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

Revision History

Revision History for Open-File Report 2007–1194

By Ellyn T. Montgomery, Marinna A. Martini, Frances L. Lightsom, Bradford Butman, Daniel J. Nowacki, and Steven E. Suttles

Posted online January 1, 2008

Version 1.1 revised and reposted online February 2009

Version 2.0 revised and reposted online June 1, 2016

The report was updated to reflect changes to the U.S. Geological Survey oceanographic time-series measurement database since the report was first published. Major updates include (1) descriptions of additional forms of data in the database and their processing, particularly data conforming to Climate and Forecast version 1.6 (CF-1.6) conventions and data in files produced at the U.S. Geological Survey Pacific Coastal and Marine Science Center,(2) additional descriptions of instruments and the processing of data from these instruments and 3) broadening the scope of the holdings to allow data from the other Coastal and Marine Geology Program centers to also be released.

Changes in version 2.0:

In the abstract, minor updates were made to the description of the report and the database.

“Conversion Factors,” “Supplemental Information,” and “Abbreviations” sections were added to the beginning of the report. These sections replace appendix 2. New sensor acronyms are included in “Abbreviations.”

In the “Introduction” section, science center names were updated, information about Digital Object Identifiers and citations was added, and the list of information included in the report was updated. References to individual scientists in the “Source of Data” subsection have been moved to the “Acknowledgments” section of the report.

The “Database Contents” section was updated to reflect the inclusion of new kinds of data files in the database. In the subsection “Spatial and Temporal Extent of the Database,” figure 3 was updated to show the locations of new experiments, and minor updates were made to the text. The subsection “Content Overview” was expanded to introduce Climate and Forecast (CF) standards and differentiate between them and Equatorial Pacific Information Collection (EPIC) standards for data models and metadata. In the “Data Quality” subsection, information was added appropriate to the inclusion of CF files in the database.

In the “Data Collection” section, minor changes were made to the introductory paragraphs. The “Tripods” subsection was renamed “Tripods and Quadpods.” The subsection “Other Sea-Floor Platforms” was added. The subsection “Instrumentation” was added; it includes links to instrument descriptions organized by measurement type. On the “Current Velocity Measurements” page, descriptions of the following instruments were added: Nortek Sentinel V, Nortek Aquadopp HR, Nortek Acoustic Wave and Current Profiler, Nortek Vector, and Sontek IQ flow monitor. The “Hydrographic Measurements” page was renamed “Water Quality Measurements,” and on this page “Nitrate Measurements” was added as a subsection. On the “Water Quality Measurements” page, descriptions of the following instruments were added: RBR Solo-T, YSI 6600 and EXO, and Satlantic ISUS. On the “Turbidity Measurements” page, information about WET Labs ECO sensors was added. On the “Pressure Measurements” page, the subsection “Pressure-Based Wave and Tide Measurements” was added, with information on the Sea-Bird Seagauge, RBR Dwave, and Onset HOBO water-level logger. On the “Images” page, the description of Imagenex sonars was expanded. The subsection “Atmospheric Measurements” was added as a new page; it includes descriptions of the Onset HOBO weather station and Down East buoy-mounted weather station.

In the “Data Processing” section (formerly “How Are the Data Processed”), the “File Naming Conventions” subsection was removed and the information in it merged with existing content in appendix 1. The “Network Common Data Form ( netCDF) Storage” subsection was moved to a separate section. “Burst and Wave Data” was added as a subsection of “Time and Orientation.” Instrument-specific processing descriptions were added for data from the following instruments: Sentinel V; Nortek Aquadopp, Aquadopp HR, and AWAC; Nortek Vector; SonTek Argonaut; YSI 6600 and EXO; Satlantic ISUS, WET Labs ECO sensor; Sea-Bird Seagauge; RBR Dwave; Onset HOBO wave logger; Down East buoy-mounted meteorology sensor; and Onset HOBO weather station. Minor updates were made to other subsections of “Data Processing.”

The “Data Validation” and “Data Management” sections were under “Data Processing, and have been promoted to the same level in Version 2. Minor updates were made to both pages to reflect the current workflow.

The “Database Access Via the Web” section was rewritten to provide instructions for using the revised database Web site. The “Software Necessary for Use of Information in the Database” and “Citing Use of This Database” subsections were removed from this section and are now separate sections. Most of the “Organization of the Experiment Pages” subsection was rewritten, including the deletion of table 7. Minor modifications were made to the links and navigation information in the “Finding Information in the Database” subsection.

The “Network Common Data Form ( netCDF) Storage Format” section is no longer a subsection of “Data Processing.” The “Global attributes”, “Variable Names” and “Conversion to Climate-Forecast (CF) Convention Compliance” subsections were split to their own pages for readability in the web version, and the subsection “Equatorial Pacific Information Collection (EPIC) Keywords” was deleted. Minor changes were made to the section name and to text within the section. Table 1 was moved to this section from the “Content Overview” subsection of “Database Contents,” and a new column was added to table 1. Tables 2, 3, 8, and 9 (version 2.0 numbering) were added, and minor changes were made to the titles, headnotes, and numbering of tables 4, 5, 6, and 7 (version 2.0 numbering).

“Software Necessary for Use of Files in the Database” is no longer a subsection of “Database Access.” Information about using MATLAB and Python to access netCDF data was modified.

“Citing Use of Data in This Database” is no longer a subsection of “Database Access.” Guidance for citing data from the database and associated reports was expanded.

The “Acknowledgments” section lists individuals previously listed in the “Source of Data” section.

In the “References Cited” list, the following publications were added: Armstrong and others (2015), Danforth (1990), Dickhudt and others (2015), Johnson (2011), and Sherwood (2014).

Appendix 1 was expanded to elaborate on the naming conventions used by the Woods Hole Coastal and Marine Science Center, including information formerly in the nonappendix “File Naming Conventions” subsection of “How Are the Data Processed.” An explanation of the naming conventions used by the Pacific Coastal and Marine Science Center was added. Figures showing nomenclature summaries of the centers’ naming conventions were added.

The content of Appendix 2 was moved to the front material- Conversion factors and Abbreviations. Appendices 3 and 4 were deleted as the information is served elsewhere.

Figures 5,6,17,20,25-27,29,30 were added to show new platforms, instruments. Figures 32-36 were added to show images of the new data server web pages. The former figure 14 was deleted. The former figure 1 is now an unnumbered cover image. Figure numbers were updated.

Version 3.0 revised and reposted online April 20, 2021

The report was updated to reflect changes to the U.S. Geological Survey (USGS) oceanographic time-series measurement data collection since the version 2.0 update. The purpose of this update is primarily to allow data in this collection to conform to the Climate and Forecast (CF) convention as a primary and sufficient method without requiring a companion Equatorial Pacific Information Collection (EPIC) data release as required in version 2.0. A method for reporting burst data using CF convention is also documented. Daniel J. Nowacki and Steven E. Suttles were added to the author byline of this report to reflect their contributions to the version 3.0 updates.

Changes in version 3.0:

Throughout the report, “NetCDF” was corrected to “netCDF.”

In “Source of Data,” specific references to the Woods Hole Coastal and Marine Science Center (WHCMSC) were replaced with references to the Coastal/Marine Hazards and Resources Program (CMHRP). A specific person is no longer named the database manager, and contact information was updated to include a general phone number and a complete postal address.

In “Database Contents,” a reference to the Coastal and Marine Geology Program was replaced with a reference to the CMHRP. A link to the home page of the data collection was added.

In “Content Overview,” text was changed to allow data releases to comply with either the CF convention or the EPIC convention, thereby removing the requirement that there always be an EPIC convention data release to the collection. Reference to the version of the CF standard was removed to allow evolution with the standard over time. CF time formatting was clarified. The final paragraph, which discussed data types not previously represented in CF, was removed and is covered in other report sections.

In “Data Quality,” a bullet was added stating that datasets conform to CF or EPIC conventions.

In “Instrumentation,” a disclaimer was added stating that instrumentation used to collect data evolves over time and that instrumentation listed should be considered representative and not comprehensive. No updates to instruments were made for version 3.0. In several of the instrument descriptions linked from this page, the URLs for accessing technical details from the manufacturer were updated. For the Down East buoy-mounted weather station, a broken link to technical specifications was removed.

In “Data Processing,” “WHCMSC” was changed to “CMHRP” to reflect program wide use of the data-processing methodology. In the second paragraph, the use of the number of samples and sampling interval to check time was clarified. In the third paragraph, the example of an exception to the creation of one data file per instrument per deployment was clarified, and a sentence that repeated information from the previous paragraph was deleted.

In “Time and Orientation,” the description of Network Common Data Form (netCDF) time was changed to follow CF conventions documentation. In the “Burst and Wave Data” subsection, a sentence describing time variables in EPIC burst data files was clarified. A description of how time and burst data variables are defined in the CF convention was added. Statements were deleted that referenced a visualization tool or the inability to represent burst and wave spectra data in the CF convention. In the “Instrument Orientation” subsection, names of specific instruments were replaced with general instrument types because specific instruments change over time.

In “Instrument Specific Processing,” a disclaimer was added stating that the processing descriptions shown represent instruments and workflows used until the release of version 2.0 (2016) and that new processing workflows are evolving with the goal of more consistency across the CMHRP. A link is provided to the Oceanographic Time-Series Data Collection overview page, which links to the latest processing code and workflow descriptions.

In “Data Management,” “dataset” was changed to “data collection” in the second paragraph. In the last paragraph, a reference to the Coastal and Marine Geology Program was removed, reference to the Oceanographic Model and Data Portal being under development was removed, “the environmental sensor map on the IOOS Data Portal” was added to the list of data aggregation sites, and links were added to the listed data portals and sites. The last sentence, regarding access through National Oceanic and Atmospheric Administration sites, was deleted.

In “Organization of Experiment Pages,” references to EPIC and CF data were changed to refer simply to data in the last of the bullet points. The final paragraph, which duplicated information from the “Data Management” section, was removed.

In “Network Common Data Format (netCDF) Storage,” text was added to allow for the use of CF naming conventions, to specify that recent files follow these conventions, and to state that the coordinate variables used as dimensions depend on the convention used. In tables 1 and 2, rows were added for the “sample” variable. In table 2, the content of time units was clarified, and the use of UDUNITS (unidata format) was recommended. In tables 2 and 3, references to version 1.6 of CF were removed.

In “Global Attributes,” the USGS program name “CMGP” was updated to “CMHRP.” The words “typical” and “typically” were added in several places to allow for situations where exact attribute usage may be different. Text was added near the beginning of the section to point users to CF conventions documentation for metadata and attributes, and to allow for new attributes as processing routines evolve. In table 6, references to CF version 1.6 were changed to refer to version 1.6 or later.

In the “Variable Names” subsection of “Network Common Data Format (netCDF) Storage,” a sentence was added to state that the CF standard name or another appropriate name is used if the EPIC key name is unavailable, and a link was added to the CF vocabulary at https://cfconventions.org/standard-names.html. In table 8, reference specifically to version 1.6 of CF was removed, the variable P_1ac was added, and the variable names T_21 and BP_915 were corrected.

In “Conversion to Climate-Forecast (CF) Convention Compliance,” the first paragraph was rewritten to reflect the evolution from requiring data compliance with the EPIC convention, to requiring compliance with the EPIC convention plus (optionally) the CF convention, to allowing compliance with CF convention only. Also described is the transition from using Matlab-based processing scripts to using python programs to generate CF-compliant files for most instruments. In table 9, references to version 1.6 of CF were removed; “or sample” was added to row 2, column 1; and rows 6 and 7 were removed. All text and bullets after table 9 were removed.

In “Necessary Software,” the third paragraph was reworded to include the program Panoply as an option for viewing CF netCDF files, and links to Panoply and ncBrowse were added. In the fourth paragraph, the USGS program name was updated from “CMGP” to “CMHRP.”

In “Acknowledgments,” the name change from “sediment transport instrumentation group” to “coastal and estuarine dynamics operations group” was noted. Individuals were added to the lists of contributors to the data collection and associated documentation as follows: Steve Suttles to the list of group leaders; Eric Marjsanik to the list of those assisting with instrumentation and data collection; Dan Nowacki to the list of those assisting with software, documentation, and data processing; and Kurt Rosenberger and David Thompson for reviewing the version 3.0 update to this report. Olivia De Meo performed leading role in getting version 3.0 documents through final review and publication.