Bathymetry

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 explicitly for bathymetry datasets and other data curation requirements are explained on this page. In addition, data management at PANGAEA and requirements for bathymetry data submission to PANGAEA are documented.

This page is mainly made for bathymetry data from multibeam echosounder data (MBES), however can also be used for data from Satellite derived bathymetry (SDB) or Light Detection and Ranging (LIDAR) data.

'''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/).



PANGAEA Bathymetry Web Map services
All submitted bathymetry data (raw data & processed 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/ (direct link to the viewer https://marine-data.de/?site=viewer), if data have a CC BY 4.0 (or CC-ZERO) data licence. If data are not under a moratorium period, also a raster image is being calculated and added to the DAM portal. Here, the (meta-)data can be explored (and are linked to the DOI). These vector & raster data are then also available through OGC Web Map services. https://maps.awi.de/services/common/pangaea_bathymetry/wms (please note, this is not a webpage, you need e.g. a GIS to use this service).

Further information can be found here.

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 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 http://doi.org/10.1002/9783527679188.oth1.

Although it is not generally agreed on, usually the authorship is given to anyone who was significantly involved in data acquisition on board or postprocessing on land.

For German research vessels raw data (archived in PANGAEA), it is very common to include the responsible scientific team on board, including all scientist (including student assistants) who were involved in monitoring, detailed survey planning or performing the survey. This can also be considered as a genuine, identifiable contribution to the content of the research data, therefore fulfilling the requirements for authorships according the Guidelines for Safeguarding Good Research Practice. ... (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: Further information about the entries can be found here:

Examples:

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 must not be cited exclusively in the abstract because references are also included in the metaheader (references) of the dataset. However, to provide credit and cite e.g. raw data if processed data are submitted to PANGAEA, you might add to the abstract: "Raw data for this study were published by (Authors, YYYY)." (followed by the full citation of the dataset in the list of references). If 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 (further, see below and examples).

For processed data please decribe whether: For raw data please decribe whether:
 * depth measurements manually cleaned from errors during processing?
 * sound velocity profile correction applied during processing?
 * navigation correction applied during processing?
 * tide correction applied during processing?
 * horizontal datum, EPSG code from raster data in this publication are?
 * sound velocity profile correction applied during acquisition?
 * are ancillary sound velocity profiles part of this data publication?
 * which device recorded the data, which ship, which cruise?
 * why have the data beeing recorded?

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 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/, 2021).

(FEEL FREE TO ADD MORE INFORMATION)

Processed data (example)
Swath sonar bathymetry data used for that dataset was recorded during RV SURVEY during cruise S143 using Kongsberg EM 122 multibeam echosounder. The cruise took place between 2016-12-12 and 2011-12-23 in the North Atlanic Ocean. Data were recorded on 8 days between 2011-12-15 and 2011-12-23. The approximate average depth of the entire dataset is around 1500m.

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 converted to MB-System format. Data were manually edited for false measurements. No further artificial sound velocity profiles were used during further processing. The data were corrected for tidal changes using data provided by the OSU Tidal Prediction Software OTPS that is retrievable through MB-System. The vertical datum of the data is now matched to mean sea level (MSL). A raster was calculated and stored in GeoTIFF format with a 25m resolution (negative values). In addition, the full resolution of avilable ASCII data and used for grid calculation are also archived in this dataset.

(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 casts and 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. In general, please always try to describe your submitted SVPs as good as possible for scientific re-use (state the origin of data, whether data are extrapolated e.g. to 12000m, etc.). You can use the following template to support your submission.

Standardized usage of Parameter
Which PANGAEA 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. 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 Metadata are extracted using the open soruce 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/, 2021). .

Please note, if you do have ancillary data, such as operational logs created on board or detailed processing reports, please add those files to the submission.

Processed data curation
Standard important parameters extracted from raster data (and ASCII data), which are mandatory to keep the data georeferenced, will be attached automatically in near future during the data curation process. Currently for raster data (and ASCII data) the curation process would be supported, if you could provide a table template during your submission, describing these parameters for each uploaded file. If you have several raster (and/or ASCII data) files to submit, based on this template, you may also prepare your own excel sheet or csv to support the submission (see parameters below). Please note that ASCII however are not recommended for further reuse

Feel free to upload bathymetry data, backscatter and/or a sidescan data, in raster (and/or ACSII) format (+ .xyz point cloud data, see below). In general, for raster data GeoTiff files (*.tif) and the grid data format (*.grd) is always preferred, since these data are usually easy to reuse, having less projection issues using standard GIS software. Please indicated whether depth values of the grid cells (also for ASCII data) contain positive or negative values (e.g. elevation / this can be indicated in the file content description). In generell you can submit any projection of the raster image, however if you do so please always add an additional GeoTiff at best with the projection WGS 84 -- WGS84 - World Geodetic System 1984, EPSG:4326. Please make sure, if you provide a “bathymetry” raster data, that they contain depth information rather than just an georeferenced image with RGB values. To submit raster images with RGB values is also fine, however they do not represent an resuable data format. In that case, always provide an raster file with true depth information (same coverage). Most dataset in PANGAEA have negative values for depth (= elevation), so we recommend to convert your data accordingly.

If you want to upload xyz files (point cloud data) to PANGAEA, you are welcome to do so. However, please also upload an auxiliary gridded raster image for each individual xyz (point cloud data) data file. In general raster data are more user-friendly (e.g. by using GIS-systems), therefore raster images are of high value for scientist. Raster images are considered as a (FAIR) interoperable data format, highly supporting the resuabblity of data by scientists, especially from other scientific domains. Raster image and point cloud data (xyz) will be published using the same doi.

Parameters for raster data are listed below (these parameter do not apply for gsf or mb-system data files. Gsf or mb-system data files will get the same parameters as for raw data ):

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/. In addition the comment may give credit to personal how was involved in the data submission and not related to the data acquisition at all, therefore not part of the author list.

Licence
PANGAEA and DAM are encouraging data submitters to submit bathymetry data under [(https://creativecommons.org/licenses/by-nc/4.0/) 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. 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 here

(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.....).

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
Simkins, Lauren M; Greenwood, Sarah L; Munevar Garcia, Santiago; Eareckson, Elizabeth; Anderson, John B; Prothro, Lindsay O (2021): Multibeam bathymetry processed data (Kongsberg EM 122 working area dataset) of RVIB NATHANIEL B. PALMER during cruise NBP150-02. PANGAEA, https://doi.org/10.1594/PANGAEA.937597, In: Simkins, LM et al. (2021): Pennell Trough, Ross Sea bathymetry and glacial landforms. PANGAEA, https://doi.org/10.1594/PANGAEA.937602

How to submit 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 title & abstract as stated above for the submission. As stated above, for processed data use the template

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. Please avoid renaming of raw data files, even if they are imperfect. If raw data from RV Sonne, RV Maria S. Merian, RV Polarstern or RV Meteor are beeing submitted, please make a comment in your submission before you upload any multibeam echosounder raw data files (e.g. .all format).

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