NDEx: A Community Resource for Sharing and Publishing of Biological Networks.

  title={NDEx: A Community Resource for Sharing and Publishing of Biological Networks.},
  author={Rudolf Tito Pillich and Jing Chen Jing Chen and Vladimir Rynkov and David Welker and Dexter Pratt},
  journal={Methods in molecular biology},
Networks are a powerful and flexible paradigm that facilitate communication and computation about interactions of any type, whether social, economic, or biological. NDEx, the Network Data Exchange, is an online commons to enable new modes of collaboration and publication using biological networks. NDEx creates an access point and interface to a broad range of networks, whether they express molecular interactions, curated relationships from literature, or the outputs of systematic analysis of… 

NDEx: Accessing Network Models and Streamlining Network Biology Workflows

This article introduces researchers to NDEx and highlights how it can simplify common tasks in network biology workflows as well as streamline publication and access to data.

Data-dependent visualization of biological networks in the web-browser with NDExEdit

NDExEdit is a web-based application where simple changes can be made to biological networks within the browser, and which does not require installation, and is designed to conform to the Cytoscape Exchange (CX) format as a data model, which is used for the data transmission by both tools.

A Guide to Conquer the Biological Network Era Using Graph Theory

This article discusses the basic graph theory concepts and the various graph types, as well as the available data structures for storing and reading graphs, and describes several network properties.

Data Journeys Beyond Databases in Systems Biology: Cytoscape and NDEx

  • W. Bechtel
  • Biology
    Data Journeys in the Sciences
  • 2020
This chapter investigates how data travels beyond databases in cell biology by focusing on Cytoscape, a platform that has been developed to represent networks, and NDEx, a database that allows for

NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.

Inventions addressing the challenges of an online data commons are described: scalability, data integration, data standardization, control of content and format by authors, and decentralized mechanisms for review.

Reproducible data integration and visualization of biological networks in R

A collection of software tools and libraries for network data integration, exploration, and visualization to document the different stages of the workflow and is accompanied by an interchangeable toolset for data exploration and network visualization.

WikiPathways: connecting communities

The growth of WikiPathways over the last three years is shown, the new communities and collaborations of pathway authors and curators are highlighted, and various technologies to connect to external resources and initiatives are described.

Reconciling Signaling Pathway Databases with Network Topologies.

This work considers signaling pathways as graphs and uses topological measures to study their structure and finds that topological characterization using graphlets (small, connected subgraphs) distinguishes signaling pathways from appropriate null models of interaction networks and quantifies topological similarity across pathway databases.

Stop Bickering! Reconciling Signaling Pathway Databases with Network Topologies

This work considers signaling pathways as graphs and uses topological measures to study their structure, and finds that topological characterization using graphlets (small, connected subgraphs) distinguishes signaling pathways from appropriate null models of interaction networks.



NDEx, the Network Data Exchange.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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.

PID: the Pathway Interaction Database

The Pathway Interaction Database (PID), a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes, serves as a research tool for the cancer research community and others interested in cellular pathways.

The Reactome pathway Knowledgebase

The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular

Bridging topological and functional information in protein interaction networks by short loops profiling

Fundamental principles of PPIN topologies are identified by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins, which define a core of interactions with high resilience.

Presenting and exploring biological pathways with PathVisio

This work presents PathVisio, a new visualization tool for biological pathways that mimics the popular GenMAPP tool with a completely new Java implementation that allows better integration with other open source projects.

KEGG: Kyoto Encyclopedia of Genes and Genomes

KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes.

CRAVAT: cancer-related analysis of variants toolkit

The Cancer-Related Analysis of Variants Toolkit (CRAVAT) is an evolving suite of informatics tools for mutation interpretation that includes mutation projecting and quality control, impact prediction and extensive annotation, gene- and mutation-level interpretation including joint prioritization of all nonsilent consequence types, and structural and mechanistic visualization.

PAV ontology: provenance, authoring and versioning

The Provenance, Authoring and Versioning ontology (PAV), a lightweight ontology for capturing “just enough” descriptions essential for tracking the provenance, authoring and versioning of web resources, is presented.