FAIRshake

4DN data portal

project

The 4D Nucleome Network aims to understand the principles behind the three-dimensional organization of the nucleus in space and time (the 4th dimension) and the role nuclear organization plays in gene expression and cellular function. The Network utilizes existing omics and imaging technologies as well as develop new ones to generate data and create resources to enable the study of the 4D Nucleome.

Tags: Project

URL(s):

https://data.4dnucleome.org/

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Project Assessments (97)

Assessment		Metrics
Target	Rubric	NIH program name is available for querying	NIH project name is available for querying	The institution that created this dataset is available	A biological assay is present and resolvable in CFDE-specified ontology (OBI)	The tool has a unique name and an informative description.	The tool can be freely downloaded or accessed from a webpage.	The tool utilizes a community-accepted ontology.	Tutorials for the tool are available on the tools homepage.	Source code is shared in a public repository and is documented.	Previous versions of the tool are made available.	Contact information is provided for the creator(s) of the tool and information describing how to cite the tool is provided.	The tool can be accessed programmatically through an API and follows community standards for open APIs.	Licensing information is provided on the tools homepage.	A standardized ID or accession number is used to identify the dataset.	The dataset is described with metadata using a formal, broadly applicable vocabulary.	Information is provided on the experimental methods used to generate the data.	The dataset is hosted in an established data repository, if a relevant repository exists.	The dataset can be downloaded for free from the repository.	Version information is provided for the dataset.	Contact information is provided for the creator(s) of the dataset.	Information is provided describing how to cite the dataset.	Licensing information is provided on the datasets landing page.	The structure of the repository permits efficient discovery of data and metadata by end users.	The repository uses a standardized protocol to permit access by users.	The repository provides contact information for staff to enable users with questions or suggestions to interact with repository experts.	Tools that can be used to analyze each dataset are listed on the corresponding dataset pages.	The repository maintains licenses to manage data access and use.	The repository hosts data and metadata according to a set of defined criteria to ensure that the resources provided are consistent with the intent of the repository.	The repository provides documentation for each resource to permit its complete and accurate citation.	A description of the methods used to acquire the data is provided.	Version information is provided for each resource, where available.	Licensing information is provided on the tools home page	The tool has a unique name and an informative description	The tool can be freely downloaded or accessed from a webpage	ANISEED database	Machine readable metadata	Tutorials for the tool are available on the tools homepage	Source code is shared in a public repository and is documented	Contact information is provided for the creator(s) of the tool and information describing how to cite the tool is provided	The tool can be accessed programmatically through an API and follows community standards for open APIs	A standardized ID or accession number is used to identify the dataset	A relevant anatomical part is present and resolvable in the UBERON Ontology	A relevant disease is present and resolvable in the MONDO Ontology	A relevant file type is present and resolvable in the EDAM Ontology	A relevant taxonomy is present and resolvable in the NCBITaxon Ontology	A relevant cell line is present and resolvable in the Cellosaurus Ontology	A landing page exists and is accessible	Globally unique identifier	Machine-readable metadata	Standardized metadata	Resource identifier in metadata	Open, Free, Standardized Access protocol	Digital resource license	Metadata license	Do the Data repository use any Identifiers?	Do the repository have metadata records/files describing the data?	In which format data is described with metadata?	Does data repository is registered in any Registry?	Does the structure of the Repository allow discovery of data and metadata by end user?	Does Data repository uses any protocol to allow access by user?	Does the data repository provide public API?	Do the data repository provide versioning information of datasets?	Does Data repository uses Title for the data resource in Data?
4DN Jupyter Hub Tool - BETA	The FAIRshake tool rubric					yes (1.00)	yes (1.00)	yes (1.00)	nobut (0.25)	yes (1.00)	no (0.00)	yes (1.00)	nobut (0.25)	yes (1.00)																						no (0.00)
4D Nucleome	The FAIRshake repository rubric																							yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	yes (1.00)	no (0.00)
4DN data portal	The FAIRshake repository rubric																							yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yesbut (0.75)	nobut (0.25)	no (0.00)
4DN Visualization Workspace	The FAIRshake tool rubric					yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)																						no (0.00)
MicroMeta - Beta tool	The FAIRshake tool rubric					yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	no (0.00)	yes (1.00)																						no (0.00)
4DN data portal	Findable and Accessible FAIR Principles for Research Data Repositories																																																							yes (1.00)	yes (1.00)	yes (1.00)	no (0.00)	yes (1.00)	yes (1.00)	yes (1.00)	no (0.00)	yes (1.00)
4DN Visualization Workspace	Common Fund Tools Assessments																																yes (1.00)	yes (1.00)	yes (1.00)		no (0.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)
4DN Jupyter Hub Tool - BETA	Common Fund Tools Assessments																																yes (1.00)	yes (1.00)	yes (1.00)		yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)
MicroMeta - Beta tool	Common Fund Tools Assessments																																yes (1.00)	yes (1.00)	yes (1.00)		yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	no (0.00)	yes (1.00)
single cell RNA-seq on hamster olfactory sensory neurons	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
single cell RNA-seq on hamster olfactory sensory neurons	NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)																yes (1.00)																						yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	no (0.00)	no (0.00)
E/L repliseq on U2OS cells (2017-08-17)	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
sciATAC-seq on F123 cells	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
5C on 6Mb of chrX	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
DpnII-seq on K562 cells	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
Bru-seq on F121-9 mESCs	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
H3K4me2 - K562	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
Dual color smFISH on fruit fly embryo (nuclear cycle 13)	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
single cell Hi-C on sorted haploid H129-1s	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
Live imaging of chromatin topology and transcription	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
RNA-seq of early embryos in vitro	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
TSA-seq SON in K562 - HS	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
NAD-seq on MEF cells (not crosslinked)	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)
TCC on IMR90 +/- Adenovirus	The FAIRshake dataset rubric														yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yes (1.00)	yesbut (0.75)	yes (1.00)	yes (1.00)	no (0.00)

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