AI Research Skills
A skill catalog that won't let you spend 6 months on a research gap that's already closed, isn't a real contribution, or isn't feasible. Every candidate thesis topic goes through a 3-gate decision dossier first — and the rest of the pipeline (literature → design → build → run → write → submit) only flows from candidates that pass.
Languages: English | 繁中 · Pipeline · Examples · Runtime contract · Glossary
What this is. A catalog of 15 Claude Code skills built around one
stubborn question most research-AI tools dodge: is this research gap
actually worth doing? The pipeline opens with a structured decision
dossier — three gates: open / contribution / feasibility — and
downstream stages (research design, manuscript drafting, reviewer
response) only fire on a candidate that clears all three. Built for graduate students, PhDs, postdocs, and
research support staff. Five plugins, one marketplace install — and
the same SKILL.md files load into Codex CLI, Gemini CLI, Cursor,
Windsurf, Hermes, OpenClaw, and generic API clients too (see
§7 Compatibility).
For literature automation, the SKILL.md catalog and the executable
research-hub runtime are separate layers; see
docs/runtime-contract.md.
📚 Part of the agentic AI learning roadmap — featured in §13–14 (research workflows).
Contents
- Install — get the skills
- Why this catalog exists
- The pipeline — what each stage delivers to the next
- Use it
- See what each skill produces
- FAQ
- Compatibility
- Limitations
1. Install — get the skills
The core asset is portable SKILL.md; Claude Code marketplace support is
the convenience layer. Use the path that matches your host:
| Host | Path |
|---|---|
| Claude Code | Marketplace install below; gets auto-triggering and claude plugin list verification. |
| Codex CLI / Cursor / Windsurf | Load the canonical repo's SKILL.md into the host's skills/rules directory, or inline it into the prompt. |
| Gemini CLI / generic API client | Inline SKILL.md as prompt or system context. |
| Hermes | Install a raw SKILL.md; this repo has Hermes 0.13.0 skill-load verification for literature-triage-matrix. |
| OpenClaw | Use a SKILL.md directory shape such as ~/.openclaw/skills/<skill>/SKILL.md when supported; not release-verified here yet. |
Full per-host recipes are in docs/install.md → Using these skills outside Claude Code.
Claude Code fastest path — 30 seconds:
claude plugin marketplace add WenyuChiou/ai-research-skills
claude plugin install research-workspace@ai-research-skillsWindows cmd.exe: run the commands one at a time. If the plugin list
does not show research-workspace@ai-research-skills, your paste probably
only executed the first line; see docs/install.md for the
single-line CMD form.
For Claude Code, the first two commands install the 11-skill
research-workspace plugin. Add the optional plugins only when you need
manuscript writing, full Zotero operations, or Claude-to-Codex/Gemini
delegation.
Additive install — stop after any step and use what you have:
# 1. Marketplace + 11 research-hub skills (6 immediately usable, pure reasoning)
claude plugin marketplace add WenyuChiou/ai-research-skills
claude plugin install research-workspace@ai-research-skills
# 2. Manuscript work — claim-evidence audit, banned-word, reviewer response
claude plugin install academic-writing-skills@ai-research-skills
# 3. Zotero CRUD (enable local API in Zotero desktop first — docs/setup-guide.md §C)
claude plugin install zotero-skills@ai-research-skills
# 4. Multi-CLI delegation (install codex / gemini CLI binaries first)
claude plugin install codex-delegate@ai-research-skills
claude plugin install gemini-delegate@ai-research-skills
# 5. Literature pipeline automation (Python CLI behind research-hub skills)
pip install research-hub-pipeline
research-hub setup --persona researcher
research-hub doctor
research-hub auto "agent-based modeling" --max-papers 3 --no-nlmBatch all 5 plugins in one go:
bash scripts/install-all.sh # macOS / Linux / git-bash
pwsh scripts/install-all.ps1 # Windows PowerShellVerify:
claude plugin list
# fastest path: research-workspace@ai-research-skills is ✔ enabled.
# full install: 5 plugins ending in @ai-research-skills are ✔ enabled.claude plugin list verifies only the Claude Code marketplace install.
It does not tell you whether Codex, Cursor, OpenClaw, Hermes, or a
generic API client has loaded the SKILL.md files. Marketplace-installed
plugins live under ~/.claude/plugins/cache/..., not ~/.claude/skills/.
Per-plugin details: docs/install.md. Python / Zotero / Git not set up yet? Start with docs/setup-guide.md. Need to know whether a skill is prompt-only or needs the Python runtime? See docs/runtime-contract.md.
I'd rather clone the repo (contributors / debugging)
git clone https://github.com/WenyuChiou/ai-research-skills.git
cd ai-research-skillsThis catalog is the registry, not a monorepo. Each plugin's source code lives in its own repo:
github.com/WenyuChiou/research-hub— 11research-workspaceskillsgithub.com/WenyuChiou/academic-writing-skills— 1 skillgithub.com/WenyuChiou/zotero-skills— 1 skillgithub.com/WenyuChiou/codex-delegate— 1 skillgithub.com/WenyuChiou/gemini-delegate-skill— 1 skill
If you're hacking on a plugin, clone its source repo, not this
catalog. This catalog only maintains marketplace.json, docs, image
assets, and the catalog-side CHANGELOG.md.
2. Why this catalog exists
You probably know the AI-for-research pain points already. The five below are the ones this catalog actually fixes — not the ones it gestures at.
P1 — "I keep re-explaining context to every new AI session"
You open a new Claude / ChatGPT session to continue yesterday's work, and the model knows nothing about your research question, the experiments you've already finished, your baselines, or the gap you closed last week. You spend the first ten minutes re-typing all of it. Tomorrow, again.
P2 — "AI confidently cites papers that don't exist"
The model writes "as Chen et al. (2024) demonstrated…" — the paper is not real. You catch it (this time). In a reviewer response, a hallucinated citation is a desk-reject.
P3 — "I've read 50 papers and still can't tell which gap is worth a thesis"
Three questions need structured answers: (1) is the gap actually still open? (2) is closing it a real contribution or a permutation of existing work? (3) can I close it in the time I have? Tools that produce a one-paragraph "research gap summary" don't answer any of them.
P4 — "AI-written prose smells like AI"
"Furthermore", "It is noteworthy that", hedged sentences with no committed claim. Reviewers (and senior co-authors) catch the smell in two paragraphs, and the manuscript drops in their priority list.
P5 — "Switching Claude / Codex / Gemini wipes my state"
You design the prompt with Claude, hand it to Codex to scaffold the code, switch to Gemini for the long-context paper synthesis. Each switch costs five minutes of re-onboarding. The cross-AI handoff is where real time disappears.
Three design principles, applied across 15 skills
The catalog is arranged around three load-bearing ideas, not a feature list:
| Principle | What it does | Solves |
|---|---|---|
1. Manifests (.research/, .paper/) |
Research state lives in checked-in YAML / Markdown files. A new AI session reads the manifest and re-onboards itself — you don't re-explain context. | P1, P5 |
| 2. Schemas with anti-leakage rules | Every cross-skill artifact has a YAML schema. A claim with empty evidence_artifacts is forced to carry status: gap + a gap_reason — never supported. A topic candidate with verdict: do-not-pursue is structurally separated from worth-pursuing ones. Downstream tools refuse to ship overconfident output. |
P2, P3, P4 |
| 3. Character-driven routing | Mechanical bulk → Codex. Long-context / CJK → Gemini. Judgment / governance → Claude. The router (research-hub-multi-ai) writes a coordination file so each delegate reads its own brief, not the parent context. |
P5 |
The 8-stage pipeline below is these three principles applied to a real research workflow.
3. The pipeline — what each stage delivers to the next
Eight stages from "I should read about X" to "the manuscript shipped". Each stage's output is the next stage's input — the handoff is mechanical, not vibes.
| # | Stage | Skill(s) | Output → next stage |
|---|---|---|---|
| 1 | Discover literature | research-hub, paper-summarize |
.bib + per-paper Key Findings notes → Stage 2 |
| 2 | Find the gap | gap-to-topic, literature-triage-matrix, notebooklm-brief-verifier, zotero-library-curator |
topic_dossier.gaps.yml (with verdict, verdict_reason) → Stage 3a |
| 3a | Frame the RQ | research-design-helper |
design_brief.md (frontmatter source: gaps.yml#G2, gap_verdict) → Stage 3b + Stage 4 |
| 3b | Plan the project | research-context-compressor, research-project-orienter |
project_manifest.yml (provenance.from_gap) → Stages 4–8 |
| 4 | Build the model | cookbook — codex-delegate for ≥5-file scaffold, Claude direct for ≤4-file or judgment work |
code in your project repo (see cookbook) → Stage 5 |
| 5 | Run & validate | research-context-compressor, research-project-orienter |
.research/ run manifests so future AI sessions skip the rescan → Stage 6 |
| 6 | Visualise & interpret | codex-delegate, gemini-delegate |
figures + analysis scripts → Stage 7 |
| 7 | Draft the manuscript | paper-memory-builder, academic-writing-skills |
.paper/claims.yml (with status enum + anti-leakage) → Stage 8 |
| 8 | Submit + respond | academic-writing-skills, research-context-compressor |
reviewer-response.md, version-tagged manifests → done |
The cross-skill handoffs (Stage 2 → 3a → 3b → 8; Stage 7 → 8) are
documented as YAML schemas, not free text. A downstream skill can
refuse to process a malformed handoff — and does, when the schema
violation would otherwise propagate (e.g. status: gap claims with no
gap_reason are rejected at Stage 7).
Cross-cutting (every stage): codex-delegate, gemini-delegate,
research-hub-multi-ai. These three sit beside the pipeline, not on
it — any stage routes mechanical / long-context / multi-AI work
through them.
Full narrative + per-stage tool tables: docs/pipeline.md.
4. Use it
Pick by goal
If you'd rather not read the full pipeline above, jump in by your immediate goal:
| Your immediate goal | Skills you'll use |
|---|---|
| Find & compare literature | research-hub + literature-triage-matrix |
| Write or revise a paper | paper-memory-builder + academic-writing-skills |
| Manage a research project | research-design-helper + research-context-compressor + zotero-library-curator |
Helping others adopt AI for research (librarian / RA / advisor)? No install needed — share this README plus docs/install.md.
Or, just describe what you want
Describe what you want in plain language — Claude Code matches your phrasing to a skill. You don't need to remember skill names.
| When you say… | Skill that activates |
|---|---|
| "Compare these 5 papers by method, data, limitations" | literature-triage-matrix |
| "Is this gap worth a thesis? Walk me through the three gates" | gap-to-topic |
| "Walk me through my research design before I start coding" | research-design-helper |
| "Audit this paragraph for banned words and overclaim" | academic-writing-skills |
Full trigger map (15 rows): docs/skill-directory.md.
If auto-trigger picks the wrong skill, name it explicitly:
"Use literature-triage-matrix to compare these 5 papers."
Already use Zotero / Obsidian / NotebookLM?
Have any of Zotero / Obsidian / NotebookLM in your workflow?
research-hubintegrates whichever of these you have as one library-management loop: search new literature (arXiv, Semantic Scholar) → Zotero metadata + ingest → per-paper notes synced to Obsidian → NotebookLM briefs verified against source bundles. All three tools are optional —research-hubadapts to whichever subset you have (or even none, in sample-dashboard mode). Python-CLI-backed;pip install research-hub-pipeline.Already run independent MCP servers for these tools (e.g.
paper-search-mcp, a Zotero MCP, a NotebookLM MCP)? They coexist — the skill orchestrates workflows, the MCPs give raw tool access. The CLI itself also exposes an MCP interface (research-hub serve). Full setup + tool-by-tool modes: research-hub project README.
All 15 skills
From research-hub (11 skills) — one install gets all
research-hub— search, ingest, organise papers across Zotero / Obsidian / NotebookLM. (Stages 1, 2)literature-triage-matrix— comparison matrix across method, data, claim, limitation. (Stage 2)notebooklm-brief-verifier— verify NotebookLM briefs against source bundles. (Stage 2)zotero-library-curator— audit Zotero, propose cleanup (preview-only withoutzotero-skills). (Stage 2)gap-to-topic— 3-gate go/no-go decision dossier for a candidate thesis/proposal topic (open? a contribution? feasible?). Emits.gaps.ymlforresearch-design-helperStage 3a handoff. (Stage 2)research-design-helper— Socratic dialog through RQ → mechanism → identifiability → validation → risk. Reads.gaps.ymlto pre-fill segments 1 + 5; Stage 4 cookbook reuses the produceddesign_brief.md. (Stages 3a, 4)research-context-compressor—.research/manifests so future AI sessions skip the rescan. (Stages 3b, 5, 8)research-project-orienter— fast orientation memo from those manifests. (Stages 3b, 5)research-hub-multi-ai— character-driven routing across Claude / Codex / Gemini. (Cross-cutting)paper-memory-builder—.paper/claims.yml+.paper/figures.yml(status enum, anti-leakage rule, file sentinels). (Stage 7)paper-summarize— fill per-paper Key Findings / Methodology / Relevance in both Obsidian and Zotero child notes afterresearch-hub auto. (Stage 1)
Standalone repos (4 plugins) — one plugin install each
academic-writing-skills— manuscript revision, claim-evidence audit (schema-aware against.paper/claims.yml), banned-word / humanize, journal format, reviewer response. (Stages 7, 8)zotero-skills— full Zotero CRUD, batch metadata, library maintenance. (Stages 1, 2, 7)codex-delegate— Claude → Codex CLI handoff for code-heavy / mechanical work. (Cross-cutting, also Stages 4, 6)gemini-delegate— Claude → Gemini CLI handoff for long-context, multilingual, or CJK work. (Cross-cutting, also Stages 6, 7)
Time + cost expectations
Rough envelope from in-session use — adjust to your input size:
| Task | Typical wall time | Conversation turns | Notes |
|---|---|---|---|
Compare 5 papers (literature-triage-matrix) |
1–3 min | 1–2 | Linear in paper count; 20 papers ≈ 5 min |
3-gate gap decision (gap-to-topic) |
5–15 min | 3–6 | Scales with candidate count + literature-recall depth |
Banned-word audit on 1 paragraph (academic-writing-skills) |
<1 min | 1 | Independent of manuscript size |
Reviewer response (6 comments) (academic-writing-skills) |
3–8 min | 3–5 | Scales with comment depth + revision required |
Audit 800-item Zotero library (zotero-library-curator) |
2–4 min | 1 | Read-only; library size matters less than tag diversity |
Summarize 5 papers per cluster (paper-summarize) |
4–10 min | 1 | One LLM call per paper; rolls back per-paper on failure |
These are maintainer-observed ranges, not benchmark numbers. Your LLM provider, network, library state, and prompt phrasing all affect the actual time.
⚠ Back up Zotero before any CRUD
zotero-library-curator is read-only — it emits a preview report.
zotero-skills can write (merge duplicates, delete items, rebind
collections). Always export a Zotero backup before letting any AI
modify your library: Zotero → File → "Export Library…" → Zotero RDF.
The skills will not do this for you.
5. See what each skill produces
Each pipeline stage's deliverable has a worked-example file. Click through to see the actual artifact a skill emits — not a description.
| Stage | What the skill produces | Example file |
|---|---|---|
| 1–2 | Literature-review deliverable (TL;DR + per-paper synthesis + tagged gap analysis) | example-literature-review-deliverable.md · .docx |
| 2 | Topic dossier with the 3-gate decision (open / contribution / feasibility) + machine-readable gap roster | example-topic-dossier.md + .gaps.yml · .docx |
| 3a | Design brief with provenance to the dossier, Socratic-walked RQ → mechanism → identifiability → validation → risk | example-design-brief.md |
| 3b | Project manifest carrying provenance.from_gap so future AI sessions skip the rescan |
example-project-manifest.yml |
| 4 | Cookbook — two paths from brief to scaffolded code (Claude-direct for ≤4 files; codex-delegate for ≥5) |
example-design-to-build.md |
| 7 | Paper claims with status: gap anti-leakage rule + figure roster with embedded-in-manuscript sentinels |
example-paper-memory-claims.yml + example-paper-memory-figures.yml |
The cross-cutting and orchestration skills (research-hub ingestion,
research-project-orienter, research-hub-multi-ai,
notebooklm-brief-verifier) don't map to a single stage deliverable —
they're exercised end-to-end in test-corpus/ from a
real dogfood run: an
orientation memo,
a multi-AI routing decision,
and a NotebookLM brief verification.
Or read docs/examples.md end to end for the
narrative tour with per-skill input/output tables.
6. FAQ
Does this work with Chinese-language literature?
Yes — skills are language-agnostic. Run them in Chinese, the output is Chinese. NotebookLM, Claude, and Gemini all handle Traditional / Simplified Chinese well.
How do I export to .docx for an advisor?
Stage 2 dossier and Stage 1–2 literature-review deliverable ship with
.docx generators — direct links in §5 above. Other stages
(design_brief.md, project_manifest.yml, claims.yml) emit
Markdown / YAML; pipe through pandoc or Word's "Open Markdown" if
needed.
7. Compatibility
The portable layer is the SKILL.md instruction file plus any bundled
references/, scripts/, and workflow contracts. Claude Code
marketplace support is one host-specific packaging layer, not the only
way to use the skills.
| Layer | What is portable | Status |
|---|---|---|
Universal SKILL.md layer |
Skill instructions, trigger descriptions, references, scripts, and .research/ / .paper/ handoff contracts |
15/15 pass strict-minimum spec (name + description, ≤500 lines) |
| Host-specific behavior | Auto-triggering, plugin marketplace install, claude plugin list, skill discovery, and rules-directory conventions |
Depends on the agent host; use that host's own list/discovery check |
| Current portability audit | Generic SKILL.md-loading hosts |
11/14 zero-edit portable in the 2026-05-10 audit; 3/14 needed cosmetic <skill-root> path edits that have since landed |
| Verified host install | NousResearch/hermes-agent 0.13.0 | literature-triage-matrix installed end to end, security scan SAFE, registered enabled; Hermes inference loop not tested |
| OpenClaw | SKILL.md-style directories such as ~/.openclaw/skills/<skill>/SKILL.md when supported by the user's OpenClaw install |
Structurally compatible target, but not release-grade verified by this repo yet |
| Other agents | Codex CLI, Gemini CLI, Cursor, Windsurf, generic API clients, and other SKILL.md-loading hosts |
Load the same SKILL.md as context or into the host's skill/rules directory; not all hosts are individually tested |
The 11/14 portability figure reflects the audit run on 2026-05-10,
when the catalog had 14 skills; gap-to-topic (added 2026-05-21, the
15th) is not yet portability-audited.
Calibrated audit + experiment transcripts:
.research/hermes-compatibility-audit.md.
For documented Codex CLI / Gemini CLI / Cursor / Windsurf / Hermes and
generic-API examples, see
docs/install.md → Using these skills outside Claude Code.
For OpenClaw, use the SKILL.md directory shape above until this repo adds
release-grade OpenClaw verification.
8. Limitations
- Assembled and tested by one graduate-student researcher; not corpus-scale-validated.
- Domain bias toward water resources and agent-based modeling; not validated for social sciences, ML, or clinical writing.
- Behavioral correctness on real-world inputs is the source repo's responsibility, not this catalog's.
- Upstream URL liveness is not machine-checked; verified manually on PRs.
- No
claude plugin installround-trip is asserted by CI; the marketplace registry is checked structurally, the actual install + trigger path is verified by the maintainer between releases (see docs/verification.md for what is and isn't covered). zotero-skillsis shipped by two plugins simultaneously (research-workspaceembeds an older copy alongside the canonical standalonezotero-skillsplugin). A bare-name invocation ofSkill(skill="zotero-skills")resolves silently to theresearch-workspaceembedded copy. To reach the canonical standalone, use the plugin-qualified formSkill(skill="zotero-skills:zotero-skills"). See docs/verification.md §2026-05-20 for the reproduction and the deferred fix.
The full design contract — including what is and is not machine-checked — is in docs/design-philosophy.md.
License
MIT. Each skill is maintained in its canonical repo — this catalog is
the index, not a monorepo. Contributions welcome via issue or PR.
New-skill proposals → either research-hub (workflow integration) or
a standalone repo (deep, single-purpose CRUD).