Efficient data management infrastructure for the integration of imaging and omics data in life science research [article]

Luis Kuhn Cuellar, Andreas Friedrich, Gisela Gabernet, Luis de la Garza, Sven Fillinger, Adrian Seyboldt, Sven zur Oven-Krockhaus, Friederike Wanke, Sandra Richter, Wolfgang M. Thaiss, Marius Horger, Nisar Malek (+3 others)
2019 bioRxiv   pre-print
As technical developments in omics and biomedical imaging drive the increase in quality, modality, and throughput of data generation in life sciences, the need for information systems capable of integrative, long-term storage and management of these heterogeneous digital assets is also increasing. Here, we propose an approach based on principles of Service Oriented Architecture design, to allow the integrated management and analysis of multi-omics and biomedical imaging data. The proposed
more » ... The proposed architecture introduces an interoperable image management system, the OMERO server, into the backend of qPortal, a FAIR-compliant web-based platform for omics data management. The implementation of an integrated metadata model, the development of software components to facilitate the communication with the OMERO server, and an extension to the data management operations of qPortal, allowed FAIR management of heterogeneous omics and biomedical imaging data within an integrated system, which facilitates metadata queries from web-based scientific applications. The applicability of the proposed architecture was demonstrated on two use cases, a plant biology study using confocal scanning microscopy, and a clinical study on hepatocellular carcinoma, with data from a variety of medical imaging and omics modalities.
doi:10.1101/2019.12.28.889295 fatcat:mpmsznhgw5g7bcrvhdovakv5f4