Publications

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83 Publications visible to you, out of a total of 83
FAIR Computational Workflows

Abstract (Expand)

ional workflows describe the complex multi-step methods that are used for data collection, data preparation, analytics, predictive modelling, and simulation that lead to new data products. They can … inherently contribute to the FAIR data principles: by processing data according to established metadata; by creating metadata themselves during the processing of data; and by tracking and recording data provenance. These properties aid data quality assessment and contribute to secondary data usage. Moreover, workflows are digital objects in their own right. This paper argues that FAIR principles for workflows need to address their specific nature in terms of their composition of executable software steps, their provenance, and their development.

Authors: Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober

Date Published: 2020

Publication Type: Journal Article

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

Abstract (Expand)

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

Formate assay in body fluids: application in methanol poisoning

Abstract

Not specified

Authors: A B Makar, K E McMartin, M Palese, T R Tephly

Date Published: 1st Jun 1975

Publication Type: Not specified

From steady-state to synchronized yeast glycolytic oscillations II: model validation.

Abstract (Expand)

UNLABELLED: In an accompanying paper [du Preez et al., (2012) FEBS J279, 2810-2822], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. Here we … validate the model by testing its capacity to simulate a wide range of experiments on dynamics of yeast glycolysis. In addition to its description of the oscillations of glycolytic intermediates in intact cells and the rapid synchronization observed when mixing out-of-phase oscillatory cell populations (see accompanying paper), the model was able to predict the Hopf bifurcation diagram with glucose as the bifurcation parameter (and one of the bifurcation points with cyanide as the bifurcation parameter), the glucose- and acetaldehyde-driven forced oscillations, glucose and acetaldehyde quenching, and cell-free extract oscillations (including complex oscillations and mixed-mode oscillations). Thus, the model was compliant, at least qualitatively, with the majority of available experimental data for glycolytic oscillations in yeast. To our knowledge, this is the first time that a model for yeast glycolysis has been tested against such a wide variety of independent data sets. DATABASE: The mathematical models described here have been submitted to the JWS Online Cellular Systems Modelling Database and can be accessed at http://jjj.biochem.sun.ac.za/database/dupreez/index.html.

Authors: F. B. du Preez, D. D. van Niekerk, J. L. Snoep

Date Published: 13th Jun 2012

Publication Type: Not specified

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