A TypeScript monorepo for a suite of academic paper tools. It uses pnpm workspaces to manage multiple packages.

1. Install dependencies:

   pnpm install

2. Configure environment variables:

   cp .env.example .env

   Update .env with your API keys and configuration:

   CROSSREF_MAILTO=your-email@example.com
   NOTION_API_KEY=your_notion_api_key
   S2_API_KEY=your_semantic_scholar_api_key
   NOTION_DATABASE_ID=your_notion_database_id

# Build all packages
pnpm build

# Run tests
pnpm test

• Local Development Server (Hot Reload):

  pnpm --filter @paper-tools/web dev

  Open http://localhost:3000 in your browser.

• Production Build (Local Verification):

  pnpm --filter @paper-tools/web build
  pnpm --filter @paper-tools/web start

• /search — Paper search. From the search result cards, you can quickly execute actions such as Save to Notion, View Graph, and Recommend.
• /graph — Citation graph visualization. Supports DOI, paper titles, and Semantic Scholar IDs as inputs. Can be automatically built via URL queries (e.g., /graph?doi=10.1145/...).
• /recommend — Displays paper recommendations based on a specified paper or your saved papers.
• /archive — List of papers saved to Notion (requires Notion authentication and database setup).
• /authors — Search authors and view profile analytics (h-index, top papers, coauthor graph, topic timeline).

• Ensure NOTION_API_KEY and NOTION_DATABASE_ID are set in your .env file (see the Setup section).
• The "Save" button will function only if the Notion configuration is valid.

• Cannot save to Notion: Check the Notion credentials in your .env file.
• Dependency errors: Run pnpm install again to ensure all packages are linked.
• Build failures: Run pnpm --filter @paper-tools/web build and inspect the logs for detailed error messages.

# Get similar papers from a single paper
node packages/recommender/dist/cli.js recommend "DOI:10.1145/3597503.3639187" --limit 10 --from recent

# Sync recommendations to Notion (excluding duplicates)
node packages/recommender/dist/cli.js sync "DOI:10.1145/3597503.3639187" --limit 10 --dry-run

# Recommend papers using all papers in your Notion DB as seeds
node packages/recommender/dist/cli.js sync-all --limit 20 --dry-run

# Search DBLP by keyword
node packages/drilldown/dist/cli.js search "software testing" --limit 20

# Search by venue (with optional year)
node packages/drilldown/dist/cli.js venue ICSE --year 2024 --limit 50

# Search Crossref
node packages/drilldown/dist/cli.js crossref "mutation testing" --limit 10

# Drill-down (BFS): Seed search -> Keyword extraction -> Deep dive
node packages/drilldown/dist/cli.js drilldown "fault localization" \
  --seed-limit 10 --depth 2 --max-per-level 15 --enrich

# Extract frequent keywords from paper titles
node packages/drilldown/dist/cli.js keywords "program repair" --top 10

• Adding the --enrich flag complements the results with DOI, citation counts, etc., via Crossref.
• Use -o <file> to save the results to a JSON file.

# Fetch BibTeX from DOI or title
node packages/bibtex/dist/index.js get "10.1145/3597503.3639187"
node packages/bibtex/dist/index.js get "coverage guided fuzzing" --key-format short

# Export BibTeX for papers in Notion DB
node packages/bibtex/dist/index.js export --format bibtex --output papers.bib

# Validate BibTeX file (or use '-' for stdin)
node packages/bibtex/dist/index.js validate papers.bib
cat papers.bib | node packages/bibtex/dist/index.js validate -

• get uses the priority order: Crossref (DOI) → DBLP (title) → Semantic Scholar (title→DOI→Crossref).
• export reads the Notion DB specified by NOTION_DATABASE_ID and generates BibTeX entries, prioritizing DOIs.
• validate detects missing required fields, duplicate keys, and duplicate DOIs.

# Resolve author by name and show profile metrics
node packages/author-profiler/dist/cli.js profile "Geoffrey Hinton"

# Resolve by Semantic Scholar Author ID
node packages/author-profiler/dist/cli.js profile 1741105 --id

# Show top cited papers
node packages/author-profiler/dist/cli.js papers "Yoshua Bengio" --top 10

# Show coauthor counts (depth 1 only)
node packages/author-profiler/dist/cli.js coauthors "Yann LeCun" --depth 1

# Save profile to Notion author database
node packages/author-profiler/dist/cli.js save "Geoffrey Hinton" --dry-run

• save utilizes NOTION_API_KEY and NOTION_AUTHOR_DATABASE_ID.
• Recommended properties for the Notion Author DB:
  • Name (title)
  • Semantic Scholar ID (text)
  • H-Index (number)
  • Citation Count (number)
  • Paper Count (number)
  • Affiliations (text)
  • Homepage (url)
  • Last Updated (date)

# Build a citation graph from a single DOI (JSON output)
node packages/visualizer/dist/cli.js graph "10.1145/3597503.3639187"

# Output in Graphviz DOT format
node packages/visualizer/dist/cli.js graph "10.1145/3597503.3639187" \
  --depth 2 --direction both --format dot -o graph.dot

# Output in Mermaid format
node packages/visualizer/dist/cli.js graph "10.1145/3597503.3639187" \
  --format mermaid

# Merge graphs for multiple DOIs and output
node packages/visualizer/dist/cli.js multi \
  "10.1145/3597503.3639187" "10.1145/3611643.3616265" \
  --depth 1 --format mermaid -o merged.md

• --direction: citing (papers citing this), cited (references), or both (default).
• --format: json (default), dot (Graphviz), or mermaid.
• --depth: BFS exploration depth (default: 1).

Note: The Web UI currently has limitations compared to the CLI tools. When saving papers from the Web UI, only English property names are recognized, and only title, DOI, and Semantic Scholar ID are populated. The CLI tools, however, correctly handle all optional properties (including Japanese names).

Required Properties:

• title (Title)
• DOI (Rich text)

Optional Properties:

• Authors (Rich text)
• Year (Number)
• Venue (Rich text)
• Citation Count (Number)
• Fields (Multi-select)
• Source (Select)
• Open Access PDF (URL)
• Semantic Scholar ID (Rich text)
• Summary (Rich text)