taxize is a taxonomic toolbelt for R. taxize wraps APIs for a large suite of taxonomic databases availab on the web.
First, install and load taxize into the R session.
install.packages("taxize")
library("taxize")
Advanced users can also download and install the latest development copy from GitHub.
This is a common task in biology. We often have a list of species names and we want to know a) if we have the most up to date names, b) if our names are spelled correctly, and c) the scientific name for a common name. One way to resolve names is via the Global Names Resolver (GNR) service provided by the Encyclopedia of Life. Here, we are searching for two misspelled names:
temp <- gnr_resolve(names = c("Helianthos annus", "Homo saapiens"))
head( temp$results )
#> submitted_name matched_name data_source_title score
#> 1 Helianthos annus Helianthus annus EOL 0.75
#> 2 Helianthos annus Helianthus annus L. EOL 0.75
#> 3 Helianthos annus Helianthus annus uBio NameBank 0.75
#> 4 Helianthos annus Helianthus annuus L. Catalogue of Life 0.75
#> 5 Helianthos annus Helianthus annuus L. ITIS 0.75
#> 6 Helianthos annus Helianthus annuus NCBI 0.75
The correct spellings are Helianthus annuus and Homo sapiens. Another approach uses the Taxonomic Name Resolution Service via the Taxosaurus API developed by iPLant and the Phylotastic organization. In this example, we provide a list of species names, some of which are misspelled, and we'll call the API with the tnrs function.
mynames <- c("Helianthus annuus", "Pinus contort", "Poa anua", "Abis magnifica",
"Rosa california", "Festuca arundinace", "Sorbus occidentalos","Madia sateva")
tnrs(query = mynames, source = "iPlant_TNRS")[ , -c(5:7)]
#> Calling http://taxosaurus.org/retrieve/f2be9ae38992ada133d90edd3a5e6322
#> submittedname acceptedname sourceid score
#> 1 Sorbus occidentalos Sorbus occidentalis iPlant_TNRS 0.99
#> 2 Festuca arundinace Festuca arundinacea iPlant_TNRS 0.99
#> 3 Abis magnifica Abies magnifica iPlant_TNRS 0.96
#> 4 Pinus contort Pinus contorta iPlant_TNRS 0.98
#> 5 Poa anua Poa annua iPlant_TNRS 0.96
#> 6 Madia sateva Madia sativa iPlant_TNRS 0.97
#> 7 Helianthus annuus Helianthus annuus iPlant_TNRS 1
#> 8 Rosa california Rosa californica iPlant_TNRS 0.99
It turns out there are a few corrections: e.g., Madia sateva should be Madia sativa, and Rosa california should be Rosa californica. Note that this search worked because fuzzy matching was employed to retrieve names that were close, but not exact matches. Fuzzy matching is only available for plants in the TNRS service, so we advise using EOL's Global Names Resolver if you need to resolve animal names.
taxize takes the approach that the user should be able to make decisions about what resource to trust, rather than making the decision. Both the EOL GNR and the TNRS services provide data from a variety of data sources. The user may trust a specific data source, thus may want to use the names from that data source. In the future, we may provide the ability for taxize to suggest the best match from a variety of sources.
Another common use case is when there are many synonyms for a species. In this example, we have three synonyms of the currently accepted name for a species.
mynames <- c("Helianthus annuus ssp. jaegeri", "Helianthus annuus ssp. lenticularis", "Helianthus annuus ssp. texanus")
(tsn <- get_tsn(mynames, accepted = FALSE))
[1] "525928" "525929" "525930"
attr(,"match")
[1] "found" "found" "found"
attr(,"uri")
[1] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=525928"
[2] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=525929"
[3] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=525930"
attr(,"class")
[1] "tsn"
library("plyr")
ldply(tsn, itis_acceptname)
submittedtsn acceptedname acceptedtsn
1 525928 Helianthus annuus 36616
2 525929 Helianthus annuus 36616
3 525930 Helianthus annuus 36616
Another task biologists often face is getting higher taxonomic names for a taxa list. Having the higher taxonomy allows you to put into context the relationships of your species list. For example, you may find out that species A and species B are in Family C, which may lead to some interesting insight, as opposed to not knowing that Species A and B are closely related. This also makes it easy to aggregate/standardize data to a specific taxonomic level (e.g., family level) or to match data to other databases with different taxonomic resolution (e.g., trait databases).
A number of data sources in taxize provide the capability to retrieve higher taxonomic names, but we will highlight two of the more useful ones: Integrated Taxonomic Information System (ITIS) and National Center for Biotechnology Information (NCBI). First, we'll search for two species, Abies procera} and *Pinus contorta within ITIS.
specieslist <- c("Abies procera","Pinus contorta")
classification(specieslist, db = 'itis')
#>
#> Retrieving data for taxon 'Abies procera'
#>
#>
#> Retrieving data for taxon 'Pinus contorta'
#> $`Abies procera`
#> name rank id
#> 1 Plantae Kingdom 202422
#> 2 Viridaeplantae Subkingdom 846492
#> 3 Streptophyta Infrakingdom 846494
#> 4 Tracheophyta Division 846496
#> 5 Spermatophytina Subdivision 846504
#> 6 Gymnospermae Infradivision 846506
#> 7 Pinopsida Class 500009
#> 8 Pinales Order 500028
#> 9 Pinaceae Family 18030
#> 10 Abies Genus 18031
#> 11 Abies procera Species 181835
#>
#> $`Pinus contorta`
#> name rank id
#> 1 Plantae Kingdom 202422
#> 2 Viridaeplantae Subkingdom 846492
#> 3 Streptophyta Infrakingdom 846494
#> 4 Tracheophyta Division 846496
#> 5 Spermatophytina Subdivision 846504
#> 6 Gymnospermae Infradivision 846506
#> 7 Pinopsida Class 500009
#> 8 Pinales Order 500028
#> 9 Pinaceae Family 18030
#> 10 Pinus Genus 18035
#> 11 Pinus contorta Species 183327
#>
#> attr(,"class")
#> [1] "classification"
#> attr(,"db")
#> [1] "itis"
It turns out both species are in the family Pinaceae. You can also get this type of information from the NCBI by doing classification(specieslist, db = 'ncbi').
Instead of a full classification, you may only want a single name, say a family name for your species of interest. The function *tax_name} is built just for this purpose. As with the classification function you can specify the data source with the db argument, either ITIS or NCBI.
tax_name(query = "Helianthus annuus", get = "family", db = "ncbi")
#>
#> Retrieving data for taxon 'Helianthus annuus'
#> db query family
#> 1 ncbi Helianthus annuus Asteraceae
I may happen that a data source does not provide information on the queried species, than one could take the result from another source and union the results from the different sources.
As mentioned most databases use a numeric code to reference a species. A general workflow in taxize is: Retrieve Code for the queried species and then use this code to query more data/information.
Below are a few examples. When you run these examples in R, you are presented with a command prompt asking for the row that contains the name you would like back; that output is not printed below for brevity. In this example, the search term has many matches. The function returns a data frame of the matches, and asks for the user to input what row number to accept.
get_uid(sciname = "Pinus")
#>
#> Retrieving data for taxon 'Pinus'
#>
#>
#>
#>
#>
#> More than one UID found for taxon 'Pinus'!
#>
#> Enter rownumber of taxon (other inputs will return 'NA'):
#> UID Rank Division
#> 1 139271 subgenus seed plants
#> 2 3337 genus seed plants
#> Input accepted, took UID '139271'.
#> [1] "139271"
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.ncbi.nlm.nih.gov/taxonomy/139271"
In another example, you can pass in a long character vector of taxonomic names (although this one is rather short for demo purposes):
splist <- c("annona cherimola", 'annona muricata', "quercus robur")
get_tsn(searchterm = splist, searchtype = "scientific")
#>
#> Retrieving data for taxon 'annona cherimola'
#>
#>
#> Retrieving data for taxon 'annona muricata'
#>
#>
#> Retrieving data for taxon 'quercus robur'
#> [1] "506198" "18098" "19405"
#> attr(,"match")
#> [1] "found" "found" "found"
#> attr(,"uri")
#> [1] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=506198"
#> [2] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=18098"
#> [3] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=19405"
#> attr(,"class")
#> [1] "tsn"
There are functions for many other sources
get_boldid()get_colid()get_eolid()get_gbifid()get_nbnid()get_tpsid()get_ubioid()Sometimes with these functions you get a lot of data back. In these cases you may want to limit your choices. Soon we will incorporate the ability to filter using regex to limit matches, but for now, we have a new parameter, rows, which lets you select certain rows. For example, you can select the first row of each given name, which means there is no interactive component:
get_nbnid(c("Zootoca vivipara","Pinus contorta"), rows = 1)
#>
#> Retrieving data for taxon 'Zootoca vivipara'
#>
#>
#> Retrieving data for taxon 'Pinus contorta'
#> [1] "NHMSYS0001706186" "NHMSYS0000494848"
#> attr(,"class")
#> [1] "nbnid"
#> attr(,"match")
#> [1] "found" "found"
#> attr(,"uri")
#> [1] "https://data.nbn.org.uk/Taxa/NHMSYS0001706186"
#> [2] "https://data.nbn.org.uk/Taxa/NHMSYS0000494848"
Or you can select a range of rows
get_nbnid(c("Zootoca vivipara","Pinus contorta"), rows = 1:3)
#>
#> Retrieving data for taxon 'Zootoca vivipara'
#>
#>
#>
#>
#>
#> More than one nbnid found for taxon 'Zootoca vivipara'!
#>
#> Enter rownumber of taxon (other inputs will return 'NA'):
#> nbnid searchMatchTitle rank
#> 1 NHMSYS0001706186 Zootoca vivipara Species
#> 2 NHMSYS0020784960 Zootoca vivipara subsp. pannonica Subspecies
#> 3 NHMSYS0001706185 Zootoca Genus
#> nameStatus
#> 1 Recommended
#> 2 Recommended
#> 3 Recommended
#> Input accepted, took nbnid 'NHMSYS0001706186'.
#>
#>
#> Retrieving data for taxon 'Pinus contorta'
#>
#>
#>
#>
#>
#> More than one nbnid found for taxon 'Pinus contorta'!
#>
#> Enter rownumber of taxon (other inputs will return 'NA'):
#> nbnid searchMatchTitle rank nameStatus
#> 1 NHMSYS0000494848 Pinus contorta var. contorta Variety Recommended
#> 2 NBNSYS0000004786 Pinus contorta Species Recommended
#> 3 NHMSYS0000494848 Pinus contorta subsp. contorta Subspecies Recommended
#> Input accepted, took nbnid 'NHMSYS0000494848'.
#> [1] "NHMSYS0001706186" "NHMSYS0000494848"
#> attr(,"class")
#> [1] "nbnid"
#> attr(,"match")
#> [1] "found" "found"
#> attr(,"uri")
#> [1] "https://data.nbn.org.uk/Taxa/NHMSYS0001706186"
#> [2] "https://data.nbn.org.uk/Taxa/NHMSYS0000494848"
In addition, in case you don't want to do interactive name selection in the case where there are a lot of names, you can get all data back with functions of the form, e.g., get_tsn_(), and likewise for other data sources. For example:
out <- get_nbnid_("Poa annua")
#>
#> Retrieving data for taxon 'Poa annua'
NROW(out)
#> [1] 1
That's a lot of data, so we can get only certain rows back
get_nbnid_("Poa annua", rows = 1:10)
#>
#> Retrieving data for taxon 'Poa annua'
#> $`Poa annua`
#> ptaxonVersionKey searchMatchTitle rank nameStatus
#> 1 NBNSYS0000002544 Poa annua Species Recommended
#> 2 NHMSYS0000461798 Poa Genus Recommended
#> 3 NHMSYS0000461804 Poa laxa Species Synonym
#> 4 NHMSYS0021060390 Poales Order Recommended
#> 5 NBNSYS0000002551 Poa glauca Species Recommended
#> 6 NBNSYS0000002547 Poa alpina Species Recommended
#> 7 NHMSYS0000456981 Poa rigida Species Synonym
#> 8 NBNSYS0000002545 Poa exilis Species Undetermined
#> 9 NBNSYS0000002551 Poa caesia Species Synonym
#> 10 NBNSYS0000160753 Poaceae Family Recommended
We've also introduced in v0.5 the ability to coerce numerics and alphanumerics to taxonomic ID classes that are usually only retrieved via get_*() functions.
For example, adfafd
as.gbifid(get_gbifid("Poa annua")) # already a uid, returns the same
#>
#> Retrieving data for taxon 'Poa annua'
#> [1] "2704179"
#> attr(,"class")
#> [1] "gbifid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.gbif.org/species/2704179"
as.gbifid(2704179) # numeric
#> [1] "2704179"
#> attr(,"class")
#> [1] "gbifid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.gbif.org/species/2704179"
as.gbifid("2704179") # character
#> [1] "2704179"
#> attr(,"class")
#> [1] "gbifid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.gbif.org/species/2704179"
as.gbifid(list("2704179","2435099","3171445")) # list, either numeric or character
#> [1] "2704179" "2435099" "3171445"
#> attr(,"class")
#> [1] "gbifid"
#> attr(,"match")
#> [1] "found" "found" "found"
#> attr(,"uri")
#> [1] "http://www.gbif.org/species/2704179"
#> [2] "http://www.gbif.org/species/2435099"
#> [3] "http://www.gbif.org/species/3171445"
These as.*() functions do a quick check of the web resource to make sure it's a real ID. However, you can turn this check off, making this coercion much faster:
system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=TRUE)) )
#> user system elapsed
#> 0.202 0.007 2.191
system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=FALSE)) )
#> user system elapsed
#> 0.001 0.000 0.000
If someone is not a taxonomic specialist on a particular taxon he likely does not know what children taxa are within a family, or within a genus. This task becomes especially unwieldy when there are a large number of taxa downstream. You can of course go to a website like Wikispecies or Encyclopedia of Life to get downstream names. However, taxize provides an easy way to programatically search for downstream taxa, both for the Catalogue of Life (CoL) and the Integrated Taxonomic Information System. Here is a short example using the CoL in which we want to find all the species within the genus Apis (honey bees).
downstream("Apis", downto = "Species", db = "col")
#>
#> Retrieving data for taxon 'Apis'
#> $Apis
#> childtaxa_id childtaxa_name childtaxa_rank
#> 1 6971712 Apis andreniformis Species
#> 2 6971713 Apis cerana Species
#> 3 6971714 Apis dorsata Species
#> 4 6971715 Apis florea Species
#> 5 6971716 Apis koschevnikovi Species
#> 6 6845885 Apis mellifera Species
#> 7 6971717 Apis nigrocincta Species
#>
#> attr(,"class")
#> [1] "downstream"
#> attr(,"db")
#> [1] "col"
We can also request data from ITIS
downstream("Apis", downto = "Species", db = "itis")
#>
#> Retrieving data for taxon 'Apis'
#> $Apis
#> tsn parentname parenttsn taxonname rankid rankname
#> 1 154396 Apis 154395 Apis mellifera 220 Species
#> 2 763550 Apis 154395 Apis andreniformis 220 Species
#> 3 763551 Apis 154395 Apis cerana 220 Species
#> 4 763552 Apis 154395 Apis dorsata 220 Species
#> 5 763553 Apis 154395 Apis florea 220 Species
#> 6 763554 Apis 154395 Apis koschevnikovi 220 Species
#> 7 763555 Apis 154395 Apis nigrocincta 220 Species
#>
#> attr(,"class")
#> [1] "downstream"
#> attr(,"db")
#> [1] "itis"
You may sometimes only want the direct children. We got you covered on that front, with methods for ITIS, NCBI, and Catalogue of Life. For example, let's get direct children (species in this case) of the bee genus Apis using COL data:
children(get_colid("Apis"))
#>
#> Retrieving data for taxon 'Apis'
#> $`20126217`
#> childtaxa_id childtaxa_name childtaxa_rank
#> 1 6971712 Apis andreniformis Species
#> 2 6971713 Apis cerana Species
#> 3 6971714 Apis dorsata Species
#> 4 6971715 Apis florea Species
#> 5 6971716 Apis koschevnikovi Species
#> 6 6845885 Apis mellifera Species
#> 7 6971717 Apis nigrocincta Species
#>
#> attr(,"class")
#> [1] "children"
#> attr(,"db")
#> [1] "col"
The direct children (genera in this case) of Pinaceae using NCBI data:
children("Pinaceae", db = "ncbi")
#> $Pinaceae
#> childtaxa_id childtaxa_name childtaxa_rank
#> 1 123600 Nothotsuga genus
#> 2 64685 Cathaya genus
#> 3 3358 Tsuga genus
#> 4 3356 Pseudotsuga genus
#> 5 3354 Pseudolarix genus
#> 6 3337 Pinus genus
#> 7 3328 Picea genus
#> 8 3325 Larix genus
#> 9 3323 Keteleeria genus
#> 10 3321 Cedrus genus
#> 11 3319 Abies genus
#>
#> attr(,"class")
#> [1] "children"
#> attr(,"db")
#> [1] "ncbi"
With accession numbers
genbank2uid(id = 'AJ748748')
#> [1] "282199"
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.ncbi.nlm.nih.gov/taxonomy/282199"
With gi numbers
genbank2uid(id = 62689767)
#> [1] "282199"
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.ncbi.nlm.nih.gov/taxonomy/282199"
Biologist often need to match different sets of data tied to species. For example, trait-based approaches are a promising tool in ecology. One problem is that abundance data must be matched with trait databases. These two data tables may contain species information on different taxonomic levels and possibly data must be aggregated to a joint taxonomic level, so that the data can be merged. taxize can help in this data-cleaning step, providing a reproducible workflow:
We can use the mentioned classification-function to retrieve the taxonomic hierarchy and then search the hierarchies up- and downwards for matches. Here is an example to match a species with names on three different taxonomic levels.
A <- "gammarus roeseli"
B1 <- "gammarus roeseli"
B2 <- "gammarus"
B3 <- "gammaridae"
A_clas <- classification(A, db = 'ncbi')
B1_clas <- classification(B1, db = 'ncbi')
B2_clas <- classification(B2, db = 'ncbi')
B3_clas <- classification(B3, db = 'ncbi')
B1[match(A, B1)]
#> [1] "gammarus roeseli"
A_clas[[1]]$rank[tolower(A_clas[[1]]$name) %in% B2]
#> [1] "genus"
A_clas[[1]]$rank[tolower(A_clas[[1]]$name) %in% B3]
#> [1] "family"
If we find a direct match (here Gammarus roeseli), we are lucky. But we can also match Gammaridae with Gammarus roeseli, but on a lower taxonomic level. A more comprehensive and realistic example (matching a trait table with an abundance table) is given in the vignette on matching.