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

Data Submission Examples

This page provides examples of data files and documentation to be used as models for different types of submissions. It was developed to help highlight measurement-specific metadata, formatting, and accompanying documents. Over time additional examples will be added for other measurements that are commonly submitted to SeaBASS. Navigate using the following menu, or scroll down the page. Each measurement type entry contains information divided into two sections, "Special Requirements" and "Example Submission", which are described next.
 
Special Requirements describes any unusual metadata headers that are specifically required for certain measurements. Additionally, this section contains required downloads for special checklist templates that must be completed and submitted along with your other documents and calibration files. These checklists were designed to standardize and preserve critical methods and analysis details that are needed for intercomparison, reprocessing, and to assist in evaluating the data for satellite validation or inclusion in algorithm development datasets.
 
The Example Submission sections include one or more example SeaBASS data files that might be helpful as a reference for which fields and headers to include, and how to arrange your data matrix. Examples of documents and calibration files that were part of a model submission are also provided.
 

Satellite Validation Match-Up Tools (Portable)

These validation match-up tools allows Users to
  1. find relevant OB.DAAC satellite granules from in situ points or a SeaBASS data file and
  2. generate coincident satellite validation match-ups for those points.
These tools are downloadable for Users to run individually, external to the official SeaBASS validation search. These tools are designed to replicate some of SeaBASS validation search's core functionality, with the exception that these tools do NOT adjust in situ data to water-leaving values.
 
These validation match-up tools are served as part of SeaDAS and apply the default recommended match-up exclusion criteria, as set forth in S.W. Bailey and P.J. Werdell, "A multi-sensor approach for the on-orbit validation of ocean color satellite data products", Rem. Sens. Environ. 102, 12-23 (2006).

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.

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.

MOBY

MOBY (Marine Optical BuoY) radiometry data are regularly used by the NASA OBPG as part of ocean color validation and vicarious calibration activities. MOBY is an autonomous buoy moored off of the island of Lanai in Hawaii. Each day it is deployed it collects several measurements of upwelling radiance from sensors on its underwater arms (at approximately 1, 5 and 9 m depth) and downwelling irradiance from sensors on its underwater arms as well as at the surface. More information about MOBY can be found on the MLML site and NOAA site.

Data Format and Submission

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.

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.)

Data Access Policy and Citation

Access to the data archived within SeaBASS follows the NASA Earth Science Data and Information Policy. 

NASA's Earth Science program was established to use the advanced technology of NASA to understand and protect our home planet by using our view from space to study the Earth system and improve prediction of Earth system change. To meet this challenge, NASA promotes the full and open sharing of all data with the research and applications communities, private industry, academia, and the general public. The greater the availability of the data, the more quickly and effectively the user communities can utilize the information to address basic Earth science questions and provide the basis for developing innovative practical applications to benefit the general public. In this regard, all users incorporating SeaBASS data into their research are expected to acknowledge both their data sources (the original data contributors and SeaBASS) and NASA, and to abide by the Access Policy.

readsb (Python)

SB_support.py is a Python module containing a set of classes designed to open, read, and manipulate data files that are in a SeaBASS format. While many of Python's built-in functions may be used to read SeaBASS files, this module leverages Python libraries and tools to efficiently read, sort, mask, and return the contained data for easy use without errors or significant intervention. Using this function, data outputs will be returned as data structures containing the file's header information (metadata) as an array of strings, the file's comments as an array of strings, the file's missing data, above detection limit, and below detection limit values (if present), the file's variable and unit lists as an Ordered Dictionary indexed by variable name, and the file's data as an Ordered Dictionary indexed by variabile name. Additionally, optional arguments flags that may be toggled are mask_missing, mask_above_detection_limit, and mask_below_detection_limit (all set true by default), which remove the header-defined values for these fill values, replacing them with NaN.