drchronx/ai-agent-research-starter-kit/checking-chembl

curl -s "https://www.ebi.ac.uk/chembl/api/data/document.json?doi=DOI"

# ✅ CORRECT - Use DOI
doi="10.1021/jm401507s"
curl -s "https://www.ebi.ac.uk/chembl/api/data/document.json?doi=$doi"
 
# ❌ WRONG - PMID won't work (will return 0 results)
pmid="24446688"
curl -s "https://www.ebi.ac.uk/chembl/api/data/document.json?pubmed_id=$pmid"  # Does NOT work!

{
  "documents": [
    {
      "document_chembl_id": "CHEMBL3120156",
      "doi": "10.1021/jm401507s",
      "title": "Discovery and development of simeprevir (TMC435), a HCV NS3/4A protease inhibitor.",
      "abstract": "Hepatitis C virus is a blood-borne infection...",
      "pubmed_id": 24446688,
      "journal": "J Med Chem",
      "year": 2014,
      "doc_type": "PUBLICATION"
    }
  ],
  "page_meta": {
    "total_count": 1
  }
}

response=$(curl -s "https://www.ebi.ac.uk/chembl/api/data/document.json?doi=$doi")
 
if [ $(echo "$response" | jq -r '.page_meta.total_count') -gt 0 ]; then
  chembl_id=$(echo "$response" | jq -r '.documents[0].document_chembl_id')
  echo "✓ Found in ChEMBL: $chembl_id"
else
  echo "✗ Not in ChEMBL"
fi

curl -s "https://www.ebi.ac.uk/chembl/api/data/activity.json?document_chembl_id=CHEMBL3120156&limit=1"

activity_url="https://www.ebi.ac.uk/chembl/api/data/activity.json?document_chembl_id=$chembl_id&limit=1"
activity_count=$(curl -s "$activity_url" | jq -r '.page_meta.total_count')
 
echo "→ $activity_count bioactivity data points"

📄 [15/127] Screening: "Discovery and development of simeprevir"
   Abstract score: 9 → Fetching full text...
   ✓ ChEMBL: CHEMBL3120156 (101 activity data points)
   → IC50 data for HCV NS3 protease inhibitors available

### [Discovery and development of simeprevir (TMC435), a HCV NS3/4A protease inhibitor](https://doi.org/10.1021/jm401507s) (Score: 9)
 
**DOI:** [10.1021/jm401507s](https://doi.org/10.1021/jm401507s)
**PMID:** [24446688](https://pubmed.ncbi.nlm.nih.gov/24446688/)
**ChEMBL:** [CHEMBL3120156](https://www.ebi.ac.uk/chembl/document_report_card/CHEMBL3120156/) (101 data points)
 
**Key Findings:**
-IC50 data for HCV NS3/4A protease inhibitors (from ChEMBL)
-Lead compound simeprevir (TMC435) approved for HCV treatment
-Structures and full activity data: [ChEMBL API](https://www.ebi.ac.uk/chembl/api/data/activity.json?document_chembl_id=CHEMBL3120156)
 
**ChEMBL Activity Summary:**
-IC50 values for HCV NS3/4A protease
-PK parameters (AUC, Cmax, clearance)
-DMPK assays (metabolic stability, permeability)

{
  "10.1021/jm401507s": {
    "pmid": "24446688",
    "status": "relevant",
    "score": 9,
    "chembl_id": "CHEMBL3120156",
    "chembl_activities": 101,
    "has_structured_data": true
  }
}

# Get all IC50 data
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity.json?document_chembl_id=CHEMBL3120156&standard_type=IC50&limit=100" > chembl_data.json
 
# Summary statistics
jq '[.activities[] | .standard_value | tonumber] | "Min: \(min), Max: \(max), Count: \(length)"' chembl_data.json

📊 ChEMBL data extracted:
   - IC50 values for HCV NS3/4A protease
   - All structures downloaded
   - Data saved to: chembl_CHEMBL3120156_ic50.json

Stage 2: Deep Dive
├─ 1. Fetch Full Text (PMC → DOI → Unpaywall)
├─ 1.5. Check ChEMBL ← ADD THIS STEP
│   ├─ Query by DOI
│   ├─ If found: note ChEMBL ID + activity count
│   └─ Report to user
├─ 2. Scan for Relevant Content
└─ 3. Extract Findings

curl "https://www.ebi.ac.uk/chembl/api/data/activity.json?document_chembl_id=ID&standard_type=MIC"

📄 [15/50] Screening: "Novel MmpL3 inhibitors..."
   Abstract score: 8 → Checking ChEMBL...
   ✓ ChEMBL: CHEMBL3456789 (34 data points)
   → Fetching full text...
   → Added to SUMMARY.md with ChEMBL link

📄 [16/50] Screening: "Another paper..."
   Abstract score: 9 → Checking ChEMBL...
   ✗ Not in ChEMBL (likely too recent or review paper)
   → Fetching full text via Unpaywall...

#!/usr/bin/env python3
import requests
import json
import sys
def check_chembl(doi):
    """Check if DOI is in ChEMBL and return summary
    IMPORTANT: Must use DOI, not PMID. ChEMBL API does not accept PMID queries.
    """
    # Query document (ONLY works with DOI)
    doc_url = f"https://www.ebi.ac.uk/chembl/api/data/document.json?doi={doi}"
    try:
        doc_response = requests.get(doc_url, timeout=10).json()
    except:
        return None
    # Check if found
    if doc_response.get('page_meta', {}).get('total_count', 0) == 0:
        return {'in_chembl': False}
    doc = doc_response['documents'][0]
    chembl_id = doc['document_chembl_id']
    # Get activity count
    act_url = f"https://www.ebi.ac.uk/chembl/api/data/activity.json?document_chembl_id={chembl_id}&limit=1"
    try:
        act_response = requests.get(act_url, timeout=10).json()
        activity_count = act_response.get('page_meta', {}).get('total_count', 0)
    except:
        activity_count = 0
    return {
        'in_chembl': True,
        'chembl_id': chembl_id,
        'activity_count': activity_count,
        'doc_type': doc.get('doc_type'),
        'title': doc.get('title')
    }
if __name__ == "__main__":
    doi = sys.argv[1]
    result = check_chembl(doi)
    if result and result['in_chembl']:
        print(f"✓ {result['chembl_id']} ({result['activity_count']} activities)")
    else:
        print("✗ Not in ChEMBL")

python3 check_chembl.py "10.1021/jm401507s"
# Output: ✓ CHEMBL3120156 (101 activities)

"Bash(curl*https://www.ebi.ac.uk/chembl/api/data/*)",
"WebFetch(domain:www.ebi.ac.uk)"