@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/drugbank-database/references/data-access.md

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+# DrugBank Data Access
+
+## Authentication and Setup
+
+### Account Creation
+DrugBank requires user authentication to access data:
+1. Create account at go.drugbank.com
+2. Accept the license agreement (free for academic use, paid for commercial)
+3. Obtain username and password credentials
+
+### Credential Management
+
+**Environment Variables (Recommended)**
+```bash
+export DRUGBANK_USERNAME="your_username"
+export DRUGBANK_PASSWORD="your_password"
+```
+
+**Configuration File**
+Create `~/.config/drugbank.ini`:
+```ini
+[drugbank]
+username = your_username
+password = your_password
+```
+
+**Direct Specification**
+```python
+# Pass credentials directly (not recommended for production)
+download_drugbank(username="user", password="pass")
+```
+
+## Python Package Installation
+
+### drugbank-downloader
+Primary tool for programmatic access:
+```bash
+pip install drugbank-downloader
+```
+
+**Requirements:** Python >=3.9
+
+### Optional Dependencies
+```bash
+pip install bioversions  # For automatic latest version detection
+pip install lxml  # For XML parsing optimization
+```
+
+## Data Download Methods
+
+### Download Full Database
+```python
+from drugbank_downloader import download_drugbank
+
+# Download specific version
+path = download_drugbank(version='5.1.7')
+# Returns: ~/.data/drugbank/5.1.7/full database.xml.zip
+
+# Download latest version (requires bioversions)
+path = download_drugbank()
+```
+
+### Custom Storage Location
+```python
+# Custom prefix for storage
+path = download_drugbank(prefix=['custom', 'location', 'drugbank'])
+# Stores at: ~/.data/custom/location/drugbank/[version]/
+```
+
+### Verify Download
+```python
+import os
+if os.path.exists(path):
+    size_mb = os.path.getsize(path) / (1024 * 1024)
+    print(f"Downloaded successfully: {size_mb:.1f} MB")
+```
+
+## Working with Downloaded Data
+
+### Open Zipped XML Without Extraction
+```python
+from drugbank_downloader import open_drugbank
+import xml.etree.ElementTree as ET
+
+# Open file directly from zip
+with open_drugbank() as file:
+    tree = ET.parse(file)
+    root = tree.getroot()
+```
+
+### Parse XML Tree
+```python
+from drugbank_downloader import parse_drugbank, get_drugbank_root
+
+# Get parsed tree
+tree = parse_drugbank()
+
+# Get root element directly
+root = get_drugbank_root()
+```
+
+### CLI Usage
+```bash
+# Download using command line
+drugbank_downloader --username USER --password PASS
+
+# Download latest version
+drugbank_downloader
+```
+
+## Data Formats and Versions
+
+### Available Formats
+- **XML**: Primary format, most comprehensive data
+- **JSON**: Available via API (requires separate API key)
+- **CSV/TSV**: Export from web interface or parse XML
+- **SQL**: Database dumps available for download
+
+### Version Management
+```python
+# Specify exact version for reproducibility
+path = download_drugbank(version='5.1.10')
+
+# List cached versions
+from pathlib import Path
+drugbank_dir = Path.home() / '.data' / 'drugbank'
+if drugbank_dir.exists():
+    versions = [d.name for d in drugbank_dir.iterdir() if d.is_dir()]
+    print(f"Cached versions: {versions}")
+```
+
+### Version History
+- **Version 6.0** (2024): Latest release, expanded drug entries
+- **Version 5.1.x** (2019-2023): Incremental updates
+- **Version 5.0** (2017): ~9,591 drug entries
+- **Version 4.0** (2014): Added metabolite structures
+- **Version 3.0** (2011): Added transporter and pathway data
+- **Version 2.0** (2009): Added interactions and ADMET
+
+## API Access
+
+### REST API Endpoints
+```python
+import requests
+
+# Query by DrugBank ID
+drug_id = "DB00001"
+url = f"https://go.drugbank.com/drugs/{drug_id}.json"
+headers = {"Authorization": "Bearer YOUR_API_KEY"}
+
+response = requests.get(url, headers=headers)
+if response.status_code == 200:
+    drug_data = response.json()
+```
+
+### Rate Limits
+- **Development Key**: 3,000 requests/month
+- **Production Key**: Custom limits based on license
+- **Best Practice**: Cache results locally to minimize API calls
+
+### Regional Scoping
+DrugBank API is scoped by region:
+- **USA**: FDA-approved drugs
+- **Canada**: Health Canada-approved drugs
+- **EU**: EMA-approved drugs
+
+Specify region in API requests when applicable.
+
+## Data Caching Strategy
+
+### Intermediate Results
+```python
+import pickle
+from pathlib import Path
+
+# Cache parsed data
+cache_file = Path("drugbank_parsed.pkl")
+
+if cache_file.exists():
+    with open(cache_file, 'rb') as f:
+        data = pickle.load(f)
+else:
+    # Parse and process
+    root = get_drugbank_root()
+    data = process_drugbank_data(root)
+
+    # Save cache
+    with open(cache_file, 'wb') as f:
+        pickle.dump(data, f)
+```
+
+### Version-Specific Caching
+```python
+version = "5.1.10"
+cache_file = Path(f"drugbank_{version}_processed.pkl")
+# Ensures cache invalidation when version changes
+```
+
+## Troubleshooting
+
+### Common Issues
+
+**Authentication Failures**
+- Verify credentials are correct
+- Check license agreement is accepted
+- Ensure account has not expired
+
+**Download Failures**
+- Check internet connectivity
+- Verify sufficient disk space (~1-2 GB needed)
+- Try specifying an older version if latest fails
+
+**Parsing Errors**
+- Ensure complete download (check file size)
+- Verify XML is not corrupted
+- Use lxml parser for better error handling
+
+### Error Handling
+```python
+from drugbank_downloader import download_drugbank
+import logging
+
+logging.basicConfig(level=logging.INFO)
+
+try:
+    path = download_drugbank()
+    print(f"Success: {path}")
+except Exception as e:
+    print(f"Download failed: {e}")
+    # Fallback: specify older stable version
+    path = download_drugbank(version='5.1.7')
+```
+
+## Best Practices
+
+1. **Version Specification**: Always specify exact version for reproducible research
+2. **Credential Security**: Use environment variables, never hardcode credentials
+3. **Caching**: Cache intermediate processing results to avoid re-parsing
+4. **Documentation**: Document which DrugBank version was used in analysis
+5. **License Compliance**: Ensure proper licensing for your use case
+6. **Local Storage**: Keep local copies to reduce download frequency
+7. **Error Handling**: Implement robust error handling for network issues

package/bin/skills/drugbank-database/references/drug-queries.md

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+# Drug Information Queries
+
+## Overview
+DrugBank provides comprehensive drug information with 200+ data fields per entry including chemical properties, pharmacology, mechanisms of action, and clinical data.
+
+## Database Contents
+
+### Drug Categories
+- **FDA-Approved Small Molecules**: ~2,037 drugs
+- **Biotech/Biologic Drugs**: ~241 entries
+- **Nutraceuticals**: ~96 compounds
+- **Experimental Drugs**: ~6,000+ compounds
+- **Withdrawn/Discontinued**: Historical drugs with safety data
+
+### Data Fields (200+ per entry)
+- **Identifiers**: DrugBank ID, CAS number, UNII, PubChem CID
+- **Names**: Generic, brand, synonyms, IUPAC
+- **Chemical**: Structure (SMILES, InChI), formula, molecular weight
+- **Pharmacology**: Indication, mechanism of action, pharmacodynamics
+- **Pharmacokinetics**: Absorption, distribution, metabolism, excretion (ADME)
+- **Toxicity**: LD50, adverse effects, contraindications
+- **Clinical**: Dosage forms, routes of administration, half-life
+- **Targets**: Proteins, enzymes, transporters, carriers
+- **Interactions**: Drug-drug, drug-food interactions
+- **References**: Citations to literature and clinical studies
+
+## XML Structure Navigation
+
+### Basic XML Structure
+```xml
+<drugbank>
+  <drug type="small molecule" created="..." updated="...">
+    <drugbank-id primary="true">DB00001</drugbank-id>
+    <name>Lepirudin</name>
+    <description>...</description>
+    <cas-number>...</cas-number>
+    <synthesis-reference>...</synthesis-reference>
+    <indication>...</indication>
+    <pharmacodynamics>...</pharmacodynamics>
+    <mechanism-of-action>...</mechanism-of-action>
+    <toxicity>...</toxicity>
+    <metabolism>...</metabolism>
+    <absorption>...</absorption>
+    <half-life>...</half-life>
+    <protein-binding>...</protein-binding>
+    <route-of-elimination>...</route-of-elimination>
+    <calculated-properties>...</calculated-properties>
+    <experimental-properties>...</experimental-properties>
+    <targets>...</targets>
+    <enzymes>...</enzymes>
+    <transporters>...</transporters>
+    <drug-interactions>...</drug-interactions>
+  </drug>
+</drugbank>
+```
+
+### Namespaces
+DrugBank XML uses namespaces. Handle them properly:
+```python
+import xml.etree.ElementTree as ET
+
+# Define namespace
+ns = {'db': 'http://www.drugbank.ca'}
+
+# Query with namespace
+root = get_drugbank_root()
+drugs = root.findall('db:drug', ns)
+```
+
+## Query by Drug Identifier
+
+### Query by DrugBank ID
+```python
+from drugbank_downloader import get_drugbank_root
+
+def get_drug_by_id(drugbank_id):
+    """Retrieve drug entry by DrugBank ID (e.g., 'DB00001')"""
+    root = get_drugbank_root()
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    for drug in root.findall('db:drug', ns):
+        primary_id = drug.find('db:drugbank-id[@primary="true"]', ns)
+        if primary_id is not None and primary_id.text == drugbank_id:
+            return drug
+    return None
+
+# Example usage
+drug = get_drug_by_id('DB00001')
+if drug:
+    name = drug.find('db:name', ns).text
+    print(f"Drug: {name}")
+```
+
+### Query by Name
+```python
+def get_drug_by_name(drug_name):
+    """Find drug by name (case-insensitive)"""
+    root = get_drugbank_root()
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    drug_name_lower = drug_name.lower()
+
+    for drug in root.findall('db:drug', ns):
+        name_elem = drug.find('db:name', ns)
+        if name_elem is not None and name_elem.text.lower() == drug_name_lower:
+            return drug
+
+        # Also check synonyms
+        for synonym in drug.findall('.//db:synonym', ns):
+            if synonym.text and synonym.text.lower() == drug_name_lower:
+                return drug
+    return None
+
+# Example
+drug = get_drug_by_name('Aspirin')
+```
+
+### Query by CAS Number
+```python
+def get_drug_by_cas(cas_number):
+    """Find drug by CAS registry number"""
+    root = get_drugbank_root()
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    for drug in root.findall('db:drug', ns):
+        cas_elem = drug.find('db:cas-number', ns)
+        if cas_elem is not None and cas_elem.text == cas_number:
+            return drug
+    return None
+```
+
+## Extract Specific Information
+
+### Basic Drug Information
+```python
+def extract_basic_info(drug):
+    """Extract essential drug information"""
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    info = {
+        'drugbank_id': drug.find('db:drugbank-id[@primary="true"]', ns).text,
+        'name': drug.find('db:name', ns).text,
+        'type': drug.get('type'),
+        'cas_number': get_text_safe(drug.find('db:cas-number', ns)),
+        'description': get_text_safe(drug.find('db:description', ns)),
+        'indication': get_text_safe(drug.find('db:indication', ns)),
+    }
+    return info
+
+def get_text_safe(element):
+    """Safely get text from element, return None if not found"""
+    return element.text if element is not None else None
+```
+
+### Chemical Properties
+```python
+def extract_chemical_properties(drug):
+    """Extract chemical structure and properties"""
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    properties = {}
+
+    # Calculated properties
+    calc_props = drug.find('db:calculated-properties', ns)
+    if calc_props is not None:
+        for prop in calc_props.findall('db:property', ns):
+            kind = prop.find('db:kind', ns).text
+            value = prop.find('db:value', ns).text
+            properties[kind] = value
+
+    # Experimental properties
+    exp_props = drug.find('db:experimental-properties', ns)
+    if exp_props is not None:
+        for prop in exp_props.findall('db:property', ns):
+            kind = prop.find('db:kind', ns).text
+            value = prop.find('db:value', ns).text
+            properties[f"{kind}_experimental"] = value
+
+    return properties
+
+# Common properties to extract:
+# - SMILES
+# - InChI
+# - InChIKey
+# - Molecular Formula
+# - Molecular Weight
+# - logP (partition coefficient)
+# - Water Solubility
+# - Melting Point
+# - pKa
+```
+
+### Pharmacology Information
+```python
+def extract_pharmacology(drug):
+    """Extract pharmacological information"""
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    pharm = {
+        'indication': get_text_safe(drug.find('db:indication', ns)),
+        'pharmacodynamics': get_text_safe(drug.find('db:pharmacodynamics', ns)),
+        'mechanism_of_action': get_text_safe(drug.find('db:mechanism-of-action', ns)),
+        'toxicity': get_text_safe(drug.find('db:toxicity', ns)),
+        'metabolism': get_text_safe(drug.find('db:metabolism', ns)),
+        'absorption': get_text_safe(drug.find('db:absorption', ns)),
+        'half_life': get_text_safe(drug.find('db:half-life', ns)),
+        'protein_binding': get_text_safe(drug.find('db:protein-binding', ns)),
+        'route_of_elimination': get_text_safe(drug.find('db:route-of-elimination', ns)),
+        'volume_of_distribution': get_text_safe(drug.find('db:volume-of-distribution', ns)),
+        'clearance': get_text_safe(drug.find('db:clearance', ns)),
+    }
+    return pharm
+```
+
+### External Identifiers
+```python
+def extract_external_identifiers(drug):
+    """Extract cross-references to other databases"""
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    identifiers = {}
+
+    external_ids = drug.find('db:external-identifiers', ns)
+    if external_ids is not None:
+        for ext_id in external_ids.findall('db:external-identifier', ns):
+            resource = ext_id.find('db:resource', ns).text
+            identifier = ext_id.find('db:identifier', ns).text
+            identifiers[resource] = identifier
+
+    return identifiers
+
+# Common external databases:
+# - PubChem Compound
+# - PubChem Substance
+# - ChEMBL
+# - ChEBI
+# - UniProtKB
+# - KEGG Drug
+# - PharmGKB
+# - RxCUI (RxNorm)
+# - ZINC
+```
+
+## Building Drug Datasets
+
+### Create Drug Dictionary
+```python
+def build_drug_database():
+    """Build searchable dictionary of all drugs"""
+    root = get_drugbank_root()
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    drug_db = {}
+
+    for drug in root.findall('db:drug', ns):
+        db_id = drug.find('db:drugbank-id[@primary="true"]', ns).text
+
+        drug_info = {
+            'id': db_id,
+            'name': get_text_safe(drug.find('db:name', ns)),
+            'type': drug.get('type'),
+            'description': get_text_safe(drug.find('db:description', ns)),
+            'cas': get_text_safe(drug.find('db:cas-number', ns)),
+            'indication': get_text_safe(drug.find('db:indication', ns)),
+        }
+
+        drug_db[db_id] = drug_info
+
+    return drug_db
+
+# Create searchable database
+drugs = build_drug_database()
+print(f"Total drugs: {len(drugs)}")
+```
+
+### Export to DataFrame
+```python
+import pandas as pd
+
+def create_drug_dataframe():
+    """Create pandas DataFrame of drug information"""
+    root = get_drugbank_root()
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    drugs_data = []
+
+    for drug in root.findall('db:drug', ns):
+        drug_dict = {
+            'drugbank_id': drug.find('db:drugbank-id[@primary="true"]', ns).text,
+            'name': get_text_safe(drug.find('db:name', ns)),
+            'type': drug.get('type'),
+            'cas_number': get_text_safe(drug.find('db:cas-number', ns)),
+            'description': get_text_safe(drug.find('db:description', ns)),
+            'indication': get_text_safe(drug.find('db:indication', ns)),
+        }
+        drugs_data.append(drug_dict)
+
+    df = pd.DataFrame(drugs_data)
+    return df
+
+# Usage
+df = create_drug_dataframe()
+df.to_csv('drugbank_drugs.csv', index=False)
+```
+
+### Filter by Drug Type
+```python
+def filter_by_type(drug_type='small molecule'):
+    """Get drugs of specific type"""
+    root = get_drugbank_root()
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    filtered_drugs = []
+
+    for drug in root.findall('db:drug', ns):
+        if drug.get('type') == drug_type:
+            db_id = drug.find('db:drugbank-id[@primary="true"]', ns).text
+            name = get_text_safe(drug.find('db:name', ns))
+            filtered_drugs.append({'id': db_id, 'name': name})
+
+    return filtered_drugs
+
+# Get all biotech drugs
+biotech_drugs = filter_by_type('biotech')
+```
+
+### Search by Keyword
+```python
+def search_drugs_by_keyword(keyword, field='indication'):
+    """Search drugs by keyword in specific field"""
+    root = get_drugbank_root()
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    results = []
+    keyword_lower = keyword.lower()
+
+    for drug in root.findall('db:drug', ns):
+        field_elem = drug.find(f'db:{field}', ns)
+        if field_elem is not None and field_elem.text:
+            if keyword_lower in field_elem.text.lower():
+                db_id = drug.find('db:drugbank-id[@primary="true"]', ns).text
+                name = get_text_safe(drug.find('db:name', ns))
+                results.append({
+                    'id': db_id,
+                    'name': name,
+                    field: field_elem.text[:200]  # First 200 chars
+                })
+
+    return results
+
+# Example: Find drugs for cancer treatment
+cancer_drugs = search_drugs_by_keyword('cancer', 'indication')
+```
+
+## Performance Optimization
+
+### Indexing for Faster Queries
+```python
+def build_indexes():
+    """Build indexes for faster lookups"""
+    root = get_drugbank_root()
+    ns = {'db': 'http://www.drugbank.ca'}
+
+    # Index by ID, name, and CAS
+    id_index = {}
+    name_index = {}
+    cas_index = {}
+
+    for drug in root.findall('db:drug', ns):
+        db_id = drug.find('db:drugbank-id[@primary="true"]', ns).text
+        id_index[db_id] = drug
+
+        name = get_text_safe(drug.find('db:name', ns))
+        if name:
+            name_index[name.lower()] = drug
+
+        cas = get_text_safe(drug.find('db:cas-number', ns))
+        if cas:
+            cas_index[cas] = drug
+
+    return {'id': id_index, 'name': name_index, 'cas': cas_index}
+
+# Build once, query many times
+indexes = build_indexes()
+drug = indexes['name'].get('aspirin')
+```