Checking ChEMBL for Structured SAR Data

Checking ChEMBL for Structured SAR Data

Overview

ChEMBL is a manually curated database of ~99,000 medicinal chemistry papers with extracted, standardized bioactivity data. If a paper is in ChEMBL, you can access structured data without parsing PDFs.

Core principle: Check ChEMBL first for medicinal chemistry papers. Curated data is more reliable than table parsing.

When to Use

Use this skill when:

• Paper describes medicinal chemistry / drug discovery
• Abstract mentions compound series, SAR, or activity data
• Paper has IC50, MIC, Ki, EC50, or other bioactivity measurements
• Before attempting to extract data from tables/figures
• Paper scored ≥ 7 in relevance evaluation

When NOT to use:

• Non-medicinal chemistry papers (cell biology, genomics, etc.)
• Papers without activity measurements
• Reviews without primary data
• Very recent papers (< 6 months, likely not curated yet)

ChEMBL API Basics

Base URL: https://www.ebi.ac.uk/chembl/api/data/

No authentication required

CRITICAL: ChEMBL can ONLY be queried by DOI, NOT by PMID

• The API returns PMID in results, but does not accept it as a query parameter
• Always use DOI for lookups: ?doi=10.1234/example
• PMID queries will return 0 results even if paper exists in ChEMBL

Two-step process:

1. Check if paper (by DOI) is in ChEMBL
2. If yes, retrieve bioactivity data

Step 1: Check if Paper in ChEMBL

Query by DOI (ONLY method that works):

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

⚠️ IMPORTANT: Must use DOI, not PMID

# ✅ 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!

If you only have PMID: Fetch DOI from PubMed first, then query ChEMBL with the DOI.

Response structure:

{
  "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
  }
}