bold is an R package to connect to BOLD Systems \url{http://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.
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')
## name taxonrep taxid taxon tax_rank tax_division parentid
## 1 Diplura Diplura 591238 Diplura order Animals 82
## 2 Diplura <NA> 603673 Diplura genus Protists 53974
## parentname
## 1 Insecta
## 2 Scytosiphonaceae
bold_tax_name(name=c('Diplura','Osmia'))
## name taxonrep taxid taxon tax_rank tax_division parentid
## 1 Diplura Diplura 591238 Diplura order Animals 82
## 2 Osmia <NA> 603673 Diplura genus Protists 53974
## 3 Diplura Osmia 4940 Osmia genus Animals 4962
## 4 Osmia Osmia 4940 Osmia genus Animals 4962
## parentname
## 1 Insecta
## 2 Scytosiphonaceae
## 3 Megachilinae
## 4 Megachilinae
bold_tax_id searches for names with BOLD identifiers.
bold_tax_id(id=88899)
## id taxid taxon tax_rank tax_division parentid parentname
## 1 88899 88899 Momotus genus Animals 88898 Momotidae
bold_tax_id(id=c(88899,125295))
## id taxid taxon tax_rank tax_division parentid parentname
## 1 88899 88899 Momotus genus Animals 88898 Momotidae
## 2 125295 88899 Momotus genus Animals 88898 Momotidae
## 3 88899 125295 Helianthus genus Plants 100962 Asteraceae
## 4 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]]$id
## [1] "CNEID3374-12"
##
## [[1]]$name
## [1] "Coelioxys funeraria"
##
## [[1]]$gene
## [1] "CNEID3374-12"
##
## [[1]]$sequence
## [1] "TATAATATATATAATTTTTGCAATATGATCAGGAATAATTGGTTCTTCATTAAGAATAATTATCCGAATAGAATTAAGAATCCCAGGATCTTGAATTAATAATGATCAAATTTATAATTCTTTTATCACAGCTCACGCATTTTTAATAATTTTTTTTTTAGTTATACCTTTTTTAATTGGAGGATTTGGTAATTGATTAGCCCCTTTAATATTAGGAGCCCCTGATATAGCTTTCCCTCGAATAAACAACATTAGATTTTGATTATTACCTCCTTCCTTATTAATACTTTTATCTAGTAATTTAATTACCCCTAGACCAGGGACAGGGTGAACTATTTACCCTCCATTATCTTTATATAATTATCANCCTTCTCCATCTGTTGATTTAGCAATTTTTTCTTTACATTTATCAGGAATTTCCTCTATTATTGGATCAATAAATTTCATTGTAACAATTTTAATAATAAAAAATTTTTCAATAAATTACAATCAAATACCTTTATTTCCATGATCAATTCTAATTACTACAATTTTATTATTATTATCATTACCTGTATTAGCAGGAGCAATTACAATATTATTATTTGATCGTAATTTAAATTCTTCATTTTTTGATCCAATAGGAGGAGGAGA---------"
##
##
## [[2]]
## [[2]]$id
## [1] "GBMIN26386-13"
##
## [[2]]$name
## [1] "Coelioxys sp. HMG-2011"
##
## [[2]]$gene
## [1] "GBMIN26386-13"
##
## [[2]]$sequence
## [1] "CGAATAAATAATATTAGATTTTGATTATTACCCCCATCACTATTATTACTTCTATTAAGTAATTTGATTAAACCAAGACCAGGTACAGGATGAACCGTATACCCTCCCTTATCTTTATATCTTTATCACCCTTCACCATCAGTTGATTTTGCAATTTTTTCTTTACATTTATCAGGAATTTCATCTATTATTGGTTCATTAAATTTTATTGTAACAATTTTAATAATAAAAAATTGATCTTTAAATTATAGACAAATATCATTATTTCCTTGATCAATTTTTATTACTACAATTTTATTATTA"
You can optionally get back the httr response object
res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$headers
## $date
## [1] "Wed, 06 Aug 2014 22:14:55 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] "AMAZ039-09"
##
## $name
## [1] "Automeris liberia"
##
## $gene
## [1] "AMAZ039-09"
##
## $sequence
## [1] "AACTTTATACTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACTTCTTTAAGATTGCTAATTCGTGCTGAATTAGGTACCCCCAGATCTTTAATTGGAGATGACCAAATTTATAATACTATTGTCACAGCCCATGCCTTCATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGACTAGTTCCTTTAATATTAGGAGCCCCAGATATAGCCTTCCCCCGAATAAATAATATAAGATTTTGACTACTCCCCCCCTCTTTAACTCTTTTAATTTCAAGAAGAATTGTAGAAAATGGTGCCGGTACCGGCTGAACCGTTTACCCCCCTCTTTCTTCTAATATTGCTCACGGAGGATCTTCAGTTGATTTAGCTATTTTTTCCTTACATTTAGCTGGAATTTCCTCAATCTTAGGAGCTATTAATTTTATTACAACAATTATTAATATACGTTTAAATAATATATCTTTTGATCAAATACCTCTATTTGTTTGAGCTGTTGGAATTACAGCATTTTTACTTCTTCTTTCATTACCTGTTTTAGCTGGAGCTATTACTATACTATTAACAGATCGTAATTTAAATACCTCTTTTTTTGACCCTGCTGGAGGGGGAGACCCTATCTTATATCAACATTTATTT"
by taxon IDs
bold_seq(ids=c('ACRJP618-11','ACRJP619-11'))
## [[1]]
## [[1]]$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] "ACRJP021-09"
##
## $name
## [1] "Lepidoptera"
##
## $gene
## [1] "ACRJP021-09"
##
## $sequence
## [1] "-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAGATTTTGACTCCTCCCCCCCTCCTTAATTTTACTAATTTCTAGTAGTATTGTAGAAAATGGAACTGGTACTGGATGAACAGTTTATCCCCCTTTATCCTCTAACACAGCTCATAGTGGAGCCTCAGTTGATTTAACTATTTTTTCCCTTCATTTAGCAGGCATTTCTTCTATTTTAGGAGCTATTAATTTCATTACTACAATTATTAATATACGATTAAATAGTCTATCATTTGATAAAATACCTTTATTTGTTTGGGCAGTAGGAATTACAGCCCTATTATTACTTTTATCTTTACCAGTCTTAGCTGGAGCTATTACTATATTATTAACTGATCGTAATTTAAACACTTCATTTTTTGACCCTGCAGGAGGTGGTGACCCTATTCTCTACCAACATTTATTT"
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 GBAH3890-08 EU726617 856421 EU726617
## 2 GBAH3894-08 EU726613 856425 EU726613
## 3 GBAH3898-08 EU726609 856429 EU726609
## 4 GBAH3899-08 EU726608 856430 EU726608
## 5 GBAH3900-08 EU726607 856431 EU726607
## 6 GBAH3902-08 EU726605 856433 EU726605
## institution_storing bin_uri phylum_taxID
## 1 Mined from GenBank, NCBI BOLD:AAA4494 20
## 2 Mined from GenBank, NCBI BOLD:AAA4494 20
## 3 Mined from GenBank, NCBI BOLD:AAA4494 20
## 4 Mined from GenBank, NCBI BOLD:AAA4494 20
## 5 Mined from GenBank, NCBI BOLD:AAA4494 20
## 6 Mined from GenBank, NCBI BOLD:AAA4494 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] "Wed, 06 Aug 2014 22:15:33 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]
## $`GBAH3890-08`
## [1] "---------------------------------------ATTCTATATATAATTTTTGCTTTATGATCTGGAATAATTGGATCAGCAATA---AGAATTATTATTCGAATAGAATTAAGTATCCCAGGATCATGAATTTCTAAT---GATCAAATTTATAATTCTTTAGTAACTGCTCATGCCTTTTTAATAATTTTTTTTCTTGTCATACCATTTTTAATTGGAGGATTTGGAAATTGATTAATTCCATTAATA---TTAGGAATTCCAGATATAGCTTTTCCTCGAATAAATAATATTAGATTTTGACTTTTACCACCATCCTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGACCTGGAACAGGATGAACAATTTATCCACCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAATTGATTTA---GCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAACATTTCCTTAAAATATATTCAATTATCCTTATTTCCTTGATCTGTATTTATTACTACTATTCTTTTACTTTTTTCTTTACCTGTATTAGCTGGA---GCAATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGTGGAGATCCAATTCTTTATCAACATTTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
##
## $`GBAH3894-08`
## [1] "---------------------------------------ATTCTATATATAATTTTTGCTTTATGATCTGGAATAATTGGATCAGCAATA---AGAATTATTATTCGAATAGAATTAAGTATCCCAGGATCATGAATTTCTAAT---GATCAAATTTATAATTCTTTAGTAACTGCTCATGCCTTTTTAATAATTTTTTTTCTTGTCATACCATTTTTAATTGGAGGATTTGGAAATTGATTAATTCCATTAATA---TTAGGAATTCCAGATATAGCTTTTCCTCGAATAAATAATATTAGATTTTGACTTTTACCACCATCCTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGACCTGGAACAGGATGAACAATTTATCCACCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAATTGATTTA---GCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAACATTTCCTTAAAATATATTCAATTATCCTTATTTCCTTGATCTGTATTTATTACTACTATTCTTTTACTTTTTTCTTTACCTGTATTAGCTGGA---GCAATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGTGGAGATCCAATTCTTTATCAACATTTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
Or you can index to a specific sequence like
res$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)
## Trace file extracted with files:
##
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/HDBNS084-03~R_1.ab1
## /Users/sacmac/github/ropensci/bold/inst/vign/bold_trace_files/TRACE_FILE_INFO.txt