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|
---
title: "bold introduction"
author: "Scott Chamberlain"
date: "2020-04-20"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{bold introduction}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
`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
```r
install.packages("bold")
```
Or install the development version from GitHub
```r
remotes::install_github("ropensci/bold")
```
Load the package
```r
library("bold")
```
### Search for taxonomic names via names
`bold_tax_name` searches for names with names.
```r
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
```
```r
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.
```r
bold_tax_id(id = 88899)
#> input taxid taxon tax_rank tax_division parentid parentname
#> 1 88899 88899 Momotus genus Animalia 88898 Momotidae
```
```r
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
```r
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
```r
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"
#>
#> $`x-xss-protection`
#> [1] "1; mode=block"
```
You can do geographic searches
```r
bold_seq(geo = "USA")
#> [[1]]
#> [[1]]$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
```r
bold_seq(researchers = 'Thibaud Decaens')[[1]]
#> $id
#> [1] "COLNO015-09"
#>
#> $name
#> [1] "Ptiliidae"
#>
#> $gene
#> [1] "COLNO015-09"
#>
#> $sequence
#> [1] "AACCTTGTATTTTATGTTCGGNGCTTGAGCTGGAATAGTCGGGACAAGTTTGAGTCTCCTTATCCGAACTGAACTCGGCACTCCAGGTTCACTAATTGGAGACGACCAAATCTACAACGTAATCGTAACAGCTCATGCTTTTGTGATGATTTTTTTTATGGTCATGCCGATTTTAATCGGAGGTTTCGGAAACTGACTTGTTCCCTTGATACTTGGAGCCCCTGATATAGCTTTCCCTCGAATGAACAACATAAGGTTCTGGCTCCTCCCCCCTTCTCTGACCCTACTTTTAATGAGAAGGATAGTAGAAAGCGGAGCAGGAACAGGGTGAACAGTTTATCCTCCCCTAGCTTCAAATATTGCTCATGGTGGAGCATCAGTTGATTTGGCGATTTTTAGGCTCCATTTAGCTGGAATCTCTTCCATTCTAGGAGCCGTAAATTTCATCACAACAATTCTCAACATACGAACTCCTCAAATAAGGTTTGATCAAATGCCATTGTTTGTTTGGGCTGTTGGAATTACAGCTCTCCTTCTTCTTCTTTCACTTCCNGTTTTAGCCGGAGCTATCACAATATTGCTAAC-------------------------------------------------------------------------"
```
by taxon IDs
```r
bold_seq(ids = c('ACRJP618-11', 'ACRJP619-11'))
#> [[1]]
#> [[1]]$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)
```r
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_)
```r
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`
```r
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
```r
bold_specimens(taxon = 'Osmia', format = 'xml')
```
```r
<?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.
```r
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"
#>
#> $`x-xss-protection`
#> [1] "1; mode=block"
```
### Search for specimen plus sequence data
The specimen/sequence combined API gives back specimen and sequence data. Like the specimen API, this one gives by default `tsv` format data, which is given back to you as a `data.frame`. Here, we're setting `sepfasta=TRUE` so that the sequence data is given back as a list, and taken out of the `data.frame` returned so the `data.frame` is more manageable.
```r
res <- bold_seqspec(taxon = 'Osmia', sepfasta = TRUE)
res$fasta[1:2]
#> $`BEECA373-06`
#> [1] "-ATTTTATATATAATTTTTGCTATATGATCAGGTATAATCGGATCAGCAATAAGAATTATTATTCGTATAGAATTAAGAATTCCTGGTTCATGAATTTCAAATGATCAAACTTATAACTCTTTAGTAACTGCTCATGCTTTTTTAATAATTTTTTTCTTAGTTATACCTTTTTTAATTGGAGGATTTGGAAATTGATTAATTCCTTTAATATTAGGAATCCCGGATATAGCTTTCCCTCGAATAAATAATATTAGATTTTGACTTTTACCCCCTTCATTAATATTATTACTTTTAAGAAATTTTATAAATCCAAGACCAGGTACTGGATGAACTGTTTATCCTCCTCTTTCTTCTCATTTATTTCATTCTTCTCCTTCAGTTGATATAGCCATTTTTTCTTTACATATTTCCGGTTTATCTTCTATTATAGGTTCGTTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAACATATCCAATTACCTTTATTTCCATGATCTGTTTTTATTACTACTATCTTATTACTTTTTTCTTTACCTGTTTTAGCAGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCTACAGGAGGTGGAGATCCAATCCTTTATCAACATTTATTT"
#>
#> $`BEECA607-06`
#> [1] "AATATTATATATAATTTTTGCTTTGTGATCTGGAATAATTGGTTCATCTATAAGAATTATTATTCGTATAGAATTAAGAATTCCTGGTTCATGAATTTCAAATGATCAAGTTTATAATTCATTAGTTACAGCTCATGCTTTTTTAATAATTTTTTTTTTAGTTATACCATTTATAATTGGAGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAATTCCTGATATAGCTTTTCCTCGAATAAATAATATTAGATTTTGATTATTACCACCATCATTAATACTTTTACTTTTAAGAAATTTTTTTAATCCAAGTTCAGGAACTGGATGAACTGTATATCCTCCTCTTTCATCATATTTATTTCATTCTTCACCTTCTGTTGATTTAGCTATTTTTTCTCTTCATATATCAGGTTTATCTTCTATTATAGGTTCATTAAACTTTATTGTAACTATTATTATAATAAAAAATATTTCTTTAAAGTATATTCAATTGCCATTATTTCCATGATCTGTTTTTATTACTACAATTCTTTTATTATTATCATTACCAGTTTTAGCAGGTGCTATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCTACAGGAGGGGGAG--------------------------"
```
Or you can index to a specific sequence like
```r
res$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.
```r
bold_trace(taxon = 'Osmia', quiet = TRUE)
```
|
