Skill: sherry-zh0u/literature-review-writing-assistant (version 1.0.0)

--- name: review-paper-writing description: | Literature review paper writing assistant — guides you through the full lifecycle: (1) Systematic search using PICO/Boolean/MeSH frameworks across arXiv, Semantic Scholar, OpenAlex, CrossRef & PubMed; (2) DOI & arXiv ID validation with cross-source conflict detection; (3) Multi-format citation output (APA 7th, MLA 9th, IEEE, BibTeX, RIS, Markdown); (4) Auto-generated structured literature review with timeline, keyword extraction & source-quality tagging. Use when drafting a review article, survey paper, or thesis background chapter — or when given a topic to compile references for. --- # Review Paper Writing Skill ## Overview This skill helps you write a thorough, well-structured literature review — from topic definition and systematic search to formatted citations and a polished markdown draft. It covers: - **Topic framing** with PICO framework - **Search strategy** (Boolean, MeSH, wildcards, proximity) - **Multi-source academic search** (arXiv, Semantic Scholar, OpenAlex, CrossRef, PubMed) - **DOI / arXiv ID validation** and conflict detection - **Citation formatting** (APA, MLA, IEEE, BibTeX, RIS, Markdown) - **Auto-generated literature review** in Markdown ## Quick Start ### 1. Run a Search ```bash python3 scripts/lit_search.py "large language model education" -n 20 --sources arxiv openalex ``` ### 2. Validate DOIs ```bash python3 scripts/lit_search.py "machine learning" --validate ``` ### 3. Format Citations ```bash python3 scripts/lit_search.py "BERT" -n 10 -f apa # APA 7th python3 scripts/lit_search.py "transformer" -n 10 -f bibtex # BibTeX python3 scripts lit_search.py "attention" -n 10 -f ris # RIS ``` ### 4. Filter Results | Flag | Effect | |------|--------| | `--published-only` | Exclude arXiv preprints | | `--preprint-only` | Only arXiv preprints | | `--min-year 2020` | Earliest publication year | | `--min-citations 50` | Minimum citation count | | `--conflicts` | Detect cross-source metadata conflicts | ### 5. Batch Mode (from file) Create `papers.txt` with one DOI/PMID/arXiv ID per line: ``` 10.48550/arXiv.2303.08774 10.48550/arXiv.2205.11916 PMID: 34567890 ``` Then: ```bash python3 scripts/lit_search.py file://papers.txt -f bibtex ``` ## Search Strategy Framework ### PICO Framework Use PICO to structure your research question: | Element | Meaning | Example | |---------|---------|---------| | **P**opulation | Target group | high school students | | **I**ntervention | Treatment or method | motivational interviewing | | **C**omparator | Control group | no intervention | | **O**utcome | Measurable result | academic performance | Convert to search terms: ``` P: student* I: "motivational interviewing" O: "academic achievement" → "motivational interviewing" AND student* AND "academic achievement" ``` ### Boolean Operators ```python # AND: all terms must appear "cognitive behavioral therapy" AND adolescent* # OR: any term may appear depression OR anxiety OR "mental health" # NOT: exclude terms animal NOT pet # Parentheses for grouping ("cognitive behavioral therapy" OR CBT) AND adolescent* ``` ### Wildcards & Truncation ```python student* → student, students, student's, students' wom?n → woman, women ``` ### Proximity Search ```python behavior N/2 change # "behavior" within 2 words of "change" "stress" ADJ3 "coping" # same sentence ``` ### MeSH (PubMed) ```python "Motor Activity"[Mesh] "Depression"[Mesh] AND "Therapy"[Mesh:Subheading] ``` ### Database-Specific Syntax ```python # PubMed "motivational interviewing"[Title/Abstract] ("Anxiety"[Mesh] OR "Anxiety Disorders"[Mesh]) AND 2020:2024[dp] # PsycINFO (OVID) exp Motivational Interviewing/ motivation interview*.tw # Web of Science TS=("motivational interviewing" AND school*) PY=2020-2024 ``` ## Source Comparison | Source | Type | API Key | Best For | |--------|------|---------|---------| | **arXiv** | Preprint | ❌ No | CS, ML, physics, stats | | **Semantic Scholar** | Published + preprint | Optional | High-citation papers | | **OpenAlex** | Published | ❌ No | Broad cross-disciplinary | | **CrossRef** | Published | ❌ No | Authoritative DOI metadata | | **PubMed** | Published (biomedical) | ❌ No | Medicine, health, biology | **Recommended combinations:** - `arxiv + semantic_scholar` → preprints + high-impact papers - `openalex + pubmed` → comprehensive academic coverage - `arxiv + openalex + pubmed` → full-spectrum search ## Quality Tags | Source | Peer Reviewed | Tag | |--------|--------------|-----| | arXiv | ❌ No | `[arXiv]` | | Journal / Conference | ✅ Yes | `[Published]` | | PubMed | ✅ Yes | `[PubMed]` | > ⚠️ arXiv papers are **preprints** — not peer-reviewed. Treat conclusions as provisional. ## Citation Formats | Format | Style | |--------|-------| | `apa` | APA 7th Edition | | `mla` | MLA 9th Edition | | `ieee` | IEEE | | `bibtex` | BibTeX (for LaTeX) | | `ris` | RIS (for EndNote/Zotero) | | `markdown` | Markdown with source tags | ## Search Workflow ``` 1. Define topic → PICO framework ↓ 2. Build search blocks → synonyms, MeSH terms, wildcards ↓ 3. Run multi-source search (parallel API calls) ↓ 4. Deduplicate by DOI / arXiv ID ↓ 5. Validate IDs (HEAD request → doi.org) ↓ 6. Detect cross-source conflicts (title, year, authors) ↓ 7. Filter → year, citations, source type ↓ 8. Format → APA / MLA / BibTeX / ... ↓ 9. Generate literature review (timeline, keywords, summary) ``` ## Configuration Edit `scripts/lit_search.py` to add your Semantic Scholar API key: ```python API_KEYS = { "semantic_scholar": "your-api-key" # Get: https://www.semanticscholar.org/api-keys } ``` Without a key, the free tier is used (1 req/sec). A key enables 1000 req/5 sec and avoids rate-limiting. ## Output Examples **Markdown output (`-f markdown`):** ``` [1] **Attention Is All You Need** * Vaswani, A., Shazeer, N., Parmar, N., et al. (2017). * arXiv: [1706.03762](https://arxiv.org/abs/1706.03762) [arXiv] *Citations: 80000* [2] **BERT: Pre-training of Deep Bidirectional Transformers** * Devlin, J., Chang, M. W., Lee, K., & Toutanova, K. (2019). NAACL-HLT 2019* DOI: [10.48550/arXiv.1810.04805](https://doi.org/10.48550/arXiv.1810.04805) [Published] *Citations: 70000* ``` **Generated review section:** ``` # Literature Review ## Statistics - **Total Papers**: 20 - [arXiv]: 8 - [Published]: 10 - [PubMed]: 2 ## Timeline - 2024: 5 papers - 2023: 8 papers - 2022: 4 papers - 2021: 3 papers ``` ## Troubleshooting | Problem | Solution | |---------|---------| | "Rate limit" from Semantic Scholar | Add API key, or switch to OpenAlex | | No results | Try fewer / broader search terms | | Too many results | Narrow date range, add AND filters | | Invalid DOI | Check format; try CrossRef validation | | arXiv ID not found | Use format `YYMM.NNNNN` (e.g., `2303.08774`) |


Security scan verdicts — ClawScan: clean | static analysis: clean | VirusTotal: clean | SkillSpector: clean (LOW)