December 16, 2020

The Wild World of Data Repositories

By Stefanie Butland. With Kara Woo, Daniella Lowenberg, Matt Jones, Carl Boettiger, Karthik Ram.

See below for speaker bios and resources including collaborative notes from the call.

There is no one-size-fits-all protocol for depositing your research data into a public repository in a way that maximizes its reuse and citation. We’ve assembled a panel that will help you understand the issues and opportunities for developing new tools and documentation.

This 1-hour event, moderated by Kara Woo, includes 5 speakers and 20 minutes for Q & A on:

Where and how to deposit data (or data + software!)
Challenges in data deposition for reuse
How to reuse data
Where are the gaps?

Speakers will cover nuances of general and domain-specific repositories (Dryad, the DataONE federation of repositories, Arctic Data Center), what curators look for, what to do when you want to deposit both data and software, designing tools to help researchers provide the right metadata to maximize reuse, making data reuse easier with R tools like piggyback, and their vision for new tools and documentation.

Index of video:

0:00 Welcome
4:50 Topic introduction from Kara Woo
7:37 Daniella Lowenberg
12:06 Matt Jones
18:08 Kara Woo
26:29 Carl Boettiger
33:45 Karthik Ram
41:32 Q & A

Speakers

Portrait of Kara Woo — Kara Woo

Kara Woo is a Principal Bioinformatics Engineer at Sage Bionetworks where she leads a team of developers building tools and infrastructure for open science. Kara is a member of the rOpenSci Code of Conduct committee. Kara on GitHub, Twitter, Website

Portrait of Daniella Lowenberg — Daniella Lowenberg

Daniella Lowenberg is the Product Manager at Dryad and Principal Investigator of Make Data Count within the California Digital Library at University of California. Daniella on GitHub, Twitter

Portrait of Matt Jones — Matt Jones

Matt Jones is Director of Informatics R&D at the National Center for Ecological Analysis and Synthesis (NCEAS), Principal Investigator of the NSF Arctic Data Center, and Director of DataONE at University of California Santa Barbara. Matt on GitHub, Twitter, Website

Portrait of Carl Boettiger — Carl Boettiger

Carl Boettiger is Assistant Professor in the Department of Environmental Science, Policy and Management at UC Berkeley, a Co-founder and strategic advisor of rOpenSci. Carl on GitHub, Twitter, Website

Portrait of Karthik Ram — Karthik Ram

Karthik Ram is a Senior Research Scientist with the Berkeley Institute for Data Science, Project Lead and Co-founder of rOpenSci, Editor for rOpenSci Software Peer Review. He has a PhD in Ecology and Evolution. Karthik on GitHub, Twitter, Website

Resources

Collaborative notes
The headache with data repositories, blog post by Sina Rüeger, with her perspectives on this community call and challenges in both using data repositories and storing data in repositories while working as a genomic data scientist
Discussion on GitHub, Read the thread that led to this Community Call
Data Repositories for everyday use, Carl Boettiger slides
Enabling culture change for meaningful data sharing, post by Karthik Ram with the COS culture change pyramid juxtaposed with current policies
Dryad API
Doing it Right. A Better Approach for Software & Data, announcement of Dryad integration with Zenodo
DataONE Skill Building Hub
Arctic Data Center Video Tutorials
ESIP Data Management Training Clearinghouse
rdryad package, interface with the Dryad data repository
rdataone package, R interface to the DataONE network of data repositories
EML package, Read and Write Ecological Metadata Language Files
datapack package, A Flexible Container to Transport and Manipulate Data and Associated Resources
Metajam package, R package to bring data and metadata into R (relying on the DataONE API)
DataPackageR package, Construct Reproducible Analytic Data Sets as R Packages
contentid package, R package for working with Content Identifiers
Content-based Identifiers for Iterative Forecasts - A Proposal, DataONE webinar by Carl Boettiger
General Repository Comparison chart, FAIRSHARING (from NIH workshop)
RDA Generalist Repository Comparison Chart
Data Repository Selection - Criteria That Matter
OpenAIRE Guidelines for Data Archives
Data Organization in Spreadsheets, Karl W. Broman & Kara H. Woo (2018) The American Statistician, 72:1, 2-10
The History and Future of Data Citation in Practice, Parsons MA, Duerr RE, Jones MB (2019) Data Science Journal, 18(1):52
A Realistic Guide to Making Data Available Alongside Code to Improve Reproducibility, arXiv preprint by Nicholas Tierney, Karthik Ram
Enforcing public data archiving policies in academic publishing. A study of ecology journals, Sholler D, Ram K, Boettiger C, Katz DS (2019) Big Data & Society.
The citation advantage of linking publications to research data, Colavizza G, Hrynaszkiewicz I, Staden I, Whitaker K, McGillivray B (2020) PLoS ONE 15(4), e0230416.

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