Below is a table of the standard field names and associated units for use in submitting data to the SeaBASS bio-optical archive. The field names are not case sensitive. Use the search bar or the find function in your browser to search the table for words or patterns found in the field names, units or descriptions. Please contact SeaBASS staff if you want to discuss adding new fields.
Special notes regarding wavelength-specific measurements: There are two different ways to indicate wavelengths (nm) in a SeaBASS file. If metadata such as date, location, or depth vary within the data, then append the wavelength number to the field name for every measurement combination. For example, downwelling irradiance ('Ed') measured at 412.3 nm is 'Ed412.3' (listed as separate columns alongside other Ed measurements, like Ed416.2, Ed419, etc.) Alternately, if date, location, and depth are assumed to be approximately constant for all measurements in the file, then use the field 'wavelength' to provide a column of the measured wavelengths and don't include them as part of the field names (this pivoted layout is commonly used for reporting spectrophotometric measurements or other measurements that use the data_type=scan keyword).
Two additional tables are provided below (Field Name Suffixes & Modifiers). The reusable naming conventions in those tables are used to create new field names without having to add dozens or hundreds of variations to the Table of Field Names and Units. For example, "_sd" (for standard deviation) appears in the table of suffixes and may be appended to any existing SeaBASS field name (e.g., "chl_sd" or "Rrs510_sd".) Similarly, field-specific names can be created ad infinitum using _bincount (i.e., number of averaged samples), and _quality. The table of modifiers allows extra information to be part of field names, typically to indicate versions of measurements that are either more specific or modified. For example, modifiers are used to denote size-fractionated measurements (see _#umfilt and _#umprefilt), specific excitation or emission wavelengths, or polarized measurements. Field names may be constructing by combing entries from multiple tables, with any applicable wavelength first, followed by "Modifiers", followed by a "Suffix".
Table of Contents
The HPLC field names are based on the SCOR (WG 78) abbreviations for each pigment as listed in:
S.W. Jeffrey, R.F.C. Mantoura, and S.W. Wright, Phytoplankton Pigments in Oceanography: Guidelines to Modern Methods, UNESCO Publishing, Paris, France, pp. 661 (1997).
The HPLC sums and ratios are described in Tables 4, 5, and 7 of:
S.B. Hooker and 15 co-authors, The Second SeaWiFS HPLC Analysis Round-Robin Experiment (SeaHARRE-2) , NASA Tech. Memo. 2005-212785, NASA Goddard Space Flight Center, Greenbelt, Maryland, pp. 112 (2005).
Usage note: Field name suffixes should be appended to the end of a field name, after any field name modifiers (such as wavelength, excitation, etc). Field name suffixes require the presence of the un-suffixed field name as a separate field entry within the same SeaBASS file (i.e., FCHECK will complain if your file contains chl_sd but not chl).
| Field Suffix | Units | Description |
|---|---|---|
| _bincount | none | The number of measurements (n) averaged into the reported value or bin in the column(s) that "_bincount" is attached to. This suffix allows (n) to be reported for individual data field. There is also a standalone field called "bincount" which may be used instead if only one bincount is needed to describe the contents of the data matrix. |
| _quality | none | An analyst-defined quality flag that is relevant to the base field name. A definition of the quality flags should be provided as metadata header comments and within accompanying documentation files. |
| _cv | unitless | Coefficient of Variation. Append "_cv" to the end of the field name it describes e.g., bb532_cv |
| _sd | same as base field's units | Standard Deviation. Append "_sd" to the end of the field name it describes e.g., chl_sd |
| _se | same as base field's units | Standard Error. Append "_se" to the end of the field name it describes, e.g., chl_se |
| _unc | same as base field's units | Uncertainty associated to the measurement. The method used to determine the uncertainty needs to be included in the metadata or comments. Please contact SeaBASS before using it. |
| _volts | Volts | Raw data in volts |
The following table provides special ways to modify field names, generally for specific cases where it is necessary to index on a second wavelength or to indicate special size filters. These modifiers go after the base name (and wavelength, if applicable) but before any suffix.
| Field Modifiers | Units | Description |
|---|---|---|
| _#ang | does not change base field's units | Collection angle. Append "_#ang" to the end of a field name to indicate the collection angle a measurment (such as VSF) was taken at, where "#" is the angle in degrees, expressed as a float or integer. (For example, if volume scattering function is measured at a collection angle of 124 degrees, the field name would be "vsf_124ang".) |
| _#cilo | does not change base field's units | Confidence interval, lower, where # is to be replaced with the percent the confidence interval was computed for. Append "_#cilo" to the end of the field name it describes to indicate the relative confidence interval at a given percentage, e.g., chl_95cilo |
| _#ciup | does not change base field's units | Confidence interval, upper, where # is to be replaced with the percent the confidence interval was computed for. Append "_#ciup" to the end of the field name it describes to indicate the relative confidence interval at a given percentage, e.g., chl_95ciup |
| _ex# | does not change base field's units | Excitation wavelength. Append "_ex#" to the end of a field name to indicate the wavelength of excitation the measurement was taken at, where "#" would be replaced by the float or integer represenation of wavelength in nm. May be used in combination with "_em#", as such: "cdmf_ex#_em#", where "_ex#" preceeds "_em#". |
| _em# | does not change base field's units | Emission wavelength. Append "_em###" to the end of a field name to indicate the wavelength of emission the measurement was taken at, where "###" would be replaced by the float or integer represenation of wavelength in nm. May be used in combination with "_ex###", as such: "cdmf_ex###_em###", where "_ex#" preceeds "_em#". |
| _#hr | does not change base field's units | Incubation time in hours. Used in NPP field name, for example:rate_13C_uptake_bottle_6h_5umfilt. |
| _#id | does not change base field's units |
_#id is used to provide user-defined field name variations associated with classification information. For example, it can be used for taxonomic groups or size classes. It must be used in conjunction with the metadata header "/id_fields_definitions" (and it is recommended to also add a human-readable list of ids as comments in the header). If "id" is used with two different base fields please number the sequentially and do not repeat the id numbers.
/id_fields_definitions=1id:nanoeukaryotes,2id:picoeukaryotes,3id:net_sample,4id:experiment_sample /fields=u_ph_1id,u_ph_2id,sample_3id,sample_4id...
Please contact SeaBASS administration to discuss use of this field before implementing it.
|
| _#umfilt | does not change base field's units |
Filter pore size in microns (i.e., measured particles are larger than # microns). e.g., ap_10umfilt
Use this suffix to report size fractionated measurements or measurements collected using atypical filter pore sizes. It is unnecessary to add this suffix for standard protocol filter pore sizes (e.g., plain "ap" is appropriate for whole water measurements, rather than "ap_0.7umfilt"). However, include all filter details in your documentation.
|
| _#umprefilt | does not change base field's units |
Filter pore size in microns that the measurement was pre-filtered through (i.e., measured particles are smaller than # microns). e.g., chl_200umprefilt
Use this suffix if needed for reporting size fractionated measurements or other cases where samples passed through a significant filter prior to the reported measurement. It is unnecessary to use this suffix if the measurement implicitly defines dissolved material, as long as standard protocol filter pore sizes were used (e.g., just write "ag", not "ag_0.2umprefilt"). However, include all filter details in your documentation.
|
| _#ppt | does not change base field's units | Parts per thousand. Append "_#ppt" to the end of a field name to indicate the solution's concentration that a measurement was taken in, where "#" is the concentration as a floating point number or integer. (For example, if absorbance is measured at 435.2 nm in a 35.3 ppt sodium-chloride solution, the field name would be "abs_nacl435.2_35.3ppt".) |
| _#size | does not change base field's units | Median bin diameter in microns. Used as a suffix for the field "PSD". |
| _#umsize | does not change base field's units | Median bin diameter in microns. Used as a suffix for the field "PSD_DNSD or PSD_DVSD". |
| _stokes1 | does not change base field's units | First Stokes parameter for characterizing polarization. |
| _stokes2 | does not change base field's units | Second Stokes parameter for characterizing polarization. |
| _stokes3 | does not change base field's units | Third Stokes parameter for characterizing polarization. |
| _stokes4 | does not change base field's units | Fourth Stokes parameter for characterizing polarization. |