Large collaborative projects need to share data during and after, within and beyond the consortium. FAIRDOM-SEEK (https://fairdomseek.org/) is an open-source software for storing, cataloguing, sharing and reusing research outcomes designed to support the principles of FAIR (Findable, Accessible, Interoperable, and Reusable) research data management. Originally developed for the needs of systems biology of microorganisms, SEEK is used in numerous projects of systems biology, systems medicine, and related domains. All data types can be handled and the use of files or references to files is possible. Users can change the visibility of files and references, making it a platform for projects and data publication. Its properties make it an interoperability resource for combining different tools for scientific work and subsequent publication of the outcomes.
The systems medicine approach to quantification and characterization of large complex systems involves integration of multipledata types (e.g. genomics, proteomics, metabolomics, phenomics, images, patient related data, etc.), stored in several specialized systems used within one project.
LiSyM-Cancer for example, uses REDCap (https://www.project-redcap.org/) as a clinical data system that manages information about patients and samples; openBIS (https://openbis.ch/) as primary system for experimental raw data and its metadata; Nextcloud (https://nextcloud.com/) for short-term raw data exchange; and OMERO for microscopic images. The harmonisation and integration of (meta)data between these platforms is mandatory to make the data comparable and publishable in open data repositories.
Here, we describe our experience in combining multiple open-source data repository systems for the benefit of large collaborative projects.