Data Publishing Workflows: Strategies and Standards Sünje Dallmeier-Tiessen (CERN) for many collaborators at CERN and in 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

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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 www.plos.org

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 www.pangaea.de

Preserving and promoting data reuse www.pangaea.de

International sharing and curation of data ww.icgc.org

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 www.zenodo.org

How to find a data repository www.re3data.org

Example: A dedicated data journal Nature Scientific Data www.nature.com/sdata/

F1000 http://f1000research.com/

Connecting articles and data Tagged Genbank entry (genetic sequence) Slide provided by H. Koers, Elsevier. Article: doi: 10.1016/j.biortech.2010.03.063

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Publish (Citable) Software

More and more examples

Published Software Papers http://openresearchsoftware.metajnl.com/

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

  DOIs for datasets 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). 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  Dataset Yancheva et al (2007). Analyses on sediment of Lake Maar. PANGAEA. doi:10.1594/PANGAEA.587840 Slides by courtesy of Dr. Jan Brase, DataCite

ORCID id www.orcid.org

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 Decide which dataset should be preserved or which dataset might be of interest for others to study or reuse Are there issues which restrict the publishing process, e.g. confidentiality for patient data? Which data product? Do I have enough materials for a dedicated data article? Which journal or repository works for me? Prepare the documentation/metadata Publish and let the others know you did Cite the dataset in the resulting papers Track who used and cited your data

HEP High-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 reuse Two important new tools

Capturing the complexity: Analysis Preservation Framework

Open it up: CERN Open Data Portal

How to publish your data Decide which dataset should be preserved or which dataset might be of interest for others to study or reuse Are there issues which restrict the publishing process, e.g. confidentiality for patient data? Which data product? Do I have enough materials for a dedicated data article? Which journal or repository works for me? Prepare the documentation/metadata Publish and let the others know you did Cite the dataset in the resulting papers 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 Science Open Data & Code Open Access Open Source Open Access Open Data & Code Open Science We are here now Slide provided by Patricia Herterich