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Submitting Marine Geophysical Data

NOAA National Centers for Environmental Information & the co-located IHO Data Center for Digital Bathymetry

This document describes current procedures to prepare various marine geophysical data sets (multibeam bathymetry, subbottom profile, water column sonar, singlebeam bathymetry, side-scan sonar and supplemental data) for submission to NOAA National Centers for Environmental Information (NCEI) & the co-located IHO Data Center for Digital Bathymetry (DCDB).

File Formats

General Information

The multibeam bathymetry database at NCEI/IHO DCDB primarily maintains raw (as collected) data files in the instrument’s vendor specific format (e.g., .all, .s7k, .xse). However, other supplemental data (sound speed profiles, tides, vessel offsets, cruise reports, etc.) and/or processed versions or products of the multibeam data are also accepted. In all submissions, the data files and cruise/survey should be well documented using metadata. 

MB Data File Formats

NCEI can accept bathymetric data from most of the commercial multibeam sonars and acquisition systems. The multibeam bathymetry data management pipeline at NCEI relies heavily on the MB-System, an open source software suite for processing and displaying seafloor mapping data. Data formats supported by the software are listed on their website. Data submitted in unsupported formats will still be accepted, but will not be discoverable through the web services provided at NCEI (Bathymetric Data Viewer). 

These data can only be accessed from the archive upon request to mb.info@noaa.gov. Processed data (if submitted) need to be delivered in an MB-System processed format or other non-proprietary format. The majority of processed data in the multibeam bathymetry database are processed MB-System, XYZ, or GSF format. If your data are not in one of the supported formats or you would like to contribute bathymetric data products, email mb.info@noaa.gov to discuss the options available at NCEI for your data.

General Information

The trackline geophysical database at NCEI primarily maintains raw (as collected) or processed data files in SEGY format. In all submissions, the data files and cruise/survey should be well documented using metadata.

Subbottom Data File Formats 

NCEI encourages data providers to provide data in SEGY format. Most commercial subbottom profilers can either collect in this format or convert from the proprietary format to community-friendly SEGY. The subbottom data management pipeline at NCEI relies heavily on SEGY to extract the navigation information necessary to generate tracklines that display the location of the data in the Trackline Geophysical Data Viewer. Data submitted in unsupported formats will still be accepted but will not be discoverable through the web services provided at NCEI. These data can only be accessed from the archive upon request to trackline.info@noaa.gov. If your data are not SEGY, please email to discuss the options available at NCEI for your data.

General Information

The water column sonar database at NCEI primarily maintains raw (as collected) data files in the instrument’s vendor specific format (e.g., .raw, .wcd). However, other supplemental data (sound speed profiles, tides, vessel offsets, biological data, cruise reports, etc.) are also accepted. NCEI has developed a data packaging tool that facilitates submitting water column sonar data and creation of accompanying metadata. If you are interested in using this tool or would like more information, please email wcd.info@noaa.gov. To enable discovery and access of the data through the Water Column Sonar Data Viewer, please ensure navigation datagrams are included in the water column data files (e.g., *.wcd).

WCSD Data File Formats

NCEI can accept files from most instruments capable of collecting water column sonar data. Currently supported instruments include Kongsberg EM series multibeam sonars (EM122, EM2040, EM302, EM3002, EM710), Reson SeaBat 7125, Simrad multibeam sonars (ME70, MS70), and Simrad single beam systems (EK500, EK60, ES60, EK80). It is preferable to have position data within the water column sonar data files. Files lacking position information may not be publicly accessible through NCEI data discovery portals. If your data are not in one of the supported formats, email wcd.info@noaa.gov to discuss the options available at NCEI for your data.

General Information

The NCEI singlebeam bathymetry database primarily contains processed singlebeam bathymetry observations. In all submissions, the data files and cruise/survey should be well documented using metadata. NCEI is able to ingest raw singlebeam data, but can only make it discoverable (via the Trackline Geophysical Data Viewer) if there is associated navigation. Navigation must either 

  1. Be provided in a separate folder under the singlebeam folder structure, or:
  2. If multibeam bathymetry was also collected during the cruise, the navigation from the multibeam database may be used. 

If no navigation is provided for raw singlebeam data, then the data will be archived, undiscoverable through NCEI data discovery portals, and only accessible upon request to trackline.info@noaa.gov.

Singlebeam Data File Formats

NCEI prefers singlebeam data to be in M77T format, as described in the documentation. Other acceptable formats for the data or navigation products include GeoJSON, GeoCSV, or ASCII 2CSV/Tab-Delimited (with format documentation). Please contact trackline.info@noaa.gov if you would like to discuss other data formats.

General Information

The side-scan sonar database at NCEI primarily maintains raw (as collected) and processed data files in JSF or HSX format. In all submissions, the data files and cruise/survey should be well documented using metadata. NCEI is able to ingest side-scan sonar data, but can only make it be made discoverable (via the Trackline Geophysical Data Viewer) if there is associated navigation. Navigation must either: 

  1. Be provided in a separate folder under the side-scan folder structure, or: 
  2. If multibeam bathymetry was also collected during the cruise, If the data was collected during a cruise that also contains multibeam data, the navigation from the multibeam database may be used.

If no navigation is provided for side-scan sonar data, then it will be archived, but undiscoverable and can only be accessed from the archive upon request to trackline.info@noaa.gov

Side-scan Sonar Data File Formats

NCEI expects side-scan sonar data files to be in JSF or HSX formats that are readable by MBSystems (format number 132, 133, 182, or 183). Acceptable supplementary navigation formats include GeoJSON, GeoCSV, ASCII CSV/Tab-Delimited (with format documentation). Please contact trackline.info@noaa.gov if you would like to discuss other data formats.

Metadata

Metadata are important documentation that provide a history of the data, as well insight into the means of long-term preservation. Please include any metadata that has been created for each cruise/dataset. NCEI uses and prefers ISO standard metadata, but accepts other standards. See the NCEI Metadata page for more information. If you are not familiar with metadata, Example ISO standard metadata records for dataset level (multibeam, singlebeam/subbottom, water column), collection/cruise level, and multibeam file level are available upon request. 

If cruise level metadata have not been created, the minimum requested metadata fields and examples are listed in the table below. Contact mb.info@noaa.gov for an Excel spreadsheet that can be used to easily populate this information for the data submission. File level metadata are also accepted if available, but not necessary. 

Processed data may include a separate metadata file or xml document which may be submitted in addition to the cruise-level spreadsheet. Please include any corrections that were applied, the nature and means by which the data were cleaned/edited, and any other corrections or conversions applied to the data. 

A DOI (digital object identifier) is a type of persistent identifier used to uniquely identify objects (in this case a particular survey or dataset). Metadata about the object is stored in association with the DOI name. For more information, see the Wikipedia page on DOIs.

Section 1: Mandatory Metadata Fields

Section 1: Mandatory Metadata Fields
Metadata Field Description of Metadata Field Example Value
SURVEY_ID Typically “ship ID, year, cruise number” PH1234
PLATFORM_NAME Name of Survey Vessel R/V Placeholder
PLATFORM_TYPE Ship, AUV, ASV, ROV etc. Ship
DATA_PROVIDER If more than one, use semi-colon to separate Example Cruise Inc.
INSTRUMENT Sonar Instrument used in data collection Reson 7125
MB_DATA_TYPE Raw, Processed, Survey Product, Composite Product, etc. If more than one, use semi-colon Raw; Processed
ASSOCIATED_DATA Ancillary or additional data types that were collected. If more than one, use semi-colon WCSD; SVP;CTD
DEPARTURE_PORT City, State for US ports. City, Country for International Ports San Juan, Puerto Rico
ARRIVAL_PORT City, State for US ports. City, Country for International Ports Charleston, South Carolina
START_DATE Date Only. DD-Mon-YYYY, acquisition start date 09-SEP-2013
END_DATE Date Only. DD-Mon-YYYY, acquisition end date 01-OCT-2013
PROJECT Specified project name or "Transit" Corals in the Florida Keys
PROPRIETARY Yes/No If "yes," provide the release date below yes
RELEASE_DATE Data embargo release date. Not applicable to public data 01-OCT-2015
REPORT Yes/No. Does a detailed report exist? If "no," information in section 3 should be populated. If "yes," list report name in comment field next to the value. yes
REPORT_PROVIDED Yes/No. Will the report be provided alongside the data? If "no," information in section 3 should be populated. yes

Section 2: Recommended Metadata

Metadata Field Description of Metadata Field Example Value
CHIEF_SCIENTIST Typically "None" for transits Jane Smith
CHIEF_SCI_ORG Affiliation of Chief Scientist A. University
MAPPING_LEAD Mapping coordinator or person responsible for mapping efforts John Doe
PLATFORM_OWNER Entity that owns the platform A. University
DATA_LICENSE If there is a license assigned to the data, provide the license type CCO-1.0
HORIZONTAL_DATUM If projected data, specify the projection and parameters NAD83/UTM zone 17N
HORIZONTAL_DATUM_UNITS_OF_MEASUREMENT   Meter
VERTCAL_DATUM Default in deep water is instantaneous sea level MLLW
VERTICAL_DATUM_UNITS_OF_MEASUREMENT   Meter
DOI If available
COMMENTS General comments regarding the cruise or dataset, if any  
OUTSIDE_LINK Web link to additional information regarding cruise, project, or funding http://www/

Section 3: Recommended Summary if No Data Report is Provided

Section 3: Recommended Summary if No Data Report is Provided
Metadata Field Description of Metadata Field Value
SYSTEM_CALIBRATION_SUMMARY Text summary of system alignment methods and procedures (e.g. patch test summary that describes how timing bias, pitch and yaw bias, roll bias, and offset values were determined). This information may also be provided in a data acquisition and processing report, if one exists. See descriptive Report
ACQUISITION_SUMMARY Text summary providing information about instruments, platforms, operations and other information related to data acquisition. How were these data collected? See descriptive Report
DATA_PROCESSOR Person or people responsible for processing the data. If more than one, use semi-colon. John Doe
DATA_PROCESSING_ORG Organization that processed the data. Example Cruise Inc.
PROCESSING_STEPS Text summary describing the processing performed on data, if any. Include information on vertical datum processing, if applicable. See descriptive Report
SOUND_VELOCITY_SENSOR Conductivity, temperature, pressure (depth) (CTD) profiler used to derive sound speed in the water column (AML Oceanographic MVP200 Moving Vessel Profiler (MVP)), and/or direct-read sound velocity measurement device (Teledyne Reson SVP-70). AML Oceanographic MVP200 Moving Vessel Profiler (MVP) for sound speed profiles and Teledyne Reson SVP-70 for surface sound speed
SOUND_VELOCITY_SAMPLING_FREQUENCY How often was sound speed in the water column estimated? Sound speed cast taken every 4 hours
POSITIONING_SENSOR Equipment used to collect position and trajectory data during survey. Applanix POS MV 320 Version 5
POSITIONING_METHOD Method of horizontal positioning of bathymetric data. Post Processed Kinematic (PPK)
ATTITUDE_SENSOR Sensor used to capture vessel attitude (roll, pitch, and heading). Applanix POS MV 320 Version 5
PURPOSE Text summary of the intentions for which the dataset was developed. Purpose includes objectives for creating the dataset and what the dataset is to support. See Descriptive Report
ABSTRACT Brief narrative summary of the resource contents. Abstract narrative should include information on general content and features; dataset application: GIS, CAD, image, database; geographic coverage: county/city name; time period of content: begin and end date or single date; and special data characteristics or limitations. This information may also be provided in a descriptive report, if one exists. See Descriptive Report

Data File Structure

The data may be delivered in one archived file (e.g., tar or zip) in a well-defined directory structure.
Please include an MD5 checksum with the delivery so NCEI can verify the integrity of the files and the completeness of the data transfer. For questions regarding MD5 checksums, contact mb.info@noaa.gov. A preferred data structure would be the following:
Sample data structure graphic.

CruisePack Data Packager Tool

NCEI CruisePack is an optional data packager tool that makes packaging cruise-based data for submission to NCEI quick and easy. This free, stand-alone tool can be easily used on most computers. It provides a simple user interface to facilitate entering metadata about the cruise and datasets and a way to specify the location of the data so that CruisePack can automatically organize the data into an accepted directory structure. Finally, it packages the data to a specified location (an external hard drive or another system) for transfer to NCEI. Using CruisePack can dramatically simplify the process of organizing data and ensure all required metadata are provided. If you are interested in using CruisePack or would like more information, please email mb.info@noaa.gov.

Data Submission Methods

Email mb.info@noaa.gov, wcd.info@noaa.gov, or trackline.info@noaa.gov, to alert a data manager of incoming data, set up your data submission, or ask any questions.

Data can be delivered to NCEI through one of the following processes:

  1. Shipping external hard drives
  2. Uploading to NCEI’s FTP server
  3. Data copy using rsync through a secure shell login (linux).

External hard drives containing a data submission can be shipped to the following address:

"Data Manager’s Name"
NOAA NCEI 325 Broadway E/NE42
Boulder, CO 80305

NCEI maintains a number of public FTP servers that allow anonymous ftp access (login: anonymous, password: email address). The servers share a single 1.0TB file system. If delivering large volumes of data (200GB), please notify a data manager prior to uploading the data.

The incoming FTP server (ftp://incoming.ngdc.noaa.gov/) allows external users to upload files. Files should be placed in the /pub/incoming/ directory. After 14 days, the files will be deleted. No external user can read files from this server. Directory listings have been disabled for the incoming FTP site.

There are multiple ways to access the incoming FTP server.

Using a Windows FTP client

Two common clients are FileZilla and WinSCP. Both are free and easy to use. For step-by-step instructions on FileZilla, see the section below.

  • Use the following FTP settings to connect:
  • Once connected, change the remote site directory to /pub/incoming
    • You will see notifications stating that the “Directory listing failed” or “550 Permission denied”. These are okay as long as you are in /pub/incoming
  • Create a directory with a name that uniquely identifies the source of your submission (e.g., your name, your institution’s name) in /pub/incoming
    • Open this new directory
  • Copy and paste (or drag and drop) your files to this directory

FileZilla step-by-step instructions

Enter incoming.ngdc.noaa.gov in the Host box and then click the Quickconnect button

Incoming Filezilla Screenshot
Incoming Filezilla Screenshot

The status will result in a red error (as seen below). This is normal.

Incoming Filezilla Screenshot error message
Incoming Filezilla Screenshot error message

Navigate to the location of data you would like to upload on the bottom left panel next to “Local site.”

Example of local site input page

Then type /pub/incoming in the space next to “Remote site” on the bottom right panel and hit enter to connect to the folder.

Pub/incoming screenshot
Pub/incoming screenshot

To create a new directory specific to your project, right-click the incoming folder, click Create directory, and enter the new directory name.

Screenshot Creating Directory
Screenshot Creating Directory

Finally, drag and drop your data from the left panel (local site) to the right panel (remote site) or right click the file and select "Upload."

Screenshot of Uploading process
Screenshot of Uploading process

Using a Linux FTP Client

  • Navigate to the directory containing your data submission
  • Typeftp incoming.ngdc.noaa.gov
  • Navigate to/pub/incoming
  • Create a directory with a name that uniquely identifies the source of your submission (e.g., your name, your institution’s name)
  • cd into the directory that you just created
  • Upload the data using the put or mput commands

When using FTP upload to submit your data, always email and let a data manager know the number of files uploaded and the total volume. This will allow the data manager to verify the data was successfully loaded to the FTP server and downloaded at NCEI.

Providing data through rsync via a secure shell login is reserved for recurring submissions from trusted providers. Email a data manager if you feel this method would be best for your data. The data manager and the IT security admin at NCEI will assess your request and determine if this method is allowable.