bold-package

bold

bold: A programmatic interface to the Barcode of Life data

A programmatic interface to the Web Service methods provided by
Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data.
Functions include methods for searching by sequences by taxonomic names,
ids, collectors, and institutions; as well as a function for searching
for specimens, and downloading trace files.

Salix Dubois

Interface to Bold Systems API

Scott Chamberlain

bold-package function

This package gives you access to data from BOLD System
http://www.boldsystems.org/ via their API
(http://v4.boldsystems.org/index.php/api_home)

About

<ul>
<li><code>bold_specimens</code> - Search for specimen data</li>
<li><code>bold_seq</code> - Search for and retrieve sequences</li>
<li><code>bold_seqspec</code> - Get sequence and specimen data together</li>
<li><code>bold_trace</code> - Get trace files - saves to disk</li>
<li><code>read_trace</code> - Read trace files into R</li>
<li><code>bold_tax_name</code> - Get taxonomic names via input names</li>
<li><code>bold_tax_id</code> - Get taxonomic names via BOLD identifiers (Deprecated)</li>
<li><code>bold_tax_id2</code> - Get taxonomic names via BOLD identifiers (improved)</li>
<li><code>bold_identify</code> - Search for match given a COI sequence</li>
<li><code>bold_identify_parents</code> - Adds guessed parent ranks (Deprecated)</li>
<li><code>bold_identify_taxonomy</code> - Adds real parent ranks.</li>
</ul>Interestingly, they provide xml and tsv format data for the specimen data,
while they provide fasta data format for the sequence data. So for the
specimen data you can get back raw XML, or a data frame parsed from the
tsv data, while for sequence data you get back a list (b/c sequences are
quite long and would make a data frame unwieldy).

Functions

bold — bold-package

This package gives you access to data from BOLD System
http://www.boldsystems.org/ via their API
(http://v4.boldsystems.org/index.php/api_home)

<ul>
<li><code>bold_specimens</code> - Search for specimen data</li>
<li><code>bold_seq</code> - Search for and retrieve sequences</li>
<li><code>bold_seqspec</code> - Get sequence and specimen data together</li>
<li><code>bold_trace</code> - Get trace files - saves to disk</li>
<li><code>read_trace</code> - Read trace files into R</li>
<li><code>bold_tax_name</code> - Get taxonomic names via input names</li>
<li><code>bold_tax_id</code> - Get taxonomic names via BOLD identifiers (Deprecated)</li>
<li><code>bold_tax_id2</code> - Get taxonomic names via BOLD identifiers (improved)</li>
<li><code>bold_identify</code> - Search for match given a COI sequence</li>
<li><code>bold_identify_parents</code> - Adds guessed parent ranks (Deprecated)</li>
<li><code>bold_identify_taxonomy</code> - Adds real parent ranks.</li>
</ul>

Interestingly, they provide xml and tsv format data for the specimen data,
while they provide fasta data format for the sequence data. So for the
specimen data you can get back raw XML, or a data frame parsed from the
tsv data, while for sequence data you get back a list (b/c sequences are
quite long and would make a data frame unwieldy).

bold-package: bold

Description

Arguments

About

Functions