che-zotero-mcp

Zotero MCP — Academic Reference Management

50 tools across 5 categories for managing academic references and building knowledge.

Tool Categories

1. Zotero Library (18 tools — Start Here)

Tool	Purpose
zotero_search	Search library by keyword
zotero_semantic_search	AI-powered semantic search (needs zotero_build_index first)
zotero_search_by_doi	Find item by DOI
zotero_get_recent	Recently added items
zotero_get_metadata	Full metadata for an item
zotero_get_collections	List all collections
zotero_get_items_in_collection	Items in a specific collection
zotero_get_tags	All tags in library
zotero_get_annotations	Highlights and notes from PDFs
zotero_get_attachments	Attached files (PDFs, etc.)
zotero_get_notes	Standalone notes
zotero_get_my_publications	Items marked as your publications
zotero_list_groups	Shared group libraries
zotero_get_config	Current API configuration
zotero_set_config	Update API configuration
zotero_find_duplicates	Detect duplicate items
zotero_normalize_titles	Fix title casing
zotero_build_index	Build semantic search index

2. Zotero Write Operations (6 tools)

Tool	Purpose
zotero_create_item	Create item manually
zotero_add_item_by_doi	Add item by DOI (auto-fills metadata)
zotero_add_attachment	Attach file to item
zotero_add_to_collection	Add item to collection
zotero_create_collection	Create new collection
zotero_delete_item	Delete item
zotero_delete_collection	Delete collection
zotero_set_in_my_publications	Toggle "My Publications" flag

3. Citation & Export (3 tools)

Tool	Purpose
zotero_to_apa	Generate APA citation
zotero_to_biblatex_apa	Generate BibLaTeX entry (APA style)
resolve_references	Resolve in-text references to DOIs

4. Academic Search (7 tools — Semantic Scholar + ORCID)

Tool	Purpose
academic_search	Search papers on Semantic Scholar
academic_search_author	Search by author name
academic_lookup_doi	Look up paper by DOI
academic_get_citations	Papers that cite a given paper
academic_get_references	References of a given paper
academic_compare_papers	Compare two papers side-by-side
orcid_get_publications	Get publications from ORCID ID
import_publications_to_zotero	Import from Semantic Scholar to Zotero

5. Knowledge Graph (13 tools)

Tool	Purpose
graph_stats	Graph overview (nodes, edges, density)
graph_add_node	Add paper/author/concept node
graph_add_edge	Add relationship edge
graph_remove_node	Remove node
graph_remove_edge	Remove edge
graph_save	Persist graph to disk
graph_neighbors	Find connected nodes
graph_shortest_path	Path between two nodes
graph_co_author_stats	Co-authorship statistics
graph_citation_network	Citation flow analysis
graph_community	Detect research communities
graph_query	Custom graph queries
graph_import_from_zotero	Import Zotero library into graph

Common Workflows

Literature Review

1. academic_search — find papers on a topic
2. academic_get_references — explore key papers' references
3. import_publications_to_zotero — add relevant papers to Zotero
4. zotero_add_to_collection — organize into collection
5. zotero_to_biblatex_apa — generate bibliography entries

Citation Generation

1. zotero_search or zotero_search_by_doi — find item
2. zotero_to_apa — for in-text or reference list
3. zotero_to_biblatex_apa — for LaTeX documents

Knowledge Graph Analysis

1. graph_import_from_zotero — populate graph from library
2. graph_community — find research clusters
3. graph_co_author_stats — identify key collaborators
4. graph_citation_network — trace influence paths

Semantic Search (First Use)

1. zotero_build_index — build vector index (one-time, takes ~30s)
2. zotero_semantic_search — search by meaning, not just keywords

Best Practices

1. Use academic_search for discovery, zotero_search for your library — don't confuse external search with local search
2. Build semantic index once — zotero_build_index only needs to run when library changes significantly
3. Use DOI whenever possible — zotero_add_item_by_doi auto-fills all metadata correctly
4. Check duplicates periodically — zotero_find_duplicates prevents bibliography bloat
5. Organize with collections — use zotero_create_collection + zotero_add_to_collection for project-based organization