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skills/brycewang-stanford/Auto-Empirical-Research-Skills/68-research-productivity-skills-literature-survey-generator

68-research-productivity-skills-literature-survey-generator

1
brycewang-stanford/Auto-Empirical-Research-Skills·Research·Audit pending·Snapshot 6a1a90734317

Summary

This source did not publish a separate summary. Review SKILL.md before using the skill.

SKILL.md

Literature Survey Generator

A multi-agent, multi-phase pipeline that produces a complete academic literature survey in LaTeX with BibTeX — from search to final compiled PDF.

When to Use

  • User wants a literature review on a topic across specific journals
  • User wants to find and synthesize recent papers in a field
  • User asks for a survey of Top 5 / Top Field journals on a topic
  • User wants automated paper search → download → review writing

Overview

The pipeline has 4 phases, each using parallel subagents where possible:

Phase 1: SEARCH (parallel per journal)
    ↓ search_{journal}.json files
Phase 2: PROCESS (3 parallel agents)
    ↓ references.bib + paper_summaries.md + pdfs/
Phase 3: DRAFT (1 agent + compilation)
    ↓ survey.tex → survey.pdf
Phase 4: REVIEW & REVISE (sequential)
    ↓ review_report.md → survey_v2.tex → survey_v2.pdf

Execution Instructions

Step 0: Setup

  1. Parse the user's request to extract:

    • Topic: The search query (e.g., "networks", "behavioral economics")
    • Journals: Which journals to search (default: Top 5 Economics)
    • Year range: Publication year(s) (default: current year)
    • Output format: LaTeX (default), Markdown, or both
  2. Create working directory:

    agent_tasks/{topic_slug}_{YYYYMMDDHH}/
    
  3. Write plan.md to the working directory documenting the execution plan.

  4. Set up task tracking with TaskCreate for the 4 phases.

Step 1: Phase 1 — Parallel Journal Search

Launch one subagent per journal (up to 10 in parallel). Each agent:

  1. Queries OpenAlex API with the journal's source ID and topic keyword
  • Queries CrossRef API with the journal's ISSN and topic keyword
  • Deduplicates results by DOI
  • Saves to search_{journal_abbrev}.json
  • Agent prompt template:

    Search for papers about "{TOPIC}" published in {JOURNAL_NAME} in {YEAR}.
    
    1. OpenAlex API (source ID: {OPENALEX_ID}):
       curl -s "https://api.openalex.org/works?filter=primary_location.source.id:{OPENALEX_ID},default.search:{TOPIC},publication_year:{YEAR}&per_page=50&[email protected]"
    
    2. CrossRef API (ISSN: {ISSN}):
       curl -s "https://api.crossref.org/journals/{ISSN}/works?query={TOPIC}&filter=from-pub-date:{YEAR}-01-01&rows=50&[email protected]"
    
    Extract: title, authors, doi, year, cited_by, pdf_urls, abstract (from inverted index), openalex_id.
    Deduplicate by DOI. Save to: {WORKDIR}/search_{ABBREV}.json
    

    Key journal identifiers (verify OpenAlex IDs via API before use):

    JournalISSNOpenAlex ID
    American Economic Review0002-8282S23254222
    Econometrica0012-9682S95464858
    Journal of Political Economy0022-3808(verify via API)
    Quarterly Journal of Economics0033-5533S203860005
    Review of Economic Studies0034-6527(verify via API)

    For non-Top-5 journals, first look up the OpenAlex source ID:

    curl -s "https://api.openalex.org/sources?search={journal+name}&[email protected]"
    

    Wait for all search agents to complete before proceeding.

    After all agents complete, do a quick tally: read each search_*.json and count papers. If total < 3, consider broadening the search terms or year range. If total > 30, the topic may need narrowing — flag this to the user.

    Step 2: Phase 2 — Process (3 Parallel Agents)

    Launch these 3 agents simultaneously:

    Agent A: PDF Downloader

    For each paper with a DOI:

    1. Query Unpaywall: https://api.unpaywall.org/v2/{DOI}[email protected]
    2. Check best_oa_location.url_for_pdf and all oa_locations[].url_for_pdf
    3. If PDF URL found, download to pdfs/{safe_filename}.pdf
    4. Verify each download is a real PDF (file > 10KB, starts with %PDF)
    5. Save pdfs/download_report.md

    Agent B: BibTeX Builder

    For each DOI:

    curl -sL -H "Accept: application/x-bibtex" "https://doi.org/{DOI}"
    
    • Clean citation keys to {firstauthor}{year}{keyword} format
    • Add foundational references cited in the introduction (if known)
    • Save to references.bib

    Agent C: Summary Extractor

    For each paper:

    1. Read abstracts from search_*.json files
    2. For missing/truncated abstracts, query OpenAlex for full inverted abstract
    3. As fallback, query Semantic Scholar (with 3s sleep between calls)
    4. Save paper_summaries.md with per-paper sections:
      • Title, Authors, Journal, DOI, Citations, Full Abstract, Key Themes
    5. Save all_papers.json (consolidated, enriched metadata)

    Wait for all 3 agents to complete before proceeding.

    Step 3: Phase 3 — Draft LaTeX Survey

    Launch 1 agent to write the survey. The agent reads:

    • paper_summaries.md (content source)
    • references.bib (citation keys)

    Survey structure (adapt based on paper count and topics):

    \documentclass[12pt]{article}
    \usepackage{amsmath,amssymb,natbib,geometry,hyperref,booktabs,setspace,array}
    \bibliographystyle{plainnat}
    
    1. Title, Author, Abstract (150-200 words)
    2. Introduction
       - Motivation for the topic
       - Selection methodology (how papers were found)
       - Brief overview of themes
       - Positioning relative to existing surveys
    3. Summary Table (booktabs: Authors, Journal, Title, Type, Key Aspect)
    4-6. Thematic Sections (group papers by theme, not by journal)
       - Each paper: 2+ paragraphs of substantive discussion
       - Critical engagement: limitations, open questions
       - Cross-references between papers where relevant
    7. Methodological Advances (compare approaches across papers)
    8. Conclusion (synthesis, gaps, future directions)
    

    Important instructions for the drafting agent:

    • Use \citet{} for in-text citations, \citep{} for parenthetical
    • Be transparent about papers with tangential relevance to the topic
    • Add critical engagement (limitations, open questions) for at least 3 papers
    • Verify all \cite keys match entries in references.bib
    • Target 8-15 pages when compiled

    After the agent saves survey.tex, compile it:

    cd {WORKDIR}
    pdflatex -interaction=nonstopmode survey.tex
    bibtex survey
    pdflatex -interaction=nonstopmode survey.tex
    pdflatex -interaction=nonstopmode survey.tex
    

    Check for errors. Fix any compilation issues before proceeding.

    Step 4: Phase 4 — Review & Revise

    4a: Review Agent

    Reads survey.tex, paper_summaries.md, references.bib. Writes review_report.md covering:

    1. Content Accuracy: Does each paper description match its abstract?
    2. Structure: Is the grouping logical? Are transitions smooth?
    3. Writing Quality: Academic tone, citation style consistency
    4. Completeness: Are all papers discussed substantively?
    5. Specific Revisions: 5-10 actionable changes with priority (HIGH/MEDIUM/LOW)
    6. Overall Score: X/10 with top 3 strengths and weaknesses

    4b: Revision Agent

    Reads review_report.md, survey.tex, paper_summaries.md. Implements ALL revision suggestions. Saves to survey_v2.tex.

    Final compilation:

    cd {WORKDIR}
    pdflatex -interaction=nonstopmode survey_v2.tex
    bibtex survey_v2
    pdflatex -interaction=nonstopmode survey_v2.tex
    pdflatex -interaction=nonstopmode survey_v2.tex
    

    Verify zero errors in the final PDF.

    Step 5: Deliver

    Report to the user:

    • Total papers found per journal
    • PDF download success rate
    • Review score and key improvements made
    • Final PDF page count and location
    • List all deliverables in the working directory

    Critical Rules

    1. File handoff, not context handoff: Every agent saves its output to a file. Never pass large content back to the main agent. Agents return only a status summary (paper count, success/failure, file paths).

    2. Parallel where possible, sequential where required: Phases 1 and 2 are parallel internally. Phase 3 depends on Phase 2 outputs. Phase 4 is sequential (review before revision).

    3. All agents get mode: auto: Subagents need Bash, Read, Write, Edit access to do their work without permission prompts.

    4. Verify before proceeding: Always compile LaTeX and check for errors between phases. Don't hand broken output to the next phase.

    5. Be transparent about relevance: Not every paper returned by keyword search is centrally about the topic. The survey should acknowledge varying degrees of relevance rather than force-fitting papers into the narrative.

    6. Respect API rate limits: OpenAlex (add mailto), CrossRef (add mailto), Semantic Scholar (3s between calls), arXiv (3s between calls).

    Customization Points

    • Different journals: Change the journal table. For any journal, look up its OpenAlex source ID first.
    • Different output format: Swap LaTeX template for Markdown if user prefers.
    • Broader search: Add NBER, SSRN, arXiv searches in Phase 1 using the academic-paper-search skill's API patterns.
    • Deeper review: Add a second review-revise cycle if the first review score < 7.
    • Zotero import: After Phase 2, optionally import all papers via zotero_add_by_doi.

    File Structure (Final)

    agent_tasks/{topic}_{timestamp}/
    ├── plan.md                  # Execution plan
    ├── search_aer.json          # Per-journal search results
    ├── search_ecma.json
    ├── search_jpe.json
    ├── search_qje.json
    ├── search_restud.json
    ├── all_papers.json           # Consolidated metadata
    ├── paper_summaries.md        # Full abstracts + key themes
    ├── references.bib            # Complete BibTeX database
    ├── pdfs/                     # Downloaded open-access PDFs
    │   ├── *.pdf
    │   └── download_report.md
    ├── survey.tex                # Initial draft
    ├── survey.pdf                # Initial compilation
    ├── review_report.md          # Quality review
    ├── survey_v2.tex             # Revised draft
    └── survey_v2.pdf             # Final PDF (deliverable)
    

    Related skills

    r-reproducibility-guideAnswering Research QuestionsBuilding Paper Screening RubricsChina-CF-StudyCleaning Up Research Sessions