/research-init

name: research-init
description: Initialize a research project with Zotero-integrated literature review. Creates or audits project-scoped sources, generates research question cards, and only writes a research proposal when the evidence gate passes.
args:
  - name: topic
    description: Research topic or keywords
    required: true
  - name: scope
    description: Review scope (focused/broad)
    required: false
    default: focused
  - name: output_type
    description: Output type (review/proposal/both). All modes produce research-question-card.md; references.bib is produced only when reliable citation metadata exists; review adds literature-review.md only when evidence is sufficient; proposal adds research-proposal.md only when the selected card passes the proposal readiness gate.
    required: false
    default: both
tags: [Research, Literature Review, Zotero, Paper Search]

/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

/research-init "transformer interpretability"

Specify Scope

/research-init "few-shot learning" focused

Specify All Parameters

/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