@bgicli/bgicli 2.1.1 → 2.2.0

package/data/skills/string-database/SKILL.md

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+---
+name: string-database
+description: "Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology."
+---
+
+# STRING Database
+
+## Overview
+
+STRING is a comprehensive database of known and predicted protein-protein interactions covering 59M proteins and 20B+ interactions across 5000+ organisms. Query interaction networks, perform functional enrichment, discover partners via REST API for systems biology and pathway analysis.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Retrieving protein-protein interaction networks for single or multiple proteins
+- Performing functional enrichment analysis (GO, KEGG, Pfam) on protein lists
+- Discovering interaction partners and expanding protein networks
+- Testing if proteins form significantly enriched functional modules
+- Generating network visualizations with evidence-based coloring
+- Analyzing homology and protein family relationships
+- Conducting cross-species protein interaction comparisons
+- Identifying hub proteins and network connectivity patterns
+
+## Quick Start
+
+The skill provides:
+1. Python helper functions (`scripts/string_api.py`) for all STRING REST API operations
+2. Comprehensive reference documentation (`references/string_reference.md`) with detailed API specifications
+
+When users request STRING data, determine which operation is needed and use the appropriate function from `scripts/string_api.py`.
+
+## Core Operations
+
+### 1. Identifier Mapping (`string_map_ids`)
+
+Convert gene names, protein names, and external IDs to STRING identifiers.
+
+**When to use**: Starting any STRING analysis, validating protein names, finding canonical identifiers.
+
+**Usage**:
+```python
+from scripts.string_api import string_map_ids
+
+# Map single protein
+result = string_map_ids('TP53', species=9606)
+
+# Map multiple proteins
+result = string_map_ids(['TP53', 'BRCA1', 'EGFR', 'MDM2'], species=9606)
+
+# Map with multiple matches per query
+result = string_map_ids('p53', species=9606, limit=5)
+```
+
+**Parameters**:
+- `species`: NCBI taxon ID (9606 = human, 10090 = mouse, 7227 = fly)
+- `limit`: Number of matches per identifier (default: 1)
+- `echo_query`: Include query term in output (default: 1)
+
+**Best practice**: Always map identifiers first for faster subsequent queries.
+
+### 2. Network Retrieval (`string_network`)
+
+Get protein-protein interaction network data in tabular format.
+
+**When to use**: Building interaction networks, analyzing connectivity, retrieving interaction evidence.
+
+**Usage**:
+```python
+from scripts.string_api import string_network
+
+# Get network for single protein
+network = string_network('9606.ENSP00000269305', species=9606)
+
+# Get network with multiple proteins
+proteins = ['9606.ENSP00000269305', '9606.ENSP00000275493']
+network = string_network(proteins, required_score=700)
+
+# Expand network with additional interactors
+network = string_network('TP53', species=9606, add_nodes=10, required_score=400)
+
+# Physical interactions only
+network = string_network('TP53', species=9606, network_type='physical')
+```
+
+**Parameters**:
+- `required_score`: Confidence threshold (0-1000)
+  - 150: low confidence (exploratory)
+  - 400: medium confidence (default, standard analysis)
+  - 700: high confidence (conservative)
+  - 900: highest confidence (very stringent)
+- `network_type`: `'functional'` (all evidence, default) or `'physical'` (direct binding only)
+- `add_nodes`: Add N most connected proteins (0-10)
+
+**Output columns**: Interaction pairs, confidence scores, and individual evidence scores (neighborhood, fusion, coexpression, experimental, database, text-mining).
+
+### 3. Network Visualization (`string_network_image`)
+
+Generate network visualization as PNG image.
+
+**When to use**: Creating figures, visual exploration, presentations.
+
+**Usage**:
+```python
+from scripts.string_api import string_network_image
+
+# Get network image
+proteins = ['TP53', 'MDM2', 'ATM', 'CHEK2', 'BRCA1']
+img_data = string_network_image(proteins, species=9606, required_score=700)
+
+# Save image
+with open('network.png', 'wb') as f:
+    f.write(img_data)
+
+# Evidence-colored network
+img = string_network_image(proteins, species=9606, network_flavor='evidence')
+
+# Confidence-based visualization
+img = string_network_image(proteins, species=9606, network_flavor='confidence')
+
+# Actions network (activation/inhibition)
+img = string_network_image(proteins, species=9606, network_flavor='actions')
+```
+
+**Network flavors**:
+- `'evidence'`: Colored lines show evidence types (default)
+- `'confidence'`: Line thickness represents confidence
+- `'actions'`: Shows activating/inhibiting relationships
+
+### 4. Interaction Partners (`string_interaction_partners`)
+
+Find all proteins that interact with given protein(s).
+
+**When to use**: Discovering novel interactions, finding hub proteins, expanding networks.
+
+**Usage**:
+```python
+from scripts.string_api import string_interaction_partners
+
+# Get top 10 interactors of TP53
+partners = string_interaction_partners('TP53', species=9606, limit=10)
+
+# Get high-confidence interactors
+partners = string_interaction_partners('TP53', species=9606,
+                                      limit=20, required_score=700)
+
+# Find interactors for multiple proteins
+partners = string_interaction_partners(['TP53', 'MDM2'],
+                                      species=9606, limit=15)
+```
+
+**Parameters**:
+- `limit`: Maximum number of partners to return (default: 10)
+- `required_score`: Confidence threshold (0-1000)
+
+**Use cases**:
+- Hub protein identification
+- Network expansion from seed proteins
+- Discovering indirect connections
+
+### 5. Functional Enrichment (`string_enrichment`)
+
+Perform enrichment analysis across Gene Ontology, KEGG pathways, Pfam domains, and more.
+
+**When to use**: Interpreting protein lists, pathway analysis, functional characterization, understanding biological processes.
+
+**Usage**:
+```python
+from scripts.string_enrichment import string_enrichment
+
+# Enrichment for a protein list
+proteins = ['TP53', 'MDM2', 'ATM', 'CHEK2', 'BRCA1', 'ATR', 'TP73']
+enrichment = string_enrichment(proteins, species=9606)
+
+# Parse results to find significant terms
+import pandas as pd
+df = pd.read_csv(io.StringIO(enrichment), sep='\t')
+significant = df[df['fdr'] < 0.05]
+```
+
+**Enrichment categories**:
+- **Gene Ontology**: Biological Process, Molecular Function, Cellular Component
+- **KEGG Pathways**: Metabolic and signaling pathways
+- **Pfam**: Protein domains
+- **InterPro**: Protein families and domains
+- **SMART**: Domain architecture
+- **UniProt Keywords**: Curated functional keywords
+
+**Output columns**:
+- `category`: Annotation database (e.g., "KEGG Pathways", "GO Biological Process")
+- `term`: Term identifier
+- `description`: Human-readable term description
+- `number_of_genes`: Input proteins with this annotation
+- `p_value`: Uncorrected enrichment p-value
+- `fdr`: False discovery rate (corrected p-value)
+
+**Statistical method**: Fisher's exact test with Benjamini-Hochberg FDR correction.
+
+**Interpretation**: FDR < 0.05 indicates statistically significant enrichment.
+
+### 6. PPI Enrichment (`string_ppi_enrichment`)
+
+Test if a protein network has significantly more interactions than expected by chance.
+
+**When to use**: Validating if proteins form functional module, testing network connectivity.
+
+**Usage**:
+```python
+from scripts.string_api import string_ppi_enrichment
+import json
+
+# Test network connectivity
+proteins = ['TP53', 'MDM2', 'ATM', 'CHEK2', 'BRCA1']
+result = string_ppi_enrichment(proteins, species=9606, required_score=400)
+
+# Parse JSON result
+data = json.loads(result)
+print(f"Observed edges: {data['number_of_edges']}")
+print(f"Expected edges: {data['expected_number_of_edges']}")
+print(f"P-value: {data['p_value']}")
+```
+
+**Output fields**:
+- `number_of_nodes`: Proteins in network
+- `number_of_edges`: Observed interactions
+- `expected_number_of_edges`: Expected in random network
+- `p_value`: Statistical significance
+
+**Interpretation**:
+- p-value < 0.05: Network is significantly enriched (proteins likely form functional module)
+- p-value ≥ 0.05: No significant enrichment (proteins may be unrelated)
+
+### 7. Homology Scores (`string_homology`)
+
+Retrieve protein similarity and homology information.
+
+**When to use**: Identifying protein families, paralog analysis, cross-species comparisons.
+
+**Usage**:
+```python
+from scripts.string_api import string_homology
+
+# Get homology between proteins
+proteins = ['TP53', 'TP63', 'TP73']  # p53 family
+homology = string_homology(proteins, species=9606)
+```
+
+**Use cases**:
+- Protein family identification
+- Paralog discovery
+- Evolutionary analysis
+
+### 8. Version Information (`string_version`)
+
+Get current STRING database version.
+
+**When to use**: Ensuring reproducibility, documenting methods.
+
+**Usage**:
+```python
+from scripts.string_api import string_version
+
+version = string_version()
+print(f"STRING version: {version}")
+```
+
+## Common Analysis Workflows
+
+### Workflow 1: Protein List Analysis (Standard Workflow)
+
+**Use case**: Analyze a list of proteins from experiment (e.g., differential expression, proteomics).
+
+```python
+from scripts.string_api import (string_map_ids, string_network,
+                                string_enrichment, string_ppi_enrichment,
+                                string_network_image)
+
+# Step 1: Map gene names to STRING IDs
+gene_list = ['TP53', 'BRCA1', 'ATM', 'CHEK2', 'MDM2', 'ATR', 'BRCA2']
+mapping = string_map_ids(gene_list, species=9606)
+
+# Step 2: Get interaction network
+network = string_network(gene_list, species=9606, required_score=400)
+
+# Step 3: Test if network is enriched
+ppi_result = string_ppi_enrichment(gene_list, species=9606)
+
+# Step 4: Perform functional enrichment
+enrichment = string_enrichment(gene_list, species=9606)
+
+# Step 5: Generate network visualization
+img = string_network_image(gene_list, species=9606,
+                          network_flavor='evidence', required_score=400)
+with open('protein_network.png', 'wb') as f:
+    f.write(img)
+
+# Step 6: Parse and interpret results
+```
+
+### Workflow 2: Single Protein Investigation
+
+**Use case**: Deep dive into one protein's interactions and partners.
+
+```python
+from scripts.string_api import (string_map_ids, string_interaction_partners,
+                                string_network_image)
+
+# Step 1: Map protein name
+protein = 'TP53'
+mapping = string_map_ids(protein, species=9606)
+
+# Step 2: Get all interaction partners
+partners = string_interaction_partners(protein, species=9606,
+                                      limit=20, required_score=700)
+
+# Step 3: Visualize expanded network
+img = string_network_image(protein, species=9606, add_nodes=15,
+                          network_flavor='confidence', required_score=700)
+with open('tp53_network.png', 'wb') as f:
+    f.write(img)
+```
+
+### Workflow 3: Pathway-Centric Analysis
+
+**Use case**: Identify and visualize proteins in a specific biological pathway.
+
+```python
+from scripts.string_api import string_enrichment, string_network
+
+# Step 1: Start with known pathway proteins
+dna_repair_proteins = ['TP53', 'ATM', 'ATR', 'CHEK1', 'CHEK2',
+                       'BRCA1', 'BRCA2', 'RAD51', 'XRCC1']
+
+# Step 2: Get network
+network = string_network(dna_repair_proteins, species=9606,
+                        required_score=700, add_nodes=5)
+
+# Step 3: Enrichment to confirm pathway annotation
+enrichment = string_enrichment(dna_repair_proteins, species=9606)
+
+# Step 4: Parse enrichment for DNA repair pathways
+import pandas as pd
+import io
+df = pd.read_csv(io.StringIO(enrichment), sep='\t')
+dna_repair = df[df['description'].str.contains('DNA repair', case=False)]
+```
+
+### Workflow 4: Cross-Species Analysis
+
+**Use case**: Compare protein interactions across different organisms.
+
+```python
+from scripts.string_api import string_network
+
+# Human network
+human_network = string_network('TP53', species=9606, required_score=700)
+
+# Mouse network
+mouse_network = string_network('Trp53', species=10090, required_score=700)
+
+# Yeast network (if ortholog exists)
+yeast_network = string_network('gene_name', species=4932, required_score=700)
+```
+
+### Workflow 5: Network Expansion and Discovery
+
+**Use case**: Start with seed proteins and discover connected functional modules.
+
+```python
+from scripts.string_api import (string_interaction_partners, string_network,
+                                string_enrichment)
+
+# Step 1: Start with seed protein(s)
+seed_proteins = ['TP53']
+
+# Step 2: Get first-degree interactors
+partners = string_interaction_partners(seed_proteins, species=9606,
+                                      limit=30, required_score=700)
+
+# Step 3: Parse partners to get protein list
+import pandas as pd
+import io
+df = pd.read_csv(io.StringIO(partners), sep='\t')
+all_proteins = list(set(df['preferredName_A'].tolist() +
+                       df['preferredName_B'].tolist()))
+
+# Step 4: Perform enrichment on expanded network
+enrichment = string_enrichment(all_proteins[:50], species=9606)
+
+# Step 5: Filter for interesting functional modules
+enrichment_df = pd.read_csv(io.StringIO(enrichment), sep='\t')
+modules = enrichment_df[enrichment_df['fdr'] < 0.001]
+```
+
+## Common Species
+
+When specifying species, use NCBI taxon IDs:
+
+| Organism | Common Name | Taxon ID |
+|----------|-------------|----------|
+| Homo sapiens | Human | 9606 |
+| Mus musculus | Mouse | 10090 |
+| Rattus norvegicus | Rat | 10116 |
+| Drosophila melanogaster | Fruit fly | 7227 |
+| Caenorhabditis elegans | C. elegans | 6239 |
+| Saccharomyces cerevisiae | Yeast | 4932 |
+| Arabidopsis thaliana | Thale cress | 3702 |
+| Escherichia coli | E. coli | 511145 |
+| Danio rerio | Zebrafish | 7955 |
+
+Full list available at: https://string-db.org/cgi/input?input_page_active_form=organisms
+
+## Understanding Confidence Scores
+
+STRING provides combined confidence scores (0-1000) integrating multiple evidence types:
+
+### Evidence Channels
+
+1. **Neighborhood (nscore)**: Conserved genomic neighborhood across species
+2. **Fusion (fscore)**: Gene fusion events
+3. **Phylogenetic Profile (pscore)**: Co-occurrence patterns across species
+4. **Coexpression (ascore)**: Correlated RNA expression
+5. **Experimental (escore)**: Biochemical and genetic experiments
+6. **Database (dscore)**: Curated pathway and complex databases
+7. **Text-mining (tscore)**: Literature co-occurrence and NLP extraction
+
+### Recommended Thresholds
+
+Choose threshold based on analysis goals:
+
+- **150 (low confidence)**: Exploratory analysis, hypothesis generation
+- **400 (medium confidence)**: Standard analysis, balanced sensitivity/specificity
+- **700 (high confidence)**: Conservative analysis, high-confidence interactions
+- **900 (highest confidence)**: Very stringent, experimental evidence preferred
+
+**Trade-offs**:
+- Lower thresholds: More interactions (higher recall, more false positives)
+- Higher thresholds: Fewer interactions (higher precision, more false negatives)
+
+## Network Types
+
+### Functional Networks (Default)
+
+Includes all evidence types (experimental, computational, text-mining). Represents proteins that are functionally associated, even without direct physical binding.
+
+**When to use**:
+- Pathway analysis
+- Functional enrichment studies
+- Systems biology
+- Most general analyses
+
+### Physical Networks
+
+Only includes evidence for direct physical binding (experimental data and database annotations for physical interactions).
+
+**When to use**:
+- Structural biology studies
+- Protein complex analysis
+- Direct binding validation
+- When physical contact is required
+
+## API Best Practices
+
+1. **Always map identifiers first**: Use `string_map_ids()` before other operations for faster queries
+2. **Use STRING IDs when possible**: Use format `9606.ENSP00000269305` instead of gene names
+3. **Specify species for networks >10 proteins**: Required for accurate results
+4. **Respect rate limits**: Wait 1 second between API calls
+5. **Use versioned URLs for reproducibility**: Available in reference documentation
+6. **Handle errors gracefully**: Check for "Error:" prefix in returned strings
+7. **Choose appropriate confidence thresholds**: Match threshold to analysis goals
+
+## Detailed Reference
+
+For comprehensive API documentation, complete parameter lists, output formats, and advanced usage, refer to `references/string_reference.md`. This includes:
+
+- Complete API endpoint specifications
+- All supported output formats (TSV, JSON, XML, PSI-MI)
+- Advanced features (bulk upload, values/ranks enrichment)
+- Error handling and troubleshooting
+- Integration with other tools (Cytoscape, R, Python libraries)
+- Data license and citation information
+
+## Troubleshooting
+
+**No proteins found**:
+- Verify species parameter matches identifiers
+- Try mapping identifiers first with `string_map_ids()`
+- Check for typos in protein names
+
+**Empty network results**:
+- Lower confidence threshold (`required_score`)
+- Check if proteins actually interact
+- Verify species is correct
+
+**Timeout or slow queries**:
+- Reduce number of input proteins
+- Use STRING IDs instead of gene names
+- Split large queries into batches
+
+**"Species required" error**:
+- Add `species` parameter for networks with >10 proteins
+- Always include species for consistency
+
+**Results look unexpected**:
+- Check STRING version with `string_version()`
+- Verify network_type is appropriate (functional vs physical)
+- Review confidence threshold selection
+
+## Additional Resources
+
+For proteome-scale analysis or complete species network upload:
+- Visit https://string-db.org
+- Use "Upload proteome" feature
+- STRING will generate complete interaction network and predict functions
+
+For bulk downloads of complete datasets:
+- Download page: https://string-db.org/cgi/download
+- Includes complete interaction files, protein annotations, and pathway mappings
+
+## Data License
+
+STRING data is freely available under **Creative Commons BY 4.0** license:
+- Free for academic and commercial use
+- Attribution required when publishing
+- Cite latest STRING publication
+
+## Citation
+
+When using STRING in publications, cite the most recent publication from: https://string-db.org/cgi/about

package/data/skills/struct-predictor/SKILL.md

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+---
+name: struct-predictor
+description: Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.
+version: 0.1.0
+metadata:
+  openclaw:
+    requires:
+      bins:
+        - python3
+      anyBins:
+        - colabfold_batch
+        - boltz
+      env: []
+      config: []
+    always: false
+    emoji: "🧱"
+    homepage: https://github.com/ClawBio/ClawBio
+    os: [macos, linux]
+    install:
+      - kind: uv
+        package: biopython
+        bins: []
+---
+
+# Struct Predictor
+
+You are the **Struct Predictor**, a specialised agent for protein structure prediction and analysis.
+
+## Core Capabilities
+
+1. **Structure Prediction**: Run AlphaFold (ColabFold), Boltz-1, or Chai locally
+2. **PDB Retrieval**: Fetch experimental structures from PDB via OpenBio
+3. **Structure Comparison**: Compute RMSD, TM-score between predicted and reference structures
+4. **Confidence Mapping**: Visualise pLDDT and PAE confidence metrics
+5. **Report Generation**: Markdown with 3D renders, confidence plots, and comparison tables
+
+## Dependencies
+
+- `colabfold_batch` or `boltz` or `chai` (at least one local predictor)
+- `biopython` (PDB parsing)
+- Optional: `pymol` (3D rendering), `py3Dmol` (interactive visualisation)
+
+## Example Queries
+
+- "Predict the structure of this protein sequence: MKWVTF..."
+- "Compare AlphaFold prediction of BRCA1 to the experimental PDB structure"
+- "Show the pLDDT confidence plot for my predicted structure"
+- "What is the RMSD between these two PDB files?"
+
+## Status
+
+**Planned** -- implementation targeting Week 4-5 (Mar 20 - Apr 2).