chembl-database-bioactivity

What it does

The skill enables an agent to query the ChEMBL public REST/JSON API to search for compounds, retrieve bioactivities (IC50, Ki, EC50, etc.), identify inhibitors for targets, perform SAR analysis, and access drug mechanisms and indications. It operates without an SDK and uses plain requests, leveraging Django-style filters in URL parameters and cursor-style pagination.

How it works

It uses the public endpoint base https://www.ebi.ac.uk/chembl/api/data with various endpoints, e.g. /molecule.json, /molecule/{chembl_id}.json, /target.json, /activity.json, /drug_indication.json, /mechanism.json, /similarity/{smiles}/{threshold}.json, and /substructure/{smiles}.json. It demonstrates constructing requests with requests.get, supplying query parameters like pref_name__icontains, molecule_properties__mw_freebase__range, target_chembl_id, standard_type, standard_value__lte, and limit. It shows how to traverse paginated results via page_meta.next and how to handle different response shapes for molecules, targets, and activities. The Quick Start and Core API sections provide concrete code blocks for retrieving a molecule by CHEMBL ID, searching by name, filtering by Lipinski-like properties, querying bioactivities, and performing structure-based searches (similarity and substructure).

When to use it

Use it for:

• Finding compounds by name, CHEMBL ID, or properties
• Querying bioactivity data (IC50, Ki, EC50) for targets
• Performing similarity or substructure searches using SMILES
• Retrieving drug mechanisms of action and indications
• Identifying inhibitors, agonists, or bioactive molecules for targets
• Analyzing SAR across compound series
• Filtering by Lipinski or other drug-likeness criteria If you need general cheminformatics tools (SMILES manipulation, descriptors), consider rdkit-cheminformatics instead. For a broader database, pubchem-compound-search is suggested.

What it can touch

• The skill uses the requests library and can touch the network to reach https://www.ebi.ac.uk/chembl/api/data. It references optional pandas for tabular analysis in examples. It does not require an API key.

Caveats

• No authentication is required for the public API. Rate limits are not published; a suggested approach is to sleep between requests (time.sleep(0.2-0.5)) in batch loops and back off on HTTP 429. The license indicated is CC-BY-SA-3.0 for the content. The description notes that the ChEMBL SDK (chembl_webresource_client) is not required, and operations can be reproduced with plain requests. The examples assume environment with Python and requests installed.