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.
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
A comma-separated list (no spaces) naming ancillary files such as cruise reports, station logs, digital images, and other associated documentation that are part of the dataset submission (provided in the relevant documents directory) and provide additional information about the experiment and cruise. Every SeaBASS submission must be accompanied by an instrumentation-methods-calibration report that describes methods: the instruments used, how they were calibrated and how data were collected and processed. Include any required checklists.
See User Resources for more information.
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:
Other accepted (but less common in SeaBASS) values include:
required
A comma-separated list (no spaces) of supplementary file names containing coefficients and techniques used to calibrate the instruments used in data collection. The named files can be found within the relevant documents folder accompanying the submitted data files.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.
optional
(m^2) Use this header to describe the area a sample occupies (e.g., for filter pad absorption measurements.)
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:
Please contact the SeaBASS staff if your associated_archives do not fit into one of these types.
conditionally required
The “associated_files” header or field can be used to link specific files within the compressed tar bundle (TGZ; the associated_archives bundle). If one link is relevant for the entire SeaBASS files, use associated_files as a header. If the links differ by data row within the data matrix, use associated_files as a field. This header should be used in conjunction with the associated_archives header, as well as the associated_file_types and associated_archive_types.
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. For additional information and examples go here.
conditionally required
Include this header if a SeaBASS file has an accompanying auxiliary or ancillary file that is being reported with the /associated_files header. For multiple entries, separate with a comma.
NOTE: This header MUST be used in conjunction with the /associated_files header.
Valid entries for this header are:
This value is an abbreviation (from the table below) specifying which, if any, method of bi-directional reflectance distribution function (BRDF) correction was applied to all relevant radiometry fields. e.g.,
/BRDF_correction=noBRDF
Alternately, one or more specific pairings of <fields-name>:<BRDF-abbreviation> may be listed comma-separated, e.g.,
/BRDF_correction=Rrs:noBRDF
Table of standardized NIR_residual_correction method abbreviations
BRDF method abbreviation |
BRDF method |
Default, if not specified |
noBRDF or NA |
No BRDF applied |
Default for all .sb files |
M02 |
Morel et al. 2002 |
Default for SeaBASS Validation files |
L11 |
Lee et al. 2011 |
|
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”.
Note: Original SeaBASS data submissions must not be BRDF corrected. BRDF may be used in alternate versions of data, or in validation outputs. See radiometry submission requirements or contact SeaBASS staff with any questions.
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.
Applicable (and required) for HPLC data. This header should contain the name of the lab where the HPLC analysis was run.
Example: /HPLC_lab=NASA_GSFC
Use in conjunction with the /HPLC_lab_technician header.
Applicable (and required) for HPLC data. This header should contain the name of the lab technician who ran the HPLC analysis.
Example: /HPLC_lab_technician=Crystal_Thomas
Use in conjunction with the /HPLC_lab header.
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,...
The numeric expression of the mass to charge ratio for a chemical compound, typically associated with the PTR-TOF/MS instrument measuring VOCC concentrations.
Use the syntax "/mass_to_charge=...,mz33.0335,mz34.0335,...", where each relevant "/fields=...,C3H6O_H,C5H8_H,..." entry has its mass to charge (m/z) ratio expressed.
If it is necessary to list multiple mass to charge raatios, then list all the values in a row, separated by commas.
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
NIR residual correction method abbreviation |
NIR residual correction method |
R06 |
Ruddick et al. 2006 |
MA95 |
Mueller and Austin 1995 |
conditionally required
Only required if a null correction was applied while calculating absorption coefficients. Generally, null corrections should be performed using absorbance, also known as optical density measurements (unitless). Please note that 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_ag:0.005,abs_ap:0.001,abs_ag:0.005
/null_correction=ag:0.005
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
Rho correction method abbreviation |
Rho correction method |
M99 |
Mobley 1999 |
Z17 |
Zhang 2017 |
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.
optional
The model of the instrument whose measurements are being reported (e.g., PRR-800). Replace any spaces in the names with underscores. If the file contains measurements from multiple instruments, 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/).
optional
Geoform Component Physiographic Setting 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/).
optional
Geoform Origin, Geoform 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/).
optional
Geoform, Geoform 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/).
optional
Geoform Type. Geoform 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/).
optional
The Rolling Deck to Repository (R2R) unique sample event number that applies to the entire data matrix. If multiple events apply to the data matrix, don't use this header. Instead, provide a column of those data values using the field name "R2R_event".
optional
Substrate Origin, Substrate 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
Substrate Class, Substrate 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
Substrate Subclass, Substrate 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
Substrate Group, Substrate 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
Substrate Subgroup, Substrate 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
Water Column Biogeochemical Feature 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/).
optional
Water Column Hydroform Subcomponent 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
Water Column Hydroform Subcomponent 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
Water Column Hydroform Subcomponent 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
Water Column Layer 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/).
optional
Water Column Salinity 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/).
optional
Water Column Temperature 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/).
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 DOI (Digital Object Identifier; see http://www.doi.org/) associated with the experiment.
assigned and entered by SeaBASS staff
The date that the files were submitted to SeaBASS.