taxize tutorial
for v0.7.5
taxize is a taxonomic toolbelt for R. taxize wraps APIs for a large suite of taxonomic databases availab on the web.
## Installation
First, install and load `taxize` into the R session.
```r
install.packages("taxize")
```
Or, install development version from GitHub
```r
if (!require("devtools")) install.packages("devtools")
devtools::install_github("ropensci/taxize")
```
```r
library("taxize")
```
## Usage
## Resolve taxonomic name
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][eol]. Here, we are searching for two misspelled names:
```r
temp <- gnr_resolve(names = c("Helianthos annus", "Homo saapiens"))
head(temp)
```
```
#> user_supplied_name submitted_name matched_name
#> 1 Helianthos annus Helianthos annus Helianthus annus
#> 2 Helianthos annus Helianthos annus Helianthus annus L.
#> 3 Helianthos annus Helianthos annus Helianthus annus
#> 4 Helianthos annus Helianthos annus Helianthus annuus L.
#> 5 Helianthos annus Helianthos annus Helianthus annuus L.
#> 6 Helianthos annus Helianthos annus Helianthus annuus
#> data_source_title score
#> 1 EOL 0.75
#> 2 EOL 0.75
#> 3 uBio NameBank 0.75
#> 4 Catalogue of Life 0.75
#> 5 ITIS 0.75
#> 6 NCBI 0.75
```
The correct spellings are *Helianthus annuus* and *Homo sapiens*.
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.
```r
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"
```
```r
lapply(tsn, itis_acceptname)
```
```
[[1]]
submittedtsn acceptedname acceptedtsn
1 525928 Helianthus annuus 36616
[[2]]
submittedtsn acceptedname acceptedtsn
1 525929 Helianthus annuus 36616
[[3]]
submittedtsn acceptedname acceptedtsn
1 525930 Helianthus annuus 36616
```
## Retrieve higher taxonomic names
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)][itis] and [National Center for Biotechnology Information (NCBI)][ncbi]. First, we'll search for two species, *Abies procera} and *Pinus contorta* within ITIS.
```r
specieslist <- c("Abies procera","Pinus contorta")
classification(specieslist, db = 'itis')
```
```
#> $`Abies procera`
#> name rank id
#> 1 Plantae kingdom 202422
#> 2 Viridiplantae subkingdom 954898
#> 3 Streptophyta infrakingdom 846494
#> 4 Embryophyta superdivision 954900
#> 5 Tracheophyta division 846496
#> 6 Spermatophytina subdivision 846504
#> 7 Pinopsida class 500009
#> 8 Pinidae subclass 954916
#> 9 Pinales order 500028
#> 10 Pinaceae family 18030
#> 11 Abies genus 18031
#> 12 Abies procera species 181835
#>
#> $`Pinus contorta`
#> name rank id
#> 1 Plantae kingdom 202422
#> 2 Viridiplantae subkingdom 954898
#> 3 Streptophyta infrakingdom 846494
#> 4 Embryophyta superdivision 954900
#> 5 Tracheophyta division 846496
#> 6 Spermatophytina subdivision 846504
#> 7 Pinopsida class 500009
#> 8 Pinidae subclass 954916
#> 9 Pinales order 500028
#> 10 Pinaceae family 18030
#> 11 Pinus genus 18035
#> 12 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.
```r
tax_name(query = "Helianthus annuus", get = "family", db = "ncbi")
```
```
#> 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.
## Interactive name selection
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.
```r
get_uid(sciname = "Pinus")
```
```
#> status rank division scientificname commonname uid genus
#> 1 active subgenus seed plants Pinus hard pines 139271
#> 2 active genus seed plants Pinus 3337
#> species subsp modificationdate
#> 1 2015/09/16 00:00
#> 2 2004/09/10 00:00
```
```
#> [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):
```r
splist <- c("annona cherimola", 'annona muricata', "quercus robur")
get_tsn(searchterm = splist, searchtype = "scientific")
```
```
#> [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()`
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:
```r
get_nbnid(c("Zootoca vivipara","Pinus contorta"), rows = 1)
```
```
#> [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
```r
get_nbnid(c("Zootoca vivipara","Pinus contorta"), rows = 1:3)
```
```
#> 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
#> 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
```
```
#> [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:
```r
out <- get_nbnid_("Poa annua")
NROW(out$`Poa annua`)
```
```
#> [1] 147
```
That's a lot of data, so we can get only certain rows back
```r
get_nbnid_("Poa annua", rows = 1:10)
```
```
#> $`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 NBNSYS0000002547 Poa alpina species Recommended
#> 6 NBNSYS0000002551 Poa glauca species Recommended
#> 7 NBNSYS0000160753 Poaceae family Recommended
#> 8 NBNSYS0000002545 Poa exilis species Undetermined
#> 9 NHMSYS0000456981 Poa rigida species Synonym
#> 10 NHMSYS0000461804 Poa minor species Synonym
```
## Coerce numerics/alphanumerics to taxon IDs
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
```r
as.gbifid(get_gbifid("Poa annua")) # already a uid, returns the same
```
```
#> gbifid phylum order family canonicalname rank
#> 1 7576620 Tracheophyta Poales Poaceae Poa annua null species
#> 2 7730008 Tracheophyta Poales Poaceae Poa annua species
#> 3 2704179 Tracheophyta Poales Poaceae Poa annua species
#> 4 6313731 Tracheophyta Poales Poaceae Poa annua varia subspecies
#> 5 7857582 Tracheophyta Poales Poaceae Poa annua pilantha subspecies
#> 6 4128771 Tracheophyta Poales Poaceae Poa annua notabilis subspecies
#> 7 6313732 Tracheophyta Poales Poaceae Poa annua supina variety
#> 8 4128718 Tracheophyta Poales Poaceae Poa annua rigidiuscula variety
#> 9 8250063 Tracheophyta Poales Poaceae Poa annua crispa variety
#> 10 5947583 Tracheophyta Poales Poaceae Poa annua maroccana variety
#> 11 7861266 Tracheophyta Poales Poaceae Poa annua supina variety
#> 12 4128778 Tracheophyta Poales Poaceae Poa annua nepalensis variety
#> 13 8157117 Tracheophyta Poales Poaceae Poa annua vivipara variety
#> 14 6085004 Tracheophyta Poales Poaceae Poa annua rivulorum variety
#> 15 7645167 Tracheophyta Poales Poaceae Poa annua lanuginosa variety
#> 16 8207852 Tracheophyta Poales Poaceae Poa annua picta variety
#> 17 8050502 Tracheophyta Poales Poaceae Poa annua villosa variety
#> 18 7572604 Tracheophyta Poales Poaceae Poa annua tomentosa variety
#> 19 8353413 Tracheophyta Poales Poaceae Poa annua triflora variety
#> 20 7665844 Tracheophyta Poales Poaceae Poa annua ovalis form
#> 21 7362863 Tracheophyta Poales Poaceae Poa annua macranthera form
#> 22 2704181 Tracheophyta Poales Poaceae Poa annua reptans form
#> 23 4128735 Tracheophyta Poales Poaceae Poa annua raniglumis subspecies
#> 24 5947756 Tracheophyta Poales Poaceae Poa annua supina subspecies
#> 25 7867993 Tracheophyta Poales Poaceae Poa annua raniglunis subspecies
#> 26 5947582 Tracheophyta Poales Poaceae Poa annua exilis variety
#> 27 8099762 Tracheophyta Poales Poaceae Poa annua humilis variety
#> 28 7456054 Tracheophyta Poales Poaceae Poa annua rivularis variety
#> 29 4128763 Tracheophyta Poales Poaceae Poa annua pilantha variety
#> 30 7853981 Tracheophyta Poales Poaceae Poa annua caespitosa variety
#> 31 7715053 Tracheophyta Poales Poaceae Poa annua racemosa variety
#> 32 7763868 Tracheophyta Poales Poaceae Poa annua brevifolia variety
#> 33 8375402 Tracheophyta Poales Poaceae Poa annua uliginosa variety
#> 34 6431931 Tracheophyta Poales Poaceae Poa annua raniglumis variety
#> 35 6313765 Tracheophyta Poales Poaceae Poa annua reptans variety
#> 36 5947556 Tracheophyta Poales Poaceae Poa annua sikkimensis variety
#> 37 8203801 Tracheophyta Poales Poaceae Poa annua stricta variety
#> 38 5947754 Tracheophyta Poales Poaceae Poa annua exigua variety
#> 39 5947811 Tracheophyta Poales Poaceae Poa annua sericea variety
#> 40 5947586 Tracheophyta Poales Poaceae Poa annua maxima form
#> 41 5947755 Tracheophyta Poales Poaceae Poa annua alpigena form
#> 42 7804763 Tracheophyta Poales Poaceae Poa annua picta form
#> 43 8422205 Tracheophyta Poales Poaceae Poa annua species
#> 44 7262139 Tracheophyta Poales Poaceae Poa annua annua subspecies
#> 45 6313730 Tracheophyta Poales Poaceae Poa annua exilis subspecies
#> 46 6431930 Tracheophyta Poales Poaceae Poa annua annua variety
#> 47 5947585 Tracheophyta Poales Poaceae Poa annua tommasinii variety
#> 48 2704180 Tracheophyta Poales Poaceae Poa annua aquatica variety
#> 49 5947584 Tracheophyta Poales Poaceae Poa annua remotiflora variety
#> 50 7427199 Tracheophyta Poales Poaceae Poa annua elatior variety
#> class
#> 1 Liliopsida
#> 2 Liliopsida
#> 3 Liliopsida
#> 4 Liliopsida
#> 5 Liliopsida
#> 6 Liliopsida
#> 7 Liliopsida
#> 8 Liliopsida
#> 9 Liliopsida
#> 10 Liliopsida
#> 11 Liliopsida
#> 12 Liliopsida
#> 13 Liliopsida
#> 14 Liliopsida
#> 15 Liliopsida
#> 16 Liliopsida
#> 17 Liliopsida
#> 18 Liliopsida
#> 19 Liliopsida
#> 20 Liliopsida
#> 21 Liliopsida
#> 22 Liliopsida
#> 23 Liliopsida
#> 24 Liliopsida
#> 25 Liliopsida
#> 26 Liliopsida
#> 27 Liliopsida
#> 28 Liliopsida
#> 29 Liliopsida
#> 30 Liliopsida
#> 31 Liliopsida
#> 32 Liliopsida
#> 33 Liliopsida
#> 34 Liliopsida
#> 35 Liliopsida
#> 36 Liliopsida
#> 37 Liliopsida
#> 38 Liliopsida
#> 39 Liliopsida
#> 40 Liliopsida
#> 41 Liliopsida
#> 42 Liliopsida
#> 43 Liliopsida
#> 44 Liliopsida
#> 45 Liliopsida
#> 46 Liliopsida
#> 47 Liliopsida
#> 48 Liliopsida
#> 49 Liliopsida
#> 50 Liliopsida
```
```
#> [1] "7576620"
#> attr(,"class")
#> [1] "gbifid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.gbif.org/species/7576620"
```
```r
as.gbifid(2704179) # numeric
```
```
#> [1] "2704179"
#> attr(,"class")
#> [1] "gbifid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.gbif.org/species/2704179"
```
```r
as.gbifid("2704179") # character
```
```
#> [1] "2704179"
#> attr(,"class")
#> [1] "gbifid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.gbif.org/species/2704179"
```
```r
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:
```r
system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=TRUE)) )
```
```
#> user system elapsed
#> 0.096 0.009 5.372
```
```r
system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=FALSE)) )
```
```
#> user system elapsed
#> 0.001 0.000 0.001
```
## What taxa are downstream of my taxon of interest?
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][wikispecies] or [Encyclopedia of Life][eol] to get downstream names. However, taxize provides an easy way to programatically search for downstream taxa, both for the [Catalogue of Life (CoL)][col] and the [Integrated Taxonomic Information System][itis]. Here is a short example using the CoL in which we want to find all the species within the genus *Apis* (honey bees).
```r
downstream("Apis", downto = "Species", db = "col")
```
```
#> name rank colid
#> 1 Apis genus 015be25f6b061ba517f495394b80f108
#> 2 Actinomadura apis species 1182a102a18b40aa19385bf5f1f53367
#> 3 Anisocentropus apis species 8891d18874dde14e44df52e931c44206
#> 4 Apis andreniformis species 7a4a38c5095963949d6d6ec917d471de
#> 5 Apis cerana species 39610a4ceff7e5244e334a3fbc5e47e5
#> 6 Apis dorsata species e1d4cbf3872c6c310b7a1c17ddd00ebc
#> 7 Apis florea species 92dca82a063fedd1da94b3f3972d7b22
#> 8 Apis koschevnikovi species 4bbc06b9dfbde0b72c619810b564c6e6
#> 9 Apis mellifera species 67cbbcf92cd60748759e58e802d98518
#> 10 Apis nigrocincta species 213668a26ba6d2aad9575218f10d422f
#> 11 Ascosphaera apis species 088549f2fb602367e84d5ffdb8c1d4fc
#> 12 Candida apis species 3219a9635d3438e8b76a645cecf87287
#> 13 Eristalis apis species 16d7c8023308d38f6bb831ed5fa82002
#> 14 Hister apis species d2d7483acf488b5ed932f49b0aa51d19
#> 15 Ifephylus apis species 9b4d00e009b58bbfc003b51bd3d0c6f0
#> 16 Impatiens nidus-apis species 6aecf448e6aa0cb46387066db94426d1
#> 17 Kirkaldykra apis species 70a68f13454abd937aabf56746f4a6ad
#> 18 Mallota apis species 10c3c3921d2ea9f9425ef9fd41914520
#> 19 Melanosella mors-apis species 4ac238f1597847dbc7998d97b8d45a0e
#> 20 Microdon apis species 9be92242562eb923e711dc24b7bbab9a
#> 21 Nosema apis species 5b2838dfd0ec15844fc6f659f7580322
#> 22 Scutirodes apis species 164ab3ac910547bc945cdbb994be1ee5
#> 23 Spiroplasma apis species 789f91571ce55de4df9821f2d05efab0
#> 24 Trichomonascus apis species 17dc4d840323e2c5b87e67a952f6dff3
#> 25 Pericystis apis species 088549f2fb602367e84d5ffdb8c1d4fc
#> 26 Pericystis apis species 088549f2fb602367e84d5ffdb8c1d4fc
#> 27 Torulopsis apis species 3219a9635d3438e8b76a645cecf87287
#> 28 Torulopsis apis species 3219a9635d3438e8b76a645cecf87287
#> 29 Apis aestuans species a517bc572c3c2697fe3bbfabc46a1493
#> 30 Apis alpina species f2781627115e4212ddab5979cdd425d2
#> 31 Apis bicornis species e67e82d00faae69da173bb31f9914056
#> 32 Apis canescens species d6b8850db971d65d6079e3a22f35e10e
#> 33 Apis clypeata species 706060924801130f6c3abf454087c100
#> 34 Apis cunicularia species ebc3c5166ce2cabf419c4c6dc332cf3b
#> 35 Apis etrusca species 6d27fd39a1d8b10050ba4e331987f3c9
#> 36 Apis globosa species 254c8e847ca4ff128bba57fe94deb98d
#> 37 Apis hispanica species e8d2057a3efeb2cfdaebe27ea8191cd5
#> 38 Apis hypnorum species dfb743f54f50b9b9dbee378473542821
#> 39 Apis ichneumonea species 13c35287e20ab9373fa445dbc44981ea
#> 40 Apis lapidaria species f8da5667af3562ebc0f6a83e1ec408f0
#> 41 Apis muscorum species 5bbfe59da5ce7fe59eb9ca3a7a45916c
#> 42 Apis mystacea species fba8e4752a7fa5939a7eae293ba633ec
#> 43 Apis obsoleta species da42bcb6cc0267903fb175f8a215aecb
#> 44 Apis rostrata species e155a4277b66d1114182cafd875afbe3
#> 45 Apis rostrata species e155a4277b66d1114182cafd875afbe3
#> 46 Apis rufa species e67e82d00faae69da173bb31f9914056
#> 47 Apis signata species 551f101ad3b9bc17b24575585b2500c1
#> 48 Apis smaragdula species 4bc5c886b061e17e9aecb537a04c616d
#> 49 Apis spinulosa species 56e7e9f854c9ed31ea6d0a06567607d0
#> 50 Apis subterranea species 3d2adff364a87bf7dd30524aa8071807
#> name_status kingdom family acc_name
#> 1 accepted name Animalia Apidae
#> 2 accepted name Bacteria Thermomonosporaceae
#> 3 accepted name Animalia Calamoceratidae
#> 4 accepted name Animalia Apidae
#> 5 accepted name Animalia Apidae
#> 6 accepted name Animalia Apidae
#> 7 accepted name Animalia Apidae
#> 8 accepted name Animalia Apidae
#> 9 accepted name Animalia Apidae
#> 10 accepted name Animalia Apidae
#> 11 accepted name Fungi Ascosphaeraceae
#> 12 accepted name Fungi Not assigned
#> 13 accepted name Animalia Syrphidae
#> 14 accepted name Animalia Histeridae
#> 15 accepted name Animalia Miridae
#> 16 accepted name Plantae Balsaminaceae
#> 17 accepted name Animalia Cicadellidae
#> 18 accepted name Animalia Syrphidae
#> 19 accepted name Fungi Not assigned
#> 20 accepted name Animalia Syrphidae
#> 21 accepted name Protozoa Nosematidae
#> 22 accepted name Animalia Noctuidae
#> 23 accepted name Bacteria Spiroplasmataceae
#> 24 accepted name Fungi Trichomonascaceae
#> 25 ambiguous synonym Ascosphaera apis
#> 26 ambiguous synonym Ascosphaera apis
#> 27 ambiguous synonym Candida apis
#> 28 ambiguous synonym Candida apis
#> 29 synonym Xylocopa aestuans
#> 30 synonym Bombus alpinus
#> 31 synonym Osmia rufa
#> 32 synonym Bembix canescens
#> 33 synonym Lestica clypeata
#> 34 synonym Colletes cunicularius
#> 35 synonym Tachytes etruscus
#> 36 synonym Exomalopsis similis
#> 37 synonym Tachytes freygessneri
#> 38 synonym Bombus hypnorum
#> 39 synonym Sphex ichneumoneus
#> 40 synonym Bombus lapidarius
#> 41 synonym Bombus muscorum
#> 42 synonym Argogorytes mystaceus
#> 43 synonym Tachytes obsoletus
#> 44 synonym Bembix rostrata
#> 45 synonym Bembix rostrata
#> 46 synonym Osmia rufa
#> 47 synonym Stictia signata
#> 48 synonym Ceratina smaragdula
#> 49 synonym Hoplosmia spinulosa
#> 50 synonym Bombus subterraneus
```
```
#> $Apis
#> childtaxa_id childtaxa_name childtaxa_rank
#> 1 7a4a38c5095963949d6d6ec917d471de Apis andreniformis species
#> 2 39610a4ceff7e5244e334a3fbc5e47e5 Apis cerana species
#> 3 e1d4cbf3872c6c310b7a1c17ddd00ebc Apis dorsata species
#> 4 92dca82a063fedd1da94b3f3972d7b22 Apis florea species
#> 5 4bbc06b9dfbde0b72c619810b564c6e6 Apis koschevnikovi species
#> 6 67cbbcf92cd60748759e58e802d98518 Apis mellifera species
#> 7 213668a26ba6d2aad9575218f10d422f Apis nigrocincta species
#>
#> attr(,"class")
#> [1] "downstream"
#> attr(,"db")
#> [1] "col"
```
We can also request data from ITIS
```r
downstream("Apis", downto = "Species", db = "itis")
```
```
#> $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"
```
## Direct children
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:
```r
children(get_colid("Apis"))
```
```
#> name rank colid
#> 1 Apis genus 015be25f6b061ba517f495394b80f108
#> 2 Actinomadura apis species 1182a102a18b40aa19385bf5f1f53367
#> 3 Anisocentropus apis species 8891d18874dde14e44df52e931c44206
#> 4 Apis andreniformis species 7a4a38c5095963949d6d6ec917d471de
#> 5 Apis cerana species 39610a4ceff7e5244e334a3fbc5e47e5
#> 6 Apis dorsata species e1d4cbf3872c6c310b7a1c17ddd00ebc
#> 7 Apis florea species 92dca82a063fedd1da94b3f3972d7b22
#> 8 Apis koschevnikovi species 4bbc06b9dfbde0b72c619810b564c6e6
#> 9 Apis mellifera species 67cbbcf92cd60748759e58e802d98518
#> 10 Apis nigrocincta species 213668a26ba6d2aad9575218f10d422f
#> 11 Ascosphaera apis species 088549f2fb602367e84d5ffdb8c1d4fc
#> 12 Candida apis species 3219a9635d3438e8b76a645cecf87287
#> 13 Eristalis apis species 16d7c8023308d38f6bb831ed5fa82002
#> 14 Hister apis species d2d7483acf488b5ed932f49b0aa51d19
#> 15 Ifephylus apis species 9b4d00e009b58bbfc003b51bd3d0c6f0
#> 16 Impatiens nidus-apis species 6aecf448e6aa0cb46387066db94426d1
#> 17 Kirkaldykra apis species 70a68f13454abd937aabf56746f4a6ad
#> 18 Mallota apis species 10c3c3921d2ea9f9425ef9fd41914520
#> 19 Melanosella mors-apis species 4ac238f1597847dbc7998d97b8d45a0e
#> 20 Microdon apis species 9be92242562eb923e711dc24b7bbab9a
#> 21 Nosema apis species 5b2838dfd0ec15844fc6f659f7580322
#> 22 Scutirodes apis species 164ab3ac910547bc945cdbb994be1ee5
#> 23 Spiroplasma apis species 789f91571ce55de4df9821f2d05efab0
#> 24 Trichomonascus apis species 17dc4d840323e2c5b87e67a952f6dff3
#> 25 Pericystis apis species 088549f2fb602367e84d5ffdb8c1d4fc
#> 26 Pericystis apis species 088549f2fb602367e84d5ffdb8c1d4fc
#> 27 Torulopsis apis species 3219a9635d3438e8b76a645cecf87287
#> 28 Torulopsis apis species 3219a9635d3438e8b76a645cecf87287
#> 29 Apis aestuans species a517bc572c3c2697fe3bbfabc46a1493
#> 30 Apis alpina species f2781627115e4212ddab5979cdd425d2
#> 31 Apis bicornis species e67e82d00faae69da173bb31f9914056
#> 32 Apis canescens species d6b8850db971d65d6079e3a22f35e10e
#> 33 Apis clypeata species 706060924801130f6c3abf454087c100
#> 34 Apis cunicularia species ebc3c5166ce2cabf419c4c6dc332cf3b
#> 35 Apis etrusca species 6d27fd39a1d8b10050ba4e331987f3c9
#> 36 Apis globosa species 254c8e847ca4ff128bba57fe94deb98d
#> 37 Apis hispanica species e8d2057a3efeb2cfdaebe27ea8191cd5
#> 38 Apis hypnorum species dfb743f54f50b9b9dbee378473542821
#> 39 Apis ichneumonea species 13c35287e20ab9373fa445dbc44981ea
#> 40 Apis lapidaria species f8da5667af3562ebc0f6a83e1ec408f0
#> 41 Apis muscorum species 5bbfe59da5ce7fe59eb9ca3a7a45916c
#> 42 Apis mystacea species fba8e4752a7fa5939a7eae293ba633ec
#> 43 Apis obsoleta species da42bcb6cc0267903fb175f8a215aecb
#> 44 Apis rostrata species e155a4277b66d1114182cafd875afbe3
#> 45 Apis rostrata species e155a4277b66d1114182cafd875afbe3
#> 46 Apis rufa species e67e82d00faae69da173bb31f9914056
#> 47 Apis signata species 551f101ad3b9bc17b24575585b2500c1
#> 48 Apis smaragdula species 4bc5c886b061e17e9aecb537a04c616d
#> 49 Apis spinulosa species 56e7e9f854c9ed31ea6d0a06567607d0
#> 50 Apis subterranea species 3d2adff364a87bf7dd30524aa8071807
#> name_status kingdom family acc_name
#> 1 accepted name Animalia Apidae
#> 2 accepted name Bacteria Thermomonosporaceae
#> 3 accepted name Animalia Calamoceratidae
#> 4 accepted name Animalia Apidae
#> 5 accepted name Animalia Apidae
#> 6 accepted name Animalia Apidae
#> 7 accepted name Animalia Apidae
#> 8 accepted name Animalia Apidae
#> 9 accepted name Animalia Apidae
#> 10 accepted name Animalia Apidae
#> 11 accepted name Fungi Ascosphaeraceae
#> 12 accepted name Fungi Not assigned
#> 13 accepted name Animalia Syrphidae
#> 14 accepted name Animalia Histeridae
#> 15 accepted name Animalia Miridae
#> 16 accepted name Plantae Balsaminaceae
#> 17 accepted name Animalia Cicadellidae
#> 18 accepted name Animalia Syrphidae
#> 19 accepted name Fungi Not assigned
#> 20 accepted name Animalia Syrphidae
#> 21 accepted name Protozoa Nosematidae
#> 22 accepted name Animalia Noctuidae
#> 23 accepted name Bacteria Spiroplasmataceae
#> 24 accepted name Fungi Trichomonascaceae
#> 25 ambiguous synonym Ascosphaera apis
#> 26 ambiguous synonym Ascosphaera apis
#> 27 ambiguous synonym Candida apis
#> 28 ambiguous synonym Candida apis
#> 29 synonym Xylocopa aestuans
#> 30 synonym Bombus alpinus
#> 31 synonym Osmia rufa
#> 32 synonym Bembix canescens
#> 33 synonym Lestica clypeata
#> 34 synonym Colletes cunicularius
#> 35 synonym Tachytes etruscus
#> 36 synonym Exomalopsis similis
#> 37 synonym Tachytes freygessneri
#> 38 synonym Bombus hypnorum
#> 39 synonym Sphex ichneumoneus
#> 40 synonym Bombus lapidarius
#> 41 synonym Bombus muscorum
#> 42 synonym Argogorytes mystaceus
#> 43 synonym Tachytes obsoletus
#> 44 synonym Bembix rostrata
#> 45 synonym Bembix rostrata
#> 46 synonym Osmia rufa
#> 47 synonym Stictia signata
#> 48 synonym Ceratina smaragdula
#> 49 synonym Hoplosmia spinulosa
#> 50 synonym Bombus subterraneus
```
```
#> $`015be25f6b061ba517f495394b80f108`
#> childtaxa_id childtaxa_name childtaxa_rank
#> 1 7a4a38c5095963949d6d6ec917d471de Apis andreniformis species
#> 2 39610a4ceff7e5244e334a3fbc5e47e5 Apis cerana species
#> 3 e1d4cbf3872c6c310b7a1c17ddd00ebc Apis dorsata species
#> 4 92dca82a063fedd1da94b3f3972d7b22 Apis florea species
#> 5 4bbc06b9dfbde0b72c619810b564c6e6 Apis koschevnikovi species
#> 6 67cbbcf92cd60748759e58e802d98518 Apis mellifera species
#> 7 213668a26ba6d2aad9575218f10d422f Apis nigrocincta species
#>
#> attr(,"class")
#> [1] "children"
#> attr(,"db")
#> [1] "col"
```
The direct children (genera in this case) of _Pinaceae_ using NCBI data:
```r
children("Pinaceae", db = "ncbi")
```
```
#> $Pinaceae
#> childtaxa_id childtaxa_name childtaxa_rank
#> 1 123600 Nothotsuga genus
#> 2 64685 Cathaya genus
#> 3 3358 Tsuga genus
#> 4 3356 Pseudotsuga genus
#> 5 3354 Pseudolarix genus
#> 6 3337 Pinus genus
#> 7 3328 Picea genus
#> 8 3325 Larix genus
#> 9 3323 Keteleeria genus
#> 10 3321 Cedrus genus
#> 11 3319 Abies genus
#>
#> attr(,"class")
#> [1] "children"
#> attr(,"db")
#> [1] "ncbi"
```
## Get NCBI ID from GenBank Ids
With accession numbers
```r
genbank2uid(id = 'AJ748748')
```
```
#> [1] "282199"
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.ncbi.nlm.nih.gov/taxonomy/282199"
```
With gi numbers
```r
genbank2uid(id = 62689767)
```
```
#> [1] "282199"
#> attr(,"class")
#> [1] "uid"
#> attr(,"match")
#> [1] "found"
#> attr(,"uri")
#> [1] "http://www.ncbi.nlm.nih.gov/taxonomy/282199"
```
## Matching species tables with different taxonomic resolution
Biologist often need to match different sets of data tied to species. For example, trait-based approaches are a promising tool in ecology. One problem is that abundance data must be matched with trait databases. These two data tables may contain species information on different taxonomic levels and possibly data must be aggregated to a joint taxonomic level, so that the data can be merged. taxize can help in this data-cleaning step, providing a reproducible workflow:
We can use the mentioned `classification`-function to retrieve the taxonomic hierarchy and then search the hierarchies up- and downwards for matches. Here is an example to match a species with names on three different taxonomic levels.
```r
A <- "gammarus roeseli"
B1 <- "gammarus roeseli"
B2 <- "gammarus"
B3 <- "gammaridae"
A_clas <- classification(A, db = 'ncbi')
B1_clas <- classification(B1, db = 'ncbi')
B2_clas <- classification(B2, db = 'ncbi')
B3_clas <- classification(B3, db = 'ncbi')
B1[match(A, B1)]
```
```
#> [1] "gammarus roeseli"
```
```r
A_clas[[1]]$rank[tolower(A_clas[[1]]$name) %in% B2]
```
```
#> [1] "genus"
```
```r
A_clas[[1]]$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
## Citing
To cite `taxize` in publications use:
> Scott Chamberlain and Eduard Szocs (2013). taxize - taxonomic search and retrieval in R. F1000Research, 2:191. URL: http://f1000research.com/articles/2-191/v2.
> Scott Chamberlain, Eduard Szocs, Carl Boettiger, Karthik Ram, Ignasi Bartomeus, John Baumgartner, Zachary Foster, and James O'Donnell (2016) taxize: Taxonomic information from around the web. R package version 0.7.5. https://github.com/ropensci/taxize
## License and bugs
* License: [MIT](http://opensource.org/licenses/MIT)
* Report bugs at [our Github repo for taxize](https://github.com/ropensci/taxize/issues?state=open)
[Back to top](#top)
[eol]: http://eol.org/
[gnr]: http://resolver.globalnames.org/
[taxosaurus]: http://api.phylotastic.org/tnrs
[ncbi]: http://www.ncbi.nlm.nih.gov/
[itis]: http://www.itis.gov/
[phylomatic]: http://phylodiversity.net/phylomatic/
[opentree]: http://blog.opentreeoflife.org/
[wikispecies]: http://species.wikimedia.org/wiki/Main_Page
[col]: http://www.catalogueoflife.org/
[iucn]: http://www.iucnredlist.org/
