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 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.

 



Table of Contents


Absorption and Attentuation Meter (AC-S)

This section addresses optical IOP measurements, in particular, absorption and attenuation meter measurements from an AC-S 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-S

Absorption and attenuation meter (AC-S) submissions should be made in conjunction with the following checklist that includes important details that need to be included with your submission. 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-S Checklist (V20191106)
( .rtf version )
 

special notes, AC-S

 "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-S 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 (V20191209)
( .rtf version )
 

special notes, ag

"Conditionally Required" metadata headers:
/null_correction (m-1) Only needed if null correction was applied to one or more abs coefficients (e.g., /null_correction=ag:0.0076)
/s_ag may be used to report calculated spectral slope (e.g., /s_ag=s_ag_300nmmin_600nmmax:0.023197)
 

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 ap filter pad 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 (V20190920)
( .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 (m-1) Only needed if null correction was applied to one or more abs coefficients
 

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

 

Download these ap filter pad guidelines

 

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

HPLC 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 )
 

Pigments, Extracted Chl (Fluorometric)

 Extracted Chl section under development.
 

required extra documents, extracted chl

N/A
 

special notes, extracted Chl

 "Conditionally Required" metadata headers:
N/A
 
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)
 

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_cover
/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

 

Last edited by Chris Proctor on 2020-02-18
Created by Chris Proctor on 2019-10-02