Data format

Three data formats are currently available. They can be easily read in Ocean Data View, or using your favorite data processing software (e.g. Python, Matlab, IDL). Matlab tools and python tools to read and manipulate files in netCDF format are also available publicly. For a thourough scientific use of the data, or for oceanographic data centers, it is advised to use the first format (marine mammal netCDF format) as it is the reference format. However, for quick investigation of the dataset, it is easier to use the second format (ODV). The third format (STD_ODV) is similar the the second, but interpolated on standard depth levels, making it the simplest to manipulate.

Hydrographic data obtained with instrumented elephant seals are provided in a netCDF format following recommandations of the ``Marine-mammals NetCDF formats and conventions'' Version 1.0 [PDF] which is derived from the Argo netCDF User's manual. 

The Argo netCDF format is a standard used to store Argo float data on Argo data servers, and thus it is well adapted to record hydrographic profile data. Because marine mammals behave very much like Argo floats from the point of view of data sampling, this format is particularly well adapted to the storage of marine mammal hydrographic data.

A single file is available for each single CTD-SRDL dataset (i.e. one tag deployment on one animal). The file name uses the SMRU naming convention (giving a deployment code, a tag identifier, and the year), with the suffix “”. Global attributes of the netCDF files provide important metadata:

  1. pi_name = name of the principal investigator
  2. species
  3. platform_code = Unique identifier number for the tag dataset
  4. wmo_platform_code = WMO number when available
  5. smru_platform_code = SMRU name (used in the file name)
  6. deployment_code = SMRU deployment code
  7. distribution_statement = "Follow MEOP data policy standards, cf. Data available free of charge. User assumes all risk for use of data. User must display citation in any publication or product using data. User must contact PI prior to any commercial use of data"
  8. citation = "The marine mammal data were collected and made freely available by the International MEOP Consortium and the national programs that contribute to it (" ;
  9. positioning_system = {“argos”,“gps”}
  10. number_of_ts_profiles = 329
  11. number_of_t_profiles = 335

The data file contains the raw and adjusted pressure, temperature, and salinity data with their associated quality flags. Adjustment equations are also stored with the corresponding coefficients. Here is a list of the most relevant variables:

  1. PI_NAME: Name of the principal investigator
  2. STATION_PARAMETERS: List of available parameters
  3. PLATFORM_NUMBER: Generic unique identifier (same as platform_code)
  4. CYCLE_NUMBER: profile index, integer ranging from 1 (first dive) to N (last dive).
  5. JULD_LOCATION: Julian day of the location relative to the 01/01/1950.
  6. LATITUDE: Latitude of the station, best estimate
  7. LONGITUDE: Longitude of the station, best estimate
  8. PRES: Sea pressure in dbar
  9. PRES_ADJUSTED: Adjusted sea pressure (in practice, pressure was not adjusted, so PRES=PRES_ADJUSTED)
  10. PRES_ADJUSTED_QC: Quality flag (1 = good data).
  11. TEMP: In-situ temperature (in degC)
  12. TEMP_ADJUSTED: Adjusted in-situ temperature (in degC)
  13. TEMP_ADJUSTED_QC: Quality flag (1 = good data).
  14. TEMP_ADJUSTED_ERROR: Rough estimate of accuracy (single value per deployment).
  15. PSAL: Practical salinity (in psu)
  16. PSAL_ADJUSTED: Adjusted practical salinity (in psu)
  17. PSAL_ADJUSTED_QC: Quality flag (1 = good data).
  18. PSAL_ADJUSTED_ERROR: Rough estimate of uncertainty (single value per deployment)
  19. SCIENTIFIC_CALIB_EQUATION: Calibration equations used to adjust data
  20. SCIENTIFIC_CALIB_COEFFICIENT: Calibration coefficients

Matlab tools and Python tools are available publicly to read and manipulate files with the netCDF format. Note also that this format can be easily read by the software Ocean Data View (using the Import/Argo formats/Float Profiles menu).

  • Second format: ODV spreadsheet (csv-like format)

While files in Argo netCDF format are meant to be the reference data files, data are also provided in Ocean Data View (ODV) spreadsheet format. Ocean Data View is a cross-platform software designed to manipulate and visualize ocean data. The ODV spreadsheet format is an ASCII format, which means that any text editor can read it. 

Contrary to the Argo netCDF files, ODV spreadsheet files contains only adjusted values that have been flagged as good. Also, the amount of metadata in the ODV spreadsheet files is kept to a minimum, i.e., SMRU name, Julian date, location, and pressure/temperature/salinity data.

  • Third format: ODV_STD spreadsheet (csv-like format)

This format is similar to the ODV spreadsheet format, except that data were interpolated on standard depth levels, making it easier to handle. The standard levels are taken from the World Ocean Database (WOD13) standard, i.e. every 5 m until 100 m, every 25 m until 500 m, and every 50 m below.

Again, contrary to the Argo netCDF files, ODV spreadsheet files contains only the adjusted values that have been flagged as good. Also, the amount of metadata in the ODV spreadsheet files is kept to a minimum, i.e., SMRU name, Julian date, location, and CTD data.

  • Complemtary file: METADATA text file

This file compiles the names and values of metadata in a simple text file. The metadata found in this file consists of the list of global attributes and their values in the corresponding netCDF file. © MEOP consortium 2015