data publishing workflows: strategies and standards sünje dallmeier-tiessen (cern) for many...

Data Publishing Workflows:Strategies and Standards

Sünje Dallmeier-Tiessen (CERN)

for many collaborators at CERN andin the RDA-WDS Data Publishing Workflows Group

Outline• Policy pressure• Solutions across disciplines• Standards

• Persistent Identifier• Data Citation• Quality Assurance, Peer Review• Licensing

• Examples in High-Energy Physics (CERN)• INSPIRE• Analysis Preservation Framework• Open Data Portal

Research data is a first class citizen

Royal Society, 1665 and 2012

Towards Open Science

Open Source

Open Access

Open Data & Code

Open ScienceWe are here now

Slide provided by Patricia Herterich, CERN

Policy pressure: STFC example

https://www.stfc.ac.uk/Resources/pdf/STFC_Scientific_Data_Policy.pdf

Policy pressure: DOE example

DMPs should provide a plan for making all research data displayed in publications resulting from the proposed research open, machine-readable, and digitally accessible to the public at the time of publication.

…the underlying digital research data used to generate the displayed data should be made as accessible as possible to the public in accordance with the principles stated above. 

http://science.energy.gov/funding-opportunities/digital-data-management/

Expectations: PLOS Data Policy

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Concerns across disciplines

Datasets are…• Not shared or lost• Difficult to discover and access• Difficult to understand > context missing

Nature, 2009

How this challenge is addressed

Example: Dedicated Data Repositories

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Preserving and promoting data reuse

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International sharing and curation of data

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ICGC – Data Publication Timeline

Time limits for publication moratoriums:

All data shall become free of a publication moratorium when either the data is published by the ICGC member project or one year after a specified quantity of data (e.g. genome dataset from 100 tumors per project) has been released via the ICGC database or other public databases.

[…]

In all cases data shall be free of a publication moratorium two years after its initial release.

https://icgc.org/icgc/goals-structure-policies-guidelines/e3-publication-policy

Zenodo – Data Repository

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How to find a data repository

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Example: A dedicated data journal

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Connecting articles and data

Tagged Genbank entry(genetic sequence)

Slide provided by H. Koers, Elsevier. Article: doi: 10.1016/j.biortech.2010.03.063

Towards Open Science

Open Source

Open Access

Open Data & Code

Open ScienceWe are here now

Slide provided by Patricia Herterich

Publish (Citable) Software

More and more examples

Published Software Papers

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STANDARDS

Licensing• Enable others to reuse your data and software • Choose the licenses or public domain dedications

accordingly• As “open” as possible

Re-Use• There are measures to demand citations to track reuse

and the impact of your work• If you re-use, cite the dataset yourself

Digital Object Identifiers (DOI names) offer a solution

Mostly widely used identifier for scientific articles

Researchers, authors, publishers know how to use them

Put datasets on the same playing field as articles

DatasetYancheva et al (2007). Analyses on sediment of Lake Maar. PANGAEA.doi:10.1594/PANGAEA.587840

URLs are not persistent

(e.g. Wren JD: URL decay in MEDLINE- a 4-year follow-up study. Bioinformatics. 2008, Jun 1;24(11):1381-5).

DOIs for datasets

Slides by courtesy of Dr. Jan Brase, DataCite

ORCID id

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Force11- Data Citation Principles

Author, Publication Year, Dataset Title, Data Repository, Version, Unique Identifier

- should include a persistent method for identification that is machine actionable and globally unique

- should facilitate identification of, access to, and verification of the specific data that support a claim.  

www.force11.org

Data Citation in Practice

Quality assurance for data: peer review

Products

• Data records in data repositories

• Data journals• Data articles

Note: standalone vs. supporting materials

QA Workflows

• Standalone or integrated?

• Blind and invited peer review

• Open peer review• Citable review reports

How to publish your data

1. Decide which dataset should be preserved or which dataset might be of interest for others to study or reuse

2. Are there issues which restrict the publishing process, e.g. confidentiality for patient data?

3. Which data product? • Do I have enough materials for a dedicated data article? • Which journal or repository works for me?

4. Prepare the documentation/metadata

5. Publish and let the others know you did

6. Cite the dataset in the resulting papers

7. Track who used and cited your data

HEPHigh-Energy Physics

Research data in HEP

Research Data on INSPIRE: starting from the paper

The underlying datasets (HEPdata)

Data Citation (Tracking)

Referenced Data

arXiv: 1311.1113

Code snippets

Code snippets

… and who gets the credit for sharing data?

Kyle’s profile on INSPIRE

Using author IDs for attributing credit

Excerpt from publication list on

Excerpt from publication list on

Make data publications count - alongside your articles

Focusing on reproducibility and reuseTwo important new tools

Capturing the complexity: Analysis Preservation Framework

Open it up: CERN Open Data Portal

How to publish your data

1. Decide which dataset should be preserved or which dataset might be of interest for others to study or reuse

2. Are there issues which restrict the publishing process, e.g. confidentiality for patient data?

3. Which data product? • Do I have enough materials for a dedicated data article? • Which journal or repository works for me?

4. Prepare the documentation/metadata

5. Publish and let the others know you did

6. Cite the dataset in the resulting papers

7. Track who used and cited your data

Conclusions• Policy pressure nationally and globally: we need data

publishing solutions

• Considerable advancements in many disciplines

We learn from best practices

• HEP with commitment to data preservation and open data releases

• First tools are available to support data preservation and data publishing

Towards Open Science

Open Source

Open Access

Open Data & Code

Open ScienceWe are here now

Slide provided by Patricia Herterich