Metadata Headers

Standard metadata headers are required in every SeaBASS file. Select a header to view its definition, or if you are just getting started, scroll down just below the table of content to see an example header.


Table of Contents


Example Header

/begin_header
/investigators=John_Smith,Mary_Johnson
/affiliations=State_University
/contact=jsmith@state.edu
/experiment=CalCOFI
/cruise=cal0101
/station=93.26
/data_file_name=pigments_cal0101.dat
/original_file_name=pigments_cal0101.xls
/documents=cal0101_readme.txt
/calibration_files=turner_cals_0012.txt
/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=tab
/fields=time,depth,CHL,PHAEO,Tpg
/units=hh:mm:ss,m,mg/m^3,mg/m^3,mg/m^3
/end_header
16:01:30    0    2.355    0.785    3.140        
16:03:45    5    2.180    1.005    3.185
16:07:53 10 1.510 -9999 -9999
16:15:11 50 0.157 -8888 0.157
...
...

 

 

Required Headers

The following headers are requird to be included in every SeaBASS file.

investigators

required

The contributor of the data file. Principal investigator is listed first, followed by any associate investigators.

 

affiliations

required

A list of affiliations (e.g. university, laboratory) for each investigator.

 

contact

required

An email address for one of the investigators or point of contact for the data file.

 

experiment

required

The name of the over-arching, long-term research project or funding program. Experiment names are used to generate a dataset-specific DOI and, generally, will contain multiple cruises or deployments and encompass data spanning multiple months or years. Please do not exceed 25 characters.

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

 

cruise

required

The name of the specific cruise (or subset of the experiment) where the data in the file were collected. Please do not exceed 25 characters.

For example: cal9802, car48, bats143, dep12.

 

station

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

The name of the station or deployment where data in the file were obtained.

 

data_file_name

required

The current name of the data file.

 

documents

required

Refers to cruise reports, station logs, digital images, and other associated documentation that provide additional information about the experiment and cruise. Every SeaBASS submission must be accompanied by an instrumentation/calibration report that describes the instruments used, how they were calibrated and how data were collected and processed.

 

See User Resources for more information.

data_type

required

Describes the general collection method for the data. Accepted values include:

  • 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)
  • sunphoto for sunphotometry data (e.g. MicroTops, PREDE)
  • mooring for moored and buoy data
  • drifter for drifter and drogue data
  • scan for discrete hyperspectral measurements
  • lidar for lidar and other active remote-sensing measurements (e.g. MPL)
  • pigment for laboratory measured pigment data (e.g. fluorometry, spectrophotometry, HPLC)
  • bottle for other types of measurements from water samples collected at discrete depths (e.g. nutrients)
  • diver for measurements made by a diver
  • auv for measurements made by an autonomous underwater vehicle (auv)
  • airborne for measurements made via an aircraft

 

calibration_files

required

Refers to supplementary files containing coefficients and techniques used to calibrate the instruments used in data collection.

start_date

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

 

end_date

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

 

start_time

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]

 

end_time

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]

 

north_latitude

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]

 

south_latitude

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]

 

east_longitude

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]

 

west_longitude

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]

 

water_depth

required

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

 

missing

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 large negative number large enough to never be confused with valid measurements. If your file includes below_detection_limit or above_detection_limit values, use different NULL values for each.

/missing=-9999

 

delimiter

required

Indicates how the columns of data are delimited. Accepted delimiters include tab, space, and comma. Only a single (1) delimiter is permitted per data file.

 

fields

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.

 

units

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 Headers

The following headers are conditionally required to be incldued in some SeaBASS files.

measurement_depth

conditionally required

If all the data in the file were collected at a discrete depth, this is that depth (in meters). Applicable (and required) for bottle samples, and 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.

Default is 0 for measurements made above the sea surface.

 

above_detection_limit

required IF file contains above_detection_limit values, optional otherwise

Refers to the numeric NULL value used a placeholder for measurements that were made but were above detection limits. If the file contains those types of values, this header is required and those values should be flagged (e.g., set to -7777 or another defined value). Above detection limit values convey some information and are not the same as "missing" values, as missing implies that data were either not measured or invalid.
 
/above_detection_limit=-7777
! Comments
!
! Measurements above detection limit are assigned the value -7777
! upper limit of detection = XYZ concentration
 
If your file contains below detection limit values, then include the header "/above_detection_limit=-7777" followed by comments that describe what the detection limit was for each relevant measurement-type.
 
 

below_detection_limit

required IF file contains below_detection_limit values, optional otherwise
 
Refers to the numeric NULL value used a placeholder for measurements that were made but were below detection limits. If the file contains those types of values, this header is required and those values should flagged (e.g., set to -8888 or another negative number that is distinct from the range of valid measurements). Below detection limit values convey some information and are not the same as "missing" values, as missing implies that data were either not measured or invalid for other reasons.
 
/below_detection_limit=-8888
! Comments
!
! Measurements below detection limit are assigned the value -8888
! lower limit of detection = XYZ concentration
 
If your file contains below detection limit values, then include the header "/below_detection_limit=-8888" followed by comments that describe what the detection limit was for each relevant measurement-type. You do not need to list the limit of detection for every measurement-type in your file, only those that use the below detection limit value (i.e. -8888.) Also, you may consolidate information where practical, for example if the limit of detection for all HPLC pigments is the same concentration (e.g. 0.001 mg/m^3) then a comment like "! HPLC pigments limit of detection = 0.001 mg/m^3" will suffice rather than listing every pigment individually.
 
 

volfilt

conditionally required

The volume filtered (in units of liters) of the field(s) 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 measurement in a /type=scan file).

Use the syntax "/volfilt=FIELD_NAME:###", for example, /volfilt=ap:0.1

If it is necessary to list multiple volumes, then list all the FIELD_NAME:### pairings in a row, separated by commas.

 

optical_depth_warning

conditionally required

Include the header using the syntax /optical_depth_warning=true if a file contains measurements that are known or suspected to be in optically shallow conditions where the bottom reflectance would impact water leaving values. Using default SeaBASS search settings, files with this header will be excluded from results. Don't include this header for typical files with measurements that are assumed to be optically deep.

Submitters: If your files contain this header, please discuss the submission with SeaBASS staff, since typical SeaBASS files are assumed to be from optically deep conditions.

associated_archives

conditionally required

Include this header using the syntax: /associated_archives=my_related_data_bundle.tgz if a SeaBASS file has an accompanying TAR archive bundle of image, auxiliary, or ancillary files. For multiple TAR bundles, separate entries with a comma.
 
This header is NOT for documentation (use /documents instead), and NOT for calibration files (use /calibration_files instead).
 
Please explicitly include the file suffix in the entry. Supported formats are: TAR, TAR.GZ, and TGZ. Please contact the SeaBASS staff if you plan to submit another format than these.
 
NOTE: Please contact the SeaBASS staff if you plan to submit a SeaBASS file using this header, as there are restrictions on allowed file types. This header MUST be used in conjuction with the /associated_archive_types header.

associated_archive_types

conditionally required

Include this header using the syntax: /associated_archive_types=DNA-FASTA if a SeaBASS file has an accompanying TAR archive bundle that is being reported with the /associated_archives header. For multiple entries, separate with a comma.
 
Valid entries for this header are: DNA-FASTQ, DNA-FASTA (for files relating to DNA analysis), benthic, or planktonic (for files relating to accompanying scientific imagery).
 
Please contact the SeaBASS staff if your tar bundle archive does not fit into one of these types.
 
NOTE: this header MUST be used in conjuction with the /associated_archives header.

associated_files

conditionally required

Include this header using the syntax: /associated_files=my_related_data_file.jpg if a SeaBASS file has an accompanying image, auxiliary, or ancillary file. For multiple files, separate entries with a comma.
 
This header is NOT for documentation (use /documents instead), and NOT for calibration files (use /calibration_files instead). This header is also NOT for generic images of instrumentation, etc; rather, this header is to be used to identify scientific imagery that is part of an observation set or used to support scientific analyses that are being reported in a SeaBASS file (e.g. - a bethic cover analysis could be accompanied by benthic cover photomosaics using this header).
 
Please explicitly include the file suffix in the entry. If submitting imagery, supported formats are: JPG, PNG, and TIF. Please contact the SeaBASS staff if you plan to submit another format than these.
 
NOTE: Please contact the SeaBASS staff if you plan to submit a SeaBASS file using this header, as there are restrictions on allowed file types. This header MUST be used in conjuction with the /associated_file_types header.

associated_file_types

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.
 
Valid entries for this header are: DNA-FASTQ, DNA-FASTA (for files relating to DNA analysis), benthic, or planktonic (for files relating to accompanying scientific imagery).
 
Please contact the SeaBASS staff if your associated_files do not fit into one of these types.
 
NOTE: this header MUST be used in conjuction with the /associated_files header.

HPLC_lab

conditionally required

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.

HPLC_lab_technician

conditionally required

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.

chemical_formula

 conditionally required

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.

 

mass_to_charge

 conditionally required

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.

 

Optional (but recommended) Headers

The following headers are optional but strongly recommend for inclusion in every SeaBASS file.

data_status

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.

 

secchi_depth

optional

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

 

cloud_percent

optional

Percent cloud cover for the entire sky.


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

 

wave_height

optional

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

 

wind_speed

optional

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

 

Optional Headers

The following headers are optional for inclusion in every SeaBASS file.

comments

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 (!).

 

original_file_name

optional

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

Designed to be a reference for the contributor.

 

area

optional

Use this header to describe the area a sample occupies.

null_correction

optional

Use this header to describe the null correction applied.

station_alt_id

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

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

 

biotic_setting

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/).

 

biotic_class

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/).

 

biotic_subclass

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/).

 

biotic_group

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/).

 

biotic_community

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/).

 

geoform_tectonic_setting

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/).

 

geoform_physiographic_setting

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/).

 

geoform_origin

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/).

 

geoform

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/).

 

geoform_type

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/).

 

substrate_origin

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/).

 

substrate_class

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/).

 

substrate_subclass

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/).

 

substrate_group

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/).

 

substrate_subgroup

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/).

 

water_column_biogeochemical_feature

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/).

 

water_column_hydroform_class

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/).

 

water_column_hydroform

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/).

 

water_column_hydroform_type

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/).

 

water_column_layer

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/).

 

water_column_salinity

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/).

 

water_column_temperature

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/).

 

Restricted Use Headers

The following headers are created by SeaBASS staff after the files have been submitted to the SeaBASS archive. Data submitters should NOT add these headers to their SeaBASS files.

identifier_product_doi

assigned and entered by SeaBASS staff

The DOI (Digital Object Identifier; see http://www.doi.org/) associated with the experiment.

 

received

assigned and entered by SeaBASS staff

The date that the files were submitted to SeaBASS.

 

Last edited by Joel Scott on 2018-11-09
Created by Chris Proctor on 2012-08-29