| name | paper-wiki |
| description | Academic literature management and survey system. Supports journal organization,
tag management, literature survey report generation, and submission recommendation.
Trigger: user mentions "literature", "paper", "survey", "journal", "submission",
"paper-wiki", or requests scan/report/recommendation on an initialized vault.
|
paper-wiki — Academic Literature Survey Skill
Manage a local Markdown literature vault. Scan, organize, tag, survey, and recommend — all from one skill.
What This Skill Does
paper-wiki turns a folder of paper Markdown files into a structured, indexed literature vault with:
- Journal organization: auto-sort papers into
paper/{direction}/{journal_abbr}/
- Tag management: multi-dimensional tagging (task, method, dataset, domain, signal, etc.)
- Survey reports: journal reports, direction reports, method/dataset stats, idea novelty surveys, literature reviews
- Submission guidance: journal scoring, revision suggestions, resubmit audits, review loops
Quick Start
- "Initialize vault" → init
- "Scan Battery papers" → scan-organize
- "Generate RESS journal report" → journal-report
- "Recommend submission target for my paper" → submission-recommend
Configuration
Configuration is read from config.json at project root. Key sections: output_lang, templates, research_workflows, web_search. For the full schema, field descriptions, and defaults, see docs/configuration.md. Before workflows that depend on vault paths, language settings, or report behavior, inspect config.json and apply its active values.
Output Language Rules
All internal content (this SKILL.md, schemas, scripts, templates) is in English. User-facing output follows output_lang from config.json: zh → Chinese, en → English. File paths, directory names, variable names, and frontmatter keys remain in English regardless of output_lang.
Report Citation Policy
All report-generation workflows must maintain a citation registry:
- Mark every evidence-bearing paper with
[N] in prose, tables, and claims. Number by first appearance; reuse numbers.
- The final References section must include every cited paper and ONLY cited papers.
- Reference format:
[N] Title. Journal, Year. DOI: xxx. URL: xxx. Source: local path or [arxiv-web].
- Omit missing fields (DOI, URL, year) rather than using placeholders.
- Before finalizing: verify citation numbers are continuous, every in-text citation has one reference entry, and every reference entry is cited at least once.
- Direction-review scope: standard 40-80 refs; deep 80-120 refs. Every reference must be cited in the body.
Full-Coverage Report Policy
For journal-report and direction-report, the evidence pipeline is mandatory. The protocol enforces screening, coverage ledger, citation traceability, and unsupported-claim risk checks. report_family.py --complete is the authoritative completion gate.
Full protocol: Load references/evidence-validation-protocol.md together with the report workflow reference file before execution.
Summary: Stage 1 builds screening/ledger evidence files → Stage 2 writes the report with full-coverage matrix → Stage 3 verifies count equality → Stage 4 runs the hard completion gate. --metadata-only overrides to the legacy deterministic path.
How Workflows Execute
SKILL.md is the dispatch layer, not the operational manual. When a user request matches a row in the routing table below:
- Load the referenced workflow file(s) from the skill directory.
- Execute the steps defined in that file.
- Do not execute a workflow from the routing table alone — catalog entries provide routing, not procedure.
- If a workflow references another workflow by name, load that workflow's reference file before using it.
Required files may include both a workflow reference file and supporting reference files. Load all listed files before execution.
Workflow Routing
Route user intent to the appropriate workflow and reference file:
| User Intent | Workflow | Reference File |
|---|
| "initialize vault" / "初始化文献库" | init | references/workflows/01-init.md |
| "scan papers" / "扫描文献", "organize by journal" / "整理期刊" | scan-organize | references/workflows/02-scan-organize.md |
| "ingest" / "入库", "process paper" / "处理论文" | ingest | references/workflows/03-ingest.md |
| "tag" / "标签", "assign tags" / "打标" | tag | references/workflows/04-tag.md |
| "journal report for XX" / "XX期刊报告" | journal-report | references/workflows/05-journal-report.md + references/evidence-validation-protocol.md |
| "direction report for XX" / "XX方向报告" | direction-report | references/workflows/06-direction-report.md + references/evidence-validation-protocol.md |
| "review paper" / "literature review" / "综述" | direction-review | references/workflows/18-direction-review.md |
| "method stats" / "方法统计", "dataset stats" | stat-report | references/workflows/07-stat-report.md |
| "idea survey" / "novelty survey" / "idea调研" | idea-survey | references/workflows/08-idea-survey.md |
| "prepare evidence for research ideas" / "idea evidence" | idea-evidence | references/workflows/19-idea-evidence.md |
| "generate research ideas" / "找idea" / "brainstorm" | idea-create | references/workflows/20-idea-create.md |
| "idea discovery pipeline" / "idea全流程" | idea-discover | references/workflows/21-idea-discover.md |
| "check novelty" / "claim novelty" / "claim查新" | idea-claim-novelty-check | references/workflows/22-idea-claim-novelty-check.md |
| "review my paper" / "adversarial review" / "多轮审稿" | auto-review-loop | references/workflows/23-auto-review-loop.md |
| "review and revise my paper for this venue" / "论文审稿改稿闭环" | paper-review-loop | references/workflows/25-paper-review-loop.md |
| "resubmit audit" / "venue transfer audit" / "转投审计" | resubmit-audit | references/workflows/24-resubmit-audit.md |
| "read this paper" / "单篇文献精读" | paper-read | references/workflows/17-paper-read.md |
| "web find" / "联网检索" / "search papers" | web-find | references/workflows/09-web-find.md |
| "daily digest" / "今日 arxiv" / "最新预印本" | web-digest | references/workflows/10-web-digest.md |
| "import web clipper" / "导入 web clipper" | web-import-clipper | references/workflows/11-web-import-clipper.md |
| "submission recommendation" / "投稿推荐" | submission-recommend | references/workflows/12-submission-recommend.md |
| "revision suggestions" / "修改建议" | revision-suggest | references/workflows/13-revision-suggest.md |
| "vault status" / "文献库状态" | status | references/workflows/14-status.md |
| "health check" / "检查" / "lint" | lint | references/workflows/15-lint.md |
| "full pipeline" / "完整流程" | pipeline | references/workflows/16-pipeline.md |
Routing notes:
- Every workflow runs independently. If preconditions are unmet, output a clear message but do NOT auto-chain unless the user explicitly requests "full pipeline".
- direction-review = literature review / survey synthesis. idea-survey = novelty/similarity analysis for a specific idea.
- For reviewer-backed workflows (idea-evidence, idea-create, idea-discover, idea-claim-novelty-check): prefer Codex-compatible MCP reviewer, otherwise dual-agent, otherwise degraded single-agent. Label degraded mode.
- For review/audit workflows (auto-review-loop, resubmit-audit, paper-review-loop): prefer Codex-compatible MCP reviewer. In Claude Code, explicitly call
codex. Fallback to dual-agent then single-agent degraded.
- Conference Seed Mode: When idea-create is triggered with an explicit conference paper file path, load
references/workflows/19-idea-evidence.md and execute its ### Conference Seed Mode section first. The routing table entry for idea-create includes this path; the activation gate is in references/workflows/20-idea-create.md.
- MCP-first web search: For web-find and web-digest workflows, MCP tools (
paper-search-mcp, arxiv-mcp-server) are preferred when available. Fallback to CLI (web_search.py) when MCP unavailable. At workflow completion, if CLI was used, output MCP installation suggestion. Do NOT auto-install MCP servers; follow official docs if user agrees.
Precondition Matrix
| Workflow | Requires | Auto-generated by |
|---|
| init | — | — |
| scan-organize | init | — |
| ingest | init | — |
| tag | ingest (≥1 canonical page) | ingest |
| journal-report | ingest (canonical pages for target journal) | ingest |
| direction-report | ingest (canonical pages) + query | ingest |
| direction-review | ingest (canonical pages with readable source_path) | ingest; web supplementation inside workflow |
| stat-report | ingest + tag | ingest, tag |
| idea-survey | init + source papers; canonical/index preferred | ingest (preferred), web-find (optional) |
| idea-evidence | init + research topic or brief. In Conference Seed Mode a verified conference paper file may serve as the seed. | user input, idea-discover Phase 0, idea-create activation gate |
| idea-create | init + topic research brief + compatible evidence pack. If conference paper file provided, Workflow 19 Conference Seed Mode must run first. | idea-evidence, idea-evidence Conference Seed Mode |
| idea-discover | init + research topic or brief. Does NOT auto-activate Conference Seed Mode. If conference paper is provided, ask user. | Phase 0 creates/updates brief |
| idea-claim-novelty-check | init + method or idea description | — |
| auto-review-loop | init + research output (paper draft, experiment report, or method proposal) | — |
| paper-review-loop | init + paper draft + target venue report or compatible resubmit-audit report | resubmit-audit can provide downstream evidence |
| resubmit-audit | init + paper draft + target venue info | resolves or generates target venue report |
| paper-read | init + one source or canonical paper | ingest (preferred) |
| web-find | init + query | init |
| web-digest | init + config.json domain_profiles | web-find |
| web-import-clipper | init + file list from clipper | init |
| submission-recommend | init + paper draft + canonical pages | journal-report |
| revision-suggest | init + paper draft + journal-report + target-journal canonical pages | journal-report |
| status | init | — |
| lint | init + scan-organize preferred | — |
| pipeline | init | orchestrates: init → scan → ingest → tag → index → status |
Workflow Catalog
| # | Workflow | Reference File | Purpose |
|---|
| 1 | init | references/workflows/01-init.md | Initialize vault directory structure and default configuration |
| 2 | scan-organize | references/workflows/02-scan-organize.md | Scan paper/ directory, optionally organize by journal |
| 3 | ingest | references/workflows/03-ingest.md | Extract metadata, generate canonical pages, convert HTML tables |
| 4 | tag | references/workflows/04-tag.md | Multi-dimensional tag analysis and assignment |
| 5 | journal-report | references/workflows/05-journal-report.md | Journal-specific full-text literature survey |
| 6 | direction-report | references/workflows/06-direction-report.md | Topic-focused full-text direction survey |
| 7 | stat-report | references/workflows/07-stat-report.md | Deterministic tag-dimension statistics |
| 8 | idea-survey | references/workflows/08-idea-survey.md | LLM/full-text idea similarity and novelty survey |
| 9 | web-find | references/workflows/09-web-find.md | Multi-source web search (OpenAlex, Semantic Scholar, arXiv) |
| 10 | web-digest | references/workflows/10-web-digest.md | Recent arXiv preprint digest by direction |
| 11 | web-import-clipper | references/workflows/11-web-import-clipper.md | Import Obsidian Web Clipper files and generate canonical pages |
| 12 | submission-recommend | references/workflows/12-submission-recommend.md | 6-dimension journal scoring and recommendation |
| 13 | revision-suggest | references/workflows/13-revision-suggest.md | 5-dimension targeted revision suggestions |
| 14 | status | references/workflows/14-status.md | Vault-wide status overview |
| 15 | lint | references/workflows/15-lint.md | Health check: errors, conflicts, stale indexes |
| 16 | pipeline | references/workflows/16-pipeline.md | Composite chain: init → scan → ingest → tag → index → status |
| 17 | paper-read | references/workflows/17-paper-read.md | MIT-style 10-phase deep single-paper reading |
| 18 | direction-review | references/workflows/18-direction-review.md | Direction-level literature review (40-80 / 80-120 refs) |
| 19 | idea-evidence | references/workflows/19-idea-evidence.md | Build evidence pack for idea generation (local + ≥50 web) |
| 20 | idea-create | references/workflows/20-idea-create.md | Generate and rank 8-12 research ideas from evidence pack |
| 21 | idea-discover | references/workflows/21-idea-discover.md | Orchestrate survey→evidence→create→novelty-check pipeline |
| 22 | idea-claim-novelty-check | references/workflows/22-idea-claim-novelty-check.md | Per-claim novelty scoring with evidence provenance |
| 23 | auto-review-loop | references/workflows/23-auto-review-loop.md | Multi-round adversarial research audit |
| 24 | resubmit-audit | references/workflows/24-resubmit-audit.md | Target-venue transfer audit with revised draft |
| 25 | paper-review-loop | references/workflows/25-paper-review-loop.md | Venue-conditioned review→revision→post-revision audit loop |
Template System
Templates live in templates/generic/. Domain-specific templates in templates/domains/{Direction}/. The template registry is tracked in config.json → templates.registry.
Status check (status workflow): reports template coverage and staleness.
Lint (lint workflow): detects missing or stale domain templates.
Regeneration threshold is set in config.json → templates.regeneration_threshold.
Safety Rules
- Never delete files in
paper/ — these are the user's original paper Markdown files
- File moves require
--dry-run first, then user confirmation before --apply
- Preserve
## User Notes — never overwrite content under this heading in any file
- Log everything — all file operations go to
workspace/logs/
- Tag priority — user tags > rule tags > manually confirmed extra suggestions (never remove user tags)
- No cross-direction moves — files stay within their research direction unless user explicitly requests
- No overwrites — if target file exists during organize, log as conflict, do not overwrite
Frontmatter Template
---
title: ""
authors: []
journal: ""
journal_abbr: ""
published_date: null
doi: ""
url: ""
source_path: ""
direction: ""
canonical_type: "research" | "survey" | "review"
tags_task: []
tags_method: []
tags_dataset: []
tags_domain: []
tags_signal: []
tags_application: []
tags_metric: []
tags_custom: []
status: "unread"
reading_priority: "medium"
updated_at: timestamp
---
<!-- User-maintained section. Scripts must never overwrite this. -->
