taxalight provides a lightweight, lightning fast query for resolving
taxonomic identifiers to taxonomic names, and vice versa, by using a
Lightning Memory Mapped Database backend. Compared to taxadb, it has
few dependencies, fewer functions, and faster performance.
If you just need to resolve scientific names to identifiers and vice
versa, taxalight is a fast and simple option. taxalight currently
supports names from Integrated Taxonomic Information System (ITIS),
National Center for Biotechnology Information (NCBI), Global
Biodiversity Information Facility (GBIF), Catalogue of Life (COL), and
Open Tree Taxonomy (OTT). Like taxadb, taxalight uses annual stable
version snapshots from these providers and presents the naming data in
the simple and consistent tabular format of the Darwin Core Standard.
You can install the released version of taxalight from CRAN with:
install.packages("taxalight")And the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("cboettig/taxalight")taxalight needs to first download and import the provider naming
databases. This can take a while, but needs to only be done once.
library(taxalight)
tl_create("itis")
#> Now we can look up species by names, IDs, or a mix. Even vernacular
names can be recognized as key. Note that only exact matches are
supported though! ITIS (itis) is the default provider, but GBIF, COL,
OTT, and NCBI are also available.
tl("Homo sapiens", provider = "itis")
#> # A tibble: 30 x 14
#> taxonID scientificName acceptedNameUsag… taxonomicStatus taxonRank kingdom
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 ITIS:944… Homo aethiopic… ITIS:180092 synonym species Animal…
#> 2 ITIS:944… Homo americanus ITIS:180092 synonym species Animal…
#> 3 ITIS:944… Homo arabicus ITIS:180092 synonym species Animal…
#> 4 ITIS:944… Homo australas… ITIS:180092 synonym species Animal…
#> 5 ITIS:944… Homo cafer ITIS:180092 synonym species Animal…
#> 6 ITIS:944… Homo capensis ITIS:180092 synonym species Animal…
#> 7 ITIS:944… Homo columbicus ITIS:180092 synonym species Animal…
#> 8 ITIS:944… Homo drennani ITIS:180092 synonym species Animal…
#> 9 ITIS:944… Homo grimaldii ITIS:180092 synonym species Animal…
#> 10 ITIS:944… Homo hottentot… ITIS:180092 synonym species Animal…
#> # … with 20 more rows, and 8 more variables: phylum <chr>, class <chr>,
#> # order <chr>, family <chr>, genus <chr>, specificEpithet <chr>,
#> # infraspecificEpithet <lgl>, vernacularName <chr>id <- c("ITIS:180092", "ITIS:179913", "Dendrocygna autumnalis", "Snow Goose",
provider = "itis")
tl(id)
#> # A tibble: 6 x 14
#> taxonID scientificName acceptedNameUsa… taxonomicStatus taxonRank kingdom
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 ITIS:180… Homo sapiens ITIS:180092 accepted species Animal…
#> 2 ITIS:179… Mammalia ITIS:179913 accepted class <NA>
#> 3 ITIS:175… Dendrocygna autu… ITIS:175044 accepted species Animal…
#> 4 ITIS:175… Anser caerulesce… ITIS:175038 synonym species Animal…
#> 5 ITIS:175… Anser hyperboreus ITIS:175038 synonym species Animal…
#> 6 ITIS:175… Chen caerulescens ITIS:175038 accepted species Animal…
#> # … with 8 more variables: phylum <chr>, class <chr>, order <chr>,
#> # family <chr>, genus <chr>, specificEpithet <chr>,
#> # infraspecificEpithet <lgl>, vernacularName <chr>For convenience, we can request just the name or id as a character
vector (paralleling functionality in taxize). If the name is
recognized as an accepted name, the corresponding ID for the provider is
returned.
get_ids("Homo sapiens")
#> Homo sapiens
#> "ITIS:180092"get_names("ITIS:179913")
#> [1] "Mammalia"library(bench)sp <- c("Dendrocygna autumnalis", "Dendrocygna bicolor",
"Chen canagica", "Chen caerulescens" )taxadb::td_create("itis", schema="dwc")
#> Registered S3 methods overwritten by 'readr':
#> method from
#> format.col_spec vroom
#> print.col_spec vroom
#> print.collector vroom
#> print.date_names vroom
#> print.locale vroom
#> str.col_spec vroom
#> Warning in overwrite_db(con, tablename): overwriting 2020_dwc_itis
#> Importing /home/cboettig/.local/share/R/contentid/data/ef/6a/ef6ae3b337be65c661d5e2d847613ebc955bb9d91d2d98d03cf8c53029cecc2a in 100000 line chunks:
#> ...Done! (in 14.38502 secs)bench::bench_time(
df_tb <- taxadb::filter_name(sp, "itis")
)
#> process real
#> 2.81s 2.84s
df_tb
#> # A tibble: 4 x 17
#> sort taxonID scientificName taxonRank acceptedNameUsag… taxonomicStatus
#> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 1 ITIS:175… Dendrocygna autum… species ITIS:175044 accepted
#> 2 2 ITIS:175… Dendrocygna bicol… species ITIS:175046 accepted
#> 3 3 ITIS:175… Chen canagica species ITIS:175042 accepted
#> 4 4 ITIS:175… Chen caerulescens species ITIS:175038 accepted
#> # … with 11 more variables: update_date <chr>, kingdom <chr>, phylum <chr>,
#> # class <chr>, order <chr>, family <chr>, genus <chr>, specificEpithet <chr>,
#> # infraspecificEpithet <chr>, vernacularName <chr>, input <chr>bench::bench_time(
df_tl <- taxalight::tl(sp, "itis")
)
#> process real
#> 29.8ms 44.8ms
df_tl
#> # A tibble: 9 x 14
#> taxonID scientificName acceptedNameUsag… taxonomicStatus taxonRank kingdom
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 ITIS:17… Dendrocygna autu… ITIS:175044 accepted species Animal…
#> 2 ITIS:17… Dendrocygna bico… ITIS:175046 synonym subspeci… Animal…
#> 3 ITIS:17… Dendrocygna bico… ITIS:175046 accepted species Animal…
#> 4 ITIS:17… Philacte canagica ITIS:175042 synonym species Animal…
#> 5 ITIS:17… Anser canagicus ITIS:175042 synonym species Animal…
#> 6 ITIS:17… Chen canagica ITIS:175042 accepted species Animal…
#> 7 ITIS:17… Anser caerulesce… ITIS:175038 synonym species Animal…
#> 8 ITIS:17… Anser hyperboreus ITIS:175038 synonym species Animal…
#> 9 ITIS:17… Chen caerulescens ITIS:175038 accepted species Animal…
#> # … with 8 more variables: phylum <chr>, class <chr>, order <chr>,
#> # family <chr>, genus <chr>, specificEpithet <chr>,
#> # infraspecificEpithet <lgl>, vernacularName <chr>bench::bench_time(
id_tb <- taxadb::get_ids(sp, "itis")
)
#> process real
#> 2.42s 2.54s
id_tb
#> Dendrocygna autumnalis Dendrocygna bicolor Chen canagica
#> "ITIS:175044" "ITIS:175046" "ITIS:175042"
#> Chen caerulescens
#> "ITIS:175038"bench::bench_time(
id_tl <- taxalight::get_ids(sp, "itis")
)
#> process real
#> 31.7ms 45ms
id_tl
#> Dendrocygna autumnalis Dendrocygna bicolor Chen canagica
#> "ITIS:175044" "ITIS:175046" "ITIS:175042"
#> Chen caerulescens
#> "ITIS:175038"Under the hood, taxalight consumes a DCAT2/PROV-O based
description
of the data provenance which generates the standard-format tables
imported by taxalight (and taxadb) from the original data published
by the naming providers. All data and scripts are identified by
content-based identifiers, which can be resolved by
https://hash-archive.org or the R package, contentid. This provides
several benefits over resolving data from a URL source:
- We have cryptographic certainty that we get the expected bytes every time
- We can automatically cache and reference a local copy. If the hash matches the requested identifier, then we don’t even need to check eTags or other indications that the version we have already is the right one.
- By registering multiple sources, the data can remain accessible even if one link rots away.
Input data and scripts for transforming the data into the desired format are similarly archived and referenced by content identifiers in the provenance trace.