Intern:Bathymetry

Page content (please note)


This page and the information provided here is addressed to PANGAEA curators and PANGAEA employees only. For PANGAEA user and data submitters please refer to https://wiki.pangaea.de/wiki/Bathymetry (external use only).

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 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) expliiatly for bathymetry data sets and other data curation requirements are explained on this page. In addition, the requirements for bathymetry data submission to PANGAEA is doumented here.

(Note, this page is currently under construction and will be updated continuously)...if you have questions, plesae contact Daniel Damaske https://www.marum.de/Daniel-Damaske.html

(Note, this page is currently under construction and will be updated continuously)

DAM Underway research data project background


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

Standardized content of data sets
To make data findable (F) and due to PANGAEA achieving 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
(more information is provided as soon as possible.....)

Standardized Title
see also https://spaces.awi.de/pages/viewpage.action?pageId=330337725

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 researh 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.

for 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.:

Constrution kit: Further information for the entries can be found here:

Examples:

Standardized Abstract
A compact Abstract is requried 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 curator.

If you do want to provide other contact information related to this dataset (e.g. Email adress), please inform the data curator.

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 Atlanic 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
Automatical entry in PANGAEA calulated from Events or PANGAEA Geocode (see below)

https://wiki.pangaea.de/wiki/Metaheader

Please note, that Minium Elevation und Maxium Elevation does not represent min / max depth values from MBES data contained in this dataset.

Note: Currently, the Coverage will be visable 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). Different information is included here.

Underway event
(update of this section is in progress)

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

Each campaign includes an so called "Underway" Event 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 aqquired during the cruise. This Event will be automatically be created during data curation.

Also, the Methods/device used to this dataset is included for Event decription. 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. The Event also 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), respectively. However, in addition occasionally you also click on these fields (a link is occasionally included here).

If the dataset is complied (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) 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 discribed above, e.g. coordinates,methods/devices, etc.. If SVP's are used for data post-proesssing (sound veleocity 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
Please note, that a script must be executed on AWI-Server to get the parameters (the script is currently under development). Please contact Daniel Damaske.

Raw data curation
The usage of PANGAEA parameter (https://wiki.pangaea.de/wiki/Parameter) for bathymetry data sets depend if raw or processed data are being submitted.

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.


 * DATE/TIME (Geocode – copy of Start of data file recording, date/time)
 * LONGITUDE (Geocode – copy of Start of data file recording, longitude)
 * LATITUDE (Geocode – copy of Start of data file recording, latitude)

In addition other parameters will be will be automatically attached while data curation process (see below).


 * Uniform resource locator/link to file (file download link)
 * file name (including file suffix, e.g. .all)
 * file format
 * file size (in kb)
 * file content
 * Data file recording duration
 * Data file recording distance
 * Ships speed (in knots)
 * Start of data file recording, date/time
 * Start of data file recording, longitude
 * Start of data file recording, latitude
 * Stop of data file recording, date/time
 * Stop of data file recording, longitude
 * Stop of data file recording, latitude

(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 automatically attached while data curation process.


 * Uniform resource locator/link to file
 * File name
 * File format
 * Raster cell size
 * File size
 * File content
 * Vertical datum
 * Horizontal datum
 * Longitude, westbound
 * Longitude, eastbound
 * Latitude, southbound
 * Latitude, northbound

(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 safty 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 visiable 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
https://doi.pangaea.de/10.1594/PANGAEA.918716 (Please note that the Abstract is currently still missing, dataset currently in review, therefore not fully accessible)

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)

(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 have may have to provide information during 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)

A upload folder will be genrated on request, here you can drop you files. Fell free to drop your data as zip- or individual files

Please also include sound velocity profiles (only SVP raw data) for raw data submission if available. If SVP have been used for data processing, you can also upload these files.

Please edit modify Titel & Abstract as stated above for the submission.

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Old content from external page
Old content from external page temporary stored here (deleted from external page)

Data from bathymetry may be archived in different versions of processing. All data are password protected by default unless free access of the author is officialy defined through the related ticket.

Processing

 * 1) Original raw data as produced by the swath sonar system in its proprietary format. A link to a software or a description for conversion to ASCII or standard format is recommended. doi:10.1594/PANGAEA.767553
 * 2) Different versions of processing steps.
 * 3) Processed and corrected but measured values in ASCII-format (latitude/longitude/depth i.e. XYZ) - use parameter Depth, bathymetric (2268). doi:10.1594/PANGAEA.418153
 * 4) Processed digital elevation model in ASCII-format (latitude/longitude/depth) - use parameter Depth, bathymetric, interpolated (102737). doi:10.1594/PANGAEA.832573
 * 5) Final map in pdf-format; optional also in original grafic (e.g. Illustrator) and/or GIS format. doi:10.1594/PANGAEA.805734, doi:10.1594/PANGAEA.805735

Metadata
A description (Metadata) must always accompany each data set:
 * Author(s)
 * Title
 * Year of publication
 * Institute as source
 * Method: type of sonar system
 * Description of processing steps and status and possible errors
 * Abstract (for final maps or in bathymetric data publications)

Workflow
workflow for bathymetry data archiving
 * on board data are stored in ships tape-drive
 * after cruise data are stored in land tape-drive (hs/datex); overview via http://ingest.awi.de/
 * SCRIPT to validate file structures
 * SCRIPT generates tar-archive
 * SCRIPT generates Pangaea import files
 * SCRIPT copies data to hs/usero/bathy (bathymetry) and hs/usero/para (parasound)
 * PI opens ticket at http://issues.pangaea.de/ with metadata
 * PI uploads import file to ticket
 * import to Pangaea by curator

Device description with formats at https://spaces.awi.de/
 * Bathymetrie - https://spaces.awi.de/confluence/display/PSdevices/Faecherecholot
 * Parasound - https://spaces.awi.de/confluence/display/PSdevices/Sedimentecholot

to be solved

 * Data authors do not care about the storage format
 * Data were not stored in tape-drive
 * Format problems while generating Pangaea import files

PANGAEA HS/bathy Folder Structure
The following folder structure shall be used for /bathy (only lower case letters alowed, only underscore sysmbol):


 * 1.) cruise/  (e.g. ps81/ or msm88_2/)


 * 2.) mbes/ or water_column/ or side_scan/


 * 3.) raw/ or processed/


 * 4.) em122/ or em712/ or ds3/ or ....


 * 4.) entire_dataset/ or transit_dataset/ or working_area_dataset/ or dataset_compilation/


 * 4.1) if working_area_dataset/ or dataset_compilation/ make subfolder with IHO-IOC GEBCO undersea feature name'' (e.g. Ascension_Fracture_Zone)