Data Management Plan

https://eurosciencegateway.eu This project was funded by the European Union’s HORIZON-INFRA-2021EOSC-01 under Grant Agreement number 101057388. D 1.1 Data Management Plan EuroScienceGateway data management and contingency management plan Work package 1 Data management plan HISTORY OF CHANGES Version Publication date Changes 1.0 2022-12-12 ● Initial version: setting up this working document 1.0 2023-01-16 ● initial list of research outputs 1.1 2023-01-24 ● addition of comments with SMP questions ● writing of generic sentences to be completed and reviewed by the consortium 1.2 2023-02-03 ● readable draft for consortium review 1.3 2023-02-20 ● remove comments 1.4 2023-02-21 ● revision ● address comments from reviewers 2.0 2023-02-28 ● address comments from reviewers ● submission 3.0 2025-10-24 ● Updated the DMP as the project has been launched. 2 Data management plan Action Number: Grant agreement ID: 101057388 Action Acronym: EuroScienceGateway (ESG) Action title: EuroScienceGateway: leveraging the European compute infrastructures for data-intensive research guided by FAIR principles Date: [2025-10-24] DMP version: [v3.0] 3 Data management plan List of Abbreviations 5 1. Executive Summary 6 2. Introduction 6 2.1. Objective and scope 6 2.2. Relation to other activities 7 2.3. DMP Change Management 7 3. Data Summary 7 3.1. Existing data/software and newly generated project outputs 7 3.2. Formats of the project outputs 8 3.3. Purpose of the data generation and re-use, relation to the project’s objectives 9 3.4. Volume of the project outputs 9 3.5. Origin/provenance of the project outputs reused or newly generated 9 3.6. Data utility 9 4. FAIR data 9 4.1. Making data findable, including provisions for metadata 10 Persistent identifiers 10 Provided metadata for discovery 10 Search keywords for discovery 10 Metadata for harvesting and indexing 10 4.2. Making data accessible 10 Repositories 10 Availability of the project outputs 11 Standardised access protocol 11 Metadata availability 11 Documentation 11 4.3. Making data interoperable 11 Data and metadata vocabularies, standards, formats and methodologies 12 Qualified references to other data 12 4.4. Increase data re-use 12 How documentation will be provided 12 Licences 12 Documentation of provenance of the data 12 Other research outputs 13 5. Resources, Security and Ethics 13 5.1. Allocation of resources 13 Costs for making data or other research outputs FAIR 13 Responsibilities for data management 13 Long term preservation of project outputs 13 5.2. Data security 13 Trusted repositories for long term preservation and curation 13 5.3. Ethics 13 4 Data management plan List of Abbreviations Abbreviation Description API Application Programming Interface CERN Conseil européen pour la recherche nucléaire (European Organization for Nuclear Research) DMP Data Management Plan DOI Digital Object Identifier DRS Data Repository Service EOSC European Open Science Cloud, a grouping of infrastructure services, projects, policies and institutions, mostly within EU, that aim to support researchers for achieving Open Science and FAIR https://www.eosc.eu ESG EuroScienceGateway (this project) FAIR Findable, Accessible, Interoperable, Reusable, a set of principles for scientific data management that emphasizes best practices and machine readability. https://doi.org/10.1038/sdata.2016.18 GA4GH Global Alliance for Genomics and Health GDPR General Data Protection Regulation, the EU law that establishes the legal framework for personal data management GTN Galaxy Training Network GUI Graphical User Interface JSON-LD JavaScript Object Notation for Linked Data MSCP Muon Spectroscopy Computational Model OAI-PMH Open Archives Initiative Protocol for Metadata Harvesting OSI Open Source Initiative PID Persistent Identifier; a long-lasting reference to a digital resource REST Representational State Transfer RO-Crate RO-Crate is the marriage of Research Objects with DataCrate TES Task Execution Service TPV Total Perspective Vortex WfExS Workflow Execution Service backend WP Work Package, a set of related activities within a project. 5 Data management plan 1. Executive Summary The deliverable D1.1, Data Management Plan (DMP), establishes the framework under which EuroScienceGateway (ESG) will generate, process, and collect data during the project’s activities. Moreover, it will define how the data will be exploited or made accessible for verification and re-use and how the data will be curated and preserved after the project is completed. Principally, the DMP describes the standards that will be used, how the project’s research data will be stored and published for verification and reuse. This maximises the findability of the results, provides the opportunities for exploitation, maximises its effects, and makes sure that project lands successfully for all stakeholders. ESG provided full open access to data, following the principles of FAIR1 use. The proper connection of included raw data with workflows and results by tracking data provenance through the entire data life cycle was a key objective. The first section of the document presents the document's purpose in the ESG project context and includes statements on the future changes and their management. The second section comments on underlying data, their handling, generation and future use, respecting and emphasising FAIR principles. The third section comprises declarations on included resources, data security and privacy as well as ethical considerations. 2. Introduction This document serves as a Data Management Plan for the EuroScienceGateway project. It provides principles, policies, and describes data as well as processes, which apply across multiple project activities. However, the digital landscape is intrinsically subject to rapid changes. Thus, this document has changed over time in order to include new settings, best practices, and technologies into the consortium policies as they occur. Consequently, change management is necessary and described in this chapter as well. In this chapter, we provide an overview of the document’s goals, relationships with other activities, and handling of changes to the data management plan. 2.1. Objective and scope The current deliverable D1.1, Data Management Plan, constitutes a guideline complying with European and national legislation on the acquiring, handling, processing, and archiving of data generated during the EuroScienceGateway project and beyond the project’s end, being updated upon influencing developments. D1.1 allows for a consortium-wide alignment around the project’s data management processes. The objective is to promote the principles of: ● FAIR data management and stewardship, as described in the paper “The FAIR Guiding Principles for scientific data management and stewardship” (Wilkinson et al. 20162); ● the GDPR (Regulation (EU) 2016/679); ● the Universal Declaration of Human Rights and the Convention 108 for the Protection of Individuals according to Automatic Processing of Personal Data; ● the national laws applying its provisions. 2 doi: 10.1038/sdata.2016.18 1 https://www.go-fair.org/fair-principles/ 6 Data management plan Although EuroScienceGateway has not managed all data assets directly, this document establishes a set of guidelines and best practices. All participants are expected to comply in their data management activities. 2.2. Relation to other activities Like other WP1 deliverables, the DMP has a cross-cutting role throughout EuroScienceGateway, providing a guideline on how partners should generate, acquire, handle, share, and curate research data during all activities carried out within and beyond the project. The DMP has been made publicly available to ensure that the entire consortium is aware of the practices that shall be followed in the conduct of those activities. 2.3. DMP Change Management EuroScienceGateway and its participants acknowledge how the data and IT services environment is evolving at a steady pace as Information Technology is rapidly becoming not only enabling, but essential to research. The EuroScienceGateway consortium updated the DMP in response to developments of associated scientific fields and indications from consortium participants. Analogously, the distribution of notifications on updates was carried out via regular meetings (WPs, WP leaders, Executive Board, General Assembly). Participants are committed to keeping track of updates, read them, and discuss contra-indicating issues. In general, changes need to be fully compliant with EU laws and best practices in scientific data management. 3. Data Summary In this chapter, we describe the various types of data the ESG consortium handles during its operational period. Some assets have been managed directly by the ESG WPs, while others will be managed by partner projects independently. However, for the purpose of general data management, each discrete data asset should fall in one of the categories described in the present chapter and be treated accordingly. 3.1. Existing data/software and newly generated project outputs Existing software that has been reused is listed below. All software will follow an Open Source Initiative (OSI)-approved licence model, which allows sharing and reuse. This software will be extended in order to be interconnected via the use of APIs. ● RO-Crate profiles for workflow run ● WorkflowHub web platform (https://workflowhub.eu) and source code (FAIRDOM-SEEK or seek4science - https://seek4science.org) ● Pulsar API ● GA4GH Task Execution Service (TES) API ● Workflow Execution Service backend (WfExS) ● Galaxy software and instances (such as UseGalaxy.eu) ● Onedata software and service instances/repositories offered by EGI-Foundation ● iRODS Open Source Data Management Software and service instances. ● Software tools developed by the MSCP and by the communities of biodiversity, climate change, and astrophysics 7 Data management plan Existing data that will be reused are biodiversity, climate change, and astrophysics datasets, including: ● Genomic data from GenomeArk repository (raw sequencing data, genome assemblies, and genome annotations) ● Copernicus, the European Union's Earth observation programme These datasets have been used to test and prove the newly developed functionalities of the software listed above. All datasets have an OSI approved open licence that allows sharing and reuse. All datasets will be reachable through permanent links or findable through permanent/public identifiers. New outputs generated by the project are listed below. ● RO-Crates profiles and specifications ● New features in the WorkflowHub software ● Maturity model for the deployment of national instances of the European Science Gateway ● Open Infrastructure as code (the actual configuration and deployment specification of usegalaxy.eu as code on GitHub) ● Pulsar API for the GA4GH TES API and TES support to WfExS ● Integration point for compute resources into Galaxy account ● Profiles used for training of the meta-scheduler ● Data analysis tools and workflows for biodiversity and climate science data ● Data and method to evaluate benefits of ESG ● Quantitative dataset, from experimental and observational studies, of astrophysical measurements ● Muon Galaxy portal ● Genome assembly and annotation portal ● EuroScienceGateway website and Galaxy Training Network (GTN) training material ● Galaxy object store plugins for Onedata integration with Galaxy ● Galaxy file source plugin for RSpace integration with Galaxy ● Galaxy Sustainability Report3 ● ZIP file importer infrastructure in Galaxy 3.2. Formats of the project outputs Open-source file formats and programming languages are widely used in ESG, as well as for existing and new software. Specifically, WorkflowHub code is mainly in Ruby (.rb), RO-Crates profiles and specifications are in JSON-LD (.jsonld), Pulsar and TES API are mostly in Python (.py), integrations with the Galaxy API are mainly done in Python, JavaScript, PHP, and Java, extension of TPV meta-scheduler is mainly done in Python. WfExS code and its software dependencies are mostly in Python (.py). The Open Infrastructure as code consists of Terraform and Ansible recipes and configuration files in YAML and JSON-like formats. Quantitative datasets for astrophysical measurements are in the format .root, which can be processed with ROOT, the open source and C++ based software, widely used and developed in the High Energy Physics community. Data and methods to evaluate benefits of ESG and the maturity model will be compiled in open tabular and text format (.txt, .md, .csv, .tsv). 3 Jain, S. (2025). Galaxy Sustainability Report (Version 1). Zenodo. https://doi.org/10.5281/zenodo.16030329 8 Data management plan 3.3. Purpose of the data generation and re-use, relation to the project’s objectives Objective 1: Accessible e-Infrastructure resources for European scientists to enable pioneering data-driven research across scientific domains. ● EuroScienceGateway created Open Infrastructure deployments (Infrastructure as Code) of Galaxy instances to be reused by local, national, and international projects. Objective 2: Support the varieties of analysis types and diverse usage patterns through efficient and smart job distribution to appropriate and sustainable infrastructures. ● The extension of Total Perspective Vortex (TPV) meta-scheduler with data locality variable in Pulsar ● The integration of different storage and compute resources into the EuroScienceGateway Open Infrastructure Objective 3: The application of FAIR principles to workflows and adoption of FAIR Digital Objects to stimulate reusable and reproducible research and enable the EOSC Interoperability Framework. ● Description of workflows executed using EuroScienceGateway as RO-Crate objects and their publication in the WorkflowHub registry Objective 4: Adoption of the EuroScienceGateway by researchers in diverse scientific disciplines. ● Use cases from the disciplines of climate change, biodiversity, and astrophysics for testing the EuroScienceGateway and for proving its benefit 3.4. Volume of the project outputs The expected size for software, specifications, methods, reports, and related documentation is less than 20 GB. 3.5. Origin/provenance of the project outputs reused or newly generated The generated software will extend the existing software previously developed by CERN or open communities, such as Galaxy project, ELIXIR, GA4GH and WorkflowHub community. Biodiversity, climate change, and astrophysics datasets that have been reused, and which originated from experimental and observational studies. 3.6. Data utility The output of this project, that is the ESG Open Infrastructure, can be used by any research community or infrastructure provider with the need to perform intensive data analysis on multidisciplinary data types, without relying on high technical skills in computer science. 4. FAIR data The ESG consortium acknowledges the primary importance of data findability: if a data asset is not findable, for practical purposes it does not exist. The consortium is therefore committed to enforcing data findability. 9