Deliverable 2.1 - Curation and Datasets Availability Plan for Non-Sensitive Life and Health Data

BioData.pt | ELIXIR Portugal • Associação BIP4DAB R. da Quinta Grande, 9 • 2780-156 Oeiras • NIPC 516416120 • biodata.pt • [email protected] Curation and Datasets Availability Plan for Non-Sensitive Life and Health Data Deliverable 2.1 – GLIM-BioData Version Author Revisor Description / Changes Date 1.0 Miguel Cisneiros Bruno Louro, Teresa Nogueira, David Palecek 31/10/2025 1. Introduction This deliverable presents the Curation and Datasets Availability Plan for non-sensitive life and health data under Work Package 2 of GLIM-BioData RDM Center. The plan outlines how datasets will be curated, governed, and made available through BioData.pt's DMPortal, a Dataverse-based repository for open and non-sensitive research data. The document defines processes for dataset submission, curation, metadata management, access authorization, and long-term sustainability. It also specifies how legal and ethical compliance will be ensured and how outreach and support structures, such as the DMPortal Helpdesk, will support data providers and users working with biodiversity omics data. 1.1. Alignment with WP2 Objectives WP2 aims to: 1. Reuse currently available non-sensitive data from the field of biodiversity omics and enhance these data by making their respective transformed data products interoperable with other data streams within Life and Health sciences. BioData.pt | ELIXIR Portugal • Associação BIP4DAB R. da Quinta Grande, 9 • 2780-156 Oeiras • NIPC 516416120 • biodata.pt • [email protected] 2. Host and plan the availability of omics diversity datasets (Task 2.1). 3. Enable biodiversity data reuse through EMO BON and EOSC FAIR-EASE use cases (Task 2.2). 4. Implement electronic laboratory notebooks to promote FAIR principles from the start of research data collection (Task 2.3). This deliverable (D2.1) is the foundation for these objectives, as it defines the curation workflows and dataset availability mechanisms on which dataset publication and data reuse will depend. 1.2. The Role of BioData.pt’s DMPortal BioData.pt's DMPortal is a national repository for non-sensitive research data in life and health sciences, operated by BioData.pt in coordination with ELIXIR Portugal. • Mission: Provide a secure, standards-compliant repository for non-sensitive biological data generated in Portugal, ensuring FAIRness and enabling open reuse and interoperability. • Integration: Metadata are harvested by national and international catalogues. Eventual migration to POLEN-FCCN platform will ensure long-term sustainability and maintenance. • Technical Core: o Dataverse platform for structured data organization and versioning. o DOI assignment for persistent identification. o Support for multiple license types and embargo periods. o Metadata validation against domain-specific schemas (Darwin Core, MIxS, ENA metadata standards). o RESTful API for programmatic access and integration. o Support for transformed data products and derived datasets. BioData.pt | ELIXIR Portugal • Associação BIP4DAB R. da Quinta Grande, 9 • 2780-156 Oeiras • NIPC 516416120 • biodata.pt • [email protected] 2. Curation Plan This Curation Plan explains how users of DMPortal should prepare, validate, preserve and share submitted biological data so it remains high-quality, ethically compliant, interoperable with Life and Health data, and reusable over time. It is written for researchers, data stewards and repository staff involved in depositing or managing non-sensitive datasets intended for open or restricted access via DMPortal. Step 1 – Pre-submission Support 1. If needed, data providers can contact the DMPortal Helpdesk. 2. Helpdesk and Data Stewards provide guidance on: o Data organization and file formats for omics data (FASTQ, FASTA, VCF, alignments) o Metadata requirements specific to biological data (taxonomic information, sampling metadata, environmental context) o Alignment with Darwin Core and MIxS standards o Licensing options (CC-BY, CC0, custom licenses) o Documentation standards for omics workflows and bioinformatics pipelines 3. Practical checklists and example metadata are provided so that users can prepare files correctly before submission. Step 2 – Submission 1. Researchers register with DMPortal through institutional authentication (LSLogin) or create a direct account. 2. Data and metadata are uploaded through the web interface or via API. 3. Files are organized into datasets with descriptive metadata following Darwin Core, MIxS, and discipline-specific schemas for omics data. 4. Submitters can provide: o Raw and/or processed data BioData.pt | ELIXIR Portugal • Associação BIP4DAB R. da Quinta Grande, 9 • 2780-156 Oeiras • NIPC 516416120 • biodata.pt • [email protected] o Transformed data products that can be integrated with Life and Health sciences data o Bioinformatics pipeline information and parameter files o Sample metadata including geospatial coordinates, environmental parameters, and sampling context Submitters select appropriate licenses and access restrictions if applicable Step 3 – Ingestion & Validation 1. Technical checks: file integrity, format validation for omics data types, virus scanning. 2. Metadata checks: a. Completeness of appropriate information b. Validation of geospatial coordinates (when applicable) c. Environmental metadata completeness (when applicable) d. Consistency with Darwin Core, MIxS and other standards e. Controlled vocabularies compliance (ENVO, MIAPPE, etc) 3. Preview and verification stage allows submitters to review their dataset before publication. Step 4 – Curation 1. Metadata enrichment using standard ontologies (ENVO, EFO and other relevant vocabularies) to improve discoverability and interoperability. 2. Capture provenance and versioning: record transformations, processing pipelines, software versions and timestamps. 3. Convert or recommend preservation-ready formats where appropriate. 4. Align records with FAIR principles. Step 5 – Monitoring & Review 1. Regular monitoring of dataset usage, citation metrics, and reuse in downstream analyses. BioData.pt | ELIXIR Portugal • Associação BIP4DAB R. da Quinta Grande, 9 • 2780-156 Oeiras • NIPC 516416120 • biodata.pt • [email protected] 2. Periodic review of metadata quality and compliance with evolving standards. 3. Tracking integration with relevant data streams and services. 4. Updates to curation policies as community standards evolve (Darwin Core, MIxS, etc). 5. Support for dataset versioning when updates are required (e.g., improved assemblies, re-annotations). 3. Dataset Availability Plan The purpose of this section is to address access levels, timelines, discovery, legal/ethical constraints and the operational roles needed to make non-sensitive biological data available in a predictable, auditable way. This plan is tailored to GLIMBioData WP2 goals, deliverables (in particular D2.2), timeline, and context. Initial implementation will focus on EMO-BON data from CCMAR as the primary pilot use case. Current DMPortal Availability Levels • Public / Aggregated Data: non-sensitive metadata or aggregated datasets openly available. • Embargoed Data: datasets with delayed public release, with metadata available immediately. Common for pre-publication datasets or those subject to moratorium periods. • Restricted access: In Dataverse, the user can mark files as “restricted” so they cannot be downloaded unless access is explicitly granted. When one restricts files, they are prompted to fill in Terms of Access (contact for access, availability status, etc.), and may also enable Request Access so users can submit requests that curators/owners review. Phased Rollout • Current Phase (2025): Internal datasets from national partners onboarded, with focus on EMO BON and EOSC FAIR-EASE pilot datasets. Migration to POLEN platform initiated. BioData.pt | ELIXIR Portugal • Associação BIP4DAB R. da Quinta Grande, 9 • 2780-156 Oeiras • NIPC 516416120 • biodata.pt • [email protected] • National Engagement Phase (2026): Expected conclusion of the migration to POLEN. Expansion of non-sensitive biological data collections from other institutions. • Federated Phase (2027 onward): Full integration with European and international biological data infrastructures (GBIF, OBIS, EOSC) for cross-border discovery, reuse, and integration with standard science data streams. Discovery & Metadata • Metadata from submissions in DMPortal should be published in national and international catalogues: o OpenAIRE for European research visibility o GBIF for terrestrial and freshwater biodiversity o OBIS for marine biodiversity o EOSC portal for FAIR-EASE integration • Alignment with biodiversity and Life and Health sciences standards: o Darwin Core for occurrence and sampling data o MIxS for genomic metadata o schema.org for enhanced web discoverability o RO-Crates for dataset packaging and annotation • Support for community-specific metadata schemas: o EMO BON metadata standards o FAIR-EASE data models o ENA submission standards • Persistent identifiers (DOIs) assigned to all public datasets. • Comprehensive search and filtering capabilities: o Taxonomic search across multiple ranks o Geospatial search with map interface o Environmental parameter filtering BioData.pt | ELIXIR Portugal • Associação BIP4DAB R. da Quinta Grande, 9 • 2780-156 Oeiras • NIPC 516416120 • biodata.pt • [email protected] o Data type and pipeline filtering o Temporal search 3.1. Implementation Example: EMO BON Reuse Case (Task 2.2) This section demonstrates how the curation and availability plan will be operationalized using the EMO-BON dataset as a pilot implementation for Task 2.2. Overview • Dataset: EMO-BON sampling data from ENA (accession: PRJEB51661) • Purpose: Building ML pipelines to screen pathogens from DNA metagenomic data • Output: Metagenomic sequences related to specific pathogens Implementation Timeline - 2025 Phase 1: Data Preparation • Download EMO-BON data subset from ENA • Document filtering and selection criteria • Transform format for analysis compatibility • Quality checkpoint: Format validation and file integrity verification Phase 2: Analysis and Transformation • Apply ML pipelines for pathogen screening • Generate derived datasets identifying virulent bacterial clones • Create RO-Crates packaging raw data, analysis scripts, and outputs • Document bioinformatics workflows with pipeline parameters and software versions BioData.pt | ELIXIR Portugal • Associação BIP4DAB R. da Quinta Grande, 9 • 2780-156 Oeiras • NIPC 516416120 • biodata.pt • [email protected] • Quality checkpoint: Pipeline reproducibility verification Phase 3: Curation • Data Steward reviews and standardizes metadata • Apply Dublin Core metadata standards • Add keywords and ontology references (Darwin Core, MIxS, ENVO) • Enhance with pathogen-specific metadata: o Taxonomic identifications using NCBI Taxonomy o Virulence factors and antimicrobial resistance markers o Environmental context (sampling locations, parameters) o Health relevance documentation • Quality checkpoint: Metadata completeness ≥95% Phase 4: Submission to DMPortal • Upload datasets through DMPortal web interface or API • Appropriate Creative Common license attribution • No embargo period • DMPortal assigns DOI for persistent identification • Quality checkpoint: DOI resolution testing, license verification Compliance Verification • No personal data involved • No sensitive data included • No ethical legislation applicable • Source citation: EMO-BON consortium properly attributed BioData.pt | ELIXIR Portugal • Associação BIP4DAB R. da Quinta Grande, 9 • 2780-156 Oeiras • NIPC 516416120 • biodata.pt • [email protected] 4. Legal & Ethical Framework Data Licensing Datasets must be published under clear, standardized licenses. DMPortal supports: • Creative Commons licenses (CC0, CC-BY preferred for maximum reuse) • CC-BY-NC when commercial restrictions are necessary • Open Data Commons licenses • Custom terms of use when necessary For biodiversity omics data, open licenses (CC0 or CC-BY) are strongly encouraged to maximize scientific reuse and integration with global biodiversity initiatives. Ethical Compliance While dealing with non-sensitive data, ethical considerations remain important for biodiversity research: • Nagoya Protocol compliance: Verification that genetic resources were accessed and used in accordance with Access and Benefit Sharing (ABS) requirements • Prior Informed Consent (PIC): Documentation of permissions for sampling in specific locations or from indigenous/local communities • Collection permits: Verification that appropriate permits were obtained for sample collection • Endangered species protection: Careful handling of location data for threatened or endangered species • Ethical guidelines: Confirmation that data collection followed institutional and national ethical guidelines • Proper attribution: Respect for intellectual property rights and acknowledgment of data sources, collectors, and indigenous knowledge