Intern: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 DAM Underway research data project. Current bathymetry data archiving concepts for PANGAEA (also with respect to further simultaneous visualisation of data and/or metadata for the DAM portal) are evaluated (Daniel Damaske, MARUM). Sustainable and scalable solutions / workflows - meaning covering all submitted bathymetry data to PANGAEA (regardless of origin, raw or processed data) - are developed. This page is currently under constrution and will be continuously updated, however main findings and guidelines shall be documented here. 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).

PANGAEA's Metaheader (https://wiki.pangaea.de/wiki/Metaheader) expliiatly for bathymetry data sets and other data curation requirements are explained on this page.

DAM Underway research data project background
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Standardized content of data sets
To make data findable (F) bathymetry data sets 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 10x larger than regular bathymetry files.

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 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 (more information is provided as soon as possible. The latest “construction kit” - incorporating all feedback - will be presented to the community very soon.....).:

Standardized Abstract
text text text https://wiki.pangaea.de/wiki/Abstract

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. More information can be found here https://wiki.pangaea.de/wiki/Reference

Standardized Coverage
text text text Automatical entry in PANGAEA calulated from Events or PANGAEA Geocode (see below) https://wiki.pangaea.de/wiki/Metaheader

Standardized usage of Events
Bathymetry data sets contain so called PANGAEA Events (https://wiki.pangaea.de/wiki/Event). Different information is included here. Each campaign included an so called "underway" Event

The "underway" Event is named CruiseID_underway-number(undefined) e.g. M127_underway-1. The event shows the starting and end point (coordinates & datetime) of the first and last data record which is contained in the dataset. 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.

Standardized usage of Parameter (for 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), which are latitude, longitude & datetime. In addition, file format, file size and file content are standard important parameters, which are mandatory to keep the data georeferenced and described.

These metadata will be automatically attached while data curation process.

Other parameters will also be automatically be created and added (more information is provided as soon as possible.....).

Standardized usage of Parameter (for processed data curation)
text text text

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 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.

(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.....).

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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

TEST AREA
Constrution kit: -