Publication date: Aug 13, 2019
Biomedical informatics has traditionally adopted a linear view of the informatics process (collect, store and analyse) in translational medicine (TM) studies; focusing primarily on the challenges in data integration and analysis. However, a data management challenge presents itself with the new lifecycle view of data emphasized by the recent calls for data re-use, long term data preservation, and data sharing. There is currently a lack of dedicated infrastructure focused on the ‘manageability’ of the data lifecycle in TM research between data collection and analysis. Current community efforts towards establishing a culture for open science prompt the creation of a data custodianship environment for management of TM data assets to support data reuse and reproducibility of research results. Here we present the development of a lifecycle-based methodology to create a metadata management framework based on community driven standards for standardisation, consolidation and integration of TM research data. Based on this framework, we also present the development of a new platform (PlatformTM) focused on managing the lifecycle for translational research data assets.
Open Access PDF
, Emam, , Elyasigomari, Matthews, A., Pavlidis, S., Rocca-Serra, P., Guitton, F., Verbeeck, D., Grainger, L., Borgogni, E., Del Giudice, G., Saqi, M., Houston, P., and Guo, Y. PlatformTM, a standards-based data custodianship platform for translational medicine research. 05181. 2019 Sci Data (6):1.
- July 29 2019 i2b2 tranSMART Training i2b2 Install and Upgrade
- Precursor-induced conditional random fields: connecting separate entities by induction for improved clinical named entity recognition.
- A clustering approach for detecting implausible observation values in electronic health records data.