The Network Data Exchange (NDEx)

Abbreviation:NDEx

Recommended

General Information

NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytoscape as well as programmatic access using a variety of languages including Python and Java. NDEx users can easily create accounts or sign in using their Google credentials thanks to the supported open authentication (OAUTH2) method and mint DOIs for their networks to use in publications or include in other resources for long term access.

This record replaces or incorporates the following deprecated resources:

Pathway Interaction Database

Homepage http://www.ndexbio.org

Developed in United States

Created in 2013

Taxonomic range

All

Knowledge Domains

In the following recommendations:

How to cite this record FAIRsharing.org: NDEx; The Network Data Exchange (NDEx); DOI: https://doi.org/10.25504/FAIRsharing.8nq9t6; Last edited: Jan. 13, 2019, 7:43 p.m.; Last accessed: Apr 21 2019 3:07 a.m.

This record is maintained by @NDExProject

Record added: Nov. 28, 2017, 9:57 p.m.
Record updated: Jan. 13, 2019, 7:43 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by '@NDExProject' at 18:23, 29 Nov 2017 (approved):

	'organizations' has been modified:
		Before:
			National Cancer Institute - ITCR Program|Government body|Funds
			UC San Diego - School of Medicine - Ideker Lab|University|Maintains
			BindingDB|Lab|Undefined
			California Digital Library (CDL)|University of California|Oakland|CA|USA|University|Undefined
			Cytoscape|Consortium|Undefined
			National Cancer Institute|Government body|Funds
		After:
			National Cancer Institute|Government body|Funds
			UC San Diego - School of Medicine - Ideker Lab|University|Maintains
			BindingDB|Lab|Undefined
			California Digital Library (CDL)|University of California|Oakland|CA|USA|University|Undefined
			Cytoscape|Consortium|Undefined
		Added:
		Removed:
			National Cancer Institute - ITCR Program|Government body|Funds

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by '@NDExProject' at 18:22, 29 Nov 2017 (approved):

	'organizations' has been modified:
		Before:
			National Cancer Institute - ITCR Program|Government body|Funds
			National Cancer Institute|Government body|Funds
			UC San Diego - School of Medicine - Ideker Lab|University|Maintains
			Cytoscape|Consortium|Undefined
			BindingDB|Lab|Maintains
			California Digital Library (CDL)|University of California|Oakland|CA|USA|University|Maintains
		After:
			National Cancer Institute - ITCR Program|Government body|Funds
			UC San Diego - School of Medicine - Ideker Lab|University|Maintains
			BindingDB|Lab|Undefined
			California Digital Library (CDL)|University of California|Oakland|CA|USA|University|Undefined
			Cytoscape|Consortium|Undefined
		Added:
			BindingDB|Lab|Undefined
			California Digital Library (CDL)|University of California|Oakland|CA|USA|University|Undefined
		Removed:
			National Cancer Institute|Government body|Funds
			BindingDB|Lab|Maintains
			California Digital Library (CDL)|University of California|Oakland|CA|USA|University|Maintains

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by 'The FAIRsharing Team' at 14:11, 29 Nov 2017 (approved):

	'domains' has been modified:
		Before:
			Cancer||http://purl.obolibrary.org/obo/DOID_162
			Genetic interaction||http://purl.obolibrary.org/obo/MI_0208
			Molecular interactions|pathways and networks||http://edamontology.org/topic_0602
			Network model|property|http://identifiers.org/mamo/MAMO_0000035
		After:
			Cancer||http://purl.obolibrary.org/obo/DOID_162
			Genetic interaction||http://purl.obolibrary.org/obo/MI_0208
			Molecular interactions|pathways and networks||http://edamontology.org/topic_0602
			Network model|property|http://identifiers.org/mamo/MAMO_0000035
			Pathway model|None|
		Added:
			Pathway model|None|
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by '@NDExProject' at 22:15, 28 Nov 2017 (approved):

	'related_standards' has been modified:
		Before:
		After:
			bsg-s001060|PAV Provenance|Authoring and Versioning
			bsg-s000572|Biological Expression Language
		Added:
			bsg-s001060|PAV Provenance|Authoring and Versioning
			bsg-s000572|Biological Expression Language
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by '@NDExProject' at 22:03, 28 Nov 2017 (approved):

	'organizations' has been modified:
		Before:
			National Cancer Institute - ITCR Program|Government body|Funds
			National Cancer Institute|Government body|Funds
			UC San Diego - School of Medicine - Ideker Lab|University|Maintains
			BindingDB|University|Undefined
			California Digital Library (CDL)|University of California|Oakland|CA|USA|University|Undefined
			Scientific Data|Publisher|Undefined
		After:
			National Cancer Institute - ITCR Program|Government body|Funds
			Cytoscape|Consortium|Undefined
			UC San Diego - School of Medicine - Ideker Lab|University|Maintains
			BindingDB|University|Undefined
			California Digital Library (CDL)|University of California|Oakland|CA|USA|University|Undefined
			Scientific Data|Publisher|Undefined
		Added:
			Cytoscape|Consortium|Undefined
		Removed:
			National Cancer Institute|Government body|Funds

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by '@NDExProject' at 21:59, 28 Nov 2017 (approved):

	'name' has been modified:
		Before: The Network Data Exchange
		After: The Network Data Exchange (NDEx)

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by 'choucygloria2007' at 10:24, 13 Nov 2017 (approved):

	'homepage' has been modified:
		Before: https://fairsharing.org/new/database
		After: https://fairsharing.org/edit/bsg-d001016

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by 'choucygloria2007' at 10:04, 13 Nov 2017 (approved):

	'dataProcesses' has been modified:
		Before:
			SSQOL
		After:
			SSQOLPLOSONE08252017
		Added:
			SSQOLPLOSONE08252017
		Removed:
			SSQOL

Support

General

blog	Informational Website
contact form	Contact Us
help	Report a Bug
online documentation	User manuals & Technical docs
twitter	Twitter Feed

Additional Information

Contact

Rudolf T. Pillich, PhD

Tools

CyNDEx - The NDEx Cytoscape App

http://apps.cytoscape.org/apps/cyndex

4.0.1

Access / Retrieve Data

Conditions of Use

Applies to: Database software

BSD-3-Clause License (Modified BSD License) (New BSD License)

Publications

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

Pillich RT,Chen J,Rynkov V,Welker D,Pratt D
Methods Mol Biol 2017

View Paper (PubMed) View Publication

NDEx, the Network Data Exchange.

Pratt D,Chen J,Welker D,Rivas R,Pillich R,Rynkov V,Ono K,Miello C,Hicks L,Szalma S,Stojmirovic A,Dobrin R,Braxenthaler M,Kuentzer J,Demchak B,Ideker T
Cell Syst 2015

View Paper (PubMed) View Publication

NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.

Pratt D,Chen J,Pillich R,Rynkov V,Gary A,Demchak B,Ideker T
Cancer Res 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts