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.
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".
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.
This page provides general SeaBASS documentation and guidelines, focusing primarily on how submissions should incorporate free-form information in external documents. 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.
1) 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)
2) External Documents and Calibration Files
- Create report(s) documenting all your methods
- Explain all methods, including those related to deployment, sampling, and analysis. Important instrument settings and calibration information must also be retained for traceability. Standalone documentation should be organized into a "documents" directory that is part of your submission. In your data files, reference the relevant external files via the "/documents" metadata headers.
Documents (and calibration files) aren't in SeaBASS format and thus don't get scanned by FCHECK. Either plain text (.txt) or .pdf format is preferred for the file format of written documentation or reports.
- Follow Data Submission Special Requirements (mandatory checklists for certain types of submissions that need to be added to your submitted documents)
- 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.
- Calibration files (if applicable) should be organized and submitted within a "documents" directory (create subfolder(s) as needed). In your data files, reference external files via the "/calibration_files" metadata headers.Notes: