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pharma-db-tools

Query public drug discovery and regulatory databases via Python HTTP APIs.

126|8|Updated Mar 10, 2026
Search Tags:#bioinformatics#drug discovery#literature search#clinical trials#cheminformatics#databases#regulatory data
One-click install
npx skills add https://github.com/DrugClaw/DrugClaw --skill pharma-db-tools
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pharma-db-tools
Source: https://github.com/DrugClaw/DrugClaw/tree/main/skills/pharma/pharma-db-tools
Command: npx skills add https://github.com/DrugClaw/DrugClaw --skill pharma-db-tools

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the process of retrieving information from various public drug discovery, translational research, and regulatory databases, saving researchers significant time and effort in data gathering.

Core Features & Use Cases

  • Comprehensive Database Access: Query PubChem, ChEMBL, BindingDB, openFDA, ClinicalTrials.gov, and OpenAlex.
  • Diverse Data Retrieval: Look up compounds, binding affinities, FDA labels, adverse events, clinical trials, and literature.
  • Use Case: When asked to find all compounds with a Ki < 1000 nM that bind to the ABL1 target, this Skill can query BindingDB using a UniProt ID and output the results to a CSV file.

Quick Start

Use the pharma-db-tools skill to query PubChem for the compound 'imatinib' and save the results to 'pharma/pubchem_imatinib.csv'.

Frequently Asked Questions about pharma-db-tools

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query PubChem for compound data using Python?▼

You can query PubChem for compound data using Python by leveraging the requests library to make HTTP API calls. This Skill automates retrieving compound properties and exporting the results to a CSV file.

What public drug discovery and regulatory databases can I query for binding affinities and clinical trials?▼

You can query PubChem, ChEMBL, BindingDB, openFDA, ClinicalTrials.gov, and OpenAlex. This Skill retrieves compounds, binding affinities, regulatory labels, adverse events, clinical trials, and literature from these public databases.

Can I find compounds with a specific binding affinity threshold for a target in BindingDB?▼

Yes, you can query BindingDB for compounds meeting specific binding affinity thresholds. This Skill can use a UniProt ID to find all compounds with a Ki < 1000 nM that bind to a specified target and output the results.

Do I need the requests library to retrieve adverse events from openFDA?▼

Yes, the requests library is required to retrieve adverse events from openFDA. This Skill uses Python with the requests library to automate HTTP API interactions with public drug discovery and regulatory databases.

What's the best way to automate literature search and clinical trial retrieval for translational research?▼

To automate literature search and clinical trial retrieval for translational research, use this Skill to query OpenAlex and ClinicalTrials.gov via public APIs. It compiles curated exports of literature and clinical trial data into accessible formats.

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