bold

Project Status: Active – The project has reached a stable, usable state and is being actively developed. cran version

bold accesses BOLD barcode data.

The Barcode of Life Data Systems (BOLD) is designed to support the generation and application of DNA barcode data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench.

This package retrieves data from the BOLD database of barcode clusters, and allows for searching of over 1.7M public records using multiple search criteria including sequence data, specimen data, specimen plus sequence data, as well as trace files.

Documentation for the BOLD API.

See also the taxize book for more options for taxonomic workflows with BOLD: https://ropenscilabs.github.io/taxize-book/

Package status and installation

cran checks Build Status codecov.io rstudio mirror downloads

Installation instructions

Stable Version

install.packages("bold")

Development Version

Install sangerseqR first (used in function bold::bold_trace() only)

For R < 3.5

source("http://bioconductor.org/biocLite.R")
biocLite("sangerseqR")

For R >= 3.5

install.packages('BiocManager')
BiocManager::install('sangerseqR')

Then install bold

devtools::install_github("ropensci/bold")

Usage

library("bold")

Search for sequence data only

Default is to get a list back

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

You can optionally get back the crul response object

res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$response_headers
#> $status
#> [1] "HTTP/1.1 200 OK"
#> 
#> $date
#> [1] "Thu, 27 Jun 2019 17:28:47 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"

Search for specimen data only

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 ASGCB255-13 BIOUG07489-F04  3955532            BIOUG07489-F04
#> 2 BEECA122-06     04-ON-0122   281152                04-ON-0122
#> 3 BEECA186-06     03-BC-0186   281216                03-BC-0186
#> 4 BEECA373-06     05-NT-0373   514740                05-NT-0373
#> 5 BEECA501-06     06-ON-0501   514868                06-ON-0501
#> 6 BEECA601-06     06-YT-0601   516953                06-YT-0601
#>                  institution_storing collection_code      bin_uri
#> 1  Biodiversity Institute of Ontario              NA BOLD:ABZ2181
#> 2 York University, Packer Collection              NA BOLD:AAC8510
#> 3 York University, Packer Collection              NA BOLD:AAC2237
#> 4 York University, Packer Collection              NA BOLD:AAI2013
#> 5 York University, Packer Collection              NA BOLD:AAC5789
#> 6 York University, Packer Collection              NA BOLD:AAB4644

Search for specimen plus sequence data

By default you download tsv format data, which is given back to you as a data.frame

res <- bold_seqspec(taxon='Osmia', sepfasta=TRUE)
res$fasta[1:2]
#> [[1]]
#> NULL
#> 
#> [[2]]
#> NULL

Or you can index to a specific sequence like

res$fasta['GBAH0293-06']
#> [[1]]
#> NULL

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.

x <- bold_trace(ids = 'ACRJP618-11', progress = FALSE)
read_trace(x$ab1)
#> Number of datapoints: 8877
#> Number of basecalls: 685
#> 
#> Primary Basecalls: NNNNNNNNNNNNNNNNNNGNNNTTGAGCAGGNATAGTAGGANCTTCTCTTAGTCTTATTATTCGAACAGAATTAGGAAATCCAGGATTTTTAATTGGAGATGATCAAATCTACAATACTATTGTTACGGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCCCTTATACTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAACAATATAAGTTTTTGGCTTCTTCCCCCTTCACTATTACTTTTAATTTCCAGAAGAATTGTTGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCACTGTCATCTAATATTGCCCATAGAGGTACATCAGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCGATTAATTTTATTACTACAATTATTAATATACGAATTAACAGTATAAATTATGATCAAATACCACTATTTGTGTGATCAGTAGGAATTACTGCTTTACTCTTATTACTTTCTCTTCCAGTATTAGCAGGTGCTATCACTATATTATTAACGGATCGAAATTTAAATACATCATTTTTTGATCCTGCAGGAGGAGGAGATCCAATTTTATATCAACATTTATTTTGATTTTTTGGACNTCNNNNAAGTTTAAN
#> 
#> Secondary Basecalls:

Large data

Sometimes with bold_seq() you request a lot of data, which can cause problems due to BOLD’s servers.

An example is the taxonomic name Arthropoda. When you send a request like bold_seq(taxon = "Arthropoda") BOLD attempts to give you back sequences for all records under Arthropoda. This, as you can imagine, is a lot of sequences.

library("taxize")

Using taxize::downstream get children of Arthropoda

x <- downstream("Arthropoda", db = "ncbi", downto = "class")
#> ══  1 queries  ═══════════════
#> ✔  Found:  Arthropoda
#> ══  Results  ═════════════════
#> 
#> ● Total: 1 
#> ● Found: 1 
#> ● Not Found: 0
nms <- x$Arthropoda$childtaxa_name

Optionally, check that the name exists in BOLD’s data. Any that are not in BOLD will give back a row of NAs

checks <- bold_tax_name(nms)
# all is good
checks[,1:5]
#>     taxid         taxon tax_rank tax_division parentid
#> 1   26059   Pycnogonida    class      Animals       20
#> 2      63     Arachnida    class      Animals       20
#> 3      74   Merostomata    class      Animals       20
#> 4  493944     Pauropoda    class      Animals       20
#> 5   80390      Symphyla    class      Animals       20
#> 6      85     Diplopoda    class      Animals       20
#> 7      75     Chilopoda    class      Animals       20
#> 8      82       Insecta    class      Animals       20
#> 9     372    Collembola    class      Animals       20
#> 10 734357       Protura    class      Animals       20
#> 11     84     Remipedia    class      Animals       20
#> 12     73 Cephalocarida    class      Animals       20
#> 13     68  Branchiopoda    class      Animals       20
#> 14 765970   Hexanauplia    class      Animals       20
#> 15     69  Malacostraca    class      Animals       20
#> 16 889450 Ichthyostraca    class      Animals       20
#> 17     80     Ostracoda    class      Animals       20

Then pass those names to bold_seq(). You could pass all names in at once, but we’re trying to avoid the large data request problem here, so run each one separately with lapply or a for loop like request.

out <- lapply(nms, bold_seq)

Citation

Get citation information for bold in R by running: citation(package = 'bold')

Meta

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