Handbook

Introduction to Barcode Of Life Data Systems (BOLD)

The Barcode of Life Data Systems (BOLD), established in 2005, is a web platform that provides an integrated environment for the assembly and use of DNA barcode data. It delivers an online database for the collection and management of specimen, distributional, and molecular data as well as analytical tools to support their validation. Over the past few years, BOLD has grown to become a powerful online workbench and the central informatics hub of the DNA barcoding community..

BOLD is freely available to any researcher with interests in DNA Barcoding. By providing specialized services, it aids in the publication of records that meet the standards needed to gain BARCODE designation in the international nucleotide sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances.

BOLD Systems Release of Version 3

The release of version 3.0 of BOLD in April 2012 represents an evolutionary update to the system. Significant revisions have been made to support an increasing diversity of workflows and an increasing volume of data. A major advance is the activation of Barcode Index Numbers (BINs), an interim taxonomic system for animals, and an annotation framework that supports rapid community based validation of barcode data.

How can I use BOLD?

This documentation provides details on BOLD functionality, data structures and best practices. It explains how to use this system to collect, manage and publish Barcode and ancillary data. It also provides details on the integrated analytical tools and web services. Online documentation is available by clicking on "Get Help" in the page footer, or by selecting "Resources" from the page header on any main page.

Figure 1-1: BOLD Home Page

For assistance with any feature of BOLD, please email the BOLD Support Team: support@boldsystems.org

To provide comments or suggestions for BOLD 3 - please click on the buttons throughout BOLD labelled "Feedback" to forward your comments. Thank you in advance!

Navigation

The interface in the newest version of BOLD improves access to commonly used features and new databases. Figure 2-1 illustrates the navigation features, which are defined in the table below.

Navigating around all sections of BOLD will retain the logged in session, so users can move easily through the system. Please see the diagram and table below for description of the navigation features.

Figure 2-1: The publication database illustrating BOLD 3.0 navigation features

Searching Public Data

Using the search bars that appear on the 4 main public databases (Primer, Publication, Public Data Portal, BINs), users can enter a combination of keywords. For example, searching “Lepidoptera Canada” in the Public Data Portal will return all of the Lepidoptera records collected in Canada.

Search domains include taxonomy(scientific names only), geography, collectors, identifiers or institutions as well as BOLD Sample IDs and Process IDs.

Below are the search guidelines (Searches are case insensitive):

• Multiple terms from the same domain can be searched to retrieve all results matching either term. For example, Anura Caudata will deliver results for records from both orders.
• Multiple terms from different domains can be searched to retrieve the intersection results. For example, Canada Aves will return results for Aves collected in Canada only.
• Quotation marks must be used for exact match retrieval of multi-word terms in a multi-term search. For example, "United States" Aves will deliver results for US birds.
• The minus operator (-) will omit certain results from the search. For example, Lepidoptera -Saturniidae will deliver results for Lepidoptera but not Saturniidae (a family within Lepidoptera).
• Combination searches are possible within and across domains. For example, "Biodiversity Institute of Ontario" Sesiidae -Manitoba will deliver results for the Sesiidae stored in the Biodiversity Institute of Ontario, but not collected in Manitoba.
• BOLD Project Codes can be searched for published projects/datasets. For example, NBCAD will return all the records from that project.
• Researchers names may be searched to find records that the researcher collected or identified. For example, "Xin Zhou" will deliver results for all records that were collected or identified by researcher Xin Zhou.

Troubleshooting for the public search bar

Search terms entered may not retrieve the desired results. There are several reasons this may have happened:

• The user has entered a typo, spelling mistake or invalid synonym instead of the proper search term.
• No records are found for searched term(s) or intersection of terms in the public database.
• Any negative symbols added to a set of searched terms must be attached directly to the front of the term that should be excluded. (IE, type "-Ontario" instead of "- Ontario")
• The search term is retrieving results from a domain that is not intended. Append the search term with a domain code, such as "[tax]", "[geo]", "[identifier]" to narrow results to only that domain.

Figure 3-1: Public Search Bar as illustrated in the Public Data Portal

Downloading Public Data

In each public database (Primer, Publication, Public Data Portal, BINs), there is also an option to download the public data available based on the search terms. This downloads includes primer sequences, bibliographies, sequences, traces, taxon ID trees, and specimen data in appropriate formats. The download option are found on the upper right hand side of the database.

Figure 4-1: Example of public downloads bar illustrating a map download

Registering for a User Account

Getting an account on BOLD expands the list of options available to a user of the system beyond access to public data and use of the identification engine. Upon signing in, users can annotate published data, helping to curate and clean the identification library. Moreover, it will be possible to submit data to BOLD and to gain access to other in-progress, private projects with the permission of the data owners. Once data is on BOLD, a large set of analytical tools are available for validation and generation of reports for publications.

Figure 5-1: Registration form for new users

After the registration form is submitted, a welcome e-mail will be sent immediately with the information needed for logging in to BOLD.

CSE this is a test1