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---
title: "bold introduction"
author: "Scott Chamberlain"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{bold introduction}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
```{r eval=TRUE, echo=FALSE, warning = FALSE, message = FALSE}
NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")
knitr::opts_chunk$set(
comment = "#>",
warning = FALSE,
message = FALSE,
collapse = TRUE,
purl = NOT_CRAN,
eval = NOT_CRAN
)
```
`bold` is an R package to connect to BOLD Systems (https://www.boldsystems.org/) via their API. Functions in `bold` let you search for sequence data, specimen data, sequence + specimen data, and download raw trace files.
### bold info
+ BOLD home page: https://boldsystems.org/
+ BOLD API docs: https://v4.boldsystems.org/index.php/api_home
See also the taxize book for more options for taxonomic workflows with BOLD: https://taxize.dev/
### Using bold
**Install**
Install `bold` from CRAN
```{r eval=FALSE}
install.packages("bold")
```
Or install the development version from GitHub
```{r, eval=FALSE}
remotes::install_github("ropensci/bold")
```
Load the package
```{r}
library("bold")
```
### Search for taxonomic names via names
`bold_tax_name` searches for names with names.
```{r cache=TRUE}
bold_tax_name(name = 'Diplura')
```
```{r cache=TRUE}
bold_tax_name(name = c('Diplura', 'Osmia'))
```
### Search for taxonomic names via BOLD identifiers
`bold_tax_id` searches for names with BOLD identifiers.
```{r cache=TRUE}
bold_tax_id(id = 88899)
```
```{r cache=TRUE}
bold_tax_id(id = c(88899, 125295))
```
### Search for sequence data only
The BOLD sequence API gives back sequence data, with a bit of metadata.
The default is to get a list back
```{r cache=TRUE}
bold_seq(taxon = 'Coelioxys')[1:2]
```
You can optionally get back the `crul` response object
```{r cache=TRUE}
res <- bold_seq(taxon = 'Coelioxys', response = TRUE)
res$response_headers
```
You can do geographic searches
```{r cache=TRUE}
bold_seq(geo = "USA")
```
And you can search by researcher name
```{r cache=TRUE}
bold_seq(researchers = 'Thibaud Decaens')[[1]]
```
by taxon IDs
```{r cache=TRUE}
bold_seq(ids = c('ACRJP618-11', 'ACRJP619-11'))
```
by container (containers include project codes and dataset codes)
```{r cache=TRUE}
bold_seq(container = 'ACRJP')[[1]]
```
by bin (a bin is a _Barcode Index Number_)
```{r cache=TRUE}
bold_seq(bin = 'BOLD:AAA5125')[[1]]
```
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 cache=TRUE}
res <- bold_specimens(taxon = 'Osmia')
head(res[,1:8])
```
You can optionally get back the data in `XML` format
```{r eval=FALSE}
bold_specimens(taxon = 'Osmia', format = 'xml')
```
```{r eval=FALSE, results='asis'}
<?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$url
res$status_code
res$response_headers
```
### Search for specimen plus sequence data
The specimen/sequence combined API gives back specimen and sequence data. Like the specimen API, this one gives by default `tsv` format data, which is given back to you as a `data.frame`. Here, we're setting `sepfasta=TRUE` so that the sequence data is given back as a list, and taken out of the `data.frame` returned so the `data.frame` is more manageable.
```{r cache=TRUE}
res <- bold_seqspec(taxon = 'Osmia', sepfasta = TRUE)
res$fasta[1:2]
```
Or you can index to a specific sequence like
```{r cache=TRUE}
res$fasta['GBAH0293-06']
```
### 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 eval=FALSE}
bold_trace(taxon = 'Osmia', quiet = TRUE)
```
|
