Fourdn Tools¶

Configuration File: fourdn_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the fourdn_tools.json configuration file.

Available Tools¶

FourDN_get_download_url (Type: FourDNTool)¶

Get download URL and DRS (Data Repository Service) API endpoint for 4DN files. Prerequisites: (1)


FourDN_get_download_url tool specification

Tool Information:

  • Name: FourDN_get_download_url

  • Type: FourDNTool

  • Description: Get download URL and DRS (Data Repository Service) API endpoint for 4DN files. Prerequisites: (1) Requires file accession - obtain by using FourDN_search_data with item_type=’File’. (2) Requires free 4DN account - create at data.4dnucleome.org, then generate access key in your profile settings. Returns download URL and instructions for command-line access with curl. Supports GA4GH DRS standard for interoperability. Use for: programmatic file download, batch processing, workflow integration.

Parameters:

  • operation (string) (required) No description

  • file_accession (string) (required) 4DN file accession (e.g., ‘4DNFIIA7E3HL’). Obtain by searching with FourDN_search_data (item_type=’File’).

Example Usage:

query = {
    "name": "FourDN_get_download_url",
    "arguments": {
        "operation": "example_value",
        "file_accession": "example_value"
    }
}
result = tu.run(query)

FourDN_get_experiment_metadata (Type: FourDNTool)¶

Get metadata for 4DN experiments including experimental design, biosource information, protocol d


FourDN_get_experiment_metadata tool specification

Tool Information:

  • Name: FourDN_get_experiment_metadata

  • Type: FourDNTool

  • Description: Get metadata for 4DN experiments including experimental design, biosource information, protocol details, and associated files. Returns experiment type (Hi-C variants, ATAC-seq, ChIP-seq), cell type, processing status, and list of output files. Prerequisites: Requires experiment accession - obtain by using FourDN_search_data with item_type=’Experiment’. Use for: understanding experimental context, finding all files from experiment, checking data provenance.

Parameters:

  • operation (string) (required) No description

  • experiment_accession (string) (required) 4DN experiment accession (e.g., ‘4DNEXHVF8WA9’). Obtain by searching with FourDN_search_data (item_type=’Experiment’).

  • include_full_metadata (boolean) (optional) Include complete API response in ‘metadata’ field (default: false). Set to true only if you need all raw fields. Omitting this reduces response size significantly.

Example Usage:

query = {
    "name": "FourDN_get_experiment_metadata",
    "arguments": {
        "operation": "example_value",
        "experiment_accession": "example_value"
    }
}
result = tu.run(query)

FourDN_get_file_metadata (Type: FourDNTool)¶

Get detailed metadata for specific 4DN files including Hi-C contact matrices, TAD (Topologically 


FourDN_get_file_metadata tool specification

Tool Information:

  • Name: FourDN_get_file_metadata

  • Type: FourDNTool

  • Description: Get detailed metadata for specific 4DN files including Hi-C contact matrices, TAD (Topologically Associating Domain) calls, A/B compartment annotations, and chromatin loop lists. Returns file type, format, size (check before downloading - files can be GBs), description, associated experiment, and biosource information. Prerequisites: Requires file accession - obtain by using FourDN_search_data with item_type=’File’. Use for: checking file details before download, understanding processing pipeline, accessing quality metrics.

Parameters:

  • operation (string) (required) No description

  • file_accession (string) (required) 4DN file accession (e.g., ‘4DNFIIA7E3HL’). Obtain by searching with FourDN_search_data (item_type=’File’).

  • include_full_metadata (boolean) (optional) Include complete API response in ‘metadata’ field (default: false). Set to true only if you need all raw fields. Omitting this reduces response size by ~97%.

Example Usage:

query = {
    "name": "FourDN_get_file_metadata",
    "arguments": {
        "operation": "example_value",
        "file_accession": "example_value"
    }
}
result = tu.run(query)

FourDN_search_data (Type: FourDNTool)¶

Search 4DN Data Portal for Hi-C chromatin conformation files and experiments. Access 350+ uniform


FourDN_search_data tool specification

Tool Information:

  • Name: FourDN_search_data

  • Type: FourDNTool

  • Description: Search 4DN Data Portal for Hi-C chromatin conformation files and experiments. Access 350+ uniformly processed Hi-C contact files from multiple technologies (in situ Hi-C, Capture Hi-C, Micro-C XL). Search by assay type, cell type, or keywords. Returns file metadata with download URLs. Note: Downloads require free 4DN account (create at data.4dnucleome.org). Use for: finding Hi-C datasets, discovering 3D genome data, accessing TAD (Topologically Associating Domain) boundaries, A/B compartments, chromatin loop calls.

Parameters:

  • operation (string) (required) No description

  • query (string) (optional) Search query (default: ‘*’ for all)

  • item_type (string) (optional) Type of item to search

  • file_type (string) (optional) Filter by file type. Common types: ‘contact list’ (processed contact matrices), ‘pairs’ (aligned read pairs), ‘cooler’ (multi-resolution contact matrices), ‘mcool’ (multi-resolution cooler), ‘hic’ (Juicer format).

  • assay_title (string) (optional) Filter by assay (e.g., ‘Hi-C’, ‘Micro-C’, ‘Capture Hi-C’)

  • biosource_name (string) (optional) Filter by cell type (e.g., ‘H1-hESC’, ‘HFFc6’, ‘GM12878’)

  • limit (integer) (optional) Maximum results to return

Example Usage:

query = {
    "name": "FourDN_search_data",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)