bold is an R package to connect to BOLD Systems via their API. Functions in bold let you search for sequence data, specimen data, sequence + specimen data, and download raw trace files.
Install
Install bold from CRAN
install.packages("bold")
Or install the development version from GitHub
devtools::install_github("ropensci/bold")
Load the package
library("bold")
bold_tax_name searches for names with names.
bold_tax_name(name = 'Diplura')
#> input taxid taxon tax_rank tax_division parentid parentname
#> 1 Diplura 591238 Diplura order Animals 82 Insecta
#> 2 Diplura 603673 Diplura genus Protists 53974 Scytosiphonaceae
#> taxonrep
#> 1 Diplura
#> 2 <NA>
bold_tax_name(name = c('Diplura', 'Osmia'))
#> input taxid taxon tax_rank tax_division parentid parentname
#> 1 Diplura 591238 Diplura order Animals 82 Insecta
#> 2 Diplura 603673 Diplura genus Protists 53974 Scytosiphonaceae
#> 3 Osmia 4940 Osmia genus Animals 4962 Megachilinae
#> taxonrep
#> 1 Diplura
#> 2 <NA>
#> 3 Osmia
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 Animals 88898 Momotidae
bold_tax_id(id = c(88899, 125295))
#> input taxid taxon tax_rank tax_division parentid parentname
#> 1 88899 88899 Momotus genus Animals 88898 Momotidae
#> 2 125295 125295 Helianthus genus Plants 100962 Asteraceae
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]]$id
#> [1] "FBAPB491-09"
#>
#> [[1]]$name
#> [1] "Coelioxys conica"
#>
#> [[1]]$gene
#> [1] "FBAPB491-09"
#>
#> [[1]]$sequence
#> [1] "---------------------ACCTCTTTAAGAATAATTATTCGTATAGAAATAAGAATTCCAGGATCTTGAATTAATAATGATCAAATTTATAACTCCTTTATTACAGCACATGCATTTTTAATAATTTTTTTTTTAGTTATACCTTTTCTTATTGGAGGATTTGGAAATTGATTAGTACCTTTAATATTAGGATCACCAGATATAGCTTTCCCACGAATAAATAATATTAGATTTTGATTATTACCTCCTTCTTTATTAATATTATTATTAAGTAATTTAATAAATCCCAGACCAGGAACAGGCTGAACAGTTTATCCTCCTTTATCTTTATACACATACCACCCTTCTCCCTCAGTTGATTTAGCAATTTTTTCACTACATCTATCAGGAATCTCTTCTATTATTGGATCTATAAATTTTATTGTTACAATTTTAATAATAAAAAACTTTTCAATAAATTATAATCAAATACCATTATTCCCATGATCTATTTTAATTACTACTATTTTATTATTATTATCACTACCTGTATTAGCTGGTGCTATTACTATATTATTATTTGATCGAAATTTAAATTCTTCTTTTTTTGACCCTATAGGAGGAGGAGACCCAATTTTATACCAACATTTA"
#>
#>
#> [[2]]
#> [[2]]$id
#> [1] "FBAPC351-10"
#>
#> [[2]]$name
#> [1] "Coelioxys afra"
#>
#> [[2]]$gene
#> [1] "FBAPC351-10"
#>
#> [[2]]$sequence
#> [1] "---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGAATAAATAATGTAAGATTTTGACTATTACCTCCCTCAATTTTCTTATTATTATCAAGAACCCTAATTAACCCAAGAGCTGGTACTGGATGAACTGTATATCCTCCTTTATCCTTATATACATTTCATGCCTCACCTTCCGTTGATTTAGCAATTTTTTCACTTCATTTATCAGGAATTTCATCAATTATTGGATCAATAAATTTTATTGTTACAATCTTAATAATAAAAAATTTTTCTTTAAATTATAGACAAATACCATTATTTTCATGATCAGTTTTAATTACTACAATTTTACTTTTATTATCATTACCAATTTTAGCTGGAGCAATTACTATACTCCTATTTGATCGAAATTTAAATACCTCATTCTTTGACCCAATAGGAGGAGGAGATCCAATTTTATATCAACATTTATTT"
You can optionally get back the httr response object
res <- bold_seq(taxon = 'Coelioxys', response = TRUE)
res$headers
#> $date
#> [1] "Tue, 15 Sep 2015 20:02:31 GMT"
#>
#> $server
#> [1] "Apache/2.2.15 (Red Hat)"
#>
#> $`x-powered-by`
#> [1] "PHP/5.3.15"
#>
#> $`content-disposition`
#> [1] "attachment; filename=fasta.fas"
#>
#> $connection
#> [1] "close"
#>
#> $`transfer-encoding`
#> [1] "chunked"
#>
#> $`content-type`
#> [1] "application/x-download"
#>
#> attr(,"class")
#> [1] "insensitive" "list"
You can do geographic searches
bold_seq(geo = "USA")
#> [[1]]
#> [[1]]$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] "BGABA657-14"
#>
#> $name
#> [1] "Coleoptera"
#>
#> $gene
#> [1] "BGABA657-14"
#>
#> $sequence
#> [1] "ACACTCTATTTCATTTTCGGAGCTTGATCAGGAATAGTAGGAACTTCTTTAAGAATACTAATTCGATCTGAATTGGGAAACCCCGGCTCATTGATTGGGGATGATCAAATTTATAATGTTATTGTAACAGCCCATGCATTCATTATAATTTTTTTTATAGTAATACCGATCATAATAGGAGGTTTTGGAAATTGATTAGTCCCGCTAATATTAGGTGCCCCAGATATAGCATTTCCTCGAATAAATAATATAAGATTTTGACTTCTTCCGCCTTCATTAACTTTACTTATTATAAGAAGAATTGTAGAAAACGGGGCGGGAACAGGATGAACAGTTTACCCACCCCTCTCTTCTAACATTGCTCATAGAGGAGCCTCTGTAGATCTTGCAATTTTTAGATTACATTTAGCCGGTGTATCATCAATTTTAGGTGCAGTTAATTTTATTACAACTATTATTAATATACGACCTAAAGGAATAACATTTGATCGCATACCTTTATTTGTATGAGCTGTAGCTTTAACTGCATTACTTTTATTATTATCTTTACCAGTATTAGCAGGTGCAATTACAATACTTTTAACTGATCGA---------------------------------------"
by taxon IDs
bold_seq(ids = c('ACRJP618-11', 'ACRJP619-11'))
#> [[1]]
#> [[1]]$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] "BLPAB406-06"
#>
#> $name
#> [1] "Eacles ormondei"
#>
#> $gene
#> [1] "BLPAB406-06"
#>
#> $sequence
#> [1] "AACTTTATATTTTATTTTTGGAATTTGAGCAGGTATAGTAGGAACTTCTTTAAGATTACTAATTCGAGCAGAATTAGGTACCCCCGGATCTTTAATTGGAGATGACCAAATTTATAATACCATTGTAACAGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGATTAGTACCCCTAATACTAGGAGCTCCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGACTATTACCCCCATCTTTAACTCTTTTAATTTCTAGAAGAATTGTCGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCCCTTTCATCTAATATTGCTCATGGAGGCTCTTCTGTTGATTTAGCTATTTTTTCCCTTCATCTAGCTGGAATCTCATCAATTTTAGGAGCTATTAATTTTATCACAACAATCATTAATATACGACTAAATAATATAATATTTGACCAAATACCTTTATTTGTATGAGCTGTTGGTATTACAGCATTTCTTTTATTGTTATCTTTACCTGTACTAGCTGGAGCTATTACTATACTTTTAACAGATCGAAACTTAAATACATCATTTTTTGACCCAGCAGGAGGAGGAGATCCTATTCTCTATCAACATTTATTT"
And there are more ways to query, check out the docs for ?bold_seq.
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 ASGCB261-13 BIOUG07489-F10 3955538 BIOUG07489-F10
#> 2 BCHYM1499-13 BC ZSM HYM 19359 4005348 BC ZSM HYM 19359 BC ZSM HYM 19359
#> 3 BCHYM412-13 BC ZSM HYM 18272 3896353 BC ZSM HYM 18272 BC ZSM HYM 18272
#> 4 BCHYM413-13 BC ZSM HYM 18273 3896354 BC ZSM HYM 18273 BC ZSM HYM 18273
#> 5 FBAPB706-09 BC ZSM HYM 02181 1289067 BC ZSM HYM 02181 BC ZSM HYM 02181
#> 6 FBAPB730-09 BC ZSM HYM 02205 1289091 BC ZSM HYM 02205 BC ZSM HYM 02205
#> institution_storing bin_uri phylum_taxID
#> 1 Biodiversity Institute of Ontario BOLD:AAB8874 20
#> 2 SNSB, Zoologische Staatssammlung Muenchen BOLD:AAD6282 20
#> 3 SNSB, Zoologische Staatssammlung Muenchen BOLD:AAP2416 20
#> 4 SNSB, Zoologische Staatssammlung Muenchen BOLD:AAP2416 20
#> 5 SNSB, Zoologische Staatssammlung Muenchen BOLD:AAE4126 20
#> 6 SNSB, Zoologische Staatssammlung Muenchen BOLD:AAK5820 20
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 httr 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] "http://www.boldsystems.org/index.php/API_Public/specimen?taxon=Osmia&specimen_download=xml"
res$status_code
#> [1] 200
res$headers
#> $date
#> [1] "Tue, 15 Sep 2015 20:12:13 GMT"
#>
#> $server
#> [1] "Apache/2.2.15 (Red Hat)"
#>
#> $`x-powered-by`
#> [1] "PHP/5.3.15"
#>
#> $`content-disposition`
#> [1] "attachment; filename=bold_data.xml"
#>
#> $connection
#> [1] "close"
#>
#> $`transfer-encoding`
#> [1] "chunked"
#>
#> $`content-type`
#> [1] "application/x-download"
#>
#> attr(,"class")
#> [1] "insensitive" "list"
The specimen/sequence combined API gives back specimen and sequence data. Like the specimen API, this one gives by default tsv format data, which is given back to you as a data.frame. Here, we're setting sepfasta=TRUE so that the sequence data is given back as a list, and taken out of the data.frame returned so the data.frame is more manageable.
res <- bold_seqspec(taxon = 'Osmia', sepfasta = TRUE)
res$fasta[1:2]
#> $`ASGCB261-13`
#> [1] "AATTTTATATATAATTTTTGCTATATGATCAGGAATAATTGGTTCAGCAATAAGAATTATTATTCGAATAGAATTAAGAATTCCTGGTTCATGAATTTCAAATGATCAAACTTATAATTCTTTAGTTACTGCTCATGCTTTTTTAATAATTTTTTTCTTAGTTATACCATTCTTAATTGGGGGATTTGGAAATTGATTAATTCCTTTAATATTAGGAATTCCAGATATAGCATTTCCACGAATAAATAATATTAGATTTTGACTTTTACCTCCTTCTTTAATACTTTTATTATTAAGAAATTTTATAAATCCTAGTCCAGGAACTGGATGAACTGTTTATCCACCTTTATCTTCTCATTTATTTCATTCTTCTCCTTCAGTTGATATAGCTATTTTTTCTTTACATATTTCTGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAACATATTCAATTACCTTTATTTCCTTGATCTGTCTTTATTACTACTATTTTATTACTTTTTTCTTTACCTGTTTTAGCAGGTGCAATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCTACAGGAGGAGGAGATCCTATTCTTTATCAACATTTATTT"
#>
#> $`BCHYM1499-13`
#> [1] "AATTCTTTACATAATTTTTGCTTTATGATCTGGAATAATTGGGTCAGCAATAAGAATTATTATTCGAATAGAATTAAGTATCCCAGGTTCATGAATTACTAATGATCAAATTTATAATTCTTTAGTAACTGCACATGCTTTTTTAATAATTTTTTTTCTTGTGATACCATTTTTAATTGGAGGATTTGGAAATTGATTAATTCCTTTAATATTAGGAATTCCAGATATAGCTTTCCCACGAATAAACAATATTAGATTTTGATTATTACCGCCATCTTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCTGGAACAGGATGAACAGTTTATCCCCCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTAGCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAATATATTCAATTGCCTTTATTTCCTTGATCTGTATTTATTACTACTATTCTTTTATTATTTTCTTTACCTGTGTTAGCTGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCTACAGGAGGAGGAGATCCAATTCTTTATCAACATTTATTT"
Or you can index to a specific sequence like
res$fasta['GBAH0293-06']
#> $`GBAH0293-06`
#> [1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAATGTTAGGGATTCCAGATATAGCTTTTCCACGAATAAATAATATTAGATTTTGACTGTTACCTCCATCTTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCTGGAACAGGATGAACAGTTTATCCTCCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTAGCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAATATATTCAATTACCTTTATTTTCTTGATCTGTATTTATTACTACTATTCTTTTATTATTTTCTTTACCTGTATTAGCTGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGGGGAGATCCAATTCTTTATCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTTTATATTTTAATTTTACCTGGATTTGGATTAATTTCTCAAATTATTTCTAATGAAAGAGGAAAAAAAGAAACTTTTGGAAATATTGGTATAATTTATGCTATATTAAGAATTGGACTTTTAGGTTTTATTGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
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)