Quick Start Guide
Video Tutorial
1. Registering an Account

An introduction to the BOLD Student Data Portal website. This video provides an overview of the system and describes how to register and create a course.
2. Submitting Data

This video follows the submission of a DNA barcode record from the specimen data all the way to the sequence. It focuses on the student interface, but it allows instructors to follow the steps students will need to undertake in order to create their records.
3. Overseeing a course

This video provides an overview of the tools available to instructors to monitor student work and participation. It also describes the steps needed in validating and approving student-generated data for publication on BOLD and GenBank.
 

Explore and Identification Interfaces

Some features of BOLD-SDP are available without an account, including exploring the public barcode data.

Exploring Taxonomy and Barcodes

This console allows the user to look up a scientific name of interest, using a variety of taxonomic databases, to determine the barcoding status of a particular taxa using the BOLD Taxonomy Browser or access and download data available in the Public Data Portal of BOLD, where specific details on individual specimens and their DNA Barcodes are available.

Explore Console Page
explore Figure 2-1: Options available for students to learn more about organisms they may want to DNA barcode

Students can search for scientific names of a species of interest using several taxonomy databases including NCBI’s (National Center for Biotechnology Information) Taxonomy Browser, ITIS (Integrated Taxonomic Information System), and EOL (Encyclopedia of Life). Simply type in a common name, click Search, and the results will open in a new page.

The BOLD Taxonomy Browser provides taxon-specific information. This information may include the number of specimens collected, the number of specimens with barcode sequences, where the specimens are stored (for example, Coastal Marine Biolabs), the geographic distribution of taxon occurrence and specimen images. Here, users can explore the taxonomic hierarchy for an organism and learn about the progress of DNA barcoding for a given group.

Taxonomy Page
taxonomypage Figure 2-2: BOLD Taxonomy Browser page for the California sheephead (Semicossyphus pulcher)

 

The BOLD Public Data Portal allows users to search among over 1 million records already generated by scientists and researchers all over the world. The Public Data Portal provides access to the actual records including all of the specimen, sequence, and trace data.

Public Data Portal Search Results
BOLD Public Figure 2-3: The Public Data Portal search results for the Monarch Butterfly, Danaus plexippus.

 

Sequence Identification

The BOLD Identification Engine can be accessed from the header menu. This ID engine will accept a DNA barcode sequence to compare for matches in the library. The Animal ID Engine has several sub-sets of the Barcode Library that can be utilized for matching COI barcodes, including the full library (All Barcode Records on BOLD), and the library of only sequences that have a species name (Species Level Barcode Records). There are also separate tabs for comparing plant and fungi sequences against the respective libraries.

The results page will return a species identification when one is possible. When a species level match cannot be made, BOLD will suggest the most likely matches. Multiple sequences can be run at the same time, and the results page will provide match results for each. On the results page, the user may view further details for the species that are the most likely matches for their queried sequence. For example, the matches can be visualized in hierarchical placement using a tree based identification system.  On the resulting taxon ID tree, the query sequence will be marked in red with BOLD sequences appearing in black.

Specimen Identification Results Page
Identification Engine Figure 2-4: BOLD ID Engine results, highlighting the most likely species match and collection location.