OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics

Abstract

Researchers are increasingly seeking to interpret molecular data within a multi-omics context to gain a more comprehensive picture of their study system. OmicsNet (www.omicsnet.ca) is a web-based tool developed to allow users to easily build, visualize, and analyze multi-omics networks to study rich relationships among lists of ‘omics features of interest. Three major improvements have been introduced in OmicsNet 2.0, which include: (i) enhanced network visual analytics with eleven 2D graph layout options and a novel 3D module layout; (ii) support for three new ‘omics types: single nucleotide polymorphism (SNP) list from genetic variation studies; taxon list from microbiome profiling studies, as well as liquid chromatography–mass spectrometry (LC–MS) peaks from untargeted metabolomics; and (iii) measures to improve research reproducibility by coupling R command history with the release of the companion OmicsNetR package, and generation of persistent links to share interactive network views. We performed a case study using the multi-omics data obtained from a recent large-scale investigation on inflammatory bowel disease (IBD) and demonstrated that OmicsNet was able to quickly create meaningful multi-omics context to facilitate hypothesis generation and mechanistic insights.

Application of a multispecies probiotic reduces gastro-intestinal discomfort and induces microbial changes after colonoscopy

“…Species annotation was allowed at 100% identity. The web-based application OmicsNet 2.0 (https://www.omicsnet.ca/; accessed 07/2022) was used to extract possible metabolite networks around the features of interest (37). The potential score which indicates the probability that a given taxon produces a metabolite was set to 90%, current, universal and metabolites without pathway annotation, were excluded from analysis.…”

Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities

“…As a tool focusing on the visualization of omics data, Visual Omics cannot compete with well-known omics analysis platforms such as Galaxy ( Afgan et al , 2018 ) and GenePattern ( Reich et al , 2006 ) in terms of the richness of data analysis functions. However, compared with some recent omics analysis tools such as NASQAR, OmincsNet 2.0 ( Zhou et al , 2022 ), PaintOmics ( Tianyuan et al , 2022 ), and even specialized omics visualization tools like esquisse ( https://github.com/dreamRs/esquisse ) and Gosling ( L'Yi et al , 2022 ), Visual Omics not only provides a more comprehensive ability to adjust graph elements but also has greater flexibility in adjustment exploration based on version control and cross-session retuning functions ( Supplementary Table S5 ). The data processing flow required between the upstream omics analysis result and the standard input of the downstream analysis may also be integrated into Visual Omics in the future.…”

Application of a multispecies probiotic reduces gastro-intestinal discomfort and induces microbial changes after colonoscopy

“…Species annotation was allowed at 100% identity. The web-based application OmicsNet 2.0 (https://www.omicsnet.ca/; accessed 07/2022) was used to extract possible metabolite networks around the features of interest (39). The potential score which indicates the probability that a given taxon produces a metabolite was set to 90%, current, universal and metabolites without pathway annotation, were excluded from analysis.…”