ELIXIR CONVERGE WP3: Common Data Management Toolkit

This task will assemble a “Common Toolkit Blueprint” and example implementation configuration of the toolkit, using already available tools. Work will be based on the emerging consensus on toolkits in use in national Nodes (in collaboration with WP1).

To facilitate integration in the diverse national contexts, emphasis will be placed on identifying and acting on interaction points (interfaces) and the necessary standardisation between tools. Specifically, we will focus on an omics oriented blueprint, centered around FAIRDOM and Galaxy, and an instance targeting sensitive human data. These starter toolkits, based on existing practices in the Nodes, will allow ELIXIR-CONVERGE to deliver tangible solutions.

Due to national priorities and infrastructure choices, we will provide Node-specific instances of these blueprints, focussing on lightweight, sustainable integration practices (API-based) and adoption of shared templates and markups (e.g. Bioschemas). This will drive interoperability between Nodes as well as facilitate capacity building and accelerated deployment of well-established, proven solutions that are integrated in the ELIXIR ecosystem of Core Data Resources, Deposition Databases, as well as analysis technologies and platforms established in EOSC-Life (e.g. Galaxy and BioContainers).

Leadership: University of Manchester (Carole Goble, ELIXIR UK)​

Participants: BSC (ELIXIR Spain), CSC (ELIXIR Finland), Heidelberg Institute for Theoretical Studies (ELIXIR Germany), SIB (ELIXIR Switzerland), University of Bergen (ELIXIR Norway), University of Luxembourg (ELIXIR Luxembourg), University of Tartu (ELIXIR Estonia), ÚOCHB (ELIXIR Czech Republic), Uppsala University (ELIXIR Sweden), VIB (ELIXIR Belgium).

In this task we will define ​processes to expand and update the toolkit. Based on the selected demonstrators (WP5), we will identify tools available to and/or provided by Nodes, evaluate them for broader usage, and assess their potential to integrate into the toolkit. Selection processes and guidelines will be developed, informed by experiences of selecting Recommended Interoperability Resources and Node data management best practices. This will be done in close collaboration with the Expert Network (WP1).

An emphasis will be on the identification of domain specific tools (e.g. BrAPI) and on guidelines and best practices for tool integration (Task 3.4) to facilitate and stimulate integration in the established ecosystem. This task, in collaboration with Task 5.2, will deliver best practice and exemplar toolkit configurations for investigator-centric data management, integrated in the portal (Task 3.3). The tools that are its components will be regularly reviewed.

Leadership: DTL-Projects (Celia van Gelder, ELIXIR Netherlands)​

Participants: ​ University of Bergen (Inge Jonassen, ELIXIR Norway ) ATHENA-RIC (ELIXIR Greece), BSC (ELIXIR Spain), CNRS (ELIXIR France), DTU (ELIXIR Denmark), EMBL-EBI, Heidelberg Institute for Theoretical Studies (ELIXIR Germany), Hungarian Academy of Sciences (ELIXIR Hungary), INESC-ID (ELIXIR Portugal), University of Ljubljana (ELIXIR Slovenia), University of Manchester (ELIXIR UK), University of Tartu (ELIXIR Estonia), ÚOCHB (ELIXIR Czech Republic), Uppsala University (ELIXIR Sweden), VIB (ELIXIR Belgium), Weizmann Institute of Science (ELIXIR Israel).

A toolkit should not be presented as a flat list of things researchers can use, since it is likely that the researchers who have the most need for a tool are not aware that a (generic) solution exists. A better approach is to present a toolkit in the form of the Data Stewardship Wizard (​https://ds-wizard.org​) which is part of the ELIXIR portfolio. The wizard guides the researcher through the development of the data management plan and can refer to all other components of the toolkit where the project and project planning calls for it.

Through integrations, building on established registries such as bio.tools (tools and services), FAIRsharing (standards, databases and policies) and TeSS (training materials), we will establish a resource that provides each user with a unique view on this whole ecosystem, allowing all stakeholders not only to discover the components, but also to identify an operational, interlinked trajectory tailored for specific use cases. This approach will promote best practices and the dissemination of the blueprints developed in Task 3.1 and 3.2.

Leadership: DTL-projects (Rob Hooft, ELIXIR Netherlands)​

Participants:Heidelberg Institute for Theoretical Studies (ELIXIR Germany), SIB (ELIXIR Switzerland), University of Bergen (ELIXIR Norway), ÚOCHB (ELIXIR Czech Republic), Uppsala University (ELIXIR Sweden), VIB (ELIXIR Belgium)

To disseminate and build capacity to use and implement the Data Management Toolkit, we will develop best practices and training materials. We will organise interactive training that helps disseminate and advance best practices, creates new stewardship and training capacity, and feeds back into the selection, as well as the development process for the toolkit (Task 3.1 and 3.2). This will be developed as workshops, hackathons and online events. These will be delivered in close collaboration with the training experts, adhering to the Training co-production model (WP2). We will target the different stakeholders: data experts (WP1), researchers as well as support staff of data generating facilities. These activities will be crucial to instill 'FAIR data at source' throughout the data life cycle, but will also provide the trainees the skills and knowledge to retroactively 'fairify' existing datasets.

The increased stewardship capacity ​using the portal (Task 3.3) and toolkits, and development capacity for ​updating, extending and sustaining the toolkits (with WP2), will ensure the long term sustainability of the developed toolkit and procedures beyond ELIXIR-CONVERGE.

Leadership: University of Luxembourg (Pinar Alper, ELIXIR Luxembourg)

Participants: ​ATHENA-RIC (ELIXIR Greece), CNR (ELIXIR Italy), CNRS (ELIXIR France), DTL-Projects (ELIXIR Netherlands), DTU (ELIXIR Denmark), EMBL-EBI, Heidelberg Institute for Theoretical Studies (ELIXIR Germany), Hungarian Academy of Sciences (ELIXIR Hungary), INESC-ID (ELIXIR Portugal), SIB (ELIXIR Switzerland), University of Bergen (ELIXIR Norway), University of Ljubljana (ELIXIR Slovenia), University of Tartu (ELIXIR Estonia), ÚOCHB (ELIXIR Czech Republic), VIB (ELIXIR Belgium), Weizmann Institute of Science (ELIXIR Israel).