encode_export_data
Export ENCODE experiment data as structured tables (CSV, TSV, JSON) for analysis in Excel, R, pandas, or sharing with collaborators. Includes metadata, publication counts, and file information.
Instructions
Export tracked experiments as a table (CSV, TSV, or JSON).
Creates a tabular export of all tracked experiments with metadata, publication counts, PMIDs, and derived file counts. Useful for loading into Excel, R, pandas, or sharing with collaborators.
PMIDs in the output can be directly used with PubMed MCP tools for further literature analysis.
WHEN TO USE: Use to create shareable tables of tracked experiments (CSV, TSV, JSON). Good for manuscripts and reports. RELATED TOOLS: encode_list_tracked, encode_summarize_collection
Args: format: Output format: - "csv": Comma-separated values (default, for Excel/spreadsheets) - "tsv": Tab-separated values (for R, pandas) - "json": JSON array (for programmatic use) assay_title: Filter by assay type (partial match) organism: Filter by organism (partial match) organ: Filter by organ (partial match)
Returns: Formatted table data in the requested format.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| format | No | csv | |
| assay_title | No | ||
| organism | No | ||
| organ | No |