Research Paper Kb

research-paper-kb

Persistent research paper knowledge base for AI agents. Ingest any paper (arXiv URL, DOI, or title) and extract structured intelligence into a permanent PAPERS.md knowledge base that survives across sessions. Never lose context on a paper again.

Trigger Conditions

Use this skill when the user: Pastes an arXiv URL (e.g. https://arxiv.org/abs/2310.12345) Pastes a DOI (e.g. 10.1038/s41586-024-07156-8) Says "add this paper to my KB" / "track this paper" / "save this paper" Says "what do we know about [paper title]" Says "update my paper KB" / "scan my PAPERS.md" Says "show me the papers I'm tracking" / "what papers have I saved"

What This Skill Does

Fetches the paper abstract, metadata, and key sections Extracts structured intelligence (method, gap, threat level, overlap) Generates a clean BibTeX entry Appends a structured entry to PAPERS.md in the workspace Updates MEMORY.md with a pointer so future sessions know the KB exists Works across sessions — the knowledge base is a file, not context

Step 1: Identify the Paper

Accept any of: arXiv URL: https://arxiv.org/abs/XXXX.XXXXX arXiv ID: 2310.12345 or 2310.12345v2 DOI: 10.XXXX/... Title string: look up via Semantic Scholar API Normalize to arXiv ID or DOI before proceeding.

Step 2: Fetch Paper Metadata

For arXiv papers — fetch the abstract page: https://arxiv.org/abs/<arxiv_id> Extract: title, authors, date, abstract, subject categories. Also fetch the Semantic Scholar API for structured metadata: https://api.semanticscholar.org/graph/v1/paper/arXiv:<arxiv_id>?fields=title,authors,year,abstract,tldr,citationCount,influentialCitationCount,fieldsOfStudy For DOI papers — use Semantic Scholar: https://api.semanticscholar.org/graph/v1/paper/<DOI>?fields=title,authors,year,abstract,tldr,citationCount,influentialCitationCount,externalIds For title lookup: https://api.semanticscholar.org/graph/v1/paper/search?query=<url_encoded_title>&fields=title,authors,year,abstract,externalIds&limit=1

Step 3: Extract Structured Intelligence

From the abstract and any available full text, extract: FieldWhat to ExtractMethodCore technical approach or contribution (1-2 sentences)Gap they claimWhat problem/limitation they say they're solvingKey resultsMain quantitative or qualitative outcomeOverlap with user's workAsk the user if context is unclear; or infer from prior PAPERS.md entries and MEMORY.mdThreat level1-5 scale: how much does this threaten the user's research? (1=unrelated, 5=directly competing)Citation countFrom Semantic ScholarRelated papersUp to 3 highly-cited related papers from the same fetch Threat level guide: 1 — Unrelated field, no overlap 2 — Adjacent method, different application 3 — Similar approach, different dataset/domain 4 — Direct competition, overlapping claims 5 — Near-identical work, same target problem

Step 4: Generate BibTeX

Generate a clean BibTeX entry. Format: For arXiv: @article{<AuthorYEARkeyword>, title = {<Full Title>}, author = {<Author1> and <Author2> and ...}, journal = {arXiv preprint arXiv:<id>}, year = {<year>}, url = {https://arxiv.org/abs/<id>}, note = {arXiv:<id>} } For published paper: @article{<AuthorYEARkeyword>, title = {<Full Title>}, author = {<Author1> and <Author2> and ...}, journal = {<venue>}, year = {<year>}, doi = {<doi>}, url = {https://doi.org/<doi>} } BibTeX key convention: FirstAuthorLastNameYearFirstContentWord (e.g., Smith2024diffusion)

Step 5: Write to PAPERS.md

• Check if PAPERS.md exists in the workspace root. If not, create it with the header:
• # PAPERS.md — Research Paper Knowledge Base
• > Auto-maintained by the `research-paper-kb` skill. Add papers with: "add this paper to my KB"
• > Last updated: <date>
• ---
• Append (never overwrite) the following entry template:
• ## [<Short Title>](<arxiv_or_doi_url>)
• **Added:** <YYYY-MM-DD>
• **Authors:** <Author1>, <Author2>, ...
• **Venue:** <arXiv / Conference / Journal>
• **Citations:** <N> (Semantic Scholar)
• **Threat Level:** <1-5> — <one-line reason>
• ### Method
• <1-2 sentence description of the core technical contribution>
• ### Gap They Claim
• <What problem/limitation they say they're solving>
• ### Key Results
• <Main outcomes, benchmarks, or claims>
• ### Overlap With My Work
• <How this relates to the user's research — ask if unclear>
• ### Notes
• <Any additional context the user provides, or leave blank>
• ### BibTeX
• ```bibtex
• <bibtex entry>
• ### Step 6: Update MEMORY.md
• After writing to PAPERS.md, append or update the PAPERS.md pointer in `MEMORY.md`:
• Find or create a section `## Research Paper KB`:
• ```markdown
• ## Research Paper KB
• PAPERS.md exists in workspace root — <N> papers tracked as of <date>
• Latest addition: <Short title> (<threat level>/5)
• Run `research-paper-kb` to add more papers
• If the section already exists, update the count and latest addition line.

Step 7: Confirm to User

• Reply with a summary:
• ✅ Added to PAPERS.md
• **[Paper Title]** (<year>)
• Authors: ...
• Threat level: X/5 — <reason>
• BibTeX key: `AuthorYearWord`
• PAPERS.md now has N papers. Run `show me my papers` to review.

Query Mode: "Show Me My Papers"

When the user asks to review their paper KB: Read PAPERS.md Summarize: total count, highest threat-level papers, recently added Optionally filter by threat level, topic, or year Offer to export BibTeX for all papers: collect all @article{...} blocks and present as a code block

Query Mode: "What Do We Know About X?"

When the user asks about a specific paper or topic: Search PAPERS.md for matching title/author/keywords Return the structured entry If not found, offer to add it: "This paper isn't in your KB yet. Want me to add it?"

Edge Cases

SituationHandlingarXiv paper not foundTry Semantic Scholar title search; if still not found, ask user to confirm titleDOI behind paywallFetch abstract from DOI.org metadata (https://doi.org/<doi> with Accept: application/json); note "full text unavailable"Paper already in PAPERS.mdDetect by title/arXiv ID match; offer to update notes or threat level insteadUser doesn't know their research areaAsk: "What's your research focus? I'll use this to assess overlap." Store in MEMORY.mdSemantic Scholar rate limitFall back to arXiv API: http://export.arxiv.org/api/query?id_list=<id>

Integration With Other Skills

This skill works best alongside: citation-management — for full BibTeX workflow and PubMed/Google Scholar search biorxiv-database — for biology/life-science preprints (use to find papers to add) cs-research-methodology — for identifying gaps and research proposals from your KB proactive-research (ClaWHub) — can feed new papers into this KB automatically

Files Modified

FileActionPAPERS.mdAppend new entry (create if missing)MEMORY.mdUpdate ## Research Paper KB section Never modifies: SOUL.md, USER.md, AGENTS.md, TOOLS.md, or any project files.

Example Interaction

User: "Add this to my KB: https://arxiv.org/abs/2310.06825" Agent: Fetches arXiv 2310.06825 → "Mistral 7B" by Jiang et al. Fetches Semantic Scholar metadata (12k citations) Extracts: method = grouped-query attention + sliding window; gap = efficient 7B model Assesses threat level vs user's work (reads MEMORY.md for context) Generates BibTeX key Jiang2023mistral Appends structured entry to PAPERS.md Updates MEMORY.md Replies: "✅ Added Mistral 7B (threat: 2/5 — efficient inference, different from your focus on X)"

Metadata

name: research-paper-kb version: 1.0.0 author: <your-github-handle> category: Academic & Research tags: [research, papers, arxiv, bibtex, knowledge-base, literature, academic, persistent-memory] summary: Persistent cross-session knowledge base for research papers. Ingest arXiv/DOI → extract method/gap/threat level → append to PAPERS.md. Never lose paper context again. requires: []