FAIRDOM-SEEK: Platform for FAIR data and research asset management

Presentation from the eScience Lab (The University of Manchester) at the ISMB/ECCB 2025 conference (view all).

Bioschemas is presented in the Bioinformatics Open Science Conference (BOSC 2025), ISMB/ECCB 2025 track as a Talk 2025-07-21 

• fairdomseek.org

Main Text of Abstract

As research becomes more data-driven, collaborative, and interdisciplinary, the need for structured, accessible, and well-curated data outputs with rich, standardized metadata is critical to ensure data is discoverable and reusable beyond its original context. Meeting these needs requires infrastructure that not only ensures long-term preservation and accessibility but also supports discoverability, reproducibility, and reuse across disciplines and domains.  FAIRDOM-SEEK platform addresses these challenges by providing a customizable, open-source, web-based catalogue designed to support FAIR (Findable, Accessible, Interoperable, Reusable) data and asset management.

FAIRDOM-SEEK utilises the widely adopted ISA (Investigation-Study-Assay) framework, originally developed for omics research, to provide contextual structure to research data. This framework allows users to link data and assets such as samples, protocols, workflows, and models within the scope of a defined experimental process. An Investigation represents a broader research question, under which multiple Studies may be conducted, each comprising one or more Assays (e.g., laboratory experiments, modelling studies). This structured approach enhances data provenance, traceability, and navigability, making it easier for collaborators and external users to interpret and reuse datasets.

Key Features and Functionalities

• Rich Data Catalogue: Users can upload and publish a wide variety of assets, including raw and processed datasets, Standard Operating Procedures (SOPs), models (e.g., SBML), presentations and publications. All assets are grouped by projects and associated with the researchers who produced them. To encourage sharing of data,  FAIRDOM-SEEK allows flexibility in the formats to accommodate real-world research practices. Common file types can be previewed directly in-browser.

• Access Control: Recognizing the academic need for phased sharing, FAIRDOM-SEEK supports fine-grained access controls, from private collaboration to public release. Researchers retain full control over when and how data is shared, enabling compliance with publishing, legal, and funding requirements.

• Interlinking and Provenance: Assets can be interlinked to describe relationships between experiments, outputs, and publications. Publications can be linked via DOI or PubMed ID, providing a complete research narrative and improving data transparency.

• Versioning and Static URLs: Every asset can be versioned with persistent identifiers, ensuring accurate citation, traceability, and reproducibility.

• Sample Management: FAIRDOM-SEEK has a flexible samples framework that allows users to generate templates for sample metadata. Both digital and laboratory samples are supported. Integration with tools like RightField allow for semantically annotated templates and spreadsheets.

• SBML Model Simulation and Annotation: Computational models adhering to the SBML standard can be annotated, visualized, and simulated directly within the platform.

Biological Applications via Project Hubs

FAIRDOM-SEEK is widely adopted across biological sciences, especially in systems biology, synthetic biology, biotechnology, and health research. Researchers use the platform to link experimental and computational data, manage sample metadata, and publish results with contextual metadata.

The platform achieves this by the creation of dedicated Project Hubs, which are customized domain specific deployments for biological projects. This allows tailored use of the platform’s core capabilities, including modified appearance, structure, and content. Some of the notable examples are:

• IBISBAKHub: Supports industrial biotechnology R&D within the Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA) infrastructure.

• WorkflowHub: Facilitates sharing of computational workflows in diverse formats (e.g., Galaxy, CWL, Notebooks).

• NFDI4Health DataHub:Serves Germany’s health research community by managing epidemiological and clinical datasets.

• deCYPher DataHub: Integrates plant multi-omics and structural biology data in a cohesive metadata-driven environment.

• MIT BioMicroCenter: Manages sample and data workflows for biological core facilities.

In addition, FAIRDOMHub, the central public instance, supports over 400 national and international biological projects, functioning as both a repository and a collaborative knowledge platform.

Open Source, Community-Driven Development

FAIRDOM-SEEK is developed and maintained by the FAIRDOM consortium (fair-dom.org), a collaboration of international researchers, infrastructure providers, and software engineers. It is built using Ruby on Rails and the source code can be downloaded from a GitHub repository (https://github.com/seek4science/seek). As an open-source platform, it:

• Encourages community contributions, extensions, and local deployments,

• Supports training, documentation, and outreach via workshops and webinars, and

• Maintains active development channels with transparent governance and user-driven feature requests.

Conclusion

In a research landscape increasingly defined by complexity, collaboration, and computational integration, FAIRDOM-SEEK provides an essential platform for FAIR data stewardship, reproducibility, and long-term knowledge sharing. In the presentation, we will showcase the core features of FAIRDOM-SEEK, demonstrate biological use cases, and discuss how the platform supports researchers in achieving effective and FAIR-aligned data and asset management.

• Project Website: https://fair-dom.org/ 
• Source Code: https://github.com/seek4science/seek 
• License: BSD 3-Clause License