| name | kegg_database |
| description | KEGG REST access via VenusFactory download tools (academic use). Use for pathway/gene/compound lookups, ID conversion, and DDI. Do NOT use for PPI networks (string_database) or enzyme kinetics (brenda_database). Non-academic use of KEGG requires a commercial license. |
| license | Non-academic use of KEGG requires a commercial license |
| metadata | {"version":"1.2","skill-author":"VenusFactory2"} |
KEGG Database
Project Tools (VenusFactory2)
| Tool | Purpose |
|---|
| download_kegg_info_by_database | Database info |
| download_kegg_list_by_database | List entries |
| download_kegg_find_by_database | Text |
| download_kegg_entry_by_id | Entry detail |
| download_kegg_conv_by_id | ID conversion |
| download_kegg_link_by_id | Cross-links |
| download_kegg_ddi_by_id | Drug–drug interaction |
All write results under required out_path (not out_dir) and return rich JSON (status + file_info).
Workflow
find / list → entry → optional link/conv.- Combine with
string_database for PPI enrichment context; brenda_database for kinetics.
Common mistakes
- Ignoring KEGG academic-use license constraints
- Confusing KEGG gene ids with NCBI Gene ids without
conv
References (progressive disclosure)
Trust order: SKILL.md → topic refs → references/legacy_guide.md (archived; may show query_kegg_* library APIs).
read_skill(skill_id="kegg_database", relative_path="references/kegg_reference.md")
read_skill(skill_id="kegg_database", relative_path="references/legacy_guide.md")
| File | When to load |
|---|
references/kegg_reference.md | REST field details |
references/legacy_guide.md | Extended tutorials after hub workflow is insufficient |
