XTENS - A JSON-based digital repository for biomedical data management

Abstract

Biomedical Science poses unique challenges in data management. Heterogeneous information - such as clinical records, biological specimens, imaging and genomic data, different technology-associated formats - must be collected and integrated to provide a unified overview of each patient. International scale research collaborations involve different disciplines (Medicine/ Biology, Engineering/IT, Physics,…). Extensive metadata is required to maximize information sharing among the partners. To properly tackle these issues, we have developed XTENS, a data repository built on a flexible and extensible JSON-based data model. The JSON data model is conceived to achieve maximal flexibility, to allow adaptive metadata management, and to perceive metadata as a dynamical process of scientific communication rather than an enduring product fixed in time. XTENS is integrated with iRODS, a data grid software that allows distributed storage, metadata file annotation and advanced policies for data curation. We have adopted the platform for a functional connectomics multicentric project where heterogeneous data sources (radiological images, electroencephalography signals) must be integrated and analysed to compute connectivity maps of the brain. To this end, we have tested the repository prototype allowing the external programs to interact with XTENS using a service-oriented REST interface. We demonstrated XTENS usefulness because we could input heterogeneous data, run the required processing tool and store the process output.