/checking-chembl

name: Checking ChEMBL for Structured SAR Data
description: Check if medicinal chemistry papers are in ChEMBL database to access curated bioactivity data
when_to_use: After finding relevant medicinal chemistry paper. When paper describes SAR data, compound series, or activity measurements. When evaluating papers with IC50, MIC, Ki, or other bioactivity values. Before attempting to parse activity tables from PDFs.
version: 1.0.0

<!-- ╔══════════════════════════════════════════════════════════════╗ ║ 本文件为开源 Skill 原始文档，收录仅供学习与研究参考 ║ ║ CoPaper.AI 收集整理 | https://copaper.ai ║ ╚══════════════════════════════════════════════════════════════╝

来源仓库: https://github.com/kthorn/research-superpower 项目名称: research-superpower 开源协议: MIT License 收录日期: 2026-04-02

声明: 本文件版权归原作者所有。此处收录旨在为社会科学实证研究者 提供 AI Agent Skills 的集中参考。如有侵权，请联系删除。 -->

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
  }
}

**Key fields:**

• `document_chembl_id` - Use this to retrieve activity data
• `doc_type` - "PUBLICATION" (from literature) or "DATASET" (deposited)
• `pubmed_id` - PMID is in the response, but cannot be used to query ChEMBL
• If `total_count` = 0, paper not in ChEMBL

**Parse response:**

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

Step 2: Get Activity Data Count

**Query activity endpoint:**

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

**Extract total count:**

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"

Step 3: Report to User and Update Summary

**Report immediately:**

📄 [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

**Add to SUMMARY.md:**

### [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)

**Always include ChEMBL status:**

• If found: Add ChEMBL ID with link and data point count
• If not found: Note "Not in ChEMBL" (still valuable information)

Step 4: Update Tracking Files

**Add to papers-reviewed.json:**

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

Optional: Extract Struc