Documentation of the U.S. Geological Survey Oceanographic Time-Series Measurement Database

The data-storage format employed for this database is Unidata's netCDF. netCDF is a general, self-documenting, machine-transportable data format created and supported by University Center for Atmospheric Research (UCAR) (https://www.unidata.ucar.edu/software/ netCDF/). netCDF was chosen because it is widely used in the climate modeling community, is independent of hardware platform and operating system, and has a variety of helper applications already developed for data access and visualization. netCDF files are typically made up of variables that contain measurements or computed values and attributes that describe the contents of the file or variables. Historical netCDF files employ attribute and variable names from one of the few oceanographic data specifications available in the 1980s, which is called EPIC (Equatorial Pacific Information Collection) (https://www.pmel.noaa.gov/epic/). EPIC was developed by the NOAA Pacific Marine Environmental Laboratory (PMEL) to analyze, manage, and display in situ oceanographic data. Newer files employ the Climate and Forecast (CF) conventions. By employing EPIC- and CF-compliant netCDF files, this database may be used by researchers from different organizations without having to translate "foreign" data types into the local vernacular. Using a known vocabulary also enhances the discovery of these data by other computers and incorporation in larger data-aggregation sites. One of the advantages of employing netCDF format is that the metadata are stored with the data.

A typical netCDF file in this database (.cdf and .nc suffixes) will have global attributes that describe what, where, when and how the data were collected. Global attributes apply to all the variables in the file, while each variable will have attributes that apply to the contents of that specific variable. The mooring number, data start date and time, data end date and time, position, instrument type, and sample rate are all metadata fields stored in the global attributes.

Most importantly, the netCDF files contain data (the actual measurements) in the variables. The variable name follows EPIC or CF conventions and describes the data it contains. A fill value is used in data variables to indicate where data were unrecoverable or missing; in most cases it is set to “1e35.” Attributes associated with each variable describe the units (for example, degrees Celsius, centimeters per second), sensor height on the tripod, data maxima and minima, and the sensor model and serial number that go with the data.

The files in the USGS database of oceanographic time-series measurements will have different dimensions depending on whether the file uses CF or EPIC conventions. Coordinate variables define the dimensions and may never have a "_FillValue" attribute, because they cannot have gaps. Table 1 lists the EPIC coordinate variable names and whether used as a dimension. Table 2 describes the CF file dimensions and coordinate systems used in the database. Table 3 displays some of the variables in the CF version that are not present in EPIC.

Table 1: Equatorial Pacific Information Collection (EPIC) coordinate variables.
[GMT, Greenwich mean time]

Table 2: Climate and Forecast (CF) coordinate variables.

Table 3: Other Climate and Forecast (CF) variables not in Equatorial Pacific Information Collection (EPIC).
[IOOS, Integrated Ocean Observing system; ID, identifier]

The details of the file elements documented are for EPIC convention. The variable names and most of the file structure are retained in the CF version, so the description applies to both forms of data. The differences between the two representations of the data are discussed in the Content Overview section