taxizesoap is an extension to taxize, but for data sources that use SOAP data transfer protocol, which is hard to support in R. This package won't go on CRAN.
Most functions in this package are different from those in taxize, but there are some of the same (e.g,. classification()). In this package, where a function is named the same as in taxize, I've added a _s at the end of the function representing the version of that function in the taxizesoap package. This is to avoid confounding effects when both packages are loaded at the same time.
| Souce | Function prefix | API Docs | API key |
|---|---|---|---|
| World Register of Marine Species (WoRMS) | worms |
link | none |
| Pan-European Species directories Infrastructure (PESI) | pesi |
link | none |
| Mycobank | myco |
link | none |
Note: Euro+Med is available through PESI.
You'll need XMLSchema and SSOAP. I have versions of these packages on my personal GitHub account that seem to work better than the versions on Omegahat, and from there you can take advantage of the easy install_github().
install.packages("devtools")
devtools::install_github(c("sckott/XMLSchema", "sckott/SSOAP"))Then install taxizesoap
devtools::install_github("ropensci/taxizesoap")Load the package
library('taxizesoap')PESI
get_pesiid(searchterm = "Salvelinus")##
## Retrieving data for taxon 'Salvelinus'
## [1] "urn:lsid:marinespecies.org:taxname:126142"
## attr(,"match")
## [1] "found"
## attr(,"uri")
## [1] "http://www.eu-nomen.eu/portal/taxon.php?GUID=urn:lsid:marinespecies.org:taxname:126142"
## attr(,"class")
## [1] "pesiid"
Worms
get_wormsid(searchterm = "Salvelinus fontinalis")##
## Retrieving data for taxon 'Salvelinus fontinalis'
## [1] "154241"
## attr(,"match")
## [1] "found"
## attr(,"uri")
## [1] "http://www.marinespecies.org/aphia.php?p=taxdetails&id=154241"
## attr(,"class")
## [1] "wormsid"
Get taxonomic classification
classification_s(get_wormsid("Salvelinus fontinalis"))##
## Retrieving data for taxon 'Salvelinus fontinalis'
## $`154241`
## name rank
## 1 Animalia Kingdom
## 2 Chordata Phylum
## 3 Vertebrata Subphylum
## 4 Gnathostomata Superclass
## 5 Pisces Superclass
## 6 Actinopterygii Class
## 7 Salmoniformes Order
## 8 Salmonidae Family
## 9 Salmoninae Subfamily
## 10 Salvelinus Genus
## 11 Salvelinus fontinalis Species
##
## attr(,"class")
## [1] "classification_s"
Get name from a WORMS id
worms_name(ids=1080)## [1] "Copepoda"
Common names from WoRMS ID
worms_common(ids=c(1080,22388,160281,123080,22388))## inputid vernacular language_code language
## 1 1080 copepods eng English
## 2 1080 hoppkräftor swe Swedish
## 3 1080 roeipootkreeften dut Dutch
## 4 22388 barnacles eng English
## 5 160281 dierluizen dut Dutch
## 6 160281 djurlöss swe Swedish
## 7 160281 lice eng English
## 8 160281 phthiraptères fra French
## 9 160281 Tierläuse deu German
## 10 123080 astéries fra French
## 11 123080 estrella de mar spa Spanish
## 12 123080 étoiles de mer fra French
## 13 123080 hitode (ヒトデ) jpn Japanese
## 14 123080 sea stars eng English
## 15 123080 Seesterne deu German
## 16 123080 sjöstjärnor swe Swedish
## 17 123080 starfish eng English
## 18 123080 tapak sulaiman zlm Malay (individual language)
## 19 123080 zeesterren dut Dutch
## 20 123080 불가사리 kor Korean
## 21 22388 barnacles eng English
Get records by ID, scientific name, common name, date, worms id, or external id.
head( worms_records(scientific=c('Salmo','Aphanius')) )## inputid AphiaID
## 1 Salmo 126141
## 2 Salmo 154470
## 3 Salmo 154471
## 4 Salmo 712455
## 5 Salmo 305943
## 6 Salmo 305944
## url
## 1 http://www.marinespecies.org/aphia.php?p=taxdetails&id=126141
## 2 http://www.marinespecies.org/aphia.php?p=taxdetails&id=154470
## 3 http://www.marinespecies.org/aphia.php?p=taxdetails&id=154471
## 4 http://www.marinespecies.org/aphia.php?p=taxdetails&id=712455
## 5 http://www.marinespecies.org/aphia.php?p=taxdetails&id=305943
## 6 http://www.marinespecies.org/aphia.php?p=taxdetails&id=305944
## scientificname authority rank
## 1 Salmo Linnaeus, 1758 Genus
## 2 Salmo (Osmerus) Linnaeus, 1758 Subgenus
## 3 Salmo (Osmerus) eperlanus (Linnaeus, 1758) Species
## 4 Salmo abanticus Tortonese, 1954 Species
## 5 Salmo albula Linnaeus, 1758 Species
## 6 Salmo albus Bonnaterre, 1788 Species
## status unacceptreason valid_AphiaID
## 1 accepted <NA> 126141
## 2 accepted <NA> 154470
## 3 alternate representation synonym 154774
## 4 accepted <NA> 712455
## 5 unaccepted <NA> 127178
## 6 unaccepted <NA> 223866
## valid_name valid_authority kingdom phylum class
## 1 Salmo Linnaeus, 1758 Animalia Chordata Actinopterygii
## 2 Salmo (Osmerus) Linnaeus, 1758 Animalia Chordata Actinopterygii
## 3 Salmo eperlanus Linnaeus, 1758 Animalia Chordata Actinopterygii
## 4 Salmo abanticus Tortonese, 1954 Animalia Chordata Actinopterygii
## 5 Coregonus albula (Linnaeus, 1758) Animalia Chordata Actinopterygii
## 6 Salmo trutta trutta Linnaeus, 1758 Animalia Chordata Actinopterygii
## order family genus
## 1 Salmoniformes Salmonidae Salmo
## 2 Salmoniformes Salmonidae Salmo
## 3 Salmoniformes Salmonidae Salmo
## 4 Salmoniformes Salmonidae Salmo
## 5 Salmoniformes Salmonidae Salmo
## 6 Salmoniformes Salmonidae Salmo
## citation
## 1 Bailly, N. (2014). Salmo Linnaeus, 1758. In: Froese, R. and D. Pauly. Editors. (2014) FishBase. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=126141 on 2014-11-22
## 2 WoRMS (2014). Salmo (Osmerus) Linnaeus, 1758. In: Froese, R. and D. Pauly. Editors. (2014) FishBase. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=154470 on 2014-11-22
## 3 Bailly, N. (2014). Salmo (Osmerus) eperlanus. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=154471 on 2014-11-22
## 4 Bailly, N. (2014). Salmo abanticus Tortonese, 1954. In: Froese, R. and D. Pauly. Editors. (2014) FishBase. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=712455 on 2014-11-22
## 5 Bailly, N. (2014). Salmo albula Linnaeus, 1758. In: Froese, R. and D. Pauly. Editors. (2014) FishBase. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=305943 on 2014-11-22
## 6 Bailly, N. (2014). Salmo albus Bonnaterre, 1788. In: Froese, R. and D. Pauly. Editors. (2014) FishBase. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=305944 on 2014-11-22
## lsid isMarine isBrackish
## 1 urn:lsid:marinespecies.org:taxname:126141 1 0
## 2 urn:lsid:marinespecies.org:taxname:154470 <NA> <NA>
## 3 urn:lsid:marinespecies.org:taxname:154471 1 1
## 4 urn:lsid:marinespecies.org:taxname:712455 1 1
## 5 urn:lsid:marinespecies.org:taxname:305943 1 1
## 6 urn:lsid:marinespecies.org:taxname:305944 1 1
## isFreshwater isTerrestrial isExtinct match_type modified
## 1 0 <NA> <NA> like 2014-11-21T14:09:38Z
## 2 <NA> <NA> <NA> like 2005-04-18T10:19:09Z
## 3 1 0 <NA> like 2013-03-22T14:42:51Z
## 4 1 <NA> <NA> like 2012-12-21T13:57:20Z
## 5 1 <NA> <NA> like 2008-02-28T14:41:08Z
## 6 1 0 <NA> like 2013-01-08T15:50:09Z
Get sources/references by ID
worms_sources(ids=1080)## inputid source_id use
## 1 1080 40 basis of record
## reference
## 1 Brusca, R.C.; Brusca, G.J. (1990). Invertebrates. Sinauer Associates: Sunderland, MA (USA). ISBN 0-87893-098-1. 922 pp.
## page url link
## 1 http://www.marinespecies.org/aphia.php?p=sourcedetails&id=40
## fulltext
## 1
Children search of WoRMS data.
head( worms_children(ids=106135) )## inputid AphiaID
## 1 106135 733743
## 2 106135 106242
## 3 106135 733262
## 4 106135 733744
## 5 106135 733263
## 6 106135 733264
## url
## 1 http://www.marinespecies.org/aphia.php?p=taxdetails&id=733743
## 2 http://www.marinespecies.org/aphia.php?p=taxdetails&id=106242
## 3 http://www.marinespecies.org/aphia.php?p=taxdetails&id=733262
## 4 http://www.marinespecies.org/aphia.php?p=taxdetails&id=733744
## 5 http://www.marinespecies.org/aphia.php?p=taxdetails&id=733263
## 6 http://www.marinespecies.org/aphia.php?p=taxdetails&id=733264
## scientificname authority rank status
## 1 Hexelasma alearum Hoek, 1913 Species unaccepted
## 2 Hexelasma americanum Pilsbry, 1916 Species accepted
## 3 Hexelasma arafurae Hoek, 1913 Species accepted
## 4 Hexelasma aucklandicum (Hector, 1888) Species unaccepted
## 5 Hexelasma aureolum Jones, 2000 Species accepted
## 6 Hexelasma brintoni (Newman & Ross, 1971) Species accepted
## unacceptreason valid_AphiaID
## 1 generic reassignment 292966
## 2 <NA> 106242
## 3 <NA> 733262
## 4 transferred to Bathylasma (see Jones, 2000) 733253
## 5 <NA> 733263
## 6 <NA> 733264
## valid_name valid_authority kingdom phylum
## 1 Bathylasma alearum (Foster, 1978) Animalia Arthropoda
## 2 Hexelasma americanum Pilsbry, 1916 Animalia Arthropoda
## 3 Hexelasma arafurae Hoek, 1913 Animalia Arthropoda
## 4 Bathylasma aucklandicum (Hector, 1887) Animalia Arthropoda
## 5 Hexelasma aureolum Jones, 2000 Animalia Arthropoda
## 6 Hexelasma brintoni (Newman & Ross, 1971) Animalia Arthropoda
## class order family genus
## 1 Maxillopoda Sessilia Pachylasmatidae Hexelasma
## 2 Maxillopoda Sessilia Pachylasmatidae Hexelasma
## 3 Maxillopoda Sessilia Pachylasmatidae Hexelasma
## 4 Maxillopoda Sessilia Pachylasmatidae Hexelasma
## 5 Maxillopoda Sessilia Pachylasmatidae Hexelasma
## 6 Maxillopoda Sessilia Pachylasmatidae Hexelasma
## citation
## 1 WoRMS (2014). Hexelasma alearum Hoek, 1913. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=733743 on 2014-11-22
## 2 WoRMS (2014). Hexelasma americanum Pilsbry, 1916. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=106242 on 2014-11-22
## 3 WoRMS (2014). Hexelasma arafurae Hoek, 1913. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=733262 on 2014-11-22
## 4 WoRMS (2014). Hexelasma aucklandicum (Hector, 1888). Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=733744 on 2014-11-22
## 5 WoRMS (2014). Hexelasma aureolum Jones, 2000. Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=733263 on 2014-11-22
## 6 WoRMS (2014). Hexelasma brintoni (Newman & Ross, 1971). Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=733264 on 2014-11-22
## lsid isMarine isBrackish
## 1 urn:lsid:marinespecies.org:taxname:733743 1 <NA>
## 2 urn:lsid:marinespecies.org:taxname:106242 1 <NA>
## 3 urn:lsid:marinespecies.org:taxname:733262 1 <NA>
## 4 urn:lsid:marinespecies.org:taxname:733744 1 <NA>
## 5 urn:lsid:marinespecies.org:taxname:733263 1 <NA>
## 6 urn:lsid:marinespecies.org:taxname:733264 1 <NA>
## isFreshwater isTerrestrial isExtinct match_type modified
## 1 <NA> <NA> <NA> exact 2013-07-03T10:40:33Z
## 2 <NA> <NA> <NA> exact 2004-12-21T16:54:05Z
## 3 <NA> <NA> <NA> exact 2013-07-03T09:26:15Z
## 4 <NA> <NA> <NA> exact 2013-07-03T10:40:33Z
## 5 <NA> <NA> <NA> exact 2013-07-03T09:26:15Z
## 6 <NA> <NA> <NA> exact 2013-07-03T09:26:15Z
Search for PESI scientific names and associated metadata.
pesi_search(scientific='Ternatea vulgaris')## input GUID
## 1 Ternatea vulgaris 67C3CC9C-624A-40C5-B63A-AB880E0300D1
## url
## 1 http://www.eu-nomen.eu/portal/taxon.php?GUID=67C3CC9C-624A-40C5-B63A-AB880E0300D1
## scientificname authority rank status
## 1 Ternatea vulgaris Kuntze Species synonym
## valid_guid valid_name valid_authority
## 1 7B5F817E-D94C-4929-956A-0ED57C94D3A0 Clitoria ternatea L.
## kingdom phylum class order family genus
## 1 <NA> <NA> <NA> <NA> <NA> <NA>
## citation
## 1 ILDIS World Database of Legumes 2010. (copyright © ILDIS). Ternatea vulgaris Kuntze. Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=67C3CC9C-624A-40C5-B63A-AB880E0300D1
## match_type
## 1 exact
Get PESI scientific names from GUIDs
pesi_name_scientific(guid='67C3CC9C-624A-40C5-B63A-AB880E0300D1')## [1] "Ternatea vulgaris"
Get PESI synonyms from GUIDs
head( pesi_synonyms(guid='A0433E13-D7B5-49F2-86BA-A1777364C559') )## input
## 1 A0433E13-D7B5-49F2-86BA-A1777364C559
## 2 A0433E13-D7B5-49F2-86BA-A1777364C559
## 3 A0433E13-D7B5-49F2-86BA-A1777364C559
## 4 A0433E13-D7B5-49F2-86BA-A1777364C559
## 5 A0433E13-D7B5-49F2-86BA-A1777364C559
## 6 A0433E13-D7B5-49F2-86BA-A1777364C559
## GUID
## 1 757B4430-51D9-4ABB-A2FF-CA18CA04AB05
## 2 74F210C9-4F53-4972-8885-E431BCBA3D07
## 3 8E7A5C45-4F19-4E12-9FC0-00664BF7BD17
## 4 E2B240D2-B3CA-4E63-8607-914239080259
## 5 0968760E-A9CD-4DD8-B3B2-427438568862
## 6 F6834328-FB47-492F-BA46-B621C19B4804
## url
## 1 http://www.eu-nomen.eu/portal/taxon.php?GUID=757B4430-51D9-4ABB-A2FF-CA18CA04AB05
## 2 http://www.eu-nomen.eu/portal/taxon.php?GUID=74F210C9-4F53-4972-8885-E431BCBA3D07
## 3 http://www.eu-nomen.eu/portal/taxon.php?GUID=8E7A5C45-4F19-4E12-9FC0-00664BF7BD17
## 4 http://www.eu-nomen.eu/portal/taxon.php?GUID=E2B240D2-B3CA-4E63-8607-914239080259
## 5 http://www.eu-nomen.eu/portal/taxon.php?GUID=0968760E-A9CD-4DD8-B3B2-427438568862
## 6 http://www.eu-nomen.eu/portal/taxon.php?GUID=F6834328-FB47-492F-BA46-B621C19B4804
## scientificname authority rank status
## 1 Charybdis maritima (L.) Speta Species synonym
## 2 Ornithogalum anthericoides (Poir.) Link ex Steud. Species synonym
## 3 Ornithogalum maritimum (L.) Lam. Species synonym
## 4 Ornithogalum squilla Ker Gawl. Species synonym
## 5 Scilla anthericoides Poir. Species synonym
## 6 Scilla lanceolata Viv. Species synonym
## valid_guid valid_name valid_authority
## 1 A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima (L.) Stearn
## 2 A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima (L.) Stearn
## 3 A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima (L.) Stearn
## 4 A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima (L.) Stearn
## 5 A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima (L.) Stearn
## 6 A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima (L.) Stearn
## kingdom phylum class order family genus
## 1 <NA> <NA> <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA> <NA> <NA>
## 3 <NA> <NA> <NA> <NA> <NA> <NA>
## 4 <NA> <NA> <NA> <NA> <NA> <NA>
## 5 <NA> <NA> <NA> <NA> <NA> <NA>
## 6 <NA> <NA> <NA> <NA> <NA> <NA>
## citation
## 1 World Checklist of Selected Plant Families (2010), copyright © The Board of Trustees of the Royal Botanic Gardens, Kew. Charybdis maritima (L.) Speta. Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=757B4430-51D9-4ABB-A2FF-CA18CA04AB05
## 2 World Checklist of Selected Plant Families (2010), copyright © The Board of Trustees of the Royal Botanic Gardens, Kew. Ornithogalum anthericoides (Poir.) Link ex Steud.. Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=74F210C9-4F53-4972-8885-E431BCBA3D07
## 3 World Checklist of Selected Plant Families (2010), copyright © The Board of Trustees of the Royal Botanic Gardens, Kew. Ornithogalum maritimum (L.) Lam.. Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=8E7A5C45-4F19-4E12-9FC0-00664BF7BD17
## 4 World Checklist of Selected Plant Families (2010), copyright © The Board of Trustees of the Royal Botanic Gardens, Kew. Ornithogalum squilla Ker Gawl.. Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=E2B240D2-B3CA-4E63-8607-914239080259
## 5 World Checklist of Selected Plant Families (2010), copyright © The Board of Trustees of the Royal Botanic Gardens, Kew. Scilla anthericoides Poir.. Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=0968760E-A9CD-4DD8-B3B2-427438568862
## 6 World Checklist of Selected Plant Families (2010), copyright © The Board of Trustees of the Royal Botanic Gardens, Kew. Scilla lanceolata Viv.. Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=F6834328-FB47-492F-BA46-B621C19B4804
## match_type
## 1 exact
## 2 exact
## 3 exact
## 4 exact
## 5 exact
## 6 exact
Search for a Candida boidinii
myco_search(filter='Name CONTAINS "Candida boidinii"')## name epithet authors nameyear mycobanknr
## 1 Candida boidinii boidinii C. Ramírez 1953 344025
## 2 Candida boidinii boidinii C. Ramírez 1954 294021
## literatureremarks literaturereferencetype literaturepagenr
## 1 NA NA 251
## 2 NA NA 100
## description_pt gender
## 1 NA Feminine
## 2 NA Feminine
## e3787
## 1 Candida boidinii C. Ramírez, Microbiología Española 6 (3): 251 (1953) [MB#344025]
## 2 Candida boidinii C. Ramírez, Revue Mycol.: 100 (1954) [MB#294021]
## wikipedia
## 1 http://en.wikipedia.org/wiki/Candida boidinii
## 2 http://en.wikipedia.org/wiki/Candida boidinii
## wikispecies
## 1 http://species.wikipedia.org/wiki/Candida boidinii
## 2 http://species.wikipedia.org/wiki/Candida boidinii
## wikimedia
## 1 http://commons.wikipedia.org/wiki/Candida boidinii
## 2 http://commons.wikipedia.org/wiki/Candida boidinii
## google
## 1 http://www.google.com/search?q=Candida boidinii
## 2 http://www.google.com/search?q=Candida boidinii
- Please report any issues or bugs.
- License: MIT
- Get citation information for
taxizesoapin R doingcitation(package = 'taxizesoap')
