NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.

@article{Pratt2017NDEx2A,
  title={NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.},
  author={Dexter Pratt and Jing Chen and Rudolf Tito Pillich and Vladimir Rynkov and Aaron Gary and Barry Demchak and Trey Ideker},
  journal={Cancer research},
  year={2017},
  volume={77 21},
  pages={
          e58-e61
        }
}
We present NDEx 2.0, the latest release of the Network Data Exchange (NDEx) online data commons (www.ndexbio.org) and the ways in which it can be used to (i) improve the quality and abundance of biological networks relevant to the cancer research community; (ii) provide a medium for collaboration involving networks; and (iii) facilitate the review and dissemination of networks. We describe innovations addressing the challenges of an online data commons: scalability, data integration, data… 

Figures from this paper

Open Data to Support CANCER Science—A Bioinformatics Perspective on Glioma Research

This work illustrates the current state of the art with examples from glioma research and shows how open data can be used for cancer research in general, and point out several resources and tools that are readily available.

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange

The NDEx Integrated Query (IQuery) is a new tool for network and pathway-based gene set interpretation that complements or extends existing resources, and combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results.

Integration of the Drug-Gene Interaction Database (DGIdb) with open crowdsource efforts

A major focus of this update was integration with crowd-sourced efforts, including leveraging the curation activities of Drug Target Commons, using Wikidata to facilitate term normalization, and integrating into NDEx for producing network representations.

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.

Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

A primary focus of this update was integration with crowdsourced efforts, leveraging the Drug Target Commons for community-contributed interaction data, Wikidata to facilitate term normalization, and export to NDEx for drug-gene interaction network representations.

On the limits of active module identification

The results clearly show that, except for the recently proposed AMIM DOMINO, the tested AMIMs do not produce biologically more meaningful candidate disease modules on widely used PPI networks than on random networks with the same node degrees.

Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases

The RCD network map was employed for interpreting the functional differences in cell death regulation between Alzheimer’s disease and non-small cell lung cancer based on gene expression data that allowed emphasizing the molecular mechanisms underlying the inverse comorbidity between the two pathologies.

Informatics Tools for Cancer Research and Care: Bridging the Gap Between Innovation and Implementation.

The advances in the understanding of the mechanisms underlying cancer have been paralleled by an explosion in computational research, which is changing the ability to work with data in new ways and at re-markable scales.
...

References

SHOWING 1-10 OF 10 REFERENCES

NDEx, the Network Data Exchange.

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

NDEx can also facilitate the integration of networks as data in electronic publications, thus making a step toward an ecosystem in which networks bearing data, hypotheses, and findings flow seamlessly between scientists.

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.

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.

Digital Object Identifier (DOI) System

The Digital Object Identifier (DOI®) System is a managed system for persistent identification of content on digital networks. It can be used to identify physical, digital, or abstract entities. The

DARPA's Big Mechanism program.

  • P. Cohen
  • Computer Science
    Physical biology
  • 2015
The Big Mechanism program aims to have machines read the literature and assemble the causal fragments found in individual papers into huge causal models, automatically, automatically.

Principled design of the modern Web architecture

  • R. FieldingR. Taylor
  • Computer Science
    Proceedings of the 2000 International Conference on Software Engineering. ICSE 2000 the New Millennium
  • 2000
The Representational State Transfer (REST) architectural style is introduced, developed as an abstract model of the Web architecture to guide the redesign and definition of the Hypertext Transfer Protocol and Uniform Resource Identifiers.

The NDEx Project

  • 2014

Cell Maps FAQ -Cancer Cell Map Initiative [Internet]. Cancer Cell Map Initiative