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It can annotate PDFs and synchronize them with a mobile PDF reader through the Zotfile plugin. Zotero can associate notes with bibliographic items.

Zotero can import and export citations from or to many formats, including Wikipedia Citation Templates, BibTeX, BibLateX, RefWorks, MODS, COinS, Citation Style Language/ JSON, refer/BibIX, RIS, TEI, several flavours of RDF, Evernote, and EndNote. Zotero also allows users to create their own customized citation styles. The house styles of most academic journals are available in Zotero, and the bibliography can be reformatted with a few clicks. Zotero users can generate citations and bibliographies through word processor plugins, or directly in Zotero, using Citation Style Language styles. Furthermore, all entries including bibliographic information and user-created rich-text memos of the selected articles can be summarized into an HTML report. Selections of the local reference library data can later be exported as formatted bibliographies. Items are organized through a drag-and-drop interface, and can be searched. Users can then add notes, tags, attachments, and their own metadata.

Zotero can also save a copy of the webpage, or, in the case of academic articles, a copy of the full text PDF. Such functionality is made possible by 'translators' – short pieces of computer code, or scripts to understand the structure of web pages and to parse them into citations using its internal formats.

Clicking this icon saves the full reference information to the Zotero library. Zotero shows an icon in the browser toolbar when a catalog entry or a resource (book, article, thesis) is being viewed on many websites (such as library catalogs or databases like PubMed, Google Scholar, Google Books,, Wikipedia, and publishers' websites).