Most headers exist as keyword=value pairs (for example /delimeter=comma). Whitespace is not allowed in values; if there are multiple values they are listed comma separated (no space), and if a single value would contain a space it is replaced with underscores (for example /investigators=John_Smith,Mary_Miller). Spaces are only allowed in freeform comment lines which begin with an exclamation point (e.g., ! This is a comment).

Table of Contents

/begin_header
/investigators=John_Smith,Mary_Johnson
/affiliations=State_University
/contact=jsmith@state.edu
/experiment=CalCOFFEE
/cruise=cal0101
/station=93.26
/data_file_name=CalCOFFEE_cal0101_pigments_20010314_R1.sb
/original_file_name=pigments_cal0101.xls
/documents=cal0101_readme.txt
/calibration_files=turner_cals_0012.txt
/calibration_date=20001212
/instrument_model=10AU_Field_Fluorometer
/instrument_manufacturer=Turner_Designs
/data_type=pigment
/data_status=final
/start_date=20010314
/end_date=20010314
/start_time=16:01:30[GMT]
/end_time=16:30:45[GMT]
/north_latitude=42.135[DEG]
/south_latitude=42.055[DEG]
/east_longitude=-72.375[DEG]
/west_longitude=-72.420[DEG]
/water_depth=250
/measurement_depth=NA
/secchi_depth=4.5
/cloud_percent=50
/wind_speed=5.0
/wave_height=1.0
!
! COMMENTS
!
! Slightly overcast, with large cumulous on horizon.  Wind from NE.  
!
! Turner fluorometer last calibrated: 12 December 2000
!
! lower limit of detection = 0.001 mg/m^3
!
/missing=-9999
/below_detection_limit=-8888
/above_detection_limit=-7777
/delimiter=comma
/fields=date,time,lat,lon,depth,CHL,CHL_sd,PHAEO,PHAEO_sd,Tpg,bincount
/units=yyyymmdd,hh:mm:ss,degrees,degrees,m,mg/m^3,mg/m^3,mg/m^3
/end_header
20010314,16:01:30,42.135,-72.375,0,2.355,0.080,0.785,0.100,3.140,3        
20010314,16:03:45,42.055,-72.420,5.5,2.180,0.005,1.005,0.009,3.185,3
20010314,16:07:53,42.100,-72.378,10,1.510,0.124,-9999,-9999,-9999,3
20010314,16:15:11,42.130,-72.380,50,0.027,0.001,-8888,-9999,0.057,3   
...

 The "comma" delimiter is used to separate data values (everything below /end_header) in the above example. Comma should be used as the delimiter. Space or tab are supported but not recommended for new submissions.

required

The contributors of the data file. The Principal Investigator (PI) is listed first, followed by any associate investigators, analysts, technicians, and students, etc. (comma-separated, no spaces).

required

A list of affiliations (i.e., university, institution, or laboratory, etc.) whose number and ordering should match the entry or entries in the investigators header (comma-separated, no spaces).

required

An email address for at least one of the investigators or point of contact for the data file. The email address of the PI must be included. Multiple email addresses may be listed comma-separated, no spaces.

required

The name of the over-arching, long-term research project or funding program. Experiment names are used to generate a dataset-specific DOI. Each /experiment is a collection of one or more /cruise, and thus it is common for experiments to encompass data spanning multiple months or years. The Experiment name should be either an acronym or short name, use underscores (no spaces), and if possible should be 25 characters or less. Data submitters should please be consistent with a consensus-selected name if data from the project are being submitted by multiple different investigators.

For example: CalCOFI, CARIACO, EcoHAB, BBOP, BTM

required

The name of the one specific cruise (or deployment, or subset of the experiment) describing the source of the data in the file, and used for linking related files. Every /cruise is organized under an over-arching /experiment, and related cruises typically share the same /experiment.

When proposing a new cruise name, avoid completely generic names. If possible, names should not exceed a length of 25 characters (no spaces allowed). Please be consistent and use a consensus-selected name if data from the same cruise are being submitted by multiple different investigators. The "cruise" header is allowed to be the same as "cruise_id" (if applicable) but sometimes a different name is more appropriate for SeaBASS.

Various example include: cal9802, car48, bats143, dep12, EXPORTSNP.

required (or optional, if station appears in /fields= list)

The name of the station or deployment where data in the file were obtained. If the data file contains measurements from multiple stations, use the value NA and include station as a column in your data matrix. NA may also be used if the data were not assigned station names.

required

The current name of the data file (i.e., a self-reference).

required

Data_type is a single keyword label that describes the general contents of the data file. This is typically the collection method or platform, but a few keywords are more specific to measurement type (e.g., pigment). Accepted values are restricted to the following:

• cast for vertical profiles (e.g. optical packages, CTD)
• flow_thru for continuous data (e.g. shipboard, underway flow through systems)
• above_water for above surface radiometry data (e.g. ASD, SIMBAD, Satlantic SAS)
• scan for discrete hyperspectral measurements (e.g., spectrophotometrically derived absorption)
• pigment for laboratory measured pigment data (e.g. fluorometry, spectrophotometry, HPLC)
• bottle (general category) for any other types of measurements from water samples collected at discrete depths (e.g. nutrients)
• mooring for moored and buoy data
• drifter for drifter and drogue data
• marine_snow_catcher for various type of marine snow catcher data

Other accepted (but less common in SeaBASS) values include:

• airborne for measurements made via an aircraft
• auv for measurements made by an autonomous underwater vehicle (auv)
• diver for measurements made by a diver
• experimental for measurements that have a non-geospatial aspect (e.g., incubations, other special laboratory measurements, etc.)
• lidar for lidar and other active remote-sensing measurements (e.g. MPL)
• net_tow for measurements captured via net (e.g., zooplankton via MOCNESS)
• sediment_trap for measurements from a sediment trap platform
• sunphoto for sunphotometry data (e.g. MicroTops, PREDE)
• taxonomy for data whose purpose is the classification or annotation of phytoplankton, zooplankton, or other marine groups

required

required

The earliest date data in the file were collected (in YYYYMMDD).

For example, a start date of March 14, 2001 would be written as /start_date=20010314

required

The latest date data in the file were collected (in YYYYMMDD).

For example, an end date of March 14, 2001 would be written as /end_date=20010314

required

The earliest time of day measurements were collected during the start_date in the file (in HH:MM:SS). Times are in Greenwich Mean Time. This header requires a [GMT] trailer.

For example: /start_time=12:30:00[GMT]

required

The latest time of day data data were collected during the end_date in the file (in HH:MM:SS). Times are in Greenwich Mean Time. This header requires a [GMT] trailer.

For example: /end_time=13:30:00[GMT]

required

The farthest north data in the file were collected (in decimal degrees). This header requires a [DEG] trailer. Latitudes south of the equator are negative.

For example: /north_latitude=42.750[DEG]

required

The farthest south data in the file were collected (in decimal degrees). This header requires a [DEG] trailer. Latitudes south of the equator are negative.

For example: /south_latitude=36.500[DEG]

required

The farthest east data in the file were collected (in decimal degrees). This header requires a [DEG] trailer. Longitudes west of the Prime Meridian are negative.

For example: /east_longitude=-68.500[DEG]

required

The farthest west data in the file were collected (in decimal degrees). This header requires a [DEG] trailer. Longitudes west of the Prime Meridian are negative.

For example: /west_longitude=-85.750[DEG]

required

The water (bottom) depth at the station where the data were collected (in meters). Use the value NA if water depth was unknown or if the file contains data from different bottom depths.

required

Refers to the NULL value used as a numeric placeholder for any missing data in the data file. Note that each row of data must contain the same number of columns as defined in the /fields and /units headers. Only one (1) missing value is allowed per file. This value MUST be non-zero. A common choice is -9999 or some other negative number large enough to never be accidentally confused with valid measurements. If your file includes below_detection_limit or above_detection_limit values, use different NULL values for each.

required

Indicates how the columns of data are delimited. Accepted delimiters include comma, space, or tab. All new submissions should use comma, and must if the data matrix contains strings. Only a single (1) delimiter is permitted per data file.

required

A list of the field names for each column of data included in the data file. Each entry describes the data in a single (1) column, and every column must have an entry.

required

A list of the units for each column of data included in the data file. Every value in /fields must have an appropriate value listed here.

conditionally required

The associated_archives header is mandatory for all submissions with associated metadata or files. This header provides the file name(s) of external bundles of files. It is typically used as part of the process of storing unprocessed files or imagery used for the results presented in the SeaBASS (.sb) file, such as planktonic imagery for IFCB, sig files for FCM, and sky photos for AOP measurements.  

The associated files should be compressed into a tar bundle (.tgz). Each TGZ file should not exceed 5Gb in size, however, each submission can provide multiple TGZ files. Multiple files can be listed similarly to the documents, separated by commas, and no spaces in the filename or list of files. The filename of the associated archive should include the experiment and cruise name, and data type, and must end with “_associated.tgz”.  

/associated_archives=Experiment_cruise_IFCB_202210-202212_associated.tgz,Experiment_cruise_IFCB_202310-202312_associated.tgz 

The submitter can compress the files using any method such as TGZ, tar.gz, or ZIP file. The files can also be uploaded individually, however, make sure they are within a folder that clearly denoted that they are associated files. The SeaBASS data manager will create the final TGZ file. Note that this header is not for general documentation (use /documents instead), and not for individual calibration files (use /calibration_files instead).

conditionally required

The associated_archive_types header is mandatory for all submissions with associated metadata or files and should accompany the associated_archives header. This header should describe each of the associated archive TGZ files. 

/associated_archive_types=planktonic,planktonic

Valid entries for this header are: 

• DNA-FASTQ 
• DNA-FASTA (for files relating to DNA analysis) 
• benthic 
• planktonic (for accompanying scientific imagery files) 
• raw (minimally processed, higher resolution data versions) 
• unbinned (Processed or QA/QC CTD data not binned) 
• metadata (Additional metadata information) 
• supplementary (for accompanying processed files)

Please contact the SeaBASS staff if your associated_archives do not fit into one of these types.  

Number of records averaged into a bin or reported measurement. List a bincount by pairing a field name with its bincount value separated by a colon. To report multiple bincounts, separate them by commas.
Examples: 

/bincount=Ed:0.005,Lu:0.001
/bincount=Ed:0.005 

What if files do not contain this header? Unless contradicted by more specific documentation, assume the defaults in the BRDF table above, i.e., .sb files = “noBRDF” and any results from SeaBASS Validation web-tools = “M02”.

The chemical formula of a reported compound, typically associated with the PTR-TOF/MS instrument measuring VOCC concentrations.

Use the syntax "/chemical_formula=...,(C3H6O)H+,(C5H8)H+,...", where each relevant "/fields=...,C3H6O_H,C5H8_H,..." entry has its true chemical formula expressed.

If it is necessary to list multiple chemical formulas, then list all the values in a row, separated by commas.

• optically_shallow: one or more data points were known or suspected to be in optically shallow conditions where the bottom reflectance would impact water leaving values
• experimental: data are either non-geospatial (e.g., non-field measurements derived under laboratory conditions) or subjectively non-geospatial (e.g., derived from measured water samples but with adjusted light levels or other experimental parameters)
• negative_data_values: the file contains one or more negative values for types of data that are nominally positive. This warning is used when calibrations or data corrections yielded negative values. Investigators generally must remove or flag negative values prior to submitting to SeaBASS, but there are cases when it is helpful to preserve (slightly) negative values.
• negative_depths: data contains one or more negative depth or pressure values, which are only allowed if it is necessary and meaningful to retain measurements above the sea-surface
• missing_required_metadata_depth: the file contains one or more data points that are missing values for the required metadata "depth". Data are typically rejected if measurement depth are missing.
• missing_required_metadata_time: the file contains one or more data points that are missing values for the required metadata "time". Data are typically rejected if measurement time data are missing.
• "ice": the file contains one or more data points that from samples taken from ice-cores, ice-leads, or under-ice seawater.

This header is a list of one or more user-defined classification categories that modify field names. This header is required if the _id modifier is used in fields.

Use the syntax "/id_fields_definitions=#id:<definition>" by listing numbered id suffix followed by the user definition. Multiple definitions may be provided; list them separated by commas. Here is an example of this metadata header paired with its use in /fields:

/id_fields_definitions=1id:nanoeukaryotes,2id:picoeukaryotes

/fields=u_ph_1id,u_ph_2id,...

conditionally required (value must be provided if depth is omitted from /fields)

The constant measurement depth (in meters) that applies to all data rows. Only provide a numerical value if all data in the file were collected at the same discrete depth, and the file omits the equivalent field named depth. For example, this is often applicable (and required) for files containing bottle samples, buoys, and moored radiometers. This header should be excluded or have the value "NA" if a single measurement depth does not apply to the file.

The default value is 0, which is also applicable for measurements made at or just above the sea surface.

This value is an abbreviation (from the table below) specifying which, if any, method of Near Infrared (NIR) residual correction is applied to all relevant radiometry fields. Alternately, one or more specific pairings of <fields-name>:<method-abbreviation> may be listed comma-separated.

Table of standardized NIR_residual_correction method abbreviations

conditionally required

This value is an abbreviation (from the table below) specifying which, if any, method of Near Infrared (NIR) residual correction is applied to all relevant radiometry fields. Alternately, one or more specific pairings of <fields-name>:<method-abbreviation> may be listed comma-separated.

Table of standardized rho_correction method abbreviations

conditionally required

The volume filtered (in units of liters) corresponding to one or more fields in a file. This header is only applicable for files with measurement(s) from a discrete sample (for example, to indicate the volume of water filtered for the ap absorption coefficient.)

Use the syntax "/volfilt=FIELD_NAME:#" by listing the field name and volume separated by a colon. For example, /volfilt=ap:0.1

If it is necessary to list multiple volumes filtered for different fields, separate the pairings with a comma.

optional

The most recent relevant calibration date for the primary instrument (as YYYYMMDD, e.g., 20190122).This header is optional but highly recommended. Omit this header if a date value is not applicable or cannot be provided." 

optional

Percent cloud cover for the entire sky.

For example: 0 indicates no clouds and 100 indicates completely overcast.

/platform_id is mutually exclusive with /cruise_id and /glider_id 
A unique value assigned to a ship deployment by the ship operator. This metadata header is synonymous with the BCO-DMO cruise_id parameter (https://www.bco-dmo.org/parameter/1102). The cruise_id is also the first portion of the SeaBASS field "R2R_event". 

 
For example:  
/cruise_id=RR1813 

optional

The condition, or status, of the data file. The value preliminary is used when the data are new and the investigator intends to analyze the data further. The value update indicates the data are being resubmitted and informs users that an additional resubmission will occur in the future. The value final is used when the investigator has no intention of revisiting the data set.

/platform_id is mutually exclusive with /cruise_id and /glider_id 
A unique value assigned to a specific glider. The glider_id parameter is similarly implemented within BCO-DMO (https://www.bco-dmo.org/parameter/1809). This term is also synonymous with the U.S. IOOS National Glider Data Assembly Center (IOOS) Glider DAC "platform_id" metadata and is implemented as the first portion of the IOOS Glider DAC "deployment" and "id" string parameters, which are part of the Climate and Forecast (CF) metadata conventions (https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html). 
 

For example: 
/glider_id= SG_219 

optional

The instrument manufacturer of the measurements that are being reported (e.g., Biospherical_Instruments_Inc.) Replace any spaces in the name with underscores. If the file contains measurements from multiple sources, list them comma separated.

/platform_id is mutually exclusive with /cruise_id and /glider_id 
A unique name assigned to oceanographic assets such as buoys, moorings, floats, drifters, towed vehicles like the Scanfish or StingRay. This could be used for towers or meteorological stations. Some organizations incorporate cruise_id and/or glider_id within platform_id, but SeaBASS has opted to keep them each defined in separate metadata headers. This is synonymous with the BCO-DMO “platform” parameter (https://www.bco-dmo.org/parameter/932), NERC “platform type” term (https://vocab.nerc.ac.uk/collection/W06/current/CLSS0001/), and the “platform_id” term within the Climate and Forecast (CF) metadata conventions (https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html). 
 

For Example: 
/platform_id=PAP_001 

optional

The secchi depth at the station where the data were collected (in meters).

optional

The wave height at the station where the data were collected (in meters).

optional

The wind speed at the station where the data were collected (in meters per second).

optional

A space for additional comments. Common comments include additional ancillary information about the data file, sea and sky states, difficulties encountered during data collection, methods of data collection, instruments used, and a description of nonstandard SeaBASS field names included in the data file. Comments must always be preceded by a exclamation point (!).

optional

The original name of the data file, if different from the current /data_file_name.

Designed to be a reference for the contributor.

optional, (use ONLY if station header is already in use)

An alternate name or identifier for the station or deployment where data were obtained.

optional

Biotic Setting, Biotic Component, level 1. CMECS Units, with no spaces, use underscores instead.

Refers to a data classifier in the Coastal and Marine Ecological Classification Standard (CMECS, https://www.cmecscatalog.org/).

optional

Biotic Class, Biotic Component, level 2. CMECS Units, with no spaces, use underscores instead.

Refers to a data classifier in the Coastal and Marine Ecological Classification Standard (CMECS, https://www.cmecscatalog.org/).

optional

Biotic Subclass, Biotic Component, level 3. CMECS Units, with no spaces, use underscores instead.

Refers to a data classifier in the Coastal and Marine Ecological Classification Standard (CMECS, https://www.cmecscatalog.org/).

optional

Biotic Group, Biotic Component, level 4. CMECS Units, with no spaces, use underscores instead.

Refers to a data classifier in the Coastal and Marine Ecological Classification Standard (CMECS, https://www.cmecscatalog.org/).

optional

Biotic Community, Biotic Component, level 5. CMECS Units, with no spaces, use underscores instead.

Refers to a data classifier in the Coastal and Marine Ecological Classification Standard (CMECS, https://www.cmecscatalog.org/).

optional

Geoform Component Tectonic Subcomponent. CMECS Units, with no spaces, use underscores instead.

Refers to a data classifier in the Coastal and Marine Ecological Classification Standard (CMECS, https://www.cmecscatalog.org/).

Refers to a data classifier in the Coastal and Marine Ecological Classification Standard (CMECS, https://www.cmecscatalog.org/).

Data-submitters do not add the following headers to their SeaBASS files. Instead, these particular headers and values are created by SeaBASS staff after the files have been submitted to the SeaBASS archive.

assigned and entered by SeaBASS staff

The date that the files were submitted to SeaBASS.