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.
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
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 ane 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. If multiple download 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.
This page provides information on how to submit data to SeaBASS. If you are new to this process, please scroll down the page to the "How to Submit" section and review the steps in the process. 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.
This page provides general SeaBASS documentation and guidelines, focusing primarly on how submissions should incorporate free-form information in external documents. This page is currently being updated (early 2020) to reflect recent changes, to better clarify certain requirements, and to provide more examples.
SeaBASS submissions have two general types of metadata, 1) self-contained metadata, e.g., machine-readable metadata headers, and text comments and 2) external documents and calibration files.
Self-contained within SeaBASS Data Files
- /documents (REQUIRED, a comma-separated list of the file name(s) of all external documentation)
- /calibration_files (REQUIRED, a comma-separated list of the file name(s) of all of external calibration files)
- Comments (OPTIONAL, text comments may be included in the header. Comment lines must start with an exclamation point. e.g., ! This is a comment)
External Documents and Calibration Files
Documentation needs to be provided that explains all methods, including those related to deployment, sampling, and analysis. Important instrument settings and calibration information must also be retained for traceability. Since it would not be efficient to include all this information within each SeaBASS data file, these data should be provided separately, and referenced via the "documents" and "calibration_files" metadata headers.
Documents and calibration files are not required to be in any special format (i.e., they aren't SeaBASS format, nor do they need to be scanned by FCHECK). For any written reports, PDF or plain text format are preferred.
Special Requirements: Please consult the Data Submission Special Requirements page to see if it includes special guidelines for the types of measurements you wish to submit. The page includes required checklists, required special metadata headers, and example data files. Check back periodically, as new content is added to that page over time to include additional data types and other updates.
These checklists are new to the community as of early 2020. The SeaBASS team welcomes feedback if you have suggestions for improving specific forms, and is interested to hear if you have requests for additional information or topics.
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.
The SeaBASS website contains several tools and options to help you find data files and products. The main options for aquiring data can be found under the "Get Data" drop-down in the main menu. The "File Search" is a good starting place as it allows you to perform custom searches for data files based on parameters such as particular measurement types (e.g. CTD, Chl, etc), investigator names, date, location and other options. Alternately, you can manually browse through files and folders using the "Archive" option, but it is generally recommended to use the File Search which simplifies downloading multiple files. The "Validation Search" allows you to search for and download post-processed datasets of successful match-ups between satellite sensors and field measurements. "NOMAD" will direct you to a specific subset of co-located measurements that were organized for algorithm development.
The "Lists" main menu option provides links to pages that contain alphabetically sorted lists of different types of information archived in SeaBASS. Visit those pages to view all contributing Investigators, Affiliations, Cruises and Experiment. These options can be useful for cross-referencing, for example, you can click on a particular cruise page to see a summary of all the associated data, or you can click on a particular investigator to see a sortable list of all the experiments and cruises they have contributed to.
The "Wiki" includes a number of articles and documents related to a variety of SeaBASS topics. You can browse through the articles or else use the search bar to look for articles that match particular keywords. For example, use the search to find an article containing a MATLAB SeaBASS file reader or a small dataset containing examples of hyperspectral Rrs measurements.
If you are interested in contributing data to SeaBASS, please visit the links under "Contribute Data" in the main menu for more information. You are also welcome to reach out with questions to the people listed under "Contact Us."
This page provides examples of data files and documentation as models to help you format different types of submissions. Measurement-specific metadata, formatting, and accompanying documents are highlighted. For each data type found in the menu below, note the sections on "Special Requirements" and "Example Submission".
The Special Requirements sections indicate any conditionally required metadata headers needed for specific types of data. Additionally, check for any Required Extra Documents. Those should be filled out and submitted 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, 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.
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.
Over time additional examples will be added.
These validation match-up tools allows Users to
- find relevant OB.DAAC satellite granules from in situ points or a SeaBASS data file and
- 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.
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