Zotero MCP Search Skill

Interface with Zotero's MCP server to search and retrieve bibliographic data using advanced semantic search and multi-strategy approaches.

Designed for plain markdown outline output: This skill generates bibliographies formatted as plain markdown outlines suitable for pasting into Logseq with:

•Outline hierarchy (nested bullets, no markdown headers)
•Compact citation format (Author, Year. Title)
•Side-by-side Chinese-English translations for improved English language search
•Plain text (no bold styling)
•Zotero item links

Context-Aware Skill: This skill automatically adapts its strategy based on the environment:

•Claude Code: Uses autonomous agents for comprehensive multi-step searches
•Claude Desktop: Uses batched manual searches with safety limits

Core Philosophy

Search comprehensively, not narrowly. Never settle for a single search attempt. Always:

•Use semantic search for conceptual discovery
•Try multiple search angles and variations
•Combine different search methods
•Iteratively refine based on results
•Ask clarifying questions when needed
•Format bibliographies for Logseq with proper outline structure

Environment Detection

Detect which environment you're running in:

•Claude Code: Agents available (Task tool), no conversation crash risk
•Claude Desktop: No agents, conversation deletion risk with large responses

How to tell: Check if Task tool is available in your tool list.

PART 1: Claude Desktop Strategy

⚠️ CRITICAL: Avoiding Claude Desktop Crashes ⚠️

KNOWN BUG: Claude Desktop has a critical bug where large MCP responses cause request timeouts that DELETE the entire conversation without warning or recovery.

Safe Search Strategy: Batched Iteration

To get comprehensive results safely, use iterative batched searches:

✅ SAFE: Multiple small searches

•Each search limited to 10-15 results maximum
•Multiple searches with different angles/filters
•Combine results across searches

❌ UNSAFE: Single large search

•limit=50 or higher in one call
•Risks conversation deletion
•No recovery possible

Recommended Approaches for Claude Desktop

Approach 1: Multi-Angle Coverage (Preferred)

Instead of one search with limit=50, do 5 searches with different angles:

code

1. Semantic search: "main concept" (limit=10)
2. Semantic search: "related concept variation" (limit=10)
3. Keyword search: "specific terms" (limit=10)
4. Tag-based search: relevant tags (limit=10)
5. Notes/annotations search: "concept" (limit=10)

This gives ~50 results from different perspectives, safer than one large call.

Approach 2: Iterative Interactive

For user-guided exploration:

code

1. First batch: limit=10
2. Present results
3. Ask: "Would you like more results, or shall I search from a different angle?"
4. Next batch based on user feedback

Default Limits for Claude Desktop

Always use these safe defaults:

•limit=10 for initial searches
•limit=15 if user explicitly needs more
•Never exceed limit=20 in a single call
•For comprehensive results: use multiple searches, not larger limits

PART 2: Claude Code Strategy

Agent-First Approach

When running in Claude Code, use autonomous agents for comprehensive searches.

When to Use Agents (Claude Code Only)

Use agents when:

•User needs comprehensive literature searches
•User asks exploratory questions ("What do I have about...")
•User needs multi-angle search coverage
•User wants thorough, curated results
•User's query is conceptual or thematic

Don't use agents when:

•User asks for a single specific paper by exact title
•User just wants to see recent additions
•User is browsing collections interactively

Agent Task Patterns

Pattern 1: Comprehensive Topic Search

User request: "Find me papers about [topic]"

Agent task:

code

Search my Zotero library comprehensively for papers about [topic].

Use multiple search strategies autonomously:

1. SEMANTIC SEARCHES (5-6 variations)
   - Try natural language phrasings
   - Try different conceptual angles
   - Use synonyms and related terms
   - No limit restrictions - get comprehensive results

2. KEYWORD SEARCHES (3-4 variations)
   - Try exact terms and variations
   - Try broader/narrower terms
   - Try related methodology terms

3. TAG-BASED SEARCHES
   - First use zotero_get_tags to discover relevant tags
   - Then search by multiple relevant tags
   - Try tag combinations

4. FULL-TEXT & ANNOTATIONS
   - Use zotero_search_notes for the concept
   - Use zotero_get_annotations to find highlights
   - Search for related concepts in notes

5. SYNTHESIS
   - Combine all results and deduplicate
   - Identify the 20-30 most relevant papers
   - Group by theme/approach if applicable
   - Provide brief relevance explanations

Return a curated list with:
- Paper metadata (title, authors, year)
- Why each paper is relevant
- Thematic groupings if applicable
- Coverage note (which strategies found what)

Pattern 2: Author-Focused Search

User request: "What do I have by/about [author]?"

Agent task:

code

Find all items related to [author] in my Zotero library.

Search comprehensively:

1. DIRECT AUTHORSHIP
   - zotero_search_items with author="[author]"
   - zotero_advanced_search with author field

2. CITATIONS & MENTIONS
   - zotero_search_notes: "[author]" (cited in my notes)
   - zotero_get_annotations: "[author]" (mentioned in highlights)
   - zotero_semantic_search: "[author]'s main concepts/theories"

3. RELATED WORK
   - Search for concepts/theories associated with this author
   - Search for methodologies they use
   - Search for co-authors

4. SYNTHESIS
   - Organize by: (1) authored by, (2) cited in my notes, (3) related concepts
   - Include temporal overview if relevant
   - Note any thematic clusters

Return organized results with context about how each item relates to [author].

Pattern 3: Concept in Context

User request: "Research about X in context Y"

Agent task:

code

Find papers about [X] in the context of [Y].

Multi-angle search strategy:

1. COMBINED SEARCHES
   - Semantic: "X in Y" + variations
   - Semantic: "Y approaches to X"
   - Advanced: keyword=X AND keyword=Y
   - Advanced: keyword=X AND keyword=[Y synonyms]

2. SEPARATE THEN CROSS-REFERENCE
   - Find strong X papers
   - Find strong Y papers
   - Identify overlap and connections
   - Check if X papers mention Y in fulltext
   - Check if Y papers mention X in fulltext

3. TAG ANALYSIS
   - Get tags related to X
   - Get tags related to Y
   - Search items tagged with both domains
   - Find bridging concepts in tags

4. ANNOTATION MINING
   - Search notes for X+Y together
   - Search notes for X and Y separately
   - Check if you've annotated connections

5. SYNTHESIS
   - Papers directly about X in Y context
   - Papers about X that discuss Y
   - Papers about Y that discuss X
   - Papers that bridge both (even if not explicit)

Return results grouped by relevance strength and connection type.

Pattern 4: Exploratory Discovery

User request: "What's related to X?" or "Explore my library for X"

Agent task:

code

Explore my Zotero library to discover all material related to [X].

Comprehensive discovery approach:

1. DIRECT SEARCHES (Cast wide net)
   - Semantic search: multiple phrasings of X
   - Keyword search: X and synonyms
   - Tag search: X-related tags
   - Notes/annotations: X mentions

2. EXPANSION PHASE
   - Analyze top results to identify:
     * Related concepts and theories
     * Related methodologies
     * Related application domains
     * Related authors
   - Search for each of these expansions

3. DEEP EXPLORATION
   - For promising papers, check fulltext for related concepts
   - Look at tags on promising papers, search those tags
   - Check annotations for related ideas
   - Look for cited works mentioned in your notes

4. THEMATIC CLUSTERING
   - Group all findings by themes/approaches
   - Identify conceptual clusters
   - Note connections between clusters
   - Highlight surprising/unexpected connections

5. SYNTHESIS
   - Core papers directly about X
   - Related theoretical frameworks
   - Methodological connections
   - Application domains
   - Surprising/tangential connections worth noting

Return a thematic map of your library's coverage of this topic.

How to Launch Agents (Claude Code Only)

Use the Task tool with subagent_type="general-purpose":

code

Task(
  description="Comprehensive Zotero search for X",
  subagent_type="general-purpose",
  prompt="[Use one of the task patterns above]"
)

PART 3: Universal Search Strategy

Multi-Method Search Approach

ALWAYS use multiple search methods in combination (in both environments):

A. Semantic Search (Primary for Conceptual Discovery)

•Use zotero_semantic_search for conceptual, thematic, or exploratory queries
•Try multiple phrasings of the same concept
•Use natural language descriptions, not just keywords
•
Example variations:
- •"theories of embodied cognition"
- •"how body influences thought and reasoning"
- •"physical experience shapes cognitive processes"
•Claude Desktop: limit=10
•Claude Code (agents): no limit restriction

B. Keyword Search (Complementary)

•Use zotero_search_items with multiple keyword variations
•Try synonyms, related terms, broader/narrower terms
•Use different word forms (singular/plural, verb/noun)
•
Example variations for "reading comprehension":
- •"reading comprehension"
- •"text understanding"
- •"literacy"
- •"comprehension strategies"

C. Advanced Search (Targeted)

•Use zotero_advanced_search for precise criteria
•Combine multiple fields (author + keyword, year + tag)
•Use for filtering after broader searches

D. Tag & Collection Filtering

•Use zotero_get_tags to discover relevant tags
•Use zotero_search_by_tag with multiple tag variations
•Use zotero_get_collections and zotero_get_collection_items for organized searches

E. Full-Text & Annotations

•Use zotero_search_notes to search annotations and highlights
•Use zotero_get_item_fulltext for content not in metadata
•Critical for finding concepts mentioned in text but not in titles/abstracts

Common Search Patterns

Pattern: "Find me papers about X"

Claude Desktop:

code

1. zotero_semantic_search: "X" (limit=10)
2. zotero_semantic_search: "X alternative phrasing" (limit=10)
3. zotero_search_items: keyword variations of X (limit=10)
4. zotero_get_tags: look for X-related tags
5. zotero_search_by_tag: if relevant tags found (limit=10)
6. zotero_search_notes: "X" (limit=10)
Result: ~50+ results safely retrieved

Claude Code:

code

Launch agent with Task tool (Pattern 1)
Agent performs comprehensive multi-strategy search
Returns curated results with synthesis

Pattern: "What do I have on [author]?"

Claude Desktop:

code

1. zotero_search_items: author="[Author]" (limit=10)
2. zotero_advanced_search: author + recent years (limit=10)
3. zotero_search_notes: "[Author]" (limit=10)
4. zotero_semantic_search: "[Author]'s main concepts" (limit=10)

Claude Code:

code

Launch agent with Task tool (Pattern 2)

Search Failure Recovery

If initial searches yield poor results:

•
Ask clarifying questions:
- •"Are you looking for theoretical or empirical work?"
- •"Any specific time period or authors?"
- •"Is this about methodology, findings, or theory?"
•
Broaden search:
- •Use more general terms
- •Remove filters
- •Try related fields/disciplines
•
Check search database status:
- •Use zotero_get_search_database_status
- •Suggest zotero_update_search_database if outdated
•
Try alternative angles:
- •If searching for method, search for problems it solves
- •If searching for theory, search for phenomena it explains
- •If searching for author, search for concepts they study

PART 4: Bibliography Output Formatting

When the user requests a bibliography or formatted output of search results:

Logseq Formatting Standards

ALWAYS use outline hierarchy (nested bullet points), NEVER use markdown headers (#): NO BOLD STYLING - use plain text for all content

Compact citation format:

code

- Main Topic - Bibliography
	- A. Category Name
		- Author(s), Year. Title (English Translation if applicable)
			- Type: Article Type
			- Journal: Journal Name, Volume X, Issue Y, Pages Z
			- Zotero: [zotero://select/library/items/ITEM_KEY](zotero://select/library/items/ITEM_KEY)
			- DOI: [if available]
			- Abstract (Chinese): [if applicable]
			- Abstract (English): [translation or original]

Format rules:

•First line: Author(s), Year. Title (English Translation)
•For Chinese authors: 黃美金 (Huang Mei-Jin)
•For multiple authors: separate with semicolons
•For no date: use "n.d."
•For no author: use institutional name or "N/A"

Translation Requirements

•
Chinese Abstracts:
- •Always provide BOTH Chinese original and English translation
- •Label clearly as Abstract (Chinese): and Abstract (English):
- •Translate comprehensively, not just summaries
•
Chinese Titles:
- •Provide English translation in parentheses after Chinese title
- •Format: 中文標題 (English Translation)
- •If English title exists in metadata, use that; otherwise translate
•
Author Names:
- •Include both Chinese characters and romanization when available
- •Format: 黃美金 (Huang Mei-Jin)

Required Metadata Fields

Each bibliography entry must include (when available):

•Title (with translations as needed)
•Authors (with Chinese/romanization)
•Date (YYYY-MM-DD or YYYY)
•Type (Journal Article, Book Chapter, Thesis, etc.)
•Journal/Publication (with volume, issue, pages)
•Zotero link (format: zotero://select/library/items/ITEM_KEY)
•Abstract (Chinese and/or English as applicable)
•DOI (if available)

What NOT to Include

•❌ No summary sections at the end of bibliographies (no totals, no "organized by themes" recap)
•❌ No markdown headers (#, ##, etc.) - use nested bullets only
•❌ No bold styling (**text**) - use plain text throughout
•❌ No item counts or statistics sections at the end

Bibliography Structure Example

code

- Indigenous Language Proficiency Certification (原住民族語言能力認證) - Bibliography
	- A. Core Certification Papers
		- 黃美金 (Huang Mei-Jin), 2003. 原住民族語言能力認證：回顧與展望 (Indigenous Language Proficiency Certification: Review and Prospects)
			- Type: Journal Article
			- Journal: 原住民教育季刊, Issue 9, Pages 5-27
			- Zotero: [zotero://select/library/items/W44VF3CG](zotero://select/library/items/W44VF3CG)
			- Abstract (Chinese): [full Chinese abstract]
			- Abstract (English): [full English translation]
	- B. Policy & Historical Context
		- [next paper...]

File Handling

When creating bibliographies:

•Save to /Users/niyaro/Desktop/ with descriptive filename
•Use .md extension
•Open in BBEdit automatically (use bbedit command)
•Confirm file creation and location to user

PART 5: Tool Quick Reference

Tool	Primary Use	Claude Desktop Limit	Claude Code (Agent)
`zotero_semantic_search`	Conceptual discovery	limit=10	No limit, use liberally
`zotero_search_items`	Keyword matching	limit=10	No limit
`zotero_advanced_search`	Precise filtering	limit=10	No limit
`zotero_get_tags`	Discover tags	No limit needed	No limit needed
`zotero_search_by_tag`	Tag filtering	limit=10	No limit
`zotero_search_notes`	Annotation search	limit=10	No limit
`zotero_get_annotations`	Highlight retrieval	limit=10	No limit
`zotero_get_item_fulltext`	Full-text access	N/A (single item)	N/A (single item)
`zotero_get_collections`	Collection discovery	No limit needed	No limit needed
`zotero_get_recent`	Recent additions	limit=10	No limit
`zotero_update_search_database`	Update index	N/A	N/A

Critical Reminders

For Both Environments

•Never use just one search method
•Never try just one search term variation
•Always check tags before searching
•Always search both metadata and full-text/annotations
•Always explain your search path
•Always refine based on initial results

Claude Desktop Specific

•🚨 SAFETY: Always use limit=10 (max 15-20) to prevent conversation deletion
•🚨 SAFETY: For comprehensive results, use multiple searches or agents, NOT large limits

Claude Code Specific

•Default to agents for non-trivial searches
•Be comprehensive - no crash limits
•Let agents explore - they can handle complexity autonomously
•Synthesize results - raw lists are not enough

Bibliography Formatting

•Format for Logseq - use outline hierarchy, not headers; NO bold styling
•Compact citation format - Author(s), Year. Title on first line
•Translate Chinese content - provide both original and English versions

Remember: This skill adapts to your environment. In Claude Code, leverage agents for comprehensive autonomous searches. In Claude Desktop, use careful batched searches with safety limits.