bold introduction

bold is an R package to connect to BOLD Systems (https://www.boldsystems.org/) via their API. Functions in bold let you search for sequence data, specimen data, sequence + specimen data, and download raw trace files.

bold info

BOLD home page: https://boldsystems.org/
BOLD API docs: https://v4.boldsystems.org/index.php/api_home

See also the taxize book for more options for taxonomic workflows with BOLD: https://taxize.dev/

Using bold

Install

Install bold from CRAN

install.packages("bold")

Or install the development version from GitHub

remotes::install_github("ropensci/bold")

Load the package

library("bold")

Search for taxonomic names via names

bold_tax_name searches for names with names.

bold_tax_name(name = 'Diplura')
#>    taxid   taxon tax_rank tax_division parentid       parentname
#> 1 603673 Diplura    genus     Protista    53974 Scytosiphonaceae
#> 2 734358 Diplura    class     Animalia       20       Arthropoda
#>   specimenrecords taxonrep     representitive_image.image
#> 1               6     <NA>                           <NA>
#> 2             308  Diplura BSOIL/GBOL20120+1540220834.jpg
#>   representitive_image.apectratio   input
#> 1                              NA Diplura
#> 2                           0.841 Diplura

bold_tax_name(name = c('Diplura', 'Osmia'))
#>    taxid   taxon tax_rank tax_division parentid       parentname
#> 1 603673 Diplura    genus     Protista    53974 Scytosiphonaceae
#> 2 734358 Diplura    class     Animalia       20       Arthropoda
#> 3   4940   Osmia    genus     Animalia     4962     Megachilinae
#>   specimenrecords taxonrep     representitive_image.image
#> 1               6     <NA>                           <NA>
#> 2             308  Diplura BSOIL/GBOL20120+1540220834.jpg
#> 3            3007    Osmia              BUSA/IMG_3061.jpg
#>   representitive_image.apectratio   input
#> 1                              NA Diplura
#> 2                           0.841 Diplura
#> 3                           1.486   Osmia

Search for taxonomic names via BOLD identifiers

bold_tax_id searches for names with BOLD identifiers.

bold_tax_id(id = 88899)
#>   input taxid   taxon tax_rank tax_division parentid parentname
#> 1 88899 88899 Momotus    genus     Animalia    88898  Momotidae

bold_tax_id(id = c(88899, 125295))
#>    input  taxid      taxon tax_rank tax_division parentid  parentname
#> 1  88899  88899    Momotus    genus     Animalia    88898   Momotidae
#> 2 125295 125295 Helianthus    genus      Plantae   151101 Asteroideae
#>     taxonrep
#> 1       <NA>
#> 2 Helianthus

Search for sequence data only

The BOLD sequence API gives back sequence data, with a bit of metadata.

The default is to get a list back

bold_seq(taxon = 'Coelioxys')[1:2]
#> [[1]]
#> [[1]]$id
#> [1] "ABEE117-17"
#> 
#> [[1]]$name
#> [1] "Coelioxys elongata"
#> 
#> [[1]]$gene
#> [1] "ABEE117-17"
#> 
#> [[1]]$sequence
#> [1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATCATTATATACATATCATCCTTCCCCATCAGTTGATTTAGCAATTTTTTYTTTACATTTATCAGGAATTTYTTYTATTATCGGATCAATAAATTTTATTGTAACAATTTTAATAATAAAAAATTATTCAATAAATTATAATCAAATACCTTTATTTCCATGATCAATTTTAATTACTACAATTTTATTATTATTATCATTACCTGTATTAGCAGGAGCTATTACAATATTATTATTTGATCGTAATTTAAATTCATCATTTTTTGACCCAATAGGAGGAGGAGATCCTATTTTATATCAACATTTATTTTG------------------------------------"
#> 
#> 
#> [[2]]
#> [[2]]$id
#> [1] "ABEE193-17"
#> 
#> [[2]]$name
#> [1] "Coelioxys rufescens"
#> 
#> [[2]]$gene
#> [1] "ABEE193-17"
#> 
#> [[2]]$sequence
#> [1] "---------------------------------------------------------------------------------------------------------------------------------------------AATAATGATATAATTTATAACTCTTTTATTACAGCTCATGCATTTTTAATAATTTTTTTTTTAGTTATACCTTTTTTAATTGGAGGATTTGGAAATTGATTAGCTCCTTTAATATTAGGAGCTCCAGATATAGCATTCCCTCGAATAAATAATATTAGATTTTGATTATTACCTCCTTCTTTATTAATATTATTAACTAGTAATTTAATTAATCCTAGACCAGGAACAGGATGAACAATTTATCCTCCTTTATCTTTATATAATTATCATCCTTCACCATCAGTAGATTTAGCAATTTTTTCTTTACATTTATCAGGAGTATCATCTATTATTGGTTCAATAAATTTTATTGTAACAATTTTATTAATAAAAAATTATTCAATAAATTATAATCAAATACCTTTATTCCCAKGATCAATTTTAATCACTACAATTTTATTATTATTATCTTTGCCTGTTTTAGCAGGAGCAATTACAATATTATTATTTGATCGAAATCTAAATTCATCCTTTTTTGACCCTTTAGGAGGAGGGGATCCAATTTTATACCAACATTTATTTTGATTTTTTGGACATCC---------------------"

You can optionally get back the crul response object

res <- bold_seq(taxon = 'Coelioxys', response = TRUE)
res$response_headers
#> $status
#> [1] "HTTP/2 200 "
#> 
#> $server
#> [1] "nginx"
#> 
#> $date
#> [1] "Mon, 20 Apr 2020 16:23:04 GMT"
#> 
#> $`content-type`
#> [1] "application/x-download"
#> 
#> $`x-powered-by`
#> [1] "PHP/5.3.15"
#> 
#> $`content-disposition`
#> [1] "attachment; filename=fasta.fas"
#> 
#> $`x-frame-options`
#> [1] "SAMEORIGIN"
#> 
#> $`x-content-type-options`
#> [1] "nosniff"
#> 
#> $`x-xss-protection`
#> [1] "1; mode=block"

You can do geographic searches

bold_seq(geo = "USA")
#> [[1]]
#> [[1]]$id
#> [1] "GBAN1777-08"
#> 
#> [[1]]$name
#> [1] "Macrobdella decora"
#> 
#> [[1]]$gene
#> [1] "GBAN1777-08"
#> 
#> [[1]]$sequence
#> [1] "---------------------------------ATTGGAATCTTGTATTTCTTATTAGGTACATGATCTGCTATAGTAGGGACCTCTATA---AGAATAATTATTCGAATTGAATTAGCTCAACCTGGGTCGTTTTTAGGAAAT---GATCAAATTTACAATACTATTGTTACTGCTCATGGATTAATTATAATTTTTTTTATAGTAATACCTATTTTAATTGGAGGGTTTGGTAATTGATTAATTCCGCTAATA---ATTGGTTCTCCTGATATAGCTTTTCCACGTCTTAATAATTTAAGATTTTGATTACTTCCGCCATCTTTAACTATACTTTTTTGTTCATCTATAGTCGAAAATGGAGTAGGTACTGGATGGACTATTTACCCTCCTTTAGCAGATAACATTGCTCATTCTGGACCTTCTGTAGATATA---GCAATTTTTTCACTTCATTTAGCTGGTGCTTCTTCTATTTTAGGTTCATTAAATTTTATTACTACTGTAGTTAATATACGATGACCAGGGATATCTATAGAGCGAATTCCTTTATTTATTTGATCCGTAATTATTACTACTGTATTGCTATTATTATCTTTACCAGTATTAGCAGCT---GCTATTTCAATATTATTAACAGATCGTAACTTAAATACTAGATTTTTTGACCCAATAGGAGGAGGGGATCCTATTTTATTCCAACATTTATTTTGATTTTTTGGCCACCCTGAAGTTTATATTTTAATTTTACCAGGATTTGGAGCTATTTCTCATGTAGTAAGTCATAACTCT---AAAAAATTAGAACCGTTTGGATCATTAGGGATATTATATGCAATAATTGGAATTGCAATTTTAGGTTTTATTGTTTGAGCACATCATATATTTACAGTAGGTCTTGATGTAGATACACGAGCTTATTTTACAGCAGCTACAATAGTTATTGCTGTTCCTACAGGAATTAAAGTATTTAGGTGATTG---GCAACT"
#> 
#> 
#> [[2]]
#> [[2]]$id
#> [1] "GBAN1780-08"
#> 
#> [[2]]$name
#> [1] "Haemopis terrestris"
#> 
#> [[2]]$gene
#> [1] "GBAN1780-08"
#> 
#> [[2]]$sequence
#> [1] "---------------------------------ATTGGAACWTTWTATTTTATTTTNGGNGCTTGATCTGCTATATTNGGGATCTCAATA---AGGAATATTATTCGAATTGAGCCATCTCAACCTGGGAGATTATTAGGAAAT---GATCAATTATATAATTCATTAGTAACAGCTCATGGATTAATTATAATTTTCTTTATGGTTATGCCTATTTTGATTGGTGGGTTTGGTAATTGATTACTACCTTTAATA---ATTGGAGCCCCTGATATAGCTTTTCCTCGATTAAATAATTTAAGTTTTTGATTATTACCACCTTCATTAATTATATTGTTAAGATCCTCTATTATTGAAAGAGGGGTAGGTACAGGTTGAACCTTATATCCTCCTTTAGCAGATAGATTATTTCATTCAGGTCCATCGGTAGATATA---GCTATTTTTTCATTACATATAGCTGGAGCATCATCTATTTTAGGCTCATTAAACTTTATTTCTACAATTATTAATATACGAATTAAAGGTATAAGATCTGATCGAGTACCTTTATTTGTATGATCAGTTGTTATTACAACAGTTCTGTTATTATTGTCTTTACCTGTTTTAGCTGCA---GCTATTACTATATTATTAACAGATCGTAATTTAAATACTACTTTTTTTGATCCTATAGGAGGTGGAGATCCAGTATTGTTTCAACACTTATTTTGATTTTTTGGTCATCCAGAAGTATATATTTTGATTTTACCAGGATTTGGAGCAATTTCTCATATTATTACAAATAATTCT---AAAAAATTGGAACCTTTTGGATCTCTTGGTATAATTTATGCTATAATTGGAATTGCAGTTTTAGGGTTTATTGTATGAGCCCATCATATATTTACTGTAGGATTAGATGTTGATACTCGAGCTTATTTTACAGCAGCTACTATAGTTATTGCTGTTCCTACTGGTATTAAAGTTTTTAGGTGATTA---GCAACA"
#> 
#> 
#> [[3]]
#> [[3]]$id
#> [1] "GBNM0293-06"
#> 
#> [[3]]$name
#> [1] "Steinernema carpocapsae"
#> 
#> [[3]]$gene
#> [1] "GBNM0293-06"
#> 
#> [[3]]$sequence
#> [1] "---------------------------------------------------------------------------------ACAAGATTATCTCTTATTATTCGTTTAGAGTTGGCTCAACCTGGTCTTCTTTTGGGTAAT---GGTCAATTATATAATTCTATTATTACTGCTCATGCTATTCTTATAATTTTTTTCATAGTTATACCTAGAATAATTGGTGGTTTTGGTAATTGAATATTACCTTTAATATTGGGGGCTCCTGATATAAGTTTTCCACGTTTGAATAATTTAAGTTTTTGATTGCTACCAACTGCTATATTTTTGATTTTAGATTCTTGTTTTGTTGACACTGGTTGTGGTACTAGTTGAACTGTTTATCCTCCTTTGAGG---ACTTTAGGTCACCCTGGYAGAAGTGTAGATTTAGCTATTTTTAGTCTTCATTGTGCAGGAATTAGCTCAATTTTAGGGGCTATTAATTTTATATGTACTACAAAAAATCTTCGTAGTAGTTCTATTTCTTTGGAACATATAAGACTTTTTGTTTGGGCTGTTTTTGTTACTGTTTTTTTATTAGTTTTATCTTTACCTGTTTTAGCTGGTGCTATTACTATGCTTTTAACAGACCGTAATTTAAATACTTCTTTTTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
#> 
#> 
#> [[4]]
#> [[4]]$id
#> [1] "NEONV108-11"
#> 
#> [[4]]$name
#> [1] "Aedes thelcter"
#> 
#> [[4]]$gene
#> [1] "NEONV108-11"
#> 
#> [[4]]$sequence
#> [1] "AACTTTATACTTCATCTTCGGAGTTTGATCAGGAATAGTTGGTACATCATTAAGAATTTTAATTCGTGCTGAATTAAGTCAACCAGGTATATTTATTGGAAATGACCAAATTTATAATGTAATTGTTACAGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGACTAGTTCCTCTAATATTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAATAATATAAGTTTTTGAATACTACCTCCCTCATTAACTCTTCTACTTTCAAGTAGTATAGTAGAAAATGGATCAGGAACAGGATGAACAGTTTATCCACCTCTTTCATCTGGAACTGCTCATGCAGGAGCCTCTGTTGATTTAACTATTTTTTCTCTTCATTTAGCCGGAGTTTCATCAATTTTAGGGGCTGTAAATTTTATTACTACTGTAATTAATATACGATCTGCAGGAATTACTCTTGATCGACTACCTTTATTCGTTTGATCTGTAGTAATTACAGCTGTTTTATTACTTCTTTCACTTCCTGTATTAGCTGGAGCTATTACAATACTATTAACTGATCGAAATTTAAATACATCTTTCTTTGATCCAATTGGAGGAGGAGACCCAATTTTATACCAACATTTATTT"
#> 
#> 
#> [[5]]
#> [[5]]$id
#> [1] "NEONV109-11"
#> 
#> [[5]]$name
#> [1] "Aedes thelcter"
#> 
#> [[5]]$gene
#> [1] "NEONV109-11"
#> 
#> [[5]]$sequence
#> [1] "AACTTTATACTTCATCTTCGGAGTTTGATCAGGAATAGTTGGTACATCATTAAGAATTTTAATTCGTGCTGAATTAAGTCAACCAGGTATATTTATTGGAAATGACCAAATTTATAATGTAATTGTTACAGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGACTAGTTCCTCTAATATTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAATAATATAAGTTTTTGAATACTACCTCCCTCATTAACTCTTCTACTTTCAAGTAGTATAGTAGAAAATGGGTCAGGAACAGGATGAACAGTTTATCCACCTCTTTCATCTGGAACTGCTCATGCAGGAGCCTCTGTTGATTTAACTATTTTTTCTCTTCATTTAGCCGGAGTTTCATCAATTTTAGGGGCTGTAAATTTTATTACTACTGTAATTAATATACGATCTGCAGGAATTACTCTTGATCGACTACCTTTATTCGTTTGATCTGTAGTAATTACAGCTGTTTTATTACTTCTTTCACTTCCTGTATTAGCTGGAGCTATTACAATACTATTAACTGATCGAAATTTAAATACATCTTTCTTTGACCCAATTGGAGGGGGAGACCCAATTTTATACCAACATTTATTT"

And you can search by researcher name

bold_seq(researchers = 'Thibaud Decaens')[[1]]
#> $id
#> [1] "COLNO015-09"
#> 
#> $name
#> [1] "Ptiliidae"
#> 
#> $gene
#> [1] "COLNO015-09"
#> 
#> $sequence
#> [1] "AACCTTGTATTTTATGTTCGGNGCTTGAGCTGGAATAGTCGGGACAAGTTTGAGTCTCCTTATCCGAACTGAACTCGGCACTCCAGGTTCACTAATTGGAGACGACCAAATCTACAACGTAATCGTAACAGCTCATGCTTTTGTGATGATTTTTTTTATGGTCATGCCGATTTTAATCGGAGGTTTCGGAAACTGACTTGTTCCCTTGATACTTGGAGCCCCTGATATAGCTTTCCCTCGAATGAACAACATAAGGTTCTGGCTCCTCCCCCCTTCTCTGACCCTACTTTTAATGAGAAGGATAGTAGAAAGCGGAGCAGGAACAGGGTGAACAGTTTATCCTCCCCTAGCTTCAAATATTGCTCATGGTGGAGCATCAGTTGATTTGGCGATTTTTAGGCTCCATTTAGCTGGAATCTCTTCCATTCTAGGAGCCGTAAATTTCATCACAACAATTCTCAACATACGAACTCCTCAAATAAGGTTTGATCAAATGCCATTGTTTGTTTGGGCTGTTGGAATTACAGCTCTCCTTCTTCTTCTTTCACTTCCNGTTTTAGCCGGAGCTATCACAATATTGCTAAC-------------------------------------------------------------------------"

by taxon IDs

bold_seq(ids = c('ACRJP618-11', 'ACRJP619-11'))
#> [[1]]
#> [[1]]$id
#> [1] "ACRJP618-11"
#> 
#> [[1]]$name
#> [1] "Lepidoptera"
#> 
#> [[1]]$gene
#> [1] "ACRJP618-11"
#> 
#> [[1]]$sequence
#> [1] "------------------------TTGAGCAGGCATAGTAGGAACTTCTCTTAGTCTTATTATTCGAACAGAATTAGGAAATCCAGGATTTTTAATTGGAGATGATCAAATCTACAATACTATTGTTACGGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCCCTTATACTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAACAATATAAGTTTTTGGCTTCTTCCCCCTTCACTATTACTTTTAATTTCCAGAAGAATTGTTGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCACTGTCATCTAATATTGCCCATAGAGGTACATCAGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCGATTAATTTTATTACTACAATTATTAATATACGAATTAACAGTATAAATTATGATCAAATACCACTATTTGTGTGATCAGTAGGAATTACTGCTTTACTCTTATTACTTTCTCTTCCAGTATTAGCAGGTGCTATCACTATATTATTAACGGATCGAAATTTAAATACATCATTTTTTGATCCTGCAGGAGGAGGAGATCCAATTTTATATCAACATTTATTT"
#> 
#> 
#> [[2]]
#> [[2]]$id
#> [1] "ACRJP619-11"
#> 
#> [[2]]$name
#> [1] "Lepidoptera"
#> 
#> [[2]]$gene
#> [1] "ACRJP619-11"
#> 
#> [[2]]$sequence
#> [1] "AACTTTATATTTTATTTTTGGTATTTGAGCAGGCATAGTAGGAACTTCTCTTAGTCTTATTATTCGAACAGAATTAGGAAATCCAGGATTTTTAATTGGAGATGATCAAATCTACAATACTATTGTTACGGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCCCTTATACTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAACAATATAAGTTTTTGGCTTCTTCCCCCTTCACTATTACTTTTAATTTCCAGAAGAATTGTTGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCACTGTCATCTAATATTGCCCATAGAGGTACATCAGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCGATTAATTTTATTACTACAATTATTAATATACGAATTAACAGTATAAATTATGATCAAATACCACTATTTGTGTGATCAGTAGGAATTACTGCTTTACTCTTATTACTTTCTCTTCCAGTATTAGCAGGTGCTATCACTATATTATTAACGGATCGAAATTTAAATACATCATTTTTTGATCCTGCAGGAGGAGGAGATCCAATTTTATATCAACATTTATTT"

by container (containers include project codes and dataset codes)

bold_seq(container = 'ACRJP')[[1]]
#> $id
#> [1] "ACRJP003-09"
#> 
#> $name
#> [1] "Lepidoptera"
#> 
#> $gene
#> [1] "ACRJP003-09"
#> 
#> $sequence
#> [1] "AACATTATATTTTATTTTTGGGATCTGATCTGGAATAGTAGGGACATCTTTAAGTATACTAATTCGAATAGAACTAGGAAATCCTGGATGTTTAATTGGGGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCCATTATAATTGGAGGTTTTGGCAATTGACTTGTACCATTAATATTAGGAGCCCCTGATATAGCATTTCCCCGAATAAATAATATAAGATTTTGACTTCTTCCCCCCTCATTAATTTTATTAATTTCAAGAAGAATTGTTGAAAATGGAGCAGGAACAGGATGAACAGTCTATCCTCCATTATCTTCTAATATTGCGCATAGAGGATCCTCTGTTGATTTAGCTATTTTCTCACTTCATTTAGCAGGAATTTCTTCTATTTTAGGAGCAATTAATTTTATTACAACTATTATTAATATACGAATAAATAATTTACTTTTTGACCAAATACCTCTATTTGTTTGAGCAGTAGGTATTACAGCTGTTCTTCTTTTATTATCATTACCAGTATTAGCAGGAGCAATTACCATACTATTAACAGATCGTAATTTAAATACTTCTTTCTTTGATCCTGCTGGAGGAGGAGATCCAATTTTATACCAACATTTATTT"

by bin (a bin is a Barcode Index Number)

bold_seq(bin = 'BOLD:AAA5125')[[1]]
#> $id
#> [1] "ASARD6776-12"
#> 
#> $name
#> [1] "Eacles ormondei"
#> 
#> $gene
#> [1] "ASARD6776-12"
#> 
#> $sequence
#> [1] "AACTTTATATTTTATTTTTGGAATTTGAGCAGGTATAGTAGGAACTTCTTTAAGATTACTAATTCGAGCAGAATTAGGTACCCCCGGATCTTTAATTGGAGATGACCAAATTTATAATACCATTGTAACAGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGATTAGTACCCCTAATACTAGGAGCTCCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGACTATTACCCCCATCTTTAACCCTTTTAATTTCTAGAAGAATTGTCGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCCCTTTCATCTAATATTGCTCATGGAGGCTCTTCTGTTGATTTAGCTATTTTTTCCCTTCATCTAGCTGGAATCTCATCAATTTTAGGAGCTATTAATTTTATCACAACAATCATTAATATACGACTAAATAATATAATATTTGACCAAATACCTTTATTTGTATGAGCTGTTGGTATTACAGCATTTCTTTTATTGTTATCTTTACCTGTACTAGCTGGAGCTATTACTATACTTTTAACAGATCGAAACTTAAATACATCATTTTTTGACCCAGCAGGAGGAGGAGATCCTATTCTCTATCAACATTTATTT"

And there are more ways to query, check out the docs for ?bold_seq.

Search for specimen data only

The BOLD specimen API doesn’t give back sequences, only specimen data. By default you download tsv format data, which is given back to you as a data.frame

res <- bold_specimens(taxon = 'Osmia')
head(res[,1:8])
#>      processid   sampleid recordID catalognum   fieldnum
#> 1  BEECA373-06 05-NT-0373   514740            05-NT-0373
#> 2  BEECA607-06 05-NT-0607   516959            05-NT-0607
#> 3  BEECA963-07 01-OR-0790   554153            01-OR-0790
#> 4  BEECB358-07 04-WA-1076   596920 BBSL697174 04-WA-1076
#> 5  BEECB438-07 00-UT-1157   597000 BBSL432653 00-UT-1157
#> 6 BEECC1176-09 02-UT-2849  1060879 BBSL442586 02-UT-2849
#>                    institution_storing collection_code      bin_uri
#> 1   York University, Packer Collection              NA BOLD:AAI2013
#> 2   York University, Packer Collection              NA BOLD:AAC8510
#> 3   York University, Packer Collection              NA BOLD:ABZ3184
#> 4 Utah State University, Logan Bee Lab              NA BOLD:AAC5797
#> 5 Utah State University, Logan Bee Lab              NA BOLD:AAF2159
#> 6   York University, Packer Collection              NA BOLD:AAE5368

You can optionally get back the data in XML format

bold_specimens(taxon = 'Osmia', format = 'xml')

<?xml version="1.0" encoding="UTF-8"?>
<bold_records  xsi:noNamespaceSchemaLocation="http://www.boldsystems.org/schemas/BOLDPublic_record.xsd"  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <record>
    <record_id>1470124</record_id>
    <processid>BOM1525-10</processid>
    <bin_uri>BOLD:AAN3337</bin_uri>
    <specimen_identifiers>
      <sampleid>DHB 1011</sampleid>
      <catalognum>DHB 1011</catalognum>
      <fieldnum>DHB1011</fieldnum>
      <institution_storing>Marjorie Barrick Museum</institution_storing>
    </specimen_identifiers>
    <taxonomy>

You can choose to get the crul response object back if you’d rather work with the raw data returned from the BOLD API.

res <- bold_specimens(taxon = 'Osmia', format = 'xml', response = TRUE)
res$url
#> [1] "https://v4.boldsystems.org/index.php/API_Public/specimen?taxon=Osmia&format=xml"
res$status_code
#> [1] 200
res$response_headers
#> $status
#> [1] "HTTP/2 200 "
#> 
#> $server
#> [1] "nginx"
#> 
#> $date
#> [1] "Mon, 20 Apr 2020 16:23:41 GMT"
#> 
#> $`content-type`
#> [1] "application/x-download"
#> 
#> $`x-powered-by`
#> [1] "PHP/5.3.15"
#> 
#> $`content-disposition`
#> [1] "attachment; filename=bold_data.xml"
#> 
#> $`x-frame-options`
#> [1] "SAMEORIGIN"
#> 
#> $`x-content-type-options`
#> [1] "nosniff"
#> 
#> $`x-xss-protection`
#> [1] "1; mode=block"

Search for specimen plus sequence data

The specimen/sequence combined API gives back specimen and sequence data. Like the specimen API, this one gives by default tsv format data, which is given back to you as a data.frame. Here, we’re setting sepfasta=TRUE so that the sequence data is given back as a list, and taken out of the data.frame returned so the data.frame is more manageable.

res <- bold_seqspec(taxon = 'Osmia', sepfasta = TRUE)
res$fasta[1:2]
#> $`BEECA373-06`
#> [1] "-ATTTTATATATAATTTTTGCTATATGATCAGGTATAATCGGATCAGCAATAAGAATTATTATTCGTATAGAATTAAGAATTCCTGGTTCATGAATTTCAAATGATCAAACTTATAACTCTTTAGTAACTGCTCATGCTTTTTTAATAATTTTTTTCTTAGTTATACCTTTTTTAATTGGAGGATTTGGAAATTGATTAATTCCTTTAATATTAGGAATCCCGGATATAGCTTTCCCTCGAATAAATAATATTAGATTTTGACTTTTACCCCCTTCATTAATATTATTACTTTTAAGAAATTTTATAAATCCAAGACCAGGTACTGGATGAACTGTTTATCCTCCTCTTTCTTCTCATTTATTTCATTCTTCTCCTTCAGTTGATATAGCCATTTTTTCTTTACATATTTCCGGTTTATCTTCTATTATAGGTTCGTTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAACATATCCAATTACCTTTATTTCCATGATCTGTTTTTATTACTACTATCTTATTACTTTTTTCTTTACCTGTTTTAGCAGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCTACAGGAGGTGGAGATCCAATCCTTTATCAACATTTATTT"
#> 
#> $`BEECA607-06`
#> [1] "AATATTATATATAATTTTTGCTTTGTGATCTGGAATAATTGGTTCATCTATAAGAATTATTATTCGTATAGAATTAAGAATTCCTGGTTCATGAATTTCAAATGATCAAGTTTATAATTCATTAGTTACAGCTCATGCTTTTTTAATAATTTTTTTTTTAGTTATACCATTTATAATTGGAGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAATTCCTGATATAGCTTTTCCTCGAATAAATAATATTAGATTTTGATTATTACCACCATCATTAATACTTTTACTTTTAAGAAATTTTTTTAATCCAAGTTCAGGAACTGGATGAACTGTATATCCTCCTCTTTCATCATATTTATTTCATTCTTCACCTTCTGTTGATTTAGCTATTTTTTCTCTTCATATATCAGGTTTATCTTCTATTATAGGTTCATTAAACTTTATTGTAACTATTATTATAATAAAAAATATTTCTTTAAAGTATATTCAATTGCCATTATTTCCATGATCTGTTTTTATTACTACAATTCTTTTATTATTATCATTACCAGTTTTAGCAGGTGCTATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCTACAGGAGGGGGAG--------------------------"

Or you can index to a specific sequence like

res$fasta['GBAH0293-06']
#> $`GBAH0293-06`
#> [1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAATGTTAGGGATTCCAGATATAGCTTTTCCACGAATAAATAATATTAGATTTTGACTGTTACCTCCATCTTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCTGGAACAGGATGAACAGTTTATCCTCCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTAGCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAATATATTCAATTACCTTTATTTTCTTGATCTGTATTTATTACTACTATTCTTTTATTATTTTCTTTACCTGTATTAGCTGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGGGGAGATCCAATTCTTTATCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTTTATATTTTAATTTTACCTGGATTTGGATTAATTTCTCAAATTATTTCTAATGAAAGAGGAAAAAAAGAAACTTTTGGAAATATTGGTATAATTTATGCTATATTAAGAATTGGACTTTTAGGTTTTATTGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"

Get trace files

This function downloads files to your machine - it does not load them into your R session - but prints out where the files are for your information.

bold_trace(taxon = 'Osmia', quiet = TRUE)

Scott Chamberlain

2020-04-20