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):

View Associations View Analytics

Project Assessments (111)


Assessment Metrics Date
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 tool’s 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 tool’s 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 dataset’s 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 tool’s 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
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)                                       Oct 20, 2022
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)                                               Oct 20, 2022
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)                                       Oct 25, 2022
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)                                       Oct 25, 2022
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)                           Oct 26, 2022
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)                           Nov 2, 2022
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)                           Nov 2, 2022
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)                                                                 May 30, 2023
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) May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
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)                                                                 May 30, 2023
sciHi-C on F121-6 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)                                                                 May 30, 2023
RNA-DNA SPRITE on pSM33 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)                                                                 May 30, 2023