'Omics-related Data

Contributing Genetic Accessions

We recommend that sequence data be submitted to national biological archiving services such as the National Center for Biotechnology Information (NCBI) GenBank or the European Nucleotide Archive (ENA) where they can be unified under a BioProject in NCBI or Study in ENA. Related metadata and supporting environmental data should be submitted to BCO-DMO to further enable discovery and re-use (see Advantages of Sharing 'Omic Data Links through BCO-DMO).

What to send to BCO-DMO

If you have metadata and additional data related to your genetic accessions (collection date, latitude, longitude, taxon names, treatment descriptions, environmental measurements, etc.), please submit them to us along with any relevant accession numbers (e.g. BioSample, SRA run id, etc). Note that submitting your accession numbers and related data in a tabular format (e.g. Excel, comma- or tab-delimited) will expedite our processing of your data. We will then create a Dataset Landing Page at BCO-DMO that is linked to your Project Page.

To submit accessions and related data, use our online Submission Tool at https://submit.bco-dmo.org/ to enter your metadata and upload data files. See the "Submitting Data" page for more information on using the Submission Tool.

(If you cannot use the online Submission Tool, you can complete the DATASET.rtf metadata form and send it to info@bco-dmo.org along with relevant data files.)

If applicable, please include the following information with your submission to BCO-DMO:

• BioProject number

• taxonomic names

• description of the types of sequences

• locations where species were collected (including latitude and longitude and cruise ID numbers, if known/applicable)

• sequencing and analysis methods (including instrument names and models)

• any other relevant information that will enable others to understand and re-use the data (e.g. published papers)

Example Datasets:

• Substrate-specific metabolic responses of model marine bacteria: https://www.bco-dmo.org/dataset/916134

• ezRAD libraries of Pocillopora spp. collected in 2019: https://www.bco-dmo.org/dataset/881853

• Accession numbers for metagenome-assembled genomes (MAGs): https://www.bco-dmo.org/dataset/868323

• Hurricane Harvey Coral Gene Expression: https://www.bco-dmo.org/dataset/817298

On these dataset landing pages, click the "View Table" or "Get Data" button at the top of the page to see the data published by BCO-DMO. Note that the related NCBI pages (like BioProject) are listed in a "Related Datasets" section on the landing page.

If you have any questions about how to submit data, please contact us at info@bco-dmo.org.

Advantages of Sharing 'Omic Data Links through BCO-DMO

'Omics is a term that refers collectively to a group of rapidly evolving multi-disciplinary fields, each seeking to quantify and describe an entire collection of biological molecules of a particular type (e.g., genome). Ocean ecosystem investigators are increasingly using ‘omic tools (e.g. genomic, transcriptomic, proteomics, and metabolomic) in their research due to their ability to document the environment status in time and space. We want to make data generators aware of the benefits of submitting 'omics data links to BCO-DMO. While there are dedicated repositories for 'omics data (Table 1), discoverability and accessibility of metadata and environmental data are often major obstacles to reusing 'omic datasets. This is generally because the specialized 'omics repositories are designed for biomedical research and often lack the ability to connect to environmental research and associated metadata.

Although BCO-DMO does not host raw sequence or mass spectrometry data, we can easily link to the repositories that do. In doing so BCO-DMO can allow researchers to discover your data and place it in its appropriate environmental context. Because BCO-DMO datasets are connected to their expeditions, environmental data associated with the meta’omic sample locations can be easily connected. Similarly, BCO-DMO connects data to grants and/or projects, allowing laboratory experimental data to be associated with 'omic data. BCO-DMO’s site is optimized for data discovery using search engines, and specific data types can be searched for within BCO-DMO’s holdings. With a minor effort in submission, all the hard work you have put into collecting your dataset can be used to help other researchers throughout the world better discover and interpret your data. You, the data generator, will benefit from submission through increased citations and collaborations.