A good reference manager will save you countless hours of tedium and frustration. Students, researchers, and volunteers who work with references should all be using one. Zotero is my preferred option, because it is free, open source, actively developed, and solves many of the problems I’ve encountered during my work. In this guide I outline the way I set up and use Zotero for my PhD work.
If you haven’t done so already, I recommended skimming the documentation to get up to speed with how Zotero works.
Setting up zotero
First up, install Zotero and Zotfile as outlined in my post on using Zotero with cloud storage providers (please note the update in that post – I no longer use Zotfile to move pdfs outside the default /Zotero/Storage directory, I just use it to rename files).
Now you can install other addons for Zotero if desired. I recommend Zutilo to help with tagging your collections. You may also be interested in the Zotero DOI Manager which can automatically validate, clean, and swap original long DOIs for official shortened versions.
Adding items to Zotero
The most common way I add items to Zotero is from the publisher page. Whether I’m searching a database or checking Google Scholar alerts, I usually end up on the publisher page if the abstract seems relevant. Simply click the Zotero icon in the browser and the item will be saved. You can change the collection on the fly with the dropdown menu.
The other way I add items is by dragging and dropping the pdf into Zotero, which will then automatically lookup the citation data in the background before attaching the pdf to a new citation in the library. If you’re using Zotfile, remember to then right click on any item(s) you’ve added this way, select ‘manage attachments,’ and then select ‘rename attachments’ so Zotero can allow Zotfile to move and rename your pdf. This extra step doesn’t need to be performed when saving in the browser as above.
Another cool way to add items is by entering an identifier after clicking the magic wand button. You can enter a DOI, ISBN, PubMedID or arXivID and Zotero will grab the citation data and add an entry. Zotero will also attach the full text if it is open access, or if you have access through your current internet connection at work or school (but not if you’re accessing content off-site through a proxy, sadly).
I like to make a few quick tweaks to items when I add them:
- Right click the title field and change the text to sentence case. Then capitalise any words after colons and any proper nouns. This ensures any in-text or bibliographic styles which require title case will be accurately implemented, as its impossible for Zotero to reliably do it the other way round.
- Add HTML code to ensure species names are italicised when printed in the bibliography. This is simple – just place <i> at the start of the name, and </i> just after the name. For example, <i>Homo sapiens</i>.
- Check authors conform to a preferred format. This helps with ‘given name disambiguation‘ which is the idea that reference managers need to differentiate between different authors. So Thomas Edward Saunders, T Saunders and T. E. Saunders would all be considered different authors by Zotero which can be annoying in some cases. To avoid this choose a preferred format and change all incoming citations to this format.
- Make sure the URL field is correct and does not contain a proxy in the address (see tips below for more proxy stuff).
- Add tags to organise references. I have two different types of tags I use:
- Status tags: These tell me important things about the reference, for example ‘to read’, if it is something important I need to cite, if it is not in English, or if it is an advance copy without a DOI, volume number, or pagination. I assign a colour to these tags so I can see this information when scrolling through my Zotero library.
- Content tags: These tell me about the content of the paper and are split into 5 groups relevant for my PhD topic. For example, one group of tags are species – what species does this paper relate to? It could be one or several. Another group of tags are types of pest management – is this paper talking about pesticides, trapping, biological control, etc.
Tags can be added on the tag tab in the right hand panel. Once tags are added to items, you can drag and drop groups of items onto a tag in the left hand panel. You can also copy all of an items tags to another item by right clicking on the item, selecting ‘Zutilo,’ then selecting copy or paste tags.
Finding items in your library
Probably the simplest way to find an item in your library is to enter terms in the search bar. By clicking the small arrow on the left of the search bar, you can choose to search either:
- Title, Year, Creator – matches against just these three fields.
- All Fields & Tags – matches against all fields, as well as tags and text in notes.
- Everything – matches against all fields, tags, text in notes, and indexed text in PDFs (this requires that PDF indexing be enabled).
You can perform more advanced searches by clicking the magnifying glass icon at the top of the library pane. Here you can filter items by the content of specific fields, and items will only show up if they satisfy all the criteria specified. You can enter the % sign as a wild card in advanced searches, substituting for zero or more characters. For example, the search term “W% Shakespeare” will match “W Shakespeare”, “W. Shakespeare” as well as “William Shakespeare”.
When you perform an advanced search you have the option of saving the search (see image above). Saved searches are continuously updated with items matching the search criteria, so they’re a powerful way to keep track of items coming in to your library or items you’re making changes to. You can also use saved searches to do things like correcting metadata associated with your citations. For example, by selecting [URL] ‘does not contain’ [%] you can always see which items require editing to ensure they don’t miss key pieces of information you may want them to have.
Another useful way to find items is to stack tags to refine your library to specific groups of citations. For example, I mentioned the way I use status tags such as ‘To read’ or ‘Important.’ By clicking several tags you can immediately filter items, for example, to show items which important, haven’t been read yet, and are going to be useful for a particular section of your document.
Zotero can also index the text inside pdfs which you can then include in your searches by selecting ‘Everything’ in the dropdown menu next to the search bar. Go to Edit -> Preferences -> Search and select ‘Rebuild index’ to index new files.
If you’re reading huge numbers of sources and trying to summarise their contents, you might like to record your thoughts about each one. Zotero features the ability to attach notes to a citation by selecting an item and clicking ‘add note’ on the toolbar or by right-clicking on a citation.
If you prefer to use your pdf viewer app to annotate the pdf itself then you can use Zotfile’s ‘extract annotations’ feature. Make sure you save the changes to the pdf, then close it and right click on the citation, select ‘manage attachments,’ and then select ‘extract annotations.’ This works by copying all of the highlights or comments you’ve added to the pdf file and pasting them into a child note attached to the citation. One of the awesome things about this feature is, for every block of highlighted text or inserted comment, Zotfile will add a little footnote directly below it: (Author, Date:Page number). This footnote is a hyperlink, which, when clicked, will open the pdf and take you to the location in the document where the annotation comes from. Super handy!
Tips & Tricks
Some bits and pieces I’ve found useful:
1. When searching for items off-campus, I make use of Zoteros automatic proxy redirection feature. The first time Zotero sees you browsing a page through an institutional proxy (e.g. a university or work proxy to allow you access to articles), it will ask if you want to store the proxy. Zotero learns which websites you visit through a proxy. You can also add these in manually by accessing Zoteros proxy preferences and using the template to add your own.
2. Shortcuts for common operations can be changed in Edit -> Preferences -> Advanced -> Shortcuts. By default they are:
- New item: Ctrl+Shift+N
- New note: Ctrl+Shift+O
- Quick search: Ctrl+Shift+K
- Copy citations to clipboard: Ctrl+Shift+A
- Copy items to clipboard: Ctrl+Shift+C
3. When viewing the library, use the ‘+’ and ‘-‘ keys next to the numpad to expand all or collapse all citations (to see attachments). If you click on the linked attachment, Zotero will provide a hyperlinked contents section in the right hand pane if the document contains one.
4. When setting up Zotero using my cloud storage guide, individual items can be deleted by right clicking and selecting ‘view file’, allowing you to delete the pdf. The citation can then be moved to trash in Zotero. If you want to delete many items at once, the easiest way to do this is with Zotfile. Open the Zotfile settings by clicking Tools -> Zotfile preferences. On the first tab, tick ‘use subfolder defined by’ and set this to %y (year), or if you already use this option to organise your files pick something else like %w (journal name). Now select all the citations you want to remove and move them into a new temporary collection (for example ‘remove’). Now select them all and right click -> Manage attachments -> Rename attachments. Zotfile will now place all of the pdfs from these citations into the folder(s) you’ve just specified. So now it’s a simple matter of opening up your base directory and deleting these folders which were just made (which removes the pdfs), and then moving the citations in Zotero to the trash.
5. When emailing pdfs, first decide if you want your annotations and highlighting to be included. If not: Right click the citation, select ‘show file’ and make a copy of this pdf (for example paste a copy to the desktop). Open the copy of the pdf in your viewer and delete these annotations. This can be accomplished in Foxit Reader by opening a pdf, clicking the ‘comments’ button in the left hand menu, selecting the first, pressing ctrl+A (to select all) and then hitting the delete key. Close the pdf and say yes to the message prompting if you’d like to save your changes to the document. Now attach the pdf to the email message and send. In Outlook, you can drag and drop the file in, or drag and drop the pdf link from within Zotero.
Thats the end of the guide! Thanks for reading, and hopefully you found it useful. Still have some questions? Know a way I can improve the guide? Please let me know in the comments below, or by tweeting me @TomSaundersNZ.