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.



Table of Contents


Absorption and Attentuation Meter (AC-S, AC-9)

This section addresses optical IOP measurements, in particular, absorption and attenuation meter measurements from an AC-meter or another similar instrument. New data submissions should be collected and reported in compliance with the most recent NASA / IOCCG protocols (i.e., Inherent Optical Property Measurements and Protocols: Best Practices for the Collection and Processing of Ship-Based Underway Flow-Through Optical Data)

required extra documents, AC-meter

Use the following checklist when creating Absorption and attenuation meter (AC-meter) submissions. Please download the following checklist, fill it in, and provide the information requested in each step. Submit it along with your other documentation and calibration information.
 
Download AC-meter Checklist (V20191106)
( .txt version )
 
If possible, your submission should preserve an extra version of your data files that have only been temperature, salinity, and pure water corrected. Preserve them as a tar bundle (the SeaBASS team can provide assistance) and in your .sb files link to  that file name using the metadata header associated_archive (/associated_archives=EXPERIMENT_CRUISE_Ac-s_OnlyTScorrected.tgz).
 
Conditionally Required metadata headers example:
/associated_archives=EXPERIMENT_CRUISE_ac-s_TSPurewater_corrected.tgz
/associated_archive_types=raw

special notes, AC-meter

 "Conditionally Required" metadata headers:
N/A
 
Noteworthy data fields in each file should nominally include:
1. relevant absorption and scattering fields
2. if binned, report column(s) of "bincount" (i.e., number averaged per bin) and a measure of uncertainty, such as standard deviation (e.g., ag440_sd)
3. if measurements were size-fractionated, report those as separate columns (see _#umprefilt fields suffix, e.g., chl_200umprefilt)
4. coincident CTD data (e.g., wt & sal)
 
Other notes:
See the AC-meter checklist download for additional information
 

Absorption, Gelbstoff / CDOM (spectrophotometer)

This section describes spectrophotometrically measured CDOM (absorbance and derived absorption coefficients, plus relevant metadata and processing information.) Examples of SeaBASS field names for these types of submissions are: abs_ag, ag, etc. New data submissions should be collected and reported in compliance with the most recent NASA / IOCCG protocols.

required extra documents, ag

Dissolved absorption submissions require supplemental documentation to preserve critical methods information. Download the following checklist, fill it out, and submit it along with your other documentation and calibration information.
 
Download ag Checklist (V20200413)
( .rtf version )
 

special notes, ag

"Conditionally Required" metadata headers:
/s_ag may be used to report calculated spectral slope (e.g., /s_ag=s_ag_300nmmin_600nmmax:0.023197)
/null_correction If applicable, report the null correction used while calculating absorption coefficients. Generally, null corrections should be performed using absorbance, also known as optical density measurements (unitless). Absorbance data should be submitted without null correction applied. List a null correction by pairing a field name with its null correction value separated by a colon. To report multiple null corrections, separate them by commas. Units are assumed to be the same as the fields used for null correction. Examples: 

/null_correction=abs_ap:0.001,abs_ad:0.005

/null_correction=ag:0.005 

 

Data fields in each file should nominally include:

1. Averaged raw absorbance, without null correction (abs_ag)

2. Standard deviation of multiple scans (abs_ag_sd)

3. Standard deviation of multiple blank scans (abs_blank_sd)

4. Measured absorption coefficient (ag)

5. (Optional) s_ag_#nmmin_#nmmax (if only 1 value is relevant to the whole file, it is typically reported in the header instead)

example submission, ag

The following bundle contains an excerpt example of a CDOM submission. The download bundle (.zip) includes two example data files, each from a different type of spectrophotometer, and several example documents and a completed CDOM Checklist file.
 
Download example CDOM submission ( .zip )
 

Absorption, Particulate (spectrophotometer)

Particulate Absorption submissions to SeaBASS include measurements of absorbance and derived absorption coefficients (and relevant metadata and processing information.) Examples of SeaBASS field names for these types of submissions are: abs_ap, abs_ad, ap, ad, aph, etc. New data submissions should be collected and reported in compliance with the most recent NASA / IOCCG protocols.

required extra documents, ap

Particulate absorption submissions require supplemental documentation to preserve critical methods information. Download whichever format you prefer, fill it out, and submit it along with your other documentation and calibration information.
 
Download ap Checklist (V20201009)
( .rtf version )
( .txt version )
 

special notes, ap

"Conditionally Required" metadata headers:
/volfilt (L) volume filtered
/area (m2) for filter pads, the area over which particles are collected onto the filter
/null_correction If applicable, report the null correction used while calculating absorption coefficients. Generally, null corrections should be performed using absorbance, also known as optical density measurements (unitless). Absorbance data should be submitted without null correction applied. List a null correction by pairing a field name with its null correction value separated by a colon. To report multiple null corrections, separate them by commas. Units are assumed to be the same as the fields used for null correction. Examples: 

/null_correction=abs_ap:0.001,abs_ad:0.005

/null_correction=ag:0.005

 

Data fields in each file should nominally include:

1. Averaged raw absorbance, without null correction (abs_ap, abs_ad)

2. Standard deviation of filter rotations for abs_ap and abs_ad (abs_ap_sd, abs_ad_sd)

3. Absorbance of blank filter subtracted from each sample (abs_blank)

4. Standard deviation of multiple blank scans (abs_blank_sd)

5. Measured ap and ad coefficient (ap, ad)

6. (Optional) Modeled ad coefficient (ad_model). Only include if applicable, e.g., insufficient pigment extraction (if so, document your computation method).

7. aph coefficient (write computation method as a comment in the header)

8. (Optional) Total uncertainty computation (ap_unc, ad_unc)

 

Other notes:

 Report any replicate filters separately

 

**See Chapter 5.3.4 the Absorption Coefficient protocol document1

 

1Neeley, A.R., Mannino, A., Reynolds, R.A., Roesler, C., Rottgers, R., Stramski, D., Twardowski, M. and Zaneveld, J.R.V., 2018. Ocean Optics & Biogeochemistry Protocols for Satellite Ocean Colour Sensor Validation: Absorption Coefficient. http://dx.doi.org/10.25607/OBP-119

 

example submission, ap

The following bundle contains a miniature example of a particulate absorption filter pad SeaBASS submission. The download bundle (.zip) includes 2 example Particulate Absorption Filter Pad SeaBASS files (one also includes size fractionated measurements) and an accompanying documents folder, which includes a cruise-specific document covering documents and calibration requirements, plus a completed ap Checklist file.
 
Download example ap filter pad submission ( .zip )
 

Particulate Organic Carbon and Nitrogen (POC, PON)

Particulate Organic Carbon (POC) and Particulate Organic Nitrogen (PON) submissions to SeaBASS should be accompanied by the checklist below as part of their documentation. Examples of SeaBASS field names for these types of submissions are: POC, PON.

required extra documents, POC, PON

POC and PON submissions require supplemental documentation to preserve critical methods information. Please download and complete the following checklist template (pick one download; whichever format you prefer) and submit it along with your other documents
 
Download POC / PON Checklist (V20190925)
( .rtf version )
( .txt version )

special notes, POC, PON

"Conditionally Required" metadata headers:

N/A

 

Data fields in each file should nominally include:

1. POC / PON values (nominally adsorption blank corrected)

2. volfilt

3. bincount and standard deviations ("_sd"), or another uncertainty metric to quantify replicates

 

Other notes:

DOC/DON adsorption ("filtrate") blank correction should be measured and applied to POC/PON.

   

Moran, S. B., M. A. A. Charette, S. M. Pike, C. A. Wicklund, M. S. Bradley, M. A. A. Charette, S. M. Pike, and C. A. Wicklund. 1999. Differences in seawater particulate organic carbon concentration in samples collected using small- and large-volume methods: the importance of DOC adsorption to the filter blank S.B. Mar. Chem. 67: 33–42.

 

example submission, POC, PON

The following bundle contains a miniature example of a POC / PON SeaBASS submission. The download bundle (.zip) includes an example SeaBASS file and an accompanying documents folder. (This example will be updated in the future with documents that also include a completed POC/PON checklist; described in "required extra documents" above)
 
Download example POC / PON submission ( .zip )
 

Dissolved Organic Carbon (DOC)

Dissolved Organic Carbon (DOC) submissions to SeaBASS should be accompanied by the checklist below as part of their documentation. Please use the recommended SeaBASS unit for DOC (DOC_L, umol/L).

required extra documents, DOC

      DOC submissions require supplemental documentation to preserve critical methods information. Please download and complete the following checklist template (pick one download; whichever format you prefer) and submit it along with your other documents

      Download DOC Checklist (V20230102)
      ( .txt version )

special notes, DOC

      "Conditionally Required" metadata headers:
      N/A


      Data fields in each file should nominally include:
      1. DOC_L (umol/L)
      2. bincount (as a data field or field suffix, i.e., doc_l_bincount) and standard deviations ("_sd"), or another uncertainty metric to quantify replicate uncertainty

      Other notes:
      Please use the recommended SeaBASS unit for DOC (DOC_L, umol/L). Even though it is customary for chemical oceanography data to be reported in mass per kg, for the purposes of remote sensing calibration, the recommended units must be normalized by volume.

Pigments, Extracted Chl (Fluorometric)

This section describes Chlorophyll-a derived fluorometrically or spectrophotometrically (e.g., "extracted" Chl), plus relevant metadata and processing information. SeaBASS field name for this type of submission is chl. New data submissions should be collected and reported in compliance with the most recent NASA / IOCCG protocols.

required extra documents, extracted chl

Extracted chlorophyll-a submissions require supplemental documentation to preserve critical methods information. Download the following checklist, fill it out, and submit it along with your other documentation and calibration information.
 
Download chl checklist (V20220420)

special notes, extracted Chl

 "Conditionally Required" metadata headers:
/volfilt header should be use to report the volume filtered if it is the same for all samples in the file. If volume filtered is different for different samples in the file, please use volfilt as a field.
 
Noteworthy data fields in each file should nominally include:
1. Chl & Phaeo as separate columns
2. If reported values were averaged from duplicate/triplicates/etc., report "bincount" (i.e., number averaged) and standard deviations (e.g., chl_sd)
3. If measurements were size-fractionated, report those as separate columns (see _#umprefilt fields suffix, e.g., chl_200umprefilt)
 
Other notes:
1. Report any fully independent replicates as separate samples
2. Report equations used for concentration computation in metadata or documentation
 

Pigments, HPLC

High performance liquid chromatography (HPLC) pigment analysis datasets consist of samples that were analyzed for a suite of chlorophylls, xanthophlls, and carotenoids.

required extra documents, HPLC

HPLC submissions require supplemental documentation to preserve critical methods information.
 
If your HPLC samples were analyzed at NASA GSFC by Crystal Thomas, do not use the download below. Instead, Crystal will provide you with a tailored version of the checklist containing the measurement and analysis section already completed with the latest updates. Using that version, fill in the beginning section (sample collection methods) and submit it along with your other SeaBASS submission documentation.
 
If your HPLC samples were analyzed at a different laboratory, please download and complete the Blank Checklist below, and submit it along with your other SeaBASS submission documentation. You may download an Example Checklist filled out by the NASA GSFC Lab if you need a reference.
 
Download HPLC Checklist (V20191008)
Blank Checklist ( .rtf version )
 

special notes, HPLC

"Conditionally Required" metadata headers:
/HPLC_lab (e.g., NASA_GSFC)
/HPLC_lab_technician (e.g., Crystal_Thomas)
/volfilt header should be use to report the volume filtered if it is the same for all samples in the file. If volume filtered is different for different samples in the file, please use volfilt as a field.
 

Data fields in each file should nominally include:

1. Individual and summed pigments (based on SeaBASS fields/SeaHARRE reports)

2. Separate columns for any size-fractionated measurements (e.g., Tot_Chl_a_20umprefilt goes in a separate column from Tot_Chl_a)

3. Include "hplc_gsfc_id" as a column if your data were analyzed at the NASA GSFC lab to preserve the lab's sample ID

 

Other notes:

  • Report any replicate filters separately
  • Use the /below_detection_limit to mask any relevant values. It is distinct from the /missing value (e.g., /missing=-9999 vs. /below_detection_limit=-8888)
  • SeaBASS files may only contain data from a single cruise or deployment. If necessary, sort and separate your data by cruise then create multiple SeaBASS files
  • An online tool (HPLC2sb) is optionally available to help convert NASA GSFC HPLC spreadsheets into SeaBASS file format. However, please read its limitations and caveats carefully. https://seabass.gsfc.nasa.gov/hplc2sb/
 

example submission, HPLC

The following download provides an example of an HPLC SeaBASS file. An updated example will be provided in the future that also includes documentation.
 
Download example HPLC file ( .zip )
 

Radiometry (in-water)

This section describes data management and submission of in-water radiometry measurements, e.g., underwater casts or sensors deployed in buoy mode.  Examples of SeaBASS field names for these types of submissions of AOPs often include: Lu, Ed, Es, etc. New data submissions should be collected and reported in compliance with the most recent NASA / IOCCG protocols.
 

required extra documents, radiometry (in-water)

In-water radiometry submissions require supplemental documentation to preserve critical methods information. Download the following checklist, fill it out, and submit it along with your other documentation and calibration information.
 
Download Radiometry (in-water) Checklist
 

special notes, radiometry (in-water)

"Optional but recommended" metadata headers:
/wind_speed
/cloud_percent
/wave_height
/heading (i.e. ship heading)
 

Data fields in each file should include:

1. Depth

2. Tilt, Roll, and/or Pitch

3. Time

 

Data fields that are optional but recommended include:

1. cond (i.e., conductivity)

2. wt (i.e., water temperature

 

Other notes

* If data from multiple sensors are expressed at common depths in the same data matrix, any offsets from the depth sensor must be described

 

Radiometry (above-water)

This section describes data management and submission of above-water radiometry (AWR), e.g., shipborne, or tower-mounted radiometers in automated or manual configurations.  SeaBASS field names for these types of submissions of AOPs usually include Rrs and Es, and often include Lt, Lsky, Lw, Lwn, and Lwnex. Data submissions from handheld instruments should include Es, Lt, Lsky, Lw, and Rrs at a minimum.

 

Some estimate of uncertainties should be provided. Ideally, these would include all sources of uncertainty from the instrument characterizations, data processing (e.g., glint correction), and environmental variability. At a minimum, variability (e.g., standard deviation) across multiple measurements for a single, averaged and submitted spectrum submitted should be reported (e.g., Rrs_unc or Rrs_std).

 

New data submissions should be collected and processed in compliance with the most recent NASA / IOCCG protocols.

 

AWR data acquisition systems typically include between one and three radiometers. Configurations with three radiometers are deployed above the sea surface and comprise two radiometers measuring skylight (Lsky) and total upwelling radiance (Lt) simultaneously with surface irradiance (Es) measured by a third radiometer equipped with a cosine collector. Fully above water systems with two radiometers typically measure Es with one and tilt the other to measure Lt and Lsky alternately. A two-radiometer system can also be configured in a skylight blocked approach (SBA) directly at the sea surface with no need to measure Lsky. Single radiometer systems typically measure Lt and Lsky alternately (by tilting) and estimate Es by measuring reflectance from a Lambertian plaque. Systems can be manually operated or fully autonomous (i.e., using a robotic platform to adjust/measure sensor geometries and a data logger to merge multiple ancillary datasets such as GPS time and position and tilt).

 

Three-radiometer AWR systems using Sea-Bird Scientific HyperOCRs or TriOS RAMSES radiometers are supported in the HyperInSPACE Community Processor (HyperCP). This software allows for protocol-driven, standardized processing of AWR with rigorous quality controls and is encouraged for the submission of validation-quality radiometry. Full radiometric characterization of radiometers for stray light, thermal response, polarization sensitivity, angular response (cosine collectors), and absolute radiometric calibration uncertainty, as described in the protocols, is strongly encouraged and used by HyperCP to deliver fully Fiducial Reference Measurement compliant, validation-quality radiometry with end-to-end uncertainty estimation. The information gathered by HyperCP and automatically formatted for SeaBASS submission simplifies the submission and review process for everyone.

 

An extensive description of measurement procedures for AWR can be found in the D-6 document prepared by the Fiducial Reference Measurements for Satellite Ocean Colour (FRM4SOC) initiative. It is written specifically for TriOS triplets, but also largely applicable to similar systems such as the Sea-Bird HyperSAS.

 

Files may be submitted as a single set of spectra (i.e., at one time stamp) with wavelength as a column, or as multiple spectra per file as rows with wavelength denoted in field names and a column for date/time.
 

For continuously sampling radiometer systems with inherent sampling rates on the order of 1 Hz, data should generally be binned to 300 s (see Ensemble_Interval metadata below).

required extra documents, radiometry (above-water)

AWR submissions require supplemental documentation to preserve critical methods information. Download the following checklist, fill it out, and submit it along with your other documentation and calibration information.

 
      Download Radiometry (above-water) Checklist
     .docx version (V20240130)

Special notes, radiometry (above-water)

When using HyperCP to process AWR, many of the headers and fields below will be supplied automatically in the SeaBASS file, provided the data are included in the processing (i.e., see HyperCP README on Ancillary data inputs here). A field log template is also provided for AWR collections here.

 

"Optional but recommended" metadata headers (if not included as fields):

  1. /wind_speed (strongly recommended)
  2. /cloud_cover (strongly recommended)
  3. /rho_correction (strongly recommended)
  4. /NIR_residual_correction (strongly recommended)
  5. /BRDF_correction
  6. /station
  7. /wave_height
  8. /water_depth

 

 

Metadata header comments (preceded by “!”):

  1. ! Percent_Light (i.e., percentage of Lt measurements retained to reduce glitter, e.g., “10”. Not for use with manual collections or SBA)
  2. ! Remove_Negatives (i.e., whether spectra with negative values were removed, e.g., “True”)
  3. ! Ensemble_Interval (i.e., duration in seconds of ensemble averaging, e.g., “300”.)

 

Data fields in each file should include (if not included as headers):

  1. Time and Date
  2. Lat/Lon (Latitude/Longitude)
  3. RelAz (Relative sun-sensor azimuth for Lt and Lsky. Not for use with SBA.)

 

Data fields that are optional but recommended include:

  1. Station
  2. SZA (solar zenith angle)
  3. AOT (aerosol optical thickness)
  4. Wind (sea surface wind speed)
  5. Cloud (percent cloud cover )
  6. *_unc (measurement uncertainty in *)
  7. Bincount (number of measurements averaged within ensemble)
  8. Heading (ship heading)
  9. Speed_f_w (speed through the water in forward “heading” direction)
  10. Tilt (instrument tilt/pitch/roll, particularly for Es)
  11. Cond(sea surface conductivity)
  12. Wt(sea surface water temperature

Backscattering measurements

This section describes backscattering measurements using scattering meters such as Hydroscat-6 (HS6) and ECO-bb. Backscattering submissions to SeaBASS should be accompanied by the checklist below as part of their documentation. For backscattering measurements using the ac-9 or ac-s please refer to the ac-meter section. 

required extra documents, bb and bbp

Backscattering submissions require supplemental documentation to preserve critical methods information. Download the following checklist, fill it out, and submit it along with your other documentation and calibration information. 
 
Download Backscattering Checklist (V20200819) 

special notes, bb and bbp

"Optional (but recommended)” metadata headers

/wind_speed (m/s) 

/cloud_percent (%) 

/wave_height (m) 

/instrument_manufacturer 

/instrument_model 

/calibration_date 

 

Data fields in each file should include: 

  1. Depth (unless depth is the same for all measurements, in which case omit the depth field and include the /measurement_depth header) 
  2. Wt (i.e., water temperature)
  3. cond (Conductivity) 
  4. sal (Salinity) 

Particle Size Distribution (PSD)

This section describes data management and submission of Particle Size Distribution (PSD) data using instruments such as LISST, UVP, coulter counter among others. PSD data can be submitted using one of the following conventions: Differential number size distribution or Differential volume size distribution. Please refer to the special notes below for correct use of headers and data fields.

required extra documents, PSD

 N/A

special notes, PSD

"Optional but recommended" metadata headers:

/instrument_model

/instrument_manufacturer

/PSD_bin_size_method=specify method used to select the nominal bin size such as arithmetic_mean or geometric_mean 

/PSD_bin_size_boundaries=please provide a comma-separated list with the bin size boundaries in increasing order, e.g., 5,9.5,15,20 ... 

 

Data fields in each file should include:

1. PSD_DNSD_###umsize=Differential number size distribution. Units: number/m^3/um 
2. PSD_DVSD_###umsize=Differential volume size distribution. Units: uL/m^3/um 

 

Data fields that are optional but recommended include:

N/A

Plankton and Other Particles

SeaBASS provides a mechanism to accept and ingest measurements of plankton and particles collected by flow cytometry and imaging-in-flow methods (e.g., IFCB, FlowCAM, UV-P, etc.). For flow cytometry data, Level 2 is defined as sums of the total abundances of each phytoplankton or bacterial group.

 

For imaging-in-flow data, Level 1b for plankton and other particle observations is defined as individual level counts with automatic (including interpretation of class scores or probabilities) and manual classifications, and biovolume and size parameters for each region of interest (ROI). An ROI is defined as a rectangular subset of pixels in a given image. The submission of a Level 1b data table for plankton and other particle observations to SeaBASS must include morphological information for each ROI and must be accompanied by documents that include relevant metadata and processing information.

 

Submissions of both types of data must be accompanied by documents that include relevant metadata and processing information.

 
Plankton and particles: imagery
Plankton and particles: Flow cytometry
Last edited by Chris Proctor on 2024-02-27
Created by Chris Proctor on 2019-10-02