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

Countries that developed this resource United States

Created in 2013

Taxonomic range

All

Knowledge Domains

Subjects

User-defined Tags

COVID-19

In the following recommendations:

Scientific Data

How to cite this record FAIRsharing.org: NDEx; The Network Data Exchange (NDEx); DOI: https://doi.org/10.25504/FAIRsharing.8nq9t6; Last edited: April 14, 2020, 9:39 a.m.; Last accessed: Jan 28 2021 7:59 a.m.

This record is maintained by @NDExProject

Record added: Nov. 28, 2017, 9:57 p.m.
Record updated: April 14, 2020, 9:31 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by 'The FAIRsharing Team' at 09:31, 14 Apr 2020 (approved):

	'user_defined_tags' has been modified:
		Before:
		After:
			COVID-19
		Added:
			COVID-19
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Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by 'The FAIRsharing Team' at 11:27, 13 Apr 2020 (approved):

	'onto_disciplines' has been modified:
		Before:
			Life Science
		After:
			Epidemiology
			Life Science
			Microbiology
		Added:
			Epidemiology
			Microbiology
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by '@NDExProject' at 19:29, 27 Jan 2020 (approved):

	'tools' has been modified:
		Before:
			CyNDEx - The NDEx Cytoscape App (for Cytoscape 3.3.x, 3.4.x and 3.5.x)|4.0.3|http://apps.cytoscape.org/apps/cyndex
			CyNDEx-2 (Core App for Cytoscape 3.7.x or higher)|3.0.1|http://apps.cytoscape.org/apps/cyndex2
		After:
			CyNDEx - The NDEx Cytoscape App (for Cytoscape 3.3.x, 3.4.x and 3.5.x)|4.0.3|http://apps.cytoscape.org/apps/cyndex
			CyNDEx-2 (Core App for Cytoscape 3.7.x and higher)|3.0.1|http://apps.cytoscape.org/apps/cyndex2
			NDEx Integrated Query|1.0|http://iquery.ndexbio.org
		Added:
			CyNDEx-2 (Core App for Cytoscape 3.7.x and higher)|3.0.1|http://apps.cytoscape.org/apps/cyndex2
			NDEx Integrated Query|1.0|http://iquery.ndexbio.org
		Removed:
			CyNDEx-2 (Core App for Cytoscape 3.7.x or higher)|3.0.1|http://apps.cytoscape.org/apps/cyndex2

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by '@NDExProject' at 19:26, 27 Jan 2020 (approved):

	'tools' has been modified:
		Before:
			CyNDEx - The NDEx Cytoscape App|4.0.1|http://apps.cytoscape.org/apps/cyndex
		After:
			CyNDEx - The NDEx Cytoscape App (for Cytoscape 3.3.x, 3.4.x and 3.5.x)|4.0.3|http://apps.cytoscape.org/apps/cyndex
			CyNDEx-2 (Core App for Cytoscape 3.7.x or higher)|3.0.1|http://apps.cytoscape.org/apps/cyndex2
		Added:
			CyNDEx - The NDEx Cytoscape App (for Cytoscape 3.3.x, 3.4.x and 3.5.x)|4.0.3|http://apps.cytoscape.org/apps/cyndex
			CyNDEx-2 (Core App for Cytoscape 3.7.x or higher)|3.0.1|http://apps.cytoscape.org/apps/cyndex2
		Removed:
			CyNDEx - The NDEx Cytoscape App|4.0.1|http://apps.cytoscape.org/apps/cyndex

Edits to 'https://fairsharing.org/FAIRsharing.8nq9t6' by 'The FAIRsharing Team' at 16:03, 08 Jan 2020 (approved):

	'organizations' has been modified:
		Before:
			UC San Diego - School of Medicine - Ideker Lab|https://healthsciences.ucsd.edu/som/medicine/research/labs/ideker/Pages/default.aspx|Maintains
			BindingDB|http://bindingdb.org/bind/aboutus.jsp|Undefined
			California Digital Library (CDL), University of California, Oakland, CA, USA|http://www.cdlib.org/|Undefined
			Cytoscape|http://www.cytoscape.org|Undefined
			National Cancer Institute, Rockville, MD, USA|https://ncifrederick.cancer.gov/Default.aspx|Funds
		After:
			National Cancer Institute, Rockville, MD, USA|https://ncifrederick.cancer.gov/Default.aspx|Funds
			BindingDB|http://bindingdb.org/bind/aboutus.jsp|Undefined
			California Digital Library (CDL), University of California, Oakland, CA, USA|http://www.cdlib.org/|Funds
			Cytoscape|http://www.cytoscape.org|Maintains
			Ideker Lab, School of Medicine, UC San Diego|http://idekerlab.ucsd.edu/|Maintains
		Added:
			California Digital Library (CDL), University of California, Oakland, CA, USA|http://www.cdlib.org/|Funds
			Cytoscape|http://www.cytoscape.org|Maintains
			Ideker Lab, School of Medicine, UC San Diego|http://idekerlab.ucsd.edu/|Maintains
		Removed:
			UC San Diego - School of Medicine - Ideker Lab|https://healthsciences.ucsd.edu/som/medicine/research/labs/ideker/Pages/default.aspx|Maintains
			California Digital Library (CDL), University of California, Oakland, CA, USA|http://www.cdlib.org/|Undefined
			Cytoscape|http://www.cytoscape.org|Undefined

	'supportLinks' has been modified:
		Before:
			blog|http://home.ndexbio.org
			contact form|http://home.ndexbio.org/contact-us/
			help|http://home.ndexbio.org/report-a-bug/
			online documentation|http://home.ndexbio.org/quick-start
			twitter|@NDExProject
		After:
			blog|https://www.linkedin.com/company/ndex-project
			blog|http://home.ndexbio.org
			contact form|http://home.ndexbio.org/contact-us/
			help|http://home.ndexbio.org/report-a-bug/
			online documentation|http://home.ndexbio.org/quick-start
			online documentation|https://www.youtube.com/channel/UCc7J1020F7e25F-zWEMtM0A
			twitter|@NDExProject
		Added:
			blog|https://www.linkedin.com/company/ndex-project
			online documentation|https://www.youtube.com/channel/UCc7J1020F7e25F-zWEMtM0A
		Removed:

	'licences' has been modified:
		Before:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Software
		After:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Software
			NDEx Terms, License and Sources|https://www.home.ndexbio.org/disclaimer-license/|Data
		Added:
			NDEx Terms, License and Sources|https://www.home.ndexbio.org/disclaimer-license/|Data
		Removed:

	'onto_disciplines' has been modified:
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			Life Science
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			Life Science
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	'dataProcesses' has been modified:
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			Browse & search
			Publish your network
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			Browse & search
			Publish your network
		Removed:

	'contact' has been modified:
		Before: Rudolf T. Pillich, PhD
		After: Rudolf T. Pillich

	'grants' has been modified:
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				5U24CA184427-02
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			5U24CA184427-02
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			5U24CA184427-02
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				5U24CA184427-02

	'miriam_id' has been modified:
		Before: None
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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

In Collections

COVID-19 Resources

NIH-supported data repositories

RDA Covid-19 WG Resources

Support

General

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

Additional Information

Contact

Rudolf T. Pillich

Tools

CyNDEx - The NDEx Cytoscape App (for Cytoscape 3.3.x, 3.4.x and 3.5.x)	http://apps.cytoscape.org/apps/cyndex	4.0.3
CyNDEx-2 (Core App for Cytoscape 3.7.x and higher)	http://apps.cytoscape.org/apps/cyndex2	3.0.1
NDEx Integrated Query	http://iquery.ndexbio.org	1.0

Access / Retrieve Data

Conditions of Use

Applies to: Data use

NDEx Terms, License and Sources

Applies to: Database software

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

Data Curation

Publish your network

https://home.ndexbio.org/publishing-in-ndex/

Data Access

Browse & search

http://www.ndexbio.org/#/search?searchType=All&searchString=&searchTer ...

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