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Protocols

NDEx specifications

Information


Unique identifier OMICS_29036
Name NDEx
Alternative name Network Data Exchange
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Allowed
Version 2.3
Maintained Yes

Maintainer


  • person_outline Florian Auer

Additional information


A R client library for NDEx is available at https://github.com/frankkramer-lab/ndexr

Publications for Network Data Exchange

NDEx citations

 (7)
call_split

New perspectives: systems medicine in cardiovascular disease

2018
BMC Syst Biol
PMCID: 5921396
PMID: 29699591
DOI: 10.1186/s12918-018-0579-5
call_split See protocol

[…] collected on the Pathguide.org website [], which currently lists over 600 resources related to biological pathway and interaction knowledge. The most prominent pathway databases are Reactome [], the Network Data Exchange (NDEx) [], the Kyoto Encyclopedia of Genes and Genomes (KEGG) [], and WikiPathways [] as well as disease-specific databases such as the Online Mendelian Inheritance in Man (OMIM) […]

library_books

Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming

2018
BMC Bioinformatics
PMCID: 5850944
PMID: 29536824
DOI: 10.1186/s12859-018-2034-4

[…] ling networks may be considered time demanding, many publicly available resources containing regulatory information currently exist such as KEGG [], Reactome [, ], Pathway Commons [], OmniPath [] and NDEX []. Some of these resources have available tools or Cytoscape [] plug-ins to extract networks given a list of molecules, such as ReactomeFIViz [] for Reactome, CyPath2 [] for Pathway Commons and […]

library_books

PyBEL: a computational framework for Biological Expression Language

2017
Bioinformatics
PMCID: 5860616
PMID: 29048466
DOI: 10.1093/bioinformatics/btx660

[…] k between disease-specific networks.We implemented lossless converters for common file formats including Node-Link JSON, JGIF, CX, and binary as well as for database formats including SQL, Neo4J, and NDEx. We also provide lossy exporters to Excel, CSV, SIF, XGMML, and GSEA to facilitate usage in other programs. Notably, we have deferred implementing a RDF (Resource Description Framework) converter […]

call_split

Multitype Network Guided Target Controllability in Phenotypically Characterized Osteosarcoma: Role of Tumor Microenvironment

2017
Front Immunol
PMCID: 5536125
PMID: 28824643
DOI: 10.3389/fimmu.2017.00918
call_split See protocol

[…] latter for molecular function annotation of the proteins containing variations. Note that pathway interaction cancer-specific data were retrieved from the Github repository () (recently integrated in NDEx, the Network Data Exchange database) (). The protein complexes were retrieved from the CORUM database (), which manually annotated resources from mammalian organisms. Comprehensive annotations in […]

library_books

Immuno Oncology Integrative Networks: Elucidating the Influences of Osteosarcoma Phenotypes

2017
Cancer Inform
PMCID: 5533255
PMID: 28804242
DOI: 10.1177/1176935117721691

[…] ons which are displayed (regions marked in light blue) are associated exclusively with cancer annotations retrieved from the PID (https://github.com/NCIP/pathway-interaction-database, now migrated to NDeX,; http://www.home.ndexbio.org/about-ndex/). Such experimentally verified associations have been mapped onto the gene-miRNA target networks.Overall, pathway landscapes revealed commonalities acros […]

library_books

Urotensin II System in Genetic Control of Blood Pressure and Renal Function

2013
PLoS One
PMCID: 3877024
PMID: 24391740
DOI: 10.1371/journal.pone.0083137

[…] lice variant was available, the longest was used as the reference sequence. Multiple peptide sequences were aligned using Teecof[email protected] web server (http://igs-server.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/i ndex.cgi) and manually inspected for accuracy . Sequences missing the biologically important C-terminal fragments of U-II or urotensin-II related peptide (URP) or sequences substantially shorter than […]

Citations

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NDEx institution(s)
Department of Medical Statistics, University Medical Center Göttingen, Göttingen, Germany; Discovery Science, Clarivate Analytics, Boston, MA, USA; Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
NDEx funding source(s)
Supported by the German Ministry of Education and Research (BMBF) grants FKZ01ZX1508 and FKZ031L0024A.

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