The NCCR Microbiomes is committed to the DORA principles. All datasets and publications generated by the NCCR are deposited on open access repositories. The NCCR proactively organises trainings and workshops, both for its members and for the larger research community, on principles and best practices in open research.
We have several ongoing Open Science initiatives to increase the interoperability and reuseability of microbiomes research.
Enabling interoperability of microbial interaction data
Mapping the interactions that occur among microbial species is key to understanding and engineering microbiomes. Synthesizing microbial interaction data from the large volumes that are produced could enable ecological insights that are not achievable from individual studies. However, data on these interactions are collected by diverse methods and are stored in innumerable locations. Many datasets are not accessible, and still more are not comparable with other datasets. To make microbial interaction data more findable, accessible, interoperable, and reuseable (FAIR), we have begun to design a Microbial Interactions Database.
The project is led by postdoctoral researcher Alan Pacheco (ETHZ), with support from PhD student Tania Miguel Trabajo (UNIL), PI Sara Mitri (UNIL), and data manager Kendra Brown. It has drawn participation from NCCR members across work packages who use a variety of methods to observe and characterize microbial interactions.
The prototype database is under development. We hope to refine and expand it over time with contributions from researchers outside the NCCR.
Encouraging Secondary Analysis of Microbiomes Data
The goal of Open Research Data is to enable data re-use, but in the past there has not been a methodical program for microbiomes researchers to learn about relevant methods. To meet this need, we have developed a five-week short course on secondary data analysis, offered during the spring semester through the UNIL Life Sciences doctoral program. In its first iteration, the course drew on expertise from NCCR postdoctoral researchers: Ricardo Arraiano Castilho (UNIL) taught a session on formulating research questions for secondary analysis; Janko Tackmann (UZH) on working with multiple raw data sets; Jeanne Tamarelle (UNIL) on systematic review and meta-analysis. Students choose their own topic for an individual research project and used methods from the course to conduct an analysis.
Although students encountered many challenges with identifying, gaining access to, and working with others’ data, they saw many opportunities for incorporating secondary data analysis in their own work. Moreover, the course kicked off a discussion of what is needed to overcome existing barriers to data re-use.
Sharing Research Protocols
Detailed research protocols are essential to enable reproducibility of results. Within the NCCR, we support researchers in developing protocols of their methods to first share internally, and eventually publish publicly. Internally, sharing methods helps with training and collaboration. Publishing protocols provides a necessary link between published data and results.