AL
Data & Repro
alphafold
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Data & Repro
TO
tooluniverse-systems-biology
Maintainer FreedomIntelligence · Last updated April 1, 2026
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels). Performs pathway enrichment, protein-pathway mapping, keyword searches, and systems-level analysis. Use when analyzing gene sets, exploring biological pathways, or investigating systems-level biology.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tooluniverse-systems-biology
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Comprehensive pathway and systems biology analysis integrating multiple curated databases to provide multi-dimensional view of biological systems, pathway enrichment, and protein-pathway relationships.
- Analyze pathways for this gene list.
- What pathways is [protein] involved in?
- Find pathways related to [keyword/process].
- Perform pathway enrichment analysis.
Source Doc
Excerpt From SKILL.md
Core Databases Integrated
| Database | Coverage | Strengths |
|---|---|---|
| Reactome | Human-curated reactions & pathways | Detailed mechanistic pathways with reactions |
| KEGG | Reference pathways across organisms | Metabolic maps, disease pathways, drug targets |
| WikiPathways | Community-curated pathways | Emerging processes, collaborative updates |
| Pathway Commons | Integrated meta-database | Aggregates multiple sources (Reactome, KEGG, etc.) |
| BioModels | Computational SBML models | Mathematical/dynamic systems biology models |
| Enrichr | Statistical enrichment | Pathway over-representation analysis |
Phase 1: Pathway Enrichment Analysis
When: Gene list provided (from experiments, screens, differentially expressed genes)
Objective: Identify biological pathways statistically over-represented in gene list
Tools Used
enrichr_gene_enrichment_analysis:
- Input:
gene_list: Array of gene symbols (e.g., ["TP53", "BRCA1", "EGFR"])library: Pathway database (e.g., "KEGG_2021_Human", "Reactome_2022")
- Output: Array of enriched pathways with p-values, adjusted p-values, genes
- Use: Statistical over-representation analysis
Use cases
- Use tooluniverse-systems-biology in research workflows aligned with this subject area.
- Follow the upstream documentation for the full working procedure.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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