Submission Instructions

This page provides instructions on how to submit data to SeaBASS as well as information about the SeaBASS File Format. If you are new to this process, please scroll down the page to the "How to Submit" section and review the steps involved. More details can be found in the other sections on this page and beneath the other topics under "Contribute Data" found in the main menu of the SeaBASS website.
 
The SeaBASS data format and structure were designed with the following in mind: To account for the continuous growth of the bio-optical data set and the wide variety of supported data types, the NASA Ocean Biology Processing Group felt it essential to develop efficient data ingestion and storage techniques. While this requires a specific data file format, the data protocols were designed to be as straightforward and effortless as possible on the part of the contributor, while still offering a useful format for internal efforts. The system was intended to meet the following conditions: simple data format, easily expandable and flexible enough to accommodate large data sets; global portability across multiple computer platforms; and web-accessible data holdings with sufficient security to limit access to authorized users.

Metadata Headers

Standard metadata headers are required in every SeaBASS file. Select a header to view its definition. Some headers are required in all SeaBASS files, some are conditionally required depending on what type of data were measured, and others are optional.
 
If you are getting started learning about SeaBASS file format, scroll down below the table of contents to see an example header.

Standardized Fields and Units

Below is a table of the standard field names and associated units for use in submitting data to the SeaBASS bio-optical archive. The field names are not case sensitive. Use the search bar or the find function in your browser to search the table for words or patterns found in the field names, units or descriptions. Please contact SeaBASS staff if you want to discuss adding new fields.

 

Special notes regarding wavelength-specific measurements: There are two different ways to indicate wavelengths (nm) in a SeaBASS file. If metadata such as date, location, or depth vary within the data, then append the wavelength number to the field name for every measurement combination. For example, downwelling irradiance ('Ed') measured at 412.3 nm is 'Ed412.3' (listed as separate columns alongside other Ed measurements, like Ed416.2, Ed419, etc.) Alternately, if date, location, and depth are assumed to be approximately constant for all measurements in the file, then use the field 'wavelength' to provide a column of the measured wavelengths and don't include them as part of the field names (this pivoted layout is commonly used for reporting spectrophotometric measurements or other measurements that use the data_type=scan keyword).

 

Two additional tables are provided below (Field Name Suffixes & Modifiers). The reusable naming conventions in those tables are used to create new field names without having to add dozens or hundreds of variations to the Table of Field Names and Units. For example, "_sd" (for standard deviation) appears in the table of suffixes and may be appended to any existing SeaBASS field name (e.g., "chl_sd" or "Rrs510_sd".) Similarly, field-specific names can be created ad infinitum using _bincount (i.e., number of averaged samples), and _quality. The table of modifiers allows extra information to be part of field names, typically to indicate versions of measurements that are either more specific or modified. For example, modifiers are used to denote size-fractionated measurements (see _#umfilt and _#umprefilt), specific excitation or emission wavelengths, or polarized measurements. Field names may be constructing by combing entries from multiple tables, with any applicable wavelength first, followed by "Modifiers", followed by a "Suffix".

 

Notes on HPLC pigment field names

FCHECK

To assist with the standardization of SeaBASS data files, the SIMBIOS Project developed feedback software, named FCHECK, to evaluate the format of submitted data files. Since then, it has been rebuilt from the ground up by the SeaBASS development team to make it available to the end-users. There are multiple ways to access this software, as explained further below. Using FCHECK, contributors may evaluate the format of their SeaBASS-compatible files prior to submission.
 
FCHECK scans files for common syntax problems, missing header information, data values outside of typical ranges, nonstandard field names or units, and also detects various other issues. It will report a summary of the types of problems detected (if any) among all the files it scanned, as well as a more detailed breakdown of issues found in each individual file. Problems are classified as either errors or warnings, depending on their severity. Errors are critical problems that must be addressed before files can be archived. Warnings should be fixed if possible, but some of them are subjective or optional and may be disregarded.

AERONET Ocean Color

The NASA OBPG routinely downloads V3 data from the AERONET-Ocean Color website for use in satellite sensor validation match-up analysis. As described by Zibordi et al. (2009), the AERONET-OC network consists of globally distributed autonomous radiometer systems maintained at fixed offshore sites. Please refer to the rest of the information in this article for details on how to acknowledge the use of AERONET-OC data and how the OBPG processes these data.

readsb (MATLAB)

readsb.m is a MATLAB function designed to open and read data files that are in a SeaBASS format. Some SeaBASS files can be opened using MATLAB's various built-in import functions, however many of the built-in methods are unsuited to efficiently open SeaBASS files without errors or significant manual intervention. Using this function, data outputs can simply be returned as either a cell array or as a structure where the names of the data field headers from the SeaBASS file are array field names (e.g. dataStructure.DEPTH, dataStructure.CHL, dataStructure.LW412). File metadata information is also returned in a separate structure (and arrays, if desired.)

Plankton and particles imagery (IFCB, UVP)

The guidelines presented below will assist the user in submitting imaging-in-flow or submersible microscopic data to SeaBASS. New metadata headers and field names have been developed for plankton and other particle data. Additionally, detailed instructions are given for the submission of documentation (protocol document, checklist, etc.), images, and additional ancillary files. The submitter must indicate in the checklist whether all ROIs in a sample were annotated. Greater detail regarding the development and application of these guidelines and requirements can be found in Neeley et al., 2021.

 
**Neeley, A., S. Beaulieu, C. Proctor, I. Cetinic, J. Futrelle, I. Soto Ramos, H. Sosik, E. Devred, L. Karp-Boss, M. Picheral, N. Poulton, C. Roesler, and A. Shepherd. (2021) Standards and practices for reporting plankton and other particle observations from images. 38 pp. DOI:10.1575/1912/27377 

Plankton and Particles Flow Cytometry

The guidelines presented below will assist the user in submitting flow cytometry data to SeaBASS. The format described herein allows for Level 2 submissions of flow cytometry data, meaning sums of total abundances of each phytoplankton or bacterial group. New metadata headers and field names have been developed for these data. Additionally, detailed instructions are given for the submission of documentation (protocol document, checklist, etc.), images, and additional ancillary files. Greater detail regarding the development and application of these guidelines and requirements can be found in Neeley et al., 2023. 

Neeley, A.R., Soto-Ramos, I. and Proctor, C. (2023) Standards and Best Practices for Reporting Flow Cytometry Observations: a technical manual, Version 1.1. Greenbelt, MD., NASA Goddard Space Flight Center, 31pp. DOI: http://dx.doi.org/10.25607/OBP-1864.2. 

Data Submission Special Requirements

When preparing a submission, check to see if the data type is in the list below. Certain types of SeaBASS data submissions have special requirements. For example, some data files need conditionally required metadata headers, and some submissions require extra "checklist" documents. These requirements and several examples are listed below, sorted by data types. This list is growing and evolving and more data types will be added in the future.

 

Check if your submission type lists any required extra documents. These checklists are designed to standardize and preserve critical methods and analysis details that are needed for intercomparison, reprocessing, to make it easier for data users to assess the data quality and to consider them for satellite validation or inclusion in algorithm development datasets. We prefer you submit a plain text (.txt) document, but if multiple format versions are offered (e.g., rich text and plain text), pick your preference and fill out the necessary sections. Rename the file in a relevant way to make it unique (e.g., add the cruise name to the end of the file name), and add it to the other documents and calibration files that are part of your submission.

 

The special notes section for each data type highlights any necessary measurement-specific metadata (e.g., conditionally required headers), fields, or formatting.

 

This page also provides example submission sections containing model data files and documentation bundles to help you format different types of submissions. These files were picked from the archive or created to serve as references. Your files might look a bit different, but hopefully the examples are helpful as a starting place from which to further adapt or improve as needed.

Plankton and other Particles (IFCB, UVP)

The guidelines presented below will assist the user in submitting imaging-in-flow or submersible microscopic data to SeaBASS. New metadata headers and fieldnames have been developed for plankton and other particle data. Additionally, detailed instructions are given for submission of documentation (protocol document, checklist, etc.), images and additional ancillary files. The submitter must indicate in the checklist whether all ROIs in a sample were annotated. Greater detail regarding the development and application of these guidelines and requirements can be found in Neeley et al., In Press.

 
**Neeley, A., S. Beaulieu, C. Proctor, I. Cetinic, J. Futrelle, I. Soto Ramos, H. Sosik, E. Devred, L. Karp-Boss, M. Picheral, N. Poulton, C. Roesler, and A. Shepherd. (2021) Standards and practices for reporting plankton and other particle observations from images. 38 pp. DOI:10.1575/1912/27377