chembl-drug

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• SKILL.md

SKILL.md (first lines)

# ChEMBL Drug & Bioactivity Lookup

Query the ChEMBL REST API to access curated drug-target interaction data, bioactivity measurements, drug mechanisms of action, and ADMET properties from the European Bioinformatics Institute.

## API Base URL

```
https://www.ebi.ac.uk/chembl/api/data
```

All endpoints accept `.json` suffix and return JSON by default. Use `format=json` as a query parameter alternatively.

## API Endpoints

### Molecule Lookup

Retrieve molecule details by ChEMBL ID or search by name:

```bash
# Get molecule by ChEMBL ID
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL25.json" | head -80

# Search molecules by name
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/search.json?q=imatinib" | head -80

# Get molecule by canonical SMILES
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule.json?molecule_structures__canonical_smiles=CC(=O)Oc1ccccc1C(=O)O" | head -60
```

### Target Lookup

Retrieve drug target information:

```bash
# Get target by ChEMBL ID
curl -s "https://www.ebi.ac.uk/chembl/api/data/target/CHEMBL2034.json" | head -60

# Search targets by gene name
curl -s "https://www.ebi.ac.uk/chembl/api/data/target/search.json?q=EGFR" | head -80

# Get target by UniProt accession
curl -s "https://www.ebi.ac.uk/chembl/api/data/target.json?target_components__accession=P00533" | head -60
```

### Bioactivity Data

Retrieve binding affinity, IC50, Ki, and other activity measurements:

```bash
# Get activities for a molecule (with pagination)
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity.json?molecule_chembl_id=CHEMBL25&limit=20" | head -100

# Get activities for a specific target
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity.json?target_chembl_id=CHEMBL2034&limit=20" | head -100

# Filter by activity type (IC50, Ki, Kd, EC50)
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity.json?molecule_chembl_id=CHEMBL941&standard_type=IC50&limit=10" | head -80

# Filter by potency threshold (pChEMBL value >= 6, i.e., activity <= 1 uM)
curl -s "https://www.ebi.ac.uk/chembl/api/data/activity.json?target_chembl_id=CHEMBL2034&pchembl_value__gte=6&limit=20" | head -80
```

### Drug Mechanisms of Action

```bash
# Get mechanism of action for a drug
curl -s "https://www.ebi.ac.uk/chembl/api/data/mechanism.json?molecule_chembl_id=CHEMBL941" | head -60

# Get all mechanisms for a target
curl -s "https://www.ebi.ac.uk/chembl/api/data/mechanism.json?target_chembl_id=CHEMBL2034" | head -80
```

### Approved Drugs

Filter for approved drugs and clinical candidates:

```bash
# Get approved drugs only (max_phase = 4)
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule.json?max_phase=4&limit=20" | head -80

# Approved drugs for a specific target
curl -s "https://www.ebi.ac.uk/chembl/api/data/mechanism.json?target_chembl_id=CHEMBL2034" | head -60

# Filter by molecule type (small molecule, antibody, etc.)
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule.json?max_phase=4&molecule_type=Small%20molecule&limit=20" | head -60
```

### ADMET and Drug Properties

```bash
# Get computed molecular properties (Lipinski, PSA, ALogP are in molecule_properties)
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL25.json" | python3 -c "import sys,json; [print(f'{k}: {v}') for k,v in json.load(sys.stdin).get('molecule_properties',{}).items()]"

# Get drug indications
curl -s "https://www.ebi.ac.uk/chembl/api/data/drug_indication.json?molecule_chembl_id=CHEMBL941&limit=10" | head -60
```

## Common Queries

```bash
# Find all drugs targeting a specific protein
curl -s "https://www.ebi.ac.uk/chembl/api/data/mechanism.json?target_chembl_id=CHEMBL1862" | head -80

# Get the ChEMBL ID for a drug by name
curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/search.json?q=metformin&limit=5" | head -40

# Get molecule image URL: https://www.ebi.ac.uk/chembl/api/data/image/CHEMBL25.svg
```

## Best Practices

1. Always include `limit` parameter to control result size; default may return thousands of records.
2. Use `offset` with `limit` for pagination through large result sets.
3. Filter bioactivity by `pchembl_value__gte=5` (10 uM) or `pchembl_value__gte=6` (1 uM) for meaningful hits.
4. Use `max_phase` to filter clinical status: 4 = approved, 3 = Phase III, 2 = Phase II, 1 = Phase I.
5. Prefer ChEMBL IDs over name searches for precise lookups; name searches are fuzzy.
6. Parse `molecule_properties` for pre-computed Lipinski descriptors, PSA, and ALogP.
7. Rate limit to 1 request per second to avoid throttling from EBI servers.

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