Pubmed Search Specialist

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

PubMed Search Specialist

Expert tool for constructing sophisticated Boolean queries to search PubMed/MEDLINE database with precision.

When to Use

• Use this skill when the task needs Build complex Boolean query strings for precise PubMed/MEDLINE literature retrieval. Trigger when user needs MeSH term mapping, Boolean query construction, advanced PubMed filters, citation searching, systematic review search strategy, or clinical query optimization.
• Use this skill for evidence insight tasks that require explicit assumptions, bounded scope, and a reproducible output format.
• Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.

Key Features

• Scope-focused workflow aligned to: Build complex Boolean query strings for precise PubMed/MEDLINE literature retrieval. Trigger when user needs MeSH term mapping, Boolean query construction, advanced PubMed filters, citation searching, systematic review search strategy, or clinical query optimization.
• Packaged executable path(s): scripts/main.py.
• Reference material available in references/ for task-specific guidance.
• Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

See ## Prerequisites above for related details.

• Python: 3.10+. Repository baseline for current packaged skills.
• dataclasses: unspecified. Declared in requirements.txt.
• requests: unspecified. Declared in requirements.txt.

Example Usage

cd "20260318/scientific-skills/Evidence Insight/pubmed-search-specialist"
python -m py_compile scripts/main.py
python scripts/main.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/main.py with the validated inputs.
4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

See ## Workflow above for related 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/main.py.
• Reference guidance: references/ contains supporting rules, prompts, or checklists.
• 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.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

python -m py_compile scripts/main.py
python scripts/main.py --help

Workflow

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Core Capabilities

• MeSH Term Mapping: Convert natural language concepts to standardized Medical Subject Headings
• Boolean Query Builder: Construct complex nested queries with AND/OR/NOT operators
• Advanced Filters: Apply study type, date, language, age, and species filters
• Search Strategy Optimization: Refine sensitivity vs specificity trade-offs

Usage Workflow

1. Concept Extraction

Extract key concepts from user's research question using PICO framework:

• Population/Problem
• Intervention
• Comparison
• Outcome

2. MeSH Term Mapping

For each concept, identify appropriate MeSH terms:

• Preferred terms (mapped to MeSH hierarchy)
• Entry terms (synonyms mapped to preferred)
• Subheadings for precision
• Explode vs Focus options

3. Boolean Construction

Build query strings following PubMed syntax:

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

4. Filter Application

Append filters as needed:

• Publication dates: from 2020 to 2024
• Article types: Clinical Trial, Review, Meta-Analysis
• Species: humans[MeSH Terms] or animals[MeSH Terms]
• Languages: english[Language]
• Age groups: adult[MeSH Terms], aged[MeSH Terms]

5. Search Strategy Output

Provide complete, copy-paste ready PubMed search string with:

• Line-by-line breakdown
• Estimated result count guidance
• Alternative strategies for sensitivity/specificity balance

Key MeSH Features

Boolean Operators

• AND: Both terms must appear (narrows search)
• OR: Either term may appear (broadens search)
• NOT: Exclude terms (use sparingly)

Operator Precedence: Use parentheses to control evaluation order.

Field Tags Reference

Clinical Query Filters

Therapy

(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])

Etiology

(risk[MeSH Terms] OR (risk factors[MeSH Terms]) OR (risk[Title/Abstract] AND factor*[Title/Abstract]))

Parameters

Example: Complete Search Strategy

Research Question: Does aspirin reduce stroke risk in diabetic patients?

Line 1 - Population:

("Diabetes Mellitus"[MeSH Terms] OR "Diabetic"[Title/Abstract] OR "Diabetics"[Title/Abstract])

Line 2 - Intervention:

("Aspirin"[MeSH Terms] OR "Acetylsalicylic Acid"[Title/Abstract] OR "aspirin"[Title/Abstract])

Line 3 - Outcome:

("Stroke"[MeSH Terms] OR "Cerebrovascular Accident"[Title/Abstract] OR "stroke"[Title/Abstract] OR "cerebrovascular"[Title/Abstract])

Line 4 - Study Type Filter:

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

Final Query:

(("Diabetes Mellitus"[MeSH Terms] OR "Diabetic"[Title/Abstract] OR "Diabetics"[Title/Abstract]) AND ("Aspirin"[MeSH Terms] OR "Acetylsalicylic Acid"[Title/Abstract] OR "aspirin"[Title/Abstract]) AND ("Stroke"[MeSH Terms] OR "Cerebrovascular Accident"[Title/Abstract] OR "stroke"[Title/Abstract] OR "cerebrovascular"[Title/Abstract]) AND (randomized controlled trial[Publication Type] OR systematic review[Publication Type] OR meta-analysis[Publication Type]))

MeSH Browser Usage

When mapping terms:

1. Check MeSH Browser for exact term hierarchy
2. Note tree numbers for related terms
3. Identify entry terms (synonyms)
4. Consider subheadings for precision
5. Decide on explode vs noexp based on scope needs