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Academic Reference Manager

User Manual
Version 6.6

Copyright 2011-2013, Third Street Software, Inc.


All Rights Reserved.

Introduction .......................................................................................................1
Key Features ............................................................................2
Sente Licensing ........................................................................5
System Requirements ...............................................................5
Checking for Software Updates ................................................5
Uninstalling Sente ....................................................................6
Getting Started..................................................................................................7
Downloading and Installing Sente .............................................7
Creating Your Sente Account ....................................................8
Creating a Sente Library ...........................................................9
Installing Your Library on a Second Device..............................10
Add References and PDFs to Your Library ...............................10
Organize Your Library Using QuickTags and Smart Collections 14
Read and Annotate PDFs.........................................................15
Cite References and Format Documents .................................16
Upgrade to a Premium Sente Account .....................................17
The Main Window .........................................................................................19
Toolbar ..................................................................................20
Tab Bar...................................................................................22
Source List .............................................................................23
Reference List ........................................................................28
Reference Editor .....................................................................32
Attachment Pane ....................................................................36
Rotating the Reference List and Attachment View ...................39
Single Collection Tabs ............................................................40
Single Reference Tabs ............................................................41
Full Screen in Lion (OS X 10.7 or higher) .................................42
Changing Default Layouts for New Tabs .................................43
Creating and Customizing a Library ....................................................45
Multiple Libraries ...................................................................45
Creating A Library ..................................................................46
Library Customization ............................................................48
Attachment Handling .............................................................49
Autolink Template Setup ........................................................54
Reference-Based Autolinks .....................................................55
Text-Selection-Based Autolinks ...............................................61
Hotwords Setup ......................................................................63
Reference Types Setup ...........................................................66
Spotlight Setup .......................................................................71
Status Setup ...........................................................................73

Web Bookmarks Setup ............................................................75


Migrating Data from Other Applications ...........................................79
Migrating Data from EndNote .................................................80
Migrating Data from Bookends ...............................................82
Migrating Data from Papers ....................................................84
Migrating Data from Mendeley ...............................................87
Migrating Data from Zotero ....................................................88
Migrating Data from Reference Manager .................................89
Importing Data from Other Systems........................................92
Adding PDFs and Other Files as New References ..........................95
Adding Files to Your Library as New References ......................95
Adding PDF Files.....................................................................96
Adding Files Other than PDFs ...............................................105
What Happens to Files After I Add Them to My Library? ........106
Targeted Browsing ....................................................................................107
Supported Sites ....................................................................108
Obtaining References Using Targeted Browsing ....................108
Obtaining Articles as References from Online Newspapers ...113
Obtaining References from Other Sites .................................115
Obtaining PDFs from the Web ...............................................116
Combining Targeted Browsing and PDF Acquisition ..............116
Obtaining Other Web Archives Using Targeted Browsing ......117
Searches .........................................................................................................119
Overview ..............................................................................119
Introduction to Searching External Data Sources in Sente .....120
What Can I Search? ...............................................................121
Creating a New Search..........................................................123
Managing Searches ..............................................................124
Searching PubMed ................................................................127
Searching Web of Knowledge ................................................130
Searching Sites that Support the Z39.50 Protocol .................133
Searching Sites that Support the SRU Protocol ......................137
Using Proxy Servers ..............................................................141
Adjusting the Update Frequency for Searches .......................141
Other Ways of Adding References ......................................................143
QuickAdd: Adding References using ISBNs, DOIs, Etc. ...........143
Creating References from Web Pages ....................................145
Printing PDFs to Sente from Other Applications ....................147

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Collections .....................................................................................................151
The All References Collection ...............................................152
Built-In Smart Collections .....................................................152
Custom Smart Collections ....................................................155
Search Collections ................................................................164
Static Collections ..................................................................165
QuickTags ......................................................................................................167
Why Use QuickTags Instead of Static Collections? .................168
Why Use QuickTags Instead of Traditional Tags? ..................169
Working with the QuickTag Palette .......................................170
Behind the Scenes ................................................................174
Designing Your QuickTag Hierarchy .....................................175
Finding References Using Tags .............................................180
Find, Browse, and Hotwords ..................................................................183
Find .....................................................................................183
Library Browser.....................................................................188
Hotwords .............................................................................191
Reading and Annotating PDFs ..............................................................195
Reading PDFs in Sente ..........................................................195
Annotating PDFs and Taking Notes ......................................197
Exporting Annotated PDFs ....................................................204
Printing Annotated PDFs .......................................................204
Some Common Questions ....................................................205
Synchronized Libraries ............................................................................207
Uses for Synchronized Libraries ............................................208
The Basics (All You Really Need to Know) ..............................208
How Synchronized Libraries Work .........................................209
Creating and Using Synchronized Libraries ...........................213
Sharing a Synchronized Library with Other People ................215
Sync Conflicts.......................................................................218
Troubleshooting Synchronized Libraries ...............................221
Working with Word Processors ............................................................225
Apple Pages .........................................................................226
Microsoft Word 2008 and 2011 ............................................227
RedleX Mellel........................................................................228
Scrivener ..............................................................................233
Nisus Writer..........................................................................235
Open Office ..........................................................................236

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Other Word Processors/Rich Text Format (RTF)/Word 2004 ..237


File Scanning.................................................................................................245
Introduction to File Scanning ................................................246
Before You Start ...................................................................250
Inserting Citations ................................................................253
Modifying In-Text Citations ..................................................255
Adding a Bibliography ..........................................................256
Scanning the File ..................................................................257
Scan-in-Place ........................................................................261
Reviewing the Scan Results ...................................................263
Rescanning a Document .......................................................264
Troubleshooting ..................................................................265
Creating and Modifying Bibliography Formats .............................269
Introduction to the Bibliography Format Editor .....................269
Bibliography Format Editor Interface Tour.............................274
Importing CSL Format Files...................................................295
Sente Preferences .......................................................................................297
Appearance Preferences .......................................................297
Bibliography Preferences ......................................................298
Output Gestures ...................................................................300
Plugins .................................................................................303
Advanced Preferences ..........................................................303

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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 find
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 final formatting of your own manuscripts.
Data Retrieval
Sente has important features that make it easy to find 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 file in Sentes web
browser, Sente will offer to automatically download, rename and file 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 find 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 find 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 define a set of custom reference statuses and
then use these to manage your personal research workflow.

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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 define 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 fields. 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 fields in Sentes
reference editor. This lets you include your own custom reference attributes and
rearrange the order of all fields to best fit your needs.
Reference Statuses. You can define your own list of reference statuses,
designed to support your personal research workflow.
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 files 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 configured 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 can be downloaded from the Apple iOS app store.

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Sente Licensing
Both the Mac and iPad versions of Sente can be downloaded and used for free. The
first time you launch either of the apps, you will create a free Basic Account on the
Sente servers.
With a free Basic Account, you can create any number of libraries, each with up to
100 references. This is more than enough references, for example, for most
undergraduate term papers.
A Basic Account also includes 250MB of space on the Sente sync servers; enough for
about 250 typical academic PDFs. This space is shared across all of the users
libraries.
To work with larger libraries, or for more sync space, an upgrade to a Premium
Account can be purchase within the app itself, or on our web site.
A Premium Account removes the restriction on library size, meaning that you can
create libraries with any number of references with a Premium Account.
A Premium Account also increases the amount of space available on the sync servers
to 1GB total.
Once an account has been upgraded to Premium, additional sync space can be
purchased on an annual basis, either from within the Mac app or from our web site.

System Requirements
Sente requires Mac OS X 10.6 or higher and an Internet connection, running on an
Intel-based computer.

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.

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

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Chapter 2

Getting Started

This chapter will help you get up and running with Sente as quickly as possible. You
will learn how to:
download and install the software on your Mac and iPad
create your Sente account for synchronizing libraries across all of your devices
(and for backing up libraries stored on only one device)
create your first library
install synchronized copies of your library on each of your Macs and iPads
add references and PDFs to your library
organize your library using QuickTags and smart collections
read and annotate PDFs
cite references in a manuscript and format the document using one of the builtin formats
upgrade to a Premium Sente account and add sync space to your account to
support synchronizing larger libraries

Downloading and Installing Sente


Sente is available for both Macs and iPads. Both versions of the software are
available for free download.

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Installing Sente for Mac


Sente for Mac is available from our web site: www.ThirdStreetSoftware.com. When
you click on the download link in Safari, a zip file will be downloaded to your
computer.
Installing Sente for iPad
Sente for iPad is available only from the Apple iOS App Store (search for Sente).

Creating Your Sente Account


To use Sente, you need to create an account on the Sente sync servers. This is true
even if you do not intend to sync libraries across devices.
Your Sente account name will be your email address. We will never use your email
address for anything other than supporting your use of Sente. We will never give
your email address to any other party for any reason. We simply need a valid email
address because many features of Sente depend on us knowing that each account is
connected to a real person.
Creating an Account on the Mac
When you first launch Sente on the Mac, you will be presented with the login /
registration screen shown below.
To create a new Sente account, click on Register as New User, then enter your email
address and select a password.
An email address will be sent to you that you must receive and act on in order for
your new account to be activated.

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The start-up screen where you either login to an existing Sente account, or create a new Sente account.

Creating an Account without a Mac


At this time, due to restrictions imposed by Apple, you cannot create a sync account
using the iPad app itself. Instead, you can either use the Mac app, or you can create
an account on our web site (there is a link on our Downloads page).

Creating a Sente Library


To create a Sente library on the Mac, use the File > New Library command.
A new library window will open, and a file save dialog will appear in which you will
tell Sente where to save the library.
By default, all Sente libraries are created as synchronized libraries. We recommend
that you leave this option checked, even if you do not intend to install the library on
another Mac or iPad, because this will make it possible to recover your library, even
if your computer fails or is stolen.

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Installing Your Library on a Second Device


Once you have created a synchronized library on any of your devices, it is a simple
matter to install it on any of your other devices, including other Macs and iPads.
Installing a Library on a Mac
To install a copy of a synchronized library on a Mac, you will need Sente on that
computer and you will need to be logged in to your Sente account on that computer.
Once you have done this, then simply access the File > Open Library menu. Your
synchronized libraries should all appear in this menu.
When you select a library from among the libraries that are available to be installed,
Sente will create the library and immediately begin downloading the contents. For
small libraries, this process can be complete in minutes; for larger libraries, it might
take many hours, depending on the speed of your network connection.
Please note that you can use this same technique to install a library that, for
example, you accidentally delete on the original computer. Or on a new Mac if your
old computer suddenly dies or is stolen. Synchronized libraries can be installed on
any Mac at any time.
Installing a Library on an iPad
To install a synchronized library onto an iPad, you will need the Sente app installed
on your iPad, and you will need to be logged in to your Sente account on that device.
Once you have done this, you can simply tap on the Open a Library entry in the
sidebar on Sente main screen.

Add References and PDFs to Your Library


There are many ways of getting references into your Sente library. You will likely
use some combination of the available methods depending on many factors. This
section will give a brief introduction to the most common methods.
Targeted Browsing
Sente includes an embedded web browser that understands the details of many
sources of academic literature. When Sente recognizes the presence of an academic
reference in a web page, it adds a target icon to the page. Clicking or tapping on
the target icon tells Sente to acquire the reference and add it to the current library.

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An example of the targeted browsing interface.

If you click on a link to a PDF in the embedded browser, Sente will normally be able
to recognize that this has happened and it will offer you several options for
downloading the PDF directly into your library.

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Acquiring a PDF in the embedded web browser.

For any of your data sources that are supported by Sente, targeted browsing
coupled with automatic PDF acquisition can make it very easy to quickly add
citations and PDFs to your library.
Searches
Sente can also search many university library catalogs and other on-line data
sources using protocols like Z39.50 and SRU. Sente also supports the E-Utils
interface to PubMed, the dominant source of biomedical literature in the world.
Searches can be created that return hundreds or thousands of references
automatically.

A PubMed search specification.

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When you create a new search, it is placed under the Searches category in the source
list, rather than directly in your main library. To add individual references from the
search results into your library, you can drag them from the results onto the All
References item in the source list.
Alternatively, you can drag the entire search into the Local Collections entry in the
source list and this will automatically add all of the search results to your library.
Furthermore, searches can be set up to run automatically, checking for new results.
This is most useful for a data source like PubMed, which has good, built-in support
for update queries. It will work for Z39.50 searches, but this can cause performance
problems for large searches.
Importing PDFs
Sente also makes it easy to import PDFs that you might already have, or that you
might acquire outside of Sente.
When you already have the citation data for a PDF in your library, you can just drag
the PDF from Finder and drop it on that reference in the main Sente window.
In the more common case, where you do not yet have the citation in your library,
you can just drag the PDF onto the All References item in the source list. This will
tell Sente to attempt to locate the citation information for you, using a process we
call QuickAdd.
With QuickAdd, Sente will look inside the PDF for information that it can use to
locate the correct citation. This is often successful for PDFs created in the last
10-15 years. When this process is successful, Sente will present you with the
citation data and you can review and/or edit this information before adding it (and
the PDF) to your library.
When Sente is unable to automatically locate the citation, it still provides you with
tools to help you find the correct citation. Simply by selecting, for example, the title
of the document in the QuickAdd sheet, you can ask Sente to search some common
data sources for the correct citation. This will often take you right to the correct
citation, so you can add it to your library with minimal effort.

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The QuickAdd sheet for creating a reference from a PDF.

Organize Your Library Using QuickTags and Smart Collections


Sente provides some very powerful tools to help you organized your library as it
grows, and to help you keep it organized as you progress in your research. One of
the most powerful of these tools is what we call QuickTags.
QuickTags are like tags in many other applications, but with the addition of the
ability to organize your tags into a hierarchy to better organize the concepts you are
working with.
Like other programs tags can be assigned to individual references by simply typing
into the Tags field at the bottom of the reference editor.
More importantly, however, QuickTags can be assigned (or removed) from one or
more reference at a time using the QuickTag Palette.
In the QuickTag palette, you can organize your tags into a hierarchy, with any
arbitrary level of nesting. And, when you explicitly assign a tag to the selected
reference(s) by clicking on the appropriate checkbox in the palette, the reference
will be immediately and automatically treated as though you had also assigned all
the parent tags to that reference, as well.

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This means that if your QuickTag hierarchy includes, say, tags reflecting geography,
you might have a top level tag for North America, with tags for Canada, USA and
Mexico under that, and each state or province under the appropriate country. In
this case, tagging a reference with the Ontario would also implicitly assign tags for
Canada and North America to the reference.

The QuickTag palette with an example QuickTag hierarchy.

Should you change the QuickTag hierarchy at any time, each citation in your library
would immediately behave as though the new implied tags had been assigned based
on the explicit tags.
Please see the chapter on QuickTags for a more detailed discussion of QuickTags.

Read and Annotate PDFs


Both the Mac and iPad versions of Sente support reading and annotating PDFs
directly within the application. And all highlighting and other annotations made in
any copy of a library are automatically reflected in all other copies of the library
almost immediately.

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PDF annotation on the iPad.

Unlike standard PDF annotation tools, Sente also integrates note taking right into
the annotation process. This means, for example, that when you select a passage to
be highlighted in a paper, you have the option of also having Sente copy the text of
the passage into a note attached to your reference. This makes it easy to review just
a summary of the important passages from you reading, and to insert quotations
from your notes into your own manuscripts.
And, because all PDF annotations and notes are automatically synchronized to all
copies of your library, you can review a few papers on the train ride to your office in
the morning and all of your highlighting and notes will be in the library on your
desktop Mac by the time you arrive.

Cite References and Format Documents


All of the Sente features highlighted thus far are designed to help you gather,
organize and comprehend the academic literature you use in your research. For
many people, the end product of their research is a journal article or a book. Sente
also helps when it comes time to prepare your own manuscripts by helping with the
details of citation and bibliography formatting.
Sente can be used in conjunction with many of the most commonly used word
processors, such as MS Word, Apple Pages, Mellel, Scrivener and many others.

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The details vary depending on the word processor, but the general process used to
have Sente format citations and bibliographies is:
1.

Open both your word processor and Sente on your Mac.

2.

Position the cursor in your document where you would like to insert a citation.

3.

Select the desired reference(s) in Sente and use the Cite command; this will
insert a citation tag (e.g, {Smith 2001}) at the cursor location in your
document.

4.

Repeat the above step for all of the references you would like to cite in your
manuscript.

5.

If you would like to have a complete bibliography added to your manuscript,


add a {bibliography} tag at the correct location, and format the paragraph the
way you would like the final paragraph to be formatted (e.g., fonts. hanging
indents, etc.).

6.

Use the Scan command in Sente, and select the desire format from the list of
available formats, to scan the manuscript, replacing the citation and
bibliography tags with properly formatted text in a new copy of your document.

With some word processors, Sente also supports the concept of scan-in-place, where
Sente simply updates the manuscript in place, rather than producing a new, scanned
document.

Upgrade to a Premium Sente Account


If you are normally working on small projects, where the limit of 100 references per
library is not a problem, and you do not need to sync more than 250MB of
attachments, you can use the free Basic Account indefinitely.
If your research needs grow, however, and you need either larger libraries, or the
ability to sync more or larger attachments, you can upgrade to a Premium Account
for a one-time charge. This will remove the library size limitation, and it will provide
you with an additional 750MB sync space (for a total of 1GB).
Finally, if you want to be able to sync even more files, you can purchase additional
sync space on an annual basis.

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Chapter 3

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 find 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 configuration 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 configured 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 fit 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 finished customizing the toolbar.

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

Tab Bar
When you first 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 filtering, 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-defined 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 modified.
Synced Collections. This category can be used to hold smart collections that
you define. 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 configuration screens
that enable you to control various aspects of your Sente library. For example,
this is where you create custom reference types and configure 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
specific 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 five stars, to each
reference in your library. The collections under By Rating make it easy to quickly
find 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 defining 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 configuring 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 configuration 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 files attached to references. For example, this is where you
tell Sente how (and if) you want the program to organize your PDF files and other
attachments.
Autolink Templates. Autolink templates generate hyperlinks based on data
from each reference to help you find 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 find 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
workflow 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 field 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 modified; 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 an up or down arrow, 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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When the library has been set up to automatically download attachments, you
will sometimes see something like :102 at the end of the sync status display.
This means that Sente is actively downloading an attachment. The number after
the colon will always be less than or equal to the main library change number,
and it will progress upward until it equals the main change number. Once all
attachments have been downloaded, the colon and the attachment change
number will disappear from the sync status display.
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:

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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 file. This icon is followed by
something like x3 when more than one file is attached to the reference.

your star rating for the reference;


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 fit 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).

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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 field on which to order the table in
the Order By list in either the main menu or the List toolbar item.
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 file.

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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
list by, say, a custom field, just add that field to the grid view. It will
immediately become one of the Order By options for the standard view.
If you drop a file onto a reference in either version of the reference list, the file
will be added to the library as an attachment on that reference. (If you want to
import a file 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 fields. 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 field 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 fields will change when you are in edit mode; for example,
most fields are configured not to be displayed in view mode if they do not have a
value. This behavior, along with the exact list of fields to be displayed for each
reference type, can be configured 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.

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.

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

Attachment Pane
Each reference in Sente can have any number of related files linked, or attached, to
it. For example, it is common to have the full text PDF of a journal article attached

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to a reference for that article. The attached files 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 files, you can
highlight passages or regions of the page using Sentes built-in annotation 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 figure in the PDF, use the Image
selection tool.
Find-in-PDF tool. The magnifying glass icon will open the Find-in-PDF window, in
which you can specify search text. When you press Return, Sente will search the

Page 37

current PDF for all occurrences of the specified text. Tapping on an entry in the
results list will cause Sente to immediately scroll to that position in the
document.

The Find-in-PDF window.

Attachment title. In the middle of the control bar you will see the name of the
displayed file type. Clicking on this name will bring up a menu of commands
with options like Reveal in Finder and Delete Attachment.

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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 find 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.
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.

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

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
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.
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 flip
back and forth between references in these collections.

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

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.
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,

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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.

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.
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 configuration 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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Sente in full screen mode.

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 find that you always want,
say, new single collection tabs to be opened in a particular configuration. 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 configuration for all new
tabs of the same type. This is done using the options in the View menu, as shown
below.

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

When you have a tab configured 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 4

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

Page 45

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.

Use the File > New Library command to create a library.

2.

A new library window will appear with a sheet for specifying the location of the
library on your computer.

3.

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 files and they will eventually corrupt the database.

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(Instead, use Sentes built-in synchronization mechanism to maintain a single


library across multiple computers; it is faster and safer than these generic
services.)

Creating a new library. Note that the Synchronize checkbox is checked by default.

4.

If you do not want the library to be synchronized, uncheck the Synchronize


checkbox.

5.

Click Save to create the library.

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 configuration options are
explained in the remaining sections in this chapter.

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Library Customization
The settings described in this chapter are all made on a library-by-library basis so
the configuration 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.

The Library Setup category in the source list.

In the rest of this chapter, we will explain how to configure:


Attachment handling -- should Sente rename and refile 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 find 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 files 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 workflow.

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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.

Attachment Handling
Attachments are files or web pages that have been attached to a reference. The
most common type of attachment is the full-text PDF file. Other items that people
often attach to references include web archives (especially for news articles or other
pages that may change over time), image files (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.
The discussion here applies only to attachments that are actually files, not to remote
URLs. URLs exist only as data in each copy of a library, not as a file, so there is
nothing to specify about how they should be handled.
Sources of Attached Files
In general terms, there are two ways in which files can be added to your copy of a
library as attachments.
The first, and perhaps most obvious, case is where you already have the file on your
computer and you are asking Sente either to attach it to an existing reference, or to
import it as a new reference (and attaching it to this new reference). In this case,
you may or may not want Sente to take over control of the original file (e.g., by
renaming and relocating it according to some rules). You may want Sente to simply
link to the existing file exactly where it exists already. Or you might want Sente to
copy or move the file, based on rules that you specify.
In the second case, the file does not already exist on your computer, and Sente is
downloading the file itself and so does not have the option of leaving it where it is.
This happens, for example, when you click on link to a PDF in Sentes embedded
web browser and ask that it be downloaded and attached to a particular reference.
It also happens when an attachment is received from the sync servers during the
normal course of library synchronization.
Files that Sente downloads onto the computer are always filed according to the rules
that you specify. This includes the rules for naming the files (usually based on
attributed of the reference to which the file is attached), and the rules for locating

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the files in the file system. The location can be either inside or outside the library
bundle. And the choice of location can be different on each computer on which the
library is installed.
Note that this has very important consequences for synchronized libraries. No
matter what the attachment handling setting are in the copy of a library where you
first add a file to a reference (e.g., you might have Sente set to just link to the
existing file), when the file is downloaded in each copy of the library during
synchronization, the file will be named and filed according the the attachment
handling rules.
Where Should You File Attachments?
One of the most fundament decisions when deciding where to file attachments is
whether they should be filed inside or outside of the library bundle.
Sente libraries are actually a special type of a folder that Finder presents as a single
file. You can open a bundle in Finder to see its contents by right-clicking on the file
in Finder and selecting the Show Package Contents command from the context
menu. If you choose to have attachments filed inside the library bundle, they will be
filed under the Contents/Attachment folder inside the bundle.
We normally recommend that you select the option to have attachments filed within
the library bundle for several reasons.
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 file itself. This makes it very easy to create backups, to
transfer the entire library to a new computer, etc.
When you first open a library from the sync server, Sente will use the Inside the
Library Bundle option for the new library. You can change this later if you prefer,
but this is the default.
Directly Accessing Attachments Stored in the Bundle

But what if you want to have access to the files 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.

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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 filed. Then
move this alias outside the bundle, to any location you choose. This will give you
immediate access to all your files from Finder, while still keeping the files 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 fixing this problem is simply a matter of
recreating the single alias file, rather than relinking each of hundreds or thousands
of references to their attachments.
To create an alias to the attachment folder:
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.

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The results of using the Show Package Contents on a Sente library.

3.

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

4.

Move the newly created alias file (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 filed.
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.

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The attachment handing setup pane.

The most important decision is where the files should be placed. The options are:
Inside the library bundle. (Recommended.)
In folder: and choose the location of the folder. 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 files 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

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Title
Article Title
Publication Title
Volume
Publication Type
Year of Publication
Unique Alphanumeric Identifier
You can also select the order of how the attachment is to be named (First name first,
year, title, etc.), and choose how many characters to limit the filename length by.
Finally, you must specify how you want Sente to handle the original file in the cases
where the file already exists on the local computer at the time you add it to your
library. The options are:
Create a copy and file/rename the copy according to the rules specified above.
Move/rename the original file according to the specified rules (this remove the
original file from its original location).
Link to the existing file. This leaves the file where it is and adds a link to the
appropriate record in the library. Note that even in this case, when the file is
downloaded during sync onto a different computer, it will be filed and named
according to the specified rules.
When you have finished entering the information for attachment handling, click the
Apply button.

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:
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.

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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 configured 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 identifiers (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 identifier, 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.

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.

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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.

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

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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 file,
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 Identifier (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
field, 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
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.

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The Autolink Setup pane.

The fields 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.
Self? Does this template refer to the actual reference? That is, is the autolink
template related specifically 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 fields from the reference, just like the URL template

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below (e.g., Search Google Scholar for {articleTitle}). See below for more on
field substitutions.
URL Template. This is the template for the URL that will be used as the link. The
fields to be inserted into the template are indicated by placing the field 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 fields.
Many of the common identifiers are useful when creating autolink templates. These
include:
CODEN
DOI
ISBN
ISSN
OAI (Open Archive Initiative number)
OCLCID
PMID (PubMed ID)
PMCID (PubMed Central ID)
PII
US LoC Control # (Library of Congress Control Number)

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Autolinks can also include regular fields, 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://
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://

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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.

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

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Just after invoking the autolink selected in the previous figure.

Configuring 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 field 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.

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Some selected-text-based autolink templates. Even though the label field 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.

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.

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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 finished 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 finished.

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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 modified.

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 fields that the
reference editor will display when showing a reference of the type selected in the
Reference Type list. There is additional configuration 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 Configuration 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 first table and then compare the
list of fields 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 field 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 field will appear at the left and the value for the
field 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 field is set to one of the unlabeled
styles, the label will appear as placeholder text when the field does not contain a
value.
Something else you will probably notice quickly is that, while the fields in the editor
appear in the same order as they appear in the reference fields list, not all of the
fields listed in the setup pane appear in the reference editor. This is because some

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fields 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 field should appear in View Mode
B indicates that the field should appear in View Mode, even if blank (if V is set
and B is not, the field will not appear in View Mode unless it contains data)
E indicates that the field should appear in Edit Mode

The reference editor.

Finally, you may notice cases where the field in the editor is called something other
than what it is called in the reference fields list. This is because it is possible to
change the label in the setup pane.
For example, Sente has two important internal fields 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 specific reference types.
To actually change these settings for a field in the reference editor fields list,
double-click on the entry in the list. A sheet will appear in which the changes can be
made.

The Reference Editor Field configuration sheet.

Rearranging Fields in the Reference Editor


To change the order in which fields are presented in the reference editor, simply
click and drag on the appropriate entries in the reference fields list and place them
in the desired locations within the list.
To remove a field from the list, simply drag it from the table and release it
elsewhere.
Removing Fields from the Reference Editor
To prevent you from overlooking fields that are present in your database, Sente will
automatically append any field that it finds in the reference to the bottom of the list
of fields in the display. This ensures that you see, for example, custom fields
imported from another reference manager.
However, this makes it a little tricky to actually prevent a field 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 fields in the setup pane will only cause it to be displayed at the
bottom of the editor along with any other field present in your data.
So, instead of removing the field from your list in the setup pane, double-click on
the field 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 field.

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 fields list for the
appropriate reference type.

Spotlight Setup
Spotlight is Apples powerful search utility for locating files 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 find specific information about library references and/or attachments
on your computer.

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Sentes support for Spotlight is configured 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 find 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 files 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 find 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 files. 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 workflow for acquiring and reviewing references. As you complete each
step in your workflow on each reference, you can adjust the status on the reference
to reflect 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.
Defining 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 field 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 find 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 find 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.
Configuring Web Bookmarks
To configure 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 reflected 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 finished making changes.

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Chapter 5

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 specific 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 fields.
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.

Open the library in EndNote.

2.

Use the File > Export command.

3.

Specify a file name and location for the export file (the Desktop may be the
most convenient location).

4.

Select XML as the export format (Save as File Type: XML).

5.

Select Show all fields for the Output Style.

6.

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.

7.

Click on Save.

Then, import the EndNote references into Sente:


1.

Launch Sente and either open the library you want to use or create a new library
in Sente.

2.

Select the File > Import command.

3.

Navigate to the EndNote XML file, 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 finished reviewing the report.

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

5.

If there are fields used in the EndNote library that are not currently in Sente, the
new fields 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 fields.

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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
fields. 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.

Launch Bookends.

2.

Manually select the references you want to export to Sente by placing a


checkmark in the checkbox to the left of each reference.

3.

Use the File > Export References command in Bookends.

4.

Select XML (EndNote 8 or later) as the format type.

5.

Place a checkmark in the checkbox next to Export attachments too by clicking


on the checkbox.

6.

Choose a location.

7.

Click the Save button and then the Okay button when the dialog box appears.

Then, import the Bookends references into Sente:


1.

Launch Sente and either open the library you want to use or create a new library
in Sente.

2.

Select the File > Import command.

3.

Navigate to the Bookends XML file (which may end in .bdb.xml), select it, and
click Open.

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 finished reviewing the report.

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

5.

If there are fields used in the Bookends library that are not currently in Sente,
the new fields 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 fields.

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 field in Bookends is
transferred to the EndNote XML output file.
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 2, without needing to export the data
from these libraries first. You will simply tell Sente where the Papers database is
stored and Sente will retrieve the data, including attachments and custom fields.
Papers 1 libraries can no longer be imported directly; instead, the references must
first be exported in a format that both programs support. For more information on
this, please see the section on Importing Papers 1 References into Sente, below.
Migrating a Papers 2 Library into Sente
To import your Papers 2 library into Sente:
1.

Launch Sente and either open the library you want to use or create a new library
in Sente.

2.

Select the File > Import command.

3.

In the file 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.

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 finished reviewing the report.

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

5.

If there are fields used in the Papers library that are not currently in Sente, the
new fields 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 Papers 1 References into Sente
Papers 1 libraries cannot be directly imported into Sente at this time. However, you
still may be able to export the Papers 1 library in a format that Sente can read, such
as EndNote XML or BibTeX.
After exporting the Papers 1 library into an output file that Sente can read, follow
these instructions to import the data into Sente:
1.

Open Sente and either open the library you want to use or create a new library
in Sente.

2.

Select the File > Import command.

3.

Navigate to the Papers2 output file, 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 finished reviewing the report.

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

5.

If there are fields used in the Papers 1 library that are not currently in Sente, the
new fields 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 fields.

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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 Papers 1 to Sente.

Migrating Data from Mendeley


A Mendeley library can be imported directly into Sente, without the need to export
the data first. Sente will import all reference data, including custom fields, 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.

Launch Sente and either open the library you want to use or create a new library
in Sente.

2.

Select the File > Import command.

3.

In the file chooser that appears, navigate to the folder containing the Mendeley
database. By default, this folder is: ~/Library/Application Support/Mendeley
Desktop. Click Open.

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 finished reviewing the report.

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

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5.

If there are fields used in the Mendeley library that are not currently in Sente,
the new fields 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 first export
the data from Zotero. Sente will import all reference data, including custom fields,
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.

Make sure Firefox is completely shut down.

2.

Launch Sente and either open the library you want to use or create a new
library.

3.

Select the File > Import command.

4.

In the file 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/Profiles/vw6pqezr.default/zotero. The
correct folder will contain a file called zotero.sqlite. Select the folder that
contains the sqlite database; do not select the database itself. Click Open.

5.

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 finished reviewing the report.

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

6.

If there are fields used in the Zotero library that are not currently in Sente, the
new fields 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 file. The RIS file contains all of the information about each
reference that was contained in Reference Manager.
If you had created any custom fields in Reference Manager, Sente will recognize the
new fields and display a results screen for new fields 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.

Launch Reference Manager.

2.

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.

3.

Use the File > Export command in Reference Manager.

4.

Choose a name and a location for the output file.

5.

Select RIS as the output format type.

6.

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).

7.

Click the Export button.

8.

If necessary, transfer the output file to a Macintosh computer that has Sente
installed.

Then, import the Reference Manager references into Sente:


1.

Open Sente and either open the library you want to use or create a new library
in Sente.

2.

Select the File > Import command.

3.

Navigate to the Reference Manager RIS file, select it, and click Open.

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 finished reviewing the report.

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

5.

If there are fields used in the Reference Manager library that are not currently in
Sente, the new fields 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 fields.

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 specifically 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.

Launch Sente and either open the library you want to use or create a new library
in Sente.

2.

Select the File > Import command.

3.

Navigate to the saved file, select it, and click Open.

4.

If Sente is unable to import the data file, an error message will appear. If Sente
is able to import the data file, a progress bar will appear.

5.

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 finished reviewing the report.

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

6.

If there are fields used in the other library that are not currently in Sente, the
new fields 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 fields.

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 specifically mentioned above and
not all of the data was imported into Sente, try exporting the data as a different
output file type. For example, if you exported the library as an RIS output file, try
exporting it as an EndNote XML file 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 6

Adding PDFs and Other Files as New


References

References in Sente can have any number of PDF and other files attached to them.
In addition, you can add PDF and other files (such as images, web archives, and
videos) to Sente and create new references for each of them. Typically these files
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 files can
be added to Sente either individually or in bulk. This chapter explains the process
of adding PDFs and other files to your library.
This chapter is about adding files, like PDFs, JPEGs, etc., that you want to have
attached to references in your library. It is not about importing data from files like
EndNote XML files. 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 files as attachments on existing references in your
library. This is accomplished by simply dragging the file or files from Finder and
dropping them onto the target reference in the reference list. All of the files
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, files 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 file 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 file from the file selector that will appear.
You can use the Add Files button on the toolbar, which will also bring up the file
selector sheet.
In each of these cases, you are indicating that each of the files being added should
appear as a new reference in the library.
In the case of PDF files, Sente can often identify the citation for the file using
information found within the file 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 files), 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 files, they will be
discussed separately below.

Adding PDF Files


PDF files are treated differently than all other types of files because Sente includes
support for some common techniques that can often be used to automatically
retrieve the correct citation details for a PDF. Other files, like images or
spreadsheets, cannot normally be handled in this way. This section covers the
process of adding PDF files. Adding other types of files is covered later in this
chapter.
PDFs That Can be Matched Using DOIs
Many modern PDF files for journal articles contain a unique identifier known as a
Digital Object Identifier, 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 files to your library, Sente will look inside the PDF for a DOI in the
first 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 files 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 field 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 first 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 configured
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 first 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 files 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 finds 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 files, 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 files 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 fill 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 first 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 filename in the reference to help you distinguish one reference from
another. This option will tell Sente to use the filename 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 files
and deal with the citation lookup later. Sente provides the same tools for finding

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the citation data after the files 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 first 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 finding 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 files that can be added as references or attachments
in Sente libraries. Images, web archives, videos, RTF, music and other files can be
added as well. The list of file types that can be added to Sente libraries is
continuously growing.
The process of adding non-PDF files 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 file to your library.

When you try to add a non-PDF file 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 file using a reference template.

When you add more than one non-PDF file 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 modified to include the
name of the file being added.

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


Exactly what Sente will do when adding a file to your library as an attachment is
determined in the Attachment Handling Setup pane. This is where you tell Sente
how files should be renamed and organized (if at all) and whether the original file
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
files.

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Chapter 7

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 finds
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 file 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 finds 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 find 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 find a reference in a web page and a potential, but not
confident, 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 satisfied 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 final 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 find 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 identified 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 filled 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 fields 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 specific 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 find 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.

Click the article title to open that web page.

2.

On the individual article web page, find the Print icon/button/link and click on
it. This is to remove advertisements from your web archive.

3.

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 file 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 files 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 specific 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 specific to your
field 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.

2.

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 find 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 file where you want it.

3.

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.

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 8

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 specified 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 specific
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 field 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 first 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 refine 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 flooding 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 filter 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 finetuning 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 Synced 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 satisfied 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 fields in the PubMed record by making selections in

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the first 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 first 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 first 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 Configuration
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 configuration
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
configuration window for the Web of Knowledge data source plugin.
To access the configuration 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 Configure Selected
Plugin button. Click this button and the configuration window will open.

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

Change the URL and update preferences in the configuration 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
first. 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 first 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 find the information
for your specific library. Another common value is Latin-1.
Username and password. Most sites do not require this information, but yours
may.
2.

Open the Z39.50 Data Source Window: File > New Search > Z39.50 Data
Sources > Other Z39.50 Data Sources.

3.

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 field and enter the information collected above into the
appropriate columns. Scroll to the right to access the User Name and Password
fields.

5.

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,

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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.

Check the Fav? checkbox so that the new site will show up in the main list of
data sources.

7.

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 first place to look first.
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 first 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 first is a
proxy that stands between you and the Internet. This kind of server is typically
configured in System Preferences in OS X. If you have such a proxy server
configured to work with Safari, it is very likely to work with Sente with no additional
configuration.
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 specific
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 flag
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 significant 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 9

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 file import. This chapter presents a few additional methods
that you may find useful in different contexts. These include:
QuickAdd. This can be used to add references using just a common identifier
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 fill in many details about a
reference from an identifier 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 identifier).
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 specific 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 find 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 10

Collections

When you first start gathering the references into your Sente library, having them
appear in a single, long list is fine. But there will come a time when you will want to
see your references organized into collections of various definitions. 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
modified, 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
defined 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 definition 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 first 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 modified 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 definitions 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
modified. 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 find references that you have
either recently added or edited.
The most obvious collections are:
Modified 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 flagged as
needing manual review of the citation data. For example, if you import a PDF
and Sente is not able to find 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 reflect 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 specified
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 specified.

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 filter criteria to the Smart Collection.
In the first 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 first 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 first criteria has been established, to signify
that the filter is to include the criteria listed above, or All of the criteria that will
follow
and Any of...available only after the first criteria has been set, to signify that
the filter 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 field contains the following value.
Does not containthe selected field does not contain the following value.
Isthe selected field is (and is only) the following value.
Is notthe selected field is not the following value.
Begins withthe selected field begins with the following value.
Ends withthe selected field ends with the following value.
Equals any ofthe selected field 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 specified 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 (filter) only, not the actual references.
To modify a smart collection, follow these steps:
1.

Either double-click the smart collection or right-click the smart collection and
choose Get Info.

2.

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 filters for certain authors and
paste it into a smart collection that filters for a range of years, the copied smart
collection will now list all references of those specific authors within the date range
specified 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 Refinement

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 refine the results. (Please
see the chapter on Searches.)
Classification

One way to refine any collection in your library is to filter for a particular keyword,
rating, or status that youve assigned to references. For example, a five-star smart
collection can take you straight to your most important references. You can use the
built-in smart collections to filter all of the references in your library by rating or
status, but if you want to be able to filter 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 filters can be defined with just a few filter 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
filter terms in a single filter 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 filter terms in the editor by clicking on the
plus (+) button next to the first term in the list. If you create three terms at the top
level and put alpha in the first, beta in the second, and gamma in the third, set
the first option (Include references that match...) to All, and set the middle option

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to contains all of these conditions, you will have created a filter 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 filter terms. Normally this is in conjunction with other terms that must also
be matched. For example, to find references by either Smith or Jones that include
the terms alpha, beta, and gamma, you would want a filter 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 filter and say we want all references with
alpha, beta, and gamma, except those references authored by Smith or Jones. Our
filter 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 filter 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
conflicts.)
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 11

QuickTags

As your research library grows, it becomes increasingly important that it stays well
organized so that you can find 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 find
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 files in a
computer file 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 reflect 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 flexible classification
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 find 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 first 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 first 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 modified at all.
Synchronization. Sente is able to synchronize both the tags on individual
references and the definitions 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 filing in
collections, will seem strange at first. 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 first 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, flexible 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, flat 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 specific to more
specific 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 find 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 first step in using QuickTags is to set up your initial QuickTag hierarchy in the
palette. When you first 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 first 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.

Add Child Tag.

This adds a tag below the selected tag.

Remove Selected Tag.

This removes the selected tag from the palette.

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 reflect the changes). This means that you do not need to
get the entire hierarchy right the first 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 reflect 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 reflected 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 reflect
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 field 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 benefit
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 file 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 file aliases or
links, each file 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 file. 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 conflict you are studying, or do you place folders for each conflict 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
Conflict 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 Conflict category to any
works that discuss specific wars or battles, and tags from the Battle Tactics category
to works that specifically 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 specific
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 field 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 specific
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 specific 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 (fiction is a
type of literature). Non-fiction might then have sub-tags like History, Biography,
etc. (a biography is a type of non-fiction 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 Non-Motorized
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 specific 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 find
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 find 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 find 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 configuring a QuickTag hierarchy and
then tagging each reference is to be able to use this information to find 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 definition 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 refine 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 12

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 specific fields. 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 configuration includes the Find
field, you can initiate a Find search by simply clicking into that field, 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 field.
Otherwise, the Find tool will appear above the reference list, as shown below.

The Find field 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 field (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 field 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 Specific Fields
You will sometimes be interested in locating references that match a search string,
but only in specific fields. 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 fields.
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
field), a menu of options will appear. This menu includes:
Commands for restricting the search to just one field in the reference (to search
only in the author names field, 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 field 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 field. 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 field to be searched. These abbreviations are:
AU: Author names
ID: Identifier
TA: Tags
KW: Keywords
TI: Title
YR: Year
Adding qualifiers 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 qualifiers to search terms in the Find operation.

Any term that does not have a prepended field code will be allowed to match any
field 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 field. 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 specific fields. 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 field.

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 first list to appear is
the list of fields that can be searched. A selection can be made in this list by using
the mouse to select one or more fields, or by using the keyboard to type the first
few characters of the desired field.

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The Browse panel with lists.

After you select a field type, the list will be updated to show all unique values for
that field 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 find all years
from 2000 to 2009.

As you make a selection in the first browse list, a new list will appear from which
you can select a different field 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-five of the available years were selected.
As you refine 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 refine the search. Here, the library of 85
references has been filtered 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 find 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 first step in using hotwords is to tell Sente the terms that you want highlighted.
Because these terms are likely to be specific to a library, this setup is done in the
Hotwords Setup pane in the main window.
To configure 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 specified 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 13

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 reflected 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 files (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 field 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 first 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 figure 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
field. 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 confirm
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 file 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 14

Synchronized Libraries

The synchronized library feature in Sente lets you:


Install synchronized copies of any library on any number of Macs and iPads,
regardless of where they are located (that is, devices do not need to be on the
same local network);
Add and edit references in any copy of the library, with the changes quickly
flowing 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 synchronized copies of a library 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 flexible than one might expect and it
can be used in ways that might not be immediately obvious to new users. Here are
some examples of how you can use synchronized libraries.
Access your library on all your Macs and iPads. This is the most basic use of
synchronized libraries. Once you turn on synchronization, you will be able to
open a synchronized copy of that library on all your devices. You can use your
library anywhere and all the changes will automatically appear in all other copies.
Your laptop or iPad can replace a folder of printed articles; you can read
anywhere, highlight, take notes, and have all that work appear in every copy of
the library immediately.
Automatic, secure backup. Whether or not you use your library on multiple
devices, you may still want to turn on synchronization because it will let you
recover your library should your computer fail, or even in the event that it is
stolen. To recover a current copy of your library, just install Sente on a new
device, log in to the sync server, and install the library again.
Share your library with collaborators. If you are working with colleagues on a
research project where it would be useful to share a common library, you can
invite them to access one of your libraries. This could be your main library, or
one created for a particular project. You control whether the collaborators can
make changes, view PDFs, etc.
Distribute a reference list to students or colleagues. Providing read-only
access to a library can be a convenient way to distribute a reference list to
students or colleagues. This could be the reading list for a course, or a
department research library, or any other sort of publication list. And, unlike
traditional static reading lists, everyones copy is automatically updated as you
update your copy of the library.

The Basics (All You Really Need to Know)


Synchronized libraries in Sente are very simple to set up and use. If you just want to
jump in and get started, here are the basics. The rest of the information in this
chapter is for people who want a deeper understand of how synchronized libraries
work, but this section should be enough to get you started.
Create a synchronized library by using the File > New Library command, making
sure the Synchronize option is checked in the sheet that will appear.

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Turn synchronization on in an existing library by using the Sync > Start


Synchronizing this Library command.
Install a copy of a synchronized library on a Mac by using the File > Open a Library
command in the main menu. Make sure you have the correct setting selected in
this sheet for how attachments should be handled.
Install a copy of a synchronized library on an iPad by using the Open a Library
command on the main screen. You will be asked about how you want
attachments handled.
Share a synchronized library with another user by using the File > Share this
Library command in the main menu. (You must have a Premium account to
share a library with another user.) You will be asked about permission settings
in the sheet that appears.
Open a library someone has shared with you by using the File > Open a Library
command, just like when you open your own libraries.
Thats it. There is a lot more information about synchronized libraries in the rest of
this chapter, but most people can get started with synchronized libraries knowing
just the information provided above. If you want to know more, then please read
on...

How Synchronized Libraries Work


Setting up a synchronized library in Sente is straightforward, but it is still useful to
understand a bit about how synchronized libraries work.
All communication involved in synchronizing libraries is done between the Sente
application, running on either a Mac or an iPad, and the Sente sync servers, using
standard web communication protocols.
This means that 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 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.

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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 files attached to the above references
All PDF annotations
All Synced Collections
The QuickTag hierarchy
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
Library Identifier
Each synchronized library is assigned a six-character alphanumeric ID. All copies of
a synchronized library will display the same value for this identifier. This can help
you diagnose any problems with the initial set-up of a synchronized library.
The library identifier is the first component of the sync status display, which is
explained in more detail later in this chapter.

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If two libraries are both copies of the same synchronized library, they will have the
same library identifier. If the identifiers are different in two different libraries, they
will not be synchronized.
Library Change Number
Each edit to a library is transmitted to the servers as a descrete operation, or
change. These changes are numbered sequentially and they are normally executed
on each client sequentially (attachments are an exception to this).
The second part of the sync status display (the part immediately after the @) is the
current change number in this copy of the library. This number is not the number
of references in the library it is the number of the most recently executed change
in the library. If two copies of the same synchronized library are both caught up
with the server, they will both display the same change number in the sync status
display.
Attachment Change Number
Attachments are handled somewhat differently from the way other edits are
handled. They use the same basic mechanisms, but they are handled at a lower
priority so the communication of very large attachment does not block the
communication of other edits.
When attachments are actively being downloaded, the attachment change number
wil be displayed at the end of the sync status display. This number will always be
less than the primary change number, because it represents Sente working through
the attachment changes that were skipped during the regular synchronization.
Automatic vs Manual Attachment Download
When a user installs a synchronized copy of a library on their Mac or iPad, they tell
Sente whether attachments should be downloaded automatically, or only as
requested by the user.
Libraries on devices with adequate local storage and reliable network connections,
like most Macs, should often be setup for automatic attachment download. As long
as Sente is running, even in the background, the files will be downloaded as soon as
they become available on the server.
Libraries on devices where storage is an issue, or that do not have fast, reliable and
non-metered Internet connections, like many iPads and some Macs, should often be

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configured for manual attachment download. When a particular PDF is desired, the
user can simply tap on the icon for the file and it will be downloaded immediately.
PDFs that are not needed on the device will consume neither local storage space,
nor network bandwidth.
It should also be noted that Sente for iPad can only sync when it is the foreground
app. Edits to references, notes, etc., can normally be handled just fine when the app
is active, but downloading attachments can take a long time and it will not progress
unless the iPad is awake, and Sente is the foreground application.
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 Conflict, which you
must resolve manually. For more information about sync conflicts, see the Sync
Conflicts 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.
The major difference between editing online and offline is that working offline
increases the likelihood of synchronization conflicts. 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 conflict 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 conflicts. All you need to
do is make sure that all of your changes in any copy are synchronized before

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working on a different copy. For example, if you were to work on a library on your
laptop or iPad during a long flight without an Internet connection, be sure to get
that device online shortly after the flight 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 conflicts 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 conflicts later in this chapter.

Creating and Using Synchronized Libraries


Creating a New Synchronized Library
When you create a new library in Sente using the File > New Library command, by
default it will be created as a synchronized library. If you do not want the library to
be synchronized, you should uncheck the Synchronize this library checkbox.

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The New Library dialog window. By default the Synchronize this library checkbox is checked.

After you select the location for the library and click on Save, Sente contacts our
sync servers, and registers the library.
All edits to the library will be immediately communicated to the sync servers, as they
are made. There is no need to remember to execute any synchronize command;
everything happens automatically.
Turning Synchronization On in an Existing Library
You can turn synchronization on for an existing, non-synchronized library using the
Sync > Start Synchronizing command in the main menu. When you do this, Sente
will register the library with the servers and begin immediately upload all of the
existing data.
The initial synchronization with the sync server may take a while. You can continue
to work on the library during this process, but it is often best to just let this initial

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upload complete before continuing work on the library. If you close Sente during
the process, it will pick up where it left off the next time you open the application.
Installing a Synchronized Library on a Second Mac
Once you have created a synchronized library on one device, it is available to be
installed on any other device.
To install a synchronized library on another Mac, use the File > Open Library
command in Sente on that Mac.
When you select a library from the server, you will be presented with a new window
and a dialog sheet in which you can tell Sente where to save the library file. You can
name the library anything you choose the name does not need to match the name
of the library on the server.
This is where you initially tell Sente whether it should download attachments
automatically or only on demand in this copy of the library.
Installing a Synchronized Library on an iPad
The process of installing a synchronized library on the iPad is very much like it is on
the Mac. In this case, the Open a Library command is found right on the main Sente
screen.
Once you select a library from the server, you will be asked about how attachments
should be handled. Be careful before choosing Automatic Download this can
consume a lot of network bandwidth (which can be expensive, depending on your
situation) and it can take up a lot of space on your device. On the other hand, if you
want to be sure you have all of your PDFs even when you do not have access to the
Internet, you will want automatic download.

Sharing a Synchronized Library with Other People


One of the most powerful aspects of synchronized libraries in Sente is the ability to
share copies of a library with other people. It is easy to share a library with any
number of people and to control what they can and cannot do in the library.

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Inviting Someone to Access a Library


The process of sharing a library begins with granting them access and sending them
an invitation. This is done using the File > Share this Library... command.
Please note that the Share this Library command is available only to users with a
Premium account. (Users with free accounts can access a library shared with them
by another user, but they cannot share their libraries with other users.)
When you invoke this command, you will be presented with a sheet in which you tell
Sente who you would like to share the library with, and what level of access they
should have.

The sheet used for sharing a library with another user.

You must specify a valid email address for the other person, and this must be the
address that they will use for their Sente sync account. The invited user will be able
to install the library on any or all of their Macs or iPads.
The user does not need to be a Sente user already. If they do not yet have a Sente
account, they will be told how to obtain the free software and create their account.

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By sharing a library with another person, you are always granting them access to
view all of the references in the library, thus the first option in the list of
permissions is always checked.
You can also grant the user access to all of the attachments (i.e., PDFs and other
files attached to references). This option should only be selected if you think that
you have the right to distribute the files to the intended recipient. For example, if
the recipient is also a member of the your academic institution and all of the PDFs in
your library were obtained under a license that they share, then it is likely that they
would have the legal right to access the files themselves.
The next option determines whether the user can change the contents of the library
by adding, removing or editing references. If you are distributing a reading list to
everyone in a class you are teaching, you probably do not want to grant them edit
permission. On the other hand, if you are sharing the library with other members of
your department or lab, you may want them to be able to add their own references
to the shared library.
The final option determines whether the user can modify important library settings
such as the QuickTag palette. This level of access should normally only be granted
to people who are very familiar with Sente and the way in which you are organizing
the library.
When you click on the Share this library button, an email message will be sent to the
specified account indicating that they have been granted access to your library.
Accessing a Shared Library
When someone is invited to access a shared library, they will receive an email
message from Sente informing them of this fact and telling them how to proceed.
The exact contents of the message will depend on several things, such as whether
the user already has a Sente account, and the level of permission being granted to
them.
If the user is not already a Sente user, they will be told how to download the free
Sente app on either their Mac or iPad, and how to set up their Sente account.
The email will also include instructions for opening the library the first time on
either device.
Shared libraries are opened in exactly the same way as other synchronized libraries,
using the File > Open Library command in the main menu.

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In the case of a library that has been shared by another user, their account name
(their email address) will be displayed alongside the library name in the list of
libraries.
Once a shared library has been installed on a device, it can be accessed just like any
other library, subject to the permissions granted by the library owner.
Changing Permissions or Revoking Access to a Shared Library
Should you want to modify the permission setting for a particular user on a shared
library, or revoke access entirely, you can do this through the Manage My Sync
Account page within Sente on either platform.
On the Mac, use the Sync > Manage My Sync Account command to open the page.
On the iPad, tap on the Manage My Sync Account item in the sidebar.
In this page, the number of users with access to each of your libraries is listed in the
main library table.
The exact list of users for each library, if any, along with their permission settings,
is found lower down on the page in a table specific to each library.
To change the permission settings, or to revoke access entirely, click on the entry
for that user. You will be taken to a page where you can modify the setting for that
user.
If you revoke access to a library, the user will be informed of this fact the next time
they open the library. They will retain the copy of the library as it existed on their
device prior to having their access revoked, but no further changes will be
communicated to that copy of the library.

Sync Conflicts
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 conflict, which must be then handled manually by the user.

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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 first that is submitted to
the sync servers will win and the second to be submitted will be rejected as a
conflict.
A far more common scenario is that one user edits many references while offline
(say, on a flight with no Internet connection). While they are on the flight, another
user might make changes to some of the same references. When the first user
finally 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 flagged as
conflicts.
When a sync conflict is detected, Sente will present a warning something like the
following:

A sync conflict warning message.

When a sync conflict 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 Conflicts 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.

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Once you decide what you want to do with each reference in the sync conflicts
collection, they can simply be deleted.
Preventing Sync Conflicts
Under most circumstances, sync conflicts are rare, but there are some ways of
working that make them more common.
Sync conflicts will be rare if everyone working on a library is connected to the
Internet while editing data. In this case, sync conflicts 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 conflicts.
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 conflicts.
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 conflict.
Resolving Sync Conflicts
When you are notified that a sync conflict has been detected, you need to decide
how to resolve the conflict.
First, it is important to note that the conflict exists only on the computer on which
the conflict 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 conflict was reported. In that library, the changes that
lost can be found in the Sync Conflicts collection in Local Collections.
If you do nothing, the changes that lost will not be reflected 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,

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those several references will be reported to you as sync conflicts. The changes to
the other references will go through without a problem. In this case, you would
locate the references in the Sync Conflicts 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.
Do You Actually Have Synchronized Libraries?
The first 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 identifier. All
copies of the same synchronized library will have the same identifier. If two libraries
have different identifiers, they are not synchronized copies of the same library and
the contents of the two libraries will not be synchronized.
Locating the Library Identifier 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.

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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:

The library sync status is also displayed in the File > Synchronization item in the main menu.

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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).
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
find 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.

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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.
Synchronizing. An up or down arrow 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 problem is that one or more of the
devices does not have an active connection to the Internet. Because Sente uses
the standard HTTPS protocol for syncing (the same protocols used when
accessing secure web pages in a browser); if you can access
www.thirdstreetsoftware.com in your web browser, you can probably sync.
(The sync connection is actually to ws1.thirdstreetsoftware.com, but this
server does not support connections from standard web browsers, so it cannot
be tested in the same way.)
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 configured 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 15

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 file scanning feature to
generate citations and bibliographies. Sente also supports a streamlined file
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 specific 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 first version to store documents in the Pages XML format.
File Scanning
Sente works with Pages documents using the file scanning interface, where citations
are first entered as citation tags (e.g., {Smith 2007}) and then are replaced with
properly formatted citations during the file 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 file
scanning process:
Apple Pages Document, Not Scannable
Apple Pages Document, Scannable
Apple Pages Document, Unscanned

The scan document options for an Apple Pages file.

Please see the chapter on File Scanning for more information.

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Rescanning
Apple Pages XML files 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 file 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 file scanning
interface, in which citations are first 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 file scanning process:
Document, Not Scannable
Document, Scannable (EndNote compatible)
Document, Unscanned

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The scan document options for a Word docx file.

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 file 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 configured 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.
Configuring Mellel
Mellel must be configured to recognize Sente. To do this, follow these steps:
1.

Launch Mellel.

2.

Open Mellel Preferences.

3.

Select the Bibliography pane.

4.

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 first 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.

2.

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 final document.

A Citation in Mellel.

3.

Insert the rest of your citations and finalize your manuscript.

4.

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 modifiers (please see
the File Scanning chapter). In cases where Mellel provides a checkbox for an edit
option, either the checkbox or the string modifier may be used.
If you double-click an inserted citation placeholder in your source manuscript, you
have access to the field code where these edits are made. Here are a few examples
of applying the modifiers to the field 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 field 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
files 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 file export menu in Scrivener 2.2 shows several file format options that Sente accepts.

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File Scanning
Sente works with Scrivener documents using the file scanning interface, in which
citations are first entered as citation tags (e.g., {Smith 2007}) and are then
replaced with properly formatted citations during the file 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 file to. For example, if you export the file in the docx format
(recommended), your output options will be:
Document, Not Scannable
Document, Scannable (EndNote compatible)
Document, Unscanned
However, if you export the file 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 files. 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 files.
Scan-in-Place
Microsoft Word docx documents can be scanned in place, where you can still edit
your document after you occasionally scan the file 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 files 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 file scanning interface, in which
citations are first entered as citation tags (e.g., {Smith 2007}) and are then
replaced with properly formatted citations during the file 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 file 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 file.

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 file scanning interface, in
which citations are first entered as citation tags (e.g., {Smith 2007}) and are then
replaced with properly formatted citations during the file 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 file 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 files 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 files; in other cases you
will need to scan the file as saved on disk.
File Scanning
Sente works with RTF, HTML, and plain text documents using the file scanning
interface, in which citations are first entered as citation tags (e.g., {Smith 2007})
and are then replaced with properly formatted citations during the file 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 file
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.

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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 final format at all
times, rather than needing to scan the file 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 file 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 specific to Word 2004 for
inserting citations and bibliographies:
1.

In a Word 2004 document, place your insertion point where you would like to
insert an in-text citation.

2.

Select Tools > Sente > Insert Citation(s). Sente will automatically launch if it
isnt running already.

3.

In the Reference Selector that appears, select one or more references.

4.

Click OK. The citation will appear as a field 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.

5.

Return to Step 1 to add more citations to your document.

6.

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.

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 field before deleting. Otherwise, the
citation may reappear when you refresh the document.

Inserted citations are maintained in fields; when deleting, be sure to select text before and
after the field to ensure the field 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 first 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 configuring 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 configure 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 Proofing

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 fields 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 final 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 find 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 final
formatting in the document, but there may be small issues until the Refresh
command is executed.

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Chapter 16

File Scanning

With most word processors, Sente uses an approach called file 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
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 file scanning:
Traditional file 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 file scanning and it will describe
the steps required to prepare a document for file scanning and to perform the file
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 file 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 file, 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 file 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 file 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 first is if you only need to edit
the scanned copy for final 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 file 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 fields. Fields can store more information than just the visible text
and Sente uses these fields 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 field. This field is intended to
contain a string of characters that uniquely identifies the reference. That is, each
reference in a library should have either no value for this field, or a string of
characters that is different from all other values in the library.
When a reference is first created, its citation ID field is empty. You can enter any
value into this field at any time. Or, you can let Sente assign a unique value to this
field automatically, as needed (as will be explained further a bit later). When Sente
generates a citation ID, it uses a template based on first 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 file 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 find 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
specified library. If it finds 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 flags 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 first 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 field. 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 field 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 specified 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 final 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
final 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
file, 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 file formats used in some word processors support the concept of
rescanning the output file. This is possible because some word processor formats
allow information to be hidden in a document, in what word processors typically
call fields. 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 file 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 file.

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
configure Sente to use those methods that you find 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
configure 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 configured 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 configured 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 workflow. 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
desired delimiters), and close the preferences pane. You can have multiple gesture
types configured to use citation tags as the output format.

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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.
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.

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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
configuration.

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

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The Cite and Scan toolbar buttons.

Using the Cite toolbar button and cmd-Y are both very easy three-step processes:
1.

Place your cursor at the proper location in your document.

2.

Select the correct reference in Sente by left-clicking on it once in the reference


table.

3.

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 file 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.
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

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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 configured 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 final 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 modifiers to the citation tags. Sente supports a number of
modifiers 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 fixed 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 final 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 file scanning process unless specifically 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 final output.

Scanning the File


At any time during the writing process you can scan the master copy of the file 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 file to be scanned.
One, it will look for all files that are currently open in any of the supported word
processors, and which are in a supported format. These files will be listed in the
menu labeled Open Document in the scan dialog window. Because you will typically
be wanting to scan a file you are currently editing, your file is likely to be in this
menu.
Alternatively, Sente lets you select any file on your computer for scanning. If you
want to scan a file that is not open in a supported word processor, select the File
option and then click on Choose to select the file from your file system.
It is important to note that Microsoft Word files must be saved in docx format, not
doc format. If you have a doc file open in Word, Sente will not include it in your list
of scannable files 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
specified in the Library menu. Only open libraries are listed, so you must first 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 specified 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 file. You can name the output
file whatever you want, but Sente will default to a name based on the input filename
plus the bibliography style name.
Output File Format
Depending on the format of the input file, you may have several options for the
format of the output file. These options determine exactly what information is
stored in the output file. These options should not be confused with the Style
options, which determine the bibliography style to be applied. Instead these
options specify the file format (e.g., RTF, docx) and, in some cases, whether the
output file should be scannable itself.

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Scannable, Not Scannable and Unscanned Options

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

The scanned file 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 file 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 files enable users to edit a draft that looks
very much like the final formatted document will look when finished.
Unscanned

If you start with a rescannable document, you can revert all of the previously
scanned citations to citation tags by scanning the file 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 file is a docx file, 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 file produced by Apple Pages, you can select any of these
output file formats:
Apple Pages Document, Not Scannable
Apple Pages Document, Scannable
Apple Pages Document, Unscanned.
Options for RTF Files

If your input file is an RTF (Rich Text Format) file, 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
file 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 fields. Fields can store more information than just the visible text
and Sente uses these fields 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
file with .backup added to the file name. The scanned citations and your edits will
be stored in the main file, 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 file 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 file scanning process is the same as the other methods of file
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 file scan results dialog window showing resolved and unresolved citations.

Resolved Citations vs. Unresolved Citations


After the file scanning process finishes, 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 file 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 specified 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 file 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 file 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 file format. (Of note,
Word docx and Apple Pages documents that have been scanned with Sentes scanin-place feature are saved in a rescannable file format.) See the output file format
specification section above for more information.
Use Caution
The normal scanning process is very safe because Sente only reads your original
documentit never modifies 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 modified 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 file just prior to each scan, at least
for several versions back.
We work hard to make sure that the file scanning process does not corrupt files 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 file scanning
issues.

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My File is Not Listed in the Scan Dialog Box


When you begin the file scanning process, you are given the choice to either scan an
open document, or find a closed file 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 file needs to be saved. If you created and worked on a document but did
not save it, the file may be missing from the list. Saving the file 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 file 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 file on the computer.
An open file is selected at the top of the window, but the file 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 file 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 file is either not specified, or cannot be written to by the current
user. Specify a filename 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 file, 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 file 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
file 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 file to scan, or your file is not saved as one of these two file 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 17

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 file,
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 first 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 definition 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
configurable, 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 modified.
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 specifications for each
reference type: one for the in-text citation and one for the bibliography entry. For
example, the APA format includes two specifications 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 specifications for the new types as well.
Each of these format specifications (e.g., book, in-text) can consist of either:
a statement that the format specification 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 specification 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 fields.
This sort of behavior can be specified 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 (first 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 find 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 reflected 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 configure 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
specified.
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 fields 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 final 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 final bibliography.
Chronologically orders the citations in each group by their dates of
publication.
Prepend, Separator, Append. Use these fields 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
defined 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 definition 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 field here (and italicized, if that option is checked). The
most common value for this text fields 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 configure the bibliography entry and in-text
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 configuration 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 configure 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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specified for any given Reference Type, and you can configure 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
definition, 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.
Definition: The Definition 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 configuring (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 Configuring Elements

If you have selected the As Shown Below option in the Definition field 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 specific 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 modified 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 fixed 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 reflected immediately in the preview area of the Bibliography Formats window.
Configuring Each Element

Immediately below the Element Type menu, some options specific to the selected
element may appear. For example, there are a number of ways to configure the
Authors element. Move down the elements list to configure 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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Configuring the Authors Element

For the Authors, Pages, and Cited Pages elements, a For plural, Prepend/Append
fields 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 field would contain , ed.
and the plural append field 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 specific 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 field, 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 specified trailing punctuation has been removed.
unless data ends with any of When checked, will override the previous field
when the specified trailing punctuation still exists after any specified 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 first 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 Specific 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 modified 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 fixed 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 final 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 specified fields. If the
reference has a value for any of the fields, 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 field 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 final
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 final 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 definitions for these formats
for examples of how conditional elements can be used to make more accurate and
flexible bibliography formats.
Configuring Other Reference Types

When youve finished setting up the Elements for your first Reference Type, select
the next type (such as Book) and then use the Copy menu to copy the setup from
the first 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.
Customized Terms

This section lets you override certain terms in the final 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.
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 first 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 configure exactly which contexts are

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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.

The Advanced Tab

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.

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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 configure 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 (first 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 find 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 reflected 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.

Click on the Show: Components radio button at the top of the window;

2.

Click on the [create new component] link at the top of the preview pane

3.

Provide a name for the new component in the sheet that appears;

4.

Edit the definition 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 first, you need only make the corrections in the component definition,
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 file for a bibliography format that you
would like to add to Sente, you can import the file (which will be imported as a Local
copy) and then modify it if you need to.
To import the CSL file, follow these steps:
1.

Quit Sente.

2.

Place the CSL file in the folder: ~/Library/Application Support/Sente/Sente 5


Bibliography Styles

3.

Restart Sente.

4.

Open the Bibliography Format Editor by using the Window > Bibliography
Format Editor command.

5.

In the list of formats on the left, scroll down until you find your new format in
the list, then place a checkmark in the checkbox next to it. (NOTE: If you
cannot find 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.)

6.

Click on the new format name and modify it, using the instructions earlier in
this chapter, if you wish to do so.

7.

Close the Bibliography Format Editor when you are finished. 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.

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Chapter 18

Sente Preferences

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

Appearance Preferences
Sente lets you configure 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 configured 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 first 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 specific 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 configure 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 configurations allows you to expand your use of Sentes citation
placement features.
Supported Formats
Sente can export data in several built-in file 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 file formats included with Sente are:
BibTeX
BibTeX (Unicode)
EndNote X
Refer
SenteXML
These export file 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 configured in the Gestures pane in Preferences.

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The Gestures preferences pane.

Supported Gestures
Sente allows you to configure 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 configured here. For example, the
PubMed and Web of Knowledge plugins can be configured 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 files, etc.

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The Advanced preferences pane.

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