94 lines
2.6 KiB
Markdown
94 lines
2.6 KiB
Markdown
---
|
|
title: "ChEMBL REST API"
|
|
task: ""
|
|
lineage_type: import
|
|
upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/chembl.md
|
|
upstream_sha: 9c9bd2e9
|
|
imported_at: 2026-06-26
|
|
prompt_class: prompt
|
|
upstream_changes: accepted
|
|
author: upstream
|
|
validated: false
|
|
---
|
|
|
|
# ChEMBL REST API
|
|
|
|
## Base URL
|
|
```
|
|
https://www.ebi.ac.uk/chembl/api/data
|
|
```
|
|
|
|
## Auth
|
|
No API key required. Fully open and free.
|
|
|
|
## Key Endpoints
|
|
|
|
| Endpoint | Description |
|
|
|----------|-------------|
|
|
| `/molecule/{chembl_id}` | Get molecule by ChEMBL ID |
|
|
| `/molecule/search?q={query}` | Free-text molecule search |
|
|
| `/target/{chembl_id}` | Get target by ChEMBL ID |
|
|
| `/target/search?q={query}` | Free-text target search |
|
|
| `/activity?molecule_chembl_id={id}` | Activities for a molecule |
|
|
| `/activity?target_chembl_id={id}` | Activities for a target |
|
|
| `/mechanism?molecule_chembl_id={id}` | Mechanism of action |
|
|
| `/drug_indication?molecule_chembl_id={id}` | Drug indications |
|
|
| `/similarity/{smiles}/{threshold}` | Similarity search (threshold 40-100) |
|
|
| `/substructure/{smiles}` | Substructure search |
|
|
|
|
## Common Parameters
|
|
|
|
- `format=json` — response format (default json)
|
|
- `limit` — results per page (default 20, max 1000)
|
|
- `offset` — pagination offset
|
|
- `order_by` — sort field (prefix `-` for descending)
|
|
- `only` — return only specified fields (comma-separated)
|
|
|
|
### Filtering operators (append to field names)
|
|
`__exact`, `__icontains`, `__gt`, `__gte`, `__lt`, `__lte`, `__in`, `__isnull`, `__startswith`, `__range`, `__regex`
|
|
|
|
## Example Calls
|
|
|
|
```
|
|
# Get molecule by ID
|
|
/molecule/CHEMBL25.json
|
|
|
|
# Search molecules by name
|
|
/molecule/search?q=aspirin&format=json
|
|
|
|
# Activities for a target with potency filter
|
|
/activity?target_chembl_id=CHEMBL240&pchembl_value__gte=6&format=json&limit=100
|
|
|
|
# Similarity search (80% threshold)
|
|
/similarity/CC(%3DO)Oc1ccccc1C(%3DO)O/80.json
|
|
|
|
# Approved drugs only
|
|
/molecule?max_phase=4&format=json
|
|
|
|
# Mechanism of action
|
|
/mechanism?molecule_chembl_id=CHEMBL25&format=json
|
|
```
|
|
|
|
## Response Format (molecule)
|
|
```json
|
|
{
|
|
"page_meta": {"limit": 20, "offset": 0, "total_count": 150},
|
|
"molecules": [{
|
|
"molecule_chembl_id": "CHEMBL25",
|
|
"pref_name": "ASPIRIN",
|
|
"max_phase": 4,
|
|
"molecule_properties": {
|
|
"full_mwt": 180.16, "full_molformula": "C9H8O4",
|
|
"alogp": 1.31, "hba": 3, "hbd": 1, "psa": 63.60
|
|
},
|
|
"molecule_structures": {
|
|
"canonical_smiles": "CC(=O)Oc1ccccc1C(=O)O",
|
|
"standard_inchi_key": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"
|
|
}
|
|
}]
|
|
}
|
|
```
|
|
|
|
## Rate Limits
|
|
No strict limit. Keep under ~10 req/sec. No auth required.
|