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research-assist

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Lightweight arXiv literature digest skill for OpenClaw — Zotero-driven interest profiling, 3-dimensional candidate ranking, abstract-first review

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<h1 align="center">research-assist</h1>

Your Zotero library already knows what you care about. Let it find next week's papers for you.

<a href="README.zh-CN.md">中文说明</a>
 ·
 <a href="SKILL.md">Skill Contract</a>
 ·
 <a href="references/workflow.md">Workflow</a>
 ·
 <a href="references/contracts.md">Contracts</a>

<code>Zotero-backed</code>
 <code>Semantic search</code>
 <code>AI-enriched digest</code>
 <code>Email delivery</code>
 <code>Feedback loop</code>

---

> **If you are an agent** (Claude Code, Codex CLI, OpenClaw, or any LLM-backed tool),
> read [`references/setup-routing.md`](references/setup-routing.md) now.
> It will walk you through an interactive setup conversation:
> choose what the user needs, ask only the relevant questions, write `config.json`, and summarize what was enabled.
> **Do not embed the full setup questionnaire here** — route there, complete setup, then return to the user's actual task.
> Once config is valid, never reopen setup during normal runs.

---

## The six-stage chain

| Stage | What happens | Output |
|---|---|---|
| **`profile_update`** | Read Zotero evidence (collections, tags, representative papers), maintain a compact research profile | `research-interest.json` |
| **`retrieval`** | Query arXiv by default, optionally add OpenAlex and Semantic Scholar, deduplicate before ranking, write candidate artifacts | Candidate JSON + batch manifest |
| **`zotero_evidence`** | Resolve exact matches and semantic neighbors from the local Zotero index for each candidate | Scored candidates with Zotero anchors |
| **`agent_patch`** | Host agent fills `recommendation`, `why_it_matters`, `caveats`, `zotero_comparison`, and final keep/drop | Review patches merged into candidates |
| **`render`** | Generate HTML digest, email body, or Telegram message from the selected subset | `.html` + delivery metadata |
| **`feedback_sync`** | Push non-destructive feedback back into Zotero: add tags, collection membership, append notes | Zotero library updated (dry_run default) |

## What it does — in 30 seconds

1. **Reads your Zotero library** — collections, tags, representative papers — and builds a compact research profile
2. **Searches arXiv by default, with optional OpenAlex and Semantic Scholar expansion** — not keywords you typed, but evidence from papers you already collected
3. **Ranks candidates** with a two-signal scorer: research-map fit + Zotero semantic affinity
4. **Lets the host agent enrich the top picks** — recommendation, why it matters, nearest Zotero anchors, caveats
5. **Delivers a clean digest** — HTML, email, or Telegram — with only the sharpest papers visible
6. **Feeds the signal back into Zotero** — tags, collections, notes — so the next run starts from a better library

A profile reads like a map: compact branches, retrieval-friendly labels, evidence from the library itself.

A digest scans fast: visible scores, nearest anchors, and AI-written recommendations that justify attention.

The loop closes in Zotero — a useful digest also improves the library it came from.

## Why this is different

| Traditional tools | research-assist |
|---|---|
| Start from a keyword list | Start from your actual library |
| Dump everything that matches | Rank, filter, keep only the sharpest |
| AI is bolted on after the fact | AI enrichment is part of the pipeline |
| Results sit in a silo | Feedback flows back into Zotero |

## Quick start

### Option A — One-click agent setup (recommended)

If you already use **Claude Code**, **Codex CLI**, **Gemini CLI**, or any LLM-backed coding assistant, paste this single message into your agent:

> **Read the README at `https://github.com/zhanglg12/research-assist` and follow `references/setup-routing.md` to set up research-assist for me interactively.**

The agent will first locate its own skill directory (or ask for an install target if its host tool has no standard one), prefer an existing host-managed skill root instead of leading with directory creation, then clone or update the repo there, ask you a few focused questions based on what you actually need (minimal digest, Zotero integration, email delivery, etc.), write `config.json`, execute the required setup commands for the chosen backend or delivery route, and verify the result before finishing. For OpenClaw, that target is typically `~/.openclaw/skills/research-assist`.

### Option B — Manual install (OpenClaw example)

#### 1. Install

If `~/.openclaw/skills/research-assist` is already your intended skill target:

```bash
if [ -d ~/.openclaw/skills/research-assist/.git ]; then
  cd ~/.openclaw/skills/research-assist && git pull --ff-only
else
  mkdir -p ~/.openclaw/skills
  git clone https://github.com/zhanglg12/research-assist ~/.openclaw/skills/research-assist
fi
cd ~/.openclaw/skills/research-assist
uv sync
```

That's it. One command installs the base Python dependencies for the skill.

#### 2. Set up config

```bash
# Inside the resolved skill root, create runtime subdirectories if missing
mkdir -p ~/.openclaw/skills/research-assist/profiles
mkdir -p ~/.openclaw/skills/research-assist/reports
cp config.example.json ~/.openclaw/skills/research-assist/config.json
cp profiles/research-interest.example.json \
  ~/.openclaw/skills/research-assist/profiles/research-interest.json
```

Then edit `~/.openclaw/skills/research-assist/config.json` for your setup.

> **If you are an agent**, do not ask the user to fill out a long config form.
> Instead, follow [`references/setup-routing.md`](references/setup-routing.md) — it tells you exactly which questions to ask based on what the user wants to do.

#### 3. Run

```bash
# Full digest: profile check → literature retrieval → rank → HTML output
uv run research-assist --action digest --config ~/.openclaw/skills/research-assist/config.json

# Ad-hoc search
uv run research-assist --action search --query "llm multi-agent planning" --top 5

# Check if profile needs refresh
uv run research-assist --action profile-refresh --config ~/.openclaw/skills/research-assist/config.json

# Sync Zotero API items into semantic index (no local sqlite needed)
uv run research-assist --action sync-index --config ~/.openclaw/skills/research-assist/config.json

# Re-render digest after agent patches are merged
uv run research-assist --action render-digest \
  --config ~/.openclaw/skills/research-assist/config.json \
  --digest-json path/to/digest.json \
  --format delivery

# Start the bundled Zotero MCP server
uv run research-assist-zotero-mcp
```

#### 4. Build a portable skill package

```bash
uv run python scripts/distribution/build_skill_package.py
unzip dist/research-assist-skill-v*.zip -d /tmp/research-assist-skill
/tmp/research-assist-skill/research-assist-skill-v*/install.sh
```

The packaged skill ships with `install.sh`, which copies the runtime files into `~/.openclaw/skills/research-assist`, creates `config.json` and `profiles/research-interest.json` if missing, rewrites fresh runtime paths to the actual install target, and runs `uv sync` when available.

After package install, run the CLI against the installed skill root:

```bash
uv run --project ~/.openclaw/skills/research-assist \
  research-assist --action digest --config ~/.openclaw/skills/research-assist/config.json
```

## Pipeline stages

```
Zotero library
    ↓
1. profile_update    → Read Zotero evidence, build a compact research map
    ↓
2. retrieval         → Query arXiv by default, optionally add OpenAlex and Semantic Scholar, deduplicate, write candidate JSON
    ↓
3. rank              → Two-signal scoring: map_match (0.30) + zotero_semantic (0.70)
    ↓
4. agent_patch       → Host agent fills: recommendation, why_it_matters, caveats, zotero_comparison
    ↓
5. render            → HTML / email / Telegram from the selected subset
    ↓
6. feedback_sync     → Push tags, collections, notes back into Zotero (dry_run by default)
```

## Key design choices

- **No LLM calls inside the pipeline.** Retrieval, ranking, and formatting are pure data operations. Intelligence comes from the calling agent.
- **Ownership boundary is strict.** The host agent fills only `candidate.review`. It cannot rewrite paper metadata, scores, or delivery wrappers.
- **Digest stays small.** The system can search wide, but the visible digest targets 5 or fewer papers. Sharper shortlist > bigger dump.
- **Feedback is non-destructive.** Zotero writeback defaults to `dry_run=true`. No automatic deletes, no speculative taxonomy rewrites.

## Feedback sync — closing the loop

The final stage pushes what you learned back into Zotero so the next run starts from a better library.

**What feedback can do:**
- Add `ra-status:*` tags (`ra-status:read_first`, `ra-status:archive`, etc.)
- Add or change collection membership
- Append structured notes with decision rationale
- Create new collections for organization

**What feedback will never do:**
- Delete items, collections, or attachments
- Modify paper metadata (title, authors, DOI)
- Apply changes without showing a dry-run plan first

**How it works:**
1. After digest review, the host agent builds a feedback payload per `reports/schema/zotero-feedback.schema.json`
2. Calls `zotero_apply_feedback` with `dry_run=true` to preview changes
3. Shows the plan to the user for confirmation
4. Only then applies with `dry_run=false`

Supported decisions: `read_first`, `skim`, `watch`, `skip_for_now`, `archive`, `watchlist`, `ignore`, `unset`

Items are matched by `item_key`, `doi`, or `title_contains`. Previous `ra-status:*` tags are replaced when a new decision is applied.

## Optional: Zotero semantic search

If you want semantic neighbors (not just exact matches), configure the local search index:

- The default recommended backend is `semantic_search.embedding_model = "qwen"`.
- No extra Python package is required for the default `qwen` path beyond `uv sync`.
- You still need a local Ollama server with `qwen3-embedding:0.6b` available:

```bash
ollama pull qwen3-embedding:0.6b
```

If setup is being driven by an agent, the agent should run that pull command and verify the backend initialization before declaring setup complete.

If you do not want local semantic search yet, set `semantic_search.enabled` to `false` and the rest of the digest pipeline still works.

```bash
uv run python - <<'PY'
from codex_research_assist.zotero_mcp.semantic_search import create_semantic_search
search = create_semantic_search()
print(search.update_database(force_rebuild=False))
PY
```

Fill these keys in `config.json`:
- `semantic_search.zotero_db_path` — path to your local `zotero.sqlite`
- `semantic_search.local_group_id` or `semantic_search.local_library_id`

## Architecture

```
config.json
    ↓
openclaw_runner.py          ← CLI entry point, markdown/HTML to stdout
    ├── profile_refresh_policy  → Should the profile be updated?
    ├── pipeline.py             → multi-source literature retrieval (arXiv default)
    ├── ranker.py               → Two-signal scoring
    ├── review_digest.py        → System-generated review fallback
    ├── review_patch.py         → Agent review patch merge
    ├── html_fmt.py             → Beautiful warm-tone HTML digest
    ├── email_sender.py         → SMTP delivery
    └── telegram_fmt/sender.py  → Telegram delivery
```

## Literature sources

`research-assist` defaults to **arXiv only**. You can expand retrieval with any combination of:

- `arxiv`
- `openalex`
- `semantic_scholar`

When multiple sources are enabled, retrieval expands the paper pool first and then deduplicates before ranking.

Add this to `config.json`:

```json
"literature_sources": {
  "enabled": ["arxiv", "openalex", "semantic_scholar"],
  "openalex": {
    "api_key": "",
    "mailto": ""
  },
  "semantic_scholar": {
    "api_key": ""
  }
}
```

Notes:

- `arxiv` remains the default and requires no extra credentials.
- `OpenAlex` works anonymously; `mailto` and `api_key` are optional but recommended.
- `Semantic Scholar` works anonymously; `api_key` is optional and can help with higher rate limits.

## Agent compatibility

research-assist is designed as an **agent-native skill**. It works with any LLM-backed tool that can read files, run CLI commands, and follow structured instructions.

| Agent / Tool | Compatibility | Notes |
|---|---|---|
| **Claude Code** | Full | Read `SKILL.md` + `references/setup-routing.md` for interactive setup |
| **Codex CLI** | Full | Same workflow; the codebase was originally scaffolded with Codex |
| **Gemini CLI** | Full | Follows the same `references/setup-routing.md` route |
| **OpenClaw** | Full | Native skill contract via `SKILL.md` |
| **Cursor / Windsurf / Cline** | Works | Can read docs and run CLI; no MCP server needed for basic usage |
| **Any MCP-capable agent** | Full + MCP | Can connect to the bundled Zotero MCP server for live library access |

The key design: all intelligence lives in the **host agent**, not inside the pipeline. The pipeline is pure data operations (retrieval, ranking, formatting). The agent decides what to enrich, what to keep, and what feedback to write back.

## For agents: how to use this skill

> **If you are an agent** reading this for the first time:
>
> 1. Read [`references/setup-routing.md`](references/setup-routing.md) to configure the skill interactively
> 2. Read [`SKILL.md`](SKILL.md) for the full skill contract — CLI usage, workflow stages, hard rules
> 3. Read [`references/workflow.md`](references/workflow.md) for stage order and controller boundaries
> 4. Read [`references/contracts.md`](references/contracts.md) for profile and review ownership rules
>
> **Important behavioral rules:**
> - Setup is a **one-time** operation. Once `config.json` is valid, do not reopen setup questions during normal runs.
> - During digest runs, use the existing config. Do not re-discuss installation options.
> - If config is missing or broken, route back to `setup-routing.md` — do not guess values.

## Reference documents

- [`SKILL.md`](SKILL.md) — Skill contract for OpenClaw / agent integration
- [`references/workflow.md`](references/workflow.md) — Stage order and controller boundary
- [`references/contracts.md`](references/contracts.md) — Profile and review ownership rules
- [`references/setup-routing.md`](references/setup-routing.md) — Interactive agent setup guide
- [`references/review-generation.md`](references/review-generation.md) — Agent-filled review behavior
- [`references/profile-map-generation.md`](references/profile-map-generation.md) — How the research map is built from Zotero evidence

## Demo data in the visuals

The README visuals use a fictional public-topic profile (Agent memory, Multi-agent planning, World models, RL systems, Tool use, Simulation) with real papers as neutral examples.

## License

This project is licensed under the [MIT License](LICENSE).

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