New: 98,000+ skills indexed from GitHub repos with 100+ stars · every skill safety-checkedBrowse top skillsTop skills
Esc to closeBrowse all skills
Submit a skillBrowse skills
Submit a skillBrowse skills

Agent skill

Pubchem Database Skill

by aipoch in aipoch/medical-research-skills

Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure…

MITAuto-check passedBackend & APIs

Install Pubchem Database Skill

skills CLI
$ npx skills add aipoch/medical-research-skills --skill pubchem-database-skill -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills pubchem-database-skill --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/pubchem-database-skill' .claude/skills/pubchem-database-skill && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
pubchem-database-skill
GitHub stars
2k
Token cost
~954 tokens
SKILL.md length
274 words
Files
4 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure…

  • Works in 3 steps: Get compound properties → Structure search (similarity) → Get bioactivity data
  • Tasks that involve REST APIs
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
  • Runs Python scripts from its folder; calls python and uv

What it does

Pubchem Database Skill is an agent skill from aipoch/medical-research-skills. Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure searches, and obtaining bioactivity data.

Its SKILL.md is about 950 tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts and reference files (for example `pubchem-database-skill_audit_result_v1.json`, `references/api_reference.md` and `scripts/pubchem_ops.py`).

It sits in Backend & APIs, covering REST APIs and Drug discovery and cheminformatics. It works with Python. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • Tasks that involve REST APIs
  • Tasks that involve Drug discovery and cheminformatics

Example prompts

  • “/pubchem-database-skill”

Requirements

  • Python 3

Workflow steps

3 steps, taken from the step headings in SKILL.md.

  1. Get compound properties
  2. Structure search (similarity)
  3. Get bioactivity data

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python
    • uv

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md. Its commands use uv, which can reach the network depending on how they are called.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Pubchem Database Skill loads about 954 tokens when it runs, and up to ~1.2k if it reads all its reference files. Until then it costs about 65 tokens; SKILL.md has 274 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~65
When it runs · the whole SKILL.md, loaded when a task matches
~954
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 274 words, ~954 tokens.

Download SKILL.mdSave it as .claude/skills/pubchem-database-skill/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
pubchem-database-skill
description
Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure searches, and obtaining bioactivity data.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

When to Use

  • You need to search for chemical compounds by name, CID, SMILES, InChI, or molecular formula.
  • You want to retrieve physicochemical properties (e.g., molecular weight, LogP, TPSA, H-bond donors/acceptors).
  • You need to perform structure-based searches, such as similarity or substructure queries.
  • You want to obtain bioactivity data (e.g., assay summaries, target information) for a given compound.
  • You are building an automated cheminformatics or drug discovery workflow that requires programmatic access to PubChem.

Key Features

  • Flexible compound search by name, CID, SMILES, InChI, or formula.

  • Property retrieval via PubChem PUG-REST and PubChemPy (e.g., MW, LogP, Canonical SMILES).

  • Structure search:

    • Similarity search
    • Substructure search

  • Bioactivity retrieval linked to PubChem BioAssay records.

  • Rate-limit aware implementation (respects PubChem’s limit of max 5 requests/sec).

  • Python function interface for seamless integration into scientific pipelines.

Dependencies

Install the required Python packages:

bash
uv pip install pubchempy requests
  • pubchempy (version: not pinned)
  • requests (version: not pinned)

Example Usage

Primary module:

  • scripts/pubchem_ops.py
1) Get compound properties
bash
python -c "from scripts.pubchem_ops import get_properties; print(get_properties(query_value='Aspirin', query_type='name'))"

Or in Python:

python
from scripts.pubchem_ops import get_properties

result = get_properties(query_value="Aspirin", query_type="name")
print(result)
2) Structure search (similarity)
bash
python -c "from scripts.pubchem_ops import structure_search; print(structure_search(query_value='CC(=O)OC1=CC=CC=C1C(=O)O', search_type='similarity'))"

Or in Python:

python
from scripts.pubchem_ops import structure_search

smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
result = structure_search(query_value=smiles, search_type="similarity")
print(result)
3) Get bioactivity data
bash
python -c "from scripts.pubchem_ops import get_bioactivity; print(get_bioactivity(cid=2244))"

Or in Python:

python
from scripts.pubchem_ops import get_bioactivity

result = get_bioactivity(cid=2244)
print(result)

Implementation Details

  • Primary script: scripts/pubchem_ops.py

  • Data sources / endpoints:

    • Compound & properties: pubchem.ncbi.nlm.nih.gov/rest/pug
    • Bioactivity: PubChem BioAssay endpoints
    • Python wrapper: PubChemPy

  • Supported operations:

    • get_properties: retrieve physicochemical properties by name/CID/SMILES/InChI/formula.
    • structure_search: perform similarity or substructure search.
    • get_bioactivity: retrieve assay and bioactivity-related data by CID.

  • Input constraints:

    • query_type must match supported types (e.g., name, cid, smiles, inchi, formula).
    • search_type must be similarity or substructure.

  • Error handling:

    • Returns structured error or None if compound is not found.
    • Handles PubChem rate limits (≤ 5 requests/sec).

  • Troubleshooting considerations:

    • Ensure network access to pubchem.ncbi.nlm.nih.gov.
    • Verify query format (e.g., valid SMILES or InChI) if results are empty.

  • Additional reference:

    • API documentation pointers: references/api_reference.md

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files (scripts, references) in scientific-skills/Evidence Insight/pubchem-database-skill of aipoch/medical-research-skills.

  • SKILL.md
  • pubchem-database-skill_audit_result_v1.json
  • references/api_reference.md
  • scripts/pubchem_ops.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Pubchem Database Skill next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Pubchem Database Skill compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Pubchem Database Skill this skillaipoch/medical-research-skills2k—~954Automated safety check: PassMIT
Bio Clinical Databases Clinvar LookupGPTomics/bioSkills1.2k2 repos~5.7kAutomated safety check: PassMIT
Zhihu Searchitwanger/toBeBetterJavaer18k—~1.5kAutomated safety check: PassNone
Fastcrudbenavlabs/fastcrud1.6k—~5kAutomated safety check: PassMIT
Cloudflare Email Servicehodgef/apiker1273 repos~2kAutomated safety check: PassMIT
FastAPI Project Templateswshobson/agents40k12 repos~901Automated safety check: PassMIT

Similar skills

  • Bio Clinical Databases Clinvar Lookup

    GPTomics/bioSkills

    Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML.

    1.2k GitHub starsUsed in 2 repos~5.7k tokens
    Backend & APIsAuto-check passed

  • Zhihu Search

    itwanger/toBeBetterJavaer

    Search Zhihu for content using the searchv3 API. An agent skill from itwanger/toBeBetterJavaer.

    18k GitHub stars~1.5k tokensUpdated today
    Backend & APIsAuto-check passed

  • Fastcrud

    benavlabs/fastcrud

    A skill your agent uses when building or modifying CRUD endpoints with FastCRUD (the fastcrud PyPI package) in a FastAPI project — covers FastCRUD, crudrouter, EndpointCreator, FilterConfig…

    1.6k GitHub stars~5k tokensUpdated 13 days ago
    Backend & APIsAuto-check passed

  • Cloudflare Email Service

    hodgef/apiker

    Send and receive transactional emails with Cloudflare Email Service (Email Sending + Email Routing).

    127 GitHub starsUsed in 3 repos~2k tokens
    Backend & APIsAuto-check passed

  • FastAPI Project Templates

    wshobson/agents

    Scaffolds FastAPI projects with a layered app layout, dependency injection through Depends, async handlers and database access, middleware and pytest setup.

    40k GitHub starsUsed in 12 repos~901 tokens
    Backend & APIsAuto-check passed

  • Build X402 Client

    coinbase/cdp-sdk

    Write code that pays for an HTTP API returning 402 Payment Required, using the x402 protocol and a CDP-managed wallet.

    204 GitHub stars~3k tokensUpdated yesterday
    Backend & APIsAuto-check passed

More from aipoch/medical-research-skills

All 567 skills in this repo

  • Academic Poster Generator

    aipoch/medical-research-skills

    Complete workflow for generating academic research posters from PDF literature; use when you need to extract paper content from PDFs and produce a LaTeX-based poster…

    2k GitHub stars~2.2k tokensUpdated 21 days ago
    Auto-check passed

  • Diagnostic Study Quality Assessment Quadas

    aipoch/medical-research-skills

    Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool.

    2k GitHub stars~1.4k tokensUpdated 21 days ago
    Auto-check passed

  • Exploratory Data Analysis

    aipoch/medical-research-skills

    Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.

    2k GitHub stars~3.7k tokensUpdated 21 days ago
    Auto-check passed

  • Iso Certification

    aipoch/medical-research-skills

    A toolkit for preparing ISO 13485:2016 certification documentation for medical device QMS.

    2k GitHub stars~1.8k tokensUpdated 21 days ago
    Auto-check passed

  • Journal Skills

    aipoch/medical-research-skills

    Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal…

    2k GitHub stars~1.7k tokensUpdated 21 days ago
    Auto-check passed

  • Latex Posters

    aipoch/medical-research-skills

    Creates academic-poster writing packages for LaTeX using beamerposter, tikzposter, or baposter.

    2k GitHub stars~1.3k tokensUpdated 21 days ago
    Auto-check passed

Works with

Categories

Questions about Pubchem Database Skill

What does Pubchem Database Skill do?

Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure…. Pubchem Database Skill is an agent skill from aipoch/medical-research-skills. Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure searches, and obtaining bioactivity data.

When should I use Pubchem Database Skill?

Pubchem Database Skill fits situations like: tasks that involve REST APIs; tasks that involve Drug discovery and cheminformatics.

How do I install Pubchem Database Skill in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill pubchem-database-skill -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/pubchem-database-skill in aipoch/medical-research-skills) into .claude/skills/pubchem-database-skill in your project. Claude Code loads it when a task matches its description.

How do I install Pubchem Database Skill in Codex?

Run `npx skills add aipoch/medical-research-skills --skill pubchem-database-skill -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/pubchem-database-skill in aipoch/medical-research-skills) into .agents/skills/pubchem-database-skill in your project. Codex loads it when a task matches its description.

Can I use Pubchem Database Skill in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill pubchem-database-skill -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pubchem-database-skill, .gemini/skills/pubchem-database-skill, .github/skills/pubchem-database-skill and .opencode/skills/pubchem-database-skill in your project.

What does Pubchem Database Skill need to run?

Going by SKILL.md and its folder, Pubchem Database Skill needs Python for the scripts in its folder and the command-line tools its instructions call (python and uv). Our summary lists: Python 3.

Does Pubchem Database Skill access the network?

SKILL.md contains no URLs. Its commands use uv, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Pubchem Database Skill safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Pubchem Database Skill use?

Pubchem Database Skill is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Pubchem Database Skill use?

About 954 tokens (SKILL.md is roughly 3.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 219 tokens, read only when the agent opens those files.

What are the alternatives to Pubchem Database Skill?

Skills that share tags, products or a category with Pubchem Database Skill: Bio Clinical Databases Clinvar Lookup (GPTomics/bioSkills, 1.2k stars), Zhihu Search (itwanger/toBeBetterJavaer, 18k stars), Fastcrud (benavlabs/fastcrud, 1.6k stars) and Cloudflare Email Service (hodgef/apiker, 127 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Pubchem Database Skill?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.