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4 Publications visible to you, out of a total of 4
BioHackEU25 report: Towards a Robust Validation Service for Data and Metadata in ARC RO-Crates

Abstract (Expand)

<p>Robust validation of both research data and its accompanying metadata is essential for ensuring adherence to FAIR principles. Current approaches often handle these aspects separately, hindering … a holistic quality assessment. Building upon previous BioHackathon work establishing ARCs (Annotated Research Context) as RO-Crates (ARC RO-Crate), we aim to develop and demonstrate an integrated validation strategy for FAIR digital objects. It distinguishes between validating the metadata descriptor and the payload data files.For the metadata descriptor, validation will ensure structural and semantic compliance to the base RO-Crate specification and the ARC-ISA family of RO-Crate profiles, using and extending the RO-Crate validator tool.For the payload data files, validation targets the actual content, since data files often require domain-specific structural and value constraints, which requires explicit schema definitions. For this, we will integrate Frictionless for checking data content against community standards (e.g. MIAPPE, as demonstrated in the HORIZON project AGENT). Crucially, this project will also explore mechanisms for specifying expected data structures’ requirements within the ARC RO-Crate itself. This aims to provide a more self-contained description of data, investigating how such internal requirements can be linked to data validation frameworks, complementing the crate’s metadata validation.The overall goal is to provide a powerful, holistic validation mechanism for ARC RO-Crates, enhancing their reliability, trustworthiness, and FAIRness. A MIAPPE-compliant plant phenomics dataset will serve as a use case. This integrated validation approach aims to streamline quality control for researchers and will be packaged as a deployable microservice, offering broad applicability across diverse research workflows.</p>

Authors: Eli Chadwick, Matthijs Brouwer, Kevin Schneider, Daniel Arend, Finn Bacall, Etienne Bardet, Sebastian Beier, Dominik Brilhaus, Xiaoming Hu, Emma Le Roy Pardonche, Timo Mühlhaus, Stuart Owen, Cyril Pommier, Heinrich Lukas Weil

Date Published: 16th Dec 2025

Publication Type: Report

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.

Abstract (Expand)

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. … It is a web-accessible repository for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship.

Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble

Date Published: 4th Jan 2017

Publication Type: Journal Article

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.

Abstract (Expand)

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. … It is a web-accessible repository for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship.

Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble

Date Published: 4th Jan 2017

Publication Type: Journal Article

RightField: Scientific Knowledge Acquisition by Stealth through Ontology-Enabled Spreadsheets

Abstract (Expand)

RightField is a Java application that provides a mechanism for embedding ontology annotation support for scientific data in Microsoft Excel or Open Office spreadsheets. The result is semantic annotation … by stealth, with an annotation process that is less error-prone, more efficient, and more consistent with community standards. By automatically generating RDF statements for each cell a rich, Linked Data querying environment allows scientists to search their data and other Linked Data resources interchangeably, and caters for queries across heterogeneous spreadsheets. RightField has been developed for Systems Biologists but has since adopted more widely. It is open source (BSD license) and freely available from http://www.rightfield.org.uk

Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Wolfgang Mueller, Finn Bacall, Jacky Snoep, Franco du Preez, Quyen Nguyen, Olga Krebs, Carole Goble

Date Published: 2012

Publication Type: Journal Article

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