brycewang-stanford/i1
skills/25-HosungYou-Diverga/skills/i1/SKILL.md
Paper Retrieval Agent - Multi-database paper fetching from Semantic Scholar, OpenAlex, arXiv Handles rate limiting, deduplication, and PDF URL extraction Use when: fetching papers, searching databases, paper retrieval Triggers: fetch papers, retrieve papers, database search, Semantic Scholar, OpenAlex, arXiv
$ install --global
skillsauthnpx skillsauth add brycewang-stanford/Awesome-Agent-Skills-for-Empirical-Research i1Install this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- i1
- description:
- |
- Use when:
- fetching papers, searching databases, paper retrieval
- Triggers:
- fetch papers, retrieve papers, database search, Semantic Scholar, OpenAlex, arXiv
- version:
- 12.0.1
⛔ Prerequisites (v8.2 — MCP Enforcement)
No prerequisites required for this agent.
Checkpoints During Execution
- 🔴 SCH_DATABASE_SELECTION →
diverga_mark_checkpoint("SCH_DATABASE_SELECTION", decision, rationale) - 🔴 SCH_API_KEY_VALIDATION →
diverga_mark_checkpoint("SCH_API_KEY_VALIDATION", decision, rationale)
Fallback (MCP unavailable)
Read research/decision-log.yaml (or .research/decision-log.yaml for legacy projects) directly to verify prerequisites. Conversation history is last resort.
I1-PaperRetrievalAgent
Agent ID: I1 Category: I - Systematic Review Automation Tier: MEDIUM (Sonnet) Icon: 📄🔍
Overview
Executes multi-database paper retrieval for systematic literature reviews. Queries Semantic Scholar, OpenAlex, and arXiv (open access), with optional Scopus and Web of Science (institutional). Handles rate limiting, deduplication, and PDF URL extraction.
Capabilities
Open Access Databases (No API Key Required)
| Database | API | PDF Availability | Rate Limit | |----------|-----|------------------|------------| | Semantic Scholar | REST | ~40% open access | 100 req/5min | | OpenAlex | REST | ~50% open access | Polite pool (email) | | arXiv | OAI-PMH | 100% | 3s delay |
Institutional Databases (API Key Required)
| Database | API Key Env | Coverage |
|----------|-------------|----------|
| Scopus | SCOPUS_API_KEY | Comprehensive metadata |
| Web of Science | WOS_API_KEY | Citation data |
Social Science Databases (Recommended for Social Science Research)
| Database | Access | Coverage | Best For | |----------|--------|----------|----------| | ERIC | Free API (IES) | 1.9M+ records | Education research, K-12, higher ed | | PsycINFO | APA subscription | 5M+ records | Psychology, behavioral science | | SSRN | Open access | 1M+ preprints | Working papers, social science | | ProQuest Dissertations | Institutional | 5M+ dissertations | Doctoral research, theses |
💡 Social science focus: These databases are essential for education, psychology, and social work research. ERIC and SSRN are freely accessible. PsycINFO and ProQuest require institutional access.
API Key Configuration
| Database | API Key Env | Coverage | Primary Discipline |
|----------|-------------|----------|-------------------|
| ERIC | ERIC_API_KEY | Education research | Education |
| PsycINFO (via APA PsycNET) | PSYCINFO_API_KEY | Psychology & behavioral sciences | Psychology |
| SSRN | — (open access) | Social science preprints | Multi-discipline |
| ProQuest | PROQUEST_API_KEY | Dissertations & theses | Multi-discipline |
ERIC API Integration Example
# ERIC API (free, no key required for basic search)
curl "https://api.ies.ed.gov/eric/?search=meta-analysis+education+technology&format=json&rows=50"
ERIC fields: title, author, source, publicationdateyear, description, subject, peerreviewed
Database Selection Guide
| Research Area | Recommended Databases | |--------------|----------------------| | Education | ERIC + Semantic Scholar + OpenAlex | | Psychology | PsycINFO + Semantic Scholar + OpenAlex | | Social Work | Semantic Scholar + OpenAlex + SSRN | | Interdisciplinary | OpenAlex + Semantic Scholar + ERIC + PsycINFO | | STEM crossover | arXiv + Semantic Scholar + OpenAlex | | Dissertations | ProQuest + OpenAlex |
Input Schema
Required:
- query: "string"
- databases: "list[enum[semantic_scholar, openalex, arxiv, scopus, wos, eric, psycinfo, ssrn, proquest]]"
Optional:
- year_range: "list[int, int]"
- max_results_per_db: "int"
- open_access_only: "boolean"
Output Schema
main_output:
databases_queried: "list[string]"
results:
semantic_scholar: "int"
openalex: "int"
arxiv: "int"
total_identified: "int"
after_deduplication: "int"
duplicates_removed: "int"
output_file: "string"
Human Checkpoint Protocol
🔴 SCH_DATABASE_SELECTION (REQUIRED)
Before executing queries, I1 MUST:
-
PRESENT database options:
Available databases for your systematic review: ✅ Open Access (recommended): - Semantic Scholar (~40% PDF URLs) - OpenAlex (~50% PDF URLs) - arXiv (100% PDF access) 🔒 Institutional (requires API keys): - Scopus (SCOPUS_API_KEY: {status}) - Web of Science (WOS_API_KEY: {status}) 📚 Social Science: - ERIC (free, education research) - PsycINFO (PSYCINFO_API_KEY: {status}) - SSRN (open access, preprints) - ProQuest Dissertations (PROQUEST_API_KEY: {status}) Which databases would you like to query? -
WAIT for explicit user selection
-
CONFIRM selection before executing
🔴 SCH_API_KEY_VALIDATION (REQUIRED)
After database selection, I1 MUST validate API keys:
-
CHECK environment for required keys:
- Semantic Scholar:
S2_API_KEY(optional but recommended for higher rate limits) - OpenAlex: Email for polite pool (optional)
- arXiv: No key needed
- Scopus:
SCOPUS_API_KEY(required if selected) - Web of Science:
WOS_API_KEY(required if selected) - ERIC:
ERIC_API_KEY(optional, basic search is free) - PsycINFO:
PSYCINFO_API_KEY(required if selected) - SSRN: No key needed
- ProQuest:
PROQUEST_API_KEY(required if selected)
- Semantic Scholar:
-
IF any selected database requires a missing key: → Call AskUserQuestion with SCH_API_KEY_VALIDATION template → WAIT for user response → If "Provide Key": Show setup instructions (
export SCOPUS_API_KEY=your_key), then re-validate → If "Skip DB": Remove from selection, re-confirm remaining databases → If "Pause": Save state, stop pipeline -
RECORD via MCP:
diverga_mark_checkpoint("SCH_API_KEY_VALIDATION", decision, rationale)
Execution Commands
# Project path (set to your working directory)
cd "$(pwd)"
# Paper retrieval (Stage 1)
python scripts/01_fetch_papers.py \
--project {project_path} \
--query "{boolean_query}" \
--databases semantic_scholar openalex arxiv
# Deduplication (Stage 2)
python scripts/02_deduplicate.py \
--project {project_path}
Query Building
I1 transforms natural language research questions into optimized Boolean queries:
Input: "How do AI chatbots improve speaking skills in language learning?"
Output:
Semantic Scholar: (AI OR "artificial intelligence" OR chatbot OR "conversational agent") AND ("language learning" OR "foreign language" OR L2) AND (speaking OR oral OR pronunciation)
OpenAlex: Same query with OpenAlex field mapping
arXiv: cs.CL AND (chatbot OR conversational) AND language
Rate Limiting Strategy
# Semantic Scholar: Exponential backoff
rate_limit = {
"requests_per_window": 100,
"window_seconds": 300,
"backoff_base": 2.0
}
# OpenAlex: Polite pool (add email)
headers = {"mailto": "[email protected]"}
# arXiv: Fixed delay
delay_between_requests = 3 # seconds
Error Handling
| Error | Action | |-------|--------| | 429 Rate Limit | Exponential backoff, max 5 retries | | 500 Server Error | Retry after 30s | | Timeout | Retry with increased timeout | | API Key Missing | STOP → trigger 🔴 SCH_API_KEY_VALIDATION checkpoint → AskUserQuestion |
Auto-Trigger Keywords
| Keywords (EN) | Keywords (KR) | Action | |---------------|---------------|--------| | fetch papers, retrieve papers | 논문 수집, 논문 검색 | Activate I1 | | search databases | 데이터베이스 검색 | Activate I1 | | Semantic Scholar, OpenAlex, arXiv | 시맨틱스칼라 | Activate I1 |
Integration with B1
I1 can call B1-systematic-literature-scout for advanced search strategy:
Task(
subagent_type="diverga:b1",
model="sonnet",
prompt="""
Help design search strategy for:
Research question: {question}
Generate:
1. Database-specific Boolean queries
2. MeSH/thesaurus terms (if applicable)
3. Grey literature sources
"""
)
Dependencies
requires: ["I0-review-pipeline-orchestrator"]
sequential_next: ["I2-screening-assistant"]
parallel_compatible: ["B1-literature-review-strategist"]
Related Agents
- I0-review-pipeline-orchestrator: Pipeline coordination
- I2-screening-assistant: PRISMA screening
- B1-literature-review-strategist: Search strategy design
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