Pubmed Search Specialist

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

Quality Checklist

Before finalizing query:

• All concepts covered with OR within, AND between groups
• MeSH terms verified against current MeSH database
• Free-text synonyms included for completeness
• Filters appropriate for research question
• Parentheses balanced and precedence correct
• Copy-paste ready for PubMed search box

Technical Difficulty

🔴 High - Requires understanding of:

• MeSH hierarchical structure and term relationships
• Boolean logic and operator precedence
• Field tag semantics and limitations
• Search sensitivity vs specificity trade-offs
• Clinical query methodology

⚠️ Verification Required: MeSH terms change annually. Always verify current MeSH version at https://meshb.nlm.nih.gov/

References

See references/mesh-structure.md for detailed MeSH hierarchy guidance. See references/boolean-examples.md for categorized query templates.

Risk Assessment

Security Checklist

• No hardcoded credentials or API keys
• NCBI API requests use HTTPS only
• API rate limits respected (max 3 requests/second without API key)
• Input validation for search terms (injection prevention)
• Output directory restricted to workspace
• Error messages sanitized (no internal paths exposed)
• API timeout and retry mechanisms implemented
• No exposure of internal service architecture

Prerequisites

# Python dependencies
pip install -r requirements.txt

# Optional: NCBI API key for higher rate limits

# Set as environment variable: NCBI_API_KEY

Evaluation Criteria

Success Metrics

• Successfully constructs valid PubMed Boolean queries
• MeSH term mapping is accurate and current
• Query syntax is copy-paste ready for PubMed
• Provides sensitivity/specificity trade-off options
• Handles complex multi-concept research questions
• Estimated result counts are reasonable

Test Cases

1. Basic Query: "diabetes treatment" → Valid MeSH-based query
2. PICO Framework: Complex clinical question → Complete search strategy
3. MeSH Mapping: Free-text term → Correct MeSH term identification
4. Boolean Logic: Multiple concepts → Properly nested AND/OR/NOT
5. Clinical Query: Therapy-focused question → Includes appropriate filters
6. API Integration: Execute search via E-utilities → Successful retrieval
7. Error Handling: Invalid search term → Graceful error with suggestions

Lifecycle Status

• Current Stage: Draft
• Next Review Date: 2026-03-06
• Known Issues:
  • MeSH terms updated annually, may need periodic validation
  • API rate limits without key
• Planned Improvements:
  • Integration with NCBI API key support for higher rate limits
  • Automatic MeSH term validation against current database
  • Support for additional databases (Embase, Cochrane)

Output Requirements

Every final response should make these items explicit when they are relevant:

• Objective or requested deliverable
• Inputs used and assumptions introduced
• Workflow or decision path
• Core result, recommendation, or artifact
• Constraints, risks, caveats, or validation needs
• Unresolved items and next-step checks

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
• If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
• Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of pubmed-search-specialist and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

pubmed-search-specialist only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

Response Template

Use the following fixed structure for non-trivial requests:

1. Objective
2. Inputs Received
3. Assumptions
4. Workflow
5. Deliverable
6. Risks and Limits
7. Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.