Handbook

GenBank & BOLD Public data submissions

BOLD shares a tightly integrated data exchange pipeline with NCBI (GenBank) that allows for automatic submission of data to GenBank. Users are only required to fill in the author and publication information, which is sent to GenBank along with the specimen, sequence, and trace data (only for COI gene) which has been transformed to the required formats. GenBank responds directly to the user with the accessions for their records to be included in publications. Accessions are also sent to BOLD to ensure bidirectional linkage.

The data exchange pipeline is further utilized to send GenBank updates to records. Identifications of records submitted through BOLD to GenBank can still be refined and updated as new information is obtained. Changes to the taxonomy of BOLD records are automatically sent to GenBank so that GenBank can gain up to date information.

How to submit records from BOLD to GenBank

BOLD has a simplified submission tool for Project Managers to submit sequences along with trace files to GenBank.

Within the Project or Dataset Console, click on Submit to Genbank. Please note that only a project or dataset manager has access to this function. If only a subset of records need to go to GenBank, then the relevant records can be submitted via a Dataset.

After submission of the form, the project or dataset will be reviewed by the BOLD staff to make sure the data meet the requirements for GenBank. The accession numbers are returned by email from GenBank to the project manager, and are associated with the records on BOLD for quick reference in the Project Summary form. GenBank accessions will appear wherever the matching sequence appear on BOLD, and will provide direct links to the GenBank page for that sequence.

GenBank puts a default 1 year privacy period on records submitted through BOLD, where the records are deposited in GenBank but are still inaccessible to the public. This privacy period allows BOLD users to gain accessions early in the manuscript writing process and removes the need for rushing to gain accessions once the manuscript is in its final stages of acceptance by a journal.

GenBank Submission Form with example data

Steps after publication

• When the manuscript is published, user will need to make the BOLD Project or Dataset public so that the sequences are accessible to the general public. The project manager can do this by clicking on Modify Project Properties within in the project or dataset and checking off the box to “Make this project publicly visible”.
• Submit a bibliography to the BOLD Publication Database following the directions in the Publication Submission Protocol. This process allows user to associate the publication details with the records on BOLD, using the GenBank Accession numbers.
• Records submitted to GenBank through BOLD are automatically kept in hold-up on GenBank for 1 year to allow time for publication. Should the article be published in less than a year, or should the authors want the sequences public on GenBank sooner, the corresponding author should contact GenBank directly to request public release. For more details on GenBank's policies, please visit their site at http://www.ncbi.nlm.nih.gov/genbank/.

Contact the BOLD support team through support@boldsystems.org with questions on any aspect of the publication process.

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