Resolve the current Zotero identity (userID, username, display name) and per-library access scopes from the configured API key, and report which library backends are available (cloud Web API and/or the desktop local API). Call this first to discover the userID — never ask the user to type a numeric ID. If no API key is configured, the server runs in local-only read mode against the desktop library (users/0).

Search or list items in a Zotero library or collection. Quick search via q (qmode: titleCreatorYear=default, matches title/creator/year only; everything=also searches notes & attachment full text). For presence checks ("is X in my library?"): a default-mode q that matches nothing auto-retries once in everything mode, so terms appearing only inside PDF text don't false-negative — pin qmode explicitly to disable. An empty everything result is reported as strong-but-not-conclusive, since un-indexed/scanned/un-synced PDFs aren't full-text searchable. Also supports boolean itemType filters (use || for OR, repeat or && for AND, leading - to negate, e.g. "journalArticle || book", "-attachment"), boolean tag filters (same syntax; escape a literal leading hyphen as "-"), since (version) for incremental queries, sort/direction, and limit/start paging. Set response_format to "detailed" to also return technical fields (version, tags, collections, DOI, url) needed before chaining a write; the default "concise" returns high-signal projections (key, itemType, title, creators, date). Reads are served from the fast desktop local API when available, otherwise the cloud Web API. Returns totalResults so you can tell when to page rather than assuming you saw everything. For conceptual/"papers about X" queries by meaning rather than exact fields, use zotero_semantic_search instead.

Fetch one item by its key, returning the full item record (itemType, all bibliographic fields, creators, tags, collections, relations, version). Optionally set include_children to also return the item's child notes and attachments. Use include to additionally request rendered output: "bib" (formatted bibliography entry), "citation" (inline citation), or "csljson" (CSL-JSON for downstream formatting); combine with style (a CSL style id, default chicago-note-bibliography) and locale. The returned version is required if you later update or delete this item.

Return the Zotero data model so you never hardcode item shapes. With no arguments, returns the schema version and the list of all item type names. With item_type, returns the valid fields and creator types for that type (the "primary" creator type is listed first). Use this to validate an item before creating or updating it: notes, attachments, and annotations are item types too but bypass the normal field/creator model.

Create new items or update existing ones in a single batch (the server auto-chunks into groups of 50). items is an ARRAY of item-data objects; each object has itemType as a plain string (e.g. "journalArticle", "book", "preprint", "report") plus its valid fields, creators (each {creatorType, firstName, lastName} or {creatorType, name}), tags ([{tag}]), and collections (array of 8-char collection keys). To UPDATE an existing item, also include its key and current version; to CREATE, omit both. Every item is validated against the Zotero schema before anything is sent — if any item is invalid, nothing is written and the problems are returned. Use zotero_schema to discover valid fields/creator types for an itemType. Writes go to the cloud Web API (requires ZOTERO_API_KEY).

Example:

{"items": [{"itemType": "journalArticle", "title": "The Role of Metadata in Machine Learning", "creators": [{"creatorType": "author", "firstName": "Ada", "lastName": "Lovelace"}], "date": "2024-01-15", "DOI": "10.1234/example.5678", "tags": [{"tag": "ml"}], "collections": ["ABCD1234"]}]}

Partially update one item (HTTP PATCH — only the fields you supply change; omitted fields are preserved). Provide item_key and a patch object of the fields to change (e.g. {"title":"New","extra":"note"} or {"tags":[{"tag":"reviewed"}]}). All field values are plain JSON strings/numbers/booleans/arrays — never wrapped in nested objects (e.g. "title": "New", NOT "title": {"title": "New"}). Optimistic concurrency is handled for you: if you pass the item's version it is used; otherwise the current version is fetched first. If the item changed on the server in the meantime (412), the update is automatically re-fetched and retried once. Writes go to the cloud Web API. Set dry_run:true to preview the field-level before→after diff without writing (arrays like tags/collections are replaced wholesale by PATCH, not merged; a dry_run call performs no write).

Move items to the trash (the safe, REVERSIBLE default) or restore them. This sets the deleted flag (1=trash, 0=restore) — it is NOT a permanent delete, so trashed items can be recovered here or in the Zotero app. Use this instead of zotero_delete_items unless you truly need irreversible removal. Provide item_keys and optional action (default "trash"). Writes go to the running Zotero desktop app for your personal library (via its local-API writes where available), otherwise to the cloud Web API.

PERMANENTLY and IRREVERSIBLY delete items by key (this purges them — it is NOT the trash). Prefer zotero_trash_items, which is reversible. This tool is disabled unless the server is started with ZOTEUS_ALLOW_DELETE=true, and additionally requires confirm: true on every call. For the personal library it goes through the running Zotero desktop app when that app supports local-API writes, otherwise the cloud Web API. The current library version is used as a precondition; the operation auto-chunks to 50 keys per request.

List, create, rename, reparent, or delete collections, and move items into or out of a collection. Set action to one of: "list" (all collections with key/name/parent), "create" (needs name, optional parent_collection key — omit for top-level), "rename" (needs collection_key + name), "reparent" (needs collection_key; parent_collection key, or omit to move to top level), "delete" (needs collection_key), "add_items" / "remove_items" (need collection_key + item_keys; collection membership lives on each item). All actions except "list" write to the cloud Web API.

List tags, or add/remove tags on items. Set action to "list" (returns library tags; supports q substring filter), "add" (add tags to each of item_keys), or "remove" (remove tags from each of item_keys). Tags are stored on the parent item's tag array, so add/remove edits the items (cloud Web API). Tag names are case-sensitive.

List, create, or delete saved-search DEFINITIONS. NOTE: the Zotero cloud Web API stores saved searches but does NOT execute them — to get the items a saved search matches, run an equivalent zotero_search_items query (or use the desktop local API when available). Set action to "list" (all saved searches with their conditions), "create" (needs name and conditions, each {condition, operator, value}), or "delete" (needs search_key). Writes go to the cloud Web API.

List the group libraries the current API key can access, with each group's id, name, type, item count, and edit permissions. Use a returned group id with the library_id/library_type:"group" parameters of other tools to operate on that group library. Requires a cloud API key.

Export items in a bibliographic format and return the raw text. Choose format (bibtex, biblatex, better-biblatex, ris, csljson, csv, mods, tei, coins, rdf_*, refer, wikipedia, bookmarks). biblatex is Zotero's STOCK translator via the cloud Web API; BBT-specific options (citation-key generation, sentence-case, biblatexExtendedNameFormat, unicode→LaTeX) are NOT available there. better-biblatex uses the local desktop Better BibTeX plugin (your configured BBT export options apply) and is only available when desktop Zotero + BBT are running; it degrades to built-in biblatex otherwise. Narrow with item_keys, collection_key, q, or item_type. A limit (default 50) is always applied. For styled human bibliographies use the bibliography tools.

Not a search — to find which items contain a term, use zotero_search_items with qmode=everything. This reads, sets, or tracks one attachment's already-extracted full text by key. action: "get" returns the indexed text content plus indexing stats for an attachment item (only attachment items have full text; returns found:false if none); "set" stores extracted text for an attachment (provide content and the indexing counts); "since" returns the map of attachment keys whose full text changed after a given library version (useful for incremental indexing). Only attachment items support full text. "get" and "since" read through the running Zotero desktop app when there is one (no cloud key needed), otherwise the cloud Web API; "set" always writes via the cloud Web API.

Retrieve an item's PDF or EPUB text for grounding. Pass a parent item_key (its best PDF/EPUB attachment is resolved automatically) or an attachment key. With query, returns the top relevant passages with locators (char offsets, nearest section, and a page); with page_range (e.g. "3-7"), returns just those pages, re-extracted from the PDF so the span is exact; with outline:true, returns the PDF's table of contents with page numbers (the cheapest way to decide which pages to read next); with none of them, returns a truncated head. Text comes from Zotero's full-text index when available; when the attachment is NOT indexed yet, the file itself is read and parsed on the fly (fallback, on by default; set fallback:false to disable), so a PDF added minutes ago still returns text (marked fulltextSource:"pdf" or "epub", with fileSource saying where the bytes came from). The file is read from the running Zotero desktop app, else straight out of the local Zotero storage folder, else downloaded from Zotero cloud storage. Page numbers are exact whenever the PDF was parsed, and otherwise an estimate (pageApprox) unless precise_pages:true. Read-only; the indexed text is served by the running Zotero desktop app when there is one, otherwise by the cloud Web API. Use this to cite a claim with a page after finding an item via zotero_search_items / zotero_semantic_search.

Return what changed in a library since a given version, for efficient incremental sync. Provide since (a library version; 0 = everything). Returns, per object type (items/collections/searches/tags), the map of keys→version that changed after since, plus the deletion log (keys removed since since). This is the version-based delta the Zotero sync algorithm uses — fetch the changed keys, then pull only those with zotero_get_item/zotero_search_items. Reads via the cloud Web API.

Upload, download, or inspect attachment files. action: "upload" stores a file as a Zotero attachment using the full File Storage protocol (provide url to have Zoteus fetch it, or file_path for a file on the machine running Zoteus; optional parent_item to attach it under an item, title, content_type) and returns the new attachment key; "download" fetches an attachment's file to a local path (provide item_key; optional save_path, default under the Zoteus data dir) and returns the path and byte count; "info" returns an attachment item's metadata. File bytes are written to / read from disk, never streamed through the conversation. Upload/download use the cloud Web API and your file-storage quota. When Zoteus runs on a different machine than Zotero, file_path refers to the server's disk, so use url instead.

Add or delete Zotero PDF annotations (highlights, underlines, notes), the same objects you create in the Zotero PDF reader. action:"add" needs parent (a regular item key OR a PDF attachment key) and annotations: each with type (highlight|note|underline, default highlight), text (the exact passage to highlight), optional comment, color, page (0-based page index). You do not need page coordinates: give the passage in text and it is located in the PDF and anchored to the exact lines it occupies, so quoting a passage is enough to highlight it. Pass page to disambiguate a passage that repeats, or occurrence to pick among repeats; pass position ({"pageIndex":N,"rects":[[x1,y1,x2,y2],...]} in PDF points, bottom-left origin) only to place a highlight yourself. action:"delete" trashes the annotations in annotation_keys. Writes go to the running Zotero desktop app for your personal library (via its connector protocol, or its local-API writes where available), otherwise to the cloud Web API.

Add a stored file attachment (e.g. a PDF full text) under an existing item. Give parent (the item key) and either url (Zoteus downloads it, then stores it) or path (a file on the machine running Zoteus). filename and content_type are inferred when omitted. Saves through the Zotero desktop app when one is reachable (Zotero 10+ local API; you may be asked once to allow Zoteus write access, choose "Always Allow"), and otherwise through the cloud Web API, which needs ZOTERO_API_KEY with file access and uses your Zotero file-storage quota. url works on every setup including a remote/hosted Zoteus that cannot see your desktop, so prefer it over path unless the file really is on the server. Returns the new attachment key.

Resolve bibliographic metadata to Zotero item-data and optionally save it to your library. action: "by_identifier" resolves a DOI, ISBN, PMID, arXiv id, or ADS bibcode (set identifier); action: "by_url" scrapes a web page (set url) and may return multiple choices to pick from. Set save_to_library:true (and optionally collection_key) to persist the resolved items — saved into the running Zotero desktop app when available, otherwise via the cloud Web API (requires ZOTERO_API_KEY); otherwise the resolved metadata is returned without saving. When a Zotero translation-server is reachable (ZOTEUS_TRANSLATION_SERVER_URL, default http://127.0.0.1:1969) it is the primary path; if none is running, DOI and arXiv ids fall back to built-in resolution (OpenAlex/Crossref and the arXiv API respectively) — the result then carries a source field ("scholar" or "arxiv"). ISBN/PMID/bibcode and web URLs require a translation-server.

Resolve a human citation-style name to a valid CSL style id and confirm it is available, or list common style aliases. action: "resolve" maps names like "APA 7th", "IEEE", "Vancouver", "Chicago", "MLA", "Nature" to the correct CSL id (e.g. apa, ieee, modern-language-association) and verifies the style can be fetched; pass the returned styleId as the style argument to zotero_format_bibliography or zotero_bibliography. action: "list" returns the built-in common aliases (any id from the CSL styles repository also works). Dependent styles are resolved to their independent parent automatically when formatting.

Render a formatted bibliography in any CSL style using citeproc-js — no Zotero library write required. Provide either items (an array of CSL-JSON objects, e.g. from zotero_import or external metadata) or item_keys (library items, which are exported to CSL-JSON first). Choose style (a name like "APA 7th" or a CSL id; default "apa"), locale (default "en-US"), and format (html/text/rtf; default html). The formatted bibliography text is returned. Use this for arbitrary items or styles; for items already in the library you can also use zotero_bibliography (server-rendered).

Produce a formatted bibliography for items already in a Zotero library, rendered server-side by Zotero in a CSL style. Provide item_keys and optionally style (name or CSL id; Zotero default is chicago-note-bibliography), locale, and linkwrap. Returns XHTML. Note: this endpoint is item-only and capped at 150 items. For arbitrary CSL-JSON or items not in the library, use zotero_format_bibliography instead.

Manage the local hybrid-search index used by zotero_semantic_search. Every job runs in the background on the server, so this tool returns immediately and never blocks on large libraries. THREE write actions, and picking the right one matters: action: "update" is the cheap one and should be the default for a library that is already indexed; action: "build" and action: "refresh" both rebuild the WHOLE index, which on a large library means many minutes and, with an API embedding provider, real spend (they differ in one thing: build resumes an interrupted build, refresh always starts over). action: "build"/"refresh" pages the library's top-level items (100-at-a-time, stopping at the server's item cap, ZOTEUS_INDEX_MAX_ITEMS, default 5000, or at a smaller limit if one is given), indexes their text (title, abstract, creators, tags) for BM25 keyword search and, if an embedding provider is configured, for vector search, persisting partial progress atomically as it goes; use it for the first build, after changing the embedding model, or to widen a previously capped build. It is ALSO the repair: if the index cannot be read at all, only action:"build" clears it, by deleting the unreadable file and opening a fresh one before rebuilding (nothing repairs it at startup or inside a query). action: "update" instead fetches only the items changed since the version the index recorded (Zotero's ?since=), re-chunks and re-embeds just those, and removes items the library no longer holds (diffed from a cheap keys-only ?format=versions census, since the deletion log is cloud-only); untouched items are never re-embedded, so adding a handful of items costs seconds instead of a full rebuild. Update falls back to a full rebuild by itself, and says so in updateNotice, when a delta would be wrong: no version stamp recorded yet, the library is now served by a different Zotero API (the desktop app and the cloud number their versions independently), or the embedding model changed. An update ALSO asks Zotero's full-text index what it has extracted since the build (that is a separate version sequence from item versions, so a PDF Zotero extracted when it was first opened changes no item version and appears in no delta) and indexes the new body text for items nothing else touched; on a library where nothing was extracted, that costs one request. A build or update interrupted by action:"stop", a crash or a restart leaves a checkpoint, and action: "build" RESUMES from it: the items already committed stay searchable and are never re-fetched or re-embedded, and only work since the last save is redone (resumedFrom on the status reports how many were inherited). action: "refresh" is the one that always starts over. A build also indexes the reader's OWN words by default: every child note, and every PDF annotation (its highlighted passage and its comment), as extra passages carrying the parent item's key — so zotero_annotate writes text that search can then find, an item with forty annotations still takes one result slot, and a hit whose snippet came from one is marked source:"note" or source:"annotation". That corpus is one paged crawl of hand-written text, orders of magnitude smaller than attachment bodies; turn it off with own_words:false or ZOTEUS_INDEX_OWN_WORDS=false. An action:"update" keeps it current for the cost of one request when nothing was written: notes and annotations are ordinary items carrying ordinary versions, so an edit, an addition and a deletion are all found by comparing the library's note/annotation keys against the ones the index holds — which is also how an index built before this existed fills its gap, once, on its first update. Set fulltext:true to ALSO index the body text Zotero extracted from each item's attachments, which is what makes semantic search match a claim buried in a PDF rather than only its title and abstract; it is off by default because it multiplies build time and index size (default cap: 40000 characters per item, tunable with fulltext_max_chars), and only attachments Zotero has already extracted are available. That pass used to be refused inside Claude Desktop, where a build that reached it killed the server process partway through with no error at all (#37); the cause was the on-device embedding model asking Electron's allocator for a block it will not serve, so the server now embeds fewer passages per call there and the build runs to completion. It is somewhat slower inside the app than in a terminal and produces exactly the same index, so a user who wants the fastest possible first build can still run one headlessly against the same ZOTEUS_DATA_DIR and let Desktop read the result. A build runs in TWO passes and reports which one it is on as phase: every item's metadata is indexed first, across the whole library, and only then are attachment bodies crawled (fulltextItemsScanned of fulltextItemsTotal). So the library is fully searchable on titles, abstracts, creators and tags long before a full-text crawl that can run for hours finishes — tell the user they can search already rather than asking them to wait for state:"done". Start a job, then POLL action: "status" every few seconds until state is "done" (or "error"); calling build or update again while one is running just returns current progress. action: "status" reports state (idle|building|done|error), operation (build|update), phase (metadata|fulltext), fetch/embed progress, itemsRemoved, index size, the active embedder, libraryVersion/libraryBackend (the version stamp an update diffs from), fulltextVersion (how far into Zotero's separate full-text sequence the index has read), resumedFrom (items inherited when a build resumed an interrupted one), itemsTotal/itemsAvailable (which differ, with a warning, when the cap stopped the crawl short of the library), ownWordsItems/ownWordsPassages (the notes and annotations indexed, with ownWordsReason if they could not be read), and (when full text was requested) fulltextItems/fulltextPassages plus fulltextReason if it produced nothing. It also reports localApiDegradedAt when the job saturated Zotero's local API and the whole session fell back to the Zotero Web API: that fallback works, so nothing errors, but the Web API is slower and rate-limited and the rest of the build takes far longer than its start suggested, so tell the user rather than letting them watch an unexplained slowdown (the crawl also backs off to one attachment at a time by itself, to let the app recover). It reports where the index is stored (storage: sqlite or memory, set by ZOTEUS_INDEX_BACKEND), storageNotice when opening that store imported or refused an older JSON index, persistError when the index could not be written to disk at all, and how the last semantic query ranked vectors (vectorScan: "codes" for the two-stage path, "exact" for a full scan of every vector, with vectorScanNotice when that needs explaining). When the embedding provider is an API (ZOTEUS_EMBEDDINGS=openai or gemini), status also reports embedRate: the batch size, the pause between requests, the estimated tokens per request and the tokens per minute the build is actually sustaining, plus passagesWithoutVectors when the index holds passages nothing has embedded yet. A build whose embedder was rate-limited to a standstill keeps every passage it indexed and stays RESUMABLE: tell the user to run action:"build" again, which embeds only the passages that have no vector and re-fetches nothing, and NOT action:"refresh", which starts the whole crawl over and pays for every vector a second time. A rate-limited request already backs off and retries by itself; if a build reports it is riding the provider's tokens-per-minute limit, the fix is ZOTEUS_EMBED_BATCH_DELAY_MS (with ZOTEUS_EMBED_BATCH_SIZE), not a smaller library. action: "stop" cancels a running job (partial data is kept and stays searchable; a stopped update leaves the version stamp untouched so the next one repeats the delta, and a stopped build leaves a checkpoint the next action:"build" resumes from). A partially built index is always usable for keyword search. Local embeddings are CPU-bound (see ZOTEUS_EMBEDDINGS), so large builds take a while: poll status rather than retrying build.

Search the library by meaning, not just keywords. Combines BM25 keyword scoring with vector similarity (when an embedding provider is configured) via reciprocal-rank fusion, and returns the best-matching items with a snippet and score. By default it searches item metadata and abstracts; if the index was built with fulltext on (zotero_index fulltext:true, or ZOTEUS_INDEX_FULLTEXT=true) it also searches the body text of attachments, and a hit whose snippet came from a PDF body is marked source:"fulltext". It ALSO searches the words the reader wrote — child notes and PDF annotations (highlight text and comments) — unless that was turned off (ZOTEUS_INDEX_OWN_WORDS=false); a hit from one is marked source:"note" or source:"annotation" and is attributed to the item it hangs off, so an item with forty annotations is one result rather than forty. mode: "auto" (hybrid, default), "keyword" (BM25 only), or "semantic" (vector only). "semantic" needs vectors in the index: when the configured embedder is not running (e.g. the on-device model runtime is not installed) it returns an error naming the cause instead of an empty result set, and "auto" keeps working as keyword search while saying so. The index must be built once before first use: when it is empty this tool starts a background build automatically (auto_build, on by default) and tells you to poll zotero_index action:"status" and retry — pass auto_build:false to opt out. For exact field/tag/itemType filtering use zotero_search_items instead; use this for conceptual/"papers about X" queries. To read the actual passages of a found item (with page locators) use zotero_get_fulltext.

Explore the EXTERNAL scholarly graph around a paper (OpenAlex, Crossref fallback). This does NOT search, list, or read your Zotero library — it queries the open web, and results are works from the scholarly web, not your items. To search or inspect YOUR library use zotero_search_items, zotero_semantic_search, zotero_get_item, or zotero_list_tags instead. Provide a doi and an action: "lookup" (metadata + citation count), "references" (works this paper cites), "citations" (works that cite this paper, most-cited first), or "related" (similar works). Set include_in_library: true to additionally flag which results your library already holds (off by default because it scans the library); otherwise every result is just a web record. limit caps results (default 20). Read-only; calls external scholarly APIs.

Discover the available Zotero tools by keyword — useful for progressive disclosure when you do not want to load every tool definition up front (the code-execution-with-MCP pattern). Pass an optional query (matched against tool names, titles, and descriptions) and detail ("names" or "descriptions", default "descriptions"). Returns the matching zotero_* tools so you can pick the right one for a task. With no query, returns the full catalog.

List tags in a Zotero library with their usage count and whether each was auto-applied by Zotero. Optional q substring filter and limit. Read-only — available even when the connector runs in read-only mode (unlike zotero_manage_tags, which also writes). For taxonomy hygiene use zotero_tag_audit.

List collections in a Zotero library (key, name, parent collection key, item count). Read-only — available even in read-only mode (unlike zotero_manage_collections, which also writes). Use the keys to scope zotero_search_items (collectionKey) or zotero_tag_audit (scope.collection_keys).

Audit a library against a controlled tag vocabulary with priority tiers. Provide the vocabulary inline as vocabulary (or a JSON file via vocabulary_path): { tags:[{name,tier?}], tiers?:[{name,required?}] }. Reports (1) off-taxonomy tags (library tags not in the vocabulary; Zotero auto-applied tags are bucketed separately unless include_auto), (2) items missing a tag from each required tier, and (3) optional per-collection coverage when scope.collection_keys is given. Read-only. Tag/auto-tag enumeration uses the cloud Web API.