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ropensci/taxizesoap

Name: taxizesoap

Owner: rOpenSci

Description: taxize but for SOAP data sources

Created: 2014-11-21 17:39:47.0

Updated: 2017-02-16 05:38:46.0

Pushed: 2017-08-07 15:44:39.0

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Size: 1794

Language: R

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README

taxizesoap

UPDATE: WORMS data source is now in taxize - for PESI and Mycobank continue to use this package.

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.

Currently implemented in `taxizesoap`

Souce	Function prefix	API Docs	API key
Pan-European Species directories Infrastructure (PESI)	`pesi`	link	none
Mycobank	`myco`	link	none

Note: Euro+Med is available through PESI.

R versions

We previously had problems with this package, where it didn't work on R > 3.2. But now those problems seem to have been solved. let us know if you run into any more problems.

Install taxizesoap

ools::install_github("ropensci/taxizesoap")

That should install two dependencies not on CRAN (XMLSchema, SSOAP). If they aren't installed correctly for you, try installing from our Drat repo.

all.packages(c("XMLSchema", "SSOAP"), repos = c("http://packages.ropensci.org", "http://cran.rstudio.com"))

If that doesn't work, try insatlling from GitHub:

all.packages("devtools")
ools::install_github("omegahat/XMLSchema")
ools::install_github("sckott/SSOAP")

Load the package

ary('taxizesoap')

Get taxonomic ids

PESI

pesiid(searchterm = "Salvelinus")
1] "urn:lsid:marinespecies.org:taxname:126142"
ttr(,"match")
1] "found"
ttr(,"uri")
1] "http://www.eu-nomen.eu/portal/taxon.php?GUID=urn:lsid:marinespecies.org:taxname:126142"
ttr(,"class")
1] "pesiid"

PESI

Search for PESI scientific names and associated metadata.

_search(scientific='Ternatea vulgaris')
             input                                 GUID
 Ternatea vulgaris 67C3CC9C-624A-40C5-B63A-AB880E0300D1
                                                                               url
 http://www.eu-nomen.eu/portal/taxon.php?GUID=67C3CC9C-624A-40C5-B63A-AB880E0300D1
    scientificname authority    rank        status
 Ternatea vulgaris    Kuntze Species is synonym of
                           valid_guid        valid_name valid_authority
 7B5F817E-D94C-4929-956A-0ED57C94D3A0 Clitoria ternatea              L.
 kingdom phylum class order family genus
    <NA>   <NA>  <NA>  <NA>   <NA>  <NA>
                                                                                                                                                                                                                 citation
 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
      exact

Get PESI scientific names from GUIDs

_name_scientific(guid='67C3CC9C-624A-40C5-B63A-AB880E0300D1')
1] "Ternatea vulgaris"

Get PESI synonyms from GUIDs

( pesi_synonyms(guid='A0433E13-D7B5-49F2-86BA-A1777364C559') )
                                input
 A0433E13-D7B5-49F2-86BA-A1777364C559
 A0433E13-D7B5-49F2-86BA-A1777364C559
 A0433E13-D7B5-49F2-86BA-A1777364C559
 A0433E13-D7B5-49F2-86BA-A1777364C559
 A0433E13-D7B5-49F2-86BA-A1777364C559
 A0433E13-D7B5-49F2-86BA-A1777364C559
                                 GUID
 757B4430-51D9-4ABB-A2FF-CA18CA04AB05
 74F210C9-4F53-4972-8885-E431BCBA3D07
 8E7A5C45-4F19-4E12-9FC0-00664BF7BD17
 E2B240D2-B3CA-4E63-8607-914239080259
 0968760E-A9CD-4DD8-B3B2-427438568862
 F6834328-FB47-492F-BA46-B621C19B4804
                                                                               url
 http://www.eu-nomen.eu/portal/taxon.php?GUID=757B4430-51D9-4ABB-A2FF-CA18CA04AB05
 http://www.eu-nomen.eu/portal/taxon.php?GUID=74F210C9-4F53-4972-8885-E431BCBA3D07
 http://www.eu-nomen.eu/portal/taxon.php?GUID=8E7A5C45-4F19-4E12-9FC0-00664BF7BD17
 http://www.eu-nomen.eu/portal/taxon.php?GUID=E2B240D2-B3CA-4E63-8607-914239080259
 http://www.eu-nomen.eu/portal/taxon.php?GUID=0968760E-A9CD-4DD8-B3B2-427438568862
 http://www.eu-nomen.eu/portal/taxon.php?GUID=F6834328-FB47-492F-BA46-B621C19B4804
             scientificname              authority    rank
         Charybdis maritima             (L.) Speta Species
 Ornithogalum anthericoides (Poir.) Link ex Steud. Species
     Ornithogalum maritimum              (L.) Lam. Species
       Ornithogalum squilla              Ker Gawl. Species
       Scilla anthericoides                  Poir. Species
          Scilla lanceolata                   Viv. Species
              status                           valid_guid      valid_name
   homotypic synonym A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima
 heterotypic synonym A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima
   homotypic synonym A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima
 heterotypic synonym A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima
 heterotypic synonym A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima
 heterotypic synonym A0433E13-D7B5-49F2-86BA-A1777364C559 Drimia maritima
 valid_authority kingdom phylum class order family genus
     (L.) Stearn    <NA>   <NA>  <NA>  <NA>   <NA>  <NA>
     (L.) Stearn    <NA>   <NA>  <NA>  <NA>   <NA>  <NA>
     (L.) Stearn    <NA>   <NA>  <NA>  <NA>   <NA>  <NA>
     (L.) Stearn    <NA>   <NA>  <NA>  <NA>   <NA>  <NA>
     (L.) Stearn    <NA>   <NA>  <NA>  <NA>   <NA>  <NA>
     (L.) Stearn    <NA>   <NA>  <NA>  <NA>   <NA>  <NA>
                                                                                                                                                                                                                                                                                                      citation
                     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
 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
                  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
                    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
                        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
                            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
      exact
      exact
      exact
      exact
      exact
      exact

Mycobank

Search for a Candida boidinii

_search(filter='Name CONTAINS "Candida boidinii"')
    _id       creation_date    last_change_date             name  epithet
 105080 03/02/2004 08:10:28 08/06/2017 14:51:37 Candida boidinii boidinii
 175286 25/12/2004 17:43:38 08/06/2017 16:37:07 Candida boidinii boidinii
    authors nameyear mycobanknr literatureremarks literaturereferencetype
 C. Ram�rez     1953     344025                NA                      NA
 C. Ram�rez     1954     294021                NA                      NA
 literaturepagenr description_pt   gender
              251             NA Feminine
              100             NA Feminine
                                                                             e3787
 Candida boidinii C. Ram�rez, Microbiolog�a Espa�ola 6 (3): 251 (1953) [MB#344025]
                 Candida boidinii C. Ram�rez, Revue Mycol.: 100 (1954) [MB#294021]
                                     wikipedia
 http://en.wikipedia.org/wiki/Candida boidinii
 http://en.wikipedia.org/wiki/Candida boidinii
                                        wikispecies
 http://species.wikipedia.org/wiki/Candida boidinii
 http://species.wikipedia.org/wiki/Candida boidinii
                                          wikimedia
 http://commons.wikipedia.org/wiki/Candida boidinii
 http://commons.wikipedia.org/wiki/Candida boidinii
                                          google
 http://www.google.com/search?q=Candida boidinii
 http://www.google.com/search?q=Candida boidinii

Contributors

Scott Chamberlain https://github.com/sckott
Francois Michonneau https://github.com/fmichonneau

ropensci/taxizesoap

README

taxizesoap

Currently implemented in taxizesoap

R versions

Install taxizesoap

Get taxonomic ids

PESI

Mycobank

Contributors

Meta

Currently implemented in `taxizesoap`