research-init

# /research-init - Zotero-Integrated Research Startup Workflow

Launch a project-scoped literature startup workflow for the research topic "$topic", with scope "$scope" and output type "$output_type".

Default behavior is evidence-first: if Zotero is unavailable, if full-paper evidence is insufficient, or if the selected Research Question Card is not ready, produce an intake/audit result instead of forcing a polished proposal.

## Usage

### Basic Usage

```bash
/research-init "transformer interpretability"
```

### Specify Scope

```bash
/research-init "few-shot learning" focused
```

### Specify All Parameters

```bash
/research-init "neural architecture search" broad both
```

## Workflow

Execute the following steps in order:

### Step 0: Intake and Capability Gate

Before creating collections or writing files:

1. Confirm the practical purpose: new project intake, literature review, proposal draft, or source audit.
2. Check whether Zotero MCP is configured and writable.
3. If Zotero MCP is unavailable, read-only, or the user asks for dry-run mode:
   - do **not** create collections,
   - do **not** import papers,
   - produce `research-question-card.md` and a source candidate/audit section,
   - either skip `references.bib` or create a stub that clearly says canonical BibTeX is unavailable unless reliable BibTeX can be generated from existing sources,
   - stop before `literature-review.md` or `research-proposal.md` unless the user explicitly provides sufficient local evidence.
4. If the topic, target venue/audience, or project boundary is ambiguous enough to change the search strategy, ask a short clarifying question before acting.

### Step 1: Create Zotero Research Collection

1. Call the Zotero MCP tool `zotero_create_collection` to create the main collection, named `Research-{Topic}-{YYYY-MM}` (extract a short PascalCase keyword from the topic, use the current year and month)
2. Create sub-collections under the main collection:
   - `Core Papers`
   - `Methods`
   - `Applications`
   - `Baselines`
   - `To-Read`
3. Record the `collection_key` for each sub-collection (needed for import in Step 2)

### Step 2: Literature Search and Import

1. Use WebSearch to find papers related to "$topic"
   - Search strategy: use the topic directly, plus variant combinations of key terms
   - Target sources: arXiv, DOI-backed publisher landing pages, conference proceedings with full-paper pages, direct PDF pages
   - Time range: focused mode searches the last 3 years, broad mode searches the last 5 years
   - Target paper count: 20-50 papers for focused scope, 50-100 for broad scope
2. **Source quality filter before extraction**:
   - Prefer candidates that expose at least one of: DOI, arXiv ID, direct PDF URL, or clear citation metadata for a full paper
   - **Explicitly avoid abstract-only pages as primary sources** when a better source exists for the same paper (for example conference abstract listings, event schedule pages, teaser pages, or pages that only contain a short abstract with no DOI/arXiv/PDF)
   - For the same title, source preference should be:
     1. DOI-backed publisher page
     2. arXiv abs/pdf page
     3. direct PDF URL
     4. full-paper proceedings landing page
     5. abstract-only page (last resort only)
   - If the discovered page is clearly abstract-only and no DOI/arXiv/PDF can be extracted, do **not** prioritize it for import; keep searching for a better source first
   - Abstract-only pages should **not** be counted toward the target paper quota unless all better identifier-bearing/full-paper sources for that title have been exhausted
3. Extract candidate DOI / arXiv ID / landing-page URL from filtered search results
4. **Classify before import**: For each paper, determine which sub-collection it belongs to (Core Papers, Methods, Applications, Baselines, or To-Read) based on its title, abstract, and venue
5. **Pre-import deduplication (two-step)**:
   - Call the Zotero MCP tool `zotero_search_items` with the DOI string when available to find potential matches
   - Call `zotero_get_item_metadata` on results to confirm the DOI field matches exactly
   - If confirmed match → skip import, log ("Already exists: {DOI} → {item_key}")
   - For papers without DOI → search by title using token overlap ratio (lowercase both titles, remove punctuation, compute intersection of words / union of words). Ratio > 0.8 = duplicate
6. **Abstract-only page guardrail (mandatory)**:
   - Before calling `zotero_add_items_by_identifier`, check whether the chosen URL is likely an abstract-only page
   - Strong signals include: URL/path contains `abstract`, page title/heading is an abstract listing, page body lacks PDF/full-text links, and no DOI/arXiv identifier is visible
   - If it is abstract-only **and** no DOI/arXiv/PDF can be recovered, prefer one of:
     - keep searching for a better source for the same title, or
     - skip this candidate for now
   - Do **not** eagerly import abstract-only pages into analytical sub-collections just to satisfy paper count
   - If an abstract-only page is imported as a last-resort placeholder, it must be treated as `To-Read` only, never as a confirmed paper source for `Core Papers`, `Methods`, `Applications`, or `Baselines`
   - When you skip such a candidate during Step 2, print this exact user-facing line in the terminal output:
     - `Skipped abstract-only page; searching better source`
7. **Smart import with collection assignment**: Call `zotero_add_items_by_identifier` with the target sub-collection's `collection_key`, `attach_pdf=true`, and `fallback_mode="webpage"`
   - Route priority is fixed: DOI / doi.org URL → arXiv ID or arXiv URL → direct PDF URL → generic landing-page URL
   - The tool will prefer proper paper/preprint items and only fall back to `webpage` when no reliable DOI/arXiv identifier is found
   - For difficult publisher pages and cookie-gated PDFs, the import path may additionally use the local Zotero connector/browser