Submission Instructions

Data Submission Policy

All data collected under the auspices of the NASA Ocean Biology and Biogeochemistry (OB&B) program are to be submitted to SeaBASS within 1-year of the date of collection. For further details, please review the SeaBASS Access Policy.

How to Submit (Overview Steps)

1. Learn about the SeaBASS data format and other submission requirements listed further below on this page.
   
   1. For a quick idea of what the SeaBASS file format looks like, go to the Metadata Headers page which begins with a relatively simple example.
   2. Consult the list of measurement types on the Data Submission Special Requirements page to see if your measurement types are there. If so, review any relevant examples and info about which fields and metadata to use.
   3. Consult the list of fields and units for each of the data parameters. If your data parameter is not listed in the table, please reach out to the SeaBASS team. 
2. Contact SeaBASS staff via email to plan out your submission before you begin formatting data. SeaBASS staff will respond to your inquiry, typically within 1-2 business days. For routine submissions, you will then be able to proceed with the steps below. For more complex scenarios and data types that are new to SeaBASS, our data managers will require more information and discussion of how to best organize and accommodate your data and documentation. When you email the SeaBASS Staff to introduce yourself, include:
   1. Your first and last name, and what institution you are affiliated with.
   2. Please indicate if your project was NASA-funded, or if your submission is voluntary.
   3. If you are not the PI or person who secured funding for the project within your laboratory or organization, please indicate that person's name and how you are connected.
   4. Indicate the project name and deployment or cruise names. In SeaBASS data are categorized under a new or existing experiment and cruise name (see Lists in the main menu), which should be coordinated if there were co-investigators.
   5. Briefly explain the measurement types of the data you wish to submit.
3. Register a SeaBASS submitter account by following the instructions further down this page. The process requires generating SSH keys and emailing the public key to SeaBASS staff. 
4. Create a draft SeaBASS file.
   1. Use the automated File Checker (FCHECK) to scan your file for format-compatibility problems. More info. Run FCHECK, fix any problems, and repeat as necessary.
   2. A suggestion is to start with just one file for practice before creating and checking all your other files.
   3. Pick thoughtful file names for your data files. Example: EXPERIMENT_CRUISE_DATATYPE_YYYYMMDDHHMM_RELEASE#.sb. More details about file naming are below in section 5.
   4. Avoid using spaces and most special characters. Full file naming guidelines are found further down this page.
5. Prepare and gather all relevant external documentation and calibration information (e.g., cruise reports, methods descriptions, calibration files, and/or fill out any SeaBASS-provided templates in the mandatory special submission requirements). Generally, these sorts of files may be provided in any format (e.g., text, PDF, DOC, etc.) Tips:
   
   1. Make sure the names listed in the metadata /documents and /calibration_files exactly match the corresponding file names.
   2. Do not use FCHECK to scan documentation. FCHECK is only needed for data files.
   3. Consult the Data Submission Special Requirements page and, if your data type is there, ensure you follow the guidelines and include the required documentation and checklists.
   4. If you have additional data or metadata files that should be linked to the submission refer to the associated metadata section below for additional information. 
6. Use your account to upload your data submission, including all documentation. If your submission includes multiple types of measurements, it is generally requested that you submit them all simultaneously as a complete package, not piecemeal.
   1. After your upload your submission, you will receive an automated email receipt within 24 hours (sent to the submitter's account plus addresses in the "contacts" metadata). Please contact us if you don't receive this confirmation within 24 hours.

   2. If your receipt email contains a section about MISSING documents and calibration files: these files were named in your metadata headers but could not be found by our automated system within your data_submission folder. The most common reasons are: 1) you forgot to upload the files, or 2) the spelling or capitalization of the documentation files does not exactly match. Please log back in and upload the relevant docs and calibration files. However, you may disregard this message if you are resubmitting or supplementing a previous submission and referencing documentation archived for the cruise (also see the “resubmission” instructions on this page). 

   3. Next, the SeaBASS team will prepare to archive your data. This involves manually reviewing your submission for completeness and performing additional QC checks. You will be emailed if revisions or more information are needed.
   4. The SeaBASS team will add a Digital Object Identifier (DOI) to your data files corresponding to the "experiment".  If the experiment is new to SeaBASS, the DOI will be reserved. New DOIs are typically formally registered on a quarterly basis. The SeaBASS team also adds the special date "received" header.
   5. You will be emailed when the data archiving is complete.
      
      
      

Request a SeaBASS Experiment and DOI

1. Experiment name: This is a short name (often an acronym) for the project. It will be part of the DOI, for example, 10.5067/SeaBASS/EXPERIMENT/DATA001
2. Experiment long name: Brief explanation of the experiment and definition of acronyms
3. Experiment description: Please provide a paragraph with information about your project. This will be part of your landing page and is an opportunity to showcase your project. Feel free to acknowledge funding, PI's, and include links to other data repositories.
4. Experiment URL: If the experiment has a webpage please send that information to us
5. Cruises: Help SeaBASS generate one or more cruise names for your Experiment. Our data is cataloged by cruises, which can be small vessels, research vessels, field campaigns, monitoring stations, and/or we can subdivide the data into time frame deployments for sampling-based projects. If the projects had research vessels, please use the cruise id. More names can be added in the future. Multiple cruises should use a consistent naming pattern, if applicable.
6. PI’s: Principal Investigators will be added to the landing page as they submit data. However, we ask for this information ahead to know more about the potential data submitters.
   
   
   

How to Resubmit (i.e. Update a Previous Submission)

SeaBASS encourages resubmissions to ensure that the best quality versions of data are available online. In the event that you need to update some or all of your data or documentation for a past submission, please follow these steps:

1. Email the SeaBASS team ahead of time to discuss what you want to resubmit. We will evaluate the best way to update your files on the back end of SeaBASS and reply to you about how to proceed.
   1. Briefly explain the reason for the resubmission. If possible, also provide a succinct description (one line or less) to explain the issue or what changed in the newer version of your data files. The SeaBASS team will use the short description to update a special metadata field (i.e., to preserve release/version history, the previous “/received” info will be kept as a comment with the short explanation appended.)
   2. Explain the scope of what files or documents need to be replaced or removed relative to the number or types of files that are currently archived.
   3. Upon request, we will try to accommodate reusing some or all of your existing documents or calibration files, if they do not need to change.

2. Update your data files (and any relevant documents) in preparation to resubmit them. Here are a few special reminders for updating SeaBASS files and metadata:

   1. File names: Remember to update your file names and the corresponding “/data_file_name” metadata header, if relevant. It is recommended that SeaBASS file names end in a release number (i.e., version number), and you should increment this integer to indicate resubmissions. For example, change myfile_R1.sb to myfile_R2.sb.
   2. /documents, /calibration_files, /associated_archives (if applicable), and /associated_files (if applicable): If these file names are different than the previous version, remember to change the metadata headers.
   3. /data_status: may need to be updated. For example, if your files were initially labeled "preliminary", change them to "final" if further changes are unlikely.
   4. optionally, provide a verbose description of the updates: The SeaBASS team will add a short description in the comment section of your data files. If you wish to go into more detail about the updates, either write your own lengthier comments in the headers or within your updated documentation.
3. FCHECK the files and fix any issues.
4. Upload your resubmission to the SeaBASS SFTP using your SeaBASS submitter account and following the normal submission process instructions. 
5. Email the SeaBASS team shortly after you transmit your resubmission to let us know you sent it, and to remind us of the scope and reason for your resubmission.
6. Automated email receipt: If your resubmission contains at least one data file, SeaBASS's automated email receipt system will trigger and send you a message within 24 hours. It won't trigger if your resubmission consisted of only non-SeaBASS files such as documentation or calibration files. If you requested SeaBASS reuse existing documents, you may disregard any warnings about missing documents in the automated email receipt.
7. The SeaBASS team will review the resubmission and email you when it is online. The old versions of files will be moved offline and replaced.
   
   
   

Data Format

The SeaBASS file format ( .sb ) is an approved NASA Earth Science Data format by NASA ESDIS (Earth Science Data and Information Systems)

SeaBASS data files are flat, two-dimensional ASCII text files. Information is organized into two sections: a metadata headers section at the top, followed by a data matrix.

• Metadata headers: are mostly keywords and values. These values and any freeform comments provide crucial context for the data. The /fields and /units headers are especially important because they define the columns in the data section beneath.
• The data matrix: contains columns of values separated by the /delimiter (arranged like a spreadsheet).

1. Core Formatting Principles
    
   • Standardized Dictionaries: Because SeaBASS archives many types of data, it relies on strict, standardized dictionaries for both headers and data columns. We provide dedicated webpages to help you find the correct Metadata Headers and Fields.
   • Delimiters: Data matrix columns must be separated by a single delimiter (comma is recommended; space or tab are accepted). Do not mix delimiters. You must spell out your delimiter in the headers (e.g., /delimiter=comma)
2. The Metadata Header Block (Top Section)
   
   
   • Header Categories: Not all headers are treated equally when creating .sb files.
     • Mandatory: Must be included in every SeaBASS file
     • Conditionally Required: Must be included for specific types of measurements.
     • Optional: Helpful for context but not required.
     • See the Metadata Headers page for more details.
   • Required Start and End tags: The block must begin with /begin_header and close with /end_header. The headers between them can be in any order.
   • No Spaces Allowed: Header values cannot contain spaces (use underscores instead). The only exception is for comment lines (which begin with ! and are allowed to contain whitespace).
   • Handling Missing Header Values: If a required metadata value is unavailable, use NA (Not Applicable). Do not use NA in the Data Matrix; use your numeric /missing value instead of NA .
   • Bracketed Units: Do not use bracketed units in headers, with the sole exception of time and location headers (e.g., [deg]). All other units are implied by the SeaBASS standard metadata headers dictionaries.
   • Time and Location Ranges: The date, time, and location headers must reflect the minimum and maximum bounds of the file (e.g., the earliest time, the farthest north latitude).
   • Experiment and Cruise Names: Use consistent names if submitting to an existing project. New names should be selected thoughtfully. These names are very important for data organization and for grouping related datasets. Note: The experiment name is critical as it becomes part of the assigned Digital Object Identifier (DOI).
3. The Data Matrix Block (Bottom Section)
    
   • Defining Columns: The columns of your data matrix are strictly defined by the /fields and /units headers. The order of your data columns must match the order listed in those headers exactly. Search the SeaBASS Fields page to find correct naming conventions. (Note: Field names and units are not case-sensitive, so Chl is recommended but CHL and chl are both acceptable).
   • Numeric Fill Values: Never use "NA" or "NaN" in the data matrix. Instead, use a specific numeric value (e.g., -9999) for missing data and define it in your headers (e.g., /missing=-9999).
     • Tip: To distinguish values that were outside detection limits, use /below_detection_limit=-8888 and /above_detection_limit=-7777
   • Coordinates & Time:
     • Latitude/Longitude must be in decimal degrees (North and East are positive; South and West are negative).
     • Time must be in GMT (UTC). If seconds were not measured, report them as 00
4. Data Matrix Layouts (Wide vs. Wavelength-Indexed)
   
   The way you arrange your rows and columns depends on the type of data you are submitting:
   
   
   • Standard / "Wide" Layout (Default for most data): This is the required layout for most measurements. Each row represents a unique measurement event (with its own date, time, latitude, longitude, and depth), and each measured parameter gets its own column.
     •    If your data includes optical wavelengths: You will still use this Wide layout, but each wavelength gets its own column. The wavelength is appended directly to the base field name (e.g., Rrs412, Rrs443, Rrs555).
   • Wavelength-Indexed Layout (Specialized for Spectrophotometric data): This alternate layout is used only for specific optical measurements where a file represents a single physical sample (e.g., one location, one time, one depth). Instead of appending wavelengths to the headers, you include a single column named wavelength. The data columns use the base field names (e.g., ap, abs_ap), and each row represents a different wavelength (e.g., 400, 401, 402).
     • Note: Because wavelength-indexed files represent a single sample, they almost always rely on the Constant Value Rule (see below) to omit the date, time, lat, lon, and depth columns from the data matrix
5. The "Constant Value" Rule for Columns
   
   

   All individual measurements must be associated with a date, time, latitude, longitude, and depth.
   
   

   • If a value changes: It must be included as a column in your data matrix. (This is typical for “Wide” files where a ship or profiler is moving).
   • If a value is constant: If any of these parameters are identical for every row in the file, you may omit that column. It will be assumed the corresponding metadata header value will automatically apply to all rows.
     • Example: If you submit a “Tall” spectrophotometer file for a single water sample, you can omit the lat, lon, date, time, and depth columns. SeaBASS file readers are designed to automatically apply the corresponding metadata header value to all rows. The /north_latitude and /south_latitude headers will be identical, and that single coordinate applies to all data rows, etc.
       
6. Scientific Processing and Reporting Best Practices
   
   
   • Consult Data Submission Special Requirements for measurement-specific instructions that supplement or supersede general submission rules.
   • Level of Processing: Data should generally be calibrated, depth-adjusted (correcting for differences between sensors and the pressure transducer), unbinned (or carefully binned), and QA/QC filtered for bad data. (Note: Binning can be appropriate. Please contact the SeaBASS administrator if you still have questions after checking the instructions in the Mandatory Special Submission Requirements).
   • Replicates and Uncertainty: Because protocols vary widely across different measurement types, always check the Mandatory Special Submission Requirements for your specific data. However, the general guidance for discrete water samples (e.g., POC, PON, extracted Chl) is:
     
     
     • Preferred: Report individual replicates as separate rows in your data matrix.
     • Alternative: If you must report replicates averaged together in a single row, you must include columns for the uncertainty (e.g., standard error _se or standard deviation _sd ) and the number of combined measurements (e.g., _bincount).
   • Intermediate Data: Please submit intermediate products calculated as part of a final reported value (e.g., submit absorbance/optical density measurements alongside the final calculated absorption coefficients). In some cases, intermediate or lower-level processed data might be appropriate to submit as associated_archives (see below; Supporting Documentation and Ancillary Files).

File Naming Guidelines

Supporting Documentation and Ancillary Files

Supporting documentation is crucial for the preservation and future use of your data. All submissions must include documentation (e.g., readmes, protocols) describing where and how the data were collected, instruments/methods used, and any post-processing steps. Measurement-specific requirements are found on the Mandatory Submission Special Requirements page. Other types of supporting files include calibration files and, in some cases, special metadata or lower-level processing datasets, processing codes, etc.

General Rules for ALL External Files:

• File Formats: Most file formats are acceptable for supporting documents (e.g., .pdf, .docx, .txt, etc.) and calibration files. They do not need to be converted into the SeaBASS .sb format. Therefore, do not run supporting files through the FCHECK tool, as it is designed exclusively to scan .sb data files.
• Exact Name Matching: The file names listed in your metadata headers MUST exactly match the actual names of the files you upload.
• No Spaces in Names: File names must not include spaces or special punctuation. Use only underscores (_) and hyphens (-).
• Header Requirements: You will use specific metadata headers to link your .sb data to external files. Many .sb files may be linked to the same external file(s).
• /documents must be included in all .sb files
• /calibration_files must be included (in rare cases there is no relevant value and then a placeholder is acceptable)
• /associated_archives must be included only for specialized data types (omit this keyword if not applicable).
  
  

Documents

Use this header within .sb files to link to your readme files, protocols, cruise reports, and mandatory checklists (required if applicable for your measurement type). When uploading your submission to SeaBASS, these should be placed in a documents/ folder. You may create additional subfolders to aid organization.

Example /documents:

/documents=Experiment_cruise_AC-s_protocol.pdf,Experiment_cruise_AC-s_checklist.txt

Calibration Files

Use this header within .sb files to link to all instrument calibration certificates and device files. These external files should also be uploaded in the documents/ folder. You may create additional subfolders to aid organization of the calibration files.

Example /calibration_files:

/calibration_files=LuZ111_Calibration_Certificate.pdf,LuZ222_Calibration_Certificate.pdf,Escal.dat

Associated Ancillary Files

Unlike documents and calibration files (which are automatically packaged whenever someone orders a SeaBASS data file), the /associated_archives workflow provides a flexible way to link large or specialized supplementary files that users must opt-in to receive. Examples include plankton imagery (IFCB, UVP), raw flow cytometry .sig files, sky photos or level-2 HDF files for above-water radiometry, and metagenomic FASTQ files.

Most types of data submissions do not require associated archives unless explicitly stated in the mandatory Data Submission Submission Special Requirements. Because this workflow is atypical and requires additional steps, contact SeaBASS for discussion before using it.

Step 1: Packaging the Files
Associated archives are stored in the SeaBASS archive as gzip-compressed tar bundles (.tgz).

• SeaBASS can compress the .tgz on your behalf: Upload your uncompressed associated files in a clearly named folder ( _associated ). The SeaBASS data manager will review them and zip the bundle(s) on your behalf which will add .tgz to their name. (See note below.)
• If you create the bundles yourself: Ensure they are compressed as .tgz , do not exceed 5GB per bundle, and names end in _associated.tgz. (Multiple bundles are allowed if you exceed the 5GB limit).
  
  
• Note: Whichever method you choose, you must declare:
  • the final intended .tgz bundle name in your .sb file’s metadata headers as /associated_archives=
  • and point to individual files within the bundle using associated_files. Step 2 below provides additional details.

Step 2: Defining the /associated_archives in .sb Metadata (Required Headers)
If you are submitting associated bundles, you must include the following two headers in your SeaBASS .sb data files that point to them:

1. /associated_archives: A comma-separated list of the compressed bundle name(s). Names always end with the suffix:_associated.tgz
2. /associated_archive_types: A description of what is inside each bundle. Valid entries include: raw, unbinned, planktonic, benthic, DNA-FASTQ, DNA-FASTA, or metadata. (Contact us if your data doesn't fit these categories).

Step 3: Linking .sb to associated_files Inside the associated_archives (Header vs. Data Column)
You must also link your .sb files to specific files (associated_files) inside the archives. How you do this depends on whether the associated_files apply to all data in the .sb file or just specific rows of data.

• Option A: Use /associated_files Header (Applies to the entire file)
  If the associated_file in the bundle is relevant to every row of data in your SeaBASS file, it is recommended to use the /associated_files and /associated_file_types headers. Using this Constant Value Rule means you do not need to list associated_file information in the fields (it would be redundant to list the same associated_file name for every row).

• Option B: Use /fields and Data Columns (Applies row-by-row)
  If different rows in your data matrix link to different files inside the bundle, you must include associated_files and associated_file_types as columns (fields) in your data matrix.
  
  
  • Important Rule: If a single row of data links to multiple files, use a pipe | to separate the file names in that column (e.g., fileA|fileB|fileC ).

Mandatory Special Submission Requirements

Format Checking and Submission

Setting up SFTP Access

• SFTP connections are secured using an SSH key. Don't worry if SSH keys are new to you, they are simply a pair of tiny text files that are specific to your computer.
• Generate a key of type RSA 4096-bit. See instructions for creating SSH keys.
• After you create your key, email the SeaBASS Administrator to request your account. Please include the following in your email:

1. Attach your public RSA SSH key
   1.    Do attach the file name ending in ".pub" (it commonly has a name like "id_rsa.pub").
   2.    Don't email us its partnering private key (it commonly has the same name without .pub, e.g., "id_rsa").
   3.    If you want to submit data from multiple computers, you are allowed to register multiple public keys and request that they are all linked to your SeaBASS SFTP account.
2. Your first and last name
3. Your affiliation/institution name
4. Your email address that will be linked to your SFTP account
5. If you are not the person who already contacted the SeaBASS team to describe your project and upcoming data submissions, please include a reminder of your connection (e.g., you work in the same lab, etc.)

• You will receive an email response (typically within 2 business days) with instructions once the SeaBASS team has created your SFTP account.  You will then have access for data submission and FCHECK requests.
  
  
  

Generating a SSH key

Your SFTP account will be secured using an SSH key. If you have never used SSH keys before, you will need to create one by running a command as explained below. An SSH key consists of two unique strings which will be saved in small plain text files. One file is public (usually its name ends in ".pub"), and the other is private (never share this one). Creating your key is a one-time process if you keep its two parts (files) stored safely on your computer. 

Note that SSH keys come in different types. Previously, SeaBASS would accept different types of SSH keys. Starting May 2023, SeaBASS will only accept RSA SSH keys that are 4096-bit encrypted. All previously submitted SSH keys must be updated to comply with the new NASA SSH key requirements.  T update your SSH key please follow the instructions below and e-mail the SeaBASS team your new RSA 4096-bit SSH key along with your SeaBASS submitter username (usually the first letter of your name followed by your last name, for example, John Smith username is jsmith). 

Please note that SSH keys are computer specific, therefore an SSH key must be generated for each computer used to upload data to the SeaBASS SFTP.  

ssh-keygen -t rsa -b 4096