alainator Researching Papers
Search open-access academic sources, download PDFs, and convert to markdown.
Tool
All commands use tools/research-tool.py:
# Search default sources (arXiv + Crossref + PMC + Unpaywall)
python3 tools/research-tool.py search "quantum time operator"
python3 tools/research-tool.py search "percolation theory" --source arxiv --max 10
# Search humanities (Semantic Scholar + Open Library + SEP + PhilPapers)
python3 tools/research-tool.py search "autopoiesis" --source humanities
python3 tools/research-tool.py search "structural realism" --source sep --download
# Search everything
python3 tools/research-tool.py search "recursive epistemology" --source all
# Download specific paper
python3 tools/research-tool.py download 2301.12345
python3 tools/research-tool.py download https://arxiv.org/pdf/2301.12345.pdf --title "Title"
# Fetch SEP entry by slug
python3 tools/research-tool.py fetch-sep structural-realism
# Convert PDF to markdown
python3 tools/research-tool.py convert _source/research/papers/paper-name.pdf
python3 tools/research-tool.py convert-all
# List and index
python3 tools/research-tool.py list
python3 tools/research-tool.py list --topic "collapse"
python3 tools/research-tool.py index
File Organization
_source/research/papers/— original PDFs_source/research/markdown/— converted markdown_source/research/sep-entries/— Stanford Encyclopedia entries_source/research/INDEX.md— catalog_source/research/last-search-results.json— most recent results
Domain Strategies
Physics/Chemistry/Biology: Default sources. Prefer recent papers (2020+). Prioritize experimental results.
Philosophy/Foundations: Use --source humanities. Domains: philosophy
of science, formal epistemology, systems theory, cognitive science.
Process
- Identify the gap or concept needing grounding
- Search appropriate sources
- Read converted markdown in
_source/research/markdown/orsep-entries/ - Present findings with relevance assessment
- Hand off to /integrating-research for canon formalization
Citations
[Author, Year] inline with ## References section. Each entry includes a one-sentence annotation. Cited science is canon science — no disclaimers.
Configuration
Set your contact email for polite API access:
export RESEARCH_TOOL_EMAIL="your-email@example.com"
Requires pdftotext (poppler-utils) or pypdf for PDF conversion.
Out of Scope
Does NOT map research onto canon formalism (use /integrating-research). Does NOT write science files (use /writing-science). Does NOT audit existing citations (use /auditing-canon).