SPV: a JavaScript Signaling Pathway Visualizer

  title={SPV: a JavaScript Signaling Pathway Visualizer},
  author={Alberto C and Gianni Cesareni},
  pages={2684 - 2686}
Summary: The visualization of molecular interactions annotated in web resources is useful to offer to users such information in a clear intuitive layout. These interactions are frequently represented as binary interactions that are laid out in free space where, different entities, cellular compartments and interaction types are hardly distinguishable. Signaling Pathway Visualizer is a free open source JavaScript library, which offers a series of pre‐defined elements, compartments and… 

Figures from this paper

SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update

Signor 2.0 now stores almost 23 000 manually-annotated causal relationships between proteins and other biologically relevant entities: chemicals, phenotypes, complexes, etc and has improved the compliance to the FAIR data principles by providing stable identifiers and downloadable data in standard-compliant formats.

CancerGeneNet: linking driver genes to cancer hallmarks

CancerGeneNet annotates curated pathways that are relevant to rationalize the pathological consequences of cancer driver mutations in selected common cancers and ‘MiniPathways’ illustrating regulatory circuits that are frequently altered in different cancers.

Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration

Myo-REG, a web portal that captures and integrates published information on skeletal muscle regeneration, is developed and is one of a kind in the myology field and allows access to information on cell and molecular interactions in the context of muscle regeneration.

Myo-REG: a portal for signaling interactions in muscle regeneration

Myo-REG, a web portal that captures and integrates published information on skeletal muscle regeneration, is developed and is one of a kind in the myology field and allows users to explore, approximately 100 cell interactions or to analyze intracellular pathways related to muscle regeneration.

Disease networks and their contribution to disease understanding and drug repurposing. A survey of the state of the art

The evolution of disease network concept during the last decade is analyzed and a data science pipeline approach is applied to evaluate their functional units to obtain a list of the most commonly used functional units and the challenges that remain to be solved.

Using the MINT Database to Search Protein Interactions

This article provides protocols for searching MINT over the Internet, using the new MINT Web Page, which contains information on more than 26,000 proteins and more than 131,600 interactions in over 30 model organisms.

Mapping the technology evolution path: a novel model for dynamic topic detection and tracking

A method for mapping the technology evolution path using a novel non-parametric topic model, the citation involved Hierarchical Dirichlet Process (CIHDP), to achieve better topic detection and tracking of scientific literature and can be helpful for understanding and analyzing the development of technical topics.



CellWhere: graphical display of interaction networks organized on subcellular localizations

This user-friendly tool helps in the formulation of mechanistic hypotheses by enabling the experimental biologist to explore simultaneously two elements of functional context: (i) protein subcellular localization and (ii) protein–protein interactions or gene functional associations.

ComplexViewer: visualization of curated macromolecular complexes

Summary Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary

Pathway Commons, a web resource for biological pathway data

A web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data.

SIGNOR: a database of causal relationships between biological entities

Assembly of large biochemical networks can be achieved by confronting new cell-specific experimental data with an interaction subspace constrained by prior literature evidence by providing a scaffold of prior experimental evidence of causal relationships between biological entities.

SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

With SignaLink 2 as a single resource, users can effectively analyze signaling pathways, scaffold proteins, modifier enzymes, transcription factors and miRNAs that are important in the regulation of signaling processes.

Cytoscape.js: a graph theory library for visualisation and analysis

Cytoscape.js is an open-source JavaScript-based graph library that can be used to render interactive graphs in a web browser and in a headless manner, useful for graph operations on a server, such as Node.js.

The complex portal - an encyclopaedia of macromolecular complexes

The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

The recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism, and a range of improvements to the integrated bioinformatics solutions are reported.

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

The International Molecular Exchange (IMEx) consortium is an international collaboration between major public interaction data providers to share literature-curation efforts and make a nonredundant

DISNOR: a disease network open resource

The gene-disease association data annotated in the DisGeNET resource is combined with a new curation effort aimed at populating the SIGNOR database with causal interactions related to disease genes with the highest possible coverage.