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]]$id
## [1] "BCHYM446-13"
##
## [[1]]$name
## [1] "Coelioxys afra"
##
## [[1]]$gene
## [1] "BCHYM446-13"
##
## [[1]]$sequence
## [1] "-------------------------------------------------------------------------------------------------------------------------------------------TTTTTAATAATTTTTTTTTTAGTTATACCATTTTTAATTGGAGGATTTGGAAATTGATTAGTACCTTTAATACTAGGAGCCCCCGATATAGCTTTTCCACGAATAAATAATGTAAGATTTTGACTATTACCTCCCTCAATTTTCTTATTATTATCAAGAACCCTAATTAACCCAAGAGCTGGTACTGGATGAACTGTANCTCCTCCTTTATCCTTATATACATTTCATGCCTCACCTTCCGTTGATTTAGCAATTTTTTCACTTCATTTATCAGGAATTTCATCAATTATTGGATCAATAAATTTTATTGTTACAATCTTAATAATAAAAAATTTTTCTTTAAATTATAGACAAATACCATTATTTTCATGATCAGTTTTAATTACTACAATTTTACTTTTATTATCATTACCAATTTTAGCTGGAGCAATTACTATACTCCTATTTGATCGAAATTTAAATACCTCATTCTTTGACC-----------------------------------------"
##
##
## [[2]]
## [[2]]$id
## [1] "FBAPB481-09"
##
## [[2]]$name
## [1] "Coelioxys afra"
##
## [[2]]$gene
## [1] "FBAPB481-09"
##
## [[2]]$sequence
## [1] "----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCCACGAATAAATAATGTAAGATTTTGACTATTACCTCCCTCAATTTTCTTATTATTATCAAGAACCCTAATTAACCCAAGTGCTGGTACTGGATGAACTGTATATCCTCCTTTATCCTTATATACATTTCATGCCTCACCTTCCGTTGATTTAGCAATTTTTTCACTTCATTTATCAGGAATTTCATCAATTATTGGATCAATAAATTTTATTGTTACAATCTTAATAATAAAAAATTTTTCTTTAAATTATAGACAAATACCATTATTTTCATGATCAGTTTTAATTACTACAATTTTACTTTTATTATCATTACCAATTTTAGCTGGAGCAATTACTATACTCCTATTTGATCGAAATTTAAATACCTCATTCTTTGACCCAATAGGAGGAGGAGATCCAATTTTATATCAACATTTATTT"
You can optionally get back the httr response object
res <- bold_seq(taxon = 'Coelioxys', response = TRUE)
res$headers
## $date
## [1] "Fri, 17 Apr 2015 19:12:26 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] "NEONV108-11"
##
## [[1]]$name
## [1] "Aedes thelcter"
##
## [[1]]$gene
## [1] "NEONV108-11"
##
## [[1]]$sequence
## [1] "AACTTTATACTTCATCTTCGGAGTTTGATCAGGAATAGTTGGTACATCATTAAGAATTTTAATTCGTGCTGAATTAAGTCAACCAGGTATATTTATTGGAAATGACCAAATTTATAATGTAATTGTTACAGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGACTAGTTCCTCTAATATTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAATAATATAAGTTTTTGAATACTACCTCCCTCATTAACTCTTCTACTTTCAAGTAGTATAGTAGAAAATGGATCAGGAACAGGATGAACAGTTTATCCACCTCTTTCATCTGGAACTGCTCATGCAGGAGCCTCTGTTGATTTAACTATTTTTTCTCTTCATTTAGCCGGAGTTTCATCAATTTTAGGGGCTGTAAATTTTATTACTACTGTAATTAATATACGATCTGCAGGAATTACTCTTGATCGACTACCTTTATTCGTTTGATCTGTAGTAATTACAGCTGTTTTATTACTTCTTTCACTTCCTGTATTAGCTGGAGCTATTACAATACTATTAACTGATCGAAATTTAAATACATCTTTCTTTGATCCAATTGGAGGAGGAGACCCAATTTTATACCAACATTTATTT"
##
##
## [[2]]
## [[2]]$id
## [1] "NEONV109-11"
##
## [[2]]$name
## [1] "Aedes thelcter"
##
## [[2]]$gene
## [1] "NEONV109-11"
##
## [[2]]$sequence
## [1] "AACTTTATACTTCATCTTCGGAGTTTGATCAGGAATAGTTGGTACATCATTAAGAATTTTAATTCGTGCTGAATTAAGTCAACCAGGTATATTTATTGGAAATGACCAAATTTATAATGTAATTGTTACAGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGACTAGTTCCTCTAATATTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAATAATATAAGTTTTTGAATACTACCTCCCTCATTAACTCTTCTACTTTCAAGTAGTATAGTAGAAAATGGGTCAGGAACAGGATGAACAGTTTATCCACCTCTTTCATCTGGAACTGCTCATGCAGGAGCCTCTGTTGATTTAACTATTTTTTCTCTTCATTTAGCCGGAGTTTCATCAATTTTAGGGGCTGTAAATTTTATTACTACTGTAATTAATATACGATCTGCAGGAATTACTCTTGATCGACTACCTTTATTCGTTTGATCTGTAGTAATTACAGCTGTTTTATTACTTCTTTCACTTCCTGTATTAGCTGGAGCTATTACAATACTATTAACTGATCGAAATTTAAATACATCTTTCTTTGACCCAATTGGAGGGGGAGACCCAATTTTATACCAACATTTATTT"
And you can search by researcher name
bold_seq(researchers = 'Thibaud Decaens')[[1]]
## $id
## [1] "BGABB1142-14"
##
## $name
## [1] "Coleoptera"
##
## $gene
## [1] "BGABB1142-14"
##
## $sequence
## [1] "TTCTTATTTGGTGCTTGATCCGCAATAGTTGGAACTTCTCTTAGATTATTAATTCGATCTGAATTAGGATCCCCAGGATCATTAATTGGTGATGATCAAATTTATAATGTAATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCAATTATAATTGGAGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCCCCTGATATAGCTTTCCCACGAATAAACAATATAAGATTTTGACTTCTTCCTCCTGCTCTCAGTTTATTAATTATAAGAAGAATTGTAGAAAGAGGGGCTGGAACAGGTTGAACTGTTTATCCTCCTCTATCAGCTAATTTAGCTCATAGAGGTTCTTCTGTAGATTTAGCTATTTTTAGCCTACATTTAGCAGGAGTTTCATCAATCCTTGGAGCTGTAAATTTTATTACTACCGTAATTAATATACGTCCTCAAGGTATAACCTTTGATCGTTTATCCTTATTTATTTGAGCAGTAAAAATTACAGCTATTCTTCTATTACTATCTCTTCCTGTTTTAGCAGGA---------------------------------------------------------------------------"
by taxon IDs
bold_seq(ids = c('ACRJP618-11', 'ACRJP619-11'))
## [[1]]
## [[1]]$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] "ACRJP167-09"
##
## $name
## [1] "Lepidoptera"
##
## $gene
## [1] "ACRJP167-09"
##
## $sequence
## [1] "-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAGTTTTTGACTTTTACCCCCCTCTTTAATTTTATTAATCTCTAGAAGAATTGTCGAAAATGGAGCAGGTACAGGATGAACAGTATATCCCCCACTTTCATCTAATATTGCTCATGGTGGTTCTTCTGTTGATTTAGCTATTTTTTCTCTTCATTTAGCCGGAATTTCCTCTATTTTAGGAGCAATTAATTTTATTACTACTATTATTAATATACGAGTTAATAATTTATCATTTGATCAAATACCTTTATTTGTTTGAGCTGTTGGTATTACTGCCTTATTACTTCTTCTTTCTTTACCAGTTTTAGCTGGAGCCATTACTATACTTTTAACAGATCGAAATCTTAATACTTCATTTTTTGACCCAGCTGGAGGAGGAGACCCAATTTTATACCAACATTTATTT"
by bin (a bin is a Barcode Index Number)
bold_seq(bin = 'BOLD:AAA5125')[[1]]
## $id
## [1] "ASARD6776-12"
##
## $name
## [1] "Lepidoptera"
##
## $gene
## [1] "ASARD6776-12"
##
## $sequence
## [1] "AACTTTATATTTTATTTTTGGAATTTGAGCAGGTATAGTAGGAACTTCTTTAAGATTACTAATTCGAGCAGAATTAGGTACCCCCGGATCTTTAATTGGAGATGACCAAATTTATAATACCATTGTAACAGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGATTAGTACCCCTAATACTAGGAGCTCCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGACTATTACCCCCATCTTTAACCCTTTTAATTTCTAGAAGAATTGTCGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCCCTTTCATCTAATATTGCTCATGGAGGCTCTTCTGTTGATTTAGCTATTTTTTCCCTTCATCTAGCTGGAATCTCATCAATTTTAGGAGCTATTAATTTTATCACAACAATCATTAATATACGACTAAATAATATAATATTTGACCAAATACCTTTATTTGTATGAGCTGTTGGTATTACAGCATTTCTTTTATTGTTATCTTTACCTGTACTAGCTGGAGCTATTACTATACTTTTAACAGATCGAAACTTAAATACATCATTTTTTGACCCAGCAGGAGGAGGAGATCCTATTCTCTATCAACATTTATTT"
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 BBHYL362-10 10BBCHY-3316 1769805 10BBCHY-3316 L#PC2010EI-002
## 2 BCHYM1499-13 BC ZSM HYM 19359 4005348 BC ZSM HYM 19359 BC ZSM HYM 19359
## 3 BCHYM411-13 BC ZSM HYM 18271 3896352 BC ZSM HYM 18271 BC ZSM HYM 18271
## 4 BCHYM413-13 BC ZSM HYM 18273 3896354 BC ZSM HYM 18273 BC ZSM HYM 18273
## 5 FBAPB700-09 BC ZSM HYM 02175 1289061 BC ZSM HYM 02175 BC ZSM HYM 02175
## 6 FBAPC355-10 BC ZSM HYM 05960 1709621 BC ZSM HYM 05960 BC ZSM HYM 05960
## institution_storing bin_uri phylum_taxID
## 1 Biodiversity Institute of Ontario BOLD:AAB8874 20
## 2 Bavarian State Collection of Zoology BOLD:AAD6282 20
## 3 Bavarian State Collection of Zoology BOLD:AAP2416 20
## 4 Bavarian State Collection of Zoology BOLD:AAP2416 20
## 5 Bavarian State Collection of Zoology BOLD:AAI1853 20
## 6 Bavarian State Collection of Zoology BOLD:AAK6070 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] "Fri, 17 Apr 2015 19:14:09 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]
## $`BBHYL362-10`
## [1] "AATTTTATATATAATTTTTGCTATATGATCAGGAATAATTGGTTCAGCAATAAGAATTATTATTCGAATAGAATTAAGAATTCCTGGTTCATGAATTTCAAATGATCAAACTTATAATTCTTTAGTTACTGCTCATGCTTTTTTAATAATTTTTTTTTTAGTTATACCATTCTTAATTGGGGGATTTGGAAATTGATTAATTCCTTTAATATTAGGAATTCCAGATATAGCATTTCCACGAATAAATAATATTAGATTTTGACTTTTACCTCCTTCTTTAATACTTTTATTATTAAGAAATTTTATAAATCCTAGTCCAGGAACTGGATGAACTGTTTATCCACCTTTATCTTCTCATTTATTTCATTCTTCTCCTTCAGTTGATATAGCTATTTTTTCTTTACATATTTCTGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAACATATTCAATTACCTTTATTTCCTTGATCTGTCTTTATTACTACTATTTTATTACTTTTTTCTTTACCTGTTTTAGCAGGTGCAATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCTACAGGAGGAGGAGATCCTATTCTTTATCAACATTTATTT"
##
## $`BCHYM1499-13`
## [1] "AATTCTTTACATAATTTTTGCTTTATGATCTGGAATAATTGGGTCAGCAATAAGAATTATTATTCGAATAGAATTAAGTATCCCAGGTTCATGAATTACTAATGATCAAATTTATAATTCTTTAGTAACTGCACATGCTTTTTTAATAATTTTTTTTCTTGTGATACCATTTTTAATTGGAGGATTTGGAAATTGATTAATTCCTTTAATATTAGGAATTCCAGATATAGCTTTCCCACGAATAAACAATATTAGATTTTGATTATTACCGCCATCTTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCTGGAACAGGATGAACAGTTTATCCCCCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTAGCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAATATATTCAATTGCCTTTATTTCCTTGATCTGTATTTATTACTACTATTCTTTTATTATTTTCTTTACCTGTGTTAGCTGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCTACAGGAGGAGGAGATCCAATTCTTTATCAACATTTATTT"
Or you can index to a specific sequence like
res$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)
##
## <bold trace files>
##
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/a12.Lep-R.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/a12.MLep-F.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/ASGCB253-13[LepF1,LepR1]_F.ab1
... cutoff