4D Nucleome Data Portal
The 4D Nucleome (4DN) Network aims to understand the principles underlying nuclear organization in space and time (the 4th dimension). The 4DN Data Portal provides a platform to search, visualize, and download nucleomics data generated by the 4DN Network and other reference datasets.
[{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "support@4dnucleome.org"}, {"contact_type": "url", "value": "https://data.4dnucleome.org/help/about/contact-us"}], "label": "4D Nucleome Network Data Coordination and Integration Center (DCIC)"}]
[{"category": "DataProduct", "description": "A comprehensive collection of Hi-C datasets generated by the 4DN Network and other reference datasets, available for search, visualization, and download.", "format": "tsv", "id": "4dn.hic", "name": "4DN Hi-C Datasets", "product_url": "https://data.4dnucleome.org/hic-data-overview"}, {"category": "DataProduct", "description": "A collection of microscopy datasets, including super-resolution microscopy and chromatin tracing data, for visualizing nuclear organization.", "format": "tsv", "id": "4dn.microscopy", "name": "4DN Microscopy Datasets", "product_url": "https://data.4dnucleome.org/microscopy-data-overview"}, {"category": "DataProduct", "description": "A specialized collection of chromatin tracing datasets that provide insights into the 3D organization of chromatin in the nucleus.", "format": "tsv", "id": "4dn.chromatin_tracing", "name": "4DN Chromatin Tracing Datasets", "product_url": "https://data.4dnucleome.org/resources/data-collections/chromatin-tracing-datasets"}, {"category": "GraphicalInterface", "description": "A web-based visualization tool for exploring and comparing genomic data, particularly suited for Hi-C and other 4DN datasets.", "id": "4dn.higlass", "name": "HiGlass", "product_url": "https://data.4dnucleome.org/tools/visualization"}, {"category": "ProcessProduct", "description": "A cloud-based Jupyter environment for analyzing 4DN data without downloading it, including example notebooks for data exploration.", "id": "4dn.jupyterhub", "name": "4DN JupyterHub", "product_url": "https://data.4dnucleome.org/tools/jupyterhub"}, {"category": "ProcessProduct", "description": "A tool for entering and accessing microscope metadata with standardized formats.", "id": "4dn.micrometa", "name": "Micro Meta App", "product_url": "https://data.4dnucleome.org/tools/micro-meta-app"}, {"category": "GraphProduct", "description": "Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access.", "dump_format": "neo4j", "id": "ubkg.neo4j", "name": "UBKG Neo4j Docker Distribution", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access.", "format": "csv", "id": "ubkg.csv", "name": "UBKG Ontology CSV Files", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}]
{"activity_status": "active", "category": "DataSource", "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "support@4dnucleome.org"}, {"contact_type": "url", "value": "https://data.4dnucleome.org/help/about/contact-us"}], "label": "4D Nucleome Network Data Coordination and Integration Center (DCIC)"}], "creation_date": "2025-06-10T00:00:00Z", "curators": [{"category": "Individual", "contact_details": [{"contact_type": "github", "value": "caufieldjh"}], "label": "Harry Caufield"}], "description": "The 4D Nucleome (4DN) Network aims to understand the principles underlying nuclear organization in space and time (the 4th dimension). The 4DN Data Portal provides a platform to search, visualize, and download nucleomics data generated by the 4DN Network and other reference datasets.", "domains": ["genomics", "biological systems", "biomedical", "medical imaging"], "homepage_url": "https://data.4dnucleome.org/", "id": "4dn", "last_modified_date": "2025-06-12T20:16:27Z", "layout": "resource_detail", "license": {"id": "https://data.4dnucleome.org/help/user-guide/faq#downloading-and-using-data-from-the-4dn-data-portal", "label": "Varies"}, "name": "4D Nucleome Data Portal", "products": [{"category": "DataProduct", "description": "A comprehensive collection of Hi-C datasets generated by the 4DN Network and other reference datasets, available for search, visualization, and download.", "format": "tsv", "id": "4dn.hic", "name": "4DN Hi-C Datasets", "product_url": "https://data.4dnucleome.org/hic-data-overview"}, {"category": "DataProduct", "description": "A collection of microscopy datasets, including super-resolution microscopy and chromatin tracing data, for visualizing nuclear organization.", "format": "tsv", "id": "4dn.microscopy", "name": "4DN Microscopy Datasets", "product_url": "https://data.4dnucleome.org/microscopy-data-overview"}, {"category": "DataProduct", "description": "A specialized collection of chromatin tracing datasets that provide insights into the 3D organization of chromatin in the nucleus.", "format": "tsv", "id": "4dn.chromatin_tracing", "name": "4DN Chromatin Tracing Datasets", "product_url": "https://data.4dnucleome.org/resources/data-collections/chromatin-tracing-datasets"}, {"category": "GraphicalInterface", "description": "A web-based visualization tool for exploring and comparing genomic data, particularly suited for Hi-C and other 4DN datasets.", "id": "4dn.higlass", "name": "HiGlass", "product_url": "https://data.4dnucleome.org/tools/visualization"}, {"category": "ProcessProduct", "description": "A cloud-based Jupyter environment for analyzing 4DN data without downloading it, including example notebooks for data exploration.", "id": "4dn.jupyterhub", "name": "4DN JupyterHub", "product_url": "https://data.4dnucleome.org/tools/jupyterhub"}, {"category": "ProcessProduct", "description": "A tool for entering and accessing microscope metadata with standardized formats.", "id": "4dn.micrometa", "name": "Micro Meta App", "product_url": "https://data.4dnucleome.org/tools/micro-meta-app"}, {"category": "GraphProduct", "description": "Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access.", "dump_format": "neo4j", "id": "ubkg.neo4j", "name": "UBKG Neo4j Docker Distribution", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access.", "format": "csv", "id": "ubkg.csv", "name": "UBKG Ontology CSV Files", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}], "publications": [{"authors": ["Dekker J", "Belmont AS", "Guttman M", "Leshyk VO", "Lis JT", "Lomvardas S", "Mirny LA", "et al."], "doi": "doi:10.1038/nature23884", "id": "https://doi.org/10.1038/nature23884", "journal": "Nature", "preferred": true, "title": "The 4D Nucleome Project", "year": "2017"}, {"authors": ["Reiff SB", "Schroeder AJ", "Kirli K", "Cosolo A", "Bakken TE", "Hodge RD", "Cort\u00e9s-Ciriano I", "et al."], "doi": "doi:10.1038/s41467-022-29697-4", "id": "https://doi.org/10.1038/s41467-022-29697-4", "journal": "Nature Communications", "title": "The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data", "year": "2022"}], "taxon": ["NCBITaxon:9606"]}