MoPS update: current status and next steps

EFSA’s Microorganisms Pipelines Service, MoPS, is progressing towards implementation as a key tool for analysing whole genome sequence data in regulatory submissions involving microorganisms.

The pilot phase has now been completed, and the system is moving towards finalisation and deployment. Availability is currently expected by the end of 2026, with mandatory use expected to begin in mid-2027.

A key feature of the planned setup is that MoPS will not be provided as a downloadable tool. Instead, EFSA is developing a controlled workspace environment in which analyses will be conducted. This means that applicants will interact with the system within EFSA’s infrastructure, rather than running a downloadable version independently. The pipeline will be shared in DevOps with full version control.

The current timeline foresees a transition from availability to full regulatory integration, with mandatory use expected to begin in mid-2027.

Although the overall framework is now clearer, EFSA is still finalising the technical setup and practical implementation of the system. The current focus is on ensuring that the workspace functions reliably and that the processes for handling genomic data are clearly defined.

Importantly, the output generated by MoPS should be understood as bioinformatics results. These outputs represent only one part of the overall safety assessment and must be interpreted together with additional evidence, such as phenotypic data, literature and other relevant scientific information. The tool therefore does not replace expert assessment, but rather supports it.

In summary, MoPS is becoming a key digital component of EFSA’s assessment framework for microorganisms. With the pilot phase completed, availability expected later this year and mandatory use planned from 2027, the system will play an increasingly central role in how microbial data are evaluated in EU regulatory submissions.