Tuesday, November 19, 2013 From rOpenSci (https://ropensci.org/blog/2013/11/19/taxize-changes/). Except where otherwise noted, content on this site is licensed under the CC-BY license.
We are building a taxonomic toolbelt for R called taxize - which gives you programmatic access to many sources of taxonomic data on the web. We just pushed a new version to CRAN (v0.1.5) with a lot of changes (see here for a rundown). Here are a few highlights of the changes.
Note: the windows binary may not be available yet…
install.packages("taxize")
library(taxize)
Each taxonomic service has their own unique ID for a taxon. We had a way to get ITIS and NCBI identifiers before - we now have functions for Tropicos, EOL, and the Catalogue of Life.
get_tpsid(sciname = "Helianthus petiolaris patens")
## 1
## 50140022
## attr(,"class")
## [1] "tpsid"
get_colid(sciname = "Pinus contorta")
## 1
## "14376216"
## attr(,"class")
## [1] "colid"
And we have a new function to get identifiers across all sources. And it’s vectorized so you can pass in many names.
get_ids(names = c("Chironomus riparius", "Poa annua"), db = c("ncbi", "itis"))
## $ncbi
## Chironomus riparius Poa annua
## "315576" "93036"
## attr(,"match")
## [1] "found" "found"
## attr(,"class")
## [1] "uid"
##
## $itis
## Chironomus riparius Poa annua
## "129313" "41107"
## attr(,"match")
## [1] "found" "found"
## attr(,"class")
## [1] "tsn"
##
## attr(,"class")
## [1] "ids"
We had a function called classification to get a taxonomic hierarchy from a particular source, ITIS or NCBI. We now have functions for Tropicos, EOL, and the Catalogue of Life. In addition, we have a function to get classifications across sources.
out <- get_ids(names = "Poa annua", db = c("ncbi", "itis"))
classification(out)
## $ncbi
## $ncbi$`Poa annua`
## ScientificName Rank UID
## 1 cellular organisms no rank 131567
## 2 Eukaryota superkingdom 2759
## 3 Viridiplantae kingdom 33090
## 4 Streptophyta phylum 35493
## 5 Streptophytina no rank 131221
## 6 Embryophyta no rank 3193
## 7 Tracheophyta no rank 58023
## 8 Euphyllophyta no rank 78536
## 9 Spermatophyta no rank 58024
## 10 Magnoliophyta no rank 3398
## 11 Liliopsida class 4447
## 12 commelinids subclass 4734
## 13 Poales order 38820
## 14 Poaceae family 4479
## 15 BEP clade no rank 359160
## 16 Pooideae subfamily 147368
## 17 Poeae tribe 147387
## 18 Poinae subtribe 640628
## 19 Poa genus 4544
## 20 Poa annua species 93036
##
##
## $itis
## $itis$`Poa annua`
## rankName taxonName tsn
## 1 Kingdom Plantae 202422
## 2 Subkingdom Viridaeplantae 846492
## 3 Infrakingdom Streptophyta 846494
## 4 Division Tracheophyta 846496
## 5 Subdivision Spermatophytina 846504
## 6 Infradivision Angiospermae 846505
## 7 Class Magnoliopsida 18063
## 8 Superorder Lilianae 846542
## 9 Order Poales 846620
## 10 Family Poaceae 40351
## 11 Genus Poa 41074
## 12 Species Poa annua 41107
Just like the classification function, synonyms now searches across sources for synonym names. However, this function only has methods for ITIS and Tropicos.
synonyms(c("Poa annua", "Pinus contorta", "Puma concolor"), db = "itis")
## $`Poa annua`
## name tsn
## 1 Poa annua var. aquatica 538978
## 2 Poa annua var. reptans 538979
## 3 Aira pumila 785854
## 4 Catabrosa pumila 787993
## 5 Ochlopoa annua 791574
## 6 Poa aestivalis 793946
## 7 Poa algida 793954
## 8 Poa annua var. annua 802116
## 9 Poa annua var. eriolepis 802117
## 10 Poa annua var. rigidiuscula 802119
## 11 Poa annua f. reptans 803667
##
## $`Pinus contorta`
## name tsn
## 1 nomatch 183327
##
## $`Puma concolor`
## name tsn
## 1 Felis concolor 180587
We have a variety of ways to get common names from scientific names for different sources. To simply things, there are two new functions to work across sources.
sci2comm(scinames = "Helianthus annuus", db = "itis")
## $`Helianthus annuus`
## comname lang tsn
## 1 common sunflower English 36616
## 2 sunflower English 36616
## 3 wild sunflower English 36616
## 4 annual sunflower English 36616
And vice versa
comm2sci(commnames = "annual blue grass", db = "tropicos")
## $`annual blue grass`
## NameId ScientificName ScientificNameWithAuthors Family
## 1 25509881 Poa annua Poa annua L. Poaceae
## RankAbbreviation NomenclatureStatusID NomenclatureStatusName Symbol
## 1 sp. 1 Legitimate !
## Author DisplayReference DisplayDate TotalRows
## 1 L. Sp. Pl. 1: 68 1753 1
We reworked the functions that interact with the ITIS service. We still have all the same functions, but there are now a number of higher level functions that make the interface to ITIS simpler. Here are some examples:
Get references associated with names.
itis_refs(c(202385, 70340))
## [[1]]
## actualPubDate isbn issn listedPubDate pages
## 1 2005-10-01 0-8018-8221-4 2005-10-01 2142
## 2 1993-01-01 1-56098-217-9 1992-01-01 xviii + 1207
## 3 1981-04-03 1981-04-03 1181
## pubComment
## 1
## 2 Corrections were made to text at 3rd printing
## 3
## pubName
## 1 Mammal Species of the World: A Taxonomic and Geographic Reference, 3rd ed., vols. 1 & 2
## 2 Mammal Species of the World: A Taxonomic and Geographic Reference, 2nd ed., 3rd printing
## 3 The Mammals of North America, vols. I and II, 2nd ed.
## pubPlace publisher
## 1 Baltimore, Maryland, USA Johns Hopkins University Press
## 2 Washington, DC, USA Smithsonian Institution Press
## 3 New York, New York, USA John Wiley and Sons, Inc.
## referenceAuthor name
## 1 Wilson, Don E., and DeeAnn M. Reeder, eds. Ursus arctos horribilis
## 2 Wilson, Don E., and DeeAnn M. Reeder, eds. Ursus arctos horribilis
## 3 Hall, E. Raymond Ursus arctos horribilis
## refLanguage referredTsn title updateDate
## 1 202385 2013-11-04
## 2 202385 2013-11-04
## 3 202385 2013-11-04
##
## [[2]]
## actualPubDate isbn issn listedPubDate pages pubComment
## 1 1988-01-01 0-913235-47-4 0097-0638 1988-01-01 vii + 277
## 2 1998-01-01 1-888569-01-8 0097-0638 1998-01-01 526
## pubName
## 1 American Fisheries Society Special Publication 16
## 2 American Fisheries Society Special Publication 26
## pubPlace publisher
## 1 Bethesda, Maryland, USA American Fisheries Society
## 2 Bethesda, Maryland, USA American Fisheries Society
## referenceAuthor
## 1 Turgeon, D. D., A. E. Bogan, E. V. Coan, W. K. Emerson, W. G. Lyons, W. Pratt, et al.
## 2 Turgeon, D. D., J. F. Quinn, Jr., A. E. Bogan, E. V. Coan, F. G. Hochberg, W. G. Lyons, et al.
## name refLanguage referredTsn
## 1 Tulotoma magnifica 70340
## 2 Tulotoma magnifica 70340
## title
## 1 Common and scientific names of aquatic invertebrates from the United States and Canada: mollusks
## 2 Common and scientific names of aquatic invertebrates from the United States and Canada: Mollusks, 2nd ed.
## updateDate
## 1 2013-04-26
## 2 2013-11-04
Get hierarchy: full, up (immediate), and down (immediate)
itis_hierarchy(tsn = 180543)
## parentName parentTsn rankName taxonName tsn
## 1 Kingdom Animalia 202423
## 2 Animalia 202423 Subkingdom Bilateria 914154
## 3 Bilateria 914154 Infrakingdom Deuterostomia 914156
## 4 Deuterostomia 914156 Phylum Chordata 158852
## 5 Chordata 158852 Subphylum Vertebrata 331030
## 6 Vertebrata 331030 Infraphylum Gnathostomata 914179
## 7 Gnathostomata 914179 Superclass Tetrapoda 914181
## 8 Tetrapoda 914181 Class Mammalia 179913
## 9 Mammalia 179913 Subclass Theria 179916
## 10 Theria 179916 Infraclass Eutheria 179925
## 11 Eutheria 179925 Order Carnivora 180539
## 12 Carnivora 180539 Suborder Caniformia 552303
## 13 Caniformia 552303 Family Ursidae 180540
## 14 Ursidae 180540 Genus Ursus 180541
## 15 Ursus 180541 Species Ursus arctos 180543
## 16 Ursus arctos 180543 Subspecies Ursus arctos alascensis 726985
## 17 Ursus arctos 180543 Subspecies Ursus arctos arctos 202383
## 18 Ursus arctos 180543 Subspecies Ursus arctos beringianus 726986
## 19 Ursus arctos 180543 Subspecies Ursus arctos californicus 726987
## 20 Ursus arctos 180543 Subspecies Ursus arctos collaris 726988
## 21 Ursus arctos 180543 Subspecies Ursus arctos crowtheri 726989
## 22 Ursus arctos 180543 Subspecies Ursus arctos dalli 726990
## 23 Ursus arctos 180543 Subspecies Ursus arctos gyas 726991
## 24 Ursus arctos 180543 Subspecies Ursus arctos horribilis 202385
## 25 Ursus arctos 180543 Subspecies Ursus arctos isabellinus 622068
## 26 Ursus arctos 180543 Subspecies Ursus arctos lasiotus 726992
## 27 Ursus arctos 180543 Subspecies Ursus arctos middendorffi 726993
## 28 Ursus arctos 180543 Subspecies Ursus arctos pruinosus 202386
## 29 Ursus arctos 180543 Subspecies Ursus arctos sitkensis 726994
## 30 Ursus arctos 180543 Subspecies Ursus arctos stikeenensis 726995
## 31 Ursus arctos 180543 Subspecies Ursus arctos syriacus 726996
itis_hierarchy(tsn = 180543, what = "up")
## parentName parentTsn rankName taxonName tsn
## 1 Ursus 180541 Species Ursus arctos 180543
itis_hierarchy(tsn = 180543, what = "down")
## parentName parentTsn rankName taxonName tsn
## 1 Ursus arctos 180543 Subspecies Ursus arctos arctos 202383
## 2 Ursus arctos 180543 Subspecies Ursus arctos horribilis 202385
## 3 Ursus arctos 180543 Subspecies Ursus arctos pruinosus 202386
## 4 Ursus arctos 180543 Subspecies Ursus arctos isabellinus 622068
## 5 Ursus arctos 180543 Subspecies Ursus arctos alascensis 726985
## 6 Ursus arctos 180543 Subspecies Ursus arctos beringianus 726986
## 7 Ursus arctos 180543 Subspecies Ursus arctos californicus 726987
## 8 Ursus arctos 180543 Subspecies Ursus arctos collaris 726988
## 9 Ursus arctos 180543 Subspecies Ursus arctos crowtheri 726989
## 10 Ursus arctos 180543 Subspecies Ursus arctos dalli 726990
## 11 Ursus arctos 180543 Subspecies Ursus arctos gyas 726991
## 12 Ursus arctos 180543 Subspecies Ursus arctos lasiotus 726992
## 13 Ursus arctos 180543 Subspecies Ursus arctos middendorffi 726993
## 14 Ursus arctos 180543 Subspecies Ursus arctos sitkensis 726994
## 15 Ursus arctos 180543 Subspecies Ursus arctos stikeenensis 726995
## 16 Ursus arctos 180543 Subspecies Ursus arctos syriacus 726996
