EPFL DIT

zoterocollecting | managing | sharing | citing

referencesmade easy

Raphaël GrolimundBibliothèque de l'EPFL December 2013

CreditIcons from the Zotero interface are produced in this document. They were cerated by MarkJames and Yusuke Kamiyamane and published under CC BY license on the author's websites:Mark James (http://www.famfamfam.com/)Yusuke Kamiyamane (http://p.yusukekamiyamane.com/)

About this documentCourse notes of the lecture given at EPFL on December 9 and 11, 2013.Course organized by the EPFL IT Department: http://dit.epfl.ch/training

Document versionv1.2 / 9.12.2013

You have the right to reuse the content of this document butderivative works should be published under CC BY-SA license. Inevery case, you should credit this document with my name and thename of the library. For further information about the license, see linkbelow.

Zotero: collecting, managing, sharing, citing references made easy byRaphaël Grolimund is licensed under a Creative CommonsAttribution-ShareAlike 4.0 International License.

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PROGRAM

Here is an overview of the course. This is more a thread than a real program.

Discover

Install

Collect Import

Setup

Manage Share

Create

More

Cite

First part of the course: Second part of the course:

Discover CreateInstall SetupImport ShareCollect CiteManage

The More section gathers some questions that go beyond the scope of this course, but thatcould be useful.

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DISCOVER

What is Zotero?

Zotero is a reference manager. It helps you collect bibliographic references, store and sortthem and manage a bibliography effortlessly.And if you are writing a paper, Zotero makes citing very easy.

Zotero has first developped as a Firefox add-on. Since January 2012, Zotero is also providedas a standalone software with exactly the same interface, but with additional compatibilitywith Chrome and Safari.

Zotero is developped since 2006 by the Center for History and New Media(http://chnm.gmu.edu/) at George Mason University (http://www.gmu.edu/), Virginia (USA).

A brief history of ZoteroOct. 2006 Zotero beta versionOct. 2007 Zotero 1.0Feb. 2010 Zotero 2.0 (sync and share features)Mar. 2011 Zotero 2.1 (Firefox 4 compliant)Jan. 2012 Zotero 3.0 (standalone version, Chrome & Safari compliant)Apr. 2013 Zotero 4.0 (major improvements with new features)

Zotero is (and has always been) a free software. Free doesn't (only) mean it's free of charge, italso means that no one owns Zotero.First developped under ECL license1, Zotero switched to GNU GPL v32 when the version 2.0was released, before switching a second time to GNU AGPL3 (version 2.1.7).

You can expect from a reference manager to :* add/import references automatically (or very easily)* create a bibliography automatically (or very easily)* help you cite while you write a paper

All these technical tasks should be done by the software. You save time for things thesoftware can't do for you:

* check if the reference data are correct and complete* read papers* sort references* select relevant references to add in the bibliography

It is important to understand that this kind of software is made to manage references, notitems. It is not means for managing a private library (with functionalities for borrowingdocuments).

Why Zotero ?

There are many reference managers. A comparison of reference managers is avaiblable onWikipedia4.

1 http://opensource.org/licenses/ecl2.php (accessed Dec. 5, 2013)2 http://www.gnu.org/licenses/gpl.html (accessed Dec. 5, 2013)3 http://www.gnu.org/licenses/agpl.html (accessed Dec. 5, 2013)4 http://en.wikipedia.org/wiki/Comparison_of_reference_management_software (accessed Dec. 5, 2013)

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Here is comparison table of the 5 most used software at EPFL.

BibTeX EndNote Mendeley Papers Zotero

free$329 (indiviual)paid by EPFL

free 59€ / $79 free

Free Proprietary

owned byThomson Reuters

Proprietary

owned byElsevier

Proprietary

owned bySpringer

Free

WindowsMac OS X

GNU/Linux

WindowsMac OS X

WindowsMac OS X

GNU/Linux

(Windows)(1)

Mac OS XWindowsMac OS X

GNU/Linux

integrated with

LaTeX

integrated with

MS WordOOo / LO

LaTeX

integrated with

MS WordOOo(2) / LO

LaTeX

integrated with

MS WordOOo / LO

LaTeX

integrated with

MS WordOOo / LO

LaTeX

N/A5Go

online storage incl.1Go

free online storageN/A

300Mofree online storage(3)

N/ASharing throughEndNote Web

unlimitedopen groups

-one

private group(4)

N/A

unlimitedopen groups

-unlimited

private groups

N/Athree

group members(4) N/Aunlimited

group members

N/A 5'000 citation styles(5) 6'700 citation styles(6) 6'700 citation styles(6) 6'700 citation styles(6)

OOo / LO stands for OpenOffice.org and LibreOffice(1) We don't recommend to use Papers for Windows (v1.5). It lacks important features included in Papers for MacOS X (v3).(2) On Mac, the OpenOffice plugin has been dropped in favor of support for LibreOffice5.(3) For more storage, see Zotero Storage Settings (login required)6.(4) For more storage, see Mendeley storage plans (login required)7.(5) http://endnote.com/downloads/styles (accessed Dec. 5, 2013)(6) http://zotero.org/styles (accessed Dec. 5, 2013)

So why Zotero? First, because it's free. You don't have to pay for it, but most of all you canhelp improve it (and you don't need to be a programmer to do it8). The community aroundZotero is huge and active.There are two more reasons to choose Zotero: it is user-friendly, powerful and compatiblewith a large number of online resources and, as a free software, you will be able to use it evenafter leaving EPFL (no restriction due to the license agreement).

5 http://www.mendeley.com/release-notes/v1_5/ (accessed Dec. 5, 2013)6 https://www.zotero.org/settings/storage (accessed Dec. 5, 2013)7 http://www.mendeley.com/upgrade/ (accessed Dec. 5, 2013)8 You don't need to be a programmer to help. You can report bugs, request new features or translate the

interface.

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Zotero interface

The interface is divided in three parts. In the left part you see the collections andsubcollections (and groups) where you file your references. When you select a(sub)collection, its content (the references) is displayed in the central part. And when youclick on a reference, all the metadata (title, author, ...) are displayed in the right part.

Personal notes

collection&groups selected collection content

selected referencemetadata

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Here are the interface buttons and their function.

New Collection... create a new collection (not a subcollection)

New Group... open Zotero website and create a new group

Actions access to import, export tools (among others) and preferences

New Item create a new empty reference

Create New item from Current Page save the current webpage (reference +complete webpage snapshot)

Add Item by Identifier add reference by entering an ISBN, DOI or PMID9

New Note create a note linked to a reference or not

Add Attachment create an attachment (snapshot, file, picture, ...) to a reference

Advanced Search query on several fields at a time (with ability to save results)

Locate access to the document (not only the reference)

Sync with Zotero Server share the Zotero library across several devices(computers, tablets, smartphones)

Toggle Tab Mode display Zotero in a browser tab (full screen)

Back to default display

9 ISBN, DOI and PMID are explained at the end of the Collect section.

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INSTALL

What do you need to install (depending on your web browser and word processor).

1. What is your web browser?

Firefox install Zotero for Firefox (go to 2)or install Zotero Standalone (go to 3)

Chrome install Zotero Standaloneand install Zotero connector for Chrome (go to 3)

Safari install Zotero Standaloneand install Zotero connector pour Safari (go to 3)

IE, Opera ou autre Not yet compatible with Zotero10

2. If you installed Zotero for Firefox : What is your word processor ?

Word install citation plugin for WordOpenOffice.org/LibreOffice install citation plugin for OpenOffice.org/LibreOfficeLaTeX11 install Autozotbib12

3. You are done! The citation plugin is included in Zotero Standalone.

10 Bookmarklets for other browsers were released. But they are still buggy. You can download them on http://www.zotero.org/downloadbookmarklet (accessed Dec. 5, 2013).

11 LaTeX is not a word processor.12 For further information, see More section.

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COLLECT

With Zotero, you collect references with a single click.Zotero scans the webpage while it is loading in the web browser. If (at least) onebibliographic reference is detected, Zotero displays an icon in the address bar (or just next toit, if you use Safari). A single click on this icon adds the reference in your Zotero library.

Firefox

Chrome

Safari

Zotero can deal with a large number of document types (the most common are shown below).

livre image

chapitre de livre vidéo

article de journal article d'encyclopédie

article de conférence article de blog

thèse page web

présentation document (générique)

If Zotero detects more than one reference on a webpage, an yellow folder icon is displayed.

Clicking on this icon open a prompt where you can select the reference you want to add inyour Zotero library. They will all be added at the same time.

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EXERCISE Add books from a library catalog or a bookstore you are used to visit.Suggestions : http://www.nebis.ch

http://www.amazon.com

Personal notes

EXERCISE Add some papers from databases you use on a regular basis.Suggestions : http://apps.webofknowledge.com/WOS (restricted access)

http://www.sciencedirect.com (restricted access)http://scholar.google.comhttp://www.arxiv.orghttp://www.plosone.org

Personal notes

EXERCISE Add a few thesis from Infoscience (EPFL Institutional Repository).Suggestion : http://infoscience.epfl.ch

Personal notes

EXERCISE Add some presentations from a website you usually use for that.Suggestion : http://www.slideshare.net

Personal notes

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EXERCISE Add some pictures from a website you like to visit.Suggestions : http://www.flickr.com

http://commons.wikimedia.org/

Personal notes

EXERCISE Add some videos.Suggestions : http://www.youtube.com

http://www.vimeo.comhttp://www.ted.com

Personal notes

EXERCISE Add a few encyclopedia entries.Suggestions : http://en.wikipedia.org

Personal notes

QUESTION What can you do if a website is not Zotero-compliant?

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For books and articles, a powerful option is provided: the Magic Wand.

ISBN, DOI and PMIDFor books, Zotero sends a request to the Library of Congress catalog based onthe provided ISBN13. If no result is found, the same request is sent toWorldCat14, the biggest library catalog in the world.

For journal papers, Zotero accepts DOI or PMID.DOI (Digital Object Identifier15) is a unique alphanumerical string assigned toan online paper. It can be a journal paper, as well as a conference paper, a thesisor any final online document. Zotero relies on CrossRef to find the documentmatching with the DOI.PMID (PubMed IDentifier) is a identifier assigned to papers in PubMed16

(bibliographical database containing biomedical literature). Indexed articles geta PMID (no every article in PubMed gets one).

EXERCISE Use the identifier to add some papers and books provided in class.

Personal notes

13 ISBN stands for International Standard Book Number. It's a unique number assigned to every published book.

14 As of January 2013, WorldCat gathers 1.5 billion item. Visit http://www.worldcat.org/ (accessed Dec. 5, 2013).

15 Further information on http://www.doi.org/ (accessed Dec. 5, 2013). ETH Zurich delivers DOI for Switzerland. See http://www.doi.ethz.ch/index_e.html (accessed Dec. 5, 2013).

16 http://www.pubmed.com (accessed Dec. 5, 2013)

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IMPORT

If already use a reference manager or store PDF on your computer, you can import them inyour Zotero library.

Import references

1. To export references from your former reference manager, choose the BibTeX or RIS fileformat.

BibTeX and RISBoth formats are standards and every reference manager should let your exportin at least one of those formats.Warning ! Don't mix up exportation format and citation style. RIS and BibTeXare exportation formats. They are used to be handled by computer, not byhumans17. Here is what it looks like.

RIS FormatTY - BOOK ID - 135 T1 - Zotero : a guide for librarians, researchers, and educators CY - Chicago A1 - Puckett,Jason PB - Association of College and Research Libraries PY - 2011/// KW - Zotero SN - 9780838985892 ER -

BibTeX Format@book{puckett_zotero_2011,

address = {Chicago},title = {Zotero : a guide for librarians, researchers, and educators},isbn = {9780838985892},shorttitle = {Zotero},publisher = {Association of College and Research Libraries},author = {Puckett, Jason},year = {2011},keywords = {\#bibliogr., \#didac2011, \#lu/vu, \#obtenu}

}

17 Citation styles are discussed in the Cite section.

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2. Import the file in Zotero (Actions > Import...).

Import PDF files (from the web)

When you download a PDF from the web using Firefox, a prompt asks if you want to save itin Zotero. By default, Zotero will try to retrieve the metadata from the PDF.

If you use another web browser, you have to download the PDF on your computer first and then drag and drop it in Zotero.

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Import PDF files (from your computer)

1. Drag and drop PDF files in the central part of the Zotero interface.

2. Select them, right-click and choose Retrieve Metadata from PDF in the dropdown

menu.

3. Zotero relies on Google Scholar to find matches.

Note : Obviously, it won't work if the PDF file has no metadata (typically an print article youscanned).

4. If any, Zotero creates a reference and joinsthe PDF as attachment.

(Optional)5. The PDF file can be renamed based on the title, author and date of the document.

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EXERCISE Add some PDF files and try to retrieve the metadata as explainedabove.(If you have PDF files on your computer, try with these. If you don't, use the oneprovided in class.)

Personal notes

EXERCISE Import the RIS file provided in class and organize the references inyour Zotero library.

Personal notes

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SETUP

The Zotero Preferences panel allows you to setup many features. Let's have a look and see themain points.

General Tab

Manages the way Zotero is displayed in the browser. You can also tell Zotero to opendownloaded RIS files and allow (or forbid) to automatically tag items withkeywords and subject headings.

Sync Tab > Settings

Sync references and files (together or not)

Search Tab

Install and update PDF Indexing tools (to retrieve references from PDF metadata).

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Export Tab

Define Default Output Format.

Cite Tab > Word Processors

Microsoft Word and LibreOffice/OpenOffice.org/LibreOffice/NeoOffice plugins management(install, update or reinstall).

Cite Tab > Styles

Citation styles management (including adding new ones from the Zotero online repository18).

Proxies Tab

Proxies management

Shortcut Tab

Define shortcuts

Advanced Tab

Access to the Data Directory on the computer and advanced Zotero setup parameters.

18 http://www.zotero.org/styles (accessed Dec. 5, 2013)

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MANAGE

Zotero provides several features to manage your library. Let's have a look at the main ones.

Organize

All the reference are included in My Library. Then, you can dispatch them in collections andsubcollections you create. You can add a reference in several (sub)collections.If a (sub)collection is selected when you collect references, they will be automatically addedin it.

EXERCISE Organize the collected references in collections and subcollections.

Personal notes

Sort

You can choose how the references are sorted. It can be based on many field. To choose afield, just click on the column header (click again to reverse the sort order).

EXERCISE Sort references based on the Date Added field (lastest first).

Personal notes

Tag

Managing and searching the Zotero library can be eased by adding tags to references.

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By default, Zotero adds keywords and subjects headings provided on the platform where thereference comes from. These tags are orange. The ones you add by yourself are blue. You canchoose not to get the keywords and subjects headings from the platform in the General Tabof the Preferences panel.

EXERCISE Add some tags (for later use).

Personal notes

Search

Zotero provides two search mode.The search field launches a quick search.

EXERCISE Run a quick search and see what happens.

Personal notes

The Advanced Search button (magnifying glass) offers more tools to build a query.

You can save a advanced search so that you don't have to type it again and again. A savedsearch collection is created (folder with magnifying glass). This collection is automatically

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updated every time you add a reference matching the query you saved.

EXERCISE Create a saved search collection and test it.

Personal notes

Create a workflowAll these management tools (tag, saved search) can help you create a simpleand powerful workflow to track what you want to read, what you already readbut was not meaningful and what you want to keep for citing.

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CREATE

There are several to create a bibliography.The two easier ways are drag and drop or copy and paste references from Zotero in a wordprocessor.You can create a bibliography to publish it online as well (right-click > CreateBibliography from Selected Items... > Output Method: Save as HTML).

EXERCISE Create a bibliography (max. one page) and print it.

Personal notes

EXERCISE Create a bibliography meant to be published online and open it in yourweb browser.

Personal notes

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SHARE

You have three ways to share your references. Each fits different needs.

Export

You can export your entire Zotero library (Actions > Export Library...), one collection(right-click > Export Collection...) or only a some references (right-click >Export Selected Items...). Choose the Format in the prompt.

Sync

You can also sync your Zotero library across several devices (computers, tablets,smartphones). It's the best way to always access your up-to-date Zotero library from anywhere(at home, at work, even while travelling).You need an account on zotero.org to be able to sync your data. Then just click on the Syncwith Zotero Server button (green arrow).

If it's the first time you sync your library, you need to enter your username and password(Actions > Preferences... > Sync Tab > Settings).

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You can choose to sync attachment or not (PDF, snapshots, ...). You have 300Mo free storagespace on your Zotero online account. It is enough for references only, but you may quicklyreach this limit if you store PDF files online.You have two options: pay for more storage space19 or choose a third-party storage service tosync PDF files (see More section).

EXERCISE Go to https://www.zotero.org/user/login/ and log in to one of thecourse account (you can also create a personal account here:http://www.zotero.org/user/register) and take a tour in the settings section.Then sync your locale Zotero library with the Zotero server.

Personal notes

Collaborate

Zotero offers a great feature for collaboration : group libraries. You can create a group, invitemembers and work together on the same collection of references. When you are part ofproject, you need to share with parnters. Easy with Zotero.

You add references in group (sub)collections the same way you do it in your own library.Notice that you can grab references from a group library and pull them to your Zotero library.

EXERCISE Create a group and invite members. Add references (change GroupSettings if necessary).

Personal notes

19 https://www.zotero.org/settings/storage (accessed Dec. 5, 2013)

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CITE

The main reason to collect reference is to be able to cite them when you write a paper.

Unless you use Zotero Standalone, you need a second tool to cite while you write: a plugin foryour word processor.You can get it here: http://www.zotero.org/support/word_processor_plugin_installationChoose the plugin depending on the operating system and word processor you are using. Thisplugin is (installed as) a Firefox add-on.

When installed, the plugin appears as a Complement Tab (in Word for Windows) or atoolbar (in OpenOffice.org/LibreOffice/NeoOffice).

LibreOffice

Word (Windows)

Word (Mac)

If you are a LaTeX user, you just need to create (export) a .bib file (Actions > ExportLibrary...) to be able to cite references in your paper20.

Citation styleThe way an in-text citation and/or a reference is formatted depends on thecitation style.See this example of a book displayed in 4 different citation styles.

Chicago Manual of Style (author-date)Puckett, Jason. 2011. Zotero : a guide for librarians, researchers, andeducators. Chicago: Association of College and Research Libraries.

IEEE[1] J. Puckett, Zotero : a guide for librarians, researchers, and educators.Chicago: Association of College and Research Libraries, 2011.

Nature1. Puckett, J. Zotero : a guide for librarians, researchers, and educators.(Association of College and Research Libraries: Chicago, 2011).

ISO-690 (auteur-date)PUCKETT, Jason, 2011. Zotero : a guide for librarians, researchers, andeducators. Chicago : Association of College and Research Libraries.ISBN 9780838985892 0838985890.

As a result, a document can look differently according to the citation styleapplied. Some information is dropped in a style (e.g. ISBN) and some others

20 In order not to have to export your library everytime you add a reference, Robin Wilson developped a pluginfor Zotero that automatically updates the .bib file when a change occurs (see More section).

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are formatted differently (e.g. author firstname). They don't always appear inthe same order.There are two main citation style families: author-date and numeric21. Author-date styles format in-text citation as below and sort bibligraphy alphabeticallybased on the first author lastname:

As Jason Puckett says at the beginning of his book « any book about softwareinevitably starts to show its age even before it makes it to the shelf » (Puckett2011, X).

Numeric styles insert a number in the text and sort references in the same orderin the bibliography:

As Jason Puckett says at the beginning of his book « Any book about softwareinevitably starts to show its age even before it makes it to the shelf » [1].

There are almost as many citation styles as there are scientific journals. You can choose astyle in the Preferences panel (Actions > Preferences... > Export Tab > DefaultOutput Format). Out of the box, Zotero provides about 15 citation styles.For your personal styles management, go to Actions > Preferences... > Cite Tab >Styles. If you need additional styles, click on the Get additional styles... link. Thisleads you to the Zotero styles repository22 (http://www.zotero.org/styles/).

EXERCISE Install the plugin corresponding to your word processor, writesomething and cite documents from your Zotero library.

Personal notes

EXERCISE Change the citation style that fit your needs.

Personal notes

21 In the Humanities field, people use a third family of styles where references are added in the footnotes.22 This repository is also used by Mendeley, Papers and some others... See http://citationstyles.org/ for more.

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MORE

If you want to go beyond the scope of the course, here are some useful tips.

Your web browser is not compatible with Zotero yet.

At the moment, only Firefox, Chrome and Safari are compatible with Zotero. Soon the Zoterobookmarklet will allow zotero user to use any other browser (including Internet Explorer andOpera). At the time of writing, this bookmarklet is still buggy.You can get it at http://www.zotero.org/downloadbookmarklet (accessed Dec. 5, 2013)

You want to install the citation plugin but Firefox is not installed.

Citation plugins (for Word or OpenOffice.org/LibreOffice/NeoOffice) are installed in Firefox.If Firefox is not installed on your computer, the only way to use them (without installingFirefox) is to use Zotero Standalone (citation plugins included).

You want to sync your PDF files with a third party service.You have 300Mo available on Zotero servers. If you want more, you can pay for that or syncyour files with a third party service. In order to be able to do that, choose a service withWebDav protocol enabled.Update settings in the Preference panel (Actions > Preferences... > Sync Tab >Settings).

You are looking for a citation style , but you don't know its name.

You may need a citation style without knowing its name, but you know what citation andreferences should look like. A great tool will help find it:http://editor.citationstyles.org/searchByExample/You can enter a reference and it will show you matching citation styles. Easy. If you find theright style, you can save it.And if it's not exactly what you need, you can edit the style through the graphic interface (nocoding!) and save it: http://editor.citationstyles.org/visualEditor/.

You need a new citation style.

If you need a citation style that doesn't exist and/or that is too different from the existingstyles, you have two ways to get it.If you XML coding skills, you can do it by yourself. All you need to know about the CSLlangage is here: http://citationstyles.org/documentation/.If don't have the required skills, you can try to do it with the new graphic interface:http://editor.citationstyles.org/visualEditor/.But the easiest way is to ask for a new style on the Zotero forum: https://github.com/citation-style-language/styles/wiki/Requesting-Styles

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You are a LaTeX user and don't want to export the .bib file again and again in order tohave an up-to-date file to use.

A PhD student, Robin Wilson, faced the same problem, so he developped Autozotbib, aZotero plugin that automatically updates the .bib file when you add new things in your Zoterolibrary.http://www.rtwilson.com/academic/autozotbib

You want to get PDF from references you have in your Zotero library.

This is currently not possible. This feature was requested by users and is planned. But notvery soon23.

You need more than one Zotero library.

You are teaching as well as publishing and you don't want to mix it all up in one Zoterolibrary.It is easy to have two different Zotero libraries on a computer by using both Zotero for Firefoxand Zotero Standalone, and to choose them not to share the same library.If you need more than two Zotero libraries, it is possible to create several Zotero libraries, butyou need to create several Firefox profiles. This is an advanced feature. Each profile cancontain a different Zotero library.

To create a second Zotero library, you need to :

1. Open Firefox ProfileManager (see Swisher et Beckwith, 2012)2. Create a new Profile3. Install Zotero and start working

Keep in mind that the citation plugin in your word processor will be able to communicatewith only one of your Zotero library. You can encounter some troubles when trying to cite.But it's easy to solve : you just need to reinstall the citation plugin in the Preferences panel(Actions > Preferences... > Cite Tab > Word Processors > Reinstall...button).

You want to have your own « Zotero server ».

For privacy concerns, you may keep your Zotero data on your own server instead of theZotero servers (that are in the USA). Mark Sample described a way to reproduce thisarchitecture with syncing and sharing functionalities (Sample, 2012).

You want to know what's happening about Zotero.

Roadmap (last updated Apr. 5, 2012): http://www.zotero.org/support/development_roadmap (accessed Dec. 5, 2013)

23 http://forums.zotero.org/discussion/26140/get-pdf-from-references-in-library/ (accessed Dec. 5, 2013)

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Some useful links

Documentation https://www.zotero.org/support/3rd Party Documentation https://www.zotero.org/support/third_party_documentationZotero Plugins https://www.zotero.org/support/pluginsUsers Forum http://forums.zotero.org/categories/Dev Forum https://groups.google.com/forum/?fromgroups#!forum/zotero-dev

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http://infoscience.epfl.ch/record/182752

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Chicago : Association of College and Research Libraries. ISBN 9780838985892.

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