Bathymetry

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Page content (please note)


Please note, bathymetry data curation SOPs in PANGAEA with respect to FAIR data principles (https://doi.org/10.1038/sdata.2016.18) are currently revised within the scope of of the German Marine Research Alliance (DAM) Underway research data project (https://www.allianz-meeresforschung.de/). This page and the information provided here is adressed to PANGAEA users and data submitters. PANGAEA's Metaheader (https://wiki.pangaea.de/wiki/Metaheader) explicitly for bathymetry datasets and other data curation requirements are explained on this page. In addition, requirements for bathymetry data submission to PANGAEA are documented.
“Please note, that this page may still be revised in the future"



DAM Underway research data project background

The German Marine Research Alliance (DAM) is a combined effort to exploit the full potential of German research vessels as mobile measuring platforms and currently involves 19 institutions and research facilities in Germany. The Underway research data project is part of DAM core area data management and digitalization (https://www.allianz-meeresforschung.de/en/activities/data-management-and-digitisation/).

DAM data portal

All submitted bathymetry data (currently only raw data) are being semi-automatically processed at PANGAEA. Tracklines and coverage polygones (footprint) of all submitted bathymetry data are extracted from the data and added to the DAM data portal https://marine-data.org/.
If a CC BY 4.0 (or CC-ZERO) is provided and data are not under a moratorium period, also a raster image is being calculated and added to the DAM portal. Here, the data can be explored (and are linked to the DOI). These raster images are then also available through OGC Web Map services.

Standardized content of datasets

To make data findable (F) and due to PANGAEAs archiving SOPs, bathymetry datasets from multibeam echosounders will be separated into two datasets, if the water column information (e.g. wcd files from Kongsbergs MBES Systems) is simultaneously being recorded during data acquisition.
This is necessary due to data curation processes, consequently reducing the download volume if it is intended to download only bathymetry data (containing only the seafloor reflector information) from PANGAEA. The water column data are usually much larger than regular bathymetry files (e.g. .all). However, both datasets will be connected / linked to each other, making it easy to find the corresponding dataset).

Standardized language

To make data FAIR, “to speak” a common language is required. PANGAEA specifically uses for bathymetry data the Natural Environment Research Council's Data (NERC) Catalogue for describing data. https://www.bodc.ac.uk/resources/inventories/nerc_data_catalogue/ https://vocab.seadatanet.org/search


Standardized Metaheader

Standardized Authors

The Authorship of (national/German) datasets is currently revised with respect to the Guidelines for Safeguarding Good Research Practice of the German Research Foundation https://www.dfg.de/download/pdf/foerderung/rechtliche_rahmenbedingungen/gute_wissenschaftliche_praxis/kodex_gwp_en.pdf. (more information is provided as soon as possible.....)

Standardized Title

To ensure the reusability (R) and interoperability (I) of datasets, metadata of similar datasets such as bathymetry data gathered from similar research missions, research vessels or research platforms should follow a common template and a common vocabulary (Generally speaking; they should look alike!). This also includes the title. Therefore, the title of bathymetry data which are entrusted to PANGAEA shall follow a certain template “construction kit”. This “construction kit” was developed within the DAM efforts (Project Underway research data). It includes the feedback of several German scientists from different institutions, PANGAEA bathymetry data submitters & data management personal. Key elements of each dataset title are incorporated, such as data type, device, platform type, platform, cruise (& area). To guarantee and fulfil FAIR standards, PANGAEA is encouraging data submitters to follow this template (also covering none German research data).

Example:
Multibeam bathymetry raw data (EM 1002 echosounder entire dataset) of RV MARIA S. MERIAN during cruise MSM55
Multibeam bathymetry raw data (Kongsberg EM122 working area dataset) of RV METEOR during cruise M127, Fictional Bank canyon, North Atlantic Ocean

The “construction kit” - incorporating all feedback - is shown below.:

Construction kit:

select data type: select data level: (device according to L22 vocabulary "Alt label" (NERC*) select: of select platform type: platform name (capital letters): during cruise Cruise ID optional: IHO-IOC GEBCO undersea feature name) optional: IHO Sea Area (1953),
Multibeam bathymetry raw data entire dataset) " RV "
Sidescan sonar processed data transit dataset) " AUV "
Water column working area dataset) " ROV "
dataset compilation)* " "
*only for processed data " "

Further information about the entries can be found here:

(device according to L22 vocabulary "Alt label" (seadatanet) optional: IHO-IOC GEBCO undersea feature name) optional: IHO Sea Area (1953),
*http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=L22 https://www.gebco.net/data_and_products/undersea_feature_names/ https://epic.awi.de/id/eprint/29772/1/IHO1953a.pdf
https://www.marineregions.org

Examples:

Multibeam bathymetry raw data (Kongsberg EM 122 working area dataset) of RV SONNE during cruise SO250 Loyd Dill Seamount, South Pacific Ocean
Multibeam bathymetry raw data (Atlas Hydrosweep DS 3 echo sounder transit dataset) of RV SONNE during cruise SO250
Multibeam bathymetry raw data (R2Sonic SONIC 2024 entire dataset) of AUV ABYSS during cruise MSM50
Multibeam bathymetry processed data (Kongsberg EM 122 entire dataset) of RV METEOR during cruise M74
Multibeam bathymetry processed data (EM 120 echosounder dataset compilation) of RV METEOR & RV MARIA S. MERIAN during cruise M74 & MSM66 ,Sardino-Balearic Abyssal Plain ,Mediterranean Sea
Water column raw data (Kongsberg EM710 entire dataset) of RV MARIA S. MERIAN during cruise MSM66 ,South Pacific Ocean

Standardized Abstract

Intending to make data more FAIR, PANGAEA requires a compact Abstract for each dataset. For more information regarding abstracts, see https://wiki.pangaea.de/wiki/Abstract.
Please note that cruise summary reports or other reference are not to be cited in the abstract because abstracts are part of the data description. If other reference shall be linked, please inform the data editor. If you would like to provide other contact information related to this dataset (e.g. Email address), please inform the data editor. Please specify in the abstract whether sound velocity profiles are part of the raw dataset publication or not. Comparatively for processed data publications, please describe your processing steps.

Raw data (example)

Multibeam bathymetry raw data using the ship's own Kongsberg EM 122 multibeam echosounder was not continuously recorded during RV MARIA S. MERIAN cruise MSM97/2. Data were recorded on 3 days between 2020-12-16 and 2020-12-19 in the Norwegian Sea and data acquisition was almost continuously monitored during the survey. Previous to the survey, gaps in already existing database were identified using the General Bathymetric Chart of the Oceans (GEBCO 2020) Type Identifier (TID) grid. These gaps were used as a base to determine the course of the ship during the cruise. During data acquisition, sound velocity measurements using sound velocity profiles (SVP) derived from CTD casts was applied on the data for data calibration. Ancillary SVP raw data (.asvp files) and SVP from CTD-cast (.txt) are part of this dataset publication. Data are unprocessed and therefore may contain incorrect depth measurements without further processing. Data can be processed e.g. with the open source software package MB-System (Caress, D. W., and D. N. Chayes, MB-System: Mapping the Seafloor, http://www.mbari.org/products/research-software/mb-system/, 2017).
(FEEL FREE TO ADD MORE INFORMATION)

Processed data (example)

Swath sonar bathymetry data used for that dataset was recorded during RV METEOR cruise M127 using Kongsberg EM 122 multibeam echosounder. The cruise took place between 25.05.2016 and 28.06.2016 in the North Atlanic Ocean. To enhance MBES data accuracy, two sound velocity profile casts were conducted in the vicinity of the working area prior to the survey using sound velocity profiler AML Oceanographic. After processing, these data were directly imported into the MBES Acquisition software Kongsberg SIS Seafloor Information System. Raw data were being converted to MB-System format. Data were manually edited for false measurements. No further sound velocity profile were used during processing of this dataset. A raster was calculated and stored in GeoTIFF format with a 25m resolution (negative values).
(FEEL FREE TO ADD MORE INFORMATION)

Standardized usage of Reference

Typically, processed datasets, which are all based of the same raw dataset (also archived in PANGAEA), are submitted to PANGAEA. These datasets will be linked to each other as a Reference Currently, all bathymetry datasets already archived in PANGAEA are reviewed and checked for relations. If a relationship is found, a linkage between both datasets is being created and is shown as Related to. More information can be found here https://wiki.pangaea.de/wiki/Reference

Standardized Coverage

Coverage is an automatic entry into PANGAEA calculated from Events or PANGAEA GEOCODE (see below): https://wiki.pangaea.de/wiki/Metaheader. Please note, that Minimum Elevation und Maximum Elevation does not represent min / max depth values measured from MBES data contained in this dataset. It is rather in this case the reference height on earth from the instrument used for the measurements.
Note: Currently, the Coverage will be visible on PANGAEA website with points having an GoogleMaps image in the background (right upper corner). It does not show the actual coverage of the surveyed area. The visible points are, instead, representing the Events (see below).

Standardized usage of Events

Bathymetry datasets contain so called PANGAEA Events (https://wiki.pangaea.de/wiki/Event). The Event links to the scientific Campaign and Basis (platform) containing further additional information. Please note that, if you browse with your mouse cursor on Campaign or Basis, a field will pop up (do not click). In some datasets, it is possible to click on these fields and a link with detailed information will be provided.
Further information for Bathymetry related events is given below.

Underway event

(update of this section is in progress)

For bathymetry data from multbeam echosounders, a so called "Underway" Event is created on board of the research vessel. The "Underway" Event is named CruiseID_0_Underway-number(undefined, ) e.g. M127_0_Underway-1. The event shows the starting and end point (coordinates & datetime) of the first and last data record of the MBES device acquired during the cruise. Also, the Methods/device used to record the data is included for Event description. Please note, that PANGAEA specific vocabulary is used here. Providing further detailed information using standard common vocabulary such as the NERC catalogue (https://www.bodc.ac.uk/resources/inventories/nerc_data_catalogue/) is currently being prepared (more information is provided as soon as possible.....).
If available, an additional link to the Sensor description hosted on https://sensor.awi.de is provided.

If the dataset is compilation of many datasets (only possible for processed data), several "Underway" Events will be used.
Note, that the prefix of the Event name contains the official cruise ID (cruise label, e.g. https://www.pangaea.de/expeditions/bybasis/Meteor%20%281986%29), not the campaign name. The suffix number does not follow any specific rule, as this number is usually chronologically created on board, which is why the numbering can differ from cruise to cruise.

SVP event(s)

If SVP casts (sound velocity profile measurements using an external device, e.g. using an AML Oceanographic Plus X sound velocity probe) or CTD casts (sound velocity derived from CTD measurements) were performed during the cruise, the acquired data files (and used for import to the acquisition software, e.g. the Kongsberg Seafloor Information, SIS) will be stored in the same raw dataset. The corresponding event of the Event list of the cruise (e.g. https://www.pangaea.de/expeditions/events/M160) will be linked to these files. This Event will contain similar information as described above, e.g. coordinates, methods/devices, etc.. If SVP's are used for data post-processing (sound velocity correction), these data files can also be submitted to PANGAEA. If possible, these SVP can be linked to the corresponding Event.

Standardized usage of Parameter

Which PANGAEA parameter (https://wiki.pangaea.de/wiki/Parameter) for bathymetry datasets will be used & added to the data files, depend on whether raw or processed data are being submitted.

Raw data curation

Standard parameters for bathymetry raw data also include PANGAEA’s so called Geocodes (https://wiki.pangaea.de/wiki/Geocode). These are standard important parameters, which are mandatory to keep the data georeferenced. These metadata for each file will be automatically created while data curation process.

Name Short Name Unit Comment
Event label Event
Binary Object Binary
Binary Object (Media Type) Binary (Type)
Binary Object (File Size) Binary (Size) Bytes
File content Content
Data file recording duration Data record duration min
Data file recording distance Data record distance m
Ship speed Ship sp knots
Number of pings Pings
Start of data file recording, date/time File start date/time
Start of data file recording, latitude File start latitude
Start of data file recording, longitude File start longitude
Start of data file, heading Start heading
Start of data file, depth Start depth
Stop of data file recording, date/time File stop date/time
Stop of data file recording, latitude File stop latitude
Stop of data file recording, longitude File stop longitude
Stop of data file, heading Stop heading
Stop of data file, depth Stop depth
DATE/TIME Date/Time Geocode – copy of 'Start of data file recording, date/time'
LATITUDE Latitude Geocode – copy of 'Start of data file recording, latitude'
LONGITUDE Longitude Geocode – copy of 'Start of data file recording, longitude'
ELEVATION Elevation Geocode – copy of 'File start depth, change of sign'

(more information (and more additional parameters) is provided as soon as possible.....).

Processed data curation

Standard important parameters, which are mandatory to keep the data georeferenced and described, will partially be attached automatically in near future during the data curation process. Nevertheless, if you could provide a table template describing these parameters for each uploaded file, this would support the data curation process. Feel free to upload a bathymetry grid, backscatter and/or a sidescan image. In general, GeoTiff files are preferred. Please indicated whether depth values of the grid cells contain positive or negative values (this can be indicated in the file content description). .

Name Short Name Value/unit Comment
Event label Event - *automated entry
Binary Object Binary *this will in PANGAEA download URL, please add the file name here
Binary Object (Media Type) Binary (Type) - *automated entry
Binary Object (File Size) Binary (Size) - *automated entry
Raster cell size Raster cell size
File content Content
Vertical datum Vertical datum
Horizontal datum Horizontal datum
Longitude, westbound Longitude west
Longitude, eastbound Longitude east
Latitude, southbound Latitude south
Latitude, northbound Latitude north

(more information is provided as soon as possible.....)

Standardized usage of Comment

Bathymetry raw and processed data, which are acquired on scientific vessels, might contain erroneous depth values and/or data artifacts. These data shall never be used for navigational purposes involving safety at sea. For safety reasons, it is widely common to state this explicitly: The comment These data should not be used for navigational purposes will be automatically included as a comment on each bathymetry dataset in PANGAEA. Please also check the PANGAEA data policy for more information: https://wiki.pangaea.de/wiki/Data_policy (page currently under construction). Bathymetry data for official nautical chart production must explicitly fulfil the requirements of the International Hydrographic Organisation (IHO) https://iho.int/.

Licence

PANGAEA and DAM are encouraging data submitters to submit bathymetry data under CC-BY 4.0 License terms, which allows sharing (copying and redistributing the material in any medium or format) and adapting (remixing, transforming, and building upon the material) the data (https://creativecommons.org/licenses/by-nc/4.0/). In this way, PANGAEA / DAM can also make the data coverage (footprint) and the trackline visible with a direct link to PANGAEA at https://marine-data.de/ in the future. Note, within the DAM efforts, coverage (footprint) and trackline off all submitted bathymetry data will be made available to the community via OGC Web Map Services (WMS). Avoid licence CC-0 & CC-BY-SA, if possible.

Which CC license choose for data? Check also https://wiki.pangaea.de/wiki/License

(Standardized usage of Data model extensions) (for raw and processed data curation)

The usage of so-called data model extensions which are further attributes is currently developed. This is a new feature for PANGAEA in order to include more standardized metadata. This new feature shall insure further findabilty (F) and interoperability(I) of the datasets (more information is provided as soon as possible.....).


Example datasets

Raw data

Damaske, Daniel; Becker, Marius (2021): Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV MARIA S. MERIAN during cruise MSM97/2. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.927786

Processed data

https://doi.pangaea.de/10.1594/PANGAEA.912259 (Please note, this is a test dataset, dataset currently in review status, therefore not fully accessible, example is also out of date...please wait to a good example)

How to submit data bathymetry data to PANGAEA and what to do?

Please submit bathymetry data here https://www.pangaea.de/submit/. During submission, you may have to provide information for the data curation process (e.g. cruise, device, etc) (more information is provided as soon as possible; you may be asked to fill out a questionnaire during data curation). Please edit/modify the titel & abstract as stated above for the submission.

Raw data

Usually for raw data, an upload area will be created for you where you can drop your files (on request). Feel free to drop your data as zip- or individual files. Please also include sound velocity profiles (only SVP raw data, e.g. MSM88_2-1_0.asvp) for raw data submission if available. Your files should not exceed a volume of 10GB, however several files can be uploaded simultaneously.

Processed data

For processed data you can use this excel file to prepare your submission template. This will highly support the data curation process. If additional SVP have been used for data processing, you can also upload these files.

PANGAEA Data Submission Form Example

Workflow: Processing of an Underway Data Submission
Field Name Explanation Content Example
Title Adapted, generalized #Standardized_Title Multibeam bathymetry raw data (Kongsberg EM122 entire dataset) of RV SONNE during cruise SO250
Author(s) #Standardized_Authors [chief scientist], [responsible scientist]
Keywords (default)
Abstract/Describe your Data #Standardized_Abstract; if the processed or raw data were already archived, the links may be placed here The survey data contain MBES measurements of the Fictional Bank canyon. No bathymetric measurements of Fictional Bank canyon were found in international databases prior to the cruise.

To enhance MBES data accuracy, two sound velocity profile casts were conducted in the vicinity of the working area prior to the survey using sound velocity profiler AML Oceanographic SVP Plus X. After processing, these data were directly imported into the MBES acquisition software Kongsberg SIS Seafloor Information System.

License #Licence The license specifies how the record can be used and modified after publication and how it must be cited by re-users. The use of the license CC-BY 4.0 is strongly recommended by PANGAEA and DAM, ensuring the re-usability of the Underway Data and the credit for the author(s). CC-BY: Creative Commons Attribution 4.0 International (default)
Data used/published in the following article/manuscript If the data is/will be published in a manuscript, please enter the details here (default)
Projects and/or Awards/Grants The project in which the data has been obtained may be named here DAM: Underway Research Data
Upload Files containing metadata information for the raw data