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Agent skill

Search Pubmed

by aipoch in aipoch/medical-research-skills

An intelligent tool for precision medical literature search using PubMed's E-utilities API.

MITAuto-check passedResearch & Science

Install Search Pubmed

skills CLI
$ npx skills add aipoch/medical-research-skills --skill search-pubmed -a claude-code

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

GitHub CLI
$ gh skill install aipoch/medical-research-skills search-pubmed --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/Other/search-pubmed .claude/skills/search-pubmed && 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
search-pubmed
GitHub stars
1.9k
Token cost
~1.3k tokens
SKILL.md length
590 words
Files
3 (incl. scripts)
Skills in repo
578
Repo updated
First seen
Licence
MIT

At a glance

An intelligent tool for precision medical literature search using PubMed's E-utilities API.

  • Works in 4 steps: Confirm the user input, output path, and… → Edit the in-file CONFIG block or… → Run python scripts/search_pubmed.py with… → …
  • Tasks that involve Academic paper search
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 10 more sections
  • Runs Python scripts from its folder; calls python

What it does

Search Pubmed is an agent skill from aipoch/medical-research-skills. An intelligent tool for precision medical literature search using PubMed's E-utilities API.

Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files, including scripts (for example `scripts/search_pubmed.py` and `search-pubmed_audit_result_v2.json`).

It sits in Research & Science, covering Academic paper search and Literature review. It works with PubMed. 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 Academic paper search
  • Tasks that involve Literature review

Example prompts

  • “/search-pubmed”

Requirements

  • Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

  1. Confirm the user input, output path, and any required config values.
  2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
  3. Run python scripts/search_pubmed.py with the validated inputs.
  4. Review the generated output and return the final artifact with any assumptions called out.

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

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

  • Network

    No URLs in SKILL.md.

    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

Search Pubmed loads about 1.3k tokens when it runs. Until then it costs about 26 tokens; SKILL.md has 590 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~26
When it runs · the whole SKILL.md, loaded when a task matches
~1.3k

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). 590 words, ~1,256 tokens.

Download SKILL.mdSave it as .claude/skills/search-pubmed/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.
name
search-pubmed
description
An intelligent tool for precision medical literature search using PubMed's E-utilities API.
license
MIT
author
AIPOCH

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

search pubmed

When to Use

  • Use this skill when the request matches its documented task boundary.
  • Use it when the user can provide the required inputs and expects a structured deliverable.
  • Prefer this skill for repeatable, checklist-driven execution rather than open-ended brainstorming.

Key Features

  • Scope-focused workflow aligned to: An intelligent tool for precision medical literature search using PubMed's E-utilities API.
  • Packaged executable path(s): scripts/search_pubmed.py.
  • Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

  • Python: 3.10+. Repository baseline for current packaged skills.
  • Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.

Example Usage

bash
cd "20260316/scientific-skills/Others/search-pubmed"
python -m py_compile scripts/search_pubmed.py
python scripts/search_pubmed.py --help

Example run plan:

  1. Confirm the user input, output path, and any required config values.
  2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
  3. Run python scripts/search_pubmed.py with the validated inputs.
  4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

  • Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
  • Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
  • Primary implementation surface: scripts/search_pubmed.py.
  • Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
  • Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Description

A script tool for precision medical literature search using PubMed's E-utilities API. Optimized for systematic reviews, meta-analyses, and evidence-based research.return total counts of relevant articles

scripts

For detailed strategies used in pubmed search, see [scripts/search_pubmed.py].

When Not to Use

  • Do not use this skill when the required source data, identifiers, files, or credentials are missing.
  • Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
  • Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.

Required Inputs

  • A clearly specified task goal aligned with the documented scope.
  • All required files, identifiers, parameters, or environment variables before execution.
  • Any domain constraints, formatting requirements, and expected output destination if applicable.
Show full SKILL.md (243 more words)Show less
  1. Validate the request against the skill boundary and confirm all required inputs are present.
  2. Select the documented execution path and prefer the simplest supported command or procedure.
  3. Produce the expected output using the documented file format, schema, or narrative structure.
  4. Run a final validation pass for completeness, consistency, and safety before returning the result.

Output Contract

  • Return a structured deliverable that is directly usable without reformatting.
  • If a file is produced, prefer a deterministic output name such as search_pubmed_result.md unless the skill documentation defines a better convention.
  • Include a short validation summary describing what was checked, what assumptions were made, and any remaining limitations.

Validation and Safety Rules

  • Validate required inputs before execution and stop early when mandatory fields or files are missing.
  • Do not fabricate measurements, references, findings, or conclusions that are not supported by the provided source material.
  • Emit a clear warning when credentials, privacy constraints, safety boundaries, or unsupported requests affect the result.
  • Keep the output safe, reproducible, and within the documented scope at all times.

Failure Handling

  • If validation fails, explain the exact missing field, file, or parameter and show the minimum fix required.
  • If an external dependency or script fails, surface the command path, likely cause, and the next recovery step.
  • If partial output is returned, label it clearly and identify which checks could not be completed.

Quick Validation

Run this minimal verification path before full execution when possible:

bash
python scripts/search_pubmed.py --help

Expected output format:

text
Result file: search_pubmed_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any

© 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 2 other files (scripts) in scientific-skills/Other/search-pubmed of aipoch/medical-research-skills.

  • SKILL.md
  • scripts/search_pubmed.py
  • search-pubmed_audit_result_v2.json

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Search Pubmed 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.

Search Pubmed compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Search Pubmed this skillaipoch/medical-research-skills1.9k—~1.3kAutomated safety check: PassMIT
Literature Reviewneflibata-feng/MyArxiv-Agent12620 repos~5.9kAutomated safety check: NotesMIT
Academic Search and Citation RouterYuan1z0825/nature-skills47k—~884Automated safety check: PassApache-2.0
Literature ReviewK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: NotesMIT
PubMed REST API Searchdavila7/claude-code-templates33k14 repos~3.9kAutomated safety check: PassMIT
Keyword Literature HarvesterJinze-Lee/codex-skills-workbench109—~952Automated safety check: PassMIT

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Works with

Categories

Questions about Search Pubmed

What does Search Pubmed do?

An intelligent tool for precision medical literature search using PubMed's E-utilities API. Search Pubmed is an agent skill from aipoch/medical-research-skills. An intelligent tool for precision medical literature search using PubMed's E-utilities API.

When should I use Search Pubmed?

Search Pubmed fits situations like: tasks that involve Academic paper search; tasks that involve Literature review.

How do I install Search Pubmed in Claude Code?

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

How do I install Search Pubmed in Codex?

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

Can I use Search Pubmed 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 search-pubmed -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/search-pubmed, .gemini/skills/search-pubmed, .github/skills/search-pubmed and .opencode/skills/search-pubmed in your project.

What does Search Pubmed need to run?

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

Does Search Pubmed access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Search Pubmed 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 Search Pubmed use?

Search Pubmed 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 Search Pubmed use?

About 1.3k tokens (SKILL.md is roughly 5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Search Pubmed?

Skills that share tags, products or a category with Search Pubmed: Literature Review (neflibata-feng/MyArxiv-Agent, 126 stars), Academic Search and Citation Router (Yuan1z0825/nature-skills, 47k stars), Literature Review (K-Dense-AI/scientific-agent-skills, 48k stars) and PubMed REST API Search (davila7/claude-code-templates, 33k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Search Pubmed?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,937 GitHub stars. The repository holds 578 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.