Academic Reference Manager

User Manual Version 6.5

Copyright 2011, Third Street Software, Inc. All Rights Reserved.

Introduction .......................................................................................................1 Key Features ............................................................................2 System Requirements ...............................................................5 Downloading and Installing Sente .............................................5 Demo Mode .............................................................................5 Launching Sente .......................................................................6 Licensing ..................................................................................7 Start-Up Options ....................................................................10 Checking for Software Updates ...............................................11 Uninstalling Sente ..................................................................11 Transferring a License to a New Computer .............................11 Some Common Questions ......................................................12 The Main Window .........................................................................................15 Toolbar ..................................................................................16 Tab Bar ..................................................................................18 Source List .............................................................................19 Reference List .........................................................................24 Reference Editor .....................................................................28 Attachment Pane ....................................................................33 Rotating the Reference List and Attachment View ...................34 Single Collection Tabs ............................................................35 Single Reference Tabs ............................................................37 Full Screen in Lion (OS X 10.7 or higher) .................................38 Changing Default Layouts for New Tabs .................................39 Creating and Customizing a Library ....................................................41 Multiple Libraries ...................................................................41 Creating A Library ..................................................................42 Library Customization ............................................................44 Attachment Handling ..............................................................46 Autolink Template Setup ........................................................51 Reference-Based Autolinks .....................................................52 Text-Selection-Based Autolinks .............................................58 Hotwords Setup ......................................................................60 Reference Types Setup ...........................................................63 Spotlight Setup .......................................................................68 Status Setup ...........................................................................70 Web Bookmarks Setup ............................................................72 Migrating Data from Other Applications ...........................................75 Migrating Data from EndNote .................................................76 Migrating Data from Bookends ...............................................78

Migrating Data from Papers ....................................................80 Migrating Data from Mendeley ...............................................83 Migrating Data from Zotero ....................................................84 Migrating Data from Reference Manager .................................85 Importing Data from Other Systems ........................................88 Adding PDFs and Other Files as New References ..........................91 Adding Files to Your Library as New References ......................91 Adding PDF Files .....................................................................92 Adding Files Other than PDFs ...............................................101 What Happens to Files After I Add Them to My Library? ........102 Targeted Browsing ....................................................................................103 Supported Sites ....................................................................104 Obtaining References Using Targeted Browsing ....................104 Obtaining Articles as References from Online Newspapers ...109 Obtaining References from Other Sites .................................111 Obtaining PDFs from the Web ...............................................112 Combining Targeted Browsing and PDF Acquisition ..............112 Obtaining Other Web Archives Using Targeted Browsing .......113 Searches .........................................................................................................115 Overview ..............................................................................115 Introduction to Searching External Data Sources in Sente .....116 What Can I Search? ...............................................................117 Creating a New Search ..........................................................119 Managing Searches ..............................................................120 Searching PubMed ................................................................123 Searching Web of Knowledge ................................................126 Searching Sites that Support the Z39.50 Protocol .................129 Searching Sites that Support the SRU Protocol ......................133 Using Proxy Servers ..............................................................137 Adjusting the Update Frequency for Searches .......................137 Other Ways of Adding References .....................................................139 QuickAdd: Adding References using ISBNs, DOIs, Etc. ...........139 Creating References from Web Pages ....................................141 Printing PDFs to Sente from Other Applications ....................143 Collections ....................................................................................................147 The All References Collection ...............................................148 Built-In Smart Collections .....................................................148 Custom Smart Collections ....................................................151

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Search Collections ................................................................160 Static Collections ..................................................................161 QuickTags .....................................................................................................163 Why Use QuickTags Instead of Static Collections? .................164 Why Use QuickTags Instead of Traditional Tags? ..................165 Working with the QuickTag Palette .......................................166 Behind the Scenes ................................................................170 Designing Your QuickTag Hierarchy .....................................171 Finding References Using Tags .............................................176 Find, Browse, and Hotwords ..................................................................179 Find .....................................................................................179 Library Browser ....................................................................184 Hotwords .............................................................................187 Reading and Annotating PDFs ..............................................................191 Reading PDFs in Sente ..........................................................191 Annotating PDFs and Taking Notes ......................................193 Exporting Annotated PDFs ....................................................200 Printing Annotated PDFs .......................................................200 Some Common Questions ....................................................201 Synchronized Libraries ............................................................................203 Uses for Synchronized Libraries ............................................204 How Synchronized Libraries Work .........................................205 Conguring Synchronized Copies .........................................209 Sample Congurations .........................................................213 Setting up a Synchronized Library .........................................218 Sync Conicts .......................................................................223 Troubleshooting Synchronized Libraries ...............................225 Working with Word Processors ............................................................231 Apple Pages .........................................................................232 Microsoft Word 2008 and 2011 ............................................233 RedleX Mellel ........................................................................234 Scrivener ..............................................................................239 Nisus Writer .........................................................................241 Open Office ..........................................................................242 Other Word Processors/Rich Text Format (RTF)/Word 2004 ..243 File Scanning ................................................................................................251 Introduction to File Scanning ................................................252 Before You Start ...................................................................256

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Inserting Citations ................................................................259 Modifying In-Text Citations ..................................................261 Adding a Bibliography ..........................................................262 Scanning the File ..................................................................263 Scan-in-Place .......................................................................267 Reviewing the Scan Results ...................................................269 Rescanning a Document .......................................................270 Troubleshooting ...................................................................271 Creating and Modifying Bibliography Formats .............................275 Introduction to the Bibliography Format Editor .....................275 Bibliography Format Editor Interface Tour ............................280 Importing CSL Format Files ...................................................301 Sente Preferences .......................................................................................303 Appearance Preferences .......................................................303 Bibliography Preferences ......................................................304 Output Gestures ...................................................................306 Plugins .................................................................................309 Advanced Preferences ..........................................................309 Registration ..........................................................................310

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Chapter 1

Introduction

Welcome to Sente (pronounced sen-tay), a powerful software tool for gathering, organizing, reviewing and citing academic literature and other material useful in academic research. Whether you are a seasoned academic researcher with years of accumulated material, or just starting out on your research career, you will nd Sente to be an essential tool in your daily work.

The Sente main window.

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Key Features
Sente helps you with all aspects of managing your academic references, from initial data retrieval through nal formatting of your own manuscripts. Data Retrieval Sente has important features that make it easy to nd and collect the references you need: Search University Libraries. Sente can search hundreds of data sources, including many university and research libraries. It is very likely that Sente can directly search the catalog of the library at your academic institution. Search Commercial Data Sources. Sente can search a number of commercial sources for academic literature, such as Web of Knowledge / Web of Science from Thomson, PubMed, the Library of Congress, WorldCat, and others. Targeted Browsing. Sente supports one-click downloading of references from dozens of websites like EBSCOHost, JSTOR, PubMed, as well as many publisher websites. Automatic PDF Download. When you click on a link to a PDF le in Sentes web browser, Sente will offer to automatically download, rename and le the PDF for you, and attach it to a reference in your library. PDF Import. Sente can also import PDFs that you already have, or which you obtain through other means, and it can help you nd the correct citation details using many different online sources. In some cases this will happen without any user action required; in other cases, you may need to click on the correct reference from a page of search results. Data Migration. Sente can import data from many other academic reference managers, including EndNote, Mendeley, Zotero, Papers, Bookends, Reference Manager and BibTeX. Library Organization As your research library grows, it will become increasingly important that it stays organized and that you be able to nd individual references quickly and easily. Here are some of the tools in Sente that will help you and your library stay organized: Custom Statuses. Sente lets you dene a set of custom reference statuses and then use these to manage your personal research workow.

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 Tags and QuickTags. Sente supports both traditional tags, as well as more powerful, hierarchical QuickTags for classifying and organizing your library. Custom Smart Collections. Sente lets you create arbitrarily complex smart collections (including Boolean logic) and then nest these collections arbitrarily deep to create a detailed hierarchy organization. Hotwords. Sente lets you dene a set of words and phrases that you would sometimes like to see automatically highlighted in each reference, including in the title, the abstract and all other elds. Having these terms highlighted can make it much easier for you to quickly scan through a large number of references. Customization Sente lets you customize many aspects of the software and your library. Reference Types and Attributes. Sente comes with built-in support for many types of references, like journal articles, books and conference proceedings. You can add any number of custom reference types if you need something that is not built-in. Also, you can add your own custom reference attributes to both the built-in and your own reference types. Reference Editor. You can modify the list and the order of elds in Sentes reference editor. This lets you include your own custom reference attributes and rearrange the order of all elds to best t your needs. Reference Statuses. You can dene your own list of reference statuses, designed to support your personal research workow. Reading and Note Taking Academic researchers spend a lot of time reading and studying the material in their research libraries. Sente makes this process easier and more efficient than it has even been before, with features like: PDF Reading and Annotation. Sente includes a built-in PDF viewer with annotation tools so you can highlight passages as you read. PDF Quoting and Note Taking. When you highlight a passage in a PDF, you can click a button to have Sente automatically create a note that includes the quoted passage. Multiple Notes per Reference. Sente lets you add as many notes as you want to any individual reference.

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Citing and Writing Sente also helps when it comes time to write up your own research. Word Processor Support. Citing to word processors including Apple Pages and Microsoft Word, RedleX Mellel, Scrivener, Nisus Writer, Open Office, and other applications that support Rich Text Format (RTF). Support for EndNote + Word Files. Full support for docx les produced using EndNote and Microsoft Word. This lets you read and write documents that can be read and edited by your colleagues who are still using EndNote and Word. And you will be able to read and edit the documents they produce, too. Custom Bibliography Format Editor. A bibliography format editor with built-in formats and the ability to edit or create your own formats. Cloud-Based Synchronization Sente includes one of the best synchronization engines around. You can maintain any number of copies of each Sente library on any number of devices. Some copies can be congured as read-only (so, for example, you can give a copy to co-workers in your department) and other copies can be fully unlocked so you can work freely on multiple devices. With Sentes synchronized libraries, every edit you make in any copy of a library is automatically and almost immediately transferred to all other copies of the library. And, because it is cloud-based synchronization, each copy of the library will catch up with all changes each time it is on the Internet. This lets you work freely while not connected to the Internet, but still have all your work synchronized the next time you are connected. iPad Support In addition to all of these tools on the Mac, Sente is also available on the iPad. Sente for iPad includes support for many of the features listed above, plus it syncs seamlessly with Sente for Mac. With Sente for iPad, you can carry your entire research library with you on your iPad. You can add new references using targeted browsing, just like on the Mac version. And you can annotate and take notes on PDFs, just like on the Mac. And, best of all, all of your information is automatically synchronized in all copies of your libraries on all devices. Sente for iPad must be purchased separately from the Apple iOS app store.

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System Requirements
Sente requires Mac OS X 10.6 or higher and an Internet connection, running on an Intel-based computer. The maximum reference library size depends on many factors, including memory and the size of other applications running concurrently with Sente. We recommend a minimum of 1GB RAM for most users. There are many Sente users with libraries in excess of 10,000 references (and some with many times that amount). Obviously, larger libraries like these work better on computers with faster processors and more RAM.

Downloading and Installing Sente

Sente is available for download from our website: www.ThirdStreetSoftware.com. The download will consist of a compressed (.zip) le you can expand by doubleclicking on it in the Finder. Then you can drag the application to any location on your computer (e.g., /Applications) and launch it from there. There is no difference between the demonstration version of Sente and the licensed version of Sente. The download you retrieve from our site as a demo will be the same program you will use if you purchase a license. The presence of a valid license changes this single program from demo mode to licensed mode.

Demo Mode
When you rst install the software, it will run in demo mode for 30 days. Sente will run without restrictions during the demonstration period, except that synchronized libraries will be limited to 50 references in size. After 30 days, the demonstration license will expire and you will need to purchase a license to continue using Sente. The unrestricted version of the Sente application is the same as the demo version, but with the license code entered to unlock the time and size restrictions. You can purchase a license for Sente at any time through our website at www.ThirdStreetSoftware.com. Immediately after your license purchase is complete, you will be sent a license code in an email. Please see the section on Licensing for more information.

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Launching Sente
Like other Mac applications, you can launch Sente by double-clicking on the Sente icon, or by clicking once on the icon if it is in the OS X dock. Accepting the Sente License When opening Sente for the rst timeand after installing an updateyou will be prompted to accept the license terms, whether you have purchased Sente or are using Sente for free during the demo time period. Scroll through the license terms and then click either Decline License (in which case Sente will quit) or Accept License.

Accept Sentes license terms.

Acknowledging Demo Mode If you have not yet entered a valid Sente license on this computer, Sente will stop during start-up to tell you that you are running a demo license, and when that license will expire. Assuming the demo period has not yet expired, you will be given the opportunity to continue in demo mode by clicking on the Continue button.

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Authorize Sente or continue with the demo version.

If you want to continue using the demo version of Sente during the 30-day free trial, simply click the Continue button. If you are ready to enter the license key and authorize Sente for full, unrestricted use, click the Authorize button and follow the steps listed under the Licensing section, below.

Licensing
At any time during or after the demo period, you can choose to purchase and install a Sente license to enable unlimited use of the software. Each single user license for Sente allows you to authorize Sente on up to three computers. To purchase a Sente license, please visit our website: www.ThirdStreetSoftware.com. Within minutes of purchasing a license, you will receive an email message from Avangate.com that includes your license code. This is the information you will need to authorize Sente on your computer(s). The Sente license key is a three-segment alphanumeric code that looks similar to the following: BC12345-ABCD-EFGH. The exact number of digits in the rst part of the license code may differ from this pattern, but it will typically be between 3 and 6 digits in length.

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If, after purchasing a Sente license, you do not receive an email message from Avangate with your license code, please check to make sure that the message was not classied as spam by your email program. To authorize a computer with a Sente license, click on the Authorize button when it stops during start-up to tell you that you are running a time-limited license.

The authorization screen in which you can enter a Sente license. Please note that Sente must be connected to the Internet to complete the authorization process.

In the next screen that appears, make sure the Use License Key tab is highlighted and enter the license key as shown in the example. The license key contains three sets of alphanumeric characters; enter each section in a separate box as shown in the image above. If you have an order code instead of a license key, click the Use Order Code tab and enter the number where shown. Troubleshooting the Licensing Process Sometimes the licensing process does not succeed. When this happens you will be presented with an error screen like that shown below:

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Error screen with information on what to do if a license key fails.

There are a few reasons why the authorization process might fail: You might not have an active Internet connection -- Sente must be able to reach our servers during the authorization process. Your license might already be in use on three computers. In this case, you can either manually de-authorize one or more of these computers to free up an authorization for your new computer, or open a support request to us to do this for you (if, for example, you no longer have access to one of the old computers). See the section below called Transferring a License to a New Computer for instructions on how to de-authorize Sente on a computer. You may have mistyped the license key. Please double-check the license key you entered. If you are still having problems authorizing your computer, please open a private support thread on our website (http://sente.tenderapp.com).

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Start-Up Options
The rst time you open Sente (and, if you place a checkmark in the Show these choices when launching Sente box, every time in the future), a What would you like to do rst? screen will appear.

The start-up options screen.

Make a selection from the list of choices and click the Continue button: Create a New, Empty Library. This is what you select when youre ready to create your rst Sente library. You may also wish to select this if you are ready to migrate a library from a different academic reference manager. Install and Open a Sample Library. If you would like to see and experiment with a sample library to get to know Sente better, choose this option. Copy and Convert a Sente 5 Library. If you have a Sente 5 library and are upgrading to Sente 6, choose this option to convert your old library into a Sente 6 library. Open an Existing Sente 6 Library. If you have previously created a library in Sente, choose this option. You will be prompted to locate the library and open it.

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 Do Not Open Any Library. Choose this option if you do not wish to open a library at this time. If you dont want this menu screen to appear again when you open Sente in the future, remove the checkmark from the box where it says Show these choices when launching Sente.

Checking for Software Updates

Be default, Sente checks for new versions automatically. When a new version is available, you will be presented with the release notes for the new version and given the option to upgrade. Although you can turn off Automatic Updates in Sente 6 Preferences, we strongly recommend that you leave it active so that you will learn about critical updates as they become available.

Uninstalling Sente
Should you need to remove Sente from your computer, you can delete the actual Sente application le from wherever you installed it (usually in the Applications folder), and remove the following les: Preferences: ~/Library/Preferences/com.thirdstreetsoftware.sente6.plist Support les: ~/Library/Application Support/Sente MS Word plugin: use a Spotlight search for SenteMenus.dot

Transferring a License to a New Computer

Your License Key allows you to authorize Sente on up to three desktop and laptop computers. To move your authorization from one computer to another, you may need to de-authorize your old computer by selecting Sente 6 > Sente 6 Preferences > Registration from the main menubar and clicking the De-authorize this computer and close Sente button. Then launch Sente on your new computer and enter your original License Key. Please note that if you purchased a license for a version of Sente older than the most recent version, you may need to re-install that older version. (For example, a license purchased for Sente 5 cannot be applied to Sente 6.)

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De-Authorize Sente on a Computer via Sente 6 Preferences > Registration.

Some Common Questions

How do I de-authorize Sente on one of my computers so that I can authorize it on another? Please see the section above, Transferring a License to a New Computer. I didnt receive my license key via emailwhat do I do? The email will arrive from Avangate. First, check your spam folder to see if it was placed there. Next, check to see if your mailbox is perhaps full. If you still are unable to locate the email, please contact Third Street Software. How many computers can I use one Sente license key on? Each single user license can be used on up to three desktop and laptop computers.

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I have a license key for an older version of Sente. Can I use it on the newest version of Sente? Unless you purchased Sente immediately before a new version was released (Sente 5 right before Sente 6 was released, for example), you will need to purchase a separate license for each major version release of Sente. Owners of older Sente licenses typically qualify for reduced pricing on the most current version. Please see our website for details. Im not able to de-authorize Sente on one of my computers / My computer hard drive crashed or failed / I cant nd my original license key. What can I do? If your hard drive fails, you are unable to de-authorize Sente on one of your computers for some reason, or you cannot nd your original license key, please contact Third Street Software for a remote de-authorization. How do I download the free trial version? Visit our website and download it from http://www.ThirdStreetSoftware.com. The free trial/demo version and the full version of Sente are the same applicationthe difference is that a license key is needed to unlock the restrictions of the demo version. I have the demo version and I paid for a licensehow do I get the unrestricted, non-demo version of Sente? The demo version and the unrestricted version of Sente are the same application; the license key unlocks the restrictions placed on the demo. Simply follow the steps above in the section called Licensing.

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Chapter 2

The Main Window

Most of your work in Sente will be done in the main window This chapter provides a brief overview of the main window and should be read by everyone new to Sente.

Sentes Main Window

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Sentes main window has several components, including: Toolbar. Many common commands can appear as buttons or other controls in the toolbar for quick access. It is not necessary to have the toolbar shown in your version of Sente, because all of the commands included in the toolbar are accessible either through the main menu, or some other means within the application. But many people nd the toolbar a convenient way to access many commonly used features in Sente. Tab Bar. When you launch Sente, the main window shows the library view of your library and the tab bar is not visible. As you open single collection tabs and single reference tabs (described below), the tab bar will appear and it will contain entries for each of the tabs you create. Source List. Present only in the main library tab, the source list (sometimes called the sidebar) provides you with access to everything in your library, including both your references and the various conguration options for your library. The selection in the source list controls what is displayed in the rest of the library view. This may be a collection of references, or a library set-up screen. Reference List. When a collection of references is selected in the source list, the references are displayed in the reference list. Reference Editor. Whenever a single reference is selected in the reference list, the details of that reference are displayed in the reference editor at the right side of the main window (if it is open). Attachment View. When the reference that is selected in the reference list has at least one attachment, such as a PDF, one of those attachments will be displayed in the attachment view. Setup Panes. If you select any item under Library Setup in the source list, you will see the selected library setup pane in place of the reference list, attachment pane and reference editor. The options in these setup panes are explained in detail in the next chapter. Each of these components (other than the Setup Panes) is described in more detail below.

Toolbar
The toolbar provides quick access to many commonly used commands. Like most Mac applications, the contents of the toolbar can be congured by the user to show only the most useful items.

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The toolbar provides easy shortcuts to many common commands.

The toolbar is not required for any function. Each command that can appear in the toolbar also appears in the main menu or somewhere else in the interface. There are some special toolbar items with more complex behavior than the most standard items. For example, the Bookmarks item has a two-part button. There is typically a small icon in the left part of the button and a small menu arrow in the right part. Clicking on the right part will call up a menu with (in this case) all of your favorite web bookmarks. Selecting one from this list will open a new view with the embedded web browser displaying the selected web page. In addition, the icon in the left part of the button will change to match the selected website. Now, clicking on the left side of the Bookmarks toolbar item will open a new web view on the same website. This makes it easy to select the same website repeatedly from the toolbar. There are a number of other two-part toolbar items that work in the same way. Customizing the Toolbar Like most application toolbars, Sentes toolbar can be customized to t your needs. To select which buttons appear on the toolbar, select View > Customize Toolbar. This will open a screen from which you can drag buttons onto the toolbar. Toolbar spaces and separators are also available to help you organize your toolbar. Click the Done button when you are nished customizing the toolbar.

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Customizing the toolbar. Most edits are accomplished using drag and drop.

Tab Bar
When you rst launch Sente, you will see the standard library view and the tab bar will not be visible. The tab bar will become visible when you open new views, such as: Single Collection Tab. If you double-click on any collection in the source list, a new tab will be created with a reference list that includes only those references in that collection. See below for more information about single collection tabs. Single Reference Tab. If you double-click on any reference in any reference list, a new tab will be opened containing only that reference and its attachments. See below for more information on single reference tabs. Web Tab. If you use any of the web view commands, a new tab will be created containing a web browser. See below for more information on web tabs. In each case, if the tab bar is not visible, it will appear and the new tab will be created.

The tab bar.

The leftmost tab will always be the library tab. The library tab is the only tab that includes the source list (see below) and cannot be closed.

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Closing all open tabs (other than the library tab) will cause the tab bar to disappear. The tabs are maintained across launches of the application, so your selected views will still be there when you exit Sente and relaunch.

Source List
The source list (sometimes called the sidebar), located on the left-hand side of the Library tab in the main Sente window, gives you quick access to your library, collections, searches, and setup commands. It provides navigational and organizational functions such as smart ltering, and works much like other Mac OS source lists such as those in Mail and iTunes. For example, any item you select in the source list will display its contents in the reference table to the right.

The source list. In the main library tab, the selection in the source list determines what is shown in the rest of the window.

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The source list includes the following categories: Library. This category includes a number of automatically-dened collections. For example, All References always includes all of the references in your library. The collections under Recent provide quick access to references that have been recently added or modied. Synced Collections. This category can be used to hold smart collections that you dene. All smart collections under Synced Collections are automatically synchronized in all copies of the library on all devices. Local Collections. This category can include smart collections, static collections and search collections. These collections are not synchronized with other copies of the library. Saved Searches. When you create a search in Sente, you have the option of saving that search for later use. This is where newly saved searches will appear. References retrieved in these searches do not automatically appear in your main list of references for the library, unless you move them there. See the section on Searches in this manual for more information. Library Setup. This category includes a number of library conguration screens that enable you to control various aspects of your Sente library. For example, this is where you create custom reference types and congure the layout of the reference editor. Each of these categories is explained in more detail below. Of note, each category in the source list can be opened and closed (shown and hidden) either by clicking on the triangle on the left side of the category or, for categories without triangles, by hovering over the category name and then clicking on Show or Hide (see image above). Items in the Library Category Everything in the Library category in the source list is generated automatically by Sente.

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The items in the Library category in the source list.

All References. If you select this entry in the source list, you will see the complete list of references in your library shown in the reference list. Recent. This entry in the source can be expanded to show a number of more specic categories, like references Added in the Last Day. These collections are often a very convenient way to access references that you have been working with lately. By Status. Sente lets you set up your own custom list of statuses for your library. Each reference may have any one status assigned to it at any one time. The sub-categories under By Status will include one collection for each of your statuses, and selecting these categories will display all references with that status. As you modify your status list for the library, the collections here will be automatically updated to match. By Rating. Sente lets you assign a rating, of from zero to ve stars, to each reference in your library. The collections under By Rating make it easy to quickly nd all references in your library with a particular rating. By Reference Type. Sente comes with support for several dozen types of references (book, journal article, etc.) and you can readily add your own custom reference types in each library. The sub-collections under By Rating are automatically generated to show all of the reference types actually in use in this library. Selecting one will show all of the references of that type. By QuickTag. One of the most powerful features in Sente is the ability to tag references with entries from the hierarchical set of tags that we call QuickTags. QuickTags are explained in detail in the QuickTags chapter of this manual. For our purposes here, it is enough to say that selecting any entry in the QuickTag list will cause Sente to reduce the contents of the reference list to only those references that have had the selected QuickTag assigned to them.

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Items in the Synced Collections Category In addition to the built-in collections in the Library category, you can create any number of arbitrarily complex smart collections. Custom smart collections kept in the Synced Collections category are automatically synchronized in all copies of a synchronized library. To create a custom smart collection in this category, use the File > New Collection > New Smart Collection in Synced Collections command in the main menu, or the toolbar equivalent. The Synced Collections category can only contain smart collections. Static collections and searches must be placed in the Local Collections category. There is more information about dening smart collections later in this manual, in the section about Collections. Items in the Local Collections Category You can also create any number of static or smart collections that will not be synchronized with other copies of your library. For example, you may be sharing a library with colleagues and you might want to create some custom collections that would not be of interest to the other users. These should be placed in the Local Collections category to prevent them from being sent to other copies of the library. To create a custom, local collection, use the File > New Collection > New Smart (or Static) Collection in Local Collections command in the main menu, or the toolbar equivalent. Items in the Library Setup Category There are many options when conguring a Sente library and these options are all accessible through the entries in the Library Setup category. To show or hide the Library Setup category, hover over the category name and then click on Show or Hide when it appears.

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The items in the Library Setup category in the source list. These are all used to modify the conguration of the current library.

The Library Setup category includes: Attachment Handling. The options in this setup pane are used to specify how Sente should handle les attached to references. For example, this is where you tell Sente how (and if) you want the program to organize your PDF les and other attachments. Autolink Templates. Autolink templates generate hyperlinks based on data from each reference to help you nd related information. The Autolink Templates setup pane is where you create and organize your Autolink templates. Hotwords. The Hotwords setup pane lets you specify which terms you would like to see highlighted (and in which color) when you turn on hotword highlighting. Hotwords can be very helpful when reviewing many references because they draw your eyes to the terms that you nd most important to your work. Reference Types. Sente lets you add your own custom reference types and reference attributes, as well as specify the exact layout of the reference editor for each reference type (built-in or custom). Spotlight. Sente lets you control how much, if any, information in Sente is indexed for Spotlight searching. You can have each individual reference indexed, or just the attachments, or both. Statuses. You can set up your own list of reference status values and then assign any one status to each reference. This is typically done to support your workow for gathering, reviewing and cataloging references. Web Bookmarks. You can specify any number of websites as your favorite websites for gathering your research material. These sites will then appear in the menus of websites throughout Sente.

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All of these settings are handled in the Library Setup panes because they are settings for each library individually, not for the application itself. (Application-wide settings are handled in Sente Preferences.) These settings are described in detail in the chapter on creating and customizing a Sente library.

Reference List
Whenever you select a folder in the source list, the references it contains are listed in the reference table. There are two available views for the reference table. One view includes several lines of information on each reference. The other view is a spreadsheet-like grid view. Reference List Status Bar On top of each version of the reference table is a status bar showing information about the current contents of the reference list. Ordered by. The name of the eld by which the table is currently ordered is shown at the left side. Reference count. The number of references currently in the reference list is shown at the right. Normally, this value will look something like 1204 references. When using tools like Find or Browse, this value will show the number of matches, along with the total numbers of references that would be shown were Find or Browse not active. For example, it might say 24 matches in 450 references. Sync status. In a synchronized library, sync status is shown just after the reference count. Typically, this value will look like L4FF23@2450. The string before the @ is the library ID (in this case, L4FF23). The value after the @ is the current change number for the library (in this case 2450). The change number always increases as a library is modied; each edit to each reference causes the number to go up. When two copies of the same synchronized library are up-to-date, they will display the same change number. When the character between the library ID and the change number in the sync status is @, this means that the library is up-to-date with the sync servers. When that character is a this means that Sente is currently processing updates. This could mean that Sente is sending changes to the sync servers or receiving edits from the servers. Once the library is up-to-date, this symbol will change back to the @ character.

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Multiple Line Version of the Reference List The standard version of the reference list shows several lines of information for each reference.

The multiple-line view in the reference table.

Each row in this version of the reference list includes information about the reference, such as: the title of the reference; the authors; the reference type (e.g., journal article, book, etc.); a thumbnail of the primary attachment, if any, otherwise a placeholder icon; small icons conveying information such as: Orange dot: Reference is unviewed. The number of unviewed references within a collection appears in the source list. Pencil: Reference has at least one associated note. Diamond: Reference data includes an abstract. Paperclip: Reference has at least one linked le. This icon is followed by something like x3 when more than one le is attached to the reference.

your star rating for the reference;

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 the current status of the reference. Grid Version of the Reference List The reference list can also be displayed as a traditional grid, or table. In this version of the reference list, each reference is represented as a single row in the table, and the table can scroll horizontally if there are too many columns to t on screen.

The grid view in the reference table.

In the grid view, you can add, remove and reorder columns to suit your needs: Add and remove columns by right-clicking in the table header and toggling individual columns on and off. The list of available columns includes any custom attributes you may have added to the library (see the Customization chapter). Rearrange columns by clicking and dragging on the column header. You can also adjust the width of columns by clicking on the divider bar between column headers. The order of references in the grid view can be changed by clicking on the header of the column you would like the table to be ordered by. For example, if you want the table ordered by article title, click on that column header. Clicking again will reverse the ordering. Alternatively, you can select the eld on which to order the table in the Order By list in either the main menu or the List toolbar item.

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Note that changing the order of references in the grid view will also change the order in the standard, multi-line view.

Right-click in the table header to select columns to be displayed.

The grid view can include columns that indicate something about the reference using small icons: Orange dot: Reference is unviewed. The number of unviewed references within a Collection appears in the source list. Pencil: Reference has at least one associated note. Diamond: Reference data includes an abstract. Document: Reference has at least one linked le. PDF: Reference has at least one linked PDF.

Features Common to Both Versions of the Reference List There are a number of features that are common to both versions of the reference list: Both versions can be ordered by any of the attributes that are currently included in the grid view. Thus, if you want to order the standard version of the reference

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list by, say, a custom eld, just add that eld to the grid view. It will immediately become one of the Order By options for the standard view. If you drop a le onto a reference in either version of the reference list, the le will be added to the library as an attachment on that reference. (If you want to import a le as a new reference, drop it onto the Library entry in the source list.) If you drag one or more references from the reference list and drop them into a static collection, those references will be added to the static collection. If you drag one or more references from the reference list and drop them into, say, a text document, they will be inserted into the document in whatever format you have selected in Sente preferences. For example, you might specify that references dragged from the reference table should be dropped as citation tags so you can easily add Sente references to your word processing documents.

Reference Editor
The reference editor in the main window can be turned on and off using either the View > Reference Editor > Open/Close Reference Editor command in the main menu, or by using the corresponding toolbar item. When visible, the reference editor is shown at the right side of the main window.

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The reference editor.

The Reference Editor allows you to seeand editthe data about each reference, along with the rating, assigned status, tags, a preview of the bibliography format, or your notes on that particular reference. At the very top of the reference editor are the status and rating elds. These can be edited at any time just by clicking on them. Next is the main body of the reference editor which shows either the reference details (or what is sometimes called the reference metadata) or your notes on the

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reference. You can switch between these two views either by clicking on the labels or by using the commands in the View > Reference Editor menu. At the bottom of the reference editor you can ask Sente to display either, or both, the tag eld or the bibliography preview. Reference Details When you are viewing the reference details, they are normally shown in read-only, or view, mode. If you click on the Edit button, the reference editor will switch to edit mode. The layout of elds will change when you are in edit mode; for example, most elds are congured not to be displayed in view mode if they do not have a value. This behavior, along with the exact list of elds to be displayed for each reference type, can be congured in the Reference Type Setup pane (see the chapter entitled Creating and Customizing a Library). You can enter and leave edit mode from the keyboard by pressing cmd-E. When you leave edit mode, keyboard focus will return to the reference in the reference list (if visible). Notes Sente lets you attach any number of notes to each reference. These can be entered manually in the notes tab in the reference editor, or they can be created while annotating PDFs in the attachment view. See the chapter Reading and Annotating PDFs for more information. Notes associated with highlighting in a PDF will be shown in the same color as the highlighting. When the mouse is over a note, a menu of commands will appear at the top of the note. This menu includes commands like expand/collapse, source (which will display the source of a note if it came from a particular location in a PDF) and others such as close, delete and copy.

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The notes pane in the reference editor.

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Bibliography Preview The preview pane shows the current reference in the selected bibliography format. This helps you to be sure that your reference includes all of the information needed when formatting a paper or manuscript in which this reference is cited. For example, in the screenshot below, the reference is being formatted in Chicago 16 AD (Author-Date) format.

The Preview pane shows the current reference formatted in one of your favorite bibliography formats.

To switch to another bibliography format, click on the format name in the preview pane and select one of the other formats. (Sente ships with dozens of bibliography formats, but only a few are normally selected as favorites at any one time. You can change this list at any time in Sente preferences.) Tags The tags pane shows all of the tags that have been assigned to this reference, including both QuickTags and regular tags. (For more information on tags in Sente, please see that chapter of this manual.)

The tags pane in the reference editor shows all of the tags that have been assigned to the selected reference, including QuickTags.

You can enter new tags manually in this pane by simply inserting the cursor and typing. You can delete tags by backspacing over them.

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As you assign and remove tags using the QuickTags palette, the entries will automatically appear (or disappear) in this eld as well.

Attachment Pane
Each reference in Sente can have any number of related les linked, or attached, to it. For example, it is common to have the full text PDF of a journal article attached to a reference for that article. The attached les are normally viewable in the attachment pane in the main window.

The attachment view in Sentes main window.

To open the attachment pane, you can either use the View > Attachment Pane > Open / Close Attachment Pane command in the main menu, or the toolbar item equivalent. At the top of the attachment pane you will see a control bar with viewing tools on it. Show Autolinks tool. On the top left is the show Autolinks tools - click on it to see a list of web pages related to this reference and attachment. Text or Image selection tool. In PDFs and some other types of les, you can highlight passages or regions of the page using Sentes built-in annotation

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tools. The choice in this control determines whether a selection made in the PDF will be a text-based selection or an image- (or region-) based selection. If you are trying to highlight or quote a passage of text in the document, use the Text selection tool. If you want to highlight or quote a gure in the PDF, use the Image selection tool. Attachment title. In the middle of the control bar you will see the name of the displayed le type. Clicking on this name will bring up a menu of commands with options like Reveal in Finder and Delete Attachment.

The menu of commands accesses by clicking on the name of the attachment at the top of the attachment view.

See the chapter Reading and Annotating PDFs for more information on working with the attachment pane.

Rotating the Reference List and Attachment View

Depending on the size and resolution of your display, and the task you are working on, you may nd it more convenient to have the reference list and the attachment view appear side-by-side instead of having the reference list above the attachment view.

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The library tab with the reference list and attachment view shown side-by-side.

To change the orientation of the reference list and attachment view in any tab: Select the View > Reference List > Display Alongside Attachments, or Display on Top of Attachments in the main menu; or Click on the Reference List item in the toolbar and select either of the above options from the menu that appears. Changing the orientation of the reference list and attachment view will affect only that tab, and any new tabs you create of the same type. For example, if you select side-by-side display in a single collection tab, the next time you open a single collection tab, it will be in side-by-side layout. Any single collection tabs already open will not be affected. This is one of those window layout options that is remembered for regular window and full screen modes independently. This means that you can set single collection tabs in window mode to be arranged top-and-bottom, but side-by-side in full screen mode.

Single Collection Tabs

Sente lets you add views to the tab bar for any collection that you have in the source list. This creates a new view containing the reference list showing just those

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references in the selected collection, and (optionally) either the reference editor, the attachment view, or both. To open a collection as a single collection view, double-click on the collection in the source list. To open a single collection tab without switching to that new tab, hold down the command key while double-clicking on the collection.

A single collection view, with the reference list and the attachment view oriented side-by-side.

Single collection tabs can be very useful for accessing and working with collections like recently added references, or the By Status collections. And, because Sente remembers your reading location within a PDF for each reference, it is easy to ip back and forth between references in these collections. Note that single collection tabs based on either built-in or custom smart collections will only be updated when you select the tab. This means, for example, that if you have a tab for references with a particular status, and you change the status of a reference in that list, the reference will not disappear until you click to another tab and back. This prevents accidental changes from causing references to suddenly disappear from view.

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Just like elsewhere in the main window, the reference list and the attachment view can be oriented either top-to-bottom or side-by-side in a single collection view. For many purposes, the side-by-side orientation may be preferred.

Single Reference Tabs

Sente also supports single reference tabs, which include only the attachment view and the reference editor. This makes it easier to focus on one reference at a time without the distraction of either the reference list or the source list. To open a single reference view on any reference, double-click on the reference in the reference list. To open a single reference tab without switching to that new tab, hold down the command key while double-clicking on the reference. Note that it is not possible to hide the attachment pane in a single reference view.

Reference opened in a single reference view.

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Full Screen in Lion (OS X 10.7 or higher)

Sente supports full screen mode under OS X 10.7 (Lion) or later. To enter full screen mode, click on the full screen icon in the window header, or select the View > Enter Full Screen command in the main menu.

Sente in full screen mode.

When Sente is in full screen mode, it occupies one of the spaces in your workspace, as controlled by Mission Control. See Apples OS X documentation for more information on this. Changes that you make to the layout of tabs in full screen mode will be remembered for full screen mode only. When you switch back to normal window mode, the tabs will revert to their conguration prior to entering full screen mode. (The list of tabs will remain the same, however.) To exit full screen mode, either click on the icon at the right edge of the menu bar, or select the View > Exit Full Screen from the main menu.

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Changing Default Layouts for New Tabs

As described above, there are many ways in which you modify the layout of each tab in Sente. As you work with the software you are likely to nd that you always want, say, new single collection tabs to be opened in a particular conguration. For example, you might always want these tabs with: the reference list side-by-side with the attachment view, and rather narrow; and the reference editor visible at a particular width. Furthermore, you might want a slightly (or very) different layout when in full screen mode for these same tabs. Sente lets you save any particular tab layout as the default conguration for all new tabs of the same type. This is done using the options in the View menu, as shown below.

The main menu commands for changing the default layout for single collection and single reference tabs.

When you have a tab congured in just the way you would like future tabs of the same type to appear, just select the appropriate option in the View menu and the details of the currently visible tab will be stored as the new defaults. The settings are stored separately for full screen and non-full screen modes, so you will have to change each of these independently. Note that changing the default layout only affects new tabs. Tabs that are already open will remain in their current layout. And changing the layout of any of these tabs does not have any effect on the defaults unless the appropriate option in the View menu is selected.

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Chapter 3

Creating and Customizing a Library

Multiple Libraries
Sente lets you create any number of libraries on your computer. This section will explain why you might choose to use more than one Sente library and the process for creating libraries. For many people, a single Sente library is adequate, but the ability to have multiple librariesperhaps synchronizedacross several desktop or laptop computers and iPads can be valuable. There are several reasons why you might want to create more than one Sente library: You might have multiple, largely non-overlapping areas of research interest. If these areas of interest are unlikely to share common references, there is little reason for them to appear in the same library, and good reason to keep them separate (e.g., if you share your library with a colleague, they are likely to be interested in only one of your research topics). You might have temporary interest in multiple topics and not want citations from these temporary interests to become a permanent part of your main research library. By placing each of these temporary topics in their own library, you can pursue them as long and as deeply as you want without cluttering your main library. When (or if) the topic ceases to be of interest to you, you can simply delete the library from your computer. You might want to create multiple, shared libraries for the purpose of collaboration. These libraries would probably contain subsets of your main research library, but they would be limited to just the references of interest in your collaboration. These collaborative libraries might even be set up to be

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editable by many people so that they can add relevant references from anywhere in the world. In this case, you might then want to copy some of these references into your main research library. You might want to create multiple libraries for the purposes of distributing reading lists to students or colleagues. For example, you might want to create a special library that includes all of the reading for a course you are teaching. As in the previous case, these references are likely to also appear in your main research library, but you really only want your students to receive those papers that are relevant to your course. You might want to split up a very large library (with, say, tens of thousands of references) into one archival library and one smaller active library for those references that you use most frequently. This can improve performance on the most active library while preserving all of the references in the archival library. One disadvantage of having multiple libraries is if the separate libraries have common topics. In this case, the libraries may end up with duplicate references or, in another example, may end up with one library having needed references and the other library not having them. It should be noted here that synchronized libraries are actually copies of one individual library. This section about how many libraries to create relates to separate, individual libraries that may or may not have synchronized copies created later for distribution to other computers or people.

Creating A Library
When youre ready to create a library, follow these steps to begin. 1. There are two ways to create a new library: a. From the Sente start-up screen, if you have Sente set to display options at start-up, select Create a New, Empty Library. b. From inside Sente, select File > New Library.

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From within sente, select File > New Library...

2.

From the new screen, choose a name for your library and the location on your computer where it will be stored. A Sente library must be stored on a local disk on your computer (that is, not on a remote, or network, disk). This is because Sente libraries include a SQLite database and SQLite does not support non-local disks. In addition, Sente libraries must not be placed in a synchronized folder, such as a Dropbox folder. Synchronization services such as Dropbox do not understand database les and they will eventually corrupt the database. (Instead, use Sentes built-in synchronization mechanism to maintain a single library across multiple computers; it is faster and safer than these generic services.)

3.

Specify the attachment handling options for the new library.

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The options available when creating a new library.

You will learn more about the attachment handling options in a section later in this chapter. For your rst library, please just use the default options (Filed, renamed and possibly synchronized by Sente, stored Inside the library bundle). Once you have created your new library, it will open with no references. You can begin using the library immediately, but there are many aspects of the library that can be customized to better meet your needs. These conguration options are explained in the remaining sections in this chapter.

Library Customization
The settings described in this chapter are all made on a library-by-library basis so the conguration is not done in Sente Preferences, but directly in each librarys main window. If you expand the Library Setup category in the source list you will see an entry for each of these items.

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The Library Setup category in the source list.

In the rest of this chapter, we will explain how to congure: Attachment handling -- should Sente rename and rele PDFs and other attachments as they are added to the library? Autolink templates -- these are automatically-generated links built using data from each reference to help you nd related information. Hotwords -- a list of words that can be highlighted to help you spot key terms as you skim through many references. Custom reference types and the reference editor -- you can add custom reference types and attributes and specify how all reference types should appear in the reference editor. Spotlight settings -- should PDFs and other les stored in Sente be indexed for Spotlight searching outside of Sente? Statuses -- a customizable list of statuses that you can assign to references to help you manage your research workow. Web bookmarks -- the list of websites that you regularly use to search for new references and related information. Each of these topics is covered in more depth below.

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Attachment Handling
Attachments are local les or remote web pages that have been attached to a reference. The most common type of attachment is the full-text PDF le. Other items that people often attach to references include web archives (especially for news articles or other pages that may change over time), image les (including charts or graphics from a paper, as well as photographs of artwork or architecture), and data archives (such as related to GenBank entries). References in Sente may have any number of attachments. Attachments can be added to references in several different ways: Files can be dragged from the Finder and dropped onto the reference in the main reference table. Files can be imported to the library (either by using the File > Import command, or by dragging the le from the Finder onto the References entry in the source list). When imported in this way, Sente will automatically create a new reference and add the le as an attachment to the new reference. Remote les can be automatically downloaded and attached to a reference when a link to the le is clicked in Sentes embedded web browser. In each case, Sente will follow the instructions captured in the Attachment Handling Setup pane to determine exactly what should be done with the le. Please note that this is one area that cannot be freely modied once synchronization is turned on for a library. It is normally best to work with these settings prior to turning sync on; otherwise, if you later change your mind about, for example, how attachment les should be named, you will have to turn sync off, change the settings and then turn sync back on. This will require copying the library manually back to every computer and iPad on which you want the library. Attachment Handling Options There are a few basic options for what Sente should do with new attachments. Sente can: Rename and le each attachment inside the library bundle; Rename and le each attachment somewhere else in the le system, outside the library bundle; Leave the original le alone and simply store a link to the le in the library. If you select this option, Sente will not be able to synchronize attachments across other computers or iPads.

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The Attachment Handling Setup screen lets you choose any of these options, and to congure the details of just how the les should be renamed and led for those options where this is to be done. However, we strongly recommend that you use the rst option (storing attachments inside the library bundle) for many reasons. These are explained in the next section. Please Store Your Attachments Inside the Library Bundle! Now that we have outlined the various attachment handling options that Sente supports, we want to convince you that one particular option is much better than all the rest. We very strongly encourage you to use the option to store attachments inside the library bundle. There are several reasons for this: You will be able to freely move the library bundle anywhere on your computer, or onto another computer, or onto any storage device, without breaking the links to the attachments. You will be able to restore the library from a backup without breaking the links. You will be able to copy the entire library, including attachments, by simply copying the library le itself. This makes it very easy to create backups, to transfer the entire library to a new computer, etc. All other options, including ling and renaming attachments outside the bundle, run the risk of having the links between the references and the attachments broken.
Directly Accessing Attachments Stored in the Bundle

But what if you want to have access to the les from Finder or through some other application? For example, many users want their attachments indexed by another application, such as DevonTHINK. Is this a good reason to choose a different option for attachment handling? Not normally. Instead of storing the attachments outside the bundle, you can simply create an alias in Finder to the folder in the bundle in which the attachments are led. Then move this alias outside the bundle, to any location you choose. This will give you immediate access to all your les from Finder, while still keeping the les safely stored inside your Sente library bundle. It is, of course, still possible to break the connection between the alias and the attachment folder inside the bundle, but xing this problem is simply a matter of recreating the single alias le, rather than relinking each of hundreds or thousands of references to their attachments. To create an alias to the attachment folder:

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1.

Right-click (or control-click) on the library bundle in Finder and select Show Package Contents from the context menu.

The context menu accessed by right-clicking (or control-clicking) on the icon for a Sente library in Finder.

2.

A new Finder window will appear. In this window, expand the folder called Contents and select the sub-folder called Attachments.

3.

RIght-click (or control-click) on the Attachments folder and select Make Alias from the context menu. A new le called Attachments alias will be created.

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4.

Move the newly created alias le (not the original Attachments folder) to any other location on your hard disk.

Once you have done this, you will be able to access the alias folder just as you would any other folder on your computer. As you add new attachments to your library, they will automatically appear here, properly renamed and led. Attachment Handling Setup Designating how attachments are to be handled is performed in the Attachment Handling Setup window. To open this section, expand the Library Setup category in the source list on the left side of the Sente window, then select Attachment Handling Setup.

The Attachment Handling Setup pane.

Choose either: Left in place and simply linked to a reference in Sente. (Not recommended for most users.) Filed, renamed, and possibly synchronized by Sente. (Recommended.)

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Please note that these items (and all items marked with an asterisk) will be the same for all copies of the library when/if synchronization is turned on. If the Filed, renamed, and possibly synchronized by Sente option is selected, then you will be able to specify where they are to be stored (inside the bundle or elsewhere), how the les should be organized into folders, and how they should be named. The most important decision is where the les should be placed. The options are: Inside the library bundle. (Recommended.) In folder: and choose the location of the folder. (Not recommended for most users.) Note that Sente will automatically create a sub-folder under whatever folder you specify here with the same name as the library. This prevents you from storing attachments from multiple libraries in the same folder hierarchy, something that would cause trouble for synchronized libraries. You also need to specify how the les should be organized. You are able to specify several levels of folders that should be created based on data within each reference. The options for each level of folder are included in the popup menus, but they include, for example: First Author Last Name First Author (Last name, forenames) First Author Last Initial Title Article Title Publication Title Volume Publication Type Year of Publication Unique Alphanumeric Identier You can also select the order of how the attachment is to be named (First name rst, year, title, etc.), and choose how many characters to limit the lename length by. Finally, you must specify whether you want Sente to delete the original le after adding a copy to the library. Toggle the Delete original les checkbox if you want Sente to automatically remove the original le after ling a copy as specied.

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When you have nished entering the information for attachment handling, click the Apply button. Changing Attachment Handling Options on an Existing, Synchronized Library Until you turn synchronization on for a library, you can freely change the attachment handling options. You can, for example, change the folder organization or le naming rules. When you do this, Sente will automatically update all attachments to use the new settings. Once you turn synchronization on, however, things get more complicated, because the attachments now likely exist on multiple computers and must be kept in sync. Even with a synchronized library, you can still change: whether the attachments are led inside or outside the bundle; whether the original le should be deleted after it is added to a library. These settings may, in fact, be different on each copy of a synchronized library. This means, for example, that you can have the attachments stored inside the bundle in one copy, but outside the bundle on another. Changing these settings does not require that sync be turned off. The rules for organizing attachments (e.g., folder structure and le naming), on the other hand, must be the same in all copies of a library and so cannot be changed once sync has been turned on. If you need to change these settings on a synchronized library, you will need to turn sync off, make the changes, and then turn sync back on. This will, in essence, create a new synchronized library (i.e., it will not stay in sync with the old synchronized copies). You will then need to replace all synchronized copies with copies of this new synchronized library.

Autolink Template Setup

Autolinks are URLs that are automatically generated by combining either information found within a reference, or some selected text, with an autolink template. Sente ships with a number of autolink templates and you can modify these or add your own. There are two kinds of autolinks:

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 Reference-based autolinks. These autolinks combine information found within a reference with a template to produce a URL based on the currently selected reference. For example, Sente ships with an autolink template that depends on the DOI attribute of a reference. When you select a reference containing a DOI, that autolink will be available. Selected-text-based autolinks. These autolinks combine selected text (e.g., selected within a PDF view in Sente) with a template to produce a URL. This type of autolink is used, for example, when adding PDFs to support easy searching based on text within the PDF. Both of these types of autolink templates are congured in the Autolinks Setup pane, and both are explained below.

Reference-Based Autolinks
Reference-based autolinks have many different uses. For example, you can use these autolinks to: Look up the publishers page for an article using the DOI; Look up the reference in an on-line literature resource such as PubMed or Web of Knowledge using one or more identiers (like PubMed ID); Look up a book at Amazon.com, the Library of Congress or WorldCat using an ISBN; Search for related references using an identier, or title, or other information within a reference; Retrieve related material from a publishers site using a DOI; Search for other works by an author on Google Scholar or some other site. Using Reference-Based Autolinks To see the list of active autolinks for a reference, select the reference in Sente and then either: Click on the autolinks button in the header of the attachment view, or Select the View > Attachment Pane > Autolinks command in the main menu.

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The autolinks button in the attachment view header.

When you do this, the attachment pane will display a page containing all of the active autolinks for the current reference.

The autolinks page in the attachment view.

If you click on any entry in the list of autolinks, that web page will be displayed in the attachment view.

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The result of clicking on one of the autolinks in the attachment view.

The autolinks that are available for any given reference will depend on the data found in the reference in your library. For example, every template that uses a DOI value (without any other values) will be active for a reference that contains a DOI. If a reference does not include a DOI, templates that use a DOI will not produce an autolink. Whenever you click on a link in the attachment view that takes you to a PDF le, Sente will automatically download the PDF and attach it to the selected reference. For example, DOI.org provides a service for locating the authoritative web pages for citations based on a citations Digital Object Identier (DOI). This service is accessed by loading a URL based on this pattern, or template: http://dx.doi.org/ {DOI} (where {DOI} is replaced with an actual DOI). That is, if the DOI for a reference is 10.123/100.456, then the correct URL for the autolink would be http://dx.doi.org/10.123/100.456. If an autolink can be generated for any given reference based on actual data in the reference, the autolink will be shown in the Autolinks page and in the main menu, under View > Attachment). For example, if a reference includes a value in the DOI eld, the doi.org autolink will be displayed when you click on the autolink icon and clicking on that link will take you to whatever page doi.org has for that reference. Sente comes with a number of built-in autolink templates, such as the DOI template mentioned above and others from PubMed and other sources. Many times, these

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web pages include links to the PDFs related to the references. It is easy to add additional templates or to modify or delete any of the existing templates. Adding and Editing Reference-Based Autolink Templates Autolink templates can be edited in the Autolinks setup tab.

The Autolink Setup pane.

The elds included for each template are: Active? Is this template active? That is, should it be considered when generating autolinks? If any of the built-in templates are not useful to you, you can either delete them entirely, or just turn them off here (by unchecking the Active? box) so that they will not be used.

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 Self? Does this template refer to the actual reference? That is, is the autolink template related specically to this reference, or is it related to similar but different references? Source. This is the source of the autolink (e.g., PubMed, Google Scholar, etc.). Label Template. This is the text that will be presented as the link in the autolinks page. The label can be just plain text (e.g., The publishers page for this reference) or it can include elds from the reference, just like the URL template below (e.g., Search Google Scholar for {articleTitle}). See below for more on eld substitutions. URL Template. This is the template for the URL that will be used as the link. The elds to be inserted into the template are indicated by placing the eld names within curly braces (e.g., {PMID} for PubMed ID). Default? Should a page generated using this template be loaded by default in the attachment view when there is no attachment? To add an autolink template, click on the New Template button. To delete an autolink, select the template in the list and press the Delete key on your keyboard. (Alternatively, uncheck the Active? checkbox to retain the autolink without using it.) Autolinks are presented on the autolinks page in the order the templates appear in the setup pane. To change the order of the templates, click and drag an entry. To restore the autolinks to their defaults, click on the Reset to Defaults. Autolink URL and Label Template Parameters When constructing an autolink template, both the URL and the label can be parameterized; that is, they can use data from within the reference. Substitution patterns embedded within the URL or label are of the form {attribute}, where the value of attribute is taken from the lists below. The patterns may contain any number of these elds. Many of the common identiers are useful when creating autolink templates. These include: CODEN DOI ISBN ISSN OAI (Open Archive Initiative number)

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 OCLCID PMID (PubMed ID) PMCID (PubMed Central ID) PII US LoC Control # (Library of Congress Control Number) Autolinks can also include regular elds, such as: affiliation articleTitle Edition intuitiveTitle (this is either the article title of the publication title, depending on the reference type) ISSN issue language pages publicationCountry publicationTitle publicationType publicationYear publisher volume These attributes may generate multiple autolinks for any particular reference: authorNames keywordValues
Examples

Here are a few autolink examples. Please note that the actual URLs shown are only examples and may not be current. To search for other PubMed articles by the same authors: Source PubMed, Label Template Articles by {authorNames}, URL Template http://

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www.ncbi.nlm.nih.gov/pubmed?term={authorNames} [Author]&cmd=DetailsSearch To search within Google Scholar for similar articles: Source Google Scholar, Label Template Articles related to {intuitiveTitle}, URL Template http:// scholar.google.com/scholar?q={intuitiveTitle} To search for PubMed articles with certain keywords: Source PubMed, Label Template Articles with keyword {keywordValues}, URL Template http:// www.ncbi.nlm.nih.gov/pubmed?term=%22{keywordValues}%22[MeSH %20Terms]&cmd=DetailsSearch

Text-Selection-Based Autolinks
Text-selection-based autolinks are used, for example, to make it easy to locate citation data when adding PDFs to your library. When Sente is unable to locate the citation data for a PDF automatically, it presents the PDF to you so you can select text (like the title) and then quickly search one of your favorite web data sources. Using Text-Selection-Based Autolinks These autolinks are currently used in two places within Sente. First, when adding PDFs to your library, you can use these templates to help locate the citation data for a PDF. Second, when reading a PDF already in your library, you can use these templates to look up, for example, a reference listed in the bibliography of the current paper.

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Invoking one of the text-selection-based autolinks while adding a PDF.

Just after invoking the autolink selected in the previous gure.

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Conguring Text-Selection-Based Autolink Templates These autolink templates are maintained in the Autolink Templates pane, just like the reference-based autolinks. The only difference between these templates and the reference-based templates is in the substitution string within the template. Instead of using a eld name within curly braces (e.g., {affiliation}), the templates include {SELECTED_TEXT}. Whatever is currently selected in the PDF at the time one of these templates is selected, will be merged with the template to produce the effective URL.

Some selected-text-based autolink templates. Even though the label eld also includes the SELECTED_TEXT string, the label is not currently used within Sente and so this will never appear anywhere.

Hotwords Setup
When skimming through a large number of references (e.g., the results of a large search) it can be helpful to have key words and phrases highlighted in titles and abstracts to draw your eyes to those terms in the text. This can make it much easier to identify those papers most directly related to your interests. Sente supports this automatic highlighting through its Hotwords feature. The highlighting of hotwords can be turned on and off using either the View > Highlight Hotwords command in the main menu, or through the Hotwords toolbar item.

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Hotwords toolbar button, turned off and on.

If hotword highlighting is turned on, the abc on the hotwords button will be highlighted, as shown in the image on the right, above.

Hotwords highlighted in the reference editor.

Hotwords are managed in the Hotwords Setup area of the Library Setup category on the source list.

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The Hotwords Setup pane.

Managing Hotwords The list of hotwords can be edited by selecting Hotwords Setup under the Library Setup category in the source list. To add a hotword to the list, click the New Hotword button at the bottom left of the Hotwords Setup window. To change the highlight color of a new hotword, click on the color box next to the hotword itself. This will bring up the color chooser and you can make your selection there. If you only want to highlight the term when it appears in exactly the combination of upper and lower case you used when you entered it, place a checkmark in the Exact Case? column. When you have nished adding the new hotword, click the Apply button. To delete a hotword from the list, double-click on the word, select it, and press the Delete key on the keyboard. Click the Apply button when you have nished.

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Reference Types Setup

Sente makes it easy to add custom reference types and attributes, and to control how all reference types are presented in the reference editor. These changes are all made in the Reference Types Setup pane.

The Reference Types Setup pane. This is where custom reference types and attributes can be added and where the layout of the reference editor for all types (custom and built-in) can be modied.

There are three lists in this setup pane: The Reference Types list, which has one entry for every type of reference that can be stored in your library. Sente ships with dozens of built-in reference types. You can add as many as you might need for your work. The Reference Editor Fields list, which shows, in order, the elds that the reference editor will display when showing a reference of the type selected in the Reference Type list. There is additional conguration information in this table that will be explained further below.

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 The Fields list, which shows all of the reference attributes that Sente knows about in this library. Sente ships with dozens of built-in reference attributes. You can add as many as you want to this list, and you can use any combination of built-in and custom attributes with any reference type. Adding a Custom Reference Type To add a new reference type to your library, click on the + button at the bottom of the Reference Type list. A sheet will appear in which you can name the new reference type.

Creating a new reference type.

If your new reference type is similar to an existing reference type, you can select that reference type in the Copy Editor Fields From drop-down menu and Sente will make a copy of the settings for that type as a starting point for your customization. Changing the Name of an Existing Reference Type You can change the display name for all reference types (custom or built-in) by double-clicking on the entry in the Reference Type list and changing the name in the sheet that appears. You can do this, for example, if you would like to change the language in which the name appears.

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Changing the display name and abbreviation for a built-in reference type.

Do not, however, change the name of any reference type in a way that fundamentally changes its meaning. The built-in types will continue to be used for their intended purpose no matter what you call them in the interface. For example, if you changed the visible name for the reference type journal article to book, Sente will continue to use that type for all journal articles that it downloads from the Internet. Changing the name does not change how Sente views the type internally. Modifying the Reference Editor Conguration for a Reference Type The reference editor is where you view and edit the contents of each reference in Sente. The way in which references are presented in this editor is controlled by the settings in the middle table in the setup pane. To get your bearing in this setup pane, you might want to select a common reference type (e.g., Journal Article or Book) in the rst table and then compare the list of elds in the second table with what you see in the reference editor when it is showing a reference of that type. One thing you will quickly notice is that some eld in the reference editor appear with labels at the left and some appear without labels. This is a difference in display style. The options are: Labeled (that is, the name of the eld will appear at the left and the value for the eld will appear after the label); Unlabeled 1, Unlabeled 2, and Unlabeled 3 (these are three styles that do not use labels; they differ in font only, with Unlabeled 1 using the largest font, and Unlabeled 3 using the smallest). When a eld is set to one of the unlabeled styles, the label will appear as placeholder text when the eld does not contain a value. Something else you will probably notice quickly is that, while the elds in the editor appear in the same order as they appear in the reference elds list, not all of the elds listed in the setup pane appear in the reference editor. This is because some

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elds are set to appear only when they actually contain data. Some may be set to appear only when the editor is in View Mode, others only in Edit Mode, and others in both modes. Here are the options: V indicates that the eld should appear in View Mode B indicates that the eld should appear in View Mode, even if blank (if V is set and B is not, the eld will not appear in View Mode unless it contains data) E indicates that the eld should appear in Edit Mode

The reference editor.

Finally, you may notice cases where the eld in the editor is called something other than what it is called in the reference elds list. This is because it is possible to change the label in the setup pane. For example, Sente has two important internal elds that it calls article title and publication title. These are used to hold the title of a component and the title of a complete published work. In the case of a journal article, one might think of them

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as article title and journal name. In the case of a book chapter, one might call them chapter title and book title. Relabeling them does not change their meaning or their behavior, it just gives them names that are more natural in the context of specic reference types. To actually change these settings for a eld in the reference editor elds list, double-click on the entry in the list. A sheet will appear in which the changes can be made.

The Reference Editor Field conguration sheet.

Rearranging Fields in the Reference Editor To change the order in which elds are presented in the reference editor, simply click and drag on the appropriate entries in the reference elds list and place them in the desired locations within the list. To remove a eld from the list, simply drag it from the table and release it elsewhere. Removing Fields from the Reference Editor To prevent you from overlooking elds that are present in your database, Sente will automatically append any eld that it nds in the reference to the bottom of the list of elds in the display. This ensures that you see, for example, custom elds imported from another reference manager. However, this makes it a little tricky to actually prevent a eld from showing up in the editor. For example, if you never care to see the BibTeX key, simply removing it

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from the list of elds in the setup pane will only cause it to be displayed at the bottom of the editor along with any other eld present in your data. So, instead of removing the eld from your list in the setup pane, double-click on the eld and change the settings so that it is not displayed in either Edit or View mode. Adding Custom Attributes The table at the right side of this setup pane lists all of the reference attributes that this Sente library knows about. Some of these attributes are used in just a few reference types, others are used in many or all reference types. You can add your own custom reference attributes here and use them in the reference editor for any combination of reference types.

Creating a custom reference attribute, or eld.

To create a new attribute type, click on the plus button on the Available Attributes list. A sheet will appear in which you can enter the name of the attribute that you want to create. To use either your custom attributes or the built-in attributes, simply drag the appropriate entry from the Attributes list onto the reference editor elds list for the appropriate reference type.

Spotlight Setup
Spotlight is Apples powerful search utility for locating les on your computer. Based on your needs, Sente can make references and attachments available for Spotlight searching. This is especially helpful when you want Sente to store library information in its bundles (which is recommended), yet you also want to be able to search for and nd specic information about library references and/or attachments on your computer.

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Sentes support for Spotlight is congured by making changes in the Spotlight Setup window, which is located in the source list under Library Setup.

The Spotlight Setup pane.

In this screen, you determine exactly what will be supported in Spotlight: Index References. This option will enable Spotlight to nd each reference in your library based on the contents of the reference attributes (title, abstract, authors, tags, etc.), but not on the content of attachments (unless the option below is also selected). Index Attached PDFs. This option will enable Spotlight to locate references in your library based on the contents of les attached to the references, but not based on the reference attributes (unless the option above is also selected). If you simply want to reproduce what you would get if the attachments were left outside the library (that is, you want Spotlight to nd the attachments, but not all of the references in Sente), then turn the indexing of references OFF, and the indexing of attachments ON. You will need to Reindex this library now after making changes so that the information will be available to Spotlight. In addition, after selecting one or both checkboxes (Index References and/or Index Attached PDFs), you may be prompted to reindex immediately.

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The prompt to reindex the library.

Please note that even if you select the Reindex this library now option, Spotlight searches will not return Sente references or attachments until after Spotlight has had a chance to work through all of the relevant les. Depending on many factors (e.g., the size of your library, the speed of your computer, etc.) this may take minutes or longer to complete.

Status Setup
Sente allows you to setup a custom list of reference statuses and to assign any one of these statuses to each reference in your library. This allows you to create your own custom workow for acquiring and reviewing references. As you complete each step in your workow on each reference, you can adjust the status on the reference to reect that work and the work remaining. Reference statuses can be applied to references in a number of ways. The Edit > Assign Status command will assign the selected status to all of the selected references in the library. Select a reference, right-click over it, open the Assign Status submenu, and select a status from the list.

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 On the top left side of the Reference Editor there is a Status menu that can be used to assign and change statuses. This will only work when there is a single selected reference. You can see all of the references that have a particular status by expanding the Library category in the source list on the left side of the Sente window, then expanding By Status. This will show a list with one smart collection for each of your status values. Selecting a status value will list in the reference table all of the references with that status. Dening Reference Statuses Your custom list of reference statuses can be edited in the Status Setup screen under the Library Setup category in the source list.

The Status Setup pane.

The values in this list appear throughout the Sente interface wherever you can change the status of a reference. Existing entries can be edited by double-clicking on the values (the status name or description) in the table. The description eld is for your use to help you remember exactly what you mean by each status.

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You can change the color that will be used when displaying references with each status by selecting the status in the table, clicking on the color square, and then using the color selector to change the color. New statuses can be added by clicking on the New Status button under the list. To delete a status, double-click over it, select it and press the Delete button on the keyboard. The order of the entries in the status setup pane determines the order in which these values will appear in menus and other lists throughout the interface. The order of these values can be changed by dragging entries in this list to a new position in the list. Of note, you will need to click on the Apply button after making changes and before moving to another window. You will be prompted if you forget to click the button. To return to the list of references in the library after making changes to this Setup section, click on All References under the Library category on the source list on the left side of the Sente window.

Web Bookmarks Setup

Sentes embedded web browser supports targeted browsing on many academic sites, such as PubMed, EBSCOhost, JSTOR, and many others. It is likely that Sente supports at least a few sites that you will nd useful in your research. To make it more convenient to access those sites, Sente lets you tailor the list of favorite bookmarks to include only those sites that you nd useful. Web bookmarks are accessed by clicking on the bookmarks toolbar button arrow:

The Bookmarks toolbar button.

Clicking on the arrow will open the list of web bookmarks, from which you can select the bookmark of your choice:

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The bookmarks menu.

You can also access the web bookmarks by using the Window > New Browser Tab command. To open a web page that is not on the list, select Open Location... at the bottom of the list (or use the cmd-L shortcut). Type in the URL of the web page you want to open. To open a blank browser tab, select Blank Browser Tab at the bottom of the list, or use the cmd-T shortcut. Conguring Web Bookmarks To congure the web bookmarks, open the Web Bookmarks Setup window, located under Library Setup in the source list.

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The Web Bookmarks Setup pane.

To add a new bookmark, click on the New Bookmark button located under the list of bookmarks. This will add a new bookmark to the list, where you can edit the title and change the URL.

Adding a new bookmark.

If you want the new bookmark to appear on the Web Bookmarks menu list, place a checkmark in the box under the Favorite? heading. To edit a current Web Bookmark, double-click on the title or URL and make your changes. You can also reorder the bookmarks by dragging entries up and down on the list. This will be reected in the bookmarks menus throughout the software. To delete a Web Bookmark, double-click on the title, select it and press the Delete key on the keyboard. Do the same for the URL. Click the Apply button when you have nished making changes.

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Chapter 4

Migrating Data from Other Applications

This chapter explains how to migrate your data from other reference manager applications into Sente, including: EndNote Bookends Papers (v1 only in this release) Mendeley Zotero Reference Manager If you have data stored in some other reference management tool, you can probably still migrate the information to Sente, using one of the many data formats that Sente supports: EndNote XML (EndNote 7 and later) Refer (both generic and EndNote) BibTeX CSA MARC21 PubMed/Medline XML

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 RefWorks SciFinder Tagged records (Medlars, Ovid, Toxline) Sente XML (the best format for importing data from another copy of Sente) Please see the appropriate section below for specic instructions on migrating your data to Sente.

Migrating Data from EndNote

In most cases it is possible to migrate an entire EndNote library, including attachments, into Sente without doing much, if any, manual cleanup afterwards. This should include attachments and custom elds. The migration instructions below assume your data is stored in EndNote 7 or later. If your library is stored in EndNote 6 or earlier, you will need to migrate it to a later version of EndNote prior to migrating to Sente. First, export references from EndNote: 1. 2. 3. 4. 5. 6. Open the library in EndNote. Use the File > Export command. Specify a le name and location for the export le (the Desktop may be the most convenient location). Select XML as the export format (Save as File Type: XML). Select Show all elds for the Output Style. If Export Selected References has a checkmark in the box and you want to export ALL references (not just references that happen to be selected), click on the checkbox to remove the checkmark. Click on Save.

7.

Then, import the EndNote references into Sente: 1. 2. 3. Launch Sente and either open the library you want to use or create a new library in Sente. Select the File > Import command. Navigate to the EndNote XML le, select it, and click Open.

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4.

If a File Import Duplicate References Report appears, review it by scrolling through the list, or copy the report to the clipboard for pasting into a text editor like Pages. Click Okay when nished reviewing the report.

A File Import Duplicate References Report appears if duplicate references are found.

5.

If there are elds used in the EndNote library that are not currently in Sente, the new elds will be added and a report will appear with the information. Click Okay to close the report.

A New Custom Fields Created by Import report shows new custom elds.

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We recommend that you spot-check your data in Sente, comparing a few random examples of references and attachments to make sure they migrated successfully from EndNote to Sente.

Migrating Data from Bookends

In general, it is normally possible to migrate references from a Bookends library to Sente and to have all of the data appear in Sente, including attachments and custom elds. Sente also scans the references being imported for any duplicates and will show a results screen for duplicates, as well. First, export references and attachments from Bookends: 1. 2. 3. 4. 5. 6. 7. Launch Bookends. Manually select the references you want to export to Sente by placing a checkmark in the checkbox to the left of each reference. Use the File > Export References command in Bookends. Select XML (EndNote 8 or later) as the format type. Place a checkmark in the checkbox next to Export attachments too by clicking on the checkbox. Choose a location. Click the Save button and then the Okay button when the dialog box appears.

Then, import the Bookends references into Sente: 1. 2. 3. 4. Launch Sente and either open the library you want to use or create a new library in Sente. Select the File > Import command. Navigate to the Bookends XML le (which may end in .bdb.xml), select it, and click Open. If a File Import Duplicate References Report appears, review it by scrolling through the list, or copy the report to the clipboard for pasting into a text editor like Pages. Click Okay when nished reviewing the report.

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A File Import Duplicate References Report appears if duplicate references are found.

5.

If there are elds used in the Bookends library that are not currently in Sente, the new elds will be added and a report will appear with the information. Click Okay to close the report.

A New Custom Fields Created by Import report shows new custom elds.

We recommend that you spot-check your data in Sente, comparing a few random examples of references and attachments to make sure they migrated successfully from Bookends to Sente.

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Troubleshooting Here are answers to some common issues related to the migration of Bookends data into Sente:
Dates did not transfer correctly

See Bookends user guide for information about how the date eld in Bookends is transferred to the EndNote XML output le.
PDFs Didnt Migrate into Sente

When exporting references and attachments from Bookends, make sure to place a checkmark in the Export attachments too checkbox.

Migrating Data from Papers

Sente can import libraries directly from Papers 1, without needing to export the data from these libraries rst. You will simply tell Sente where the Papers database is stored and Sente will retrieve the data, including attachments and custom elds. Papers2 libraries cannot currently be imported directly; instead, the references must rst be exported in a format that both programs support. For more information on this, please see the section on Importing Papers2 References into Sente, below. Migrating a Papers 1 Library into Sente To import your Papers 1 library into Sente: 1. 2. 3. Launch Sente and either open the library you want to use or create a new library in Sente. Select the File > Import command. In the le selector that appears, select the folder containing the Papers database. Do not navigate into this directory. By default, the location is: ~/ Documents/Papers. If you have relocated the database, the current location can be found from the Papers > Preferences > Library tab. Click Open. If a File Import Duplicate References Report appears, review it by scrolling through the list, or copy the report to the clipboard for pasting into a text editor like Pages. Click Okay when nished reviewing the report.

4.

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A File Import Duplicate References Report appears if duplicate references are found.

5.

If there are elds used in the Papers library that are not currently in Sente, the new elds will be added and a report will appear with the information. Click Okay to close the report.

We recommend that you spot-check your data in Sente, comparing a few random examples of references and attachments to make sure they migrated successfully from Papers to Sente. Importing Papers2 References into Sente Papers2 libraries cannot be directly imported into Sente at this time. However, you still may be able to export the Papers2 library in a format that Sente can read, such as EndNote XML or BibTeX. After exporting the Papers2 library into an output le that Sente can read, follow these instructions to import the data into Sente: 1. 2. 3. Open Sente and either open the library you want to use or create a new library in Sente. Select the File > Import command. Navigate to the Papers2 output le, select it, and click Open.

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4.

If a File Import Duplicate References Report appears, review it by scrolling through the list, or copy the report to the clipboard for pasting into a text editor like Pages. Click Okay when nished reviewing the report.

A File Import Duplicate References Report appears if duplicate references are found.

5.

If there are elds used in the Papers2 library that are not currently in Sente, the new elds will be added and a report will appear with the information. Click Okay to close the report.

A New Custom Fields Created by Import report shows new custom elds.

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It is advised that you spot-check your data in Sente, comparing a few random examples of references and attachments to make sure they migrated successfully from Papers2 to Sente.

Migrating Data from Mendeley

A Mendeley library can be imported directly into Sente, without the need to export the data rst. Sente will import all reference data, including custom elds, and attachments. Sente also scans the references being imported for any duplicates and will report any detected duplicates. To import the Mendeley references into Sente: 1. 2. 3. Launch Sente and either open the library you want to use or create a new library in Sente. Select the File > Import command. In the le chooser that appears, navigate to the folder containing the Mendeley database. By default, this folder is: ~/Library/Application Support/Mendeley Desktop. Click Open. If a File Import Duplicate References Report appears, review it by scrolling through the list, or copy the report to the clipboard for pasting into a text editor like Pages. Click Okay when nished reviewing the report.

4.

A File Import Duplicate References Report appears if duplicate references are found.

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5.

If there are elds used in the Mendeley library that are not currently in Sente, the new elds will be added and a report will appear with the information. Click Okay to close the report.

We recommend that you spot-check your data in Sente, comparing a few random examples of references and attachments to make sure they migrated successfully from Mendeley to Sente.

Migrating Data from Zotero

A Zotero library can be imported directly into Sente, without the need to rst export the data from Zotero. Sente will import all reference data, including custom elds, and attachments. Sente also scans the references being imported for any duplicates and will report any detected duplicates. To import the Zotero references directly into Sente, follow these steps: 1. 2. 3. 4. Make sure Firefox is completely shut down. Launch Sente and either open the library you want to use or create a new library. Select the File > Import command. In the le selector that appears, navigate to the folder containing the Zotero database. This directory can be found by clicking on the Show Data Directory button in the Advanced tab in Zotero preferences (accessed through the Zotero gear menu). The folder path should look something like (but not exactly like): ~/Library/Application Support/Firefox/Proles/vw6pqezr.default/zotero. The correct folder will contain a le called zotero.sqlite. Select the folder that contains the sqlite database; do not select the database itself. Click Open. If a File Import Duplicate References Report appears, review it by scrolling through the list, or copy the report to the clipboard for pasting into a text editor like Pages. Click Okay when nished reviewing the report.

5.

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A File Import Duplicate References Report appears if duplicate references are found.

6.

If there are elds used in the Zotero library that are not currently in Sente, the new elds will be added and a report will appear with the information. Click Okay to close the report.

We recommend that you spot-check your data in Sente, comparing a few random examples of references and attachments to make sure they migrated successfully from Zotero to Sente.

Migrating Data from Reference Manager

Sente can import data from Reference Manager when its library contents are exported in RIS format. The two main tasks in migrating library data from Reference Manager to Sente are to export the references from Reference Manager, and then to import the data into Sente. During the migration process, Sente reads the data contained in the Reference Manager RIS le. The RIS le contains all of the information about each reference that was contained in Reference Manager. If you had created any custom elds in Reference Manager, Sente will recognize the new elds and display a results screen for new elds after the import process. Sente also scans the references being imported for any duplicates and will show a results screen for duplicates, as well.

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First, export references and attachments from Reference Manager: 1. 2. Launch Reference Manager. Manually select the references you want to export to Sente by placing a checkmark in the checkbox to the left of each reference. If you want to export all of the references, you will be able to select that option from within the dialog box. Use the File > Export command in Reference Manager. Choose a name and a location for the output le. Select RIS as the output format type. If you want to export all of the references, place a checkmark in the checkbox next to All references in list by clicking on the checkbox. If you want to export only the references you marked, place a checkmark in the box next to Marked reference(s). Click the Export button. If necessary, transfer the output le to a Macintosh computer that has Sente installed.

3. 4. 5. 6.

7. 8.

Then, import the Reference Manager references into Sente: 1. 2. 3. 4. Open Sente and either open the library you want to use or create a new library in Sente. Select the File > Import command. Navigate to the Reference Manager RIS le, select it, and click Open. If a File Import Duplicate References Report appears, review it by scrolling through the list, or copy the report to the clipboard for pasting into a text editor like Pages. Click Okay when nished reviewing the report.

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A File Import Duplicate References Report appears if duplicate references are found.

5.

If there are elds used in the Reference Manager library that are not currently in Sente, the new elds will be added and a report will appear with the information. Click Okay to close the report.

A New Custom Fields Created by Import report shows new custom elds.

We recommend that you spot-check your data in Sente, comparing a few random examples of references and attachments to make sure they migrated successfully from Reference Manager to Sente.

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Importing Data from Other Systems

If your reference manager is not specically listed in this chapter, you still may be able to migrate your data into Sente. Sente can import data in many different formats, including: EndNote XML (EndNote 7 and later) Refer (both generic and EndNote) BibTeX CSA MARC21 PubMed/Medline XML Reference Manager (RIS) RefWorks SciFinder Tagged records (Medlars, Ovid, Toxline) Sente XML To import data in any of these formats: 1. 2. 3. 4. 5. Launch Sente and either open the library you want to use or create a new library in Sente. Select the File > Import command. Navigate to the saved le, select it, and click Open. If Sente is unable to import the data le, an error message will appear. If Sente is able to import the data le, a progress bar will appear. If a File Import Duplicate References Report appears, review it by scrolling through the list, or copy the report to the clipboard for pasting into a text editor like Pages. Click Okay when nished reviewing the report.

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A File Import Duplicate References Report appears if duplicate references are found.

6.

If there are elds used in the other library that are not currently in Sente, the new elds will be added and a report will appear with the information. Click Okay to close the report.

A New Custom Fields Created by Import report shows new custom elds.

We recommend that you spot-check your data in Sente, comparing a few random examples of references and attachments to make sure they migrated successfully from your other reference manager application to Sente.

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Troubleshooting Here is some information on some common issues related to migrating data from other reference management systems.
Missing Fields

If you tried migrating your data from a library not specically mentioned above and not all of the data was imported into Sente, try exporting the data as a different output le type. For example, if you exported the library as an RIS output le, try exporting it as an EndNote XML le and importing it into a new Sente library, then compare the libraries to see if the data was imported correctly.

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Chapter 5

Adding PDFs and Other Files as New References

References in Sente can have any number of PDF and other les attached to them. In addition, you can add PDF and other les (such as images, web archives, and videos) to Sente and create new references for each of them. Typically these les would be located on your computer, attached to emails, or exist as web pages online. While web page archives can be added to Sente individually, other les can be added to Sente either individually or in bulk. This chapter explains the process of adding PDFs and other les to your library. This chapter is about adding les, like PDFs, JPEGs, etc., that you want to have attached to references in your library. It is not about importing data from les like EndNote XML les. That process is covered elsewhere in this manual.

Adding Files to Your Library as New References

Files can be added to your library in several ways. First, you can add any number of les as attachments on existing references in your library. This is accomplished by simply dragging the le or les from Finder and dropping them onto the target reference in the reference list. All of the les dropped in this manner will be added to your library as attachments on that reference. This path is fairly straightforward and will not be discussed further here. Second, les can be added to your library as new references. For example, if you receive a PDF from a colleague in an email message, you might want to add the PDF

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as a reference to your library. This second type of addition can be initiated in several different ways: You can drag a le from Finder and drop it on the All References category in the source list. You can use the File > Add PDFs and Other Files command from the main menu and select the le from the le selector that will appear. You can use the Add Files button on the toolbar, which will also bring up the le selector sheet. In each of these cases, you are indicating that each of the les being added should appear as a new reference in the library. In the case of PDF les, Sente can often identify the citation for the le using information found within the le itself (e.g., a DOI). In this case, Sente makes it as easy as possible to get the right citation data into the new references in the library. In other cases (e.g., JPEGs or MP4 les), Sente does not know how to obtain the citation data, so it leaves the process of data entry to the user. Because of this fundamental difference between different types of les, they will be discussed separately below.

Adding PDF Files

PDF les are treated differently than all other types of les because Sente includes support for some common techniques that can often be used to automatically retrieve the correct citation details for a PDF. Other les, like images or spreadsheets, cannot normally be handled in this way. This section covers the process of adding PDF les. Adding other types of les is covered later in this chapter. PDFs That Can be Matched Using DOIs Many modern PDF les for journal articles contain a unique identier known as a Digital Object Identier, or DOI. Here is a typical DOI: 10.1126/science.1157784. This one happens to identify a paper published in Science in 2009. DOIs are very useful because they uniquely identify a reference and they can be used to locate the citation data for that reference.

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When you add PDF les to your library, Sente will look inside the PDF for a DOI in the rst few pages and it will attempt to locate the citation details using this value. If it is successful, it will display the Citation Lookup sheet with both the PDF and the citation details so you can review the match.

The Citation Lookup sheet showing a successful DOI lookup.

If the citation looks correct, you can make any edits you want (e.g., assign a status or QuickTags) and then add the reference to your library. The PDF will be automatically added as an attachment on the new reference. PDFs That Cannot be Matched Using DOIs Sente will not be able to locate the citation data automatically for some of the PDFs you try to add to your library. When this happens, Sente provides some useful tools to help you locate the citation data on the web and to create references using targeted browsing. (See the chapter on Targeted Browsing for general information on this topic. This chapter only covers those aspects of targeted browsing unique to the process of adding les to your library.) If Sente is not able to locate the citation data using an embedded DOI, it will display the Citation Lookup sheet open to the web search tab, as shown below.

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The web search tab shown when DOI-based lookup fails.

When this happens, there are two basic approaches that you can use to getting the correct citation data into your library: Web searches, plus targeted browsing, and Manual data entry. These are covered in the following sections. Citation Lookup Using a Web Search Depending on your eld and the data resources available to you (perhaps through your institution), you probably have access to several sources of references on the web. For example: PubMed (biomedical) ArXiv (physics) EBSCOhost (many disciplines) Google Scholar (many disciplines)

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Sente makes it easy to search any of these sources (and others) using information found in the PDF you are adding combined with text-selection-based autolinks. To use this feature, begin by selecting some text from the PDFthe title is often the most useful. When you do this, a popup menu will appear like the one shown below.

The popup menu used to initiate a web search for citation data.

In this popup menu you will see, among other things, two groups of websites, with the following labels: Search for selected text at: Copy text and visit: The rst group of links are generated from text-select-based autolinks. These are sites that accept search strings as part of the URL and which have been congured in the Autolink Template setup pane (see the Creating and Customizing a Library chapter for more information). If you select one of these options, the web view should then display the search results found by searching on the selected text.

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The second group of links are your favorite bookmarks. These will duplicate some of the sites listed in the rst group, if you have autolink templates to some of your favorite sites (as you likely will). If you select one of this second group of links, Sente will load the selected site into the web view and copy the selected text from the PDF onto the clipboard. You will then have to paste the text into the search box and initiate the search.

Search results with targeted browsing. If the correct reference is listed, click on the target to add it to your library.

In both cases, you will then see the search results. If the site is supported by targeted browsing, you will see small target icons next to each reference in the results page. Clicking on a target will cause Sente to download the citation data, prepare it for entry into your library and show you the results in the reference editor tab. To accept this reference and add it to your library, along with the PDF as an attachment, click on the Add New Reference button.

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After clicking on a target, the selected reference will be shown in a reference editor where you can make any edits you need. The Add New Reference button is also enabled. Clicking on this button will complete the process.

Manual Data Entry As a last resort, you may have to turn to manual data entry to add the citation details to the new reference. You can do this either directly in the reference editor tab in the Citation Lookup sheet, or you can simply switch to that tab and immediately click on Add New Reference to add the reference without any citation details. You will then be able to edit the reference at any time in the future using the normal reference editor in the main window. Working with Batches of PDFs There will be times when you will have more than one PDF you want to add to your library. In this case, you can use any of the methods mentioned above to initiate the addition (drag and drop, File > Add PDFs and Other Files, etc.) and Sente will work through the list of les one-by-one. In this case, you will notice a few additional features that may be useful.

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For example, unless you have changed the default settings (see below for more on this), Sente will automatically use whatever status, rating and tags you assign to one reference during the add, to the next reference as a default. You can, of course, change these settings, but it is common to want all of the references in a batch to have some of the same settings. In addition, if at any time you want to have Sente automatically accept DOI-based matches, or automatically create blank references for those without a DOI-based match, you can select those options in the Options menu. This will take effect as soon as you tell Sente what to do with the reference current in the sheet. Options Various aspects of the process of adding PDFs can be controlled using the Options menu in the Citation Lookup sheet.

The Options menu in the Citation Lookup sheet. Always Automatically Accept DOI Matches

This setting tells Sente never to require user input when a DOI lookup nds a citation for the PDF. Thus, if you have this option selected and you drop multiple PDFs onto Sente, and they all result in successful citation lookups using DOI matches found within the les, you will not have to do anything else to complete the process.
For This Batch, Automatically Accept DOI Matches

This is like the previous setting, but it will apply only to the les remaining in this batch. This setting is always turned off when a new set of PDFs is added to Sente.

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For This Batch, Automatically Create New, Blank References When DOI Lookup Fails

This option tells Sente to skip any semi-automatic citation lookup (e.g., targeted browsing) or manual data entry for those PDFs that could not be matched using the DOI lookup. All such references will be added to the library as blank references without any further interaction with the user.
Default to Last Rating, Status and Tags

These settings determine whether Sente will automatically ll in any of these values when creating new references, based on the values you assigned in the previous reference. For example, suppose you are adding a batch of PDFs that you know are all related to a particular topic and you want to remember to read all of them in the near future. You drag all of the references onto Sente and it begins the add process. When it stops to let you review the rst match, you might change the status of the new reference to To Be Read and assign a couple of tags. When you click on Add, that reference will be added to the library. When Sente stops to show you the next match, the same status and tags will have been automatically applied before the reference is presented for approval. You can, of course, change these values, but in many cases you will want the same values, so you will not have to do anything more.
Use Filename as Default Title

When creating new, blank references, it can sometimes be useful to have the original PDF lename in the reference to help you distinguish one reference from another. This option will tell Sente to use the lename as the default title for all new references. If citation lookup retrieves a real title, this default will not be used.
Include PubMed in DOI Lookups

Users in the biomedical sciences will typically want Sente to favor citation data found in PubMed over data found in other resources, like CrossRef. If you work in the biomedical sciences, you should make sure this setting is turned on; otherwise turn it off because it will simply slow down citation searches. Doing the Citation Lookup After Adding PDF Files to the Library While it is very efficient to perform the citation lookup during the process of adding PDFs to your library, there will be times when you will simply want to add the les and deal with the citation lookup later. Sente provides the same tools for nding

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the citation data after the les are in the library that it provides during the add process.

To look up a citation for an existing PDF reference, right-click over the reference/PDF and select Look Up Citation Using PDF from the context menu or select the reference(s) and then use Edit > Reference > Look Up Citation Using PDF from the main menu.

To add a batch of PDFs without performing any manual citation lookup, initiate the process as usual (drag and drop, File > Add PDFs and Other Fiels, etc.) and, when the Citation Lookup sheet appears, click on Options and select both of these options: For this Batch, Automatically Accept DOI-Based Matches, and For this Batch, Automatically Create New, Blank References when DOI Lookup Fails. Then click on the desired action for the rst PDF (shown in the sheet). This reference will be processed, and the two options you set above will cause Sente to quickly work through the entire batch, creating blank references as needed. Then, when you are ready to work on nding the citations for the blank references. you can select the references in the main reference list and execute the Edit > Reference > Look Up Citation Using PDF.

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Adding Files Other than PDFs

PDFs are not the only types of les that can be added as references or attachments in Sente libraries. Images, web archives, videos, RTF, music and other les can be added as well. The list of le types that can be added to Sente libraries is continuously growing. The process of adding non-PDF les to your library is quite a bit different from what is described above. The process is initiated in exactly the same way (drag and drop, File > Add Files, etc.) but from there everything changes.

The sheet for adding a single non-PDF le to your library.

When you try to add a non-PDF le to your library, you will be presented with an Add Reference sheet in which you can enter the initial reference details. You can enter as much or as little information as desired. Clicking on the Add to Library button will complete the operation.

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The sheet for adding more than one non-PDF le using a reference template.

When you add more than one non-PDF le at one time, you will be presented with a reference template sheet. You can enter as much information as you want in this sheet and that information will be used for all new references created as part of this process. This lets you set, for example, the reference type, status, author, etc., once and have it applied automatically to all of the new references. In addition, the title of each reference will be automatically modied to include the name of the le being added.

What Happens to Files After I Add Them to My Library?

Exactly what Sente will do when adding a le to your library as an attachment is determined in the Attachment Handling Setup pane. This is where you tell Sente how les should be renamed and organized (if at all) and whether the original le should be removed from its original location after it is added to the library. Please see the chapter on library setup for more information on the available options. The settings in the Attachment Handling setup pane apply to both PDF and non-PDF les.

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Chapter 6

Targeted Browsing

One easy way to add references to your Sente library is by using the feature we call Targeted Browsing. Whenever Sente loads a web page in its embedded browser, it looks to see if it can identify reference data on the page and, when it nds references, it adds target icons to the page. If you click on one of these targets, Sente will automatically download all of the data on the reference that it can from the website and display it to you for possible inclusion in your library. In this way, targeted browsing can eliminate all of the steps typically required to add a reference from the web to your library (e.g., downloading the reference in a useful format and then locating the downloaded le on your computer and importing it). Targeted browsing can also be used to update existing references in your library. For example, if your original entry was created using pre-publication data, targeted browsing can be used to update the record with the publication details once they become available. Finally, Sentes embedded browser also makes it easy to acquire PDFs for new or existing references. When Sente detects that you have clicked on a link to a PDF, it offers several options, including automatically downloading and attaching the PDF to the current reference. By combining targeted browsing and automatic PDF acquisition, you can often add a new reference, along with the full text, to your library with just a few clicks.

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Supported Sites
Targeted browsing works with dozens of the most important academic websites, including: Google Scholar HighWire Press JSTOR PubMed Amazon.com The US Library of Congress WorldCat any web page that includes COinS data for embedded citations many more. Obviously, Sente can only access sites requiring a subscription if you already have access to the site (e.g., through your institution). If you cannot access the data using Safari, you will not be able to access it using Sente. New sites are being added all the time, and Third Street Software welcomes suggestions for new sites via email; click the envelope icon in the upper right-hand corner of the page during targeted browsing to send your suggestions. The PDF acquisition feature works with almost every website.

Obtaining References Using Targeted Browsing

Sentes embedded web browser can appear either as a web tab in the main window, or within the attachment view in any other type of tab. Targeted browsing and PDF acquisition are supported in both places. When a web page is loaded, Sente looks through the contents for reference data. When it nds something it thinks is a reference, it adds a small icon near the information. There are three versions of this icon, each representing a different situation. The most common image you will see is a target, which means that Sente has found a reference that it believes is not in your current library.

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Sometimes Sente will nd a reference that it believes is already in your library. In this case, the image will be a small Sente icon. If you hover the pointer over this image, Sente will show you a summary of the reference from your library that it believes matches the reference on the page. Occasionally, Sente will nd a reference in a web page and a potential, but not condent, match in your library. In this case, the image it adds will be a solid red circle. This means that there was enough information to identify a possible match in your library, but not enough information from one source or the other to be sure that the two are, in fact, the same reference.

An example of a web page in which Sente has detected references that can be downloaded.

If you click on any one of the icons described above, Sente will automatically download as much information about the reference as it can from the source website. Often, this will be more information than was displayed on the web page

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you were viewing. Sente will then present the reference to you as a potential new reference. After downloading all of the available citation data, Sente reconsiders the question of whether the reference is actually in your library already. Because Sente often has more information at this step than it did when it originally loaded the web page, the answer about whether the reference is already in your library may change. If at this point Sente determines that the reference is not, in fact, in your library, it will present the data to you in a sheet that lets you add the reference. In this sheet you can also edit the reference, assign a status, tags, rating, etc., and even add notes. Once you are satised with the entry, clicking the Add to Library button will add the reference to your library.

The acquisition sheet for a reference that is not currently in your library.

On the other hand, if Sente determines that the new reference matches something in your library, it will present a sheet in which you can ask Sente to update the existing reference from the information gathered from the website. There are several common scenarios in which this might happen. For example, if you originally acquired the reference from an on-line source prior to the actual publication of the article, the data might be incomplete. Once the nal version appears in print (or on-line), the missing information will become available. Or, you

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might have acquired the original reference from a source (like Google Scholar) that provides only minimal entries, and then acquire the complete reference from a resource with more complete data. In any case like these, you can use targeted browsing to update your incomplete references from records you nd on the web.

The acquisition sheet for a reference that matches one already in your library.

The acquisition sheet for the case where Sente has identied a matching reference in your library includes a standard reference editor, just like the case of a new reference. You can edit the incoming reference just as you would expect. In addition, Sente will present you with two options: Add as a New Reference. This option lets you override the mechanism by which Sente would normally merge the two references together. When complete, this operations will result in two different references in your library, even though to Sente they appear to represent the same citation. Update Reference. This option will perform an automatic merge of the new reference and the existing reference. Data missing in the existing reference will be automatically lled in from the incoming reference. Keywords will be merged. If there are values in the existing reference that you want overwritten by the new data, you should open a reference editor on the existing reference and delete

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those values from the existing reference; the new values will then be added when the merge takes place. The Targeted Browsing Summary Bar When you are using targeted browsing, you will also notice that Sente adds a region at the top of each page summarizing its success in identifying references on the page.

The yellow targeted browsing summary bar appears at the top of the results page.

The summary bar will show the number of references found on the page, and how many of those references appear to be new. If you wish, you can click on the target icon in this summary bar to acquire all of the references shown on the page and add them to your library. If you do so, the Add References Using Template sheet will appear and allow you to enter any information (reference data, status, rating, or tags) related to all of the references. (Individual reference data may overwrite any bibliography elds you change, such as author or date.) After you click the Add to Library button, all of the references will be added to your library. They will all be listed under Recent > Added but not yet viewed category in the source list.

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The references acquired from the summary bar are listed in the Added but not yet viewed category in the source list.

Later, when you are ready to view the references listed in the Added but not yet viewed category, you can search for more information on the web related to each individual reference. For more information on how to do this, please see the section about using Citation Lookup on references already in your library. Sometimes this summary will indicate that Sente was unable to identify any references on the page. This can happen, even when there clearly are references on the page, for several reasons: the website, or at least the specic type of page, is not yet supported by Sente; something about the site has changed and broken Sentes ability to detect references on a page that used to work. Whenever you nd a page that you think Sente should support, but does not, you can click on the envelope icon in the summary bar to send us a request to investigate. If the site is one that we have supported in the past, we will normally try to correct the problem as quickly as possible. If we have not yet added support for the site, our decision about whether to add support will depend, in part, on the number of requests we receive from users.

Obtaining Articles as References from Online Newspapers

Sente currently supports a few online newspapers such as the New York Times, from which you can easily acquire articles using targeted browsing.

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The New York Times, showing 150 references that can be added to the library.

To add the reference to your library, without attaching the article as a web archive, click the target icon and edit the Add Reference information as needed, then uncheck the box marked Attach a copy of the current web page and click the Add to Library button. To add the entire article to your reference as a web archive (a copy of the web page as it is right now, not a link to the web page which could potentially change in the future), follow these steps: 1. 2. 3. Click the article title to open that web page. On the individual article web page, nd the Print icon/button/link and click on it. This is to remove advertisements from your web archive. Click the target icon and edit the Add Reference information as needed. Make sure there is a checkmark in the Attach a copy of the current web page box, then click the Add to Library button. (If the reference already exists in your library, the button choices will be Add as New Reference or Update Reference).

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Example of newspaper article saved as a web page archive.

Obtaining References from Other Sites

While Sente supports many sites with the targeted browsing feature, there are many websites that are notat least not yetsupported by Sente. Obtaining references from these sites is a bit more difficult, but can still often be done without resorting to manual data entry. The key to obtaining references from unsupported sites is to use the best export option supported by the site and then import the resulting le into Sente. In general, the best formats for exporting data from a website are: EndNote XML BibTeX If neither of these is supported, you can fall back to using any other supported format and trying it in Sente. The preferred formats will normally result in better data in Sente, but sometimes it is necessary to use other formats and then clean up the data afterward.

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Obtaining PDFs from the Web

The other important capability in Sentes embedded web browser is the ability to automatically download PDF les and attach them to new or existing references. This can reduce the normal process of acquiring PDFs from multiple, complex steps to one simple step. Whenever you click on a link to a PDF, Sente detects this and presents you with several options: You can attach the PDF to the current reference (that is, the reference currently selected in this tab, if any); You can attach the PDF to the last reference you acquired through targeted browsing in this tab, if any; You can have Sente create a new reference and attach the PDF to it; Or, you can just have Sente display the PDF in the browser without attaching it to any reference in your library.

The Add File sheet that appears after clicking on a link to a PDF in the web browser

Combining Targeted Browsing and PDF Acquisition

As you work to gather research material in Sente, the exact order of steps needed to add each reference to your library, along with the full text and any related material, will depend on your specic context and the nature and quality of the on-line resources you are using. We recommend that you start with this approach:

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1.

Whenever possible, start by acquiring the citation data using targeted browsing on a site that returns high quality data. Data sources that are specic to your eld are more likely to have higher quality data than more general sites, like Google Scholar. On the other hand, Google Scholar sometimes includes reference that cannot be found in other sources. Start with the best data source available to you. Next, move on to locating the full text (when desirable). In some cases this will just involve clicking on a link on the same page where you clicked on the target. In other cases, you may have to switch over to the autolink display for the reference and follow some of those links to the publishers page, or some other repository. When you nd and click on a link to a PDF, you will be asked if you want to attach it to your last acquired reference. This is the most reliable way of getting the le where you want it. If your citation data is incomplete, use the autolinks page again to locate the reference on an alternative data source. Then, if the page is supported in targeted browsing, click on the target (or, more likely, the Sente icon) to download that sites version of the reference. Click on the Update button to update the existing reference with the data found on the second site. You will then need to review the results to make sure that you have the fullest possible record.

2.

3.

For more information about autolinks, please see the section of the manual on Using Autolinks. This is just a starting point for the process of acquiring references and PDFs. There are times when it makes more sense to start with downloading the PDF and letting Sente use an embedded DOI for locating the citation data. In the end, you will need to try several approaches to see which works best for your research.

Obtaining Other Web Archives Using Targeted Browsing

Occasionally while searching for references, you may come across an entire web page that you would like to save as a reference. You can do so by attaching a web archive, which is a picture of the web page as it is right now, not a link to the web page which could potentially change in the future. To create a web archive and attach it to a new reference, simply right-click (or cmd-click) within the web page to access the context menu, then select the option to Create a New Reference from this Web Page.

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The context menu in the embedded web browser within Sente.

When you select this command, Sente will open the Add Reference sheet, in which you can edit the citation data. Make sure to place a checkmark in the box to Attach a copy of the current web page, then click the Add to Library button. For additional information on obtaining and attaching web archives, please see the section on Creating References from Web Pages.

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Chapter 7

Searches

This section provides an overview of Searches and information on how to perform searches, including: What can be searched Creating a new search Managing searches Searching PubMed Searching Web of Knowledge Searching sites that support the Z39.50 protocol Searching sites that support the SRU protocol Using proxy servers

Overview
Whether youre exploring a new subject or trying to stay current on a topic that you already know well, Sentes ability to automatically keep on top of the literature can be invaluable. Some data sources support direct searching by software like Sente by supporting what is known as an Application Programming Interface (API). This is not the same thing as a web interface intended for use by people through their web browser. A search API is a protocol that lets programs like Sente perform searches and parse the results. It is normally easier to gather large amounts of data from sources that

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support an API than it is from sources that only support a web interface. For sources that only support web interfaces, you should use targeted browsing. This section discusses Sentes features for searching data sources that support APIs.
Note that Searches initially require an Internet connection, but after the search results have populated in Sente, they can be reviewed even when Sente is offline.

Introduction to Searching External Data Sources in Sente

There are a few data sources that support proprietary APIs that programs like Sente can use. Many other libraries and other data sources instead support one of the two most common generic search protocols, Z39.50 and SRU. Many data sources, including many libraries and literature databases (like PubMed and Web of Knowledge) provide interfaces that let software like Sente perform searches and retrieve results without any user interaction. Sente can search these sites for references matching criteria specied by the user and automatically download dozens, hundreds, or even thousands of resulting references at one time. This is often the most efficient way to obtain large collections of references on a topic. Further, some of these same data sources also make it easy to retrieve only new results for a given search. The best example of this is PubMed. This makes it possible for users to set up standing searches in Sente and to have these searches updated on even a daily basis. When new results are found, Sente will draw your attention to them by adding a count of unread references to the name of each search in the source list.

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This example shows 150 unread/unviewed references in the instructional design search.

If you are looking for particular papers, or are unable to compose suitably specic searches within Sente, then you may need to use targeted browsing to locate and download most of your references. But if there is a data source in your eld that supports direct searching, using Sentes external search feature may be the best way for you to quickly and easily build large collections of relevant literature.

What Can I Search?

Almost all libraries today maintain their catalogs in a database of some sort, and most use one of the commercial packages designed for the purpose. Most of these systems provide both a web-based interface that users can employ to search the catalog, and an Application Programming Interface (API) that software like Sente can use for the same purpose. The same is also true of many of the online literature sources like Thomson Web of Knowledge, Ovid, and EBSCOhost. Sente can search many different sources of academic literature around the world, including: PubMed, from the US National Library of Medicine Web of Knowledge / Web of Science, from Thomson Ovid (using Z39.50) JSTOR (using SRU) Most university and academic libraries, using either the Z39.50 or SRU search protocols

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Some data sources are freely available, such as PubMed and most university libraries. Others such as Web of Science, Ovid, and JSTOR require you to have an account before you can use Sente to search them. Sente cannot provide you with access to any data source that you do not already have access to, but it does make using these data sources easier. Searching Library Catalogs with Z39.50 and SRU The most commonly supported protocols for searching library databases is called Z39.50. This protocol is supported by the majority of libraries around the world. If you are a student or faculty member at a college or university, there is a good chance that the institutions library supports the Z39.50 protocol. SRU is another, somewhat less common, protocol for searching library catalogs. Some institutions support both Z39.50 and SRU; others support just one or the other. Sente ships with the Z39.50 and SRU protocol information built in for many libraries, so the rst step in determining whether you can search your library is to look in the list of sites that comes with Sente to see if your library is listed there. If the library you would like to access is not present in Sente, it can be added assuming that your library supports one of these two protocols. To add the library, you will need to locate the required information for your library (e.g., network address, catalog name, etc.). This can often be found by searching Google for the name of your library and either Z39.50 or SRU. Other Data Sources Sente includes built-in support for some proprietary protocols, including those provided by PubMed and Thomsons Web of Knowledge. PubMed is freely available and does not require an account. Web of Knowledge is available only by subscriptions (institutional subscriptions are the most common), and authentication is usually by IP address. If your institution subscribes to Web of Knowledge or Web of Science, you will probably be able to access it through Sente while you are on the campus network. Because these are dedicated protocols, no additional information is required to access these sites.

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Proxies To get full access to some resources, you may need to work through a proxy server. For example, if you want to access a restricted source like Web of Knowledge from off-campus, you may need to access the site through a computer on-campus that has been set up to relay requests to the World of Knowledge site. In general, if you can access a data source through Safari, you should be able to access the same source through Sente. If the site requires a log-in, you may need to initiate the session using Safari, then continue the session using Sente.

Creating a New Search

Regardless of the data source you want to search, start by selecting File > New Search Then select a data source to bring up an appropriate search dialog.

Use File > New Search to create a new search.

When you click Execute Search, Sente may offer to let you rene your search criteria if the results include more than 100. Sente also limits the maximum number of references that a search can return to 1,000 by defaultthis keeps you from accidentally ooding your library with references.
You can change the default thresholds for refining searches and downloading in Advanced Preferences (Sente 6>Sente 6 Preferences>Advanced).

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Once you approve the search, Sente will begin retrieving references in the background. This can take up to several minutes depending on the nature of your search. The results appear in a new Search Collection inside the currently selected Collection or library. Automatic Updates Sente automatically keeps your Search Collections up-to-date by scanning the data source for new and updated references daily. Because of this, generally it is not useful to manually delete references from a Search Collection because theyll reappear at the next update. Instead, you could place a Smart Collection inside your Search Collection to help lter out unwanted references. The unviewed dot will always appear on new references, so you can easily spot the most recently added references. Of note, you can also right-click over any reference and select Set to Viewed (or Set to Not Viewed).

Managing Searches
This section explains how searches are managed within Sente. It is important to understand this information if you are using searches to obtain information for your library. New Searches and the Searches Category Whenever a new search is created in Sente, it is automatically placed in the Saved Searches category in the source list. These searches are stored within the library bundle, but not in the actual library itself, so the references returned by the search are not automatically included in what you see when you click on the References item in the source list.

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The tip about searches that appears when you create a new search.

Searches kept under the Saved Searches category in the source list are not synchronized if the library is synchronized with other copies of the same library. In essence, each search in the Saved Searches category in the source list is like a separate library included in the same package as the main library. If you move or copy the library, these searches will continue to appear in the library, but the references contained within the search are not automatically included in the library itself. This is done for several reasons: Exploratory searches. You might be creating exploratory searches, each of which might return many unwanted references. If you are successful in netuning the search parameters to the extent that almost all returned references are useful, then the search can be moved into the main library. But, until then, keeping the search in the Searches category makes it easy, for example, to delete the search and all of its references. Reference streams. You might want to set up a number of broad searches that you know will return many more references than you want in your library, but you want a chance to see all the results and select the desired references manually. For example, you might set up a search on a particular journal so that all articles from that journal are returned as each new issue is published. As you review the new search results, you would manually copy selected references from the search into the main library.

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Moving a Search into the Main Library If you have a search where you want most of the results in your main library, and you think this will continue to be the case as the search is updated over time, you can move the search into the main library. If you do this, all references currently in the search results, along with all new results returned over time, will be automatically added to your main library. In addition, these references will then be synchronized with any other synchronized copies of the same library. To move a search into your main library, simply drag the search entry from the Saved Searches category in the source list into the Local Collections category. Note that you cannot place a search in the Shared Collections category in a synchronized library. This is because doing so would cause the search to be automatically updated on each computer with a copy of the library. By placing it in the Local Collections category, the search will be updated on one computer and the results will be automatically propagated to all other synchronized copies. For the reasons listed above, you should not create duplicate searches on multiple copies of a synchronized library. Instead, create the search on the computer on which Sente is used most often and place the search in the Local Collections category in that copy (if desired). The search results will be automatically propagated to all other copies by Sente, rather than re-downloaded multiple times from the original data source. Automatic Update Frequency Searches in Sente can be set to automatically check for new results in the data source at regular intervals. When new results are found, they will be added to the search results (and the main library, if the search is in the Collections category in the source list). Some data sources (like PubMed) make it easy to query for new results for a search. In this kind of data source, Sente is able to ask for only those references that have been added or updated since the last time the search was updated. For data sources such as these, setting the update frequency to daily can be very useful, and doing so places little load on either your computer or the remote server. On the other hand, sites supporting Z39.50 or SRU generally do not have a good method for locating only new results. In general, the update frequency for these searches should be set to be much less frequent, or automatic updating should be turned off entirely.

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The update frequency on a new search is set to a default value based on the data source. For PubMed, it is set to update each day. For Z39.50 and SRU searches, it is set to update every 30 days. Deleting Searches As long as a search is in the Searches category in the source list, itand all of its resultscan be deleted simply by selecting it in the source list, right-clicking over it and selecting Delete. This means that if you are not satised with a search, rightclicking over it and selecting Delete will remove the search and all of its results from your computer. Once a search has been moved into the main library, however, deleting the search from the source list will remove the search, but not the results. All references that the search returned prior to being deleted will remain in the main library after the search is deleted.

Searching PubMed
PubMed is a large collection of biomedical literature maintained by the US National Library of Medicine. Access to PubMed is free and generally unrestricted. Creating a PubMed Search To search PubMed, use the File > New Search > PubMed command. This will open a search editor for a new search.

Search Editor for a New PubMed Search

For simple searches, you can simply enter the search term into the single search blank in the editor and click on the Execute Search button. You can search for or exclude terms from particular elds in the PubMed record by making selections in

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the rst two drop-down boxes. To add criteria, click the plus (+) button. Use asterisks in your search terms to indicate wildcards.

A PubMed search with complex criteria.

In the example shown above, Sente searches for references that include acetaminophen AND (ibuprofen OR diphenhydramine), and you can extend this logic into deeply nested queries. There are advanced options available for PubMed searches, which can be seen by clicking on the Show Advanced Options button. This is where you can specify, for example, that you would only like articles published after a particular date, or which are written in English.

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More search criteria is available in the Advanced Options.

It is also possible to create searches using Boolean logic (e.g., all references by either Smith or Jones that mention both alpha and beta). The rst time a search is executed, it will be placed in the Saved Searches category in the source list. Searches in this category are stored in the library bundle, but are not automatically included in the main library (that is, the search results can only be seen by selecting the search in the source list, not in the References category). For more information, see the section on Managing Searches in this chapter.

This example shows 150 unread/unviewed references in the instructional design search.

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Adjusting the Automatic Update Frequency for PubMed Searches By default, PubMed searches are set up to be automatically updated every day with new results (provided Sente has access to an Internet connection). This means that if Sente is running, it will check PubMed for new results at least once per day. Even though the check for new results at PubMed is efficient, you might want to adjust the update frequency or turn it off entirely. This can be done by going to Sente 6 > Sente 6 Preferences > Advanced and changing the search update criteria there. Note that changing the search update preferences here will affect all of your searches.

Searching Web of Knowledge

Thomson maintains two commonly used data sources, called Web of Knowledge and Web of Science. Both support a proprietary protocol for remote searches that Sente is able to use. Creating a Search To search either the Web of Knowledge or the Web of Science, select the File > New Search > Web of Knowledge command in the main menu. This will open a search editor for a new search. In this editor, you can specify: The database to be searched, including PsycINFO, Derwent, Current Contents and others. The date range to be considered. The search terms.

Web of Knowledge/Web of Science Search Editor

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It is also possible to create searches using Boolean logic (e.g., all references by either Smith or Jones that mention both alpha and beta). The rst time a search is executed, it will be placed in the Saved Searches category in the source list. Searches in this category are stored in the library bundle, but are not automatically included in the main library (that is, the search results can be seen only by selecting the search in the source list, not in the References category). For more information, see the section on Managing Searches in this chapter. Adjusting the Automatic Update Frequency By default, Web of Knowledge searches are set up to be automatically updated every seven (7) days with new results. This means that if Sente is running and has an Internet connection, it will check Web of Knowledge for new results at least once per week. You might want to adjust the update frequency or turn it off entirely. This can be done by going to Sente 6 > Sente 6 Preferences > Advanced and changing the search update criteria there. Note that changing the search update preferences here will affect all of your searches. Special Conguration The Web of Knowledge search uses the Thompson ESTI SOAP API. This service is separate from the standard web interface and its access may require conguration of a special proxy address, depending on your institution. You can change the URL that Sente uses to access the Web of Knowledge in the conguration window for the Web of Knowledge data source plugin. To access the conguration window, open Sente 6 > Sente 6 Preferences and select the Plugins tab. Then locate the Web of Knowledge data source plugin in the list of plugins (under Name) and select it. This will enable the Congure Selected Plugin button. Click this button and the conguration window will open.

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Select the Web of Knowledge Data Source line and click Congure Selected Plugin

Change the URL and update preferences in the conguration editor and click the Save button.

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Searching Sites that Support the Z39.50 Protocol

Z39.50 is the search protocol most commonly supported by academic libraries. Z39.50 is intended to be used by software, not by people, so there is no standard user interface to the protocol. Instead, if you provide software like Sente with a few key items of information, you will be able to search the library (or other collection) right from within Sente, rather than through, say, an online card catalog. Using a Built-In Z39.50 Server Sente ships with the information needed to search many university libraries using the Z39.50 protocol. Your institution may be in this list, so this is the place to look rst. To do this, use this command: File > New Search > Z39.50 Data Sources > Other Z39.50 Data Sources. This will open up the Z39.50 data source window, where the sites are listed alphabetically.

Accessing library catalogs that use the Z39.50 protocol.

If the library you would like to search is in the list, all you need to do is check the Fav? box and this library will be added to the list of Z39.50 sites available for new searches.

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List of sites that allow searches via the Z39.50 protocol.

Creating a Z39.50 Search Any of the Z39.50 data sources listed in Sente can be searched using the File > New Search > Z39.50 Data Sources option in the main menu. A search editor will be opened where you can specify one or more search terms.

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The File > New Search > Z39.50 Data Sources will open a menu of your favorite Z39.50 sources.

When a search is executed for the rst time, it will be added to the Saved Searches category in the source list. The returned references will not be automatically added to your main library. For more information on this, please see the section on Managing Searches in this chapter. Adding a New Z39.50 Site Sente ships with the connection information needed to search many libraries with the Z39.50 search protocol, but your library may not be on that list. If the library you would like to search supports Z39.50 but is not in the list of built-in Z39.50 sites, you can easily add it to Sente. Here are the steps to add a new Z39.50 data source to Sente: 1. Locate the following information for your site:

Hostname or IP address of the Z39.50 server. Note that this normally is not the same as the website that you would use to search the catalog manually. For example, you might normally use www.mylibrary.edu, but the Z39.50 server might be Z3950.mylibrary.edu.

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 Port number. This is a positive integer that indicates which port on the server is used for Z39.50 connections. Collection name. This is the name of the catalog on the server that you will be searching. Encoding. The method used for encoding non-ASCII characters. Most servers use ANSEL encoding, so start with that value if you cannot nd the information for your specic library. Another common value is Latin-1. Username and password. Most sites do not require this information, but yours may. 2. 3. Open the Z39.50 Data Source Window: File > New Search > Z39.50 Data Sources > Other Z39.50 Data Sources. Add a new entry to the list by clicking on the plus (+) button.

The plus (+) button adds a new line at the bottom.

4.

Double-click in each eld and enter the information collected above into the appropriate columns. Scroll to the right to access the User Name and Password elds. Test the connection. After entering the required information for a new site, it is a good idea to let Sente test the connection. Select the new source in the list and click on the Test the Connection button. Sente will attempt to communicate with the server using the information you have provided. If the connection succeeds,

5.

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you should then be able to perform searches on this site. If the connection does not succeed, you will need to double-check the information you entered about the site. If this all appears to be correct, then you may need to contact the technical support staff at the library for assistance. (It might be, for example, that the Z39.50 parameters on the website are out-of-date.) 6. 7. Check the Fav? checkbox so that the new site will show up in the main list of data sources. Close the data source menu and begin searching the new site using the File > New Search > Z39.50 Data Sources command on the main menu.

Send Us the Information on a New Site If you have added the data on a new Z39.50 site, you might want to consider sending the information to us at our support address. We will include the information in a later release of Sente so that others will not have to track down the information themselves.

Searching Sites that Support the SRU Protocol

Similar to Z39.50, SRU is a search protocol that lets software like Sente search library catalogs and other sources of academic literature. While not as commonly supported as Z39.50, there are many libraries that use this protocol. SRU stands for Search/Retrieval by URL and is a standard search protocol used by literature databases such as OAIster, the British Library, JSTOR, and others. Some SRU data sources (like JSTOR) restrict access to subscribers, but many do not. Built-In SRU Servers Sente ships with the information needed to search many libraries using the SRU protocol. Your institution may be in this list, so this is the rst place to look rst. To do this, use this command: File > New Search > SRU Data Sources > Other SRU Data Sources. This will open up the SRU data source window, where the sites are listed alphabetically.

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List of sites that allow searches via the SRU protocol.

If the library you would like to search is in this list, all you need to do is check the Fav? box and this library will be added to the list of SRU sites available for new searches. Creating an SRU Search Any of the SRU data sources listed in Sente can be searched using the File > New Search >SRU Data Sources option in the main menu. A search editor will be opened where you can specify one or more search terms.

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The File > New Search > Web (SRU) Data Sources will open a menu of your favorite SRU sources.

Example Search of Library of Congress Online Catalogue

When a search is executed for the rst time, it will be added to the Saved Searches category in the source list. The returned references will not be automatically added to your main library. For more information on this, please see the section on Managing Searches in this chapter. Adding a New SRU Site If the library you would like to search is not in the list already, you can easily add it. The only information required for SRU is the URL of the server. Simply click on the plus (+) button, enter the name and URL for the server, and check the Fav? checkbox (which will make the new entry appear in the main menu).

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The plus (+) button adds a new line at the bottom.

Testing a New Data Source After entering the required information for a new site, it is a good idea to let Sente test the connection. Select the new source in the list and click on the Test the Connection button. Sente will attempt to communicate with the server using the information you have provided. If the connection succeeds, you should then be able to perform searches on this site. If the connection does not succeed, you will need to double-check the information you entered about the site. If this all appears to be correct, then you may need to contact the technical support staff at the library for assistance. (It might be, for example, that the URL listed on the website is out-of-date.) Send Us the Information on a New Site If you have added the data on a new SRU site, you might want to consider sending the information to us at our support address. We will include the information in a later release of Sente so that others do not have to track down the information themselves.

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Using Proxy Servers

A proxy server is a server that acts as a gateway to other computers. Proxies can be set up for various reasons (e.g., for security, or to provide remote access to restricted servers). In some cases, you may need to access external data sources through a proxy server. There are two general types of proxy server that you may encounter. The rst is a proxy that stands between you and the Internet. This kind of server is typically congured in System Preferences in OS X. If you have such a proxy server congured to work with Safari, it is very likely to work with Sente with no additional conguration. The second kind of proxy you are likely to encounter is a server that provides you with access to restricted sites. One of the most common servers of this type is EZProxy. Many academic libraries maintain EZProxy servers to provide access to subscription services to their patrons. In many cases, you can simply change the URL in the bookmark for a site to have Sente go through this type of proxy server. Please consult your technical library staff for additional information on your specic proxy server.

Adjusting the Update Frequency for Searches

Most searches in Sente can be set up to occasionally check for new results for the original search. When new references are found for an existing search, they are automatically downloaded and added to the search collection with the Unread ag set to draw your attention to them. Some data sourcesmost notably PubMedare very efficient at handling search updates. Their programming interface is designed to download only new articles since the last time the search was executed. Because the protocols are well-suited to regular updates, searches on these data sources can be set to update on a daily basis with little impact on performance. Other data sources do not support update queries, so searches must be re-executed from scratch each time. Sente makes this as transparent as possible to users, but it can place a signicant burden on the computer and network connection each time an update is performed. For this reason, we recommend updating searches on Z39.50 and SRU sites much less frequently, if at all. To adjust the update frequency for searches, open Sente 6 > Sente 6 Preferences > Advanced and changing the search update criteria there. Note that changing the search update preferences here will affect all of your searches.

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Chapter 8

Other Ways of Adding References

There are many ways to get references into your Sente library, given how important this is to your research process. We have already seen searches, targeted browsing and several forms of le import. This chapter presents a few additional methods that you may nd useful in different contexts. These include: QuickAdd. This can be used to add references using just a common identier such as an ISBN or a DOI. For example, if you have a book in your hands, you can often use QuickAdd to automatically gather all of the citation details from just the ISBN. Creating References from Web Pages. You can create new references from any web page, using either Sentes embedded web browser, or Apples Safari browser. Sente will also offer to capture a copy of any web page visited with Sentes web browser as an attachment for future reference. Print to Sente. Anything you can print from any other application in OS X can be sent to Sente as a PDF. Sente will create a new reference and include the PDF as an attachment. These operations are described below in more detail.

QuickAdd: Adding References using ISBNs, DOIs, Etc.

Even in cases where you have a reference in hand, but the reference data is not readily available online, you may still be able to avoid doing manual data entry by using Sentes QuickAdd feature, which can often ll in many details about a reference from an identier such as an ISBN.

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To use QuickAdd, select the File > New Reference > QuickAdd command. The QuickAdd sheet will be displayed where you can enter the ISBN (or other identier). Sente will then attempt to look up the reference details.

QuickAdd Sheet

When one or more reference suggestions is returned, click on the correct reference and then click the Accept button. If the correct reference does not appear on the list, click the Cancel button.

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Select the reference from the list and click Accept.

Creating References from Web Pages

In some cases, you may want to create a reference from a specic web page. For example, if you are gathering news reports and one or more of the sites you use is not yet supported by Sentes targeted browsing feature, you might want to add a web page to your library as a web archive of the news article. This can be accomplished either through Sentes embedded web browser, or Safari. In both cases, Sente is able to automatically create an archive copy of the web page and attach it to the new reference for you. In most cases, you will get the best results if, prior to creating the new reference, you switch to what many sites call the Print View of the web page (that is, a reformatted version more suitable to printing). This will often reduce the clutter on the page and provide you with a more useable result.

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Creating a Reference from a Web Page in Sente If you are viewing the web page you would like to save as a reference within Sentes embedded browser, either in a web tab or in the attachment view, you can simply right-click (or cmd-click) within the web page to access the context menu, and select the option: Create New Reference from this Web Page. This option is also available from the File > New Reference menu.

The context menu in the embedded web browser within Sente.

When you select this command, Sente will open the Add Reference sheet, in which you can edit the citation data. You can also change the setting about automatically attaching a copy of the web page to the new reference.

The Add Reference sheet after selecting the command to create a new reference from a web page.

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Creating a Reference from a Web Page in Safari There will be times when you will be using Safari, and not Sentes embedded web browser, when you nd a web page from which you would like to create a reference. In this case, the steps are slightly different, but the results are the same as in the case mentioned above. To add the new reference to Sente, click and drag the icon in the address bar in Safari (do not just drag the text of the URL; you need to grab what is called the favicon in the address bar). Drag this icon onto Sente and drop it over the References entry in the source list.

Drag the icon immediately to the left of the URL onto All References in Sente to add a web page from Safari as a reference or attachment.

Again, Sente will present you with the Add Reference sheet where you can edit the citation data and keep or change the option of including a copy of the web page as an attachment.

Printing PDFs to Sente from Other Applications

Sente also supports creating references from PDFs generated by the Print operation in any other application. To do this, select the Print command in the other application. Then, after adjusting the print options so that you have the right pages included, click on the PDF menu in the print dialog and then, from the menu that appears, select Save PDF to Sente.

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The PDF print menu in Safari: Select Save PDF to Sente.

The PDF menu in the print dialog from Mail.

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Sente will receive a copy of the generated PDF and open the Add Reference sheet where you can edit the citation details. If Sente is not open at the time you save the PDF to Sente, it will open automatically. Sente will open the Add Reference sheet in which you can manually edit the citation details for the new reference.

The Add Reference sheet opens in response to printing a PDF to Sente.

After you click Add to Library, the new reference will be created and the PDF will be added as an attachment.

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Chapter 9

Collections

When you rst start gathering the references into your Sente library, having them appear in a single, long list is ne. But there will come a time when you will want to see your references organized into collections of various denitions. You might, for example, want all the references associated with a particular project, or all of those that discuss a particular topic. Sente has a number of powerful tools for organizing your library into collections and these are all discussed in this chapter. In particular, this chapter covers: The All References collection. This is a special collection that always includes all references in a library. Built-in smart collections. These are collections that Sente creates and maintains automatically for you, based on information such as date added or modied, status, rating, QuickTags, type, etc. Custom smart collections. These are collections that you create based on a set of rules about which references they should include. Smart collections can be dened based on complex Boolean conditions, and they can be nested arbitrarily deeply, so you can create rather powerful hierarchies. Search collections. These are collections that include the instructions for searching a remote data source, such as PubMed or WorldCat. Search collections include both the search denition and the references that have been returned by the search. Static collections. These are traditional, folder-like collections into which you can place references. The use of static collections is discouraged for several

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reasons; please see the section on Static Collections in this chapter for more information.

The All References Collection

The rst collection listed under the Library heading in the source list is All References. If you click on this collection, the reference list will show all of the references in your library. You can then use tools like Find and Browse to search the list for particular references. While this collection is called All References, there are some references stored in your library that will not appear in this collection: References in the Trash collection (under Local Collections) are excluded. References found only in search collections (under Saved Searches in the source list). These references are not added to your regular library until you either move individual references, or entire searches, into your main library. There is more information on each of these special collections later in this chapter.

Built-In Smart Collections

Everything else listed under the Library heading in the source list are built-in smart collections created and maintained automatically by the software. Some of these are based on static criteria (e.g., references added in the last week) and some are based on information under your control (e.g., statuses and QuickTags).

The top-level categories of built-in smart collections.

This list includes subcategories such as: Recent, including recently added and recently modied references.

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 By Status, which lists each of your custom statuses and the references with those statuses. This list is automatically updated as the list of statuses changes. Please see the chapter on Creating and Customizing a Library for more information about Reference Statuses. By Rating, which lists the different star ratings and shows the references to which each rating has been assigned. By QuickTag, which shows references that have had each of the entries in the QuickTags palette assigned to them. The hierarchy of smart collections based on QuickTags is automatically kept in sync with the hierarchy in the QuickTag palette. Please see the chapter on tagging for more information about QuickTags. By Type, which breaks down your library by type of reference. In general, these built-in smart collection denitions are not directly controlled by the user. That is, it is not possible to move, rename, add, or delete these categories directly. On the other hand, changes to either the status list or the QuickTags palette will cause those entries in these built-in smart collections to also be modied. For example, if you create a new entry in the QuickTags palette, it will show up in these smart collections as soon as the edit to the QuickTag palette is committed. These built-in smart collections reduce the need for custom smart collections in a library, but they do not eliminate it. For example, if you want to see all of the papers that are tagged with both of two tags, you will need to create your own smart collection based on those conditions. Please see the section in this chapter on Custom Smart Collections. The Recent Collections There are a number of smart collections that help you nd references that you have either recently added or edited. The most obvious collections are: Modied in the last day / week / month. Added in the last day / week / month. These work about as you would expect. It is currently not possible to adjust the time ranges used to create these smart collections. In addition to these, there are a couple of other collections:

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 Added but not yet viewed. These are references that are still marked Unviewed in your library. Added and needs data review. These are references that Sente has agged as needing manual review of the citation data. For example, if you import a PDF and Sente is not able to nd the citation data for the paper, it will mark the reference as needing data review. Note that as you work with references in these last two collections they will not automatically move out of the collection until you manually switch away from the collection and back. For example, if you click on a reference in the not yet viewed collection, you might expect it to immediately move out of the collection, because it has now been viewed, but this will not happen until the next time you open this collection. The By Status Collections Sente automatically maintains a complete set of built-in smart collections based on your custom reference status list. This list is maintained in the Library Setup panes; as you make changes to your status list, the collections under By Status will be updated to reect the changes. The By Rating Collections If you assign star ratings to references, they will automatically appear in these By Rating collections. Each rating category will appear in this list, whether or not there are any references that match the criteria. The By QuickTag Collections The QuickTags listed under the By QuickTag category in the Built-In Smart collection are those QuickTags that have been added to the QuickTag palette, and the hierarchy in the collection list will exactly match the hierarchy in the QuickTag palette. The collection list will change whenever the QuickTag palette is edited (note that edits will not be saved until the palette is closed). Please see the chapter on QuickTags for more information about tagging.

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The By Type Collections Each reference in your library should have a reference type (e.g., journal article or book). For collections with a wide variety of types of references, it can be useful to view all the references of a particular type. Only those reference types that are actually in use in your library will appear under the By Type category.

Custom Smart Collections

This section provides an overview of Custom Smart collections and instructions for using the Smart collections, including: Creating Custom Smart collections The Smart collection Editor Editing Custom Smart collections Copying Custom Smart collections Working with Custom Smart collections Complex Queries Overview As mentioned in the section about Built-In Smart collections, a smart collection is a collection of references whose exact contents are determined by applying a set of criteria (e.g., has an author named Smith) to the references in the parent collection. Only those references from the parent collection that match the specied criteria are included in the smart collection. (In the case of top-level smart collectionsthat is, those without a parent collectionthe entire library is treated as the parent.) In addition to the Built-In Smart collections (please see the section in this chapter about Built-In Smart Collections), you can create your own custom smart collections in either the Synced Collections or Local Collections categories. These smart collections can be nested arbitrarily deeply, making it possible to create very sophisticated subsets of your library. Of note, custom smart collections saved in the Synced Collections categories will be synchronized to all synced copies of the library; custom smart collections saved in the Local Collections categories will remain only in that copy of the library.

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Creating Custom Smart Collections To create a new smart collection, you can use: The File > New Collection command in the main menu. This will bring up a submenu of options including: New Smart Collection Under XYZ (where XYZ is the name of the collection currently selected in either Local Collections or Synced Collections). New Smart Collection in Synced Collections, which will place the new smart collection at the top level in the Synced Collections category in the source list, allowing the collection to be synchronized with other copies of the library. New Smart Collection in Local Collections, which will place the new smart collection at the top level in the Local Collections category in the source list, keeping the collection local to this library only and not synchronizing it with other copies of the library. New Static Collection in Local Collections, which will place the static collection at the top level in the Local Collections category in the source list. Static collections are not recommended and will not be synchronized with other copies of the library. Please see the section on Static Collections for more information.

The new Smart Collection will be placed under the instructional design collection because it is selected in the source list.

The New Collection command in the toolbar, if one has been placed there (see Customizing the Toolbar for more information). The sub-options are similar to the above.

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The New Collection command in the toolbar.

In each of these cases, Sente will open a smart collection editor in which you can specify the criteria to be applied when selecting references. The Smart Collection Editor When you create a new smart collection, the Smart Collection Editor appears. This is where you will enter your criteria for the new custom smart collection.

The Smart Collection Editor, where criteria is specied.

Simply use the drop-down lists to choose your criteria, click on a plus (+) button to add additional criteria or the minus (-) button to delete a criteria, and click the Apply and/or OK buttons to apply the lter criteria to the Smart Collection. In the rst line of the Smart Collection Editor, your choices are to include references that match: Any of the conditions, or All of the conditions For the sets of criteria, your rst options are: Any Field Any of the available values, such as Publication Type, Year of Publication, Keyword, etc.

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 or All of...available only after the rst criteria has been established, to signify that the lter is to include the criteria listed above, or All of the criteria that will follow and Any of...available only after the rst criteria has been set, to signify that the lter is to include the criteria listed above, and Any of the criteria that will follow.

First Set of Available Criteria to Choose From in the Smart Collection Editor

The second set of options are: Containsthe selected eld contains the following value. Does not containthe selected eld does not contain the following value. Isthe selected eld is (and is only) the following value. Is notthe selected eld is not the following value. Begins withthe selected eld begins with the following value. Ends withthe selected eld ends with the following value. Equals any ofthe selected eld equals any of the following values.

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Second Set of Available Criteria to Choose From in the Smart Collection Editor

The text box on the right side of the criteria line is where you type the value that is to be matched according to the criteria you specied with the previous two options. Please make sure to check your spelling! Editing Custom Smart Collections To rename a smart collection, right-click over the collection and select Rename, enter the new name and click Okay. To delete a smart collection, right-click over the collection and select Delete. Note that this will delete the collection (lter) only, not the actual references. To modify a smart collection, follow these steps: 1. 2. Either double-click the smart collection or right-click the smart collection and choose Get Info. Modify the criteria shown and proceed as though you were creating a new smart collection.

Copying Custom Smart Collections If you want to apply the same criteria to another collection in your library, optiondrag the smart collection to copy it to another folder (or simply drag to move it instead); the smart collection will derive its contents from its new parent. For example, if you copy a custom smart collection that lters for certain authors and paste it into a smart collection that lters for a range of years, the copied smart collection will now list all references of those specic authors within the date range specied by the parent collection.

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Working with Custom Smart Collections You can use smart collections for a variety of specialized purposes:
Search Renement

Rarely will your online search extract exactly the references you need from a data source. Generally, your search will be broad enough to capture what you need, while also including additional unwanted references. The solution? Place a custom smart collection inside your Saved Searches collection to rene the results. (Please see the chapter on Searches.)
Classication

One way to rene any collection in your library is to lter for a particular keyword, rating, or status that youve assigned to references. For example, a ve-star smart collection can take you straight to your most important references. You can use the built-in smart collections to lter all of the references in your library by rating or status, but if you want to be able to lter just the references in one of your custom smart collections by rating, status, keyword or another criteria, you can create a smart collection to do this and place it within the parent custom smart collection.
Favorite Journals

Use a smart collection to create a newsletter of new articles from a few of your favorite journals. To do this, just create a smart collection that only accepts references from your favorite publications, and copy the smart collection to all of your Saved Searches collections. In this way, you can view the parent Saved Searches collection to see everything, or just the child smart collections to see only items from your favorite publications. Wondering whats been published since your last check? Look for the orange dots in the reference table.

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Setting up a Smart Collection to gather references from your favorite journals. Multiple Searches

Often a single online search wont be enough to get what you want; you might need to run different sets of search criteria against a data source, or you might need to search several different data sources. The solution is to place all of these similar search collections into a single collection. Complex Queries Most lters can be dened with just a few lter terms. Sometimes, however, it is important to be able to create searches with more complex logic. Sente supports what is known as Boolean logic for these complex queries. This section explains how to use Boolean logic in Sentes smart collection editor.
Multiple Filter Terms with AND

The simplest form of Boolean logic is probably when you want to combine multiple lter terms in a single lter and only return those records that match all of the terms. For example, you might want only those references that include alpha and beta and gamma. This would often be represented as: alpha AND beta AND gamma In Sente, this is accomplished by adding lter terms in the editor by clicking on the plus (+) button next to the rst term in the list. If you create three terms at the top level and put alpha in the rst, beta in the second, and gamma in the third, set the rst option (Include references that match...) to All, and set the middle

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option to contains all of these conditions, you will have created a lter that requires references to match alpha, beta, and gamma.

Multiple Filter Terms with AND Using OR

Sometimes it is important to be able to locate references that match any one of several lter terms. Normally this is in conjunction with other terms that must also be matched. For example, to nd references by either Smith or Jones that include the terms alpha, beta, and gamma, you would want a lter that looks like: (Smith OR Jones) AND alpha AND beta AND gamma In Sente, this would be done by adding the top level clauses for alpha, beta, and gamma, just like in the previous example. Then you would add another clause for and Any of... and this clause will automatically create two sub-clauses. One of these would be set to An author name contains Smith and the other to An author name contains Jones. One can think of the Sente query then as being: All of (alpha AND beta AND gamma AND Any of (Smith OR Jones)) This same logic can be applied to any depth in the smart collection editor.

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Multiple Filter Terms with AND and OR Using NOT

Sometimes you might want all references except references containing certain criteria. Take, for example, the above lter and say we want all references with alpha, beta, and gamma, except those references authored by Smith or Jones. Our lter would look like: alpha AND beta AND gamma (NOT Smith OR Jones) In Sente, this would be done by adding the top level clauses for alpha, beta, and gamma, just like in the previous example. Then you would add another clause for and Any of... and this clause will automatically create two sub-clauses. One of these would then be set to An author name does not contain Smith and the other to An author name does not contain Jones. The Sente query then would be: All of (alpha AND beta AND gamma AND Any of (NOT Smith OR Jones)) Again, this same logic can be applied to any depth in the smart collection editor.

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Multiple Filter Terms with AND, NOT, and OR

Search Collections
Sente also supports a special type of collection that holds both references, and the search instructions for retrieving references from a particular data source. For example, you might create a search on PubMed for articles by a particular author. When you create such a search, Sente creates a search collection to hold the results as well as the original search criteria. The Saved Searches Category When you create a search, Sente will automatically place the new search collection in the Saved Searches category in the source list. This is a special category of data that is stored inside your library bundle, but the references are not included in the All References category in the source list.

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The Saved Searches category. This is where all new searches are initially stored.

You can work with search collections in the Saved Searches category much like you would work with any other collection in your library. For example, you can place smart collections under a search collection to lter the search results on any arbitrary criteria. You can move any number of references from a search collection in Saved Searches into your main library by selecting them and dragging them onto the All References category for your library. You can also move the entire search into your main library by dragging the search collection itself (not the references within the collection) onto the Local Collections category in the source list. When you do this, all references in the search collection will be added to your library, along with any new search results that are retrieved at a later date. If you delete a search collection in Saved Searches, the search, along with all of the references returned by that search, will be deleted. This will not affect references that you have manually copied into your main library. Search results deleted in this way are not moved to the Trash collection; they are simply deleted from your library bundle. Much more information about searches can be found in the chapter called Searches.

Static Collections
Sente also supports organizing references in what we call static collections. These are collections into which you simply drag or copy references.

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Please Do Not Use Static Collections! Please note that while the software continues to support static collections, their use is discouraged. There are several reasons for this: Static collections are more difficult to maintain that other options. In particular, we strongly encourage people to adopt QuickTags as their primary organization tool in Sente. Please see the chapter on QuickTags for more information. Static collections are not synchronized. Static collections can only be created in the Local Collections category in Sente and collections in this category are not synchronized. This means that whatever organization you create in one copy of your library using static collections will not be replicated in other copies. (The fundamental reason that we do not support synchronization of static collections is because techniques that we use for synchronization, which work so well for individual references and smart collections, do not work well for static collections. The amount of information that would need to be transferred to the sync servers is too large and there is too much opportunity for creating sync conicts.) The bottom line is that we think there are much better ways of organizing your library than by using static collections. We continue to support them because there are many Sente users who started with the software in a much earlier version and who have a lot of time invested in this style of organization, but we are encouraging all new users to avoid the use of static collections, and all long-time Sente users to invest the time in migrating to a QuickTag and smart collection based approach. And, if the above information is not enough, you should know that we may simply eliminate traditional static collections in a future release. So, please, do not use static collections when organizing your library!

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Chapter 10

QuickTags

As your research library grows, it becomes increasingly important that it stays well organized so that you can nd what you need when you need it. In this chapter we describe QuickTags, a feature that is unique to Sente, and one that many users nd indispensable. For many users, the QuickTag feature in Sente has completely replaced the use of organizational tools like static collections and made many common organizing tasks much easier. You may have used other programs that support the concept of tagging. In these applications, tags are usually short strings of text that you can assign to any number of objects (documents, web pages, references, etc.). These programs also usually include a simple interface for retrieving objects based on their tags. The concept of QuickTags in Sente extends this idea by including an interface for arranging the list of available tags into a hierarchy, much like you arrange les in a computer le system. This enables you to represent far more complex organizations quite naturally. Furthermore, searches based on QuickTags use this hierarchy to return results based on both explicit tags (those that you explicitly assigned) and implied tags (tags which were not explicitly assigned by the user, but which are implied by tags that were assigned). Because implied tags are based on the hierarchy as it exists when you are doing the search, the results automatically reect your current thinking about how the tag hierarchy should be structured, typically with little or no effort on your part. Hierarchical QuickTags in Sente are a more powerful and exible classication system than anything you are likely to have used before. Yet you can start simply,

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with only a basic understanding of how QuickTags work, and gradually enhance your approach as you become comfortable with the tools and ideas. We would encourage you to start by reading through this chapter to get an overview of QuickTags and then give QuickTags a try on a small scale in your own library. We think you will soon nd QuickTags to be both intuitive and very effective for organizing even the largest of libraries.

A sample QuickTag hierarchy shown in the QuickTag palette. The tags that have been explicitly assigned by the user to the selected reference are checked. The implied tags are shaded blue, but not checked.

Why Use QuickTags Instead of Static Collections?

When many people start using Sente, their rst instinct is to organize their references by placing them into collections. Collections in Sente have some rather nice features that make this particularly attractive. Despite this, however, we recommend the use of QuickTags and smart collections rather than static collections for organizing your library. So, why not just use collections if they are already familiar and supported in Sente? Here are a few reasons: Efficiency. Placing references into static collections is done by dragging and dropping the reference into the target collections. This is pretty efficient, but it is even quicker to click a few boxes in the QuickTag palette. Further, because

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the entire QuickTag palette is reproduced in the main menu, you can assign custom keyboard shortcuts to your most commonly used tags. Maintainability. When you rst place a reference into the appropriate collections, things seem fairly simple. But as your thoughts about organization evolve, you are likely to want to change the collection hierarchy and where individual references are placed within that hierarchy. This is not as simple to accomplish as you might expect, because of the way in which static collections work. For example, if you originally placed a reference three levels down in your collection hierarchy, it will appear in each of the parent collections as well as in the target collection. This means that it may need to be moved from each of those collections if your organization changes. With tags, however, you can change the hierarchy quite simply, and in many cases the references will not need to be modied at all. Synchronization. Sente is able to synchronize both the tags on individual references and the denitions for custom smart collections based on tags (or any other smart collections for that matter). Sente is not able to synchronize static collections. This means that if you organize your library using tags and smart collections, this organization will be automatically replicated in all copies of your library. Some of these advantages will be made more clear as you read through the rest of this chapter. If you are not yet convinced that tags are superior to static collections for organizing your library, please keep reading. As the developers of Sente, we are convinced that tags are superior to static collections, so this is where we are placing our energy. We know that for some users the idea of tagging, rather than ling in collections, will seem strange at rst. We think over time you will come to see that tagging is actually the superior option.

Why Use QuickTags Instead of Traditional Tags?

If you already use tags in another software application, you may be wondering what Sentes QuickTags can offer that traditional tags do not. Traditional tags are, after all, fairly powerful and useful. You can typically assign tags by simply clicking on an entry in a list of tags, or by typing the rst few characters of the tag and the software will autocomplete for you. After that, searching based on tags is often easy and rapid. Sente supports this type of tagging, so why not just use it? Because QuickTags are much more powerful, exible and efficient to use. The most important differences between QuickTags and traditional tags are:

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 Hierarchical Tag Dictionary. While most programs that support tagging work with simple, at lists of tags, Sentes QuickTags are organized in a hierarchy. This supports far more powerful and useful organization strategies. You can have, for example, a hierarchy of tags that range from less specic to more specic terms, or from a single large category to smaller and smaller subcategories. There is no practical limit to the depth of the QuickTag hierarchy. Implied Tags. One important aspect of how Sente implements QuickTags is the concept of implied tags. If you explicitly assign a tag a few levels down in a QuickTag hierarchy, the reference will behave as though all the parent tags of that tag were also assigned. Further, as you edit and rearrange the hierarchy, Sente keeps up because the implied tags are evaluated as queries are run, not just when the original tag is assigned. This means that you have to assign fewer tags to each reference to get the desired results, and you can change your tag hierarchy over time. In general, you will not have to update the tags you originally assigned to each reference as you make these changes. Automatic Smart Collections. Sente also automatically creates and maintains a built-in smart collection hierarchy that matches the QuickTag hierarchy in a library. This makes it easy to quickly nd all references that have been tagged with any tag (either explicitly or implicitly) without having to manually maintain the smart collection hierarchy. Each of these concepts will be explained more fully in the pages that follow. The best way to learn about QuickTags is to work with them. The rest of this chapter will explain both the mechanics of working with QuickTags and the ideas behind how they should be used.

Working with the QuickTag Palette

Most operations involving QuickTags are done in the QuickTag palette, which is normally seen in the small utility window accessed through the Window > QuickTag Palette command or by clicking on the QuickTags button in the toolbar.

The QuickTags toolbar button.

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Editing the QuickTag Hierarchy The rst step in using QuickTags is to set up your initial QuickTag hierarchy in the palette. When you rst open the palette (Window > QuickTag Palette), you will see some default entries. These are simply placeholders and should be replaced with values that are meaningful in your work.

The default QuickTag palette window.

To make changes to the QuickTag hierarchy, you rst need to click on the lock icon to unlock the palette. When you do this, the footer of the window will change to display the available editing commands.

The buttons at the bottom of the QuickTag palette after clicking Unlock.

The following commands are available when editing the QuickTag palette: Add Tag. This adds a tag as a peer to the selected tag. This adds a tag below the selected tag. This removes the selected tag from the palette.

Add Child Tag.

Remove Selected Tag.

Rename. Click on the current name to rename the tag. Sente will ask you whether you want to change the tag on all references to which it had previously been assigned.

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 Rearrange. Drag a tag onto a new parent or top level. The changes to implied tags on all references will immediately take effect. Lock. Clicking on the lock icon will take the palette out of edit mode. This will also cause Sente to update the automatic, tag-based, built-in smart collections and it will cause the updated palette to be propagated to all other copies of a synchronized library.

After making changes to the QuickTags, click on the lock to apply the changes.

You can edit the QuickTag palette at any time and Sente will normally help ensure that the library keeps up with the changes in the appropriate way (e.g., by offering to update all references to reect the changes). This means that you do not need to get the entire hierarchy right the rst time. Start by adding some values that you think make sense and begin using them. As your thinking evolves, you can update the palette to reect your new ideas. For help in designing your QuickTag hierarchy, please see the section entitled Designing Your QuickTag Hierarchy below. Viewing Assigned Tags When you select a reference in the reference table, the QuickTags that have been assigned to that reference are reected in the QuickTag palette. Any tag that has been explicitly assigned to the reference is marked with a checkmark, and the tag value is colored blue. Any implied tags (tags that have not been explicitly assigned, but which are implied by other, explicitly assigned tags) are colored blue, but the checkbox is left unchecked.

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The QuickTag palette with more than one reference selected in the reference table.

When you select more than one reference in the reference table, the QuickTag palette represents the combined state of all these references: Any tag that has been explicitly assigned to all of the references is checked. Any tag that has been explicitly assigned to some, but not all, of the references will be shown with a dash in the checkbox to indicate mixed-state. Any tag that is implied on any reference is shaded blue. (Note that there is no concept of mixed-state for implied tags.) Assigning and Removing Tags Once you have added some values to the QuickTag palette, you are ready to begin assigning tags to your references. The simplest case is assigning tags to a single reference. Just select the reference in the main reference list in Sente and click on the desired tag in the palette. To remove the tag, just click again. The checkboxes in the palette will always reect the current state of the selected reference. Assigning tags to multiple references works the same way. In this case, select several references in the reference table and assign a tag by clicking on it in the palette. Removing the tag by clicking again.

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In each case, if you assign a tag that is not at the top level of the hierarchy, you should see all the parent tags back to the top level turn blue to indicate that they are implied by the one you explicitly assigned. More information on implied tags and how they work can be found later in this chapter.

Behind the Scenes

You can use QuickTags and tags in Sente without understanding the details of how they are implemented, but there are times when it is helpful to know a bit more about the internal design. Here are the important details about how tags are implemented: All tags, both QuickTags and regular tags, are stored as simple strings of text in each reference. Entries in the QuickTag palette are also just simple strings of text, organized in a hierarchy. You cannot add two entries to the QuickTag palette with the exact same value. There are no links between the entries in the palette and the tags stored in each reference, other than the fact that they might contain identical values. This has several consequences: If you enter a tag manually in the tags eld that happens to exactly match an entry in the palette, it will behave exactly the same as if the value had been assigned through the palette. If you add an entry to the palette that happens to match a tag on one or more references, those references will behave exactly as though they had been tagged with that tag using the palette. If you copy a reference from one library to another, all tags assigned to that reference will be carried along to the new library. As above, if any of those tags happen to match entries in the palette, they will behave as though they were originally tagged through the palette. The rule about no two entries in the QuickTag palette having the same value means that you will often have to make the values more precise than you might have otherwise. For example, you might be tempted to create two entries called Other, one under a parent called Language and the other below Region. Instead, you would need to consider names like Other Language and Other Region to keep them distinct.

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Designing Your QuickTag Hierarchy

For many Sente users, the QuickTags feature is the single most useful tool for organizing their library. For these users, QuickTags make classifying and accessing references easier and more efficient than any approach. But to get the most benet from QuickTags, it is important to think carefully about how you set up your QuickTag hierarchy. This section introduces the most important concepts to understand during this process. There are two key ideas that should be kept in mind when designing your QuickTag hierarchy: First, the QuickTag hierarchy should be viewed as a collection of independent hierarchies, rather than as a single hierarchy. That is, each top level tag is typically the root of an independent hierarchy. Second, each of these independent hierarchies should be either what is commonly called a containment hierarchy or an is-a hierarchy. Other types of hierarchies will often lead to confusion and inefficiency. These two concepts are explained in more detail below. Multiple, Independent Hierarchies Modern, hierarchical computer le systems are obviously powerful, and they affect the way many people think about organizing information, but they are not, in fact, very good models for organizing complex data. The main problem is that, without resorting to a complex system of le aliases or links, each le is stored in a single location in the hierarchy of folders on a computer. This structure starts to break down as soon as you care about more than one aspect of a le. For example, if you are classifying material on military history, do you put folders for topics like battle tactics and political context under folders for each conict you are studying, or do you place folders for each conict under folders for battle tactics and political context? Neither answer is obviously correct and both are difficult to maintain and use. With QuickTags you can treat each of these as separate dimensions on which you want to classify your material. You would do this by creating several hierarchies within the QuickTag hierarchy, each starting from a different top-level term, and assigning one or more tags from each relevant hierarchy to each reference as appropriate.

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For example, in the case of military history, you might create a top-level tag called Conict with sub-tags for the World War I, World War II, the American Civil War, etc. Under each of these you might create tags for particular battles within each war. Then, you might create another top-level tag called Battle Tactics, with sub-tags for Offensive Tactics and Defensive Tactics, and so on. With a design like this, you would assign tags from the Conict category to any works that discuss specic wars or battles, and tags from the Battle Tactics category to works that specically deal with those topics. Many works would be tagged with at least one tag from each top level category. With this approach, you would never have to wrestle with deciding whether you wanted to create a folder for specic battles inside a folder on tactics, or the other way around. Nor would you have to decide which aspects of a work were most important -- you would simply assign all relevant tags to each reference. One way to think about these multiple hierarchies is to consider that they represent different dimensions on which you might classify each work. It is common to end up with QuickTag hierarchies with several different dimensions, or sub-hierarchies. Types of Hierarchies Starting with the idea that the QuickTag hierarchy is really a collection of several, distinct sub-hierarchies, one then needs to decide how to design each of these hierarchies. Because of the way QuickTags work in Sente, it is often best if each hierarchy is either a containment hierarchy or an is-a hierarchy. These are explained below.
Containment Hierarchies

A containment hierarchy is one in which all child tags are parts of, or contained within, the parent tag. For example, the tag 20th Century might have the sub-tags Early 20th Century and Late 20th Century (the early 20th century is part of the 20th century). Or a tag related to the eld of study might be Economics, with sub-tags for Microeconomics and Macroeconomics (Microeconomics is part of the study of economics). Or here is a larger example related to geography:

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A sample containment hierarchy based on geography.

In each case, the child tags represent either a part of, or something contained within, the parent tag. Using any containment hierarchy, you would tag a reference with the most specic applicable tag. All parent tags will be implied by this assignment. Searches within Sente will behave as though all of the implied tags were also assigned to the reference. For example, if you tag a reference with Chile from the geography hierarchy example shown above, and later search for references tagged with South America, the reference would be returned because the South America tag is implied by the Chile tag. Furthermore, because the QuickTag hierarchies are evaluated as they are used (rather than when tags are assigned), if you were to introduce a new level in the geography hierarchy for Western Hemisphere, and move everything shown above to be below this new tag, any reference tagged Chile would immediately be returned in a search for references tagged Western Hemisphere because that would now be implied.

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In containment hierarchies, it is usually best to make all child tags represent nonoverlapping concepts or spaces. For example, if one were expanding the geography example to include specic states within the United States, these might go directly under the United States tag. If one later wanted to add larger regions (e.g., Western States, Southern States, etc.) to the hierarchy, the individual state tags should be moved to be under the new region tags, rather than leaving them at the same level as the new tags. If this is not done, the implied tags will yield incorrect results. In containment hierarchies, it is common to make the top-level tag of the hierarchy be a description of the hierarchy, rather than an actual member of the hierarchy. For example, in the geography example above, the top-level tag might be Geography. This lets you collapse all geography-related tags under one parent tag.
Is-A Hierarchies

The other common type of hierarchy used in Sente is sometimes called an is-a hierarchy, or a class hierarchy. In this type of hierarchy, each child is an example of, or a sub-class of, the parent. For example, if one were to classify writing, one might have a top level tag Literature, with sub-tags for Fiction and Non-Fiction (ction is a type of literature). Non-ction might then have sub-tags like History, Biography, etc. (a biography is a type of non-ction literature). As another example, one might be studying modes of transportation:

A sample is-a hierarchy based on transportation vehicles.

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If you consider each tag in the example above, you could say it is an example of the parent tag. For example, a Sedan is a Passenger Car, which in turn is a Motorized Vehicle. As with a containment hierarchy, references should normally be tagged with just the most appropriate tags from an is-a hierarchy. In our example above, a work that discusses non-motorized transportation in general should be tagged NonMotorized Vehicles but a work that discussed different types of bicycles explicitly should be tagged with each type of bicycle (and not Non-Motorized Vehicles, which will be automatically implied). One way to decide which level of tag to apply is to ask yourself whether you would expect a particular reference to be returned if you were to search on each of the tags under consideration. For example, a paper describing trends in personal transportation in China may discuss bicycles extensively. Tagging such a reference with only the Non-Motorized Vehicles tag would mean that a search on Bicycles would miss this paper. On the other hand, if it makes little distinction between various types of bicycles, tagging the paper with Road Bikes and/or Mountain Bikes would mean that searches on either of these terms would return the paper, even though it has little to say on either specic subject. In the case of an is-a hierarchy, the top-level node is typically the most generic term in the hierarchy (unlike in a containment hierarchy -- see the Containment Hierarchies section, above). Putting It All Together When you set up your QuickTag palette as described above, with several independent hierarchies, each either a containment or an is-a hierarchy, you will nd that you can quickly classify new references as you enter them into your library. You will get used to asking yourself questions like What region of the world does this reference discuss? or Which modes of transportation are considered? Part of the power of this approach becomes apparent when you nd yourself looking for a subset of your references that you may not have explicitly considered before. For example, though your primary interest might be personal transportation trends in China, you are likely to have collected many references that cover other forms of transportation elsewhere in the world. Should you later want to nd all references that discuss air transportation in North America and Europe, it would be easy to create a new smart collection based on a new collection of your existing tags, as will be described below.

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Finding References Using Tags

The reason one goes to the effort of carefully conguring a QuickTag hierarchy and then tagging each reference is to be able to use this information to nd references quickly and easily in the future. Sente provides several useful tools for searching within your library using QuickTags. (There is a fuller description of each of these methods elsewhere in this manual; this is just a brief introduction to searching based on QuickTags.) Built-In, QuickTag-Based Smart Collections. As you modify the QuickTag palette, Sente automatically maintains a parallel set of built-in smart collections in the source list. This makes it easy to select all references tagged (either explicitly or implicitly) with any of your tags.

The built-in smart collections based on QuickTag hierarchy.

Custom smart collections. When you want to locate references with a combination of tags, you can create a custom smart collection. Each such collection can include tests on tags as well as other criteria (e.g., all references tagged Bicycles and China published before 1970).

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A custom smart collection denition based on tags.

The Library Browser. One can do quick, ad hoc searches based on QuickTags using Sentes library browser (cmd-B). The library browser will provide feedback as you rene your search by showing only those tags that are actually present in the remaining subset of the data.

Using tags in the library browser.

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Chapter 11

Find, Browse, and Hotwords

Sente includes several tools for locating and viewing references contained in your library: Find, for searching by free text; the Library Browser, for locating references based on their attributes, like author name, journal name, publication year, etc; and, Hotwords, for highlighting words and phrases you select to help you quickly scan references visually. Each of these is explained in detail below.

Find
The Find command lets you perform free-text searches on your library. By default, Find will search anywhere within a reference for matches. Alternatively, it can be told to look only in specic elds. This lets you locate references that contain the string white, but only in an author name, and not in abstracts or titles. When you perform a search using the Find command, you can save the search as a smart collection so you can repeat the search at any time in the future by simply clicking on the saved collection.

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How to Use Find If you have the toolbar visible, and your toolbar conguration includes the Find eld, you can initiate a Find search by simply clicking into that eld, typing your search string, and then pressing Enter.

The Find and Browse items in the toolbar.

You can also initiate a Find by executing the View > Find command in the main menu, or by pressing the keyboard shortcut for this command, cmd-F. In this case, if the FInd toolbar item is visible, keyboard focus will be transferred to that eld. Otherwise, the Find tool will appear above the reference list, as shown below.

The Find eld that is used when the toolbar item is not visible.

In either case, you can enter the search string and press Enter to initiate the search. As long as a Find operation is active (with the Find panel still open) and a Reference Editor is open (such as Bibliography Fields or Summary), all occurrences of the search string will be highlighted in the Reference Editor to help you spot the text that matched your search.

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Highlighted search string in the reference editor.

To return to your original reference list, you can: Click the x in the Find eld (either in the toolbar or in the Find panel), Use the View > Find... command in the main menu, or Type cmd+F. Saving the Find Operation as a Smart Collection If you are using the Find panel (and not the Find eld in the toolbar), you can click on the Save button to create a smart collection based on the contents of the Find operation. (See the Collections chapter for more information.)

A Find operation saved as a smart collection.

Saving the search operation in Find will create a new Smart Collection under Local Collections in the source list on the left side of the main Sente window. Now, whenever you click on your new Smart Collection in the source list, you will see upto-date results of the Find operation you just performed, without needing to go

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through the Find steps agains. For more information, please see the Collections chapter. Restricting a Find to Specic Fields You will sometimes be interested in locating references that match a search string, but only in specic elds. For example, you may be looking for a paper that contains a particular term in the title, and you do not want to see all of the papers that include that term in any other elds. If you click on the magnifying glass at the left end of the Find text box (where it initially says Enter search terms in the Find panel, although not in the toolbar Find eld), a menu of options will appear. This menu includes: Commands for restricting the search to just one eld in the reference (to search only in the author names eld, for example). A list of the most recently used search terms (search history). A command for clearing the search history list.

The Find drop-down menu.

If you select one of the Search only entries in this list, your search will return references where the contents of the selected eld match your search string. Restricting Individual Terms in a Find You can also create searches that combine individual terms, each of which can be independently limited to a particular eld. For example, you can search for all references that have an author name of White and include the word mRNA in the title.

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This is accomplished by prepending each term with the two-letter abbreviation for the eld to be searched. These abbreviations are: AU: Author names ID: Identier TA: Tags KW: Keywords TI: Title YR: Year Adding qualiers to each search term can be helpful in restricting or narrowing the resulting list of references. For example, if the search blank contains AU:Smith, it will only match Smith if it occurs in one of the authors names.

An example of adding qualiers to search terms in the Find operation.

Any term that does not have a prepended eld code will be allowed to match any eld in the reference. Searching for Phrases Normally, if you specify more than one word in a Find operation, each word is matched independently. To specify a phrase, surround the word with quotation marks. For example, typing gene expression in the search box will return only the references that contain the phrase gene expression in any eld. Entering TI:gene expression in the search box will return the references that contain gene expression as a phrase in the title only.

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Library Browser
Sente also includes a powerful library browser that makes it easy and quick to sort through even very large libraries based on values found in specic elds. By selecting matching criteria in sequence, you can gradually pare down your reference list to obtain the results you want. You can also save your browse operation as a smart collection for easy reuse. How to Use Browse The library browser is activated by using the View > Browse option in the main menu, by pressing cmd+B, or by clicking on the Browse item in the toolbar.

The Browse toolbar item, along with the Find eld.

The library browser always operates on the currently selected collection. To browse your entire library, select the References entry under Library to display all of the references in the library. When you activate Browse, the Browse panel will appear at the top of the Sente window and this panel will always include at least one list. The rst list to appear is the list of elds that can be searched. A selection can be made in this list by using the mouse to select one or more elds, or by using the keyboard to type the rst few characters of the desired eld.

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The Browse panel with lists.

After you select a eld type, the list will be updated to show all unique values for that eld in the current collection. For example, if you select Year, you will see only those years for which you actually have references. You can make selections in this list either with the mouse or the keyboard. If you use the keyboard, your keystrokes will appear in the list header to show you what you have typed.

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A selection in the library browser made using the keyboard. Here the user has typed 200 to nd all years from 2000 to 2009.

As you make a selection in the rst browse list, a new list will appear from which you can select a different eld to search. To move to the next browse list, you can press the Tab key on the keyboard (use shift+Tab to move backward to the previous browse list). In the next list of browse criteria, make a value selection either by clicking or by typing. To remove a restriction from the search, click on the x in the upper right-hand corner of the appropriate browse list. This will remove the restriction represented in that list from the search, leaving all of the other restrictions active. As you enter your browsing criteria, the number of selected terms is shown in the list header. For example, Year (2 of 45) would mean that in the Browse list, two out of forty-ve of the available years were selected. As you rene your search, the number of matching references is updated in the bar on top of the reference list.

The count of matching references is continually updated as you rene the search. Here, the library of 85 references has been ltered down to just 2 references.

To return to your original reference list, you can: Click the Browse icon in the toolbar, Use the View > Browse command in the main menu, or Type cmd+B.

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Using Browse to Create a Smart Collection When you have set up the library browser to nd the records you are searching for, you can have Sente automatically create a smart collection using the same criteria that you used by clicking on the Save button in the browse panel. Then you can recreate the search at any time just by selecting the new smart collection in the source list. You wont need to have the browse panel open when you click on the search results saved in the smart collection in the future.

The Browse saved as a Local Collection (years 2010 & 2011, reference type: Book).

Hotwords
Hotwords is a different kind of tool for looking through your library. Instead of searching for references matching particular criteria, the hotwords feature highlights terms of interest to help you spot references, and terms within a reference, as you manually sort through your library. For example, suppose your research interests include mitochondria. When you are looking through a large number of references returned by a search, it might be helpful to have mitochondria and mitochondrial automatically highlighted in titles, abstracts, etc., to help you spot these terms. This is what the hotwords feature in Sente lets you do.

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How to Use Hotwords The rst step in using hotwords is to tell Sente the terms that you want highlighted. Because these terms are likely to be specic to a library, this setup is done in the Hotwords Setup pane in the main window. To congure hotwords, expand the Library Setup category in the source list and select the Hotwords entry.

The Hotwords Setup pane.The color selector is visible for the selected entry in the list.

Each term is shown in this list highlighted as it will be in your own data. To add a new term, click on the New Hotword button. When a term is selected in the list, a color selector will be visible. Click in the color selector to call up the standard color chooser. It is often useful to have all variations of a single term (or even related terms) highlighted in the same color. Click the Apply button to apply your changes.

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Once you have set up your personal list of hotwords, you can toggle hotword highlighting on and off either by: using the View > Highlight Hotwords command in the main menu, or by clicking on the Hotwords toolbar item.

The Hotwords toolbar item, with hotwords turned off.

The Hotwords toolbar item with hotwords turned on.

Once you have toggled hotwords on, all of your specied terms will be highlighted in the selected colors in the reference list and in the reference editor in Sentes main window.

The main window with hotwords highlighting turned on.

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Chapter 12

Reading and Annotating PDFs

Another powerful feature of Sente is the ability to read and annotate PDFs, as well as to edit and/or delete the annotations, and to save or print the annotated versions. This chapter will cover: Reading PDFs Annotating PDFs with highlights Creating comments/notes Quoting portions of text Copying portions of text or images Taking snapshots of regions of a PDF document Saving copies of annotated PDFs Printing annotated PDFs with or without the annotations Common questions related to reading and annotating PDFs.

Reading PDFs in Sente

Sentes embedded PDF viewer lets you read and annotate PDFs right from within the program. Any highlighting or note-taking that you do in the embedded viewer is automatically reected in all synchronized copies of the library on all devices.

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The PDF viewer is active in the attachment view when the displayed attachment is a PDF. When the attachment view is showing other types of les (e.g., web archives, images or videos), the PDF tools are not available. The attachment view (and thus the PDF viewer) is available in any tab in the main Sente window. Clicking on the Attachment View icon in the toolbar, or selecting the appropriate command under View in the main menu, will open or close the attachment view.

Clicking the paperclip icon in the View toolbar button will open or close the Attachment pane in the main window.

When you want to read, highlight and take notes on a PDF, it is often useful to open the reference in a single reference tab. To do this, double-click on the reference in the reference list.

A PDF attachment open in a single reference tab, with areas highlighted and quoted in Notes.

While you will normally want to view the PDF right from within Sente, you may occasionally want to open the PDF in your default PDF viewing application (e.g.,

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Preview or Acrobat). To open a PDF in your default PDF application, click on the attachment name at the top of the attachment view and select Open from the menu that will appear. This will enable you to read the PDF document in your default application, but any annotations you make on the document will not be saved within Sente and will not be propagated to any synchronized copies of the library.

To open a PDF in another application outside of Sente, click on the attachment name (PDF in this image) and select Open from the menu.

Annotating PDFs and Taking Notes

Annotating PDFs (e.g., highlighting and taking notes) begins with making a selection in the PDF with the mouse. Once you have made a selection, a popover window will appear from which you can select one of the annotation commands. The options in this popover will depend on the type of selection you have made. You can make two types of selections within a PDF: Text. A text selection selects words, phrases and sentences within a PDF, without regard to how the text appears on the page. Image. An image selection selects a rectangular region of the page, exactly as it appears. Even if the region contains words or sentences, an image selection makes no effort to extract the words. To toggle between these two types of selection, click one of the two icons located on the top right side of the bar above the attachment. The icon with the A in the blue box is the text selection tool and the empty rectangle icon is the image-select tool used to select rectangular areas on a page.

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The controls for switching between text-select and image-select modes are the A in the blue box and the empty rectangle.

To make a text selection, click on the blue icon with the A in the top bar and then click and drag the mouse within the PDF. There are some PDFs (notably PDFs that have been scanned as images and not OCRed) where this will not select any text. In this case, you will have to use the image-select mode. To make an image selection, click on the empty rectangle icon in the top bar and then click and drag a rectangular selection in your document. In either case, an annotation popover will appear from which you can select the annotation commands you need. Highlighting Text Passages To highlight a text passage in a PDF document, simply select the text as described above. When you release the left mouse button, the text annotation popover will appear.

The text annotation popover.

Select a color from the palette and then click Highlight and your text will be highlighted in the color you chose. Note that if you choose the color on the far right side that is grey with a line through it, no highlight color will appear over the text. To change the highlight color of a highlighted portion of text, left-click once over the highlighted text, select another color, and click Highlight again.

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To remove the highlight from a section of text, left-click once over the highlighted text, select the color on the far right (the grey box with the line through it), then click Highlight and the text will no longer be highlighted. Create a Note from a Text Selection In addition to highlighting text passages in PDFs, you can also ask Sente to automatically add notes on these passages to your library. Such notes can include that highlighted passage as a quotation, along with your own comments, a note title and the page number from the PDF where the note was created. To create a note from a passage of text: select the desired text, as described above; in the text annotation popover that appears, select the highlighting color (if you want the passage to be highlighted when you are done); if you want just to create a note without quoting the selected text passage, click on Comment; if you want to quote the selected text in your notes, click on Quote. A note will be created in your library (including the quoted text if that option was selected) and it will be displayed in the Notes tab in the reference editor, with the cursor placed in the comment eld for the note. In addition, a note icon will be automatically placed next to the passage in the PDF to indicate that you have a note on this passage in your library. There are two versions of this icon: the grey version indicates that there is a note without comments; the yellow version indicates that there is a note with comments.

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The Note icon appears next to the commented text and the comment appears in the Notes View.

The rst words of the selected text will be used as the title of the new note. When you select a region using Image select mode, the title of the new note will indicate that it is a snapshot. You can, of course, edit the title to be whatever you choose. Highlighting Images, or Regions You can also highlight arbitrary rectangular regions in a PDF using the Image selection mode. To highlight a region: select the Image selection mode in the top bar (the empty rectangle icon); click and drag the mouse to outline the region of interest in the PDF; in the image annotation popover that appears, select the desired highlighting color and line weight; and click Highlight.

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Preparing to highlight a region with a heavy, purple box.

After applying the highlighting.

Creating a Note from an Image Selection You can also create notes based on image, or region, selections in your PDFs. This lets you, for example, create a note that includes a graph or other gure from your reference. To create a note from a region of a page in a PDF: select the desired region, as described above;

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 select the highlighting color and line weight from the region annotation popover, if you want the region to be highlighted when you are done; click on Comment if you want to create a note without capturing the selected image as the quotation; or click on Snapshot if you want to create a note that includes the selected region as the quotation.

The image, or region, annotation popover just prior to creating a note with the snapshot.

In either case, a note will be created and the cursor will be placed in the comment eld. The note icons will also appear in the document itself, following the same rules as for text notes.

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The PDF after highlighting a region and creating a note including a snapshot of that region.

Changing Highlighting Color You can change the color used to highlight text or a region of a PDF by clicking on the highlighting (or the note icon, if present), selecting the new color in the annotation popover, and then clicking Highlight. Deleting Notes and PDF Annotations To delete the note from within the PDF view, click on either the highlighting or the note icon (depending on what was created; either of these may not be present). A popover will appear containing a Delete button. Click that button and then conrm your intentions in the sheet that will appear.

Deleting note alone, or deleting note and highlighting together.

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Copying Text and Images Whenever you have one of the annotation popovers on the screen, you can place the selected text or image on the system pasteboard by clicking on the Copy button. When the selection is an image, you will be able to paste it into many, but not all, applications, depending on whether the application is designed to accept images from the pasteboard.

Exporting Annotated PDFs

You can save a copy of an annotated PDF document while in the Attachment View by exporting it. Simply click on the arrow next to the name of the document in the middle of the header bar (which may just say PDF or File reference), go to the Export submenu, and select With Sente Annotations, then select the le name and location for saving.

Exporting a copy of the PDF with or without annotations.

Printing Annotated PDFs

To print the PDF document either with or without annotations, you can use the File > Print command or use the Print button command on the toolbar. (If the Print button is not on your toolbar, please see the chapter on Customizing the Toolbar.)

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Print PDF with or without annotations.

Some Common Questions

I have a PDF and I want to highlight the text, but the text select tool wont let me select any text. What can I do? Some PDFs do not allow text selection, either because they have not been OCRed or for some other reason related to how PDFs store text within the document. Instead of using the text select tool, try switch to image select mode and highlighting a region on the page. You will still be able to highlight it and place a copy of the image in your Notes.

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Chapter 13

Synchronized Libraries

The synchronized library feature in Sente lets you: Install synchronized copies of any library on any number of computers and iPads, regardless of where they are located (that is, a local network connection is not required); Add and edit references in any copy of the library, with the changes quickly owing to all other copies; Read PDFs, take notes and highlight text in any copy at any time, with all changes appearing in all copies almost immediately; Provide copies with restricted editing permissions to other users when appropriate; Create copies without PDFs to comply with copyright restrictions; Create lightweight copies that only download PDFs (or other attachments) when you actually need them, thus conserving disk space when needed. This chapter will provide you with an overview of synchronized libraries in Sente and it will describe the steps required to create and install synchronized copies on any Mac or iPad.

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Uses for Synchronized Libraries

Sentes synchronized library feature is more exible than one might expect and it can be used in ways that might not be immediately obvious to new users. This section will describe some common ways to use synchronized libraries. Keeping Your Library Current on Multiple Devices The most common use for synchronized libraries is to keep one or more libraries up-to-date on several computers used by one person. For example, you might have a desktop computer at home and at your office, plus a laptop or iPad that you use while on the road. If you place a synchronized copy of your library on each computer, you will always have access to the most recent updates to your library. This means that changes you make on your computer at the office are available on your computer at home that evening. And on your laptop when you travel. And on the iPad that you now carry instead of le folders stuffed with PDFs. When your standing searches in the copy of your library at work nd new references on your research topic, those references appear in all copies almost immediately. As you read a PDF on your iPad on the bus ride home, highlighting passages and taking notes, the highlighting and notes appear in all copies by the time you arrive home. Changes made in any copy show up in all other copies almost immediately, no matter where they are located. Sharing a Library with Collaborators Another use for synchronized libraries is to share them with collaborators. You and your peers may be working on a research paper or a research project, for example. You can create a synchronized library lled with all of the resources needed for your research and share copies of the library with your collaborators. Not only will everyone be able to have access to that research library, they will be able to access it from any of their devices, including their iPads. The synchronized library copies will always stay up-to-date and identical on all of the computers. Because Sente lets you set different permission levels on each copy of a synchronized library, you can, for example, provide copies of a library that allow new references to be added and edited, but which prevent changes to the QuickTag palette used to keep the library organized.

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Distributing Read-Only Copies of a Library Another common use for synchronized libraries is as a mechanism for distributing references and PDFs to students or colleagues. In this case, you would create restricted copies of your library that let users view, but not edit, the contents of the library. You would then distribute these read-only libraries to the appropriate people through emails or from a website. Then not only would the recipients have access to the contents of the library on the day they rst receive the library, they would also quickly receive updates as you add new references to your copy. Because Sente Viewer for iPad is a free application, anyone with an iPad can view your library on their iPad at no cost. If the people using a read-only copy of your library maintain their own research libraries in Sente, they can easily copy references and attachments from their copy of your library to their own library. Using Synchronized Libraries as a Backup Although this is something you normally might not think of, a synchronized library can also serve as an effective backup mechanism. If you only have one computer, you might not think you have a need for the synchronized library feature in Sente. But if you turn synchronization on for your library, make a synchronized copy of that library and store the copy somewhere other than on your computer (e.g., on a CDROM, USB drive, or in your email account stored on a server), you can still recover your Sente library should you ever lose your computerand still have the very last changes you made before the computer was lost. All you would then need to do is install Sente on your replacement computer, restore the backup copy you made months ago, open it in Sente and wait while it catches up with all the changes you made since initially creating the backup copy.

How Synchronized Libraries Work

The Basics Setting up a synchronized library in Sente is straightforward, but it is still useful to understand a bit about how synchronized libraries work. With synchronized libraries in Sente there is no master copy that has to be online, and computers (including iPads) do not have to be in close proximity or connected to each other on the same network in order to synchronize. Instead, a history of all

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changes to a synchronized library is stored on our synchronization servers and each copy of the library will synchronize with those servers whenever it is online, downloading any changes made on other computers or by other users and uploading any edits you made while offline. In brief, here is how you set-up and use synchronized libraries: 1. 2. 3. 4. 5. The rst step is to turn Synchronization on, which will transmit information about the current state of your library to our servers. Next, you create a synchronized copy of the library with the desired permissions and content. Then you transfer the new, synchronized copy to a different device (desktop, laptop, or iPad). After that, you can open the library copy on the other device and it will automatically start synchronizing. You can make edits on any copy of the library (subject to permission settings) and all versions of the library will be synchronized.

These steps will be described in more detail below. What Information Is Synchronized Most of the information in a synchronized library is automatically copied to all other copies of the library, but not everything. Here is a description of what is, and what is not, synchronized. The following information is automatically synchronized between all copies of a synchronized library: All references in the Library category in the source list (this includes all references that you see when you select the All References entry in the source list just below Library) All notes on all of the above references All PDFs and other les attached to the above references (assuming the copy was created with the necessary permission settings, and assuming that the library is congured so that Sente is managing the attachments) All PDF annotations (again subject to permissions) All Synced Collections The QuickTag hierarchy

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 The status dictionary The following items are not synchronized between multiple copies of a synchronized library. If you want these items to be the same in all copies of a library, they will have to be edited manually in each copy. Everything in the Local Collections category in the source list Bibliography formats Hotwords Everything in the Saved Searches category References in the Trash collection Attachments that are not being managed by Sente What Happens When You Turn Sync On When you rst turn synchronization on for a library, Sente contacts our sync servers, creates an account for the library, and encrypts the credentials required to access this account, then stores them inside the library bundle. Each synchronized library is assigned a six-character alphanumeric ID. All copies of a synchronized library will display the same value for this identier. This can help you diagnose any problems with the initial set-up of a synchronized library. All communication between Sente and our sync server is done using port 993. This is the port normally used for the secure IMAP protocol (which is, in fact, what Sente uses for sync communications). Some institutions have rewalls that block this port, but Sente must be able to communicate over this port for sync to work. You cannot maintain a synchronized copy of a library behind a rewall that blocks traffic on port 993. After the account is created and the credentials are assigned, information about the current state of the library is uploaded to the account on the sync server. All data sent back and forth over the Internet is always encrypted and occurs in the background. The initial synchronization with the sync server may take a while. You can continue to work on the library during this process, but you will not be able to create a synchronized copy of the library until this initial synchronization process with the server has nished. If you close Sente during the process, it will pick up where it left off the next time you open the application.

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Once the initial upload of information is completed, you can create a synchronized library. What Happens When You Create a Synchronized Copy When you create a synchronized copy, you are presented with a number of options that control, for example, what operations will be permitted in the new copy, and how much data should be pre-populated in the copy. These options are explained in detail later in this chapter. Once all of these options are selected, Sente will create the encrypted copy with the same credentials needed to synchronize with the server. If any attachments are included with the library copy, they will be led inside of the copy but can be moved later, if desired. Finally, the copy is moved to another computer or iPad and then opened in Sente on that device, at which time the library will immediately contact the Sente sync servers and catch up with any changes made since the copy was created. If the copy was not pre-populated, this rst synchronization may take some time given how much data must be downloaded. What Happens When You Edit a Synchronized Library Your Sente library knows how to communicate with the Sente sync servers, so synchronization can and will occur in the background as long as there is an open Internet connection. You can work offline with the library, but it is important to let the library synchronize with the servers as often as possible. If you are online while you are making changes, each edit is committed locally and then transmitted to the sync servers. The sync servers check to make sure that your changes were made to the most current version of the reference. If they were, your new version is made the new official version and the other synchronized library copies are updated with the new information. If you were not working on the most current version of the reference, your edit is marked as a Sync Conict, which you must resolve manually. For more information about sync conicts, see the Sync Conicts section below. What Happens While Your Library is Offline When your library is offline, you can still make changes. Each edit is committed locally and the changes are queued up for synchronization. The next time the computer is online, the synchronized process described above is carried out.

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The major difference between editing online and offline is that working offline increases the likelihood of synchronization conicts. If you edit a reference while offline, the changes will be committed the next time the library is online, unless the reference is edited in another copy of the library before then. When Sente tries to commit the changes you made while offline, if it detects that the same reference was edited in another copy of the library while you were offline, your changes will be rejected by the server and marked as a sync conict in your local library. If you are the only user of a synchronized library (but you use it on multiple computers), you can work in such a way as to prevent sync conicts. All you need to do is make sure that all of your changes in any copy are synchronized before working on a different copy. For example, if you were to work on a library on your laptop or iPad during a long ight without an Internet connection, be sure to get that device online shortly after the ight and let Sente sync all the changes you made in transit. On the other hand, when several different people have permission to edit a library, if you were to work offline for an extended period, there is a chance that you will have made a change to one or more references that someone else edited while you were offline. In this case, when you let your copy synchronize, the changes you made to these references will be marked as sync conicts and will require manual intervention on your part. For this reason, it is best to avoid changing many references while offline if others might be editing the same references. There is more information about handling sync conicts later in this chapter.

Conguring Synchronized Copies

Each copy of a synchronized library can be congured to support different levels of user permissions. These conguration options are presented in the sheet that appears when you select the File > Synchronization > Create Synchronized Copy command.

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The options available when creating a new synchronized copy of a library.

Unrestricted vs. Restricted Libraries One of the most basic questions to answer when creating a synchronized copy of a library is whether the copy is for your own use (in which case you will want to be able to do anything in any copy of the library without restriction) or for someone elses use (in which case you will probably want to limit what they can do). An Unrestricted copy of a library allows the user to view, add, modify, and delete references and attachments, as well as change Sente library settings. This is the most common option to use if you are setting up synchronized libraries on multiple computers for your own use.
A Restricted copy of a library allows you to control how other users (and yourself

on other computers) can use the copies of the synchronized library. For example, you can set restrictions to allow other users to only be able to view the references and attachments; to be able to view them and make changes; or to have full access (including permission to delete references and/or attachments). These options are explained below. Options for Restricted Copies of a Library When you create a restricted copy of a library, you can specify just which operations can be done on that copy.

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Reference Permissions

Do you want people to be able to add and delete references? To change (modify) references? Or to only view the references and not be able to add, modify or delete them? Select one of these options in the References drop-down list: View onlycan only view the references and cannot add, change, or delete them Add and modifycan add, view and change references, but cannot delete them Add, modify, and deletecan add, view, change, and delete references (full control)
Attachment Permissions

This option controls how people can access library attachments, like PDFs. Select one of the following: No accesscannot view, add or delete attachments View onlycan view attachments, but cannot add or delete them Addcan add and view attachments, but cannot delete them Add and deletecan add, view, and delete attachments (full control)
Shared Collections Permissions

Control whether the denitions of shared smart collections can be modied in this copy of the library by selecting one of the following: View onlycan only view the shared collections; cannot modify them. Modifycan view and modify shared collections (full control)
Library Settings Permissions

Select one of these options to determine whether or not other people can change the library settings, such as the QuickTag palette and the status dictionary: View onlycannot change library settings Modifycan change library settings (full control) Pre-Population Options You can control how much data is placed in the synchronized library copy when it is rst created. Do you want the copy to be fully pre-populated so that little time is

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needed to initially synchronize the library? Do you need a very small le size that you can email instead? Select one of the following pre-population options: Nothing (smallest le, slowest initial sync)This option will result in the smallest le possible, with no detailed information about the references or attachments. Once the le is opened in Sente, it will begin synchronizing and the reference information and attachments (if any) will begin to download. This process may take a long time, depending on the size of the library and whether attachments are set to be downloaded on demand or as soon as they are available (see below). This option may be the best option for sending libraries via email, but if you will be transferring the library using another method, you might want to select one of the other options to speed up the initial sync. All current referencesOnly information about the references will be included in the le (no attachments). This will normally produce a smaller le and allow for faster synchronization on the new computer or iPad. All references and attachments (quickest initial sync)This option creates the largest le in size, but allows for a faster initial synchronization on the new computer or iPad. All of the references and attachments are included in the le that is transferred, so initial synchronization will be very quick when the library is opened for the rst time. Attachment Handling Options You also need to specify when Sente should download attachments in this copy of the library. Assuming you having congured the library to include attachments at all, your choices are to have Sente download each attachment as soon as it is available, or only when the user indicates that they would like to see the le. The On demand option tells Sente to download attachments only when the user asks to view them. This saves room on the device and may be the best option for the iPad. Of course, it is not possible to download attachments when the device is offline, so the lack of an Internet connection may leave you unable to view some of your attachments. The As soon as they are available option tells Sente to download all attachments as soon as they are available on the sync server. The Not applicable is automatically selected if this copy of the library does not have access to attachments. It is important to understand that even when you congure a copy of a library to download attachments on demand, once they are downloaded they remain in the

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library as long as you need them. In other words, if you ask Sente to download a PDF, that PDF will be downloaded and saved in the library for quick access at any time. Thus, if you were about to get on a plane without Internet access, you would download any PDFs you were hoping to read during the ight and they would all be available to you even when you lost your Internet connection. It is also possible to delete the local copy of any attachment without removing the le from the synchronized library. Thus, if you want to free up some space in any library, you can delete the local copies of some of your attachments. Then, should you later want these deleted attachments, you can simply download them just as you would if the library were set to Download on Demand. There are things you should consider when selecting among the attachment handling options: Will this copy of the library reside on a computer with limited disk space? If so, you may want to select Download on Demand so that only those attachments that are currently of interest are actually downloaded, thus saving space on the computer. Will this copy of the library normally be left open in Sente and stay connected to the Internet? If so, then Sente will receive synchronization messages at any hour of the day or night, and therefore can process incoming attachments immediately, making them available essentially immediately. If the library will be open only occasionally, then this copy of the library will have to catch up each time it is opened. This means that it may fall quite far behind the other copies, especially if it has been congured to download all attachments as soon as they are available. This may make Sente slow to use, and it will have a hard time catching up because downloading attachments can be very time-consuming. Will this copy of the library be installed on an iPad? If so, it is very unlikely that Sente will be left running long enough to stay current on all attachments. In this case you probably want to download the attachments only as needed.

Sample Congurations
To help you understand how these various conguration options can be used, let's take a look at several common situations. Suppose you have installed Sente on your desktop computer in your office and you want to create copies of your library for your own use on the following devices: Your desktop computer at home Your laptop computer, which you tend to use mostly when traveling

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 Your iPad, which you use regularly for reading new papers In addition, you might want to create copies for: A research assistant who will be helping to gather new references A collaborator located at another institution Students in a class you are teaching We will describe below how you might set up a synchronized copy for each of these scenarios. Obviously, the details of your situation will be different from the scenarios presented here, but these should help you understand how one selects the conguration options when creating synchronized copies of a library. Conguring a Copy for Your Desktop Computer at Home Suppose you have your main Sente library on your desktop computer in your office and you would like to place a synchronized copy of your entire library on your computer at home. This computer has plenty of disk space and a fast Internet connection, and it is normally always turned on. In addition, it is easy for you to transfer the synchronized copy to your home computer on a USB drive, so having a large synchronized copy is not a problem. In this case, we would recommend settings similar to the following: Create an Unrestricted Copy, because this will be for your own use and you should be able to do anything on the copy at home that you can do at the office. Pre-populate with All references and attachments, because you will be transferring the library on a USB drive and this will get the new copy up-andrunning as quickly as possible. Attachments should be downloaded As soon as they are available, because your computer is always on (so it will stay current as long as Sente is running and the library is open) and disk space is not an issue. Conguring a Copy for Your Laptop In this scenario, lets assume you mainly use your laptop when commuting or traveling. This laptop has limited disk space and is not always connected to the Internet, and you dont want to have to wait for a long period of time for attachments to download. You will be able to transfer the synchronized copy to your laptop on a USB drive, but you may have limited space and so dont want to store all of the attachments on your laptop; you want to pick and choose which attachments to download, when you are ready to review them.

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 Create an Unrestricted Copy, because this will be for your own use and you should be able to do anything on this copy that you can do in any other copy. Pre-populate with All current references, because you will be transferring the library on a USB drive and this will get the new copy up-and-running as quickly as possible, but you may have limited disk space and will want to choose which attachments to download. Attachments should be downloaded On demand, because your laptop is not always on and may have limited disk space. With this option, you will be able to choose which attachments you wish to download and will generally not have to wait for a long synchronize process when you rst open the library in Sente. Conguring a Copy for Your iPad Say, for example, that you like to use your iPad for reading papers. It may or may not always be connected to the Internet, but Sente and the library are not always open and the iPad has limited storage space. The synchronized copy will be transferred via iTunes on your desktop computer. These are the options that you might want to use when setting up the synchronized library copy for your iPad: Create an Unrestricted Copy, because this will be for your own use and you should be able to do anything in this copy that you can do in any other copy. Pre-populate with All current references, because you will be transferring the library via iTunes on your desktop computer and this will get the new copy upand-running as quickly as possible, but you may have limited disk space on the iPad and will want to choose which attachments to download. Attachments should be downloaded On demand, because your iPad has limited storage space and because downloading all PDFs as they become available would mean that Sente would rarely catch up with your other copies. With this option, you will be able to choose which attachments you wish to download and will generally not have to wait for a long synchronize process when you rst open the library in Sente on your iPad. Conguring a Copy for Use by a Research Assistant You may wish to create a synchronized library copy for a research assistant. You might want the research assistant to be able to have full access to the references and attachments, but not be able to change the shared collections or the library settings. Lets assume that the research assistant has a desktop computer with plenty of disk space and a fast Internet connection, and it is normally always turned on. In addition, it is easy for you to transfer the synchronized copy to the research

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assistants computer over the local network, so having a large synchronized copy is not a problem. In this scenario, these settings would be recommended: Create a Restricted Copy, because you want to be able to control how the research assistant can modify the library. In the References option, select either Add, modify, and delete (if you want the research assistant to have full control over the references) or Add and modify (for add, view and modify control over the references, but without the ability to delete references). In the Attachments option, select either Add or Add and delete, depending on whether or not the research assistant should have full control over attachments. In the Shared Collections option, select View only to allow the research assistant the ability to view shared collections but not modify them. In the Library Settings options, select View only to allow viewing of the library settings, but not the ability to change the settings. Pre-populate with All references and attachments. Attachments should be downloaded As soon as they are available, because the research assistant will typically open the library each day and disk space is not an issue. Conguring a Copy for Use by a Collaborator at Another Institution In this example, you are sharing your library with a collaborator at another institution. You want the collaborator to have full control of the references, attachments, and shared collections, but not of the library settings. You may not know whether your collaborator has a desktop computer or laptop, or whether or not it is always connected to the Internet. Available disk space may or may not be an issue. Finally, you may need to transfer the library copy via email or by uploading it to a web server. Create a Restricted Copy, because you want to be able to control how your collaborator can modify the library. In the References option, select Add, modify, and delete to allow the collaborator full control over the references. In the Attachments option, select Add and delete, to allow the collaborator full control over attachments. (If attachments will not be shared with your collaborator, you may choose to select the No access option instead.) In the Shared Collections option, select Modify to allow your collaborator the ability to view and modify shared collections.

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 In the Library Settings options, select View only to allow viewing of the library settings, but not the ability to change the settings. Pre-populate with Nothing (smallest le, slowest initial sync), because you will be emailing the library copy as an attachment or uploading it to a web server and this option creates the smallest le size. Attachments should be downloaded As soon as they are available if you know that disk space is not an issue. Conguring a Copy for Use by Students in a Class You are Teaching In this scenario, you are teaching a class and have a set of papers for the students to read during the semester. You will be updating the library during the semester and want the students always to have the most up-to-date version of the library. You want the students to have view-only access to the library. You also have no knowledge of whether the students will be using desktop computers, laptops or iPads. Finally, you want to be able to either email the library to the students or upload it to a web server so that students can download it. These are the options we recommend you select for this scenario: Create a Restricted Copy, because you want the students to have view-only control over the library. In the References option, select View only so that the students will only be able to view the references and not change them. In the Attachments option, select View only, because you want the students to be able to view the attachments, but not change them. In the Shared Collections option, select View only so that students will not be able to modify the shared collections. In the Library Settings options, select View only to allow viewing of the library settings, but not the ability to change the settings. Pre-populate with All current references, because the library is relatively small except for the attachments, and this will reduce the time required for the initial sync. Attachments should be downloaded On demand because you know that many students will access the library on their iPads and this will limit the amount of time Sente needs to catch up on sync when it is launched.

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Setting up a Synchronized Library

This section provides step-by-step instructions for the operations required to set up synchronized copies of a library, including: Creating a synchronized copy of a library Installing a synchronized library on another computer Installing a synchronized library on an iPad Creating a synchronized copy of a library as a backup How to: Create a Synchronized Copy of a Library 1. 2. Open the library. Select the File > Synchronization > Create Synchronized Copy command.

The Synchronization > Create Synchronized Copy menu command.

3.

If you have not previously turned sync on for this library, you will be asked whether you want to do this. You must turn sync on prior to creating a synchronized copy. Read the dialog box information and click on the appropriate button.

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The Turn Synchronization ON dialog box.

4.

Once you turn Synchronization on, the library will begin synchronizing with the Sente servers and a dialog box will show the progress.
The library synchronization may take some time. To continue working while the synchronization process continues, click the Dismiss button.

The Synchronization Progress dialog box. When the synchronization process has completed, a Synchronization is complete message will appear. Click the Proceed button to continue.

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The Synchronization is Complete dialog box.

5.

Select the appropriate options.

See the Conguring Synchronized Copies section.

The options for creating a synchronized copy.

6. 7.

Click on the Create button when all of the options have been selected. Type the library name, select the location where the synchronized library will be placed, and click the Create Synchronized Copy button.

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The Save dialog box.

8.

Click the Okay button when the process is completed.

The Synchronized Copy Completed dialog box.

9.

Read the message about your synchronized copy, then click either the Show in Finder button or the Okay button.

The Synchronized Copy is Ready dialog box.

The synchronized copy of the library is now ready to be transferred to and installed on another computer or iPad, uploaded to a web server, or distributed via email.

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How To: Install a Synchronized Copy on Another Computer 1. Transfer the synchronized copy le to the new computer.
Copy or move the le onto a CD, USB thumb drive, portable hard drive or other storage media, then transfer the le to the new computer. Alternatively, the library copy can be downloaded from an email or web server onto the new computer.

2.

Open Sente on the new computer, then open the synchronized library le.
The library copy will begin to synchronize with the server. If the Pre-populate option was set to All current references or All references and attachments (quickest initial sync) and/or if the Attachment option was set to As soon as they are available, it may take a while to fully populate the new synchronized library.

How To: Install a Sente Library on an iPad 1. 2. 3. 4. 5. 6. 7. If Sente is not already installed on the iPad, download the application and install it. Connect the iPad to the computer. If iTunes does not open automatically on the desktop or laptop computer, open it manually. Click on the iPad name on the list under DEVICES in iTunes. Click on the Apps tab in the iTunes window. Scroll down to the File Sharing section and click on the Sente icon. Add the synchronized copy of the Sente library.
Either drag and drop the synchronized copy of the Sente library onto the Sente Documents box or click on the Add... button and select the le using that method.

8. 9.

Click the Sync button in iTunes. Detach the iPad from the computer when the synchronization with iTunes has nished.

10. Open Sente on the iPad. 11. Tap on the Libraries button and choose the library from the list.
The synchronization process will begin and may take a while, depending on which prepopulation and attachment options were selected.

How To: Create a Synchronized Copy as a Backup 1. 2. Follow the steps under How to: Create a Synchronized Copy of a Library to create the library copy. Save the le in a location away from the computer, such as on a web server, USB device, or another computer.

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3.

If it becomes necessary, re-install the backup library copy, then open it in Sente and allow it to synchronize completely.

Sync Conicts
Normally, changes made on any copy of a synchronized library are immediately propagated to all other open copies as soon as they are made. This means that even if two people are editing the same library at the same time, they will be seeing each others changes in close to real time. This ensures that each user will be seeing, and editing, the most current data at all times. However, there are cases in which one user might make a change to an outdated version of a reference. When this happens, the change will be rejected by the sync servers as a sync conict, which must be then handled manually by the user. Theoretically, but not commonly, two people could be editing the very same reference at the same time, each making a change to some attribute on that reference. If their edits exactly overlap in time, then the rst that is submitted to the sync servers will win and the second to be submitted will be rejected as a conict. A far more common scenario is that one user edits many references while offline (say, on a ight with no Internet connection). While they are on the ight, another user might make changes to some of the same references. When the rst user nally connects to the Internet and begins the Sente sync process, changes they made to references that were also edited by the second user will be agged as conicts. When a sync conict is detected, Sente will present a warning something like the following:

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A sync conict warning message.

When a sync conict is encountered, the version of the reference that won will appear in all copies of the library. The version of the reference that lost will be placed in the Sync Conicts collection in Local Collections in the copy of the library where those (rejected) changes were made. By retaining both copies of the reference, Sente makes it easier to re-do any lost edits, as appropriate. Once you decide what you want to do with each reference in the sync conicts collection, they can simply be deleted. Preventing Sync Conicts Under most circumstances, sync conicts are rare, but there are some ways of working that make them more common. Sync conicts will be rare if everyone working on a library is connected to the Internet while editing data. In this case, sync conicts can only occur if the very same reference is edited by two people at exactly the same time. On the other hand, one of the strengths of Sentes sync mechanism is that it supports editing while offline. As long as you are a bit careful about how this is done, you will rarely experience sync conicts.

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For example, if you are the only person editing a synchronized library, and you make sure that you connect your computer to the Internet after making changes, but before working on a different copy, you will not have sync conicts. Or, if there are multiple people editing a library, if you limit the scope of edits that are made while offline (e.g., wait until you are online to make edits like assigning tags or statuses to large numbers of references), then you will not often generate a sync conict. Resolving Sync Conicts When you are notied that a sync conict has been detected, you need to decide how to resolve the conict. First, it is important to note that the conict exists only on the computer on which the conict was reported. All copies of the library have the same data for the references in question, and this version is the one that beat the changes made on the computer on which the conict was reported. In that library, the changes that lost can be found in the Sync Conicts collection in Local Collections. If you do nothing, the changes that lost will not be reected in the library proper. For these changes to appear in the library, you must make the edits again on the newer version of the references. For example, suppose you assign a particular QuickTag to a hundred references while offline. While you are offline, someone else updates several of these references in some way. Then, when you take your copy of the library back online, those several references will be reported to you as sync conicts. The changes to the other references will go through without a problem. In this case, you would locate the references in the Sync Conicts collection, select the same references in the main library, and then re-assign the QuickTag.

Troubleshooting Synchronized Libraries

Synchronized libraries normally just work. Sometimes, however, things may not seem to be working as expected. This section will describe how you can determine whether or not sync is actually working and, if not, what can be done to address the situation.

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Do You Actually Have Synchronized Libraries? The rst thing to check, especially with newly created synchronized libraries, is that both libraries are actually synchronized copies of the same library. Every copy of a synchronized library has a six-character alphanumeric identier. All copies of the same synchronized library will have the same identier. If two libraries have different identiers, they are not synchronized copies of the same library and the contents of the two libraries will not be synchronized.
Locating the Library Identier and Change Number in Desktop Sente

In desktop Sente, the library ID and change number for a library are found in the header above the reference list.

The synchronization status display above the reference list in the main window. In this example, the library ID is L6FAAA and the library is current as of change #1704.

When Sente is actively processing updates (either sending changes to the sync server, or receiving and processing changes from the server), the sync status display will change slightly: the @ will be replaced with an arrowhead. As soon as all pending changes have been processed, the arrowhead () will change back to the @ symbol. The library ID and related synchronization information can also be seen in the File > Synchronization menu, as shown below:

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The library sync status is also displayed in the File > Synchronization item in the main menu. Locating the Library ID on the iPad

For libraries on the iPad, the library ID can be found in the Synchronization pane, accessed by tapping on the Synchronization entry in the list at the left side of the screen (in landscape orientation).

The Synchronization pane on the iPad. This library has ID LE9FB0.

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What if the Library IDs are missing or different?

If you check the library IDs on two libraries that you think should be syncing and nd that they have different IDs, or either library is missing an ID entirely, the libraries will not sync with one another. To achieve the goal of synchronized libraries, you should go back and reread the earlier part of this chapter and carefully follow the steps for creating synchronized libraries. Remember that there is no way to connect two independent libraries and have them start syncing. Instead, you need to start with a single library and create synchronized copies of that library. Are They in Sync? Once you have determined that you have two copies of a single synchronized library, you should then check to see if Sente thinks that they are in sync. Each copy of a synchronized library has a current change number. Over time, this number should increase in all copies of a synchronized library and the value should be exactly the same in all copies when they are all current with respect to the server.
Locating the Change Number on the iPad

The change number for a synchronized library on the iPad is found in the same synchronization status pane as the library ID (see above).
What if the Change Numbers are Not the Same?

If the change numbers on two copies of a synchronized library are the same, the content of the two libraries should be the same (see below if this is not the case). If the change numbers are not the same, the one with the lower value has fallen behind the other copy. In most cases, each copy will catch up all on its own, but there are some reasons why this may not happen right away. Focusing on the copy with the lower change number, you should note the current synchronization status. Synchronized. The @ symbol indicates that Sente believes this copy of the library is current with respect to the sync servers. You should not normally see two libraries, both online, with the same library IDs, displaying Synchronized status, but with different change numbers. If this happens, please contact us for support.

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 Synchronizing. The symbol indicates that Sente is currently processing updates. This could mean that Sente is sending changes to the sync servers or receiving edits from the servers. Once the library is up-to-date, this symbol will change back to the @ character. In general, no further action is required until the library reaches the Synchronized state. Offline. If the computer is offline, Sente will be unable to synchronize with other copies of the library. The most common causes for this are: (1) The device in question is not connected to the Internet. You can test the Internet connection by attempting to open any remote web page in a browser on the device. (2) The device is located behind a rewall that is blocking traffic on Port 993. Sente cannot synchronize a library unless it can communicate over this port to the sync servers. Either the rewall conguration must be changed to permit traffic on Port 993, or the device moved to another location. (3) The sync servers are down for some reason. If you suspect this to be the case, you can either contact us using our support email address, or simply wait for an hour or two and check again. The few outages that we experience are normally resolved within a few hours. Still Not Working? If you have checked everything listed above and the library IDs and change numbers match, the two libraries should be identical unless they have been congured to be different. For example, a library that was set up not to include attachments will always differ in this respect from copies containing attachments. So, if you get to this point, but still believe that you have a case in which you have two copies that claim to be identical but are not, you will need to contact us for support. We will likely want to see both copies so that we can look carefully at their exact states to determine the nature of the problem.

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Chapter 14

Working with Word Processors

Sente makes it easy to cite references in your manuscripts. Through Sentes bibliography formats, you can insert citations and bibliographies that are automatically formatted to your publishers or institutions requirements. Sente integrates with many word processors and also outputs bibliographies in Rich Text Format for use in any word processor that supports RTF. For most current word processors, youll use Sentes le scanning feature to generate citations and bibliographies. Sente also supports a streamlined le scanning process called scan in place for Microsoft Word and Apple Pages documents. When you use the scan-in-place option to scan an open Word or Pages document, Sente will automatically replace the open document with the document resulting from the scan (after saving a copy of the original). And, because the rescannable option is always used for the output format for Word docx and Apple Pages documents, you can just keep editing where you left off. When working with Sente and Word 2008 or later, you can exchange documents with users who are still using EndNote with Wordincluding users running on Windows. You can open documents they send to you, make changes such as adding and editing citations, and send them the new document, which they will then be able to open and edit on their computer. The only requirement is that documents be stored in docx (not doc) format. Since different word processors interact with Sente differently (Word 2004 and RedleX Mellel, for example), please select your word processor from the list below the next section and read the information specic to that application.

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Apple Pages
Sente can work with documents prepared in Apple Pages starting with the Pages 08 version, which was the rst version to store documents in the Pages XML format. File Scanning Sente works with Pages documents using the le scanning interface, where citations are rst entered as citation tags (e.g., {Smith 2007}) and then are replaced with properly formatted citations during the le scan operation. Please see the chapter on File Scanning for more information and step-by-step instructions. Output Options These are the output options available for Apple Pages documents during the le scanning process: Apple Pages Document, Not Scannable Apple Pages Document, Scannable Apple Pages Document, Unscanned

The scan document options for an Apple Pages le.

Please see the chapter on File Scanning for more information.

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Rescanning Apple Pages XML les support the concept of rescanning, where scanned documents can be editedincluding changes to the actual citations in the document and then scanned again to produce a properly formatted document. Please see the File Scanning chapter for more information and instructions on how to rescan Apple Pages documents. Scan-in-Place Apple Pages documents can also be scanned in place, where you can still edit your document after you occasionally scan the le and update recently added citations. Please see the chapter on File Scanning for more information on scan-in-place.

Microsoft Word 2008 and 2011

Sente can work with documents prepared in Word 2008 and 2011 because they use the docx format. (Note: For Word 2004, please see the section called Microsoft Word 2004 because the interface and instructions are different.) File Scanning Sente works with Word 2008 and 2011 docx documents using the le scanning interface, in which citations are rst entered as citation tags (e.g., {Smith 2007}) and then are replaced with properly formatted citations during the scan operation. Please see the chapter on File Scanning for more information and step-by-step instructions. Output Options These are the output options available for Microsoft Word 2008 and 2011 documents during the le scanning process: Document, Not Scannable Document, Scannable (EndNote compatible) Document, Unscanned

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The scan document options for a Word docx le.

Please see the chapter on File Scanning for more information. Rescanning Microsoft Word 2008 and 2011 documents support the concept of rescanning, where scanned documents can be edited, even including changes to the actual citations in the document, and then scanned again to produce a properly formatted document. Please see the File Scanning chapter for more information and instructions on how to rescan Word 2008 and 2011 documents. Scan-in-Place Microsoft Word 2008 and 2011 documents can also be scanned in place, where you can still edit your document after you occasionally scan the le and update recently added citations. Please see the chapter on File Scanning for more information on scan-in-place.

RedleX Mellel
Mellel is the word processing program from Redlers (www.redlers.com). Mellel has built-in support for reference management software, and it can be congured to recognize Sente as your reference manager.

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Enabling the Mellel Plugin Sente ships with a plugin for Mellel and this is active by default. If for some reason it has been deactivated, it can be reactivated in Sente 6 > Sente 6 Preferences. Conguring Mellel Mellel must be congured to recognize Sente. To do this, follow these steps: 1. 2. 3. 4. Launch Mellel. Open Mellel Preferences. Select the Bibliography pane. Select Sente from the Bibliography Application menu.

Choosing Sente as the bibliography application in Mellel.

Inserting Citations & Bibliographies in Mellel When Sente is running the background, you can insert citations and generate bibliographies using Mellels standard bibliography commands. In this process, youll rst insert unformatted citation tags into your Mellel document and then scan to format in-text citations and a bibliography. You can use the Mellel Unscan button to revert back to citation tags.

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1.

In Mellels Bibliography palette, click the Find in Reference Database button to insert a citation from Sente. You can also select references in Sente and use CMD-Y to insert them directly into your Mellel document. Inserted citations appear as unformatted placeholders in your document. Citations inserted directly adjacent to each other will be merged into a single citation in your nal document.

2.

A Citation in Mellel.

3. 4.

Insert the rest of your citations and nalize your manuscript. In the Bibliography palette, click the Scan button.

The Scan button in Mellel.

5.

In the dialog box that appears, select a bibliography format from the list of your favorites. The format controls how your inserted citations and bibliography will appear when the document is scanned.

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Selecting a bibliography format in Mellel.

6.

Click Scan Document to initiate the scan. The scan replaces citation tags with formatted citations and appends a bibliography.

When scanning, it is important that the current Sente library (the library most recently accessed) is the library that contains the citations in your Mellel document. If there are references that cannot be resolved, Sente will display a dialog box summarizing the issues. Editing In-Text Citations In Mellel, you have access to all of the standard in-text citation modiers (please see the File Scanning chapter). In cases where Mellel provides a checkbox for an edit option, either the checkbox or the string modier may be used. If you double-click an inserted citation placeholder in your source manuscript, you have access to the eld code where these edits are made. Here are a few examples of applying the modiers to the eld codes: Insert \any text\ just before the # sign to append text to the citation, such as page numbers.

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An example of an edited citation for appending text.

Prepend a % sign to the beginning of the eld code to show only the date in the citation tag (while leaving the bibliography entry unaffected).

An example of an edited citation for date only.

Check Exclude from Final Document to render the citation invisible while leaving its bibliography entry unaffected (or, alternatively, prepend the citation tag with !).

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Check Exclude from Final Document to render the citation invisible while leaving its bibliography entry unaffected.

Scrivener
Scrivener is the content-generation software program from Literature and Latte (www.literatureandlatte.com/). With Scrivener, you have the option to export your les in three format types that Sente can work with: docx, RTF, and plain text (TXT). It is recommended that you choose the Microsoft Word (DOCX) option, especially if you wish to produce a rescannable document. Please see the section on Microsoft Word 2008 and 2011 for more information.

The le export menu in Scrivener 2.2 shows several le format options that Sente accepts.

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File Scanning Sente works with Scrivener documents using the le scanning interface, in which citations are rst entered as citation tags (e.g., {Smith 2007}) and are then replaced with properly formatted citations during the le scan operation. Please see the chapter on File Scanning for more information and step-by-step instructions. You can add Sente as your Bibliography/Citations manager in Scrivener by opening Scrivener Preferences and clicking on the General tab. Next to the heading Bibliography Manager, click the Choose... button, navigate to your Sente application and select it. (It may be located in your /Applications folder.) Output Options The output options for your Scrivener document will depend on which format type you export your le to. For example, if you export the le in the docx format (recommended), your output options will be: Document, Not Scannable Document, Scannable (EndNote compatible) Document, Unscanned However, if you export the le as an RTF document, your output options after scanning will be limited to the following (with no Scannable option): Scanned RTF Scanned RTF with EndNote codes for Word 2004 Scanned RTF with Sente codes for Word 2004 Unscanned RTF Please see the information in this chapter about working with Microsoft Word 2008 and 2011 documents and/or working with RTF les. Please also see the chapter on File Scanning for more information on scanning documents. Rescanning Microsoft Word docx documents support the concept of rescanning, where scanned documents can be edited, even including changes to the actual citations in the document, and then scanned again to produce a properly formatted document. Please see the File Scanning chapter for more information and instructions on how to rescan docx documents.

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Rescanning is not supported for documents stored in RTF format. Therefore, it is recommended that you export your Scrivener documents as docx les. Scan-in-Place Microsoft Word docx documents can be scanned in place, where you can still edit your document after you occasionally scan the le and update recently added citations. Please see the chapter on File Scanning for more information on scan-inplace. Documents saved in RTF format cannot be scanned in place. Therefore, it is recommended that you export your Scrivener documents as docx les if you wish to use Sentes scan-in-place feature.

Nisus Writer
Sente can work with documents prepared in the Nisus Writer word processors (Nisus Writer and Nisus Writer Express) that are stored in RTF format. File Scanning Sente works with Nisus Writer documents using the le scanning interface, in which citations are rst entered as citation tags (e.g., {Smith 2007}) and are then replaced with properly formatted citations during the le scan operation. Please see the chapter on File Scanning for more information and step-by-step instructions. Output Options These are the output options available for RTF formatted documents (including Nisus Writer documents stored in RTF format) during the le scanning process: Scanned RTF Scanned RTF with EndNote codes for Word 2004 Scanned RTF with Sente codes for Word 2004 Unscanned RTF

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Scan document options for an RTF le.

Please see the chapter on File Scanning for more information. Rescanning Rescanning is not supported for documents stored in RTF format, including Nisus Writer documents.

Open Office
Sente can work with documents prepared in the Open Office Writer word processor stored in RTF format. File Scanning Sente works with Open Office Writer documents using the le scanning interface, in which citations are rst entered as citation tags (e.g., {Smith 2007}) and are then replaced with properly formatted citations during the le scan operation. Please see the chapter on File Scanning for more information and step-by-step instructions. Output Options These are the output options available for RTF formatted documents (including Open Office Writer documents stored in RTF format) during the le scanning process:

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 Scanned RTF Scanned RTF with EndNote codes for Word 2004 Scanned RTF with Sente codes for Word 2004 Unscanned RTF Please see the chapter on File Scanning for more information. Rescanning Rescanning is not supported for documents stored in RTF format, including Open Office Writer documents.

Other Word Processors/Rich Text Format (RTF)/Word 2004

Sente works with a number of other word processors, but the les must be in either RTF, HTML, or plain text format (with the exception of Word 2004; please see below). In some cases, Sente will be able to identify open les; in other cases you will need to scan the le as saved on disk. File Scanning Sente works with RTF, HTML, and plain text documents using the le scanning interface, in which citations are rst entered as citation tags (e.g., {Smith 2007}) and are then replaced with properly formatted citations during the le scan operation. Please see the chapter on File Scanning for more information and stepby-step instructions. Output Options These are the output options available for RTF formatted documents during the le scanning process: Scanned RTF Scanned RTF with EndNote codes for Word 2004 Scanned RTF with Sente codes for Word 2004 Unscanned RTF Please see the chapter on File Scanning for more information.

NOTE: I tried saving and scanning an HTML le with citations and a plain text document with citations and neither worked. Is this still supported? Its mentioned in several places.

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Rescanning Rescanning is not supported for documents stored in RTF format. Microsoft Word 2004 Sente is able to work with Microsoft Word documents on the Macintosh for versions 2004, 2008 and 2011. However, the interface and instructions for Word 2004 differ from those of the later versions of Word. If you are using Word 2004, please read the information provided in this section. If you use Word 2008 or 2011, please read that section instead. Sente includes a plugin for working with Word 2004 that supports dynamic updating of the original document, similar to what is called Cite While You Write in EndNote. Using this plugin will enable you to work with your document in its nal format at all times, rather than needing to scan the le to produce a second, formatted copy.
Installing the Word 2004 Plugin

The Word 2004 plug may have been installed during the original installation of Sente. If it was not installed then, it can be installed at any time using the Sente 6 > Sente 6 Preferences window. In the Bibliography tab in Preferences, select the Word 2004 tab.

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The Microsoft Word 2004 plugin instructions.

To install the plugin, select the Automatically install/update the MS Word 2004 integration le button. In rare cases, it may be necessary to control exactly where the plugin is placed. This can be done using the manual option in this tab.
The Sente Menu in Word 2004

When the Word 2004 plugin is active, a Sente menu appears in the Tools menu in Word.

Sente commands available in Microsoft Word 2004.

Launch Sente opens Sente if it isn't running, or brings it to the front if it's running in the background. The other menu commands will also launch Sente automatically as part of their function. Auto refresh automatically rebuilds all citations and the bibliography whenever a reference is added to the document. Insert Citation(s) places one or more citations at the insertion point. Edit Citation lets you manually edit any citation youve inserted. Group/Ungroup Citations toggles whether adjacent inserted citations are merged into a single citation group. Insert Bibliography creates a bibliography based on your inserted citations and places it at the insertion point.

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 The Format selector shows which bibliography format is determining the structure of your in-text citations and bibliography. Refresh Document rebuilds all citations and the bibliography if, for example, youve moved or added citations.
Inserting Citations & Bibliographies in Word 2004

The steps to insert citations and bibliographies in Word 2004 are a little different than in other word processors. These are the instructions specic to Word 2004 for inserting citations and bibliographies: 1. 2. 3. 4. In a Word 2004 document, place your insertion point where you would like to insert an in-text citation. Select Tools > Sente > Insert Citation(s). Sente will automatically launch if it isnt running already. In the Reference Selector that appears, select one or more references. Click OK. The citation will appear as a eld structured according to the selected Bibliography Format. If you are citing multiple references, Word will merge the information into a single citation. To create or edit a bibliography format, see the chapter on Creating and Modifying Bibliography Formats. Return to Step 1 to add more citations to your document. At any time, you can select Tools > Sente > Insert Bibliography. Using the selected bibliography format, Word will build a bibliography from your inserted citations and place it at the insertion point.

5. 6.

Deleting a Citation

If you want to remove a citation from your document, be sure to highlight at least one text character before and after the citation eld before deleting. Otherwise, the citation may reappear when you refresh the document.

Inserted citations are maintained in elds; when deleting, be sure to select text before and after the eld to ensure the eld is removed.

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Selecting a Bibliography Format

You can select a different bibliography format even after youve inserted citations and a bibliography. When you change the format via Tools > Sente > Format, Word updates your entries.
Modifying a Format in Use

Word 2004 is quite forgiving regarding changes. You can even modify the selected bibliography format in Sente while your Word document is open; just choose Refresh Document to see the results.
Controlling Character and Paragraph Formatting

The rst time you insert a citation into a document, Sente adds two new styles to your Word 2004 documents style sheet: SenteCitation and SenteBibliography. These are automatically applied to in-text citations and bibliographies, respectively. By conguring these two styles (see Working with Styles, below), you can control the look of your citations and bibliographies. All changes you make to the SenteCitation and SenteBibliography style will be preserved regardless of whether you add more citations, refresh the document, or change the bibliography format.
Working with Styles

Although Sentes bibliography formats can apply bold, italic, and underline to elements of your bibliography entry, all other aspectssuch as font, indentation, and marginsare determined by the SenteCitation and SenteBibliography styles in Word. Through these styles, you can set up global formatting rules to apply to all citations and bibliographies in your document. Once you insert a citation into your document, you can access these styles in Word 2004 by selecting Format > Style.

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Using the Sente paragraph and character styles to control formatting of bibliographies and citations in Microsoft Word 2004.

Select one of the Sente styles in your Styles list and click Modify to congure its format. This allows you to, for example, set up a hanging indent for your generated bibliographies, or set all of your citations to appear as superscript.
Disabling Proong

To prevent Word 2004 from grammar- and spell-checking your citations and bibliography, do this for each style: in the Modify Style window, choose Format > Language and check Do not check spelling or grammar.
Editing Citations and Bibliography Entries Directly

To avoid creating unnecessary work, you should always try to use Sentes Bibliography Format Editor combined with Word styles to achieve the results you want. Remember, you can also go back into Sente and edit the original references, if needed.

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Editing Citations

If you need to manually edit an inserted citationsuch as to append page numbers click in the citation in your Word document and then select Tools > Sente > Edit Citation; your changes will remain even after refreshing the document.
WARNING: Do NOT edit your citations directly in your Word document because your changes will be lost when you refresh the document. Editing Bibliography Entries

You can edit bibliography entries directly in your Word 2004 document. However, edits to bibliography elds are NOT retained after the document is refreshed. You may need to refresh if you add, delete, or move citations, or change the bibliography formattherefore, direct editing of a bibliography entry is generally only useful as a nal step in manuscript preparation.
Performance

Each time a citation is added to your document, Sente must reconsider all existing citations to see if there is any impact on the appearance of any citations. This works well for relatively small documents, but can be slow on very large documents (what constitutes large will depend on your computer speed, document complexity, and other factors). This means that as your document grows in length and number of citations, you may come to nd that the time it takes to perform operations on citations is becoming disruptive to your work. In this case, we recommend turning autoupdating off in the document (in the Tools > Sente menu). This will tell Sente to delay updating all of the citations in the document until you execute the Refresh command. In general, the formatting will still appear to be very close to the nal formatting in the document, but there may be small issues until the Refresh command is executed.

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Chapter 15

File Scanning

With most word processors, Sente uses an approach called le scanning for formatting citations and bibliographies. File scanning is the approach Sente uses when working with: Microsoft Word 2008 and 2011 (but not Word 2004) Apple Pages Nisus Writer
Is this still supported? I couldnt get it to work with 6.5v4

And any word processor that can save documents in RTF, HTML or plain text. With most of these word processors, Sente supports two types of le scanning: Traditional le scanning, in which the user performs all of their edits in a source document and they use the scanning process to produce a formatted output document, and Scanning-in-place, in which the user is able to edit the formatted version of the document, so you are always working with formatted version of your manuscript. This chapter will provide you with an overview of le scanning and it will describe the steps required to prepare a document for le scanning and to perform the le scanning operation itself. This chapter does not explain the details of how to work with any particular word processor. The information here applies to all word processors that Sente supports with the le scanning interface.

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Introduction to File Scanning

File scanning is a technique for adding properly formatted citations and reference lists to a document. When scanning a le, Sente reads an original document containing temporary citation tags, collects the citation data from a Sente reference library, and produces a copy of the original document in which the temporary citation tags have been replaced with properly formatted citations and, optionally, with a complete bibliography. Traditional File Scanning In the traditional le scanning process, there are two copies of a document: The source copy, or the original, containing the complete text of the document, plus temporary citation tags. In Sente, citation tags typically look like {Smith 2007}. Also, somewhere near the end of the document, there may be a tag that looks like {bibliography} to indicate where the bibliography is to be placed. The scanned copy is produced during the le scanning process and includes all of the original text, with properly formatted citations replacing the citation tags, and the bibliography replacing the bibliography tag. In this approach, the scanned copy of the document will not be used for edits because any changes made will be lost the next time the original document is scanned. There are two exceptions, however. The rst is if you only need to edit the scanned copy for nal format or content changes after the scan process has been performed for the last time. The second exception is when the second copy is, itself, scannable. This case is explained later in this chapter. Scan-In-Place With some word processors, Sente supports an enhanced version of le scanning in which Sente is able to format the citations in the same copy of the document that you are editing. This is called scan-in-place. With scan-in-place, when Sente scans your source document, it replaces citation tags with formatted citations, but these citations are stored in what some word processors call elds. Fields can store more information than just the visible text and Sente uses these elds to hold the information required to allow it to rescan the document later. In addition, Sente automatically interacts with your word processor to make a copy of your source document, and to replace it with the scanned output document. The scanned output document is automatically reopened to just where you were when

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you started the scan operation, so it appears as though there is a single copy of your document. Citation IDs, Citation Tags and Delimiters Each reference in a Sente library has a citation ID eld. This eld is intended to contain a string of characters that uniquely identies the reference. That is, each reference in a library should have either no value for this eld, or a string of characters that is different from all other values in the library. When a reference is rst created, its citation ID eld is empty. You can enter any value into this eld at any time. Or, you can let Sente assign a unique value to this eld automatically, as needed (as will be explained further a bit later). When Sente generates a citation ID, it uses a template based on rst author name plus year of publication. Sente will ensure that each generated citation ID is unique within the library at the time of creation. A citation tag is a temporary marker placed in the master version of a document that consists of a citation ID surrounded by delimiting characters (e.g., curly braces). For example, if the citation ID for a reference is Smith 2001 then a citation tag referring to this reference would be {Smith 2001}. Delimiters are the characters that surround the citation ID to make up a citation tag in the original document. These delimiters (curly braces, by default) are intended to be characters that are only used as delimiters within the document. That is, if the default curly braces are used as delimiters for citation tags, there should not be any curly braces in the document that are not part of a citation tag. What Happens During File Scanning During le scanning, Sente reads through the master document looking for citation tags based on the delimiter you selected. That is, if you are using the default curly braces as delimiters, Sente will nd all text enclosed in curly braces and consider each string to be a citation ID. Sente will then look up each citation ID in the specied library. If it nds exactly one reference in the library with that citation ID, it will use that reference when formatting the output document. If the library includes either no references with that citation ID, or more than one reference with that citation ID, Sente considers that citation tag to be unresolved and it ags it as an error. Note that Sente does not analyze the contents of the citation tag to look up references. For example, if it encounters a citation tag like {Smith 2001} it does not look for a reference with a rst author of Smith published in 2001. Instead,

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Sente looks for a reference in the library that has a citation ID of Smith 2001. This might be a paper written by Jones and published in 1996the only thing that matters is the value stored in the citation ID eld. Obviously, reading the original document will be more difficult if the citation IDs do not have meaningful relationships to the related citations, and when Sente generates citation IDs it tries to make them meaningful, but in the end the citation ID eld is just a string of characters. When a scan is successful and all citation tags are successfully matched with individual references in your library, Sente will produce a second copy of the document in the specied format (e.g., APA, MLA, etc.). In this second version of the document, all of the citation tags will have been replaced with properly formatted citations. Similarly, if there is a bibliography tag, it will have been replaced with the complete bibliography.

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The File scanning process starts with a master document that includes citation tags and produces a scanned document in which these have been replaced with properly formatted text.

The Writing / Editing Process In general, you will want to use the File > Scan Document command or the scan-inplace toolbar button (for Word docx and Apple Pages documents) regularly throughout the writing process to verify that all of the citation tags in the document are correct and that the nal format meets your needs.

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In most cases, you will then need to return to the original document to continue editing. You will normally not want to edit the output document, except to make nal tweaks just prior to completion, because any changes you make in the output document will be lost if you rescan the original document. Rescanning Normally when you scan a master document to produce a scanned version of the le, the scanned version cannot be edited and scanned again because the information that Sente needs to recognize citations was lost in the scanning process. However, the le formats used in some word processors support the concept of rescanning the output le. This is possible because some word processor formats allow information to be hidden in a document, in what word processors typically call elds. Sente can use this feature to store enough information to let it continue to recognize citations even after they have been converted to formatted text. Sente can produce rescannable documents for these word processors: Microsoft Word 2008 and 2011 (not 2004) Apple Pages When scanning documents created in these word processors, you will have the option of specifying that the output le should be rescannable. When you do this, the output document will be properly formatted, with all citation tags having been replaced with formatted citations, but additional information will be stored in the document to support scanning this output document. This means that you would be able to edit the scanned document, including adding and removing citations, and then be able to scan the edited version to produce a new, scanned output le.

Before You Start

There are a few items that you need to think about before you begin working with a document that you will be scanning with Sente. In particular, you should: Decide how you want to get citations into your document. Sente supports several methods for inserting citations into a document and you should congure Sente to use those methods that you nd the easiest and most efficient.

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 Select the citation tag delimiters for the document. All citation tags in a document should use the same delimiters (curly braces are the default). You may want to use something other than the default if you are using curly braces elsewhere in the document. This section provides you with more detail on these items. Select the Command to be Used to Insert Citation Tags While citation tags can be typed into a document manually, most users will want to congure one of the supported commands to insert citation tags in your documents. For example, you could decide to use the copy / paste command to insert citation tags in your documents. Any one or more of the following commands can be congured to use citation tags: Drag and Drop Drag and Drop with the Option key () held down Drag and Drop with the Command key () held down Drag and Drop with the Shift key () held down Copy and Paste Cite (cmd-Y) and the Cite toolbar button For most word processors, the Cite toolbar button and/or cmd-Y will be the most useful. These two methods are the same as the the File > Cite in Word Processor command, and all three congured as Cite (cmd-Y) under Other Gestures in the Gestures preferences pane. (More on that later.) To use any of these three methods, insert the cursor in your document where you want the citation tags to be added, switch to Sente, select the desired reference(s) and either click on the Cite toolbar button, press cmd-Y on the keyboard, or use File > Cite in Word Processor. Sente will then insert the citation tags and automatically switch focus back to the word processor application. (Note: If the Cite button is not available on your toolbar, please see the section on Customizing the Toolbar.) Any of the other commands can also be used for this purpose if they are more convenient for your workow. Each of the supported gestures can be connected to any of the supported formats using the commands in Preferences. Simply open Sente 6 > Sente 6 Preferences, click on the Gestures tab, select the desired output for each of the different gesture methods (in this example, citation tags with the

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desired delimiters), and close the preferences pane. You can have multiple gesture types congured to use citation tags as the output format.

The Gestures preferences pane.

For more information on setting the various output options, please see the section on Output Gestures. Select the Citation Tag Delimiter Before you being inserting citation tags into your document, you should decide which of the citation tag delimiter options you will use in the document. Sente supports the following options for citation tag delimiters: Curly braces: {Smith 2007} Square brackets: [Smith 2007] Parentheses: (Smith 2007) Dash-braces: -{Smith 2007}It is important to choose a delimiter set that will not be used elsewhere in the document other than in citation tags. For example, if mathematical equations containing curly braces are used throughout the document, curly braces should not be used as delimiters for citation tags.

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For most documents, curly braces are a good default because they do not commonly appear in text. However, the dash-brace delimiter may be needed in documents that make extensive use of braces, parentheses and brackets.

Selecting citation tags with curly braces for Cite button and cmd-Y gestures in Sente 6 > Sente 6 Preferences, Gestures tab.

See the section on Output Gestures for more information about gesture conguration.

Inserting Citations
As you write your document, you will want to insert citation tags at the appropriate places in the text. Adding Citation Tags Automatically Sente allows you to quickly and easily insert citation tags by simply selecting the reference in the reference list and either clicking the Cite toolbar button or using

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the cmd-Y keyboard shortcut.. (If the Cite button is not located on your toolbar, please see the section on Customizing the Toolbar.)

The Cite and Scan toolbar buttons.

Using the Cite toolbar button and cmd-Y are both very easy three-step processes: 1. 2. 3. Place your cursor at the proper location in your document. Select the correct reference in Sente by left-clicking on it once in the reference table. Either click the Cite button on the toolbar or use the cmd-Y keyboard shortcut.

The citation tag will be placed at the cursor location in your document. You may also use the File > Cite in Word Processor menu command, if you choose. Manual Entry If you prefer, you can enter the citation tags manually. There is nothing special about citation tagsthey are simply text that the le scanner in Sente can recognize. This means that you can always just type the tags in manually, as long as the citation IDs match the references in the library. The only drawback to the manual entry method (other than the typing) is that when the other methods are used, Sente will automatically generate a citation ID for each reference if one does not already exist. When you type in the citation tag manually, the citation ID may not yet exist for the reference. In this case, the tag you typed in will show up as unresolved during the scanning process. If you then drag the reference from the reference table in Sente onto the unresolved citation in the results window, Sente will automatically assign the tag you entered to the reference, so the tag will resolve correctly in the next scan. Footnotes Some bibliography formats require that citations appear in footnotes rather than in the body of the text. In these formats there is typically a superscripted number in the text at the point you want to refer to the citation, and then a footnote with that number at the bottom of the page. The citation is then included in the footnote.

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Sente can generate properly formatted citations for footnotes, but it cannot create the actual footnotes in the document. Therefore, if you are working on a document in which citations should appear in footnotes, you will need to create the footnotes manually using the word processor and then insert the citation tags into the footnotes. Again, what is inserted into the document (e.g., citation tags versus full citations) depends on what is congured in the Gestures tab of Preferences. Please see the section on Output Gestures for more information.

Modifying In-Text Citations

You may want to modify the nal formatted citation in some wayto add cited pages, perhaps, or to limit the output to just the year of the publication. This is accomplished by adding modiers to the citation tags. Sente supports a number of modiers that can be applied to in-text citation tags to change the output in various ways:
Cited Pages (@)

Many bibliography formats support the concept of cited pages and call for different ways of displaying page numbers in a citation. For example, (Smith 2007, 83-85) might be appropriate for one format, while (Smith, A., Stories, pp. 83-5) might be appropriate for another. As long as you include the page numbers in the citation marker, Sente will format them appropriatelyincluding dropping digits if the bibliography format calls for it. To include cited pages, type a page or page range following @ in the marker, such as: {Smith 2007@83-85}. Note that for the @ notation to have any effect, the bibliography format must include a cited pages element.
Append and Prepend Text (\...\)

You can add any xed text to a citation marker by enclosing the text in backslashes before or after the citation ID: {Smith 2007\, Chapter 2\} might become Smith, A. 2007, Chapter 2. {\As found in: \Smith 2007} might become (As found in: Smith, A., Stories.).

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Year Only (%)

Sometimes you only want the year of publication to appear in the nal output, rather than the complete citation. In this case, prepend the citation ID with a percent sign: As Smith said {%Smith 2007} would become As Smith said (2007).
Bibliography Only (!)

If you dont want a citation to appear at all (for example, when youve already discussed the reference in the text), but you still want the reference to appear in the bibliography, you can insert a citation ID and then hide it by prepending an exclamation point: {!Smith 2007}.
Suppress Superscripting (_)

If the bibliography format youre using calls for superscripting all citations, you can override that in individual citations by prepending the citation ID with an underscore: {_Smith 2007}.
Strip Enclosing Punctuation (*)

To omit any enclosing punctuationlike parenthesesplace an asterisk before the citation ID: {*Smith 2007}. In this case, if the bibliography format would normally produce (Smith, 2007), it would instead produce Smith, 2007.

Adding a Bibliography
Sente will not automatically add a complete list of references, or bibliography, during the le scanning process unless specically told to do so. This is accomplished using the bibliography tag. To tell Sente to insert a bibliography during the scanning operation, insert the text {bibliography} at the desired location. If you are using something other than the default delimiters for citation tags, you should replace the curly braces in the above example with the delimiters you are actually using. Formatting the Bibliography Tag Normally, the {bibliography} tag should appear in its own paragraph in the document and the formatting of that paragraph should be the formatting you want to have applied to the generated bibliography.

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For example, if you want the bibliography formatted with a hanging indent and double-spacing, apply that formatting to the paragraph containing the bibliography tag and this will carry through to the nal output.

Scanning the File

At any time during the writing process you can scan the master copy of the le to produce a formatted version. This will cause Sente to check all citation tags in the document to make sure they refer to exactly one reference in the library, and it will produce a formatted document for your review. With Microsoft Word docx and Apple Pages documents, Sente offers a scan-in-place feature that allows you to continue working on the document as you occasionally scan newly inserted citation tags. For more information about scan-in-place, please review the information below and then see the scan-in-place section. To initiate a scan operation, select the File > Scan Document command or click on the Scan button if it is present on the toolbar.

The Cite and Scan toolbar buttons.

Either of these methods will bring up the Scan Dialog window in which you set various options for the scanning process. These options are explained below.

The scan dialog window appears when you select File > Scan Document or click the Scan toolbar button.

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Selecting the File to Scan Sente provides two ways of specifying the le to be scanned. One, it will look for all les that are currently open in any of the supported word processors, and which are in a supported format. These les will be listed in the menu labeled Open Document in the scan dialog window. Because you will typically be wanting to scan a le you are currently editing, your le is likely to be in this menu. Alternatively, Sente lets you select any le on your computer for scanning. If you want to scan a le that is not open in a supported word processor, select the File option and then click on Choose to select the le from your le system. It is important to note that Microsoft Word les must be saved in docx format, not doc format. If you have a doc le open in Word, Sente will not include it in your list of scannable les because the format is not docx. Style Any of Sentes bibliography styles can be selected as the output style. The menu next to the Style item contains all of the styles you have selected as a favorite. (If you want to change the entries in this menu, open the Bibliography Format Editor and adjust which entries are marked as a favorite.)

The list of favorite citation style options.

Library All references in a document must be found in a single Sente library. This library is specied in the Library menu. Only open libraries are listed, so you must rst open the library you wish to use.

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Delimiters Before you began entering citation tags in your document, you selected one of the options for citation tag delimiters (curly braces by default) in Preferences. You need to make sure that the same delimiters are specied in the scan dialog window so that Sente will recognize your citation tags.

Delimiter options in the scan document window must match the delimiters used in your document.

Scan-in-Place Scan-in-place is an option where your Word docx or Pages document can be scanned occasionally as you continue editing it. For more information, please see the section on Scan-in-Place below. Output File Name and Location This is where you tell Sente where to save the output le. You can name the output le whatever you want, but Sente will default to a name based on the input lename plus the bibliography style name. Output File Format Depending on the format of the input le, you may have several options for the format of the output le. These options determine exactly what information is stored in the output le. These options should not be confused with the Style options, which determine the bibliography style to be applied. Instead these options specify the le format (e.g., RTF, docx) and, in some cases, whether the output le should be scannable itself.

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Scannable, Not Scannable and Unscanned Options

When working with some input le formats, like Word docx or Apple Pages, you will have the option of selecting output le formats like: Scannable, Not Scannable, and Unscanned.

The scanned le format options for a Word docx document. Not Scannable

This is the default (and, in some cases, only) output format. In this type of output, all temporary citation tags will have been replaced with properly formatted citations. It is not possible to add new citations to this type of document; instead, all editing must be performed in the original document and that le is the one that should be rescanned after edits are made.
Scannable

Some word processor formats (e.g., Pages and Word .docx) can include data that is not normally visible to the user. This capability means that Sente can produce a scanned document that can be edited, including the insertion of additional citation tags, and then rescanned. Scannable les enable users to edit a draft that looks very much like the nal formatted document will look when nished.
Unscanned

If you start with a rescannable document, you can revert all of the previously scanned citations to citation tags by scanning the le and selecting Unscanned as

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the output format. This is particularly useful for making sure that the correct citations are included in the document.
Options for Microsoft Word docx Files

If your input le is a docx le, you can select any one of: Document, Not Scannable. Document, Scannable (EndNote compatible) Document, Unscanned.
Options for Apple Pages Files

If you are working with a le produced by Apple Pages, you can select any of these output le formats: Apple Pages Document, Not Scannable Apple Pages Document, Scannable Apple Pages Document, Unscanned.
Options for RTF Files

If your input le is an RTF (Rich Text Format) le, you can select any one of these output formats: Scanned RTF Scanned RTF with EndNote codes for Word 2004 Scanned RTF with Sente codes for Word 2004 Unscanned RTF. Start the Scan Once you have selected the desired options in the File Scan Dialog Window, you can simply click on the Scan button to start the scan operation.

Scan-in-Place
For Word docx and Apple Pages documents, Sente supports an enhanced version of le scanning called scan-in-place. This allows Sente to format citations in the same

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copy of the document that you are editing, allowing you to easily rescan after adding new citation tags. When Sente scans your source document during scan-in-place, it replaces citation tags with formatted citations, but these citations are stored in what some word processors call elds. Fields can store more information than just the visible text and Sente uses these elds to hold the information required to allow it to rescan the document later. In addition, Sente automatically interacts with your word processor to make a copy of your source document, and to replace it with the scanned output document. The scanned output document is automatically reopened to just where you were when you started the scan operation, so it appears as though there is a single copy of your document. If you look where your document is stored, however, you will see a le with .backup added to the le name. The scanned citations and your edits will be stored in the main le, which is rescannable if you wish to continue editing it either now or on another day. To use scan-in-place, follow the directions above for le scanning, but place a checkmark in the Scan-in-place checkbox in the scan document dialog box. Remember that only Word docx and Apple Pages can be scanned in place.

To use Scan-in-Place for Word docx or Apple Pages documents, place a checkmark in the Scan-in-place checkbox before clicking the Scan button.

The scan-in-place le scanning process is the same as the other methods of le scanning, except that you can rescan your document as you edit it, as many times as you want to. In addition, the scan results window (see below) appears only if there are any unresolved citations.

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Reviewing the Scan Results

When Sente has complete the scan operation, it will display the Scan Results dialog window. This window will tell you whether Sente encountered any problems during the scan and help you resolve any that may have occurred.

A sample le scan results dialog window showing resolved and unresolved citations.

Resolved Citations vs. Unresolved Citations After the le scanning process nishes, you will be shown the results. The table in this dialog window includes a list of citation tags found in the document. Unresolved citations are listed in red. By default, both of the Show checkboxes are checked, indicating that both resolved and unresolved citation tags should be included in the list. You can display only resolved or unresolved citations by checking the appropriate boxes. Correcting Unresolved Citations There are two basic reasons why a citation would be listed as unresolved in this list: There is no reference in the library with the exact citation ID from the citation tag. This might be because you typed in the citation tag manually and either made a mistake, or never added the citation ID to the appropriate reference.

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 There were two or more references in the library with that exact citation ID. This can happen if you update the citation ID on a reference manually and mistakenly change it to a value that it already in use. In either case, you need to change either the citation tag in the document, or the citation ID on the desired reference so that the two match (and no others). If you simply mistyped the citation tag, you should normally correct the tag in the document. If you entered the tag manually, but did not add it to the reference, then you will want to add the citation ID to the reference in the library. This can be done manually, of course, or you can simply drag the reference from Sentes main reference list onto the appropriate row in the scan results table and Sente will automatically assign the correct citation ID to the reference. If there are two or more references with the same ID in the library, you will need to change one of them to something else. After making any corrections either to the document or the library, you can use the Start Over command to re-do the scan using the new values in the library. If Sente is unable to match a citation and you click the Save and Open button without correcting the citation, **UNRESOLVED** will appear at that location in the document.

Rescanning a Document
A few word processors use le formats that support the concept of rescanning an already scanned document, a process in which new citations can be incorporated into a document that already contains formatted citations. This section will explain how to use rescanning. When is Rescanning Supported? When you scan an original document containing citation tags, these tags are normally replaced with formatted text. Sente can recognize the citation tags in the original document because they are always surrounded with the specied delimiters. But in the output document there is no reliable way for Sente to recognize the formatted citations, because they are just text. This is true for le formats such as RTF, HTML, and plain text.

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There are other formats, however, that allow Sente to store additional information in the output le which Sente can use to keep track of the citation tags used in the original document. These formats include Word docx and Apple Pages format. In these formats, you can add new citation tags to the output document and execute the scan operation on that document, and Sente will merge the old and new citations to produce a new output document where all of the citations have been included. In order to be able to scan a document that was itself produced during a scan, the output document must have been created in a rescannable le format. (Of note, Word docx and Apple Pages documents that have been scanned with Sentes scanin-place feature are saved in a rescannable le format.) See the output le format specication section above for more information. Use Caution The normal scanning process is very safe because Sente only reads your original documentit never modies the contents of the original documentso nothing can be lost, even in the event of a serious bug or system error. Rescanning, however, is not as safe, because you switch to editing a document that Sente has modied and, if something goes wrong, there is always the possibility of data being lost. For this reason, we recommend that you use rescanning with caution. In particular, we recommend that you keep intermediate copies of your document as you are working, so that you can always fall back to a recent version if something goes awry. For example, save and keep each version of the le just prior to each scan, at least for several versions back. We work hard to make sure that the le scanning process does not corrupt les in any way, but word processing documents are very complex and there is no way for us to test our code in every possible circumstance, so there may be cases that are not handled properly.

Troubleshooting
File scanning helps simplify the task of inserting and formatting citations and bibliographies and usually it works easily and correctly. However, sometimes problems may arise. This section will help you solve some common le scanning issues.

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My File is Not Listed in the Scan Dialog Box When you begin the le scanning process, you are given the choice to either scan an open document, or nd a closed le on the computer to be scanned. All open documents that are saved in a format that Sente recognizes will appear in the dropdown list for the open document option. If your open document does not appear on the list, here are some common reasons why: The word processor is not yet supported by Sente. Sente supports Word 2004, 2008 and 2011, Apple Pages, Mellel, Nisus Writer, TextEdit, rich text format (RTF), HTML, and others, but there are still word processors that are not yet supported by Sente. If your document is not saved in one of these currently supported formats, it will not appear on the drop-down list. The le needs to be saved. If you created and worked on a document but did not save it, the le may be missing from the list. Saving the le may resolve this problem. The Word 2008 or 2011 document is not saved in the docx format. Sente is only able to read Word 2008 and Word 2011 documents that are saved in the docx format. Documents saved in the doc format will not appear in the dropdown list. The Scan Button is Grayed Out In the scan dialog box where you select the document to be scanned and specify a number of options to be used during the scan operation, there is a button at the bottom that starts the scan process. Sometimes this button is grayed outor is inactivatedand the reasons for this may not always be clear. Here are the most common reasons why the button may be grayed out and cannot be pressed: No input le is selected in the top section of the window. Select either a document that is currently open (which has been saved in the proper format of one of the supported word processors), or select a closed le on the computer. An open le is selected at the top of the window, but the le has unsaved changes. (This will be indicated by the text Unsaved Changes in the item name). Click the Cancel button, save the changes, and return to Sente to start the le scanning process again. There is no selected library in the library drop-down list. Make sure that the library with the references being cited is open in Sente and selected from this list.

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 The output le is either not specied, or cannot be written to by the current user. Specify a lename in a location on the computer that you have permission to write to. The required scanner plugin is disabled in Sentes Preferences. For example, if you are trying to scan a Word 2008 docx le, you will need to make sure that the Word 2008 docx scanner plugin is enabled. (NOTE: All plugins are enabled by default.) The Bibliography Isnt Properly Formatted If the bibliography is not properly formatted after the le is scanned, please make sure that the paragraph containing the bibliography tag itself is formatted. The references cited will use the same format that the bibliography tag has before the le scan. If you want the bibliography to have a hanging indent and be doublespaced, for example, make sure that the paragraph containing the bibliography tag is formatted with a hanging indent and double-spacing. The Scan-in-Place Option is Grayed Out Scan-in-place can be used with Word docx and Apple Pages documents only. If the checkbox for Scan-in-Place is grayed out, you either have not selected a Word docx or Apple Pages le to scan, or your le is not saved as one of these two le types. Still Not Working? If, after reviewing these possible problems, you are still not able to successfully scan a document, please contact us at our support address.

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Chapter 16

Creating and Modifying Bibliography Formats

Sente comes with many built-in bibliography formats, including many of the most popular formats, such as MLA, Chicago and others. Most users can simply select one of these built-in formats and let Sente take care of the rest. However, if you need a format that is not included with Sente, you may need to either modify an existing format, or create a new format to meet your needs. This is done using the Bibliography Format Editor in Sente. Your custom formats become available as menu choices for all bibliographies you create. They also become selectable for print, copy/paste, drag/drop, send to le, and send to word processor formats.

Introduction to the Bibliography Format Editor

Sente comes with quite a few bibliography formats pre-installed. Many users will never need to do anything but to pick one of the most popular formats from the lists of favorite formats presented at various places in the Sente user interface. Some users, however, will need to dig deeper than this to either select one of the less common formats, or to modify a built-in format, or even to create a new format from scratch. All of these tasks are performed using the Bibliography Format Editor. To open the Bibliography Format Editor, use the Window > Bibliography Format Editor command.

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When the window rst opens, it will contain a list of all installed and custom bibliography formats in the list at the left. A preview (using built-in sample data) for the format selected in the format list will be shown in the preview pane at the right.

The Bibliography Format window, showing the favorite bibliography formats in the list on the left.

Favorites The checkbox at the top of the format list is used to control whether the format list includes all known formats, or only those that you have indicated are favorites. If you are looking for a format that is not among the favorites, simply uncheck the Show Favorites Only box to see all of the available options. Each of the formats with a checkmark in the box will be included in menus of formats elsewhere in Sente.

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The Preview At the right side of the window is a preview of the bibliography format selected at the left. Just above the preview pane, there are two radio buttons that control the contents of the preview. Normally you will want to select the Reference Types option to see what the format will look like in use. The Components option is used when editing formats, and will be explained below. Within the preview pane, there is a complete list of all Sente reference types, including any custom types you may have added. By default, the preview for each type is collapsed and clicking on the disclosure triangle next to the type will show the preview. Note that while it is easy to expand all of the reference types in the preview, this will slow down performance because more previews need to be updated every time something about the format denition changes. Also by default, there are two versions of each reference type displayed in the preview: in-text and bibliography. Exactly what is displayed in the preview pane is congurable, as will be discussed later. Editing As you move your mouse around the preview pane, you will see that different portions of the preview become highlighted. The highlighting shows you which element in a format your pointer is hovering over. In some cases, this will be a simple element (like the article title) and in other cases, this may be a component built out of several simple elements or other components. When you click on the preview, the highlighting for the current element changes to yellow and, if it is not open already, the editing drawer will open and the element you clicked on will be selected. This makes it easy to jump right to whatever part of the format you want to work on.

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The Format Editor drawer (at right) is where you set up the look of citations and bibliographies for custom (Local) formats you create.

Before making any changes to a built-in format, you need to make a local copy using the Duplicate button at the bottom of the format list. If you attempt to change a built-in format, you will be warned that your changes will not be saved. This allows us to update the built-in formats with each release, without overwriting any formats that you have modied. Whenever you make a change to the selected format, a black dot appears in the red close button at the top of the window to indicate that there are unsaved changes. The format will be saved automatically whenever you switch to another format or close the window. To save the format manually, just press cmd-S. The rest of this chapter explains some of the concepts behind Sentes bibliography formats and the details of setting up and modifying bibliography formats.

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Concepts
Bibliography Format

A bibliography format in Sente is a set of rules about how citations should be presented both in the body of a document (i.e., in-text citations) and in the list of works cited, or bibliography, which is typically at the end of a document. Each bibliography format in Sente includes two different specications for each reference type: one for the in-text citation and one for the bibliography entry. For example, the APA format includes two specications for how book references should be presented, one for in-text and the other for the bibliography, and two for each other reference type. Also, when you add custom reference types to Sente, you can easily add format specications for the new types as well. Each of these format specications (e.g., book, in-text) can consist of either: a statement that the format specication for a different reference type should be used (e.g., same as Book Chapter), or a list of elements indicating exactly which information should be presented and how it should be formatted (e.g., authors, publisher, etc.).
Elements

Individual elements in a format specication can be simple elements, like Publication Title, or components, each of which can contain any number of other elements.
Conditions

Many bibliography formats have complex rules about where and when certain attributes of a reference should appear. Sometimes it is important, for example, to be able to add or remove punctuation based on the presence or absence of particular elds. This sort of behavior can be specied in Sente using the Conditions menu on any element in any format. See below for more information on using conditions on elements.
Components

Components are an important tool for building and maintaining complex formats. For example, in most formats, the list of authors for each reference in a

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bibliography follows some basic rules that are the same for all types of references. By creating a component that contains an Authors element, with all of the correct options set (rst author format, other author format, punctuation, etc.), and then using this component instead of a new author element, all of the options only need to be set correctly in one place. Should you nd something you need to change in the author format, you would only need to make the change in that one place and the change would automatically be reected everywhere that component was used. Further, because components can contain any number of elements, it is possible to build up rather complex components that capture a lot of rules about a format. For example, some formats begin each bibliography entry with the authors followed by the year of publication, and the year should be the year of original publication, if different from the year of re-publication. Using conditional tests such as reference has an original date of publication, you can create a component that always works, no matter what the details of any particular reference may be.

Bibliography Format Editor Interface Tour

Here is a brief tour of the settings contained on each of the tabs in the format editor. The tour will include: The General Tab The Bibliography Entries Tab The RTF Tab The Advanced Tab

Bibliography Format Editor Tabs

The General Tab The General tab is where you congure some global formatting rules that apply to bibliographies and citations generated within word processing documents.

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The General Tab Bibliography Formats Options

The top section of the General tab is where a number of format-wide options are specied. Order Bib. by: The selection here determines how the entries in the bibliography will be ordered. Occurrence in document causes bibliography entries to appear in same order as their citations do in the document.

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 Author full names, then date orders entries alphabetically by the full names of all authors, then chronologically for entries that have identical authors. Author surnames, then date orders entries alphabetically by all author surnames, then chronologically for entries that have identical authors. First author, then date orders entries as above except additional authors are ignored. Author names, then title orders entries alphabetically by all author names, then alphabetically by title. In-text citation value orders entries by the content of their in-text citations. For example, you would want to order by citation value if your format will reproduce the in-text citation, such as (Smith, 1997), at the beginning of each bibliography entrythis way the entries can be ordered by this initial citation value. Prepend, Separator, Append. Use these elds to place text before, after, and between bibliography entries. Usually these will be paragraph breaks represented by \n. Append a, b, to year as needed. This determines whether Sente will automatically append letters to the end of the year of publication to distinguish otherwise identical citations. Clean up extra spaces. If checked, Sente will ensure that each bibliography entry has no leading or trailing spaces, and no runs of more than one space in a row internally.
In-Text Citation Format Options

These setting affect the nal appearance of in-text citations. Order Citations by: determines how citations within a citation group (multiple citations place at the same location in a document) are ordered. As entered does not change the order of the citations with citation groups. Alphabetically reorders the citations within each group to be alphabetical. As in bibliography reorders the citations within each group to match the order in which the references appear in the nal bibliography. Chronologically orders the citations in each group by their dates of publication. Prepend, Separator, Append. Use these elds to place text before, after, and between citation information.

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 Use numeric ranges in citation groups (e.g. 1-3) applies only when using a bibliography format that places citation numbers in the text. If checked, Sente will replace 1, 2, 3, 4 with 1-4. Omit delimiter between repeated authors tells Sente not to place the Separator dened above between two references that have the same authors. This enables Sente to generate output like Smith 1998, 2001; Jones 2000 when citing two papers by Smith and one by Jones. (In this case, the comma is provided by the format denition itself, but this option eliminates the semicolon that would otherwise be automatically generated.) Superscript tells Sente to place the resulting in-text citations in superscript. Use ibid: tells Sente that the format uses some form of Ibid. to handle repeated references. If this is checked, then everything that would have been outputted for the second and successive occurrences of a reference should be replaced with the value in the text eld here (and italicized, if that option is checked). The most common value for this text elds is, of course, Ibid. Note that cited pages will still be printed even with Ibid. Italicize italicizes the form of Ibid. chosen (if the box is checked). The Bibliography Entries Tab In a single Bibliography Format, you can congure the bibliography entry and intext citation for any number of reference types, such as journal article, book, book chapter, etc. For each reference type, you set up the bibliography entry and in-text citation by stringing together a sequence of Elements and specifying rules for applying punctuation and spacing around each Element. As you assemble Elements for each reference type, you can review sample output in the Bibliography Formats window.

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The Bibliography Entries Tab

Ref. Type: Sente references always have a Reference Type; when Sente formats a bibliography entry or in-text citation, it uses the conguration for the appropriate Reference Type within a Bibliography Format. This way, for example, your format knows to treat a journal article entry differently than a newspaper article entry. Select the Reference Type you want to congure from the Ref.Type menu; if you dont see the one you want, make sure its checked in the Display Sample Types menu in the Bibliography Formats window. Occurrence: Most Bibliography Formats are applied in two places: in the in-text citations and in the bibliography or reference list that appears at the end of a manuscript. These are known as occurrences of your format that may be

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specied for any given Reference Type, and you can congure each Reference Type/Occurrence combination independently. For example, the In-text Occurrence of your Journal Article Reference Type might include just two ElementsAuthors and Year of Publicationso that an in-text citation for a journal article would look like Smith et al. 1999.

An In-text occurrence of a Bibliography Format might include just two Elements

Although there are only two basic occurrences for each reference type in a format denition, sometimes you want to see how, say, the In-Text style will appear in a particular context (e.g., when it is the second time a reference is cited in your document). To accomplish this, you can readily add previews to the preview pane to show each reference under a variety of conditions. Denition: The Denition menu provides some alternatives to using the string of Elements: As Shown Below means the format will use the Elements youve arranged them in the Elements list. Choose Not implemented to disable formatting for the selected reference type. When Sente formats an entry with a reference type that is not implemented, it inserts Not Imp into your bibliography. If the Reference Type/Occurrence combination youre conguring (such as Book chapter/In-text) has the same format as one youve already set up (such as Journal article/In-text), youll be able to select it hereas Same as Journal article (In-text), for example. This allows you to maintain a single set of formatting rules and have it applied in many different instances.

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Adding and Conguring Elements

If you have selected the As Shown Below option in the Denition eld above, you will be able to add elements to the format for the selected reference type. To add a new element to the end of the list, click on the + button, and then select the type of element in the pop-up menu below the list. To move the selected element up and down the list, use the Up and Down buttons.

Specifying the Element Type in a Bibliography Entry

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In addition to the standard bibliographic elements, you can include the Abstract and Notes. Some elements exhibit specic behavior: Author roles include Authors, Editors, Translators, Artists, Compilers, Directors, Illustrators, Lyricists, Orchestrators, Performers, Photographers, Producers, Reporters, Series Editors, and Writers. Each name in a reference can be assigned any one of these roles. Alternate title, Description, Intuitive Title, and Translated title allow you to choose the capitalization rules (as found in reference, force sentence case, etc.) and choose whether or not to use the shortened title, if available. Cited pages and Pages will display a page number or page range if the citation marker has been modied to include cited pages. See the Working with Word Processors section. Date elements have choices for date formats. Keywords and Tags have a box to input the separator. Paragraph separator includes a checkbox for additional indent and choices for indentation style. Static text allows you to insert any xed text. Year of publication (w/ a,b,c) includes a checkbox for using a 2-digit year.
Viewing Sample Output

When your elements list is complete, select any item in the list. In the preview area of the Bibliography Formats window, the sample output for that element is highlighted in yellow.

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Changes to an Element are reected immediately in the preview area of the Bibliography Formats window. Conguring Each Element

Immediately below the Element Type menu, some options specic to the selected element may appear. For example, there are a number of ways to congure the Authors element. Move down the elements list to congure each one, and review your changes in the preview area of the Bibliography Formats window.
Some Elements can be configured for automatic case changes, such as forcing title case. Sente maintains a list of terms that arent affected by case change rules, such as and, or, but, in, etc., and you can edit this list in Sente 6 > Sente 6 Preferences, Bibliography tab. There you can also set up a custom list of terms that always appear in a specified exact case.

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Conguring the Authors Element

For the Authors, Pages, and Cited Pages elements, a For plural, Prepend/Append elds appear. This allows you to specify certain punctuation that may be required before or after these elements only when there is more than one of them. For example, in the case of editors (or authors, etc.), if there is only one editor, the normal prepend and append values will be used. If there are two or more editors, the plural values will be used. This makes it possible to have a single editor appear like this: John Smith, ed. and to have multiple editors appear like this: John Smith and Adam Jones, eds.. In this case, the singular append eld would contain , ed. and the plural append eld would contain , eds..

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Prepend and Append options for multiple pages and authors.

For the Journal/book name element, you can ask the Format to use either the full name or abbreviation.

The Publication Title (same as the Journal/book name Element) can call for the full name or the abbreviation, when known. Sente stores known full names and abbreviations in the Journal Dictionary.

To view and edit the list of journals that Sente uses to distinguish full names from abbreviations, choose Window > Journal Dictionary from the main menu. Sente knows the names and abbreviations for several hundred journals, but you can edit any titles, abbreviations, and ISSNs. You can also add and delete titles.

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Journal Dictionary Common Settings

Some settings can be used on all elements, regardless of type. Others are specic to particular element types. Here are the common setting shared by all elements: Remove trailing punctuation. When checked, will strip all occurrences of the trailing punctuation you specify. For example, if you enter .; in this eld, all trailing periods and semicolons will be stripped from the selected Element. Add trailing punctuation characters. When checked, will append punctuation to the Element after any specied trailing punctuation has been removed. unless data ends with any of When checked, will override the previous eld when the specied trailing punctuation still exists after any specied trailing punctuation has been removed. Prepend and Append add any characters after any checked operations above have been performed. Type a space to add a space, \n to insert a line break, and \t to insert a tab. Font allows you to apply common font treatments to the Element. Replacement text if element missing allows you substitute text (such as unknown) when a reference contains no data for that Element. Depends on enables you to make the inclusion of the element conditional. See the Conditional Elements section below for more information.

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Working with Punctuation

Its often important to correct trailing punctuation for elements like Journal/book name and Article/chapter title. In these cases, the example shown below often works.

Controlling Punctuation for an Element

This format rst strips all periods and semicolons from the end of the article/ chapter title, then adds back a periodunless the title already ends in a question mark. Finally, the format appends a space at the end. The result is that every article/chapter title will end with either a period or a question mark, followed by a space.
Setting for Specic Element Types

Many element types have special settings in addition to those listed above. Some of these are below: Alternate title, Description, Intuitive Title, and Translated title allow you to choose the capitalization rules (as found in reference, force sentence case, etc.) and choose whether or not to use the shortened title, if available.

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 Cited pages and Pages will display a page number or page range if the citation marker has been modied to include cited pages. See the section on Modifying In-Text Citations for more information. Date elements have choices for date formats. Keywords and Tags have a box to input the separator. Paragraph separator includes a checkbox for additional indent and choices for indentation style. Static text allows you to insert any xed text. Year of publication (w/ a,b,c) includes a checkbox for using a 2-digit year.
The Conditions Menu

Each element in a bibliography format, including components, can be included conditionally, if desired. For example, it is possible to have an entire component not appear if the reference does not have both a translated title and a publisher. The conditions under which an element should appear in the nal output are captured in the conditions menu shown here:

The Conditions Menu in the Bibliography Format Editor

This menu contains a number of sub-menus, including: Reference has all of... When one or more selections are made in this sub-menu, all of the selected elements must exist for the current element to be included in the output. Reference has none of When one or more selections are made in this submenu, the reference must have values for none of the specied elds. If the reference has a value for any of the elds, the element will not appear. Reference has at least one of At least one of the elements selected in this sub-menu must exist for the current eld to be included in the output. Reference lacks one or more of At least one of the elements selected in this sub-menu must be missing for the current element to be included in the output. Reference is of type(s) The reference being rendered must be one of the types selected in this sub-menu for the current element to appear in the nal output.

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 Reference is not of type(s) The reference being rendered must not be one of the reference types selected in this sub-menu for the current element to appear in the nal output. Conditions in context This sub-menu includes various contexts that can be tested for when determining whether an element should be rendered. The options are shown below. Selecting options in this sub-menu enables you to, for example, indicate that the list of authors should not be included when the reference is the second (or subsequent) reference in a group of references, and the authors are the same as the immediately preceding reference.

Context Sub-Menu

The more complex formats (such as APA, MLA, Chicago) make extensive use of conditional elements. Please take a look at the built-in denitions for these formats for examples of how conditional elements can be used to make more accurate and exible bibliography formats.
Conguring Other Reference Types

When youve nished setting up the Elements for your rst Reference Type, select the next type (such as Book) and then use the Copy menu to copy the setup from the rst typeusually, only minor changes will be needed to adapt your format for each Reference Type.

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Copying a Sequence of Elements from Another Reference Type If the Reference Type/Occurrence combination youre configuring is exactly identical to another combination youve already configured, dont make a copy. Instead, specify the existing combination using the Definition menu this way, you can maintain the configuration in just one place.

The RTF Tab The Rich Text Format settings only apply when youre using a Bibliography Format as a drop/paste and printing format; they dont affect how Sente generates citations and and bibliographies within word processors. Indentation determines the style of paragraph indentation to be used in the bibliography. Font sets the font to be used. Size determines the point size for the text in the bibliography. Line spacing is used to modify the space between lines in the bibliography. Paragraph spacing adjusts the amount of space between each entry in the bibliography.

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The RTF Tab

The Advanced Tab Advanced bibliography format settings allow you to customize certain terms and to customize the preview.

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The Advanced Tab Customized Terms

This section lets you override certain terms in the nal output. This lets you replace English terms with other languages or symbols. The values you can override include: and This is often replaced with the equivalent in another language or something like & et al. Some formats use and others or some other text instead of the traditional et al.

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Contexts Used in this Format

Different formats have very different rules about how references appear in different contexts. For example, some formats make a distinction between the rst and subsequent occurrences of a reference; other do not. Some format citations differently if there are several references in a row from the same author, and others do not. Sente supports all of these conditions (and more) but displaying them in the preview can be overwhelming, especially when no single format cares about all of the possible contexts. Therefore, Sente lets you congure exactly which contexts are displayed in the preview pane to make it easier for you to create and modify bibliography formats. By showing only the contexts that the format actually cares about, you are not distracted by a lot of identical references in the preview. Fundamentally, there are two different contexts: in-text and the bibliography. Almost all formats want references formatted differently when they are presented in the text of a document and when they are presented in the bibliography. These are the two contexts included by default in the preview display. You can add or remove contexts as appropriate for each format. When you add a new context, you specify the conditions that should be simulated in the preview display for the context, using the Context conditions menu. For example, if you are creating a format that uses dashes in the bibliography when a reference has the same authors as the previous reference, you can add a context for bibliography entries with the same authors as the previous reference. When Sente formats this entry in the preview, it will act as though it is formatting a reference with the same authors as the previous reference so the formatting rules based on this condition will be applied in the preview. Without the ability to congure these contexts for the preview, you would only be able to test many complex formats by setting up real data where the conditions were met, and this would be a tedious process.

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Context Conditions in the Advanced Tab of the Bibliography Format Editor

Creating and Using Components Components are an important tool for building and maintaining complex formats. For example, in most formats, the list of authors for each reference in a bibliography follows some basic rules that are the same for all types of references. By creating a component that contains an Authors element, with all of the right options set (rst author format, other author format, punctuation, etc.), and then using this component instead of a new author element, all of the options only need to be set correctly in one place. Should you nd something you need to change in the author format, you would only need to make the change in that one place and the change would automatically be reected everywhere that component was used.

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Further, because components can contain any number of elements, it is possible to build up rather complex components that capture a lot of rules about a format. For example, some formats begin each bibliography entry with the authors followed by the year of publication, and the year should be the year of original publication, if different from the year of re-publication. Using conditional tests such as reference has an original date of publication, you can create a component that always works, no matter what the details of any particular reference may be. To create a new component: 1. 2. 3. 4. Click on the Show: Components radio button at the top of the window; Click on the [create new component] link at the top of the preview pane Provide a name for the new component in the sheet that appears; Edit the denition using the details drawer.

Creating a New Component

Once this has been done, you will have access to the new component in the list of element types in the drawer, so you can use it just like any built-in element type.
Example: Author Lists

As a simple example of a component, consider the case where the format for each of the reference types uses the same format for the list of authors. While there are many differences between the format for a book and the format for a journal article, the format for the list of authors in both cases would typically be identical. One could just add an Authors element to both the Book and Journal Article formats, and specify the same rules in both places (e.g., name format, list format, punctuation, use of et al., etc.). Or you could create an Author List component, specify the rules inside that component, and just use the component instead of an Authors element in each of the reference type formats.

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In addition to making the original creation of a new format easier, this method makes it much easier to make corrections. For example, if you get the et al. rules wrong at rst, you need only make the corrections in the component denition, rather than in each of the reference type formats.

Importing CSL Format Files

Occasionally you may need to use a bibliography format that is not included in Sentes list of formats. If you have a CSL le for a bibliography format that you would like to add to Sente, you can import the le (which will be imported as a Local copy) and then modify it if you need to. To import the CSL le, follow these steps: 1. 2. 3. 4. 5. Quit Sente. Place the CSL le in the folder: ~/Library/Application Support/Sente/Sente 5 Bibliography Styles Restart Sente. Open the Bibliography Format Editor by using the Window > Bibliography Format Editor command. In the list of formats on the left, scroll down until you nd your new format in the list, then place a checkmark in the checkbox next to it. (NOTE: If you cannot nd the new format in the list and all of the formats listed have checkmarks in the checkboxes, go to the top of the list and remove the checkmark from the Show Favorites Only box.) Click on the new format name and modify it, using the instructions earlier in this chapter, if you wish to do so. Close the Bibliography Format Editor when you are nished. If there is a checkmark in the box next to the name of your new format, it will appear in the list of favorite bibliography styles elsewhere in Sente.

6. 7.

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Chapter 17

Sente Preferences

Sente preferences are accessed via Sente 6 > Sente 6 Preferences. This chapter covers what can be modied in Sente 6 Preferences.

Appearance Preferences
Sente lets you congure many aspects of the appearance of the application.

The Appearance preferences pane.

Currently, you can modify the font used in the source list and in the grid version of the reference list.

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Other appearance preferences will be added in future releases.

Bibliography Preferences
There are several settings that affect the formatting of documents and bibliographies. Microsoft Word 2004 Plugin Sente can work with all versions of Microsoft Word from Word 2004 and on. For Word 2008 and later, there is nothing that needs to be congured to make it work. For Word 2004, there is a Word plugin that needs to be installed. This is done using the MS Word 2004 tab in the Bibliography preferences pane.

The Microsoft Word 2004 tab in the Bibliography preferences pane.

Title Case Words Sente includes a list of words that should not be automatically capitalized when using the Title Case setting in a bibliography format. Typically, this list includes small words like a and in.

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When converting text to title case, Sente will leave any word in this list in lower case, unless the word appears at the beginning of a phrase.

The Title Case tab in the Bibliography preferences pane.

For example, with the word a in the Title Case list, Sente will produce the following text in title case: A New Direction Going in a New Direction Economics: A New Direction In this last example, the word a was capitalized because it is the rst word in the phrase that starts after the colon. The characters that are considered to end phrases are also set here, along with the sentence-ending characters. Exact Case Words Sente can also be taught to leave some words exactly as they are in the original text by placing them in the Exact Case list. This is particularly useful for acronyms, or special terms like gene symbols, where case must be preserved exactly.

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The Exact Case tab in the Bibliography preferences pane. To add new words, click the + and then double-click to type in the word.

This list can also include phrases. This makes it possible to indicate that Top Ten should always be capitalized, but top and ten should not be, unless they appear in that specic phrase.

Output Gestures
Sente supports many different export formats (e.g., Sente XML, APA 6, etc.) and many different gestures by which you can export data (e.g., drag and drop, copy and paste, etc.). This section explains how you match each gesture with the desired format to best meet your needs. For example, you could congure Sente so that dragging a reference into a word processor places a citation tag, but copying and pasting a reference into an email message places a citation in Chicago Notes style. Having multiple congurations allows you to expand your use of Sentes citation placement features. Supported Formats Sente can export data in several built-in le formats, or in any built-in or userdesigned bibliography format. Please see the chapter on Working with Word

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Processors for more information about how to export data. Below is a summary of information about formats supported by Sente. The built-in le formats included with Sente are: BibTeX BibTeX (Unicode) EndNote X Refer SenteXML These export le formats can be accessed through the File > Export command. Sente can also output references as: Sente URLs. These are URLs that point to the reference within Sente. If you click on one of these in most other applications, Sente will automatically open and display the correct reference. Citation Tags. These are the placeholders that you insert into documents that you will be scanning with the File > Scan Document command. You can also specify which delimiters are to be used in the tags (e.g., braces). Please see the chapters on Working with Word Processors and File Scanning for more information on these topics. Sente URLs and citation tags are congured in the Gestures pane in Preferences.

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The Gestures preferences pane.

Supported Gestures Sente allows you to congure what each of these gestures will produce: Drag and Drop Drag and Drop with the Option key () held down Drag and Drop with the Command key () held down Drag and Drop with the Shift key () held down Copy and Paste Cite (cmd-Y) and the Cite toolbar button Connecting Gestures to Formats Each of the supported gestures can be connected to any of the supported formats using the commands in preferences. Simply select the desired output for each of the different gesture methods and close the preferences pane.

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Plugins
Sente comes with a number of plugins that provide important features in the software. For the most part, you will not need to make any changes in this preference pane. There are, however, a few plugins that can be congured here. For example, the PubMed and Web of Knowledge plugins can be congured to use alternate URLs. This can be useful when working through a proxy server.

The Plugins preferences pane.

Advanced Preferences
The Advanced pane in Sente preferences contains settings that control some detailed aspects of Sentes behavior. Examples include how often searches are updated, how many references searches should be limited to, how long to wait before a reference is marked as viewed, whether or not to automatically accept DOI matches for added les, etc.

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The Advanced preferences pane.

Registration
The Registration preference pane includes licensing information for your installation of Sente on this computer.

The Registration preferences pane.

If you wish to remove a Sente license from one of your computers, you can do this in the Registration pane. Simply click on the De-authorize this computer and close Sente button. Sente will de-authorize the computer and exit. This will free up the authorization to be used on a different computer. (Each single user Sente license can be used on up to three computers at one time.)

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