FAIR data in a generic data repository presented by Lars Holm Nielsen during the OpenAIRE workshop Services to support FAIR data, Vienna: https://www.openaire.eu/openaire-workshop-making-services-fair-vienna-april-24th-2019

1. 1Linking Open Science in Austria, Vienna, April 24, 2019
This work is licensed under Creative Commons Attribution 4.0 International, except where noted on the specific slide.
Lars Holm Nielsen
CERN, IT Department
FAIR data in a generic data repository

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Credit: Dave Hill, CC-BY-NC-SA 2.0 Generic. https://www.flickr.com/photos/dmh650/4031607067/in/gallery-wlef70-72157633022909105/

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Credit: By Brian Herzog / licensed under Creative Commons Attribution-NonCommercial-ShareAlike 2.0 — https://www.flickr.com/photos/herzogbr/6756173595/in/gallery-wlef70-72157633022909105/

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Credit: By Bryan Tong Minh / CC-BY-2.5 (http://commons.wikimedia.org/wiki/File:Brand_bouwkunde_-_TU_Delft_-_13_Mei_2008.jpg)

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Don’t do it yourself!

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Plan
Collect
AnalysePublish
Re-use
Research data lifecycle
Archived data
Active
data

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Funded by

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Behind Zenodo
CERN Data Centre
- ~300PB disk
- ~400PB tape
- ~110k CPUs
Services
- Digital repositories
- Data preservation
for High-Energy
Physics.

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Zenodo
Upload Describe Publish

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How can
a generic data repository
provide services
for FAIR data?

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Case study: Taxonomic treatments
Enghoff H. 2018. A mountain of millipedes VII: The genus Eviulisoma Silvestri, 1910, in the Udzungwa Mountains, Tanzania, and related species from other Eastern Arc Mountains. With notes on
Eoseviulisoma Brolemann, 1920, and Suohelisoma Hoffman, 1963 (Diplopoda, Polydesmida, Paradoxosomatidae). European Journal of Taxonomy 445: 1–90. https://doi.org/10.5852/ejt.2018.445
Describe the discovery of new biological species
Example:
Journal article describing 22 new millipedes,
published in European Journal of Taxonomy

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Treatments: Data in disguise

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Treatments: Material
Enghoff H. 2018. A mountain of millipedes VII: The genus Eviulisoma Silvestri, 1910, in the Udzungwa Mountains, Tanzania, and related species from other Eastern Arc Mountains. With notes on
Eoseviulisoma Brolemann, 1920, and Suohelisoma Hoffman, 1963 (Diplopoda, Polydesmida, Paradoxosomatidae). European Journal of Taxonomy 445: 1–90. https://doi.org/10.5852/ejt.2018.445
Collection code
Geographic coordinates Date collected Collector

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Treatments: Figures

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Treatments: Relations
Article
Treatment
Material
Figure
Author

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Locked up data
Unanswerable questions:
•How many species have been described by my collection?
•Give me a list of all new species?
•Retrieve all images for a given taxon?
•What’s know about a geographic region?
•Treatments:
•Past 260 years: ~10+ millions published
•Every year: ~17k new / ~130k augmented

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Unlocking FAIR treatments?

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Overview of process
PDF Text and data mining
Article
Treatment
Material
Figure

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Example

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Key features provided
•Persistent identifier management and registration
•Widely adopted metadata schemas (DataCite, JSON-LD, …)
•Indexing and registration in searchable resources
Findable Accessible

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Digital Object Identifier
Credit: Screenshot of article (free to read) Copyright 2011 Federation of European Microbiological Societies.
Credit: Reference list from https://doi.org/10.1371/journal.pntd.0003884

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Digital Object Identifier
Credit: Screenshot of https://www.ncbi.nlm.nih.gov/pubmed/22098502 obtained on 2017-05-21

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Digital Object Identifier
http://doi.org/10.5281/zenodo.1100973
https://zenodo.org/record/1100973
Resolvable

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Digital Object Identifier
http://doi.org/10.5281/zenodo.1100973
https://zenodo.org/record/1100973
Persistent

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Digital Object Identifier
http://doi.org/10.5281/zenodo.1100973
Globally unique

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Digital Object Identifier
Metadata

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Indexing and reuse

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Key challenge
Material-level vs. treatment-level:
Geospatial / Temporal
Generic vs domain-specific

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Key challenge (solution)
•Map metadata to DataCite with detail loss.
•Simplified custom metadata (searchable):
•Key-value pairs based on vocabulary (JSON-LD)
• http://rs.tdwg.org/dwc/terms/collectionCode
•Domain-specific metadata files (not searchable)
•DarwinCore XML

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How can
a generic data repository
provide services
for FAIR data?

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Zenodo for FAIR data
• Stable home
• Key for Findable & Accessible data
• Metadata (both generic and domain specific)
•Key for Interoperable & Reusable data

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It takes an ecosystem
ORCID, ZooBank, Publishers, ….

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FAIR data in action!
It takes an ecosystem of independent services
Data repositories provide a stable home
Thank you! zenodo.org