Bathymetry

Page content (please note)


Please note, bathymetry data curation SOP'S 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 data sets 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 are extracted from the data and added to the DAM data portal https://marine-data.org/. If CC BY 4.0. or 3.0 license is provided and data are not under a moratorium period, also raster data are being calculated and added to the DAM portal. Here, the data can be found (visualized) and are directly linked to the DOI. These data are then also available through OGC Web Map services.

Standardized content of data sets
To make data findable (F) and due to PANGAEAs archiving SOPs, a bathymetry datasets will be separated into two data sets, if the water column information (e.g. wcd files from Kongsbergs MBES Systems) is simultaneously being recorded during bathymetry 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 about 5x larger than regular bathymetry files. (However, datasets will be connected / linked to each other)

Standardized Authors
The Authorship of (national) 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 data sets, metadata of similar data sets such as bathymetry data mostly gathered during specific research missions from research vessels or other research platforms, should follow a common template and using common vocabulary. This is also including 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 is including the feedback of several German scientist from different institutions, PANGAEA bathymetry data submitters & data management personal. Key elements of each data set title are incorporated, such as data type, data level, device, platform type, platform, cruise (& area). PANGAEA is encouraging data submitters to follow this template in order make the data as FAIR as possible.

Example: 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: Further information about the entries can be found here:

Examples:

Standardized Abstract
A compact Abstract is required for data in PANGAEA, thus making the data more FAIR. For more information please open https://wiki.pangaea.de/wiki/Abstract. Please note, do not cite cruise summary reports in the abstract or other reference. Keep in mind, the abstract is part of the data description. If other reference shall be linked, rather inform the data editor. If you do want to provide other contact information related to this dataset (e.g. Email address), please inform the data editor. Please add to the description, whether sound velocity profiles are part of the raw data set publication or not. Comparatively for processed data publications, please describe your processing steps.

Raw data (example)
''Swath sonar bathymetry data using Kongsberg EM 122 multibeam echosounder was recorded during RV METEOR cruise M127 (WHAT, HOW). The cruise took place between 25.05.2016 and 28.06.2016 in the North Atlantic Ocean (WHEN). 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 (WHY). 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 (WHAT, WHEN & WHY). After processing, these data were directly imported into the MBES acquisition software Kongsberg SIS Seafloor Information System.''

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

Processed data (example)
''Swath sonar bathymetry data used for that dataset was recorded during RV METEOR cruise M127 using Kongsberg EM 122 multibeam echosounder (WHAT, HOW). The cruise took place between 25.05.2016 and 28.06.2016 in the North Atlanic Ocean (WHEN). 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 (WHAT, WHEN & WHY). After processing, these data were directly imported into the MBES Acquisition software Kongsberg SIS Seafloor Information System (WHEN & HOW). 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). ''

(more information is provided as soon as possible; feel free to provide more detailed processing information here, but keep it as compact as possible.....)

Standardized usage of Reference
Typically, processed data from one entire cruise are delivered to PANGAEA which are built on the “same” raw dataset also archived in PANGAEA. These datasets shall be linked as a Reference to each other. Currently, all bathymetry datasets already archived in PANGAEA are reviewed and checked. 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
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 from MBES data contained in this dataset. 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 points are representing the Events.

Standardized usage of Events
Bathymetry data sets 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 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 Underway data, 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 compiled (dataset compilation) of many dataset (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. In addition, the suffix number does not follow a specific rules, since this number is chronologically being created mostly already on bord, therefore 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 cast (sound velocity derived from CTD measurements) were made during the cruise, the data files which were acquired (and used for import to the acquisition software, e.g. the Kongsberg Seafloor Information, SIS) during the cruise will be stored within the same raw data set. 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-processsing (sound velocity correction), these data files can be also submitted to PANGAEA. If possible, these SVP can be also linked to the corresponding Event.

Standardized usage of Parameter
Which PANGAEA parameter (https://wiki.pangaea.de/wiki/Parameter) for bathymetry data sets will be used & added to the data files depend if raw or processed data are being submitted.

Raw data curation
Standard parameters for bathymetry raw data include also 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.

(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 be in automatically attached in near future while data curation process. However, if you could provide a table (e.g. Excel file) describing these parameters per uploaded file, this would support the data curation process. Feel free to upload a bathymetry grid, backscatter and/or sidescan image. In general, GeoTiff files are favoured. Please indicated whether depth values of the grid cells are positive or negative vale (this can be indicated in the file content description). .

(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 widly common to state this explicitly. Therefore 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 PANGAEA data policy https://wiki.pangaea.de/wiki/Data_policy (page currently under construction). Bathymetry data for official nautical chart production must explicitly fulfil requirements of the International Hydrographic Organisation (IHO) https://iho.int/. This comment is visible on PANGAEA data set page.

Licence
PANGAEA and DAM are encouraging data submitters that bathymetry data are submitted with CC-BY 4.0 License terms, which allows share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) the data (https://creativecommons.org/licenses/by-nc/4.0/) This allows also PANGAEA / DAM in future to make data coverage and the trackline visible at https://marine-data.de/ with a direct link to PANGAEA. Within the DAM efforts, coverage and trakline shall also be made available to the community via OGC Web Map Services (WMS). Avoid licence like CC-BY-ND-NC if possible.

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



Raw data
Bartholomä, Alexander; Holler, Peter; Wisshak, Max (2020): Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV MARIA S. MERIAN during cruise MSM55. Senckenberg am Meer, Wilhelmshaven, PANGAEA, https://doi.org/10.1594/PANGAEA.923421

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 oalso ut of date)

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

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.

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.