Finn Bacall

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About Finn Bacall:

No description specified

SEEK ID: https://fairdomhub.org/people/318

Location: United Kingdom

ORCID: https://orcid.org/0000-0002-0048-3300

Joined: 21st Sep 2009

Expertise: Programming

Tools: Ruby on Rails, Javascript, HTML

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SEEK

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FAIRDOM

FAIRDOM is establishing a support and service network for European Systems Biology. FAIRDOM is a joint action of ERA-Net ERASysAPP and European Research Infrastructure ISBE to establish a data and model management service facility for Systems Biology. Our prime mission is to support researchers, students, trainers, funders and publishers by enabling Systems Biology projects to make their Data, Operating procedures and Models, Findable, Accessible, Interoperable and Reusable (FAIR).

Projects: FAIRDOM, FAIRDOM user meeting, FAIRDOM Community Workers

Web page: http://fair-dom.org

SysMO

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep

Web page: http://sysmo.net/

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FAIRDOM

FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.

Programme: FAIRDOM

Public web page: http://fair-dom.org/

Start date: 1st Nov 2014

Organisms: Not specified

SysMO DB

The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:

facilitates and maximises the potential for data exchange between SysMO research groups;
maximises the ‘shelf life’ and ...

Programme: SysMO

Public web page: http://www.sysmo-db.org/

Organisms: Not specified

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University of Manchester - Department of Computer Science

ROR ID: Not specified

Department: Not specified

Country: United Kingdom

City: Manchester

Web page: http://www.cs.manchester.ac.uk/

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Submitter: Finn Bacall

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: 1 hidden item

Organisms: No organisms

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Created: 24th Mar 2020 at 09:16

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BioHackEU25 report: Towards a Robust Validation Service for Data and Metadata in ARC RO-Crates

FAIRDOM

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<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 …

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

DOI: 10.37044/osf.io/zah28_v1

Citation: Preprint. https://doi.org/10.37044/osf.io/zah28_v1

Created: 17th Dec 2025 at 08:07

Flexible Metadata Structuring for Research Data Management Through the FAIRDOM-SEEK Platform - Implementing Tailored and Complex Metadata Schemes in SEEK

FAIRDOM

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Modern research projects increasingly require hybrid metadata approaches that balance adherence to domain-overarching, as well as domain-specific community standards with flexibility for project- or … resource-specific metadata. The FAIRDOM-SEEK platform [1] is a widely used research data management system designed to support diverse domains, from systems biology to health research data, by integrating standardized metadata models (e.g., the ISA framework [2]) with customizable extensions. To address this need, we introduce the Extended Metadata feature in SEEK, which allows researchers to extend core metadata schemas with user-defined fields, hierarchies, and semantic annotations while ensuring interoperability with domain-specific standards. We demonstrate this capability through two use cases: 1. NFDI4Health Local Data Hubs (LDH) [3],[4]: In the context of the German National Research Data Infrastructure for Personal Health Data (NFDI4Health [5]), we have developed Local Data Hubs (LDH) based on the SEEK platform. These hubs support federated data structuring and sharing for sensitive health data from clinical trials, epidemiological studies, and public health research and allow to connect local platforms to the central metadata repository of NFDI4Health, the German Health Study Hub. Given the complexity of the NFDI4Health metadata schema (MDS) [6], the SEEK-based LDH software utilizes the Extended Metadata feature to fully represent the schema, allowing for flexible project-defined metadata extensions. 2. FAIR Data Station (FAIR-DS) [7]: Based on the ISA-framework, with the addition of Observation units from MIAPPE [8], the FAIR-DS is a web application that enables users to create and manage metadata according to FAIR principles. Using packages and terms configured through the UI, it generates Excel spreadsheets which are then populated to gather the metadata. FAIR-DS is then used to validate the metadata and generates RDF datasets representing the content. SEEK has been updated to allow Extended Metadata and Sample Types to be configured automatically via these RDF datasets, and also the content can be imported, and updated, in a single action. The Extended Metadata feature allows users to define additional metadata attributes to be tailored to specific data types, ensuring compliance with standards. When creating a resource, users can select an Extended Metadata type from a dropdown menu, dynamically triggering the rendering of associated metadata input forms within the web interface. This enables seamless integration of resource-specific metadata (e.g., clinical trial study metadata) alongside core descriptive fields. Currently, only instance administrators can create, manage (enable/disable), and delete additional attributes for specific resource types (e.g., ISA items such as Investigation, Study, Assay, as well as Projects and Models) based on specific schemas (e.g., the NFDI4Health MDS). Attribute types range from simple (e.g., string, text, date, integer, Boolean) to complex (e.g., controlled vocabularies linked to ontologies, nested hierarchical structures), with validation rules for mandatory or optional fields. Regular expressions are introduced to ensure correct input formatting. Metadata schemas can be created through backend seed files, JSON uploads, or FAIR-DS RDF imports. These schemas are programmatically accessible via the SEEK REST API, enabling automated metadata creation and retrieval. This ensures interoperability with external tools while adhering to FAIR data principles.

Authors: Xiaoming Hu, Stuart Owen, Frank Meineke, Finn Bacall, Carole Goble, Wolfgang Müller, Martin Golebiewski

Date Published: 2025

Publication Type: Conference Paper

DOI: 10.5281/zenodo.16736322

Citation: Zenodo. https://zenodo.org/doi/10.5281/zenodo.16736322.

Created: 1st Jan 2026 at 17:43

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

FAIRDOM

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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. …

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

PubMed ID: 27899646

Citation: Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.

Created: 5th Dec 2016 at 07:31, Last updated: 8th Dec 2022 at 17:26

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

LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, TRALAMINOL, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 Disease Map

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Date Published: 4th Jan 2017

Publication Type: Journal Article

PubMed ID: 27899646

Citation: Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.

Created: 13th Nov 2019 at 14:52, Last updated: 8th Dec 2022 at 17:26

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

FAIRDOM, Example use cases

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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 …

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

DOI: 10.1007/978-3-642-33876-2_42

Citation: Knowledge Engineering and Knowledge Management 7603:438-441,Springer Berlin Heidelberg

Created: 17th Apr 2017 at 18:03, Last updated: 8th Dec 2022 at 17:26

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FAIRDOM-SEEK: A platform for FAIR data and research asset management

FAIRDOM

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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. 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 enables scientists ...

Creators: Phil Reed, Munazah Andrabi, Stuart Owen, Finn Bacall, Xiaoming Hu, Maja Rey, Martin Golebiewski, Flora D'Anna, Jacky Snoep, Wolfgang Müller, Carole Goble, Ulrike Wittig, Kevin De Pelseneer