Zotero is capable of much more than just saving sources and creating citations or bibliographies. It can also take several more roles in your research workflow:
Along with the PDF reader, the Zotero 6 release also came with the full release of Zotero's native iOS app.
Zotero for iOS has the full features of Zotero - saving items from the web, organizing items, reading and annotating PDFs.
There are other mobile tools that work with Zotero, including for non-iOS users. You can learn more about ways to work with Zotero on mobile devices on the Zotero "Mobile" support page.
One reason to use a reference management software like Zotero instead of storing sources as bookmarks in a browser or pasting citations and links into a Word document is the ability to easily organize, connect, and search items in Zotero.
Collections and subcollections
You can create a new collection by right-clicking on "My Library" in the left-side pane of the Zotero app. Collections function like playlists - anything added to a collection is also in your library and items can be in as many collections as you'd like.
The Zotero browser connector will save items to whatever collection you have open in the app, with the option of changing the destination in a dropdown menu that appears under the browser connector when you save a new item.
You can also nest additional subcollections within a collection. All items in the subcollections will appear in the collection, but not in other subcollections. This can be used, for example, to separate different types of sources you're using for a project or course.
Tags are descriptive words or phrases attached to an item that help you categorize and find it again later. Tags work similarly to how keywords work in some databases. You can tag items based on topic, methods, or however is useful for your workflow. Zotero also automatically adds tags when items are saved from databases that have subject headings or controlled keywords applied to items, and these are marked with an orange-red tag instead of the blue user-added tag. Tags are searchable, and you can also filter your collection by tags using the tag cloud in the bottom left pane of the desktop app.
Related items are a third way to organize or express connections between items, along with collections and tags. The "Related" tab of the right pane when you select an item shows other items you've set as related. Like tags, there are many ways to use related items. You may want to link articles from the same author, a book review and a book, a paper explaining a piece of software and that software or website, or connect a note to an item without attaching the note. Clicking on the related item in this window will take you to that item in the closest level of sub/collection.
Notes in Zotero
You can create notes, small text files, in Zotero. These can be create by either clicking the small notepad icon in the top row or by right clicking the item you want to add a note to and selecting "add note". Notes created via the notepad button in the top row can also be unattached to any item.
Notes are flexible and can be used to record whatever information you may want to store alongside a source or a collection. Notes can be exported or inserted into documents using Word or Google Docs plugins.
Zotero has a search function to help locate items in your library. This is helpful if you're a long-time Zotero user who has thousands of saved items and scrolling to look for them is inefficient, or if you're joining a new group library and want to see if particular authors, topics, or items are found there - perhaps to add them if not.
Zotero's search function has both a simple "quick" search and an advanced search. The small search box near the top of the desktop app is the quick search box. Quick search has three options for what fields are searched:
Zotero's advanced search is somewhat hidden. The advanced search menu can be opened by clicking on the magnifying glass icon in the top row of the desktop app.
The advanced search lets you choose individual fields, exclude terms, require multiple terms to be found, or allows you to see results for any of several terms. This is effectively Boolean logic ("Match all" = AND; "Match any" = OR, "does not contain" = NOT), but Zotero's advanced search only supports simple single operator searches. Please see the support page, linked below, for details on how to construct complex multi-Boolean searches using Saved Searches.
Saved searches appear as collections in your library and automatically add items in your library that match the search criteria to the collection. This can be a useful tool in organizing your library.
Zotero has long been able to download PDFs and attach them to items in your library, but the Zotero 6 release (2022-03-17) brought the ability to open, read, and mark up those PDFs in Zotero itself. Zotero's PDF reader has functionality typical of a PDF reader, including searching in document text and highlighting text or areas of the PDF. Deep integration with Zotero means that comments on the PDF can be turned into a note attached to the reference in Zotero.
Opening PDFs in Zotero
PDFs in your library can be opened in the Zotero standalone by double clicking on the attached PDF or by right clicking on either the item or the attached PDF and selecting "View PDF". They will open as new tabs in Zotero.
Creating a Timeline
The "Timeline" feature of Zotero visualizes a collection or a selection of items on a timeline, which can be a useful tool for writing literature reviews or similar projects where the progression of scholarship on a topic is relevant.
You can create a timeline by selecting a collection, subcollection, or group of items and then going to Tools > Create Timeline.
Manipulating the timeline
By default, the timeline is organized by date of publication. You can also sort by the date the item was added to your Zotero library or last modified in the library.
The timeline view has a text entry box that can be used to filter the items shown on the timeline, which works as a keyword search of the titles displayed. The "Highlight" text entry boxes next to the filter box behave similarly, but instead of only showing results for a keyword, the highlight boxes will highlight it in the corresponding color.
The chronological range shown in the timeline can be adjusted by changing the "band" settings. The bands represent different timeframes, with the first/top band showing items and the lower bands indicating the location of items chronologically with tick marks. By default the first band is set to "month", the second to "year", and the third to "decade". This works well with the assumption that the most common use of the Timeline will be to look at the chronology of published academic literature.
Different band settings may be useful if the scope of the project is narrower or broader than the default bands. For example, if I wanted to visualize a collection of news articles that covered an emerging situation in order to see how coverage changed throughout the time period, I could set the first band to day and the second band to month. If I was working with a collection of classical texts, I may want to set the third band to millennium, the second to century, and the third to year.
The "Duplicate Items" Collection
Zotero automatically checks items in your collection for duplicates. Specifically, it compares the title, DOI, and ISBN fields. If two items have the same information in these fields, it checks author/creator names and year of creation to determine if they're duplicates. Duplicates may have different information in other fields, but Zotero does not consider this.
Suspected duplicates are added to the "Duplicate Items" collection, found in your library below any collections you have and above the trash.
When you select an item in the duplicates collection, it will automatically select the other items Zotero considers duplicates as well and give you the option to merge the items in the right-hand pane. You should always opt to merge duplicates rather than delete one, as the merge saves any tags, collection locations, or citations via the word processor plugins.
The right-hand pane also gives you several options for how to merge the items. You can choose which of the items will survive the process as well as choose field-by-field which information you want to add to that item if other the other items being merged differ in those fields.