We hope you will join us for our next Generalist Repository Ecosystem Initiative (GREI) event, the Virtual GREI workshop on January 24 & 25.

Virtual Generalist Repository Ecosystem Initiative (GREI) Workshop

Tuesday, January 24 11am-4pm ET & Wednesday January 25 11am-3:30pm ET Registration and agenda at: https://datascience.nih.gov/news/grei-workshop-january-24-25-2023

This 2-day virtual workshop is presented by the seven generalist repositories participating in the Generalist Repository Ecosystem Initiative (GREI), sponsored by the NIH Office of Data Science Strategy.

The GREI workshop will focus on GREI's vision of developing collaborative approaches for data management and sharing through inclusion of the generalist repositories in the NIH data ecosystem, and to better enable search and discovery of NIH-funded data in the generalist repositories. The workshop is aimed at researchers of all stages including those funded by NIH and those who support data sharing at academic institutions, funders, publishers, repositories, and beyond.

The workshop will feature keynote speakers and panel discussions with leaders in open data from the research community, NIH, and data community organizations. Interactive training sessions led by GREI repositories will present use-case-specific guidance on sharing and discovering data in generalist repositories. The workshop will also gather community feedback to inform future GREI work to enhance support for NIH data sharing with common functionality, interoperability, and “coopetition” among generalist repositories.

Agenda Highlights

• Keynotes by:
  • Martha Whitehead, Harvard University
  • Tim Errington, Center for Open Science 
• Research Community Panel featuring guest speakers: 
  • Robin Champieux, Oregon Health & Science University 
  • Sean Mooney, University of Washington 
  • Alisa Surkis, New York University 
  • Jason Williams, Cold Spring Harbor Laboratory 
  • Moderator: Kristi Holmes, Northwestern University
• NIH Stakeholder Perspectives Panel featuring guest speakers: 
  • Cindy Danielson, NIH Office of Extramural Research (OER) 
  • Jaime Guidry Auvil, National Cancer Institute (NCI) 
  • Jennie Larkin, National Institute on Aging (NIA) 
  • Jessica Mazerik, NIH HEAL Initiative 
  • Rebecca Rodriguez, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) 
  • Moderator: Mark Hahnel, Figshare
• Interactive training sessions focusing on: 
  • Using generalist repositories to share data 
  • Discovering and reusing data in generalist repositories

We're excited to share our plans for Zenodo in the coming 6-12 months.

TL;DR - See our demo site for Zenodo's next-generation platform based on InvenioRDM.

Next-generation platform

We are currently in the process of moving Zenodo on top of our next-generation platform based on InvenioRDM. InvenioRDM is a digital repository platform born out of Zenodo and developed together with 25 other partners.

For institutions/domains, InvenioRDM enables them to provide the "Zenodo-experience" in their own repositories. For Zenodo, InvenioRDM enables us to collaborate with partners on the technical platform underpinning Zenodo.

InvenioRDM is already being used in production system today, see for instance:

• https://data.caltech.edu
• https://repository.tugraz.at

The ZenodoRDM project

The move to InvenioRDM is being managed and coordinated through our ZenodoRDM project. The focus of the project is to migrate Zenodo.org with the existing feature set to InvenioRDM and provide backward compatibility to our users.

The largest challenge in the project is by far the full data migration process. Zenodo today has almost 3 million records, 300k users and many API integrations, and thus we're doing our outmost to minimize disruptions during the data migration process and ensure existing API integrations will continue to work unaffected.

Milestones

Our project is designed to start early on with the data migration, and continue it as a main activity throughout the entire project. Thus, a large fraction of each milestone is dedicated to data migration.

In addition for each milestone, we'll work with specific users to validate that everything works as supposed.

The milestones for the project

• MS2 Themed demo-site with initial data migration
• MS3 Legacy API support
• MS4 Basic feature set completion
• MS5 Normal feature set completion
• MS6 Advanced feature set completion
• MS7 Support operations
• MS8 Launch

Timeline

We are expecting to go-live with the new platform in Autumn 2023.

What's new

The move to InvenioRDM will also provide some long awaited new features for Zenodo. See below what's coming, or even better, check out the new features for yourself on our demo site.

State of demo site

We have loaded a partial dump of 1M records and a couple of communities from Zenodo into the demo site. The records are not connected with user accounts and thus cannot be edited. You can create new communities and test the new upload form and get a feeling for some of the changes we've made.

Community members

InvenioRDM supports having members with different roles - that means multiple users can curate records and/or see closed access content in the communtiy. Zenodo will come with the following community roles:

• Reader: A reader is a member of the community and can view restricted files owned by the community.
• Curator: A curator can in addition to a reader also edit/accept/decline records in a community.
• Manager: A manager can in addition to curators also manage members of a community.
• Owner: An owner has full administrative access to a community, and can change all settings as well as delete the community.

More about communities

Reviews

Submission to communities now enable the curator and uploader to have a conversation directly on the platform. Curators of the community will receive the review request, and can have a conversation with the submitter, as well as preview the submitted record. Both the submitter and curator can edit and update the record under review until it's published:

More about review

Upload form

Our upload form have also gotten a larger overhaul. You'll for instance find the following changes:

• Creator auto-completion from ORCID
• Affiliations auto-completion from ROR.
• Subjects auto-completion from e.g. OECD Fields of Science and Technology vocbulary.
• New improved license selection and funder/award integration.

FAQ

Will your APIs be backward compatibile?

Yes, we do our outmost to ensure backward compatibility of our APIs, and your integration will continue to work on the new platform as well.

Will I be required to update my API integration ?

After Zenodo on InvenioRDM has been launched (Autumn 2023), we will deprecate some of our existing APIs. We will provide a migration period of 1-year for the transition. New features, will only be available on the new API.

Where do I find documentation of your new REST API?

You can find the documentation for our new REST API in the InvenioRDM documentation.

Will the community curators be able to edit my existing records?

No. You will have to opt-in to allow community curators to edit the metadata of records already uploaded on Zenodo. Metadata of new records you upload after the launch will by default be editable by curators (and you'll be asked to confirm).

Will feature X still work?

Yes, we will provide backward compatiblity for all existing features.

Cross posted from Northwestern

A new award to Northwestern University Feinberg School of Medicine and the European Organization for Nuclear Research (CERN) will enhance capabilities of data management and sharing for National Institutes of Health-funded researchers through the Generalist Repository Ecosystem Initiative (GREI), led by the NIH Office of Data Science Strategy.

This modernization of the data ecosystem aligns with the NIH Strategic Plan for Data Science and includes search and discovery of NIH-funded data in generalist repositories. The GREI establishes a common set of cohesive and consistent capabilities, services, metrics, and social infrastructure across repositories, and facilitates the adoption of FAIR principles to better share and reuse data.

Zenodo joins the GREI through a partnership between Northwestern University and CERN, led by Kristi Holmes, PhD, director of Galter Health Sciences Library and Learning Center and professor of Preventive Medicine in the Division of Health and Biomedical Informatics, and Tim Smith, PhD, head of IT Communication, Education and Outreach at CERN. The Zenodo GREI team features expertise and leadership from both sites, including Jose Benito Gonzalez Lopez, PhD, head of Institutional Repositories at CERN; Lars Holm Nielsen, InvenioRDM product manager at CERN; Matthew Carson, PhD, senior data scientist and head of Digital Systems at Galter Library; and Sara Gonzales, senior data librarian at Galter Library and community manager for InvenioRDM. Additional team members will be recruited in the coming months.

Since its launch almost 10 years ago, Zenodo has served as an open, dependable home for science, enabling researchers to share and preserve a wide range of interdisciplinary research outputs. Zenodo was established through the European Commission OpenAIRE program and is operated by CERN. Zenodo houses over 2 million records and a petabyte of data, serving 15 million user visits from around the world annually.

Over the past several years, CERN and Northwestern have partnered with the Invenio Open Source Community (IOSC) to develop InvenioRDM, a turnkey, scalable, and top-of-the-class user experience software for repositories, forming a strong and sustainable foundation for Zenodo. The InvenioRDM software is dedicated to offering a reliable environment for science, empowering preservation, credit, discovery, and sharing while maintaining integrity in its responsiveness to the evolving needs of the research community, including data sharing policy compliance.

“Our strong and efficient partnership with Northwestern through the InvenioRDM project has shown how effective we can be with our complementary skills and common goals,” Smith said. “The GREI allows us to take this partnership to the next level in delivering a useful service to NIH-funded researchers. We are excited that the NIH is supporting us and entrusting us with this task.”

The NIH Office of Data Science Strategy, formed in 2018 within the Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI), leads implementation of the NIH Strategic Plan for Data Science through scientific, technical, and operational collaboration with the institutes, centers, and offices that comprise NIH. DPCPSI also plans and coordinates the NIH Common Fund’s support of trans-NIH initiatives and research.

“Modern research requires collaboration and thoughtful, feature-rich technology for success,” Holmes said. “We’re thrilled to build on our longstanding partnership with CERN to advance our shared commitment to FAIR practices and we look forward to working together and with the GREI partners to achieve the goals of the program.”

The Zenodo GREI project is supported by the NIH Office of Data Science Strategy/Office of the NIH Director pursuant to OTA-21-009, “Generalist Repository Ecosystem Initiative (GREI)” through Other Transactions Agreement (OTA) Number 1 OT2 DB000013-01.

Situated within the Northwestern University Clinical and Translational Sciences (NUCATS) Institute, Galter Library is the only library embedded within a CTSA hub. NUCATS is supported, in part, by the National Institutes of Health’s National Center for Advancing Translational Sciences, Grant Number UL1TR001422.