Introduction to

Zotero

Compiled by: Dr. F. Patrick Graz, 2011

Table of Contents
1. Getting started with Zotero..........................................................3 What is Zotero?...................................................................................................4 The Zotero interface............................................................................................5 2. Developing your reference library.................................................9 Adding and removing library entries.................................................................10 More than the minimum....................................................................................14 Organizing your references...............................................................................16 Storing files with your citation information........................................................18 Storing your thoughts in Zotero........................................................................20 3. Inserting citations into texts.......................................................21 Setting your document preference....................................................................22 Inserting single citations...................................................................................23 Formatting a citation.........................................................................................24 Inserting multiple sources.................................................................................25 Inserting and formatting the list of references..................................................26 Adding styles from the Internet.........................................................................28 4. Securing your database..............................................................29 Copying your database......................................................................................30 Web-based backup............................................................................................31 5. Collaborating with others...........................................................35 Creating a new group........................................................................................36 Adding references to your group.......................................................................37 6. Appendixes................................................................................ 39 Installation of Zotero.........................................................................................40 Installation of cite-while-you-write....................................................................42

1. Getting started with Zotero

Anyone who has ever had to write a scientific or technical article will have had to cite existing, published material. At the end of the artical we would typically insert a bibliography that lists only those works that we included in the text (although we may have read many more). Sorting out a bibliography can be a nightmare when your thesis or report cites 200 articles or more. You end up spending hours ticking references off in the text and cross-checking these against the reference list. And when that is done we have to make sure that the formatting of the references is consistent... The joy is repeated when you receive comments on your work. And you have to go through the whole process again. Reference management software such as Zotero, Endnote or Refworks help us with this task. We introduce Zotero here because it is free of charge and simple to use yet fairly sophisticated.

Objectives
At the end of this section you should be able to: appreciate the usefulness of referencing software, have a working copy of Zotero installed, have Cite-While-You-Write installed, be familiar with the Zotero interface.

Prerequisites
Before you start this section, you need to have completed: have attained basic computer & Internet skills have the Mozilla Firefox (3.6 or later) installed

In this section:
What is Zotero?.......................................................4 The Zotero interface...............................................5

F. Patrick Graz

Getting started with Zotero

What is Zotero?
Zotero (pronounced zoh-TAIR-oh) is free software that helps you with the management of your references. The software does a number of things that we are going to look at further. These include: inserting references in the text you write and formatting these to specific requirements; keeping track of the references you have already cited in the text; generate and format a list of the references you have included in your text.
You can team up to create a centralized Zotero database that is accessible by your research team

You will admit that these capabilities can save you quite a bit of time in the long-run. But there are a number of further functions that are quite important: keeping notes on the references you have read the electronic equivalent of writing in the margin, retaining a set of tags, creating dynamic collections based on searches within your Zotero database, collaborating with other researchers through the web. To use the software, however, you need to enter your references into a Zotero library data base. Although this might seem to be a real drag, the effort is well worth it. My own collection amounts to well over a thousand references. Fortunately you don't have to type all the information in by hand. When you are browsing the table of contents of a journal Zotero will often recognize what you are doing and the software can be prompted to download specific citations for you.

Citation information is not the same as the article itself.

Remember, though, that you need to distinguish between the actual article and the citation information. These are not the same. So while Zotero may get the information about an article, it will not get the actual article for you.

The Zotero interface

Collections

References

Citation Inform.

When you click on the Zotero link in the Firefox status bar, the Zotero window will open, as in the above illustration. The library we show above already contains a lot of references. When you click on your new installation the three columns are going to be blank, although you may have a sample reference. In the Collections column you see a number of categories into which the references have been classified. Collections allow you to organize your references into topics. The References column presents a list of the references within the collection selected in the collections window. You can list all the references within your library by listing the contents of the collection My Library. The final column shows the Citation Information that you have collected for each reference.

In a new installation the three columns will be empty.

Getting started with Zotero Above the three columns is a set of icons most of which provide access to sub-menus. Icon colours may vary, depending on the theme you have enabled on your desktop. Managing collections / groups Managing citations Managing the Zotero window

Managing the Zotero window

The three icons that manage the Zotero window allow you to close the window (the red field with the x) or maximize Zotero within the browser window. The Zotero window is limited to the Firefox window. When you first start the add-on it may only cover the lower portion of the browser. Sometime, however, you want to use the entire window when you manage your references (As shown in the illustration below). In that case, use the centre icon.

Once you have maximized your Zotero window the Toolbars and navigation bar of Firefox also disappear. They will reappear when you restore the Zotero window (by clicking the button again) or close it.

The last icon in the group is used to synchronize your database with the Zotero server. This has two advantages: you have a backup of your reference library, and you can transfer your library to other computers via the Internet. Using the Sync functionality is a more advanced feature that we will deal with later.
You can back up your reference library to the Zotero server.

Collections & Groups

Collections permit you to sort your references into categories that have meaning to you. For instance, you are interested in Water points, in Rangeland management and in GIS. By assigning your references to different collections you are able to keep them organized, almost as if you were stacking books of similar subject matter in a bookshelf. Groups on the other hand permit you to share your reference collection with other people who have similar interests. Those people who are members of a group will be able to copy and may even update the references. This is useful when you are collaborating with other researchers. Working with Groups is also a more advanced feature that we will deal with later. Now that you have an idea of what you are working with, have a browse through the various menu options. We are going to deal with a number of them, but some you will need to explore yourself.

Getting started with Zotero

2. Developing your reference library

Once you have installed the Zotero extension it is time to start adding references to the database an empty database is of little use. In this section we show you various methods that you can use to add the citation information. Here we show you three possible methods of data entry - all three have their uses. We can not overemphasize, though, that you need to cross-check any data you download from Internet sources a number of journal home pages seem to have their own format of serving the citation data and these may not be directly compatible with Zotero. You need to make sure that it is consistent with your database. This is not difficult, and does not take much effort. And it is well worth the trouble.

Objectives
At the end of this section you should be able to: Add items to your Zotero library

Prerequisites
Before you start this section, you need to have completed: the installation of the Zotero extension in Firefox.

In this section:
Adding and removing library entries....................10 More than the minimum.......................................14 Organizing your references..................................16 Storing files with your citation information...........18 Storing your thoughts in Zotero............................20

F. Patrick Graz

Developing your reference library

Adding and removing library entries

Your citation information is the core of your Zotero Library. It is therefore, of the utmost important to manage this information carefully make sure that your entries are correct and that you have all what is necessary. As we have already alluded to previously you can enter references in a number of different ways. We are going to look at three approaches, specifically: entering citation information manually (using the keyboard); downloading citation information; downloading entire reference lists. Later on you will note that you can also add references from shared libraries to your own list simply through drag& drop.

Entering reference information manually

To add a new reference manually, select the New Item menu (see margin). Here you will already see a list of the most commonly used types of information resources, for example journal article. If you select the More option you will obtain a list of all the types of material that the Zotero library can support. Let us work through an example and add the following reference information to your library: Hardy, M. B., Hurt, C. R., & Bosch, C. H. (1999). Veld condition assessment. In N. Tainton (Ed.), Veld Management in South Africa (pp. 194-206). Pietermaritzburg, South Africa: University of Natal Press. In the New Item Menu select Book Section from the list. You should now have an empty template in the right most column, similar to the one shown in the margin. (Also note the four tabs at the top.) Move your mouse to the grey space next to the word title and you should see a highlighted field. Now click in the highlight and add the title of the 10

Empty template for a new journal article

article. Make sure that you enter the text in Sentence Case, i.e. only the first letter and names are capitalized. To add the first author you click on the author field last to enter the last name, and first to enter the author's first names and / or initials. Authors may have more than one initial. These initials should be separated by spaces. If you don't do this then Zotero will only provide the first initial when you try to generate a reference list. The second (and any additional) author can be added by clicking on the + sign following the author you entered. Make sure, though, that you retain the same order of authors as shown on the document you would cite. To add the editor of the book section you are entering, you would first add the person as an additional author. You then select the down-arrow preceding the word author and obtain a list of different author types. From this list you select 'editor'. The illustration in the margin shows an example of the completed citation for the book section we provided above. Then add all the other information you have, but enter as much of the citation information as you can. For a journal article the absolute minimum should be the : title, author, publication name, volume, pages, and date.
Separate initials with a space

There are different types of authors

Be aware though, that some journals require additional information in their references, for instance the issue number or DOI number or a journal abbreviation. In those instance you would have to add this information later, when you want to publish with one of these journals.
Completed citation for book section.

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Developing your reference library

Downloading citation information

Publishing houses now provide journal articles on the Internet and allow you to download the citation information. Sometimes this is referred to as Exporting the citation.
NOTE: As we indicated previously, the importing of citations is not without errors. Some journals import well, others don't. So whenever you have downloaded the information you will need to check if the information was placed into the correct fields.

To download citation information for individual journal articles you access the to the repository in which the journal is kept (In the example below an article in Ecohydrology is on Wiley Interscience.). When you look at the abstract page a new icon may appear in the navigation bar (a white page, circled)

To download the information, simply click on the icon and Zotero will create a new record in your database.

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If the icon is missing see if you can find a link on the page to export the citation information. Make sure that you check anything you import. But if all else fails you will need to revert to manual entry you will find that copy & paste is a wonderful tool-set.

Select the formats Procite or RIS if you are prompted to choose.

Downloading reference lists

Sometimes you want to import the citation information of more than one article a single journal issue of a journal, or even all its entries. To do so, navigate to the table of contents for the particular issue in question. A new icon may now appear in the navigation bar (yellow folder shown below).

Clicking on the icon will call up a list of the articles in the particular issue. Now select the articles that you are interested in (all of them, if that is what you want) and press OK.

All the identified references will now be copied to your Zotero database. Again, it is essential for you to ensure that the import was accurate.

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Developing your reference library

Deleting library entries

In some cases it is necessary to delete entries from your library. For instance, you found that you have duplicated information, or you want to remove a note. To delete any library entry you right-click on the entry and select Delete Selected Item from Library... from the context menu.

More than the minimum

So far we have only considered the actual citation information. But this is the bare minimum of what you need. Consider, for instance, that you also want the keywords that are listed with articles. Such information, as well as any notes you might want to keep about an article, are stored under the tabs

Enter keywords - tags

Keywords are an important component of any citation library. They help you FIND your references again!

Most journal articles provide you with a list of keywords that are applicable to the specific contents. These keywords can be included in the Tags tab. Keep each of your keywords as a separate entry this has two advantages: 1) When you enter keywords manually Zotero will try to recognize what you are typing and suggest existing keywords. This helps you to develop a certain consistency. 2) When you want to search your database on the keywords, the individual tags permit you to refine the search. Unfortunately the tags often need editing when you downloaded the citation information you will frequently find that they are provided in a single entry, only separated by a semi-colon or a comma. You will need to separate them manually.

Keeping notes with your citations

The Notes tab provides you with space to keep your own ideas about a specific article it's like keeping notes in the margin of a printed copy. For example, your article contains an interesting figure or table that you might want to refer to later. You 14

could then create an entry in the Notes to help you remember where to find it. Similarly, a term or concept might be defined by the author (for instance the concept of piosphere was coined by Lange in 1969). You obtained the article and now copy out the exact definition into a note, together with a page number, so that you don't have to go searching for it within the article. The following figure shows an example of a citation with three notes attached to it. The notes can be edited at any time.

It is very important to remember that Zotero allows you to search all your notes you don't have to remember what article contained the definition of the piosphere if you have copied it out in a note Zotero can find it for you.

Linking related articles

The final tab, Related, allows you to link two articles. For instance, you have citation of the original of a specific sampling method. that another person has modified. You may then relate the two articles. Consider, for instance, that the Braun-Blanquet system for estimating cover abundance was first published in 1932. Later the system was modified and published by Sutherland in 2006. You may now link the two citations so that you can refer back and forth with ease. Alternatively you have two articles that seem to concur, or contradict each other, and you want to remind yourself of the existence of this relationship. Zotero also permits you to relate an article to a note in another. To relate two articles simply click on the add 15

Developing your reference library button in the Relate tab of the first article and select the related one Zotero will insert the relate you specify, as well as the reverse relate.

Organizing your references

So far we have only looked at getting citation information into a library, but it's all in one big heap called My Library. This makes it a little difficult to find the references you might want to work with. To some degree you can use your Tags to organize the library, but it would be easier if you could establish groupings of references. This is possible in two ways, either by using collections or by using saved searches. Both have their advantages.

Collections
A collection is very much like a folder that you might create on your computer system. Actually, the icon that marks a collection looks like a folder. But there is an important difference between collections and folders. A citation can belong to more than one collections without it needing to be stored twice. So once you have the citation information you can add it to as many collections as you like and not worry about having to keep the information synchronized. For example, you have a reference on modeling the impact of water-points in savanna rangelands. You might have a collection for citations on waterpoints, one for savanna related information and one for modeling. Which collection is the most suitable? Well, since you can assign the same reference to many collections you don't have to make that decision. To create a new collection you would simply click on the icon and you will be prompted to supply a name for it. Once you click on the OK button the collection will be added under My Library and Zotero will move to it. Since the collection is new it will of course be empty. You can now either add new citation information directly within the collection, or you can drag-and16

drop existing citations into it. If you choose to create new citations within the group you will also find it under My Library from there you can drag it to any other.

Saved searches
Saved searches are very much like an automatic collection. While you need to decide what to include in a collection and move the relevant citations into it, saved searches use specific criteria to do the job for you. Let us use the example on modeling the impact of water-points in savanna rangelands again. If you have added tags on modeling, water-points and savanna to the citation information you can use three different saved searches rather than collections. Why bother? Well, the saved search is updated from My Library every time you click on it. This means that any new citation that you may have added and tagged accordingly will automatically appear in the group. But there is more! Zotero can be told not only to search the tags for your search criteria, but also the title, abstract and any notes you have stored as part of your library. To create a new saved search right-click on the My Library and select New saved search. Enter a suitable name and set the search criteria. To add more criteria you simply click on the plus sign at the end of a line, and to remove a criterion click on the corresponding minus sign.

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Developing your reference library

Storing files with your citation information

Consider that you may have started collecting a lot of material, such as .PDF files containing journal articles, image files containing maps or other electronic files. As you continue studying and reading these files accumulate and you end up developing a custom folder structure so that you can find the files again. This works well for some people, if they continuously interact with their folder structure. Once you get started with your reference library you may want to save the documents and the citation information together. This means that you will not be required to keep track of folder structures and file names. Zotero permits you to store a copy of an existing file as part of the library. The software creates a folder called Storage in the directory in which you keep your database. Then for each file you add Zotero will add an additional subfolder and link it to your citation information. These folders have very strange names a code. This means that when you store a file as part of library then the easiest way to retrieve it is through Zotero. Alternatively, you can retain your folder structure and simply tell Zotero where to find your files. Zotero then only stores the path and name of the file. To store a file with your library or link to it you need to have a copy of the file already on your system (or an accessible network drive).

Now, click on the paper-clip on the toolbar and you will be given the following options:

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Attach snapshot of current page: Will copy the page you are currently viewing in your browser into your Zotero library. Attach link to current page: Will copy a link to the web page you are currently viewing in your browser into your Zotero library. Attach stored copy of file... Prompts you to select a file on your system that will be copied to the storage folder within your library. Attach link to file... Prompts you to select a file on your system to which Zotero will store a link. Select the option you want and simply follow the prompts. When you have selected the file (or web page) Zotero will add a marker (a plus-sign) to your entry.
Important Note If you store links to a file on your system you need to make sure that this link will always remain in tact. If the link is broken, then Zotero will not be able to locate the file for you any-more. This can happen when you rename or move a folder! If you have to switch between Windows and Linux installations then you should keep copies of your files in Zotero rather than link to files. The two operating systems have different naming conventions for folders and you will only see the files in the operating system under which you created the link!

Changing the name of a stored file

When you have stored a copy of a file with your citation information you might want to change its name to reflect the author's name and contents. This is useful if you are exchanging files with other researchers. To change the name of the file you would rightclick on the name of the file and select: Rename file from parent meta-data
If you share files you need to remember copyright issues.

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Developing your reference library

Storing your thoughts in Zotero

You may, in the past, have kept notes on a specific subject while you were developing your thoughts towards a research project or report. At this stage you might have started a new document, but without references. Unfortunately you might only remember some aspects of your thought, but can not remember where you stored it, or what the file name was. Since Zotero can be used to search your library for articles based on your notes and keywords, you might want to store such thoughts in your Zotero database. Just as you can add a note to an article, you can also keep searchable notes in your library.

Select the New Note item on the main toolbar and select Add standalone note. Zotero will add a new note at the bottom of your library. This note can also be linked to existing references. So, while your are developing your thoughts you can already start selecting certain references that might be relevant.

Viewing your copied or linked file

To view the file that you have stored with your citation you may either double-click on the citation in central pane or expand the plus sign and doubleclick on the file name. Alternatively, right-click on the citation information in the central pane and select View PDF.

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3. Inserting citations into texts

So far we have only dealt with the development of the Zotero database or citation information. This is important in itself, as you would not be able to continue with the next section which is to cite. In this section we deal with the features related to the adding of citations to a document you may be working on. We then show you how you use Zotero to compile a list of references for you only including the references you actually cited. Cross-checking the reference list/bibliography and citations in the text can be very time consuming. I recall the hours I spent on cross-checking my M.Sc. Thesis (that was before reference management software was readily available). The examples that we provide here will be based on OpenOffice.org Writer but the tasks are identical when using LibreOffice or MS Word TM.

Objectives
At the end of this section you should be able to: insert and format single citations in a document, insert and format multiple citations in a, document, and create a list of references

Prerequisites
Before you start this section, you need to have completed: the establishment of a Zotero (sample) database the installation of the word-processor plugin.

In this section
Setting your document preference.......................22 Inserting single citations.......................................23 Formatting a citation............................................24 Inserting multiple sources....................................25 Inserting and formatting the list of references.....26 Adding styles from the Internet............................28

F. Patrick Graz

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Inserting citations into texts

Setting your document preference

Before you start inserting a lot of references you may want to choose the citation style in which the references are to be formatted. Different disciplines and journals have different preferences. For instance, APA is very popular in the arts and humanities, while other citation styles may be more frequently used in the sciences. The document preferences permit you to set parameters for every new document that you create, but also for existing documents that you want to add citations to. Zotero remembers the settings you used previously and suggests them as the default setting for the next document you create. This is useful if you have a consistent preference. Open a new text document and click on the circled icon on the Zotero toolbar to open the Document preferences dialogue box, as shown below.

APA is the prescribed reference style at UNAM

Here you can specify the citation style you want to use (highlighted here is the Chicago Manual of Style (Autor-Date format)) Then, depending on the word-processor you use, and the interoperability you require between users of OpenOffice.org or MS Office you need to specify if you are going to use Reference Marks or 22

Bookmarks. (Reference marks permit you to edit your citation format, Bookmarks do not allow you to do this readily) Once you have chosen your basic settings, select OK and you're done. The preferences are not set in stone, but can be changed. For instance, you might decide that you want to use a different citation style (say, change it to a Harward style) or you need to improve interoperability between word processors.
Settings can be changed

Inserting single citations

Now that you have set the preferences for your document you are ready to insert citations. When you have reached a point where you want to insert a reference click on the Insert Citation icon to open the Add / Edit Citation dialogue box as shown below.

To insert a citation select the one you want and click OK. The citation we selected in the box above would have produced - (Folgarait 1998) - in accordance with the rules of the Chicago Manual that we selected in the citation preferences.

If you want to have a look at the reference list that you could already create with one reference, skip to the last section. - but come back here to learn more about formatting.

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Inserting citations into texts

Formatting a citation
Sometimes we want to format the citation a little differently, for instance we want to add a page number or prefix the name with something (say: 'see also'), or only have the year in brackets. To do so, you may either edit an existing citation or modify the citation as you enter it. If you want to edit an existing citation move your cursor on to the citation in question and select the Edit Citation icon on the toolbar. This opens the same dialogue box you used to insert the citation in he first place (as we have shown on the previous page). Now select the Show Editor option to open the citation editor - your dialogue box should now look as follows:

You can now, for instance by adding page numbers or prefixes in the fields provided above the editor. Why don't you try the following: add the word See into the prefix field, add the number 1230 into the Page field. As you type, you should see the changes appear in the editor.

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While you can change settings in the Editor you should avoid doing so, as this removes the link between the Zotero database and the citation. This means that changes to the citation style will not be updated in the text, only in the reference list. If you do need to make modifications, however, you can always come back to this before you submit the document.

Although you can edit manually, try to avoid doing so.

Inserting multiple sources

In some cases you may want to cite a number of different authors to support a particular point. Select the Insert Citation icon and open the dialogue box again. Then select the Multiple Sources option. You may then select the references from the list and add them to list to be cited using the arrow (circled in the illustration below). To remove a citation from the multiple sources list, select the source in question and use the arrow pointing to the left. In the illustration we have already added two authors and selected the Show Editor option to show the effect. You may prefix the individual citations and add page numbers to them as you did previously. To do this select the entry in the right hand column and add the information you need in the relevant fields.

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Inserting citations into texts

Inserting and formatting the list of references

Once your document is complete you can generate a reference list or bibliography using the Insert Bibliography option on the toolbar. We have generated a sample of such a reference list using the Chicago Manual we initially chose when we set the preferences.
Belnap, J. 2006. The potential roles of biological soil crusts in dryland hydrologic cycles. Hydrological Processes 20, no. 15: 3159-3178. doi:10.1002/hyp.6325. Folgarait, P J. 1998. Ant biodiversity and its relationship to ecosystem functioning: a review. Biodiversity and Conservation 7, no. 9: 1221-1244. doi:10.1023/A:1008891901953. Graz, F. P. 2008. The woody weed encroachment puzzle: gathering pieces. Ecohydrology 1, no. 4: 340-348. doi:10.1002/eco.28. Stafford Smith, D.M., and S.R. Morton. 1990. A framework for the ecology of arid Australia. Journal of Arid Environments 18: 255-278.

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However, you may not be satisfied with the formatting, and now decide to use a different style. This you can do by changing the preferred style in the document preferences. For instance, the same list as above formatted for the journal Basic and Applied Ecology would look like this:
Belnap, J. (2006). The potential roles of biological soil crusts in dryland hydrologic cycles. Hydrological Processes, 20, 3159-3178. Folgarait, P. J. (1998). Ant biodiversity and its relationship to ecosystem functioning: a review. Biodiversity and Conservation, 7, 1221-1244. Graz, F. P. (2008). The woody weed encroachment puzzle: gathering pieces. Ecohydrology, 1, 340348. Stafford Smith, D., & Morton, S. (1990). A framework for the ecology of arid Australia. Journal of Arid Environments, 18, 255-278.
The style is not in the default list of styles, but can be added from the Internet

In some cases you may want to (or need to) add citations even after you have generated the list. This is easily done actually Zotero does the task for you. Every citation you add after the reference list is generated will automatically be inserted into it in the correct place. Similarly, any citation you remove will also be removed from the list.

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Inserting citations into texts

Adding styles from the Internet

While some journals use existing, standard citation styles, others have their own. Also, some universities require their students to cite only in APA or only in Harvard or Chicago styles.

What styles are installed

When you install Zotero you also add a number of predefined styles. To see which ones you already have go the Preferences (actions menu), select Cite and the Styles tab.

Installing additional styles

Additional citation styles are available on the Internet at: http://www.zotero.org/styles from where they can be downloaded freely. If you navigate to this page you will find a bulleted list of the available styles for particular journals. For instance: Ecology [Install] (2010-07-26 02:21:30) Ecology Letters [Install] (2010-09-11 04:14:37) Ecoscience [Install] (2010-07-26 02:21:30) When you hover the mouse over the name of the journal you will be provided with an example of what the citation would look like. You can use Zotero to do the installation and follow the hyper-link provided under the Styles tab (Actions menu Preferences - Cite ). This will take you to the exact same page. Select the style that you are interested in and click on the install hyperlink opposite it. You will be prompted to confirm the installation. If you are using a computer on which Zotero is not installed, you can type in the URL in any webbrowser. You would then right-click on the Install option across the style you are interested in and select Save link As... or Save Target or similar, depending on the browser you use, and save the relevant .csl file. You will now, however, need to copy the downloaded file to your Zotero styles collection.

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4. Securing your database

So far we have shown you how to create your own data-base and how to use the cite-while-you-write functionality. These are, for most users, the most important features. Just think how frustrated you would be if you lost your library...

Objectives
At the end of this section you should be able to: create a user account on the Zotero servers Sync your files over the internet.

Prerequisites
Before you start this section, you need to have completed: creating your own data-base, have access to the Internet.

In this section:
Copying your database.........................................30 Web-based backup...............................................31

F. Patrick Graz

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Securing your database

Copying your database

Where is my reference library stored
The location in which you store your Zotero library is not quite a trivial issue you need to know where it is so that you can keep a backup copy. To find the files associated with your library you should select Preferences (Actions menu) and Advanced option. Near the top you will find a button: Show Data Directory. Clicking this button will open a file browser on your system and show you all the folders and files that are associated with your reference library. Typically the folder would contain:
You need to copy all these files and folders to your backup folder.

locate, storage (documents you stored in your library), styles (the citation styles you have installed), translators (filters to download references),

and a series of files starting with zotero.sqlite with various extensions. The file zotero.sqlite is the file that contains your library. The files that have a number followed by .bak are backup files that Zotero generates automatically. If you want to back up the library you must copy all these files and folders to your backup device or folder.

Changing the library location

Zotero give you the option to change the location of your library. You might want to do this because you have a scheduled system backup. Or you might want to store your library on a network-drive that is backed up centrally. To prepare the new data location directory, go to the folder under which you want to store your library and create a sub-folder called Zotero. If you already have data in your library you need to copy all the folders and files across to the new location (see previous section). You should do this before you restart Firefox otherwise Zotero will create the necessary file and folder structures automatically. 30

Now select the Custom radio button under Preferences (Actions menu) and Advanced and browse to the new folder. Click OK to select the new location. The next time that you start Firefox it will point to the new location. If you copied your files across then your existing library will be visible when you start Zotero.

Web-based backup
However, you may reach the stage where you have several computers running your Zotero library at work and at home. Which one was the most current? Did you change things on both workstations? Synchronizing the individual installations will address this problem, and will make sure that the most current version of each database entry can be found. We will now work through the Sync functionality that permits you to back your data-base to a server on the Internet. From there you can install it on any other machine that is also connected. Storing your database on the Zotero server is free just like the software but requires you to create an account at Zotero. If you have linked .pdf files to your data-base entries then the amount of disk space that is available to you will not be sufficient in the long-run.
Syncing also gives you the entry point into working collaboratively. linking to existing groups and creating your own.

Setting up your Zotero account

Creating your own account in Zotero is a relatively simple process, since most of the procedure is guided by a series of prompts. Open up the Zotero preferences through the Actions menu, and select the Sync options (shown below). The image below shows a (fictitious) person who already has a user account. Click on the Create Account hyperlink to open a new Firefox window at: http://zotero.org/user/register where you create the account. Fill in the information that is requested, and register.

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Securing your database

Make a note of your user name and password!

Make a note of your user name and password!!

You will be sent a registration key by email, to confirm the registration process. The email will prompt you to follow a hyperlink if you click on it you will automatically complete the registration. Once your registration is complete you will need to enter your Zotero user-name and password into the Sync preferences (in the figure above). But there is more to do before you synchronize your account.

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Setting the Sync preferences

Before you start the Sync function for the first time you may want to consider the settings. In the Settings tab all options are ticked. This option set may require a long time to Sync. So consider what your needs and limitations are - a slow Internet connection can be frustrating if you have selected a set of options that requires a lot of uploading or downloading. Sync Automatically This setting prompts the software to sync every time you open the Zotero window. Initially this may seem irritating, especially if you have a slow Internet connection. However, the value of Sync is that you always have a copy of the most current version of your database on the Internet. Sync Attachment Files in My Library using... This means that all attachments in your personal database would be copied to the Zotero server. While this is not a bad thing to do, you may quickly run out of server-space. Depending on your needs, you are able to purchase additional server space so consider if this is necessary. Sync Attachment Files in Group Libraries... The final setting in this tab permits you to Sync attachments in Group libraries. While this may seem to be an attractive option to swap information with other users, remember that the material you make available may have a copyright.

Click on the Sync icon to synchronize manually

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Securing your database

Resetting
You should use this option with care!

The options provided here permit you to recover your database from the server if it has been corrupted.

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5. Collaborating with others

So far you have worked more or less in isolation from other researchers. But think of the advantages if you could copy the references prepared by others, and share your effort with them at the same time. Consider for instance that you may be part of a research group with similar interest. It is then likely that you will refer to similar material. In such instances it would make more sense to have a combined repository of all the citations any newcomer can link into the repository. In this section we are going to show you how to prepare a library that you can share with others.

Objectives
At the end of this section you should be able to: Create a group account in Zotero

Prerequisites
Before you start this section, you need to have completed: establishing a Zotero user account (Sync)

In this section:
Creating a new group...........................................36 Adding references to your group..........................37

F. Patrick Graz

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Collaborating with others

Creating a new group

Creating a new group is a relatively simple matter, but you can do this only if you already have a user account on the Zotero server. Clicking on the New Group icon (circled) will take you to the Zotero user page, and you will be prompted to log into your account. Complete the login. You will now be prompted to create a new group, as shown below. The group that is created in the example below is called Rangeland Management and is open to all Zotero users (Public, Open Membership). Initially, however, you might want to consider creating a group with Private Membership. You can change the setting later to Open, Public Membership once you feel more comfortable.

Click on Create Group to proceed to the settings page. Here you are able to change the name of your group (say, for instance that you detected a typing mistake) and indicate what sector you work in. This makes it easier for others to find your group. You will also note that you can change the group type.

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Select the settings that are most appropriate for your specific case or conditions. Once you have saved the settings, look at the Library tab in the browser window. Here you will be able to set the general access to your group. The Members tab shows you the people who have joined your group. This screen allows you to set the functions that group members may take either as Member or as Admin. While you were editing the various settings you may have noted that your group was added to the left hand Zotero window. The time interval between you creating the group and its appearance in your Zotero window will depend on your Internet connection.

Adding references to your group

Once your new Group Library appears in your Zotero window you can start adding references. This is done through a straight forward drag-and-drop from your existing records. creating a new entry directly into the group library. You will need to determine which is the most appropriate. Although it is tempting to store your references on the Internet directly, it is important to make sure that you have your own copy. What would you do if you had difficulties with your Internet connection or service provider? Consider also that you may have given write access to other group members who may destroy a reference by accident or change it to something that you don't agree with (and this you could find out too late). It is therefore useful to create a collection of references that you can then drag-and-drop into the group folder. Keep in mind though, that this would overwrite the changes other group members have made! So be careful! 37

Collaborating with others

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6. Appendixes
Installation of Zotero............................................40 You need Firefox before you can run Zotero.....40 Online Installation of Zotero..............................40 Downloading Zotero and installation offline.....41 Installation of cite-while-you-write........................42 Online installation.............................................42 Downloading extension and installation offline... . 42

F. Patrick Graz

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Appendixes

Installation of Zotero
You need Firefox before you can run Zotero
Since Zotero is an add-on of the Mozilla Firefox web browser you need to have a working copy of the browser installed before you can proceed. This is not part of these notes, but the installation is very simple. The steps can be found on the home page of the software www.mozilla.com. The software is free so you don't need to worry about potential costs or licensing. There are two possible approaches to installing the Zotero extension. Either directly over the Internet, or by downloading the .xpi file and then through a simple drag-and-drop.

Online Installation of Zotero

When Firefox is installed go the Zotero home page at: www.Zotero.org and select download This will download the file to your computer and start the installation. The image on the right is the prompt you should obtain. Once you click the Install Now button, Zotero will be installed within Firefox. When restart Firefox you should see the word Zotero in the bottom right hand status bar of your open browser window, as we show on the next page.

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Zotero home page with the extension already installed.

Downloading Zotero and installation offline

If you want to install Zotero on a computer that is not attached to the Internet, you will need to download the extension, transfer it with a memory stick and continue with the installation offline. Using any web browser continue to the Zotero home page at www.Zotero.org. Download by right-clicking on the download button. Your browser will pop up with a menu where you select Save Link as or Save Target as (or similar) to store the extension somewhere on your computer or memory stick. You now need to transfer the file to the computer on which you want to install the software. Open Firefox as well as the folder containing the Zotero extension. Now simply drag-and-drop the extension into the main browser window. You will then be prompted, to verify what you want to do, and restart Firefox to finalize the installation. You can now start using the Zotero add-on to develop your database. But there is more...

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Appendixes

Installation of cite-while-you-write
Without the word-processor integration add-on you will not be able to utilize the more interesting features of the reference manager, i.e. inserting your references into your document and to generate the reference list. Therefore, the second thing you need to install is the link between Zotero and your word-processor. On the Zotero home page and follow the link Download Word-processor plugins and select the extension relevant to your word processor When you have completed the installation of this extension, it will appear as though nothing has happened. However, when next you open your word processor you will find an additional toolbar (shown on the right), In MS Word 2007 the toolbar will be provided under the Add ins tab.

Online installation
As above, you have the option of installing directly over the Internet (online), or downloading and then installing. To continue with the online installation navigate to: Download word processor plugins on the Zotero home page and then the link showing your wordprocessor. Click on the link to start the downloading and installation. The procedure will then proceed in a manner similar to the one we described for the main installation of Zotero.

Downloading extension and installation offline

On the Zotero home page and follow the link Download word processor plugins, and find the extension relevant to your word processor For the off-line installation you need to right-click on the link and save the extension to your hard disk or memory stick. As above, drag-and-drop the .xpi file into an open Firefox window, and follow the prompts.

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