The evolution of standards and data management practices in systems biology.

Abstract

Mol Syst Biol. (2015) 11: 851 Systems biology involves the integration of multiple heterogeneous data sets, in order to model and predict biological processes. The domain's interdisciplinary nature requires data, models and other research assets to be formatted and described in standard ways to enable exchange and reuse. Infrastructure for Systems Biology Europe (ISBE) is a project to establish essential, centralized services for systems biology researchers throughout the systems biology lifecycle. A key component of ISBE is to support the management, integration and exchange of data, models, results and protocols. To inform further ISBE development, we surveyed the community to evaluate the uptake of available standards, and current practices of researchers in data and model management. The survey addressed four key areas as follows: 1. Standards usage; 2. Data and model storage before publication; 3. Sharing in public repositories after publication; 4. Reusability of data, models and results. The survey was sent to major mailing lists targeting the systems biology and computational biology communities and advertised at relevant consortia meetings. It elicited 153 responses, from 17 countries across 6 continents, with a cross section of the systems biology community represented (Appendix Fig S1). Lessons from the survey are being implemented as part of an ISBE supporting project, FAIRDOM (www.fair-dom.org). To understand how uptake of standards has developed, we compared our findings to a previous study by Klipp et al in 2007. Fig 1 shows a summary of the survey results (detailed results in Dataset EV1). A number of acronyms are used within the text, details of which can be found in Table 1. Figure 1. Survey summary. View this table: Table 1. Glossary of acronyms Formatting …