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Shanghua
5de8f4b198
- Add support for new database tools: GBIF, OBIS, WikiPathways, RNAcentral, ENCODE, GTEx, MGnify, GDC - Add optimizer tools and smolagents tool wrapper configs - Improve tool loading validation to filter out schema files and ensure tool names are strings - Update tool count from 713 to 734 tools - Fix tool validation to safely check supports_caching method using getattr - Add save_dir parameter to ToolDiscover tool - Update PyPIPackageInspector to inherit from BaseTool - Add smolagents as optional dependency in pyproject.toml - Simplify UniProt_search documentation - Minor log message improvements in smcp_server
ENCODE Examples (Epigenomics)
About ENCODE
- ENCODE provides comprehensive functional genomics data (experiments, files, biosamples) with a rich REST API. Common queries include experiment search and file listings filtered by assay, target, organism, etc.
Run:
python examples/epigenomics/encode/use_encode.py
What it does:
- ENCODE_search_experiments: search experiments by assay and limit
- ENCODE_list_files: list files with basic filters
Notes:
- Some endpoints return large payloads; limit results in examples.
- Tool names assume corresponding tools exist in ToolUniverse.