# Paper Summarize > After research-hub ingests a cluster of cited papers, fill the per-paper Key Findings + Methodology + Relevance sections in BOTH Obsidian markdown and the Zotero child note. Use when the user says "fill the TODO Key Findings/Methodology blocks left by research-hub auto", "I just ran auto and don't know what these papers are about", or "summarize the papers in cluster X". Invokes a supported LLM CLI on each paper's abstract. NOT for summarizing the user's own manuscript draft — that's `paper-memory-builder`. NOT for cluster-level briefs — that's `research-hub notebooklm generate`. This skill is per-cited-paper only. If the user says "extract claims from these papers", disambiguate before acting: their own manuscript draft → `paper-memory-builder`; a cross-paper comparison matrix → `literature-triage-matrix`; per-cited-paper Key Findings → this skill. - Skill: `wenyuchiou/paper-summarize` (Agent Skill, multi-file: 2 files) - Install (CLI): `npx skillmds@latest add wenyuchiou/paper-summarize` - Raw SKILL.md: https://api.skillmd.com/api/skills/wenyuchiou/paper-summarize/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: AI & ML - Author: WenyuChiou (https://skillmd.com/u/wenyuchiou) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/wenyuchiou/paper-summarize --- # paper-summarize The `auto` pipeline ingests metadata + abstract only — Summary / Key Findings / Methodology / Relevance stay as `[TODO]` skeletons in both Obsidian and Zotero. Cluster-level summarization (NotebookLM brief, crystals) does NOT fill per-paper notes. So after `auto`, the user has nothing scannable per paper without opening the PDF. This skill fills that gap. One LLM call per paper, JSON-validated, written to both vault systems atomically (rollback the markdown change if Zotero write fails so the two stay in sync). ## When to use Trigger phrases: - "Summarize the papers in cluster X." - "Fill the TODO Key Findings for X." - "I just ran `auto X` and the notes are empty — give me real summaries." - "Update Zotero notes for cluster X with what each paper actually says." Not for: - Generating a single CLUSTER-LEVEL summary — that's `research-hub notebooklm generate` (NotebookLM brief). - Filling Q&A on the cluster — that's `research-hub crystal emit/apply`. - Reading PDFs — abstract-only by design. PDF parsing is out of scope; the LLM is told to mark "[PDF needed]" if abstract is too thin. - Verifying brief vs source — that's `notebooklm-brief-verifier`. ## Inputs - Cluster slug (must already exist in the vault under `raw//`) - Optional LLM CLI override (`claude`, `codex`, `gemini`, `opencode`, `aichat`, `cursor`, or configured custom adapter) - Optional `--apply` flag (default off, dry-run) The skill reads each paper's frontmatter (DOI, year, zotero-key) + the `## Abstract` body block. Papers with empty abstract get a "PDF needed" marker rather than hallucinated findings. ## Outputs For each paper, three sections are rewritten: 1. **Obsidian markdown** at `raw//.md`: - `## Key Findings` callout block (3–5 bullets) - `## Methodology` callout block (one sentence) - `## Relevance` callout block (1–2 sentences linking to the cluster topic) - Anchor IDs (`^findings`, `^methodology`, `^relevance`) preserved. 2. **Zotero child note** for the paper's parent item (looked up via `zotero-key` frontmatter): - Existing note HTML overwritten with `

Summary` + Abstract + Key Findings `
    ` + Methodology + Relevance. - If no child note exists, one is created. Both writes must succeed for a paper to count as "applied". A Zotero write failure rolls back the markdown change so the two systems stay in sync. ## Failure modes - **No LLM CLI on PATH**: prompt is saved to `/.research_hub/artifacts//summarize-prompt.md`. The user pipes it through their LLM manually and re-runs with `--apply`, or calls the `apply_cluster_summaries` MCP tool with the parsed payload. Exit code 0; ok=True. - **LLM returns malformed JSON**: report is `ok=False` with `error="LLM response had no parseable JSON object"`. No writes. - **Paper slug in payload not in cluster**: that entry is skipped with reason logged; other entries still applied. - **Empty key_findings / methodology / relevance**: entry skipped. - **Zotero write fails for one paper**: that paper's markdown change is rolled back; other papers still applied. ## Verification This skill's contract is exercised end-to-end by the test suite. The suites stub the LLM CLI but execute real Obsidian markdown writes against a fixture vault and real Zotero child-note writes against a mocked Zotero adapter. Rollback semantics (markdown rolls back if Zotero write fails) are explicitly tested. ```bash # Run the full paper-summarize suite (23 tests) python -m pytest -q \ tests/test_v069_summarize.py \ tests/test_v073_parallel_summarize.py \ tests/test_v080_resummarize.py ``` Coverage breakdown: | Test file | Count | What it covers | |---|---|---| | `tests/test_v069_summarize.py` | 17 | Prompt builder shape, validator (rejects unknown slugs / empty fields / wrong types), Obsidian + Zotero apply path, rollback when Zotero fails, no-LLM-on-PATH fallback | | `tests/test_v073_parallel_summarize.py` | 3 | Parallel summarize across multiple clusters, ordering, error isolation | | `tests/test_v080_resummarize.py` | 3 | Re-summarize behaviour: idempotent on same input, overwrite on different LLM output, --no-zotero path | For a manual smoke check against a live vault: ```bash # Dry-run (emit prompt + show LLM output, no writes) research-hub summarize --cluster # Live run (writes to Obsidian + Zotero) research-hub summarize --cluster --apply # Override LLM research-hub summarize --cluster --llm-cli codex --apply # Obsidian-only (skip Zotero — useful when Zotero is offline) research-hub summarize --cluster --apply --no-zotero ``` After applying, scan `raw//*.md` — every paper's `## Key Findings` callout should have real bullets instead of `[TODO]`. ## Operating notes - Findings-first: the prompt instructs the LLM to state the result, not "The paper shows that…". - Anchored to the abstract: every Key Finding must trace to something the abstract claims. The LLM is told to mark uncertain claims with `[likely]`. - Idempotent: re-running on a cluster with already-filled findings will overwrite them with whatever the LLM produces this run. Use `--no-zotero` or `--no-obsidian` if you want to preview one side first. - Same dual-write discipline as the abstract-sync helpers in `.scratch/`: one transactional unit per paper.