Reference Retrieval Skill

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

Reference Retrieval Skill

Core Function

This skill helps users quickly retrieve and filter high-quality, highly relevant references from PubMed based on natural language descriptions.

Workflow

Step 1: Construct Boolean Query

1. Analyze intent: Understand user semantics, extract core medical keywords (MeSH Terms preferred).
2. Construct Boolean query:
   • Logical operators: Use AND (intersection), OR (union), NOT (exclusion).
   • Truncation: Use * to match variants (e.g., diagno* matches diagnosis, diagnostic).
   • Example: For "metformin treatment of type 2 diabetes", construct: Metformin AND "Diabetes Mellitus, Type 2" AND (Therapy OR Treatment).

[!TIP] About Escaping: If the query contains double quotes " (e.g., phrase search), you must wrap the entire query in single quotes or escape internal double quotes with \" to avoid command-line parsing errors.

• Correct: python scripts/pubmed_search.py 'Metformin AND "Type 2 Diabetes"'
• Correct: python scripts/pubmed_search.py "Metformin AND \"Type 2 Diabetes\""

Step 2: Execute Search

Prefer LitSense for semantic search; only use PubMed Boolean search when precise control or complex Boolean logic is needed.

Scenario A: Semantic/Natural Language Search (LitSense) [Preferred] Suitable for direct natural language queries or finding literature related to complex statements.

python scripts/litsense_search.py "natural language query"

Scenario B: Basic Boolean Search (PubMed) Suitable when a precise Boolean query has been constructed.

python scripts/pubmed_search.py "YOUR_BOOLEAN_QUERY"

• --max: Returns 20 articles by default; specify --max 50 for more.

Step 3: Evaluation & Iteration

If initial results are inadequate (too few, low relevance, or empty), must automatically iterate, up to 5 rounds.

1. Analyze cause:
   • Zero results: Keywords may be misspelled or too specific.
   • Irrelevant results: Keywords are ambiguous or Boolean logic is incorrect.
2. Refine query:
   • Broaden scope: Remove non-essential AND conditions, add OR synonyms.
   • Narrow scope: Add qualifiers (e.g., diagnosis, therapy), or use field tags [ti].
   • Switch API: If LitSense search fails or lacks precision, try constructing a precise Boolean query for PubMed.
3. Iterate:
   • Repeat the cycle: modify query, run script, evaluate results.
   • Limit: Maximum 5 retries. If still no satisfactory results after 5 attempts, report tried strategies and request more information from the user.

Step 4: Filter & Present

After the script returns JSON results, filter 3-5 best references based on these criteria:

1. Selection criteria:

   • Relevance: Title/abstract must directly address the user's question.
   • Article type: Prefer Review, Systematic Review, Meta-Analysis. Then high-quality RCT or Original Article. Never cite Letters, Editorials, or Comments.
   • Recency: Prefer literature from the past 5-10 years (exceptions for classic foundational works).
   • Open Access (OA): If looking for OA/free literature, check for is_oa: true or pmcid field in results, indicating free full text via PMC.

2. Output format: Present results strictly in the following structure:

   I. Citation Marking Add citation markers at key points in the response content (or in user-provided text).

   • Format example: ...effectively improved prognosis [1]. or ...treatment efficacy [1].
   • Language should match the user's query language.

   II. References List references in citation order, format as follows:

   [1] PMID: 34479503 | Title. Journal. https://pubmed.ncbi.nlm.nih.gov/34479503/
   
   Citation rationale: Briefly explain why this reference supports the stated point.
   
   [2] ...

   PubMed link generation rules:

   • Always provide direct link: https://pubmed.ncbi.nlm.nih.gov/{pmid}
   • For example, PMID 34479503 becomes: https://pubmed.ncbi.nlm.nih.gov/34479503

   [!NOTE] Example: [1] The augment of regulatory T cells undermines the efficacy of anti-PD-L1 treatment in cervical cancer. BMC Immunol. https://pubmed.ncbi.nlm.nih.gov/34479503/

Important Notes

• Accuracy: A query that is too broad yields irrelevant results; too narrow may yield nothing. If results are few, try reducing search terms.
• Language consistency: Never auto-translate. Summary language must match the user's query language.
• Search language: Always translate non-English keywords to accurate English medical terms for searching (searches must use English), but present final results matching the user's language.

When to Use

• Use this skill when the user explicitly needs to perform the core task of reference-retrieval-skill and has provided the minimum executable input.
• Use this skill when you need a structured deliverable rather than general advice.
• Use this skill when the current task can be completed using this skill's bundled scripts, templates, or reference materials.