REST API for Taxonomy Browser

The BOLD Taxonomy Web Service provides an interface to query the BOLD Taxonomy Browser.

Information can be retrieved by querying a Taxon Name or BOLD Taxonomy ID.

Web service end points

Data Types

For the Taxon Data Retrieval endpoint, the following data types can be specified. Multiple data types can be specified in a comma delimited list, using the dataType parameter.

General Parameters Description
dataType

Specifies the datatypes that will be returned.
Types are explained below

Examples:

  • dataTypes=all returns all data.
  • dataTypes=basic,images returns basic taxon information as well as specimen images.

basic

Returns basic taxonomy info.
Includes taxid, taxon name, tax rank, tax division, parent taxid, parent taxon name.

Example response: 
{"taxid":88899,"taxon":"Momotus","tax_rank":"genus","tax_division":"Animals","parentid":88898,"parentname":"Momotidae"}

stats

Returns specimen and sequence statistics.
Includes public species count, public BIN count, public marker counts, public record count, specimen count, sequenced specimen count, barcode specimen count, species count, barcode species count.

Example response: 
{"stats":{"publicspecies":2,"publicbins":3,"publicmarkersequences":{"COI-5P":5},"publicrecords":5,"specimenrecords":"41","sequencedspecimens":"20","barcodespecimens":"20","species":"3","barcodespecies":"2"}}

geo

Returns collection site information.
Includes country, collection site map.

Example response: 
{"country":{"Brazil":3,"Mexico":2,"Panama":10,"Guatemala":1,"Peru":9,"Bolivia":6,"Ecuador":2},"sitemap":"http:\/\/www.boldsystems.org\/index.php\/TaxBrowser_Maps_CollectionSites?taxid=88899"}

images

Returns specimen images.
Includes copyright information, image URL, image metadata.

Example response: 
{"images":[{"copyright_institution":"Smithsonian Tropical Research Institute","specimenid":2616730,"copyright":"Matthew J. MIller","imagequality":3,"photographer":"Oscar López","image":"BSPBB\/MJM_7406_IMG_2302_l+1345760782.JPG","fieldnum":"MJM 7406","sampleid":"MJM 7406","mam_uri":null,"copyright_license":"CreativeCommons - Attribution Non-Commercial","meta":"Lateral","copyright_holder":"Matthew J. MIller","catalognum":"","copyright_contact":"[email protected]","copyright_year":"2012","taxonrep":"Momotus momota","aspectratio":1.586,"original":true,"external":null}]}

sequencinglabs

Returns sequencing labs.
Includes lab name, record count.

Example response: 
{"sequencinglabs":{"Biodiversity Institute of Ontario":10,"Smithsonian Tropical Research Institute":6,"Mined from GenBank":2,"Royal Ontario Museum":2}}

depository

Returns specimen depositories.
Includes depository name, record count.

Example response: 
{"depositry":{"Universidade de Sao Paulo, Departamento de Botanica":1,"Museo Argentino de Ciencias Naturales, Bernardino Rivadavia":3,"Mined from GenBank, NCBI":2,"Smithsonian Tropical Research Institute":10,"Universidade Federal de Minas Gerais":1,"Universidad Nacional Autonoma de Mexico, Instituto de Biologia":2,"Coleccion Boliviana de Fauna":3,"Museo Nacional de Ciencias Naturales":3,"Universidad de San Carlos de Guatemala, Escuela de Biologia":1,"Centro de Ornitologia y Biodiversidad":9,"Royal Ontario Museum":1,"Instituto Nacional de Pesquisas da Amazonia":1}}

thirdparty

Returns information from third parties.
Includes wikipedia summary, wikipedia URL, GBIF map.

Example response: 
{"wikipedia_summary":"<b><i>Momotus<\/b><\/i> is a small genus of the motmots, a family of near passerine birds found in forest and woodland of the Neotropics. They have a colourful plumage, which is green on the back becoming blue on the flight feathers and the long tails. The barbs near the ends of the two longest central tail feathers fall off, leaving a length of bare shaft so that tails appear racket-shaped. \n\n<i>Momotus<\/i> species, like other motmots, eat small prey such as insects and lizards, and will also take fruit. They nest in tunnels in banks, laying about four white eggs.","wikipedia_link":"http:\/\/en.wikipedia.org\/wiki\/Momotus","gbif_map":"http:\/\/data.gbif.org\/species\/2475289\/overviewMap.png"}

all

Returns all information. Identical to specifying all data types at once.

Example response: 
{"taxid":88899,"taxon":"Momotus","tax_rank":"genus","tax_division":"Animals","parentid":88898,"parentname":"Momotidae","stats":{"publicspecies":2,"publicbins":3,"publicmarkersequences":{"COI-5P":5},"publicrecords":5,"specimenrecords":"41","sequencedspecimens":"20","barcodespecimens":"20","species":"3","barcodespecies":"2"},"country":{"Brazil":3,"Mexico":2,"Panama":10,"Guatemala":1,"Peru":9,"Bolivia":6,"Ecuador":2},"sitemap":"http:\/\/www.boldsystems.org\/index.php\/TaxBrowser_Maps_CollectionSites?taxid=88899","images":[{"copyright_institution":"Smithsonian Tropical Research Institute","specimenid":2616730,"copyright":"Matthew J. MIller","imagequality":3,"photographer":"Oscar López","image":"BSPBB\/MJM_7406_IMG_2302_l+1345760782.JPG","fieldnum":"MJM 7406","sampleid":"MJM 7406","mam_uri":null,"copyright_license":"CreativeCommons - Attribution Non-Commercial","meta":"Lateral","copyright_holder":"Matthew J. MIller","catalognum":"","copyright_contact":"[email protected]","copyright_year":"2012","taxonrep":"Momotus momota","aspectratio":1.586,"original":true,"external":null}],"sequencinglabs":{"Biodiversity Institute of Ontario":10,"Smithsonian Tropical Research Institute":6,"Mined from GenBank":2,"Royal Ontario Museum":2},"depositry":{"Universidade de Sao Paulo, Departamento de Botanica":1,"Museo Argentino de Ciencias Naturales, Bernardino Rivadavia":3,"Mined from GenBank, NCBI":2,"Smithsonian Tropical Research Institute":10,"Universidade Federal de Minas Gerais":1,"Universidad Nacional Autonoma de Mexico, Instituto de Biologia":2,"Coleccion Boliviana de Fauna":3,"Museo Nacional de Ciencias Naturales":3,"Universidad de San Carlos de Guatemala, Escuela de Biologia":1,"Centro de Ornitologia y Biodiversidad":9,"Royal Ontario Museum":1,"Instituto Nacional de Pesquisas da Amazonia":1},"wikipedia_summary":"<b><i>Momotus<\/b><\/i> is a small genus of the motmots, a family of near passerine birds found in forest and woodland of the Neotropics. They have a colourful plumage, which is green on the back becoming blue on the flight feathers and the long tails. The barbs near the ends of the two longest central tail feathers fall off, leaving a length of bare shaft so that tails appear racket-shaped. \n\n<i>Momotus<\/i> species, like other motmots, eat small prey such as insects and lizards, and will also take fruit. They nest in tunnels in banks, laying about four white eggs.","wikipedia_link":"http:\/\/en.wikipedia.org\/wiki\/Momotus","gbif_map":"http:\/\/data.gbif.org\/species\/2475289\/overviewMap.png"}

Taxonomy ID Service

URL: http://www.boldsystems.org/index.php/API_Tax/TaxonData?<Parameter 1>&<Parameter 2>&...

Description: Retrieves taxonomy information by BOLD taxonomy ID.

Results: JSON encoded data.

Examples: To retrieve basic taxonomy and stats for taxon with ID 88899. 

http://www.boldsystems.org/index.php/API_Tax/TaxonData?taxId=88899&dataTypes=basic,stats
returns the following results:

{"taxid":88899,"taxon":"Momotus","tax_rank":"genus","tax_division":"Animals","parentid":88898,"parentname":"Momotidae","stats":{"publicspecies":2,"publicbins":3,"publicmarkersequences":{"COI-5P":5},"publicrecords":5,"specimenrecords":"41","sequencedspecimens":"20","barcodespecimens":"20","species":"3","barcodespecies":"2"}}

To retrieve basic taxonomy for taxon with ID 88899 and its parent taxa. 

http://www.boldsystems.org/index.php/API_Tax/TaxonData?taxId=88899&dataTypes=basic&includeTree=true
returns the following results:

{"88899":{"taxid":88899,"taxon":"Momotus","tax_rank":"genus","tax_division":"Animals","parentid":88898,"parentname":"Momotidae"},"88898":{"taxid":88898,"taxon":"Momotidae","tax_rank":"family","tax_division":"Animals","parentid":339,"parentname":"Coraciiformes"},"339":{"taxid":339,"taxon":"Coraciiformes","tax_rank":"order","tax_division":"Animals","parentid":51,"parentname":"Aves"},"51":{"taxid":51,"taxon":"Aves","tax_rank":"class","tax_division":"Animals","parentid":18,"parentname":"Chordata","taxonrep":"Aves"},"18":{"taxid":18,"taxon":"Chordata","tax_rank":"phylum","tax_division":"Animals","parentid":1,"taxonrep":"Chordata"}}

Taxon Data Retrieval Description
taxId

Specifies the taxon to retrieve information for.

  • taxId=88899
includeTree
(optional)

Returns a list containing information for parent taxa as well as the specified taxon. True or false.

  • includeTree=true

Taxon Name Service

URL: http://www.boldsystems.org/index.php/API_Tax/TaxonSearch?<Parameter 1>&<Parameter 2>&...

Description: Retrieves taxonomy information by taxon name.

Results: JSON encoded array of one or more taxa with taxId as key

Examples: To retrieve basic information for taxa with the name Diplura. 

http://www.boldsystems.org/index.php/API_Tax/TaxonSearch?taxName=Diplura
returns the following results: 

>{"24810":{"taxid":24810,"taxon":"Diplura","tax_rank":"genus","tax_division":"Animals","parentid":211734,"parentname":"Dipluridae"},"307122":{"taxid":307122,"taxon":"Diplura","tax_rank":"order","tax_division":"Animals","parentid":82,"parentname":"Insecta","taxonrep":"Diplura"}}

Taxon Name Parameters Description
taxName

Specifies the taxon name to return information for.

Examples:

  • taxName=Momotus
fuzzy

true or false. Specifies if the search should only find exact matches. All searches are case sensitive

Examples:

  • fuzzy=true

Notes