Concept for acquisition and storage of process data and metadata to improve traceability and reproducibility in biomedicine

Abstract

Methods for the generation of engineered heart muscle (EHM) from induced pluripotent stem cells and application in experiment are advanced at the Institute of Pharmacology and Toxicology in Göttingen. Documentation and data capture do not adhere to latest developments of digital research. A comprehensive information system infrastructure is the foundation of further advances toward automation of lab processes. A data management system concept is proposed, prototypically deployed, and evaluated that should enable traceability of assets within the lab and reproducibility of published assays and results. Challenges, approaches, and software solutions are investigated by literature search and assessment. System requirements are defined based on regulations, best practises, and analysis of the local processes. Overarching goals are to enable research process, to maximize usability, to ensure information security, to favour dynamic extension, to maximize sustainability, and to increase reporting quality of results. These are translated into an architecture framework for a comprehensive research laboratory data management system. The proposed framework uses a service integration approach to combine five core components into a central portal site: electronic laboratory notebook, laboratory information management system, data integration and analysis system, research data management system, and multiple experiment-specific systems. Practical application of the concept is demonstrated by implementing a prototype system. The prototype integrates an existing electronic lab notebook, existing EHM process database, and a newly introduced research data management system by means of a custom developed portal and integration component based on the Drupal framework. Evaluation of the deployed prototype’s contribution to process quality shows moderately positive results. The overall architecture and developed tools are promising foundation for subsequent advancements.