SEPIA: A Scalable System for Integrated Sample Metadata Management
Abstract
SEPIA: Sample Essentials, Persistent Identifiers & AttributesSEPIA is a scalable system for managing sample metadata and assigning persistent identifiers. It links samples with datasets, people, and investigations through a REST API and web interface. Piloted at HZB, SEPIA streamlines sample management, enhances collaboration, and ensures research data are traceable and accessible.
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Highlight Highlight https://nubes.helmholtz-berlin.de/f/576928966 In order to make everyone's work as easy as possible, we have prepared the following layouts, which can be selected very easily and quickly (Select Home > Layout). All layouts are available as a 3-column or 4-column layout variant and are created in this order for each variant: •Basic •Basic with Logo Placeholder •Hub AST •Hub Earth and Environment •Hub Energy •Hub Health •Hub Information •Hub Matter •HMC Office •HMC Projects For more information (i.e. how to select and apply a Layout, how to install and add Theme Colours etc, please read the TEMPLATE READ ME here: https://nubes.helmholtz-berlin.de/f/576928966 Important: To make sure everything works well, please download this Template so that you can use PowerPoint instead of working directly in the Cloud. General Why SEPIA? Why SEPIA Matters Mojeeb Rahman Sedeqi1,2 // Rolf Krahl1// Katherine Rial1,3 // Heike Görzig1,2 SEPIA: A Scalable System for Integrated Sample Metadata Management Sample Essentials, Persistent Identifiers & Attributes 1 Helmholtz-Zentrum Berlin für Materialien und Energie 2 Helmholtz Metadata Collaboration 3 ROCK-IT Contact: [email protected] [email protected] Beamline & Lab Integration – Supports seamless metadata entry and retrieval across workflows. SEPIA – Sample Metadata Platform FAIR & Interoperable – Enhances reproducibility and collaboration through FAIRaligned metadata. Complete Sample Records – Flexible metadata for provenance, keywords, contributors, and timelines. Global Identifiers – Worldwide, institutionindependent sample PIDs via IGSN and DataCite. Objectives of SEPIA Challenges •Thousands of samples measured every year at Matter facilities. •Metadata tracking often limited to safety or beamline operations. •There is a growing need to catalogue all chemicals, objects, and artifacts analyzed at beamlines. •Some samples are also examined elsewhere or modified between measurements, making tracking crucial. Scientific Benefits •Ensures scientific reproducibility through complete sample records. •Provides transparent provenance across preparation & measurement cycles. •Integrates with FAIR principles: •Findable (PIDs) •Accessible (API) •Interoperable (standards) •Reusable (rich metadata) Primary / Metadata Objectives •Assign Persistent Identifiers (PIDs) to samples using IGSN & DataCite. •Ensure global sample identification, independent of any institution. •Accept pre-existing PIDs to preserve sample history. •Track sample modifications, location history, and experiments over time. •Record static and dynamic metadata depending on sample type such as: (basic info, related items, contributors & affiliations, keywords, Sample-type fields and contextdependent attributes) References [1] Krahl, R., Sedeqi, M. R., & Rial, K. (2024, November 5). Enhancing Research Data Annotation: The SEPIA Sample Database for Metadata Storage and Exchange. Helmholtz Metadata Collaboration Conference 2024 (HMC 2024), online. Zenodo. https://doi.org/10.5281/zenodo.14041060 [2] FAIR Data Maturity Model WG. (2020). https://doi.org/10.15497/rda00050 [3] Collaboration, T. I. C. A. T. (2014). The ICAT Project. The ICAT Collaboration. https://doi.org/10.5286/SOFTWARE/ICAT System Architecture How SEPIA Works? •Database for sample metadata (chemicals, objects, provenance). •Minting of PIDs via IGSN & DataCite. •Integrable with new HZB ID Management. •Tracking of sample activities before, during, and after measurements. Facility & Collaboration Benefits •Unifies sample tracking across: •Beamlines •Laboratories •Institutions •Supports: •Cross-experiment comparison •Collaborative research workflows Solution: SEPIA •Centralized, persistent, FAIR-compliant sample metadata platform. •Supports complete sample tracking before, during, and after experiments. Technical Implementation •PostgreSQL relational database as backend. •Flask REST API following OpenAPI specifications. •Next.js, Typescript, TailwindCSS, and Shadcn UI for the frontend. •Tightly integrated with ICAT. https://codebase.helmholtz.cloud/hzb/research_data_management/sepia Why SEPIA Matters … Next Steps •Expand database and workflow functionalities. •Enhance UI/UX based on user feedback. •Develop API for automated data input/output. Acknowledgments This work was supported by the Helmholtz Metadata Collaboration (HMC), an incubator-platform of the Helmholtz Association within the framework of the Information and Data Science strategic initiative; the NFDI consortium DAPHNE4NFDI funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 38/1 – project number 460248799; and the Helmholtz Digital Research Infrastructure ROCK-IT.