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4DNucleome Data Portal

Abbreviation:4DN

General Information

The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data.

Homepage https://data.4dnucleome.org/

Countries that developed this resource United States

Created in 2016

Taxonomic range

Drosophila melanogaster

Gallus gallus

Homo sapiens

Mus musculus

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: 4DN; 4DNucleome Data Portal; DOI: https://doi.org/10.25504/FAIRsharing.CugtbQ; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Sep 25 2021 10:19 p.m.

This record is maintained by 4DNucleome DCIC (4dn_dcic)

Record added: April 17, 2019, 4:59 p.m.
Record updated: Feb. 9, 2021, 3:34 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.CugtbQ' by 'The FAIRsharing Team' at 15:34, 09 Feb 2021 (approved):

	'onto_domains' has been modified:
		Before:
			Experiment report
			Experimental measurement
			Nucleic acid sequence
			Workflow
			chromosome
			data transformation
		After:
			Experimental measurement
			Nucleic acid sequence
			Workflow
			chromosome
			data transformation
		Added:
		Removed:
			Experiment report

Edits to 'https://fairsharing.org/FAIRsharing.CugtbQ' by 'The FAIRsharing Team' at 11:56, 12 Oct 2020 (approved):

	'standardsImplemented' has been modified:
		Before:
			Experimental Factor Ontology
			FASTQ Sequence and Sequence Quality Format
			Big Browser Extensible Data Format
			bigWig Track Format
			Binary Alignment Map Format
			Common Workflow Language
			BEDgraph
			Pairs file format
			Cooler file format
		After:
			Experimental Factor Ontology
			FASTQ Sequence and Sequence Quality Format
			Big Browser Extensible Data Format
			bigWig Track Format
			Binary Alignment Map Format
			Common Workflow Language
			BEDgraph
			JavaScript Object Notation
			JavaScript Object Notation for Linking Data
			Pairs file format
			Cooler file format
		Added:
			JavaScript Object Notation
			JavaScript Object Notation for Linking Data
		Removed:

	'supportLinks' has been modified:
		Before:
			help|https://data.4dnucleome.org/help/user-guide
			online documentation|https://data.4dnucleome.org/help/about/about-dcic
			online documentation|https://data.4dnucleome.org/help/user-guide/biosample-metadata
		After:
			help|https://data.4dnucleome.org/help/user-guide
			help|https://data.4dnucleome.org/help/user-guide/rest-api
			online documentation|https://data.4dnucleome.org/help/about/about-dcic
			online documentation|https://data.4dnucleome.org/help/user-guide/biosample-metadata
			twitter|@4dn_dcic
		Added:
			help|https://data.4dnucleome.org/help/user-guide/rest-api
			twitter|@4dn_dcic
		Removed:

	'onto_domains' has been modified:
		Before:
			Experiment report
			Experimental measurement
			Nucleic acid sequence
			chromosome
			data transformation
		After:
			Experiment report
			Experimental measurement
			Nucleic acid sequence
			Workflow
			chromosome
			data transformation
		Added:
			Workflow
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.CugtbQ' by 'The FAIRsharing Team' at 20:27, 17 Apr 2019 (approved):

	'organizations' has been modified:
		Before:
			NIH Common Fund, USA|https://commonfund.nih.gov|Funds
		After:
			NIH Common Fund, USA|https://commonfund.nih.gov|Funds
			Data Coordination and Intregration Center|http://dcic.4dnucleome.org/|Maintains
		Added:
			Data Coordination and Intregration Center|http://dcic.4dnucleome.org/|Maintains
		Removed:

	'supportLinks' has been modified:
		Before:
		After:
			help|https://data.4dnucleome.org/help/user-guide
			online documentation|https://data.4dnucleome.org/help/about/about-dcic
			online documentation|https://data.4dnucleome.org/help/user-guide/biosample-metadata
		Added:
			help|https://data.4dnucleome.org/help/user-guide
			online documentation|https://data.4dnucleome.org/help/about/about-dcic
			online documentation|https://data.4dnucleome.org/help/user-guide/biosample-metadata
		Removed:

	'description' has been modified:
		Before: A platform to search, visualize, and download nucleomics data.
		After: The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data.

	'dataProcesses' has been modified:
		Before:
			4DN REST API
		After:
			Submit Data
			Analysis and Visualization
			Browse Data
		Added:
			Submit Data
			Analysis and Visualization
			Browse Data
		Removed:
			4DN REST API

	'onto_domains' has been modified:
		Before:
			chromosome
		After:
			Experiment report
			Experimental measurement
			Nucleic acid sequence
			chromosome
			data transformation
		Added:
			Experiment report
			Experimental measurement
			Nucleic acid sequence
			data transformation
		Removed:

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://data.4dnucleome.org/help/user-guide/rest-api|4DN REST API
		Added:
			REST|https://data.4dnucleome.org/help/user-guide/rest-api|4DN REST API
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.CugtbQ' by '4dn_dcic' at 17:20, 17 Apr 2019 (approved):

	'standardsImplemented' has been modified:
		Before:
		After:
			Experimental Factor Ontology
			Binary Alignment Map Format
			Big Browser Extensible Data Format
			bigWig Track Format
			FASTQ Sequence and Sequence Quality Format
			BEDgraph
			Common Workflow Language
		Added:
			Experimental Factor Ontology
			Binary Alignment Map Format
			Big Browser Extensible Data Format
			bigWig Track Format
			FASTQ Sequence and Sequence Quality Format
			BEDgraph
			Common Workflow Language
		Removed:

	'related_databases' has been modified:
		Before:
		After:
			Gene Expression Omnibus
			Sequence Read Archive
			ENCODE Project 
		Added:
			Gene Expression Omnibus
			Sequence Read Archive
			ENCODE Project 
		Removed:

	'onto_disciplines' has been modified:
		Before:
		After:
			Life Sciences
		Added:
			Life Sciences
		Removed:

	'dataProcesses' has been modified:
		Before:
		After:
			4DN REST API
		Added:
			4DN REST API
		Removed:

	'onto_domains' has been modified:
		Before:
		After:
			chromosome
		Added:
			chromosome
		Removed:

	'tools' has been modified:
		Before:
		After:
			Submit 4DN|1.1.0|https://github.com/4dn-dcic/submit4dn
		Added:
			Submit 4DN|1.1.0|https://github.com/4dn-dcic/submit4dn
		Removed:

Support

General

help	User Guide
help	Rest API Documentation
online documentation	About DCIC
online documentation	Biosample metadata
twitter	@4dn_dcic

Additional Information

Contact

4DN Helpdesk

Tools

Submit 4DN

https://github.com/4dn-dcic/submit4dn

1.1.0

Access / Retrieve Data

Conditions of Use

Data Curation

Submit Data

https://data.4dnucleome.org/help/submitter-guide/online-submission

Data Access

Analysis and Visualization	https://data.4dnucleome.org/help/analysis-and-visualization
Browse Data	https://data.4dnucleome.org/browse/?award.project=4DN&experimentset_ty ...

REST Web Services

4DN REST API

https://data.4dnucleome.org/help/user-guide/rest-api

Publications

The 4D nucleome project.

Dekker J,Belmont AS,Guttman M,Leshyk VO,Lis JT,Lomvardas S,Mirny LA,O'Shea CC,Park PJ,Ren B,Politz JCR,Shendure J,Zhong S
Nature 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Experimental Factor Ontology

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by 4DNucleome DCIC (4dn_dcic)

Funds

NIH Common Fund, USA (Government body)

Maintains

Data Coordination and Intregration Center (Consortium) Lead

Grant Number(s)

1U01CA200059-01 (NIH Common Fund, USA)

4DNucleome Data Portal

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