NDEx-The Network Data Exchange

Last updated: February 1st, 2021

Overview

The NDEx Project provides an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge.
One of the goals of the project is to create a home for models that are currently available only as figures, tables, or supplementary information, such as networks produced via systematic mining and integration of large-scale molecular data.
The NDEx project does not compete with existing pathway and interaction databases, such as Pathway Commons, KEGG, or Reactome; instead, NDEx provides a novel, common distribution channel for these efforts, preserving their identity and attribution rather than subsuming them.

Why NDEx?

What can I do with NDEx ? Why should I care to use it? These are very common questions that scientists might ask when presented a new tool they have never used before... There are many ways you can benefit from using NDEx for everyday work and collaboration, like a "Dropbox" for networks!

You can begin by reviewing the NDEx FAQ or browsing anonimously the network models available on the NDEx Public Server; when you sign up for an NDEx account, you get 10 GB of free cloud space, enough to store many of your own networks. Your networks start out as private to you, but you can share them to collaborate with other NDEx users or groups. You can also share a network with anyone using a Shareable URL, just paste it into email or documents! >> Learn More...

Distribute and Publish

NDEx includes features to support data distribution and access according to FAIR principles and is registered on FAIRsharing.org . Individual users and organizations can make networks public, findable and accessible in NDEx; each public network has its unique, stable URL and can always be downloaded either manually or programmatically, via our REST API.
NDEx lets you specify Licenses and Request DOIs for your networks to include in grant proposals or publications thus enabling papers to link directly to the data. Readers can now go from static figures to interactive, actionable data objects in just a few clicks! Vice versa, networks linking out to the papers they support provide you with new opportunities for discovery and citation.
NDEx is recommended by Scientific Data, Springer Nature and the PLOS family of journals. >> Learn More...

Cytoscape Integration

Cytoscape is the leading desktop application for network visualization and analysis and NDEx its built-in back-end cloud component. If you use Cytoscape for your work, you can easily save your networks in your NDEx account and preserve all visual style and layout information. In addition, networks viewed in the NDEx Web UI can be seamlessly opened in Cytoscape with just one click! >> Learn More...

Programmatic Access

Programs can read, write, and query NDEx via a REST API. You can build your workflows with NDEx as a source for networks, a destination for networks that you generate, or even as an intermediate location to link different components of a pipeline. We provide client libraries in Python, R and Java, and web applications can access NDEx via JavaScript. >> Learn More...

The Cytoscape Ecosystem of Services and Applications

NDEx is one of the pillars supporting the evolution of the Cytoscape ecosystem of tools and resources supporting network genomics. The shift to a Service Oriented Architecture paves the way for Cytoscape in the cloud, facilitating the use of network techniques that can be accessed conveniently in a web browser and flexibly integrated into modern data science workflows. Web applications can leverage the Cytoscape ecosystem in many ways, ranging from simple connections such as importing public networks from NDEx or sending gene lists to another ecosystem application, to deep integration where their functionality is primarily based on ecosystem services, data resources, or access to the Cytoscape desktop. A good example of such a web app is the Integrated Query (IQuery). IQuery is a model for a web app that builds workflows from ecosystem resources: it uses NDEx as source of pathways/networks to query, displays the results using cytoscape.js, interfaces to the Cytoscape desktop via CyREST and can save query results to NDEx.