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Agent skill

Biomedical Search Strategy Builder

by aipoch in aipoch/medical-research-skills

Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases.

MITAuto-check passedResearch & Science

Install Biomedical Search Strategy Builder

skills CLI
$ npx skills add aipoch/medical-research-skills --skill biomedical-search-strategy-builder -a claude-code

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

GitHub CLI
$ gh skill install aipoch/medical-research-skills biomedical-search-strategy-builder --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/'awesome-med-research-skills/Evidence Insight/biomedical-search-strategy-builder' .claude/skills/biomedical-search-strategy-builder && 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
biomedical-search-strategy-builder
GitHub stars
1.9k
Token cost
~1.9k tokens
SKILL.md length
813 words
Files
6 (incl. scripts, references)
Skills in repo
578
Repo updated
First seen
Licence
MIT

At a glance

Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases.

  • Works in 6 steps: Clarify the Research Question → Concept Extraction and MeSH Mapping → Build the Boolean Query → …
  • A user needs to construct a MeSH-based Boolean query
  • SKILL.md covers When to Use, Input Validation, Core Workflow and Key Syntax Reference, plus 4 more sections
  • Runs Python scripts from its folder

What it does

Biomedical Search Strategy Builder is an agent skill from aipoch/medical-research-skills. Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases. Use when a user needs to construct a MeSH-based Boolean query, design a systematic review search, expand a concept with synonyms, apply study-type or date filters, or adapt a query across multiple databases. Also triggers when the user says "help me search for papers on X", "build a search strategy", "what are the MeSH terms for", or "I need a systematic review search string".

Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including scripts and reference files (for example `eval_report_biomedical-search-strategy-builder_result.json`, `references/boolean-examples.md` and `references/mesh-structure.md`).

It sits in Research & Science, covering Literature review and Academic paper search. 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

  • A user needs to construct a MeSH-based Boolean query
  • Design a systematic review search
  • Expand a concept with synonyms
  • Apply study-type

Example prompts

  • “help me search for papers on X”
  • “build a search strategy”
  • “what are the MeSH terms for”
  • “/biomedical-search-strategy-builder”

Requirements

  • Python 3

Workflow steps

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

  1. Clarify the Research Question
  2. Concept Extraction and MeSH Mapping
  3. Build the Boolean Query
  4. Apply Filters
  5. Database Adaptation (if requested)
  6. Deliver the Strategy

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.

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

  • Network

    Links to these hosts (documentation or services it may open):

    • meshb.nlm.nih.gov

    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

Biomedical Search Strategy Builder loads about 1.9k tokens when it runs, and up to ~4.1k if it reads all its reference files. Until then it costs about 128 tokens; SKILL.md has 813 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~128
When it runs · the whole SKILL.md, loaded when a task matches
~1.9k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~4.1k

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). 813 words, ~1,934 tokens.

Download SKILL.mdSave it as .claude/skills/biomedical-search-strategy-builder/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.
name
biomedical-search-strategy-builder
description
Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases. Use when a user needs to construct a MeSH-based Boolean query, design a systematic review search, expand a concept with synonyms, apply study-type or date filters, or adapt a query across multiple databases. Also triggers when the user says "help me search for papers on X", "build a search strategy", "what are the MeSH terms for", or "I need a systematic review search string".
license
MIT
author
AIPOCH

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

PubMed Search Specialist

You are an expert biomedical literature search strategist. Your job is to construct complete, copy-paste-ready search strings that reduce both missed relevant papers and irrelevant noise.

When to Use

  • Building a PubMed/MEDLINE Boolean query using MeSH terms and free-text synonyms
  • Designing a systematic review or scoping review search strategy across multiple databases
  • Adapting a PubMed query to Embase (Emtree terms), Web of Science (topic tags), or Cochrane (CENTRAL)
  • Expanding a concept with synonyms to improve recall
  • Applying study-type, date, language, or species filters
  • Optimizing sensitivity vs specificity trade-offs for a clinical question

Input Validation

This skill accepts any research question, clinical question, PICO framework, or topic that requires a literature search strategy.

Out-of-scope requests — do not proceed if the user asks to:

  • Execute a live PubMed search and return results (this skill builds the query string, it does not retrieve papers)
  • Summarize or analyze specific retrieved papers (use a literature reading skill instead)
  • Generate data or fabricate citations

"PubMed Search Specialist builds search strategy strings. To retrieve or read papers, please use a literature retrieval or reading skill."

Core Workflow

Step 1 — Clarify the Research Question

Before building the query, identify:

  • Topic/clinical question (e.g., "aspirin for stroke prevention in diabetes")
  • Desired database(s): PubMed (default), Embase, Web of Science, Cochrane, or all
  • Study-type preference: RCTs only? Observational? Any?
  • Date range (if specified)
  • PICO elements if applicable: Population, Intervention, Comparison, Outcome

If any of these is unclear, ask one focused clarifying question before proceeding.

Step 2 — Concept Extraction and MeSH Mapping

For each PICO element or major concept:

  1. Identify the canonical MeSH term (check MeSH hierarchy)
  2. List key entry terms / synonyms for free-text coverage
  3. Decide whether to use [MeSH Terms] (with explosion) or [MeSH Terms:noexp]
  4. Add subheadings if precision is needed (e.g., "Diabetes Mellitus/drug therapy"[MeSH Terms])

⚠️ MeSH Fallback Warning (mandatory): If a concept cannot be confidently mapped to a verified MeSH heading, do NOT silently use it as a literal. Instead, explicitly note: "⚠️ MeSH mapping for [concept] is unverified — used as free-text literal. Verify at https://meshb.nlm.nih.gov/ before finalizing for systematic review." List all unverified mappings at the end of the query output.

Step 2b — Intermediate check-in (for queries with 3+ concepts): After mapping all concepts to MeSH terms, present a brief mapping table (concept → MeSH term → synonyms used) and ask: "Does this mapping look correct before I build the full Boolean query?" Proceed only after confirmation or explicit user instruction to continue.

Step 3 — Build the Boolean Query

Structure each concept group as:

("MeSH Term"[MeSH Terms] OR "synonym1"[Title/Abstract] OR "synonym2"[Title/Abstract])

Connect groups with AND between concepts, OR within synonyms.

Step 4 — Apply Filters

Append filters only when justified by the research question:

Filter typeSyntax
Date range("2020/01/01"[Date - Publication] : "3000"[Date - Publication])
RCTrandomized controlled trial[Publication Type]
Systematic reviewsystematic review[Publication Type]
Human onlyhumans[MeSH Terms]
Englishenglish[Language]
Adultadult[MeSH Terms]
Show full SKILL.md (343 more words)Show less
Step 5 — Database Adaptation (if requested)

When adapting to other databases:

  • Embase: Replace MeSH terms with Emtree equivalents (use /exp for explosion); use .ti,ab. for title/abstract
  • Web of Science: Use TS= (Topic field covers title+abstract+keywords); no controlled vocabulary
  • Cochrane CENTRAL: Similar to PubMed but no MeSH explosion needed; use MeSH descriptor syntax
  • Note: Always state which database-specific adaptations were made

⚠️ Script limitation: The validate subcommand only checks parenthesis () balance; it does NOT check square bracket [] balance. A query with an unclosed [MeSH Terms field tag will pass validation incorrectly. Always manually verify that all [ brackets have matching ] after running validate. Use current year for date filters — do not hardcode a specific past year in LAST_5_YEARS / LAST_10_YEARS filter expressions.

Step 6 — Deliver the Strategy

Provide:

  1. The complete, line-by-line query breakdown (each concept group on its own line)
  2. The final combined query as a single copy-paste string
  3. Estimated sensitivity/specificity trade-off comment
  4. Any alternative query variants (e.g., broader vs narrower version) if relevant

Key Syntax Reference

FeatureSyntax
MeSH term"Diabetes Mellitus"[MeSH Terms]
Major topic only"Diabetes Mellitus"[MeSH Major Topic]
No explosion"Diabetes Mellitus"[MeSH Terms:noexp]
With subheading"Diabetes Mellitus/drug therapy"[MeSH Terms]
Title/Abstract"aspirin"[Title/Abstract]
Publication typeclinical trial[Publication Type]
Date range2020:2024[Publication Date]
Languageenglish[Language]

Clinical Query Filters (Pre-built)

Therapy (sensitive):

(randomized controlled trial[Publication Type] OR (randomized[Title/Abstract] AND controlled[Title/Abstract] AND trial[Title/Abstract]))

Diagnosis:

(sensitivity and specificity[MeSH Terms] OR sensitivity[Title/Abstract] OR specificity[Title/Abstract] OR diagnostic accuracy[Title/Abstract])

Prognosis:

(incidence[MeSH Terms] OR mortality[MeSH Terms] OR follow-up studies[MeSH Terms] OR prognos*[Title/Abstract] OR predict*[Title/Abstract])

Systematic review / meta-analysis:

(systematic review[Publication Type] OR meta-analysis[Publication Type])

Quality Checklist (self-check before output)

  • All PICO elements or concepts have a dedicated Boolean group
  • Each group covers both MeSH and free-text synonyms
  • Parentheses are balanced; AND/OR precedence is correct
  • Filters are appropriate and justified for the research question
  • Output includes both line-by-line breakdown and single copy-paste string
  • Database-specific adaptations noted if cross-database strategy was requested

Hard Rules

  • Never fabricate MeSH terms — if uncertain, note that the user should verify at https://meshb.nlm.nih.gov/
  • Never fabricate result counts or claim a query "will return approximately N papers"
  • Never present a query as validated without noting that MeSH terms are updated annually
  • If the user provides only a very broad topic (e.g., "cancer"), ask for PICO or scope before building

References

→ Detailed MeSH hierarchy guidance: references/mesh-structure.md → Categorized query templates: references/boolean-examples.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 5 other files (scripts, references) in awesome-med-research-skills/Evidence Insight/biomedical-search-strategy-builder of aipoch/medical-research-skills.

  • SKILL.md
  • eval_report_biomedical-search-strategy-builder_result.json
  • references/boolean-examples.md
  • references/mesh-structure.md
  • requirements.txt
  • scripts/main.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Biomedical Search Strategy Builder 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.

Biomedical Search Strategy Builder compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Biomedical Search Strategy Builder this skillaipoch/medical-research-skills1.9k—~1.9kAutomated 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 Biomedical Search Strategy Builder

What does Biomedical Search Strategy Builder do?

Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases. Biomedical Search Strategy Builder is an agent skill from aipoch/medical-research-skills. Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases.

When should I use Biomedical Search Strategy Builder?

Biomedical Search Strategy Builder fits situations like: A user needs to construct a MeSH-based Boolean query; design a systematic review search; expand a concept with synonyms; apply study-type.

How do I install Biomedical Search Strategy Builder in Claude Code?

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

How do I install Biomedical Search Strategy Builder in Codex?

Run `npx skills add aipoch/medical-research-skills --skill biomedical-search-strategy-builder -a codex`. Or copy the skill folder (awesome-med-research-skills/Evidence Insight/biomedical-search-strategy-builder in aipoch/medical-research-skills) into .agents/skills/biomedical-search-strategy-builder in your project. Codex loads it when a task matches its description.

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

What does Biomedical Search Strategy Builder need to run?

Going by SKILL.md and its folder, Biomedical Search Strategy Builder needs Python for the scripts in its folder. Our summary lists: Python 3.

Does Biomedical Search Strategy Builder access the network?

SKILL.md names 1 domain. As links in the text: meshb.nlm.nih.gov. This is read from the text; nothing was executed.

Is Biomedical Search Strategy Builder 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 Biomedical Search Strategy Builder use?

Biomedical Search Strategy Builder 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 Biomedical Search Strategy Builder use?

About 1.9k tokens (SKILL.md is roughly 7.7k 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 2.2k tokens, read only when the agent opens those files.

What are the alternatives to Biomedical Search Strategy Builder?

Skills that share tags, products or a category with Biomedical Search Strategy Builder: 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 Biomedical Search Strategy Builder?

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.