MINERVA—a platform for visualization and curation of molecular interaction networks

Abstract

Our growing knowledge about various molecular mechanisms is becoming increasingly more structured and accessible. Different repositories of molecular interactions and available literature enable construction of focused and high-quality molecular interaction networks. Novel tools for curation and exploration of such networks are needed, in order to foster the development of a systems biology environment. In particular, solutions for visualization, annotation and data cross-linking will facilitate usage of network-encoded knowledge in biomedical research. To this end we developed the MINERVA (Molecular Interaction NEtwoRks VisuAlization) platform, a standalone webservice supporting curation, annotation and visualization of molecular interaction networks in Systems Biology Graphical Notation (SBGN)-compliant format. MINERVA provides automated content annotation and verification for improved quality control. The end users can explore and interact with hosted networks, and provide direct feedback to content curators. MINERVA enables mapping drug targets or overlaying experimental data on the visualized networks. Extensive export functions enable downloading areas of the visualized networks as SBGN-compliant models for efficient reuse of hosted networks. The software is available under Affero GPL 3.0 as a Virtual Machine snapshot, Debian package and Docker instance at http://r3lab.uni.lu/web/minerva-website/. We believe that MINERVA is an important contribution to systems biology community, as its architecture enables set-up of locally or globally accessible SBGN-oriented repositories of molecular interaction networks. Its functionalities allow overlay of multiple information layers, facilitating exploration of content and interpretation of data. Moreover, annotation and verification workflows of MINERVA improve the efficiency of curation of networks, allowing life-science researchers to better engage in development and use of biomedical knowledge repositories.

The Atlas of Inflammation-Resolution (AIR)

“…We used OpenLayer and Google Maps based techniques to bring the AIR to the web-browser for easy visualization implemented on the MINERVA platform developed by University of Luxembourg 35 . Considering various user groups (clinicians, research scientists, pharmaceutical companies), we divided the AIR into three layers ( Figure 3).…”

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

“…We used the Interaction NEtwoRk visualization (MINERVA) web service 22 , to allow for content queries, custom dataset visualizations and feedback submission to manual curators. Custom datasets, particularly simulation results, can be visualized in a map context using the COBRA Toolbox 13 .…”

Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges

“…Another area to explore in future work is a better connection to the concept of disease maps, such as the Parkinson's disease map, 154 which can be queried computationallyand thus potentially integrated into mass spectral workowsvia interfaces such as MINERVA. 155 While hypothesis generation can begin already from data snapshots on patients and controls at certain time points, in reality the prioritisation and discovery of "driving" neurotoxicants will depend on forming high quality, long term datasets involving cohorts where participants are recruited even before any symptoms are displayed, so that long term trends become clear. Ideally, this would be extended across multiple cohorts to allow hypothesis development in one cohort and replication in another based on chemical-environmental strat-ication.…”