identifier from Catalogue of Life (https://www.catalogueoflife.org).- bold
a
numeric. Unique taxonomic identifier from Barcode of Life (http://www.boldsystems.org).- ncbi
a
numeric. Unique taxonomic identifier from National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov).- verbose
a
logical. Should extra information be reported on progress?- ...
further arguments to be passed to
httr::GET().
Value
An object of class mgSearchTaxonomy, which is a data.frame including
all taxa matching the query.
Details
Taxon names of the taxonomy table were validated with
TNRS (see https://tnrs.biendata.org and/or GNR
might not be the taxon name documented in the original publication.
In order to identify relevant networks with the original name, use
search_nodes().
The validation of taxon names was performed by an automated procedure and if there is any doubt, the original names recorded by authors should be regarded as the most reliable information. Please report any issue related to taxonomy at https://github.com/mangal-interactions/contribute/issues/new/choose/.
Examples
# \donttest{
search_taxonomy("Acer")
#> Data retrieval 100%
#>
#> Data retrieval 100%
#>
#> Data retrieval 100%
#>
#> Data retrieval 100%
#>
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#>
#> Data retrieval 100%
#>
#>
#> id original_name node_level network_id taxonomy_id
#> 1 2629 Acer negundo taxon 19 2
#> 2 2630 Acer saccharinum taxon 19 3
#> 3 8895 Acer shirasawanum taxon 948 3117
#> 4 8923 Acer ukurunduense taxon 948 3144
#> 5 8930 Acer japonicum taxon 948 3151
#> created_at updated_at taxonomy.id
#> 1 2019-02-22T18:48:49.433Z 2019-02-22T18:48:49.433Z 2
#> 2 2019-02-22T18:48:49.465Z 2019-02-22T18:48:49.465Z 3
#> 3 2019-02-25T20:52:53.654Z 2019-02-25T20:52:53.654Z 3117
#> 4 2019-02-25T20:52:54.835Z 2019-02-25T20:52:54.835Z 3144
#> 5 2019-02-25T20:52:55.175Z 2019-02-25T20:52:55.175Z 3151
#> taxonomy.name taxonomy.ncbi taxonomy.tsn taxonomy.eol taxonomy.bold
#> 1 Acer negundo 4023 28749 583069 100987
#> 2 Acer saccharinum 75745 28757 583072 101028
#> 3 Acer shirasawanum 66216 NA 5613162 485602
#> 4 Acer caudatum 290844 NA 2888949 102168
#> 5 Acer japonicum 47966 837855 2888970 448667
#> taxonomy.gbif taxonomy.col taxonomy.rank
#> 1 3189866 90203e29e2f59e5754167f89b9eba3cc species
#> 2 3189837 1582ed5db846e241f3e18da418a2a477 species
#> 3 7263086 25b4371fbbdc5b1cd43fad895050cc05 species
#> 4 7263099 1211e426bdec174da9a7526348c26fb9 species
#> 5 8010851 3388e995334d5638aeb11ef84f98b319 species
#> taxonomy.created_at taxonomy.updated_at
#> 1 2019-02-21T21:17:12.585Z 2019-06-14T15:20:36.273Z
#> 2 2019-02-21T21:17:12.637Z 2019-06-14T15:20:36.328Z
#> 3 2019-02-22T00:31:49.729Z 2019-06-14T15:24:56.217Z
#> 4 2019-02-22T00:31:52.729Z 2019-06-14T15:24:57.854Z
#> 5 2019-02-22T00:31:53.328Z 2019-06-14T15:24:58.251Z
# Retrieve higher classification
tsn_acer <- search_taxonomy("Acer")$taxonomy.tsn
#> Data retrieval 100%
#>
#> Data retrieval 100%
#>
#> Data retrieval 100%
#>
#> Data retrieval 100%
#>
#> Data retrieval 100%
#>
#> Data retrieval 100%
#>
#>
# }