litbase

Source: https://github.com/aipoch/medical-research-skills

LitBase

An academic paper reading and research development system running inside Claude Code (or any compatible agent environment). Built for biomedical researchers who want to find papers, build structured reading notes, track discussion insights, and ultimately synthesize their literature base into a research proposal.

Paper source: Semantic Scholar — free, no login required, 200M+ papers across all disciplines.

---

Quick Start

Step 1 — Edit config.json with your research folder path:

{
  "data_dir": "/path/to/your/research/folder",
  "s2_api_key": "optional — leave empty to use free tier",
  "mode": "auto"
}

Step 2 — Open this folder in Claude Code, then type /setup.

The setup command configures everything automatically — no terminal commands needed.

---

Commands

Command	When to use	What it does
/setup	First use	Guided research profile setup; auto-configures environment
/feed	Daily	Updates search terms → searches Semantic Scholar → recommends papers
/read	Per paper	Submit a PDF path, DOI, or abstract → generates 4-section structured note
/discuss [keyword]	Deep dive	Locate a paper note by author/title/keyword and discuss; auto-records insights
/recap	Weekly review	Reading overview, framework completeness map, next-step recommendations
/update	Direction shift	Sync research direction changes to memory and search terms
/sync	Maintenance	Cross-document consistency check; literature integrity audit
/propose	Proposal stage	Synthesizes reading notes into a Research Foundation Document (RFD) for downstream protocol design

---

Note Structure

Each paper analysis is structured in four sections:

Section	Content
I. Paper Weight	Journal/conference rank, IF, database indexing (SSCI/Scopus/etc.), Q-rank; each author's institution, position, h-index; citation count and yearly average; overall assessment
II. Paper Highlights	Methodological innovation / critique of systemic problems / significance of the research object
III. Transferable Elements	Theory framework, method details, conceptual tools — each tagged to which part of the user's own paper it can support
IV. How to Use in Your Paper	Literature review positioning, suggested citation phrases (English), methodological precedent, research motivation

---

Research Foundation Document (RFD)

The /propose command generates an RFD — a structured synthesis of the user's accumulated literature base. It serves as a standardized upstream input to any downstream protocol design skill.

RFD sections: Study Population & Clinical Context → Focused Research Question (P/E/C/O/D/T) → Theoretical Framework & Mechanistic Basis → Methodological Precedents → Identified Research Gaps → Literature Source Index.

All citations in the RFD are sourced exclusively from the user's confirmed reading list. No fabricated references.

---

Capability Tiers

LitBase adapts to its runtime environment automatically:

Tier	Environment	PDF reading	Paper search	Notes storage	State persistence
A	Web Claude, any LLM chat	Native upload	WebSearch / WebFetch	Artifact output	Session card (paste at session start)
B	Manus, file-capable agents	Claude Read tool	WebFetch → S2 API	File system	MEMORY.md
C	OpenClaw / Claude Code	Claude Read tool (+ optional pdftotext)	WebFetch → S2 API (+ optional Python)	File system	Claude persistent memory

---

Dependencies

Dependency	Purpose	Required?
Python (stdlib)	Runs paper search and metadata scripts	Optional — WebFetch fallback available
pdftotext (poppler)	PDF text extraction	Optional — Claude native PDF reading available
Claude Code	Executes skill commands	Required for Tier C

No API key required for Semantic Scholar. An optional free key raises rate limits.

---

Literature Integrity

All commands follow the rules in LITERATURE_HARD_RULES.md:

• No fabricated PMIDs, DOIs, titles, authors, citation counts, or study data.
• All citations in notes and proposals must be traceable to user-provided papers.
• Unverifiable claims are labeled explicitly rather than omitted silently.

---

File Structure

litbase/
├── SKILL.md                        ← skill manifest (this file)
└── core/                           ← open this folder in Claude Code
    ├── CLAUDE.md                   ← project rules (auto-loaded)
    ├── README.md
    ├── config.json                 ← user config (data_dir, API key, mode)
    ├── search_config.json          ← search terms (maintained by Claude)
    ├── settings.local.json         ← Claude Code permissions template
    ├── install.sh                  ← optional manual setup script
    ├── commands/
    │   ├── setup.md
    │   ├── feed.md
    │   ├── read.md
    │   ├── discuss.md
    │   ├── recap.md
    │   ├── update.md
    │   ├── sync.md
    │   └── propose.md
    ├── references/
    │   ├── LITERATURE_HARD_RULES.md
    │   └── SESSION_CARD_TEMPLATE.md
    ├── scripts/
    │   ├── recommend.py            ← optional: Semantic Scholar search
    │   ├── lookup_paper.py         ← optional: paper metadata query
    │   └── rename_pdfs.py          ← optional: PDF batch rename
    ├── memory/
    │   └── MEMORY.md
    └── notes/
        └── WORKFLOW.md

data_dir/                           ← path set in config.json
  notes/
    reading_list.md
    YYYY-MM-DD/
      recommendations.md
      Author_Year_Keywords/
        Author_Year_Keywords.pdf
        Author_Year_Keywords.md
    recaps/
      YYYY-MM-DD_recap.md
    proposal/
      YYYY-MM-DD_RFD.md