Zotero tips & tricks
This page contains practical information you need for using the Zotero system for collecting and organizing references and using them as citations in documents.
The page is found at the URL http://wiki.bio.dtu.dk/teaching/index.php/Zotero_tips_%26_tricks.
Any questions or comments should be addressed to Henrik Nielsen, firstname.lastname@example.org.
First, you have to install Firefox as a browser (but it does not have to be your default browser). Then, using Firefox, you go to the Zotero homepage (http://www.zotero.org/) and click the download button.
After restarting Firefox, click the "zotero" button in the lower right corner to open the interface (if you think it takes up too much space, it can be changed to a single "Z" using the Zotero preferences).
- Under General/Miscellaneous select "Automatically attach associated PDFs and other files when saving items" — this is one of Zotero's strongest features, don't miss it.
- Under General/Miscellaneous deselect "Automatically take snapshots when creating items from web pages" — if this is on, you needlessly include hundreds of small files in your library. Take snapshots manually when needed.
- Under Search, install pdftotext and pdfinfo — these are necessary for retrieving metadata from PDFs.
- Under Advanced/OpenURL, enter the Resolver address "http://sfx.cvt.dk.globalproxy.cvt.dk/sfx_local" and set Version to "1.0" — this is necessary for using the Library Lookup function.
One more customization is recommended:
- Click the button above the right pane, choose "Manage Lookup Engines..." and in the window that pops up, double-click "Google Scholar Search" and click OK.
Getting information into Zotero
There are (at least) five ways to get references into Zotero:
From a web page with a site translator
When Firefox displays a page for which there is a "site translator", there will be a Zotero-derived symbol in the address bar. The appearance of the symbol will depend upon the type of item that will be generated from the page — if it is an article, it will look like this: . Click it, and an article item is automatically created.
Sites with "site translators" capable of generating references include:
- NCBI Pubmed abstract pages .
- NCBI Pubmed search results (all displayed items will be saved with one click).
- Article abstract pages from most scientific journal websites . If available, the PDF will be downloaded as an attachment.
- Note: if the paper is not open access, you need to log in with the DTIC proxy bookmarklet.
- Note: for some journals (e.g. J. Biol. Chem.), you need to be on the abstract page for the PDF saving to work, while NCBI Pubmed will refer you to the full text page. Click "Abstract" before you click the symbol in the address bar.
- Web of Science abstract pages .
- Google Scholar search results .
- Amazon book pages .
Note that some sites that do not harbour literature references nevertheless have Zotero site translators. This includes, e.g., Flickr picture pages , where the site translator gives you access to download the picture (even in those cases where Flickr itself doesn't). There's also a site translator for YouTube, but it only downloads information about the video, not the actual video file.
From another database format
From a PDF
If you already have the PDF of an article, you you can add it to your database like this:
- drag the PDF file to the Zotero central window. Note: take care that you don't drop it on top of an existing entry in the database (this will make the PDF an attached item); drop it between two items or after the last item, so it becomes an item of its own.
- right-click the newly added PDF and choose "Retrieve Metadata for PDF" in the menu
then magically the naked PDF is converted to a bibliographical entry with the PDF as an attachment.
Note: this trick works by looking up the PDF in the Google Scholar database. If the article is not indexed in the database, it will not work.
From an identifier code
This trick also works if you have the DOI (Digital Object Identifier) of an article (often printed near the bottom of the first page). You can also use the PMID (PubMed ID) of an article, but this is generally less useful, since you usually would have to look this up in PubMed anyway, and then you could just click the symbol in the address bar.
Getting the PDF if you have the reference
If you have entered reference information manually or through import from another database format, you subsequently might want to have the PDF (or to get more detailed information, such as the abstract, into your database). This can be done via the "Locate" function which is accessed by clicking the button above the right pane. Click one of these possibilities:
- Library Lookup: This will open a search results page from the DTU library (if you have entered the correct OpenURL, see Customizing Zotero). Clicking the "Go" button will then, if you are lucky, lead you to the article webpage from where you can get the PDF. If the full text is not electronically accessible via DTIC (e.g. if the item is a book), the search results page will unfortunately not lead you directly to the form where you can order the item.
- CrossRef Lookup: This will often lead you directly to the relevant article webpage. You may then have to log in to the DTU library with the DTIC proxy bookmarklet before you can download the PDF.
- Google Scholar Search: This will open a search results page in Google Scholar. Try this if you cannot get the PDF by the above methods, because Google Scholar will quite often supply alternative links to the full text if it is found anywhere on the web. (Note: This is not available by default, you have to add it using "Manage Lookup Engines...", see Customizing Zotero).
Organizing your Zotero database
There is a search field above the central pane in the Zotero window. Just write (part of) an author name or a title word in the field, and the list of items will be filtered to those that contain the name or word.
There is also an advanced search option: click the button, and the Advanced Search window will open. Here, you can specify which field in the database to search. To add more fields, click the button to the right of the search line.
Note: While simple search searches only the current collection, Advanced Search searches the entire library. To search a specific collection in Advanced Search, choose "Collection" as the field and select it from the menu that appears.
You can add tags to an item by clicking the "Tags" tab in the right Zotero pane and then clicking the "Add" button.
Tags are automatically added to articles that you add using the PubMed site translator, if the articles have MeSH terms. Some journal site translators also add keywords as tags.
Existing tags in your library are displayed in the bottom half of the left pane in the Zotero window. Click a tag to filter the list of items to those containing the tag.
Collections can be used as folders to organize your Zotero database.
You add items to a collection by dragging and dropping them onto the collection pane (the upper half of the left pane in the Zotero window).
You can see the contents of a collection by clicking on it in the collection pane.
An item can easily belong to several collections. Just drag-and-drop it several times.
Note: You do not remove an item from a collection by dragging it to another collection. To remove an item from a collection, right-click the item and choose "Remove Selected Item" (or select the item and hit "Delete") while the collection is selected in the collection pane. This will not delete the item from the library.
To delete an item from the library, right-click the item and choose "Delete Selected Item from Library..." (or select the item and hit "Delete" while the library is selected in the collection pane). This will move your item to the "Trash" library. Empty the "Trash" library to free up disk space by right-clicking it and selecting "Empty Trash".
Collections can contain subcollections. To create a subcollection, right-click a collection and choose "New Subcollection" or drag-and drop an existing collection onto another collection. Note: adding an item to a subcollection does not automatically add it to the parent collection.
You add a note to a Zotero item by selecting it, clicking the "Notes" tab in the right pane and clicking the "Add" button. You can now write information about the item, e.g. which relevance the article has for your own research.
Note that the editor window that comes up is a real wysiwyg HTML-editor: you can use bold and italics, sub- and superscript, text and background colour, headings, itemized or enumerated lists, embedded links etc.
You can also create a "standalone" note as an item of its own by clicking the button and selecting "Add Standalone Note". This can e.g. be used to have a note in each collection reminding yourself of what the collection is for.
Adding and viewing attachments
There are several ways to add an attachment to a Zotero item:
- If you have added the item from a journal home page with a site translator, the full text PDF may already be added as an attachment.
- If you click the button you have four possibilities:
- Attach Snapshot of Current Page: Use this if you want to keep an exact copy of a web page as it was when you saw it. Useful e.g. for saving notes on an article from a discussion forum or a news item about the article.
- Attach Link to Current Page: This basically attaches a bookmark to your item. Useful e.g. when an article describes a web server or database that you might want to use in the future.
- Attach Stored Copy of File...: Stores a copy of a file in the Zotero database, e.g. the full text PDF, the supplementary materials, a picture of the authors, whatever.
- Attach Link to File...: If you want to save disk space, you can store a link instead of a copy, but if you subsequently move or rename your file on the disk, the link will be useless.
- Right-clicking an item gives you the same four possibilities as above.
- Finally, you can simply add an attachment (Stored Copy of File) by dragging any file and dropping it onto an item.
When an item in Zotero has one or more attachments (including Notes), there will be a symbol on the left of the item. Click it to see a list of the attachments. Double-click an item to view it in the default way (defined by your Firefox setup).
If you want to see where a particular Zotero attachment actually resides on your disk, select it, click the button above the right pane, and select "Show File". This will open an explorer window showing the file.
You can also copy a file from Zotero by dragging an attachment and dropping it onto an explorer window, an email attachment pane, or similar.
Getting information out of Zotero
Making a bibliography from one or more items
If you click a single item in Zotero and drag it to an editing window, e.g. in Word or your mail program, it will be converted to a bibliographic entry. You can also select several items by holding down Ctrl while you click, and then drag all of them to the editing window to create a bibliography.
The format in which the bibliography will be set depends on the setting in Preferences/Export. There is only a limited number of styles to choose from; if want another one, use the mechanism described below.
Via the right-click menu
Select one or more items and right-click, and choose "Create Bibliography from Selected Items...". This opens a window where you are prompted to select a bibliography style and a mode of output. There is a lot of bibliography styles to choose from; if you don't find you preferred format in the list, open "Preferences", click on "Cite" and the "Styles" tab, then click "Get additional styles...". This will open a web page where you can choose from more than 1000 styles and install one or more of them. Once installed, they will appear in the list of styles to choose from.
Instead of right-clicking items in the centre pane, you can also right-click a collection in the collection pane and make a bibliography from the entire collection.
Instead of a bibliography, you can also choose to make a report. This will create a web page with all the information in the selected items or the selected collection.
Exporting to other formats
If you want to use BibTeX, EndNote, RefMan or similar for inserting citations in your document, you can export your Zotero database or parts of it to other formats. Simply right-click one or more items in the centre pane, or a collection or the entire library in the collection pane, and choose "Export...". A window will open with an option to export to various formats. Use the format "RIS" for importing into EndNote or RefMan.
Using the Word and OpenOffice extensions
You can also use Zotero directly as a citation tool, if you install the extensions for Word and/or OpenOffice (the OpenOffice extension also works for NeoOffice and LibreOffice). You install the extension(s) from http://www.zotero.org/support/word_processor_plugin_installation . The plugins are installed as Firefox extensions, which then somehow manipulates with your word and/or OpenOffice installation.
Note: Firefox must be running while you use the extensions!
Once installed, the Zotero extension will add a new toolbar or menu (depending on platform). In the following, I will assume you have a toolbar.
When you want to insert a citation in the text, you click the button. The first time it is clicked in a new document, the Document Preferences window will open and let you choose the Citation style (the same list that you get when you create a bibliography from the right-click menu in Zotero -- remember that you can add more citation styles in Preferences). Then the Add/Edit Citation window will open and let you select which item to cite. Note that you can choose a collection to search in the left pane of the window, if that makes it easier to find what you're looking for.
If you want to cite two or more references in the same place in a document, don't insert two citations after each other! Insert one citation with multiple sources by clicking on the "Multiple sources" button in the Add/Edit Citation window, this will ensure the correct formatting.
Creating the bibliography
You can also use the button to make manual edits in the bibliography; but this should only be done in the final phase of editing, because the edited entries in the bibliography will no longer be updated to reflect changes in your Zotero database or your bibliography style. Their numbers in the bibliography will also not be updated correctly when citations are moved or deleted!
Synchronization & collaboration
Synchronization via the Zotero server
If you use Zotero on more than one computer, you will want to synchronize your database so that it is identical on all computers. You will probably also want to have your Zotero data backed up. Both these goals can be achieved with a Zotero account.
You sign up for a (free) Zotero account on http://www.zotero.org/ by following the "Register" link. Then you open "Preferences" in Zotero, click "Sync" and enter your Zotero Username and Password. Chack "Sync automatically" and your bibliography database is backed up and synchronized. To enforce a manual sync, click the button above the right pane.
If you also want to back up and synchronize attachment files in your Zotero library, there is a catch: a free Zotero account only includes 100MB of space (that could fill up quickly if you save many large PDFs). There are two solutions to this:
- Pay for a Zotero account upgrade
- Use a WebDAV server. We have an (experimental) one for CBS staff (ask me for details if you are a CBS student). Let me know if there is need for an Institute-wide WebDAV server for Zotero usage.
Synchronization via Dropbox
An alternative to using the Zotero server is to place your Zotero database in a directory that is synchronized via Dropbox. For this, you need a (free) account from https://www.dropbox.com/ and the Dropbox client installed on your computers. Then, you need to change the Zotero Storage Location to a directory under your "My Dropbox" directory; this is done in "Preferences" under "Advanced".
The advantage is that you have 2GB of space for free. The downside is that this does not give you the possibility to create group libraries (see below).
Collaboration via group libraries
If you have a Zotero account associated with your Zotero installation (see above), you can create or link to a group library by clicking the button above the left pane. This will take you to the Zotero groups page (via the login page if you are not already logged in) where you can create a new group or search for an existing group.
The groups you are a member of can be found in the bottom of you list of collections. The point is that your collaborators can now log in and join the group you have created, and you can all cite the same database.
You copy items from your library to the group libraries by dragging and dropping, just like adding them to a collection. There is a difference, however: dragging and dropping an item to a group library creates a new copy of the item, so any changes you make to the new copy will not be reflected in your own library, and vice versa.