che-zotero-mcp

What this skill does

# 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