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The Library

The library is where references are managed. Its layout and use follow Zotero's main window: collections and tags on the left, the reference table in the middle, and the details of the selected reference on the right.

Two views

One library has two views:

  • The full view is a window of its own called Library. It can also be moved into the writing window as a tab with Open Library as Tab in Main Window. Everything related to managing references is done here: multiple selection, merging, checkups, import and export, editing.
  • The sidebar view is the References page in the right pane of the writing window. While writing you use it to search references and insert citations; it does not manage anything.

Each view remembers its own current collection, search term and selection, but sorting, columns and display options are shared: change one in either view and the other follows.

Adding references

  • Create by hand: the New Reference button in the toolbar of the library window; choose a reference type and fill in the fields in the right pane.
  • Add by identifier: enter a DOI, ISBN, arXiv ID and so on; see Adding by identifier.
  • Add from a URL, and the browser window: see Browser Window and Adding from a URL.
  • Import a file: File > Import…, or File > Import from Clipboard; see Importing and Exporting References.
  • Add an attachment: File > Add Attachment adds a file to the library as a standalone attachment; you can also drag files into the reference table. PDFs and ebooks have their metadata retrieved automatically if the setting is on.

A new reference goes into the collection you are currently looking at.

Dragging in the reference table: drop a file from disk on a reference row to make it a child attachment of that reference; drop it between rows or in empty space to add it as a standalone attachment in the collection you are looking at. Hold a modifier key while dropping to change what happens: on macOS, Command moves the file (the original goes to the Trash after the copy is stored) and Command plus Option links it; on other systems, Shift moves and Shift plus Ctrl links. Child notes and child attachments in the table can be dragged onto another reference row to move them under that reference, and standalone notes and attachments can be dropped on a reference row the same way; dropped between rows or in empty space, child notes and child attachments become standalone items (and go into the selected collections if you are looking at a collection).

Collections

The collection tree on the left can hold collections at several levels, sorted by name within a level. Dragging references onto a collection adds them to it; one reference can be in several collections. Removing a reference from a collection only ends its membership; the reference is not deleted.

The tree also has a few fixed rows:

  • Library: all references;
  • Unfiled References: references that are in no collection;
  • Recently Read, Duplicate Items and Retracted Items: three virtual rows described below, which can be hidden from their context menu and shown again;
  • Trash.

Show References from Subcollections is in the View menu: when on, selecting a collection also lists the references of all its subcollections.

Tags

The lower left holds the tag selector: click a tag to filter, and several tags are combined by intersection. Tags can have colors (at most nine colored tags per library; colors belong to the whole library), and can be renamed and deleted. Show Automatic controls whether tags added automatically by lookups are listed.

Dragging items onto a tag in the tag selector adds that tag to them; hold Shift (Command on macOS) while dragging to remove it instead. References, notes, attachments and the annotations under an attachment can be dragged together. Pressing a digit key 1 to 9 adds or removes the matching colored tag on the selected items, and 0 removes all colored tags.

Tags are stored as a list, so a tag containing a comma, semicolon or space is stored as it is and never split.

  • Quick search: the search field at the upper right of the middle pane, with several modes (title, creator and year; all fields and tags; everything).
  • Tag filter: combined with quick search; the filters are intersected.
  • Advanced search: combine conditions; conditions can match at four levels (references, attachments, notes, annotations), and a search can be saved as a saved search that appears in the collection tree.

The Everything mode also searches the full text of attachments such as PDFs, EPUBs and web snapshots. The full-text index is built in the background; its progress is shown on the Advanced page of the settings, see Settings.

Notes and attachments

  • A reference can have child notes and child attachments; press the triangle before the reference in the table to expand it. There can also be standalone notes and standalone attachments without a parent reference.
  • An attachment can be a file stored in the library or a link to a local file or a web address; see Attachments.
  • Double-click a PDF, EPUB or web snapshot attachment to open it in the built-in reader, where you can annotate; annotations are stored in the library.
  • Select a note and the right pane shows the note editor directly.

The trash

Deleting references, collections and saved searches only moves them to the trash, from where you can restore them in the Trash row. A reference in the trash keeps its collection memberships, which return when it is restored. The trash can be emptied by hand; under Miscellaneous on the General page of the settings you can set after how many days items in the trash are deleted automatically. Permanent deletion cannot be undone.

Most actions in the library can be undone with Edit > Undo, creating and importing included.

Duplicate items

The Duplicate Items row lists suspected duplicates. When a group of duplicates is selected, the right pane shows the merge pane: choose the master reference and pick field by field whose value to keep. After merging, the merged-away references go to the trash, and their attachments, notes, tags and collection memberships are moved to the master. The application makes a database backup before merging.

Two references can be merged only if their CSL type and their reference type are the same.

Retractions

The application checks your references against the Retraction Watch list, marks retracted references with a red cross and lists them in the Retracted Items row. For a DOI only the first characters of its hash are sent, so the DOI itself never leaves your computer; a PubMed ID is not hashed, and its first digits are sent (for a short ID, the whole ID), as in Zotero. To turn the check off, set retractionsEnabled to false in the Config Editor at the bottom of the Advanced page of the settings, see Settings. When you add a retracted reference to a citation in the citation dialog you also get a warning.