Molgenis – Omics Data Management

MOLGENIS helps to find, capture, exchange, manage and analyse scientific data. It is fully customizable: data structure, user interface, and layout can be fully changed. Molgenis is a web-based application for the management of scientific data. The entire data model, consisting of various entities and variables, is highly flexible and configurable. A user-friendly interface allows capturing, exchanging, and exploitation of large amounts of data. Molgenis helps to make the data FAIR and makes it easy to share and reuse data. The fine-grained permission system allows exposing of the appropriate data without exposing (sensitive) data. Genomic data can be visualized right out of the box. Molgenis further allows running computational scripts for data analysis. Molgenis also offers a REST API to connect to the data from an analysis script or a custom plugin.

Molgenis APP

We created a user login to illustrate the use of Molgenis as an administrator. The Molgenis app in the GitHub BIBBOX repository has been extended by a FAIR Data Point and a Provenance Access Point.

Login Credentials Admin:
Username: “admin”
Password: “admin”

Link to the Molgenis instance

Link to the Molgenis FAIR Data Point›

Login Credentials:
The FDP does not require a login to browse the stored information.


Molgenis specifies a data model using Excel files in a very specific format: The EMX file format. One single file describes all relations in the database and holds all the data at the same time. An integrated user management system enables the definition of roles and individual access rights, allowing users to only view or edit the data.

Molgenis data overview


Molgenis can be customized in different ways and offers the possibility of developing applications, as the BBMRI-ERIC project shows.

BBMRI-ERIC based on Molgenis