Tutorial for taxadb
Carl Boettiger, Kari Norman
2020-02-06
Source:vignettes/articles/intro.Rmd
intro.RmdThe goal of taxadb is to provide fast,
consistent access to taxonomic data, supporting common tasks
such as resolving taxonomic names to identifiers, looking up higher
classification ranks of given species, or returning a list of all
species below a given rank. These tasks are particularly common when
synthesizing data across large species assemblies, such as combining
occurrence records with trait records.
Existing approaches to these problems typically rely on web APIs,
which can make them impractical for work with large numbers of species
or in more complex pipelines. Queries and returned formats also differ
across the different taxonomic authorities, making tasks that query
multiple authorities particularly complex. taxadb creates a
local database of most readily available taxonomic authorities,
each of which is transformed into consistent, standard, and
researcher-friendly tabular formats.
Install and initial setup
To get started, install the development version directly from GitHub:
devtools::install_github("ropensci/taxadb")
library(taxadb)
library(dplyr) # Used to illustrate how a typical workflow combines nicely with `dplyr`Create a local copy of the Catalogue of Life (2018) database:
td_create("col")
#> Importing 2019_common_col.tsv.bz2 in 100000 line chunks:
#>
[-] chunk 2
[\] chunk 3
[|] chunk 4
[/] chunk 5 ...Done! (in 9.042107 secs)Read in the species list used by the Breeding Bird Survey:
bbs_species_list <- system.file("extdata/bbs.tsv", package="taxadb")
bbs <- read.delim(bbs_species_list)Getting names and ids
Two core functions are get_ids() and
get_names(). These functions take a vector of names or ids
(respectively), and return a vector of ids or names (respectively). For
instance, we can use this to attempt to resolve all the bird names in
the Breeding Bird Survey against the Catalogue of Life:
birds <- bbs %>%
select(species) %>%
mutate(id = get_ids(species, "col"))
head(birds, 10)
#> species id
#> 1 Dendrocygna autumnalis COL:35517330
#> 2 Dendrocygna bicolor COL:35517332
#> 3 Anser canagicus COL:35517329
#> 4 Anser caerulescens COL:35517325
#> 5 Chen caerulescens (blue form) <NA>
#> 6 Anser rossii COL:35517328
#> 7 Anser albifrons COL:35517308
#> 8 Branta bernicla COL:35517301
#> 9 Branta bernicla nigricans COL:35537100
#> 10 Branta hutchinsii COL:35536445Note that some names cannot be resolved to an identifier. This can
occur because of miss-spellings, non-standard formatting, or the use of
a synonym not recognized by the naming provider. Names that cannot be
uniquely resolved because they are known synonyms of multiple different
species will also return NA. The filter_name
filtering functions can help us resolve this last case (see below).
get_ids() returns the IDs of accepted names, that is
dwc:AcceptedNameUsageIDs. We can resolve the IDs into
accepted names:
birds %>%
mutate(accepted_name = get_names(id, "col")) %>%
head()
#> species id accepted_name
#> 1 Dendrocygna autumnalis COL:35517330 Tringa flavipes
#> 2 Dendrocygna bicolor COL:35517332 Picoides dorsalis
#> 3 Anser canagicus COL:35517329 Setophaga castanea
#> 4 Anser caerulescens COL:35517325 Bombycilla cedrorum
#> 5 Chen caerulescens (blue form) <NA> Icteria virens
#> 6 Anser rossii COL:35517328 Somateria mollissimaThis illustrates that some of our names, e.g. Dendrocygna bicolor are accepted in the Catalogue of Life, while others, Anser canagicus are known synonyms of a different accepted name: Chen canagica. Resolving synonyms and accepted names to identifiers helps us avoid the possible miss-matches we could have when the same species is known by two different names.
Taxonomic Data Tables
Local access to taxonomic data tables lets us do much more than look
up names and ids. A family of filter_* functions in
taxadb help us work directly with subsets of the taxonomic
data. As we noted above, this can be useful in resolving certain
ambiguous names.
For instance, Trochalopteron henrici gucenense does not resolve to an identifier in ITIS:
get_ids("Trochalopteron henrici gucenense")
#> [1] NAUsing filter_name(), we find this is because the name
resolves not to zero matches, but to more than one match:
filter_name("Trochalopteron henrici gucenense")
#> # A tibble: 2 x 17
#> sort taxonID scientificName taxonRank acceptedNameUsa… taxonomicStatus update_date kingdom phylum class order family genus
#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 1 ITIS:9… Trochaloptero… subspeci… ITIS:916117 synonym <NA> Animal… Chord… Aves Pass… Leiot… Troc…
#> 2 1 ITIS:9… Trochaloptero… subspeci… ITIS:916116 synonym <NA> Animal… Chord… Aves Pass… Leiot… Troc…
#> # … with 4 more variables: specificEpithet <chr>, vernacularName <chr>, infraspecificEpithet <chr>, input <chr>
filter_name("Trochalopteron henrici gucenense") %>%
mutate(acceptedNameUsage = get_names(acceptedNameUsageID)) %>%
select(scientificName, taxonomicStatus, acceptedNameUsage, acceptedNameUsageID)
#> # A tibble: 2 x 4
#> scientificName taxonomicStatus acceptedNameUsage acceptedNameUsageID
#> <chr> <chr> <chr> <chr>
#> 1 Trochalopteron henrici gucenense synonym Trochalopteron henrici ITIS:916117
#> 2 Trochalopteron henrici gucenense synonym Trochalopteron elliotii ITIS:916116Similar functions filter_id, filter_rank,
and filter_common take IDs, scientific ranks, or common
names, respectively. Here, we can get taxonomic data on all bird names
in the Catalogue of Life:
filter_rank(name = "Aves", rank = "class", provider = "col")
#> # A tibble: 35,398 x 21
#> sort taxonID scientificName acceptedNameUsa… taxonomicStatus taxonRank kingdom phylum class order family genus
#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 1 COL:35… Sturnella mag… COL:35520416 accepted species Animal… Chord… Aves Pass… Icter… Stur…
#> 2 1 COL:35… Tauraco porph… COL:35530219 accepted infraspe… Animal… Chord… Aves Muso… Musop… Taur…
#> 3 1 COL:35… Pyroderus scu… COL:35534370 accepted infraspe… Animal… Chord… Aves Pass… Cotin… Pyro…
#> 4 1 COL:35… Dromaius minor COL:35552206 synonym infraspe… Animal… Chord… Aves Casu… Droma… Drom…
#> 5 1 COL:35… Lepidocolapte… COL:35525495 accepted species Animal… Chord… Aves Pass… Furna… Lepi…
#> 6 1 COL:35… Casuarius pap… COL:35552204 synonym infraspe… Animal… Chord… Aves Casu… Casua… Casu…
#> 7 1 COL:35… Forpus modest… COL:35536431 accepted species Animal… Chord… Aves Psit… Psitt… Forp…
#> 8 1 COL:35… Pterocnemia p… COL:35552203 synonym infraspe… Animal… Chord… Aves Rhei… Rheid… Rhea
#> 9 1 COL:35… Ceyx lepidus … COL:35532279 accepted infraspe… Animal… Chord… Aves Cora… Alced… Ceyx
#> 10 1 COL:35… Rhea tarapace… COL:35552202 synonym infraspe… Animal… Chord… Aves Rhei… Rheid… Rhea
#> # … with 35,388 more rows, and 9 more variables: specificEpithet <chr>, infraspecificEpithet <chr>, taxonConceptID <chr>,
#> # isExtinct <chr>, nameAccordingTo <chr>, namePublishedIn <chr>, scientificNameAuthorship <chr>, vernacularName <chr>,
#> # input <chr>Combining these with dplyr functions can make it easy to
explore this data: for instance, which families have the most
species?
filter_rank(name = "Aves", rank = "class", provider = "col") %>%
filter(taxonomicStatus == "accepted", taxonRank=="species") %>%
group_by(family) %>%
count(sort = TRUE) %>%
head()
#> # A tibble: 6 x 2
#> # Groups: family [6]
#> family n
#> <chr> <int>
#> 1 Tyrannidae 401
#> 2 Thraupidae 374
#> 3 Psittacidae 370
#> 4 Trochilidae 338
#> 5 Muscicapidae 314
#> 6 Columbidae 312Using the database connection directly
filter_* functions by default return in-memory data
frames. Because they are filtering functions, they return a subset of
the full data which matches a given query (names, ids, ranks, etc), so
the returned data.frames are smaller than the full record of a naming
provider. Working directly with the SQL connection to the MonetDBLite
database gives us access to all the data. The taxa_tbl()
function provides this connection:
taxa_tbl("col")
#> # Source: table<2019_dwc_col> [?? x 19]
#> # Database: duckdb_connection
#> taxonID scientificName acceptedNameUsa… taxonomicStatus taxonRank kingdom phylum class order family genus specificEpithet
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 COL:31… Limacoccus br… COL:316423 accepted species Animal… Arthr… Inse… Hemi… Beeso… Lima… brasiliensis
#> 2 COL:31… Coccus bromel… COL:316424 accepted species Animal… Arthr… Inse… Hemi… Cocci… Cocc… bromeliae
#> 3 COL:31… Apiomorpha po… COL:316425 accepted species Animal… Arthr… Inse… Hemi… Erioc… Apio… pomaphora
#> 4 COL:31… Eriococcus ch… COL:316441 accepted species Animal… Arthr… Inse… Hemi… Erioc… Erio… chaoticus
#> 5 COL:31… Eriococcus ch… COL:316442 accepted species Animal… Arthr… Inse… Hemi… Erioc… Erio… chathamensis
#> 6 COL:31… Eriococcus ch… COL:316443 accepted species Animal… Arthr… Inse… Hemi… Erioc… Erio… chilensis
#> 7 COL:31… Eriococcus ci… COL:316444 accepted species Animal… Arthr… Inse… Hemi… Erioc… Erio… cingulatus
#> 8 COL:31… Eriococcus ci… COL:316445 accepted species Animal… Arthr… Inse… Hemi… Erioc… Erio… cistacearum
#> 9 COL:31… Eriococcus bu… COL:316447 accepted species Animal… Arthr… Inse… Hemi… Erioc… Erio… busariae
#> 10 COL:31… Eriococcus au… COL:316450 accepted species Animal… Arthr… Inse… Hemi… Erioc… Erio… australis
#> # … with more rows, and 7 more variables: infraspecificEpithet <chr>, taxonConceptID <chr>, isExtinct <chr>,
#> # nameAccordingTo <chr>, namePublishedIn <chr>, scientificNameAuthorship <chr>, vernacularName <chr>We can still use most familiar dplyr verbs to perform
common tasks. For instance: which species has the most known
synonyms?
taxa_tbl("col") %>%
count(acceptedNameUsageID, sort=TRUE)
#> # Source: lazy query [?? x 2]
#> # Database: duckdb_connection
#> # Ordered by: desc(n)
#> acceptedNameUsageID n
#> <chr> <dbl>
#> 1 COL:43082445 456
#> 2 COL:43081989 373
#> 3 COL:43124375 329
#> 4 COL:43353659 328
#> 5 COL:43223150 322
#> 6 COL:43337824 307
#> 7 COL:43124158 302
#> 8 COL:43081973 296
#> 9 COL:43333057 253
#> 10 COL:23162697 252
#> # … with more rows