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USGS Coastal and Marine Geology Program

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

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Network Common Data Format (NetCDF) Storage

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) ( 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. We 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) ( EPIC was developed by the NOAA Pacific Marine Environmental Laboratory (PMEL) to analyze, manage, and display in situ oceanographic data. By employing EPIC-compliant NetCDF, 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 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 are typically four dimensional, where time, depth, latitude, and longitude are the dimensions (and coordinate variable names). Coordinate variables are those used to describe the dimensions of the measurement variables. The time dimension corresponds to the number of samples in the file. Sample measurement time (see Data Processing) is computed from coordinate variables named "time" and "time2". Depth may have one or more values (if a vertical current profile was measured at 14 heights above the bed by an ADCP, the depth dimension would have 14 values). Latitude and longitude have single values because our observations are from static platforms, but were defined as dimensions to preserve the option of employing drifting instruments that have time-varying position. Coordinate variables (time, time2, depth, lat, lon, freq, dir) 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-1.6 file dimensions and coordinate systems used in the database. Table 3 displays some of the variables present in the CF version that are not present in the EPIC version.

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

Variable name Contents (units)Used as dimension?
timeTime (true Julian day) Yes
time2Time (milliseconds since 00:00 GMT) No
depthZ: measurement depth (meters) (may be scalar or vector): convention is positive down in EPIC, so 10 meters below the surface is represented as 10.Yes
latY: latitude (decimal degrees)Yes
lonX: longitude (decimal degrees)Yes

Table 2: Climate and Forecast version 1.6 (CF-1.6) coordinate variables.

Variable name Contents (units) Used as dimension?
timeTime (seconds since 1970-01-01T00:00:00Z)Yes
zAltitude bins (meters): convention is positive up, so 10 meters below the surface is represented as -10.Yes (if profile)
latitudeY: (decimal degrees north)No
longitudeX: (decimal degrees east)No

Table 3: Other Climate and Forecast version 1.6 (CF-1.6) variables not in Equatorial Pacific Information Collection (EPIC).
[IOOS, Integrated Ocean Observing system; ID, identifier]

Variable name Description Used as dimension?
Feature_type instanceUnique string defining the fileNo
crsCoordinate reference systemNo
platformLink to IOOS station IDNo
sensor depthDepth of sensor (if profile)No


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.

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Page Last Modified: Wednesday, 06-Dec-2017 13:16:59 EST