How to publish data in PANGAEA

23 August 2023

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Dr. Flavia Höring

Data management consultant for DAM research missions

Data curator at PANGAEA

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Today‘s info event

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PANGAEA - Organisation

Hosted by:

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Managed by:

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Team

PANGAEA - Clients

• Research projects

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• Institutions

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• Individual researcher

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PANGAEA - Content

Data sets: > 420 000

Measurements: ~ 25 billion

Projects: > 800

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New datasets per year: ~ 10,000

PANGAEA - Data types

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Focus on georeferenced observational and experimental data:

• Tabular data of e.g. environmental time series, biodiversity, sediment samples…

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• Binary files e.g. images, movies, netCDF files…

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DON’T SUBMIT:

• Model data
• Nucleotide sequence data (e.g. FASTA files)
• Software code

PANGAEA – Website�

https://pangaea.de/

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FAIR data publishing in PANGAEA�

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Full citation with DOI!

METADATA

FAIR data publishing in PANGAEA�

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METADATA

Open Access Licence

FAIR data publishing in PANGAEA�

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DATA

Benefits of FAIR data publication�

• Citation – appropriate attribution and credit
• Reusability – Data sharing and collaboration
• Reproducibility of findings
• Increasing the efficiency of research

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Looking for help? Check out the Wiki!

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Website: https://wiki.pangaea.de/

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Submission guidelines, templates and more

Data and metadata preparation

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Step 1: Prepare the data

• Preferred format for data tables is TAB-delimited text files (UTF-8 encoding) or Excel-format
• Position(s) (latitude/longitude in decimal degree) must be provided for every sample, observation and measurement carried out anywhere on earth
• Include a third dimension, e.g. water depth, altitude, depth in sediment …
• Date/Time must be provided in the ISO-format (e.g. 1954-12-07T13:34:11) as coordinated universal time (UTC)
• Parameters are always accompanied by a unit
• Event/station ID as first column
• Explain abbreviations
• Read guidelines at: https://wiki.pangaea.de/wiki/Data_submission

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Campaigns and events

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Already available campaigns and events: https://pangaea.de/expeditions/

Parameters

• Parameter names: Mix of relevant standard vocabularies (e.g. WoRMS, IUPAC) and community standards
• Complete parameter list: https://www.pangaea.de/lists/parameter/all-byname
• Check out similar datasets in PANGAEA database

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Most important: Full parameter name with unit!

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Data examples

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Date/Time and Depth are missing!

Unit is missing!

Abbreviation

not explained!

No unique event labels

Data examples

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From generic template for field observation data: https://wiki.pangaea.de/wiki/Best_practice_manuals_and_templates

Step 2: Prepare the metadata�

• Data authors (≠ paper authors): Contributors to collection and processing of data
• Titles and abstracts for each dataset (≠ paper, see https://wiki.pangaea.de/wiki/Abstract )
• (Preliminary) paper citation & other references
• Projects/awards
• Include separate metadata files/tables:
• Multiple abstracts/dataset titles
• Campaign info and Event table

(if not listed at https://pangaea.de/expeditions/)

• Parameter table (full names, units, PIs, methods, comments)

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Examples – Campaign & Event information

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Red parameters are mandatory!

From generic template for field observation data: https://wiki.pangaea.de/wiki/Best_practice_manuals_and_templates

Examples – Parameter information

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From generic template for field observation data: https://wiki.pangaea.de/wiki/Best_practice_manuals_and_templates

Please provide the primary instrument of measurement for each parameter.

• Syntax: Instrument type, Manufacturer, Model name [further infos]
• For more details, see https://wiki.pangaea.de/wiki/Method

Step 3: Data submission

• Data prepared
• Metadata prepared
• Ready for submission

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Processing time: up to several months

Access restriction/Moratorium up to two years can be requested

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Please submit your data as early as possible!

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Step 3: Data submission�

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Submission form –�Basic information

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• General dataset title
• Authors
• Keywords
• General abstract
• License

Submission form - References

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• Any references or manuscripts (in prep)
• Full reference, if available
• Please include the DOI!

Submission form – Projects and Grants

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• Add related projects/funding

Submission form – File upload

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• Data and metadata files
• Max. file size: 100MB
• Max. number of files: 20
• Please request an upload link for larger/more files

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For datasets of 100s of GBs or TBs, please contact us first!

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Submission form – Submit

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• Add comment
• Request moratorium
• Accept PANGAEA’s terms of use

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Submission done !

An issue was created in our ticket system.

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Step 4: Data curation – Processing steps�

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Dataset status

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Update of paper reference is possible

Automatic registration after 28 days

Access to the data may be restricted for up to 2 years!

Make your data citation count!

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Data availability statement:

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e.g. “All data are available in the public repository, PANGAEA, https://doi.org/

10.1594/PANGAEA.004444 (Höring et al., 2022).”

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Please always add the full citation of the data to the reference list of your paper!

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Only refer to persistent links!

Information on how to contact us�

• General inquiries: https://pangaea.de/contact/

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• Your submission: Comment via Ticket system (https://issues.pangaea.de/browse/PDI-XXXXX)

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• Questions about this event: Flavia Höring (Email: fhoering@marum.de)

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• Please fill in the feedback form for this event:

https://cloud.marum.de/apps/forms/s/8tjbnWSanSTz8zaYM2pYmm6S

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FAIR data publishing in PANGAEA�

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See https://www.openaire.eu/how-to-make-your-data-fair,

Wilkinson, et al., Scientific Data, 2016 http://doi.org/10.1038/sdata.2016.18

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Title/Abstract – Guidelines�

An individual abstract/title must be provided for each dataset!

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Title:

• Include information about the WHAT, WHERE & WHEN

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Abstract:

• Include information about the WHAT, WHERE, WHEN, WHY & HOW
• May contain necessary references
• For details, see https://wiki.pangaea.de/wiki/Abstract

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AVOID

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Copying the manuscript title/abstract

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Using abbreviations

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Interpreting results

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Licenses�

CC-BY: Creative Commons Attribution 4.0 International

• Data is freely available to everyone
• Usage requires to “cite”/”attribute” the original author(s)
• No further restrictions on usage

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CC-BY-SA: Creative Commons Attribution-ShareAlike 4.0 International

• Attribution required
• If data gets included into works (e.g., paper), the resulting work must be CC-BY-SA licensed, too

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CC0: Creative Commons Zero 1.0 Universal

• Public Domain
• No attribution required, but recommended according to Good Scientific Practice

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Step 4: Data curation - Flow�

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Web Portal – submission, search, review datasets

Ticket System – communication, documentation, organization

Editorial System – Curation, Editorial

PANGAEA Wiki – Help, SOPs

Tools

Make your data citation count!

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Data availability statement:

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“All data are available in the public repository, PANGAEA, https://doi.pangaea.de/

10.1594/PANGAEA.004444 .”

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(Meta-)Data Access & Reuse for Data Science

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• Various entry points to explore and re-use data (frontend, APIs, community specific portals…)
• Support of commonly used tools (e.g. Python and R)

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PANGAEA search:

• https://wiki.pangaea.de/wiki/PANGAEA_search

Python module ‘pangaeapy’:

• https://github.com/pangaea-data-publisher/pangaeapy

R package ‘pangaear’:

• https://docs.ropensci.org/pangaear/