scieee AI-readable full text Open interactive document viewer

Slide Deck for "FAIRway Advanced Course: A Pathway to Good Practices and Optimised Research Data Management Processes"

Aguiar Castro, João; Tomasino, Maria Paola; Muñoz Mérida, Antonio; Babo, Camila; Ventura, Carolina

Abstract

This resource compiles the complete set of slide decks developed for the advanced training session FAIRway: A Pathway to Good Practices and Optimised Research Data Management Processes, delivered as part of the FAIRway Project under the National Programme for Open Science and Open Research Data (PNCDAI), within the Portuguese Recovery and Resilience Plan (PRR). Corresponding to Deliverable D3.1, the session focused on build capacity in Research Data Management (RDM) and in the practical implementation of the FAIR principles, drawing on real-world examples and case studies from the partner institutions INESC TEC, CIIMAR, and CIBIO-BIOPOLIS. The resource includes several thematic slide decks covering conceptual, methodological, and hands-on components across the research data lifecycle. Included Materials Module 1 - FAIRness in Research, by Camila BaboIntroduces the foundational concepts of FAIR, the role of metadata, identifiers, ontologies and licensing, and tools and criteria for assessing the FAIRness of datasets. Module 2 - Data Management Plans and Stakeholder Engagement, by João Aguiar CastroExamines institutional practices and challenges in RDM, synthesising findings from interviews and surveys across partner institutions. Discusses the strategic role of Data Management Plans, common pitfalls, and the importance of collaboration between researchers and data stewards.The module also includes the segment “From Data Management Plans to Data Publication”, which explains the relationship between early planning and the final stages of depositing datasets. The session also included examples of DMPs and a Zenodo demonstration to complement the presentation. Module 3 - Data Submission to FAIR Repositories (ENA, BioStudies, GBIF, PANGAEA, OBIS), by Antonio Muñoz, Maria Paola Tomasino and Carolina VenturaProvides guidance on domain-specific metadata standards, community requirements and submission processes for major life-science and environmental repositories, such as ENA, BioStudies, GBIF, and PANGAEA. The session included practical demonstrations of dataset preparation, metadata structuring, and editorial review workflows. This module was complemented with a detailed presentation about PANGAEA. Module 4 - Electronic Laboratory Notebooks (ELNs), by Maria Paola Tomasino and Carolina VenturaPresents the benefits of ELNs for structured documentation, reproducibility and metadata capture, highlighting how ELNs support FAIR workflows and institutional data governance. Includes insights from the CIIMAR pilot implementation of eLabFTW. These slide decks support the development of effective Research Data Management practices and the practical application of the FAIR principles. They offer guidance on structuring, documenting and sharing research data; introduce relevant repositories and standards; and illustrate how FAIR-aligned workflows can be implemented across diverse research environments. The resource reflects the collaborative effort of the FAIRway team to strengthen institutional capacity for responsible data stewardship.

Full text

A pathway to good practices and optimised Research Data Management Processes Antonio Muñoz | [email protected] 04/12/2025 Module 3: Data submission to FAIR repositories (ENA, BioStudies, GBIF, Pangaea, OBIS) FAIR data Repositories ENA SRA Generic repositories Zenodo BioStudies Sequence repositories Specific repositories GBIF PANGAEA OBIS Dryad BioImage eBird ERDDAP FAIR data Repositories FAIR data Repositories SUBMISSION TO A SEQUENCE REPOSITORY - They accept different formats from raw reads, processed reads or alignments (Fastq, BAM, CRAM). - All the information in the three big repositories is synchronized (EBI, NCBI, DDBJ) - These repositories provide the infrastructure to make your data FAIR FAIR sequence data Repositories SRA: The SRA is NIH's archive of high-throughput sequencing data and is part of the International Nucleotide Sequence Database Collaboration (INSDC) that includes the NCBI Sequence Read Archive (SRA), the European Bioinformatics Institute (EBI), and the DNA Database of Japan (DDBJ). ENA: The European Nucleotide Archive (ENA) provides a comprehensive record of the world’s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation ENA data submission ENA data submission ENA data submission Sample submission Sample submission Sample submission Raw reads submission Raw reads submission Raw reads submission Raw reads submission Raw reads submission Analysis submission Command-line submission Online submission Transfer options ● Webin File Uploader ● FileZilla Online submission Transfer options ● Webin File Uploader ● FileZilla ● FTP Upload sequence data Submitted record SUBMISSION TO A GENERIC REPOSITORY Normally intended for submission of data that does not fit into other more specific repositories FAIR depending on the submitter Sometimes used even for specific data because it has fewer requirements The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. Generic data repository BioStudies submission BioStudies submission BioStudies submission BioStudies submission BioStudies submission Online form exclusively GBIF submission Submission types: - Occurrence - Sampling Event - Checklist - Metadata only GBIF submission GBIF submission Darwin Core standard GBIF submission Darwin Core standard GBIF submission Darwin Core mappings GBIF submission Basic Metadata GBIF submission Basic Metadata GBIF submission Basic Metadata GBIF submission Event publication GBIF submission Event registration