| name | string_database |
| description | STRING PPI networks and enrichment via VenusFactory download tools. Use for interaction networks, partners, GO/KEGG enrichment, homology across 5000+ species. Do NOT use for sequence homology search (protein_sequence_similarity_search) or KEGG pathway entries alone (kegg_database). |
| license | Unknown |
| metadata | {"version":"1.2","skill-author":"VenusFactory2"} |
STRING Database
Overview
Hub exposes download_string_* tools only. Lower-level query_string_* helpers in src/tools/database/string/ are not LangChain tools.
Project Tools (VenusFactory2)
| Tool | Key args | Purpose |
|---|
| download_string_map_ids | identifiers, out_dir, species (default 9606) | Name → STRING ID |
| download_string_network | identifiers, out_dir, required_score | PPI TSV |
| download_string_network_image | identifiers, out_dir | Network PNG |
| download_string_interaction_partners | identifiers, out_dir, limit | Partners TSV |
| download_string_enrichment | identifiers, out_dir | GO/KEGG/Pfam enrichment |
| download_string_ppi_enrichment | identifiers, out_dir | PPI enrichment JSON |
| download_string_homology | identifiers, out_dir | Homology TSV |
Workflow
download_string_map_ids (validate gene/protein names)- Network and/or partners + enrichment
- Plan a score-bar figure even if network PNG exists
Common mistakes
- Calling
query_string_* as hub tools
- Wrong
species taxon (human=9606)
- Score threshold too high → empty network
References (progressive disclosure)
Trust order: SKILL.md (hub tools & envelopes) → topic refs → references/legacy_guide.md (archived; may be outdated).
read_skill(skill_id="string_database", relative_path="references/legacy_guide.md")
Load legacy only after the hub workflow in this file is insufficient.
