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pubchem-database▌

google-deepmind/science-skills · updated Jun 4, 2026

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$npx skills add https://github.com/google-deepmind/science-skills --skill pubchem-database
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### Pubchem Database

  • ›name: "pubchem-database"
  • ›description: "Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule."
skill.md
name
pubchem-database
description
> Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.

PubChem Database

Prerequisites

  1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
  2. User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://pubchem.ncbi.nlm.nih.gov/docs/citation-guidelines and https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest, then (2) create the file recording the notification text and timestamp.

Quick Start

PubChem queries are executed via a robust Python wrapper script to respect terms-of-service and handle complex JSON parsing. This script allows safe multi-agent use of APIs.

Example: Resolve a chemical name to its Compound ID (CID)

uv run scripts/pubchem_api.py resolve --name "aspirin" --output result.json

Core Rules

  • Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
  • Read the generated JSON output file, and process it with jq or code.
  • Verify Facts: ALWAYS verify information retrieved from memory with a database query if the user asks for a specific fact that can be checked in PubChem. Do not rely solely on internal knowledge.
  • Notification: If this skill is used, ensure this is mentioned in the output.

Core Capabilities

1. Compound Resolution (Name or InChI to Identifiers) Convert chemical/trade names or InChI strings into PubChem CIDs, SMILES, and InChIKeys.

uv run scripts/pubchem_api.py resolve --name "ibuprofen" --output result.json
# OR
uv run scripts/pubchem_api.py resolve --inchi "InChI=1S/C3/c1-3-2/i1+1" --output result.json

2. Physical & Chemical Property Retrieval Fetch computed properties (e.g., MolecularWeight, XLogP, TPSA).

uv run scripts/pubchem_api.py properties --cid 2244 --output result.json

3. Synonyms and Trade Names Find alternative names and brand names.

uv run scripts/pubchem_api.py synonyms --cid 2244 --output result.json

Advanced Context

4. Safety and Hazard Information (GHS) Retrieve Global Harmonized System hazard statements and handling precautions (uses PUG-View).

uv run scripts/pubchem_api.py safety --cid 2244 --output result.json

5. Drug and Medication Information Fetch FDA pharmacology data, mechanism of action, and therapeutic uses (uses PUG-View).

uv run scripts/pubchem_api.py pharmacology --cid 2244 --output result.json

6. Custom Heading (PUG-View) Retrieve any specific heading from the PUG-View system (e.g., 'Geometry', 'Crystal Structures').

uv run scripts/pubchem_api.py view --cid 3939 --heading "Crystal Structures" --output result.json

7. Image Generation Retrieve 2D chemical structure images. The script returns a Markdown-formatted image link.

uv run scripts/pubchem_api.py image --cid 2244 --output result.json

Complex Search & Biology

8. Structure-Based Searching (Similarity & Substructure) Find molecules similar to a SMILES string or containing a specific substructure.

uv run scripts/pubchem_api.py similarity --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --output result.json

and

uv run scripts/pubchem_api.py substructure --smiles "C1=CC=CC=C1" --output result.json

9. BioAssay & Target Interactions Identify genes or proteins a chemical interacts with.

uv run scripts/pubchem_api.py assays --cid 2244 --output result.json

Advanced Usage & Workflows

10. Cross-references (Xrefs) Fetch identifiers cross-referenced with a CID (e.g., PatentID, PubMedID).

uv run scripts/pubchem_api.py xrefs --cid 2244 --type "PatentID" --output result.json

11. Property Range Search Find CIDs within a specific property range. Supported features include: molecular_weight, heavy_atom_count, xlogp, tpsa, h_bond_donor_count, h_bond_acceptor_count, rotatable_bond_count, exact_mass, monoisotopic_mass, and complexity.

uv run scripts/pubchem_api.py range --feature molecular_weight --min 400.0 --max 400.05 --output result.json

12. Custom PUG-REST Query Execute a raw path against the PUG-REST API.

uv run scripts/pubchem_api.py query --path "compound/cid/2244/xrefs/PatentID/JSON" --output result.json

Fallback Search Strategies

If direct resolution by name or formula fails (e.g., for complex compounds or specific ions):

  • Search for parent/neutral molecule: If searching for an ion or salt, try searching for the neutral parent compound.
  • Deconstruct complex formulas: If a complex formula returns no results, try searching for major components or ligands.
  • Use substructure or similarity search: If you have a SMILES string or can generate one for a component, use it to find related compounds.

Complex Queries and Multi-Step Tasks

how to use pubchem-database

How to use pubchem-database on Cursor

AI-first code editor with Composer

1

Prerequisites

Before installing skills in Cursor, ensure your development environment meets these requirements:

  • ›Cursor installed and configured on your development machine
  • ›Node.js version 16.0+ with npm package manager (verify with node --version)
  • ›Active project directory or workspace where you want to add pubchem-database
2

Execute installation command

Execute the skills CLI command in your project's root directory to begin installation:

$npx skills add https://github.com/google-deepmind/science-skills --skill pubchem-database

The skills CLI fetches pubchem-database from GitHub repository google-deepmind/science-skills and configures it for Cursor.

3

Select Cursor when prompted

The CLI will show a list of available agents. Use arrow keys to navigate and space to select Cursor:

◆ Which agents do you want to install to?
│
│ ── Universal (.agents/skills) ── always included ────
│ • Amp
│ • Antigravity
│ • Cline
│ • Codex
│ ●Cursor(selected)
│ • Cursor
│ • Windsurf
4

Verify installation

Confirm successful installation by checking the skill directory location:

.cursor/skills/pubchem-database

Reload or restart Cursor to activate pubchem-database. Access the skill through slash commands (e.g., /pubchem-database) or your agent's skill management interface.

⚠

Security & Verification Notice

We perform automated surface-level scans (Gen AI Scanner, Socket, Snyk) during installation. These checks detect common vulnerabilities but do not guarantee complete security. Always review skill source code and verify the publisher's reputation before production use.

Skills execute code in your development environment. Always verify the publisher's identity, review recent commits, and test in isolated environments before production deployment.

Additional Resources

›View source code on GitHub›Skills CLI documentation›Learn more about Cursor›What are agent skills?

List & Monetize Your Skill

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Use Cases▌

Task Automation & Efficiency

Automate repetitive workflows and reduce manual effort

Example

Generate reports, summarize documents, draft communications

✓

Save 3-5 hours per week on routine tasks

Knowledge Enhancement

Learn new skills, understand complex topics, get expert guidance

Example

Explain concepts, provide examples, suggest learning resources

✓

Accelerate learning and skill development by 2x

Quality Improvement

Enhance output quality through reviews, suggestions, and refinements

Example

Review drafts, suggest improvements, catch errors

✓

Improve work quality by 30-40% with less effort

Implementation Guide▌

Prerequisites

  • ›Claude Desktop or compatible AI client with skill support
  • ›Clear understanding of task or problem to solve
  • ›Willingness to iterate and refine outputs

Time Estimate

15-45 minutes depending on use case complexity

Installation Steps

  1. 1.Install skill using provided installation command
  2. 2.Test with simple use case relevant to your work
  3. 3.Evaluate output quality and relevance
  4. 4.Iterate on prompts to improve results
  5. 5.Integrate into regular workflow if valuable

Common Pitfalls

  • ⚠Expecting perfect results without iteration
  • ⚠Not providing enough context in prompts
  • ⚠Using skill for tasks outside its intended scope
  • ⚠Accepting outputs without review and validation

Best Practices▌

✓ Do

  • +Start with clear, specific prompts
  • +Provide relevant context and constraints
  • +Review and refine all outputs before using
  • +Iterate to improve output quality
  • +Document successful prompt patterns

✗ Don't

  • −Don't use without understanding skill limitations
  • −Don't skip validation of outputs
  • −Don't share sensitive information in prompts
  • −Don't expect skill to replace human judgment

💡 Pro Tips

  • ★Be specific about desired format and style
  • ★Ask for multiple options to choose from
  • ★Request explanations to understand reasoning
  • ★Combine AI efficiency with human expertise

When to Use This▌

✓ Use When

Use when skill capabilities match your task, clear ROI on time saved, and you can validate outputs. Best for repetitive tasks, learning, and quality improvement.

✗ Avoid When

Avoid when task requires deep expertise you can't validate, involves sensitive decisions, or when learning process is more valuable than speed of completion.

Learning Path▌

  1. 1Familiarize yourself with skill capabilities and limitations
  2. 2Start with low-risk, non-critical tasks
  3. 3Progress to more complex and valuable use cases
  4. 4Build expertise through regular use and experimentation

Discussion

Product Hunt–style comments (not star reviews)
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general reviews

Ratings

4.4★★★★★48 reviews
  • ★★★★★Li Gill· Dec 28, 2024

    pubchem-database fits our agent workflows well — practical, well scoped, and easy to wire into existing repos.

  • ★★★★★Diya Chawla· Dec 28, 2024

    Solid pick for teams standardizing on skills: pubchem-database is focused, and the summary matches what you get after install.

  • ★★★★★Dhruvi Jain· Dec 20, 2024

    pubchem-database reduced setup friction for our internal harness; good balance of opinion and flexibility.

  • ★★★★★Valentina Khan· Dec 20, 2024

    Registry listing for pubchem-database matched our evaluation — installs cleanly and behaves as described in the markdown.

  • ★★★★★Yusuf Flores· Dec 8, 2024

    I recommend pubchem-database for anyone iterating fast on agent tooling; clear intent and a small, reviewable surface area.

  • ★★★★★Hiroshi Menon· Dec 4, 2024

    Keeps context tight: pubchem-database is the kind of skill you can hand to a new teammate without a long onboarding doc.

  • ★★★★★Zara Desai· Nov 27, 2024

    pubchem-database reduced setup friction for our internal harness; good balance of opinion and flexibility.

  • ★★★★★Mei Verma· Nov 23, 2024

    pubchem-database has been reliable in day-to-day use. Documentation quality is above average for community skills.

  • ★★★★★Mateo Li· Nov 19, 2024

    pubchem-database is among the better-maintained entries we tried; worth keeping pinned for repeat workflows.

  • ★★★★★Oshnikdeep· Nov 11, 2024

    I recommend pubchem-database for anyone iterating fast on agent tooling; clear intent and a small, reviewable surface area.

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