Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research: JabRef is an open-source, cross-platform citation and reference management tool.

To get started, please follow the installation instructions and familiarize yourself with the basics of JabRef.

Use the Search icon at the top left of this page to find what you're looking for. To learn more about JabRef's features, please follow the links below.

Collect

• Add new entries manually or the based on the reference text

• Search across many online scientific catalogs like CiteSeer, CrossRef, Google Scholar, IEEEXplore, INSPIRE, Medline/PubMed, MathSciNet, Springer, arXiv, and zbMATH

• Import options for over 15 reference formats

• Easily retrieve and link full-text articles

• Fetch complete bibliographic information based on identifiers such as ISBN, DOI, PubMed-ID and arXiv-ID

• Extract metadata from PDFs

• Import new references directly from the browser with one click using the official browser extension for Firefox, Chrome, Edge and Vivaldi

Organize

• Edit the bibliographic information using a convenient user interface

• Group your research into hierarchical collections and organize research items based on keywords/tags, search terms or your manual assignments

• Advanced search and filter features

• Complete and fix bibliographic data by comparing with curated online catalogs such as Google Scholar, Springer or MathSciNet

• Customizable citation key generator

• Manage field names and their content

• Customize and add new metadata fields or reference types

• Fix common mistakes, automatically upon save if you wish

• Find and merge duplicates

• Attach related documents: 20 different kinds of documents supported out of the box, completely customizable and extendable

• Automatically rename and move associated documents according to customizable rules

• Keep track of what you read: relevancy, ranking, priority, printed, quality-assured, read status

Cite

• Native BibTeX and biblatex support

• Cite-as-you-write functionality for external applications such as Emacs, Kile, LyX, Texmaker, TeXstudio, Vim and WinEdt

• Format references in one of the many thousand built-in citation styles or create your style

• Support for Word and LibreOffice/OpenOffice for inserting and formatting citations

Share

• Many built-in export options or create a custom export format

• Library is saved as a simple text file, and thus it is easy to share with others e.g. via Dropbox and is version-control friendly

• Work in a team: sync the contents of your library via a SQL database

JabRef is highly customizable and adapts to you, not the other way around.

If you want to dive even deeper, have a look at the advanced information about JabRef.

Entries can be created from a reference text.

In case you have a reference string, JabRef offers the functionality to convert the text to BibTeX (or biblatex). For this, JabRef uses the technology offered by Grobid.

Example:

O. Kopp, A. Armbruster, und O. Zimmermann, "Markdown Architectural Decision Records: Format and Tool Support", in 10th ZEUS Workshop, 2018.

1. Click Library and select "New entry from plain text..." Alternatively, you can press Ctrl+Shift+N.

2. The "Plain Reference Parser" window opens

3. Paste the reference text:

4. Click "Add to current library"

5. The result is selected in the entry table:

To add a new entry, select Library → New entry..., press CTRL + N​ or click on the dedicated icon of the toolbar.

A dialog window is displayed. By default, 5 common types of entries are displayed:

For other types of entries, click on Others. That expands the window and displays the other entry types available:

Finally, the entry editor opens and let you fill in the various fields.

JabRef provides you with many ways to add a new entry.

JabRef is not intended to be a tool for mass download of citations. The purpose of the Web search is to easily gather a few entries directly from within JabRef. If you use the search functionality too extensively you might get blocked (for some time). To fetch entries from an online database, choose View → Web search, and the search interface will appear in the side panel. Select the database you want to search (e.g., arXiv) in the dropdown menu. Note that it might be necessary to scroll downwards to find certain fetchers. An example for this is provided in the image below. You may opt to download the abstracts along with the cite information for each entry, by checking the Include abstracts checkbox.Then enter the words of your query, and press Enter, or the Search button. The results are displayed in the . Some online services support advanced search queries. These are described below at the respective fetcher.

Apart from fetching entries by using a full search, it is also possible to directly .

Mass downloading of articles

Using a Proxy Server

If you need to use an HTTP proxy server, you can configure JabRef to use a proxy using the "Network" preferences (File → Preferences → Network).

Search Syntax

JabRef searches the databases by using the specified keywords. One can use quotes (") to keep words togehter: An example is "process mining". It is also possible to restrict the search to dedicated fields:

Thereby, JabRef supports following fields:

One can usually combine different searches using the Boolean operators AND and OR. Thereby, the default operator is OR.

Examples

• author:smith and author:jones: search for references with authors "smith" and "jones"

• author:smith or author:jones: search for references with either author "smith" or author "jones"

• author:smith and not title:processor: search for author "smith" and omit references with "processor" in the title

Supported databases

ACM Portal

• the Guide to Computing Literature that is a bibliographic collection from major publishers in computing with over one million entries.

arXiv

Bibliotheksverbund Bayern (BVB)

Biodiversity Heritage Library

CiteSeerX

Collection of Computer Science Bibliographies (CCSB)

Crossref / Unpaywalll

The Unpaywall database has a very simple structure: it has one record for each article with a Crossref DOI. It harvests from many sources to find Open Access content, and then matches this content to these DOIs using content fingerprints. So for any given DOI, we know about any OA versions that exist anywhere.

To fetch entries from Unpaywall indirectly through Crossref, choose Search → Web search, and the search interface will appear in the side pane. Select Crossref in the dropdown menu. To start a search, enter the words of your query, and press Enter or the Fetch button.

DBLP

DOAB

DOAJ

It is possible to limit the search by adding a field name to the search, as field:text. The supported fields are:

Google Scholar

Traffic limitations

Google scholar can block "automated" crawls which generate too much traffic in a short time. To unblock your IP, doing a Google scholar search in your browser might help. You will be asked to show that you are not a robot (a CAPTCHA challenge). If no CAPTCHA appears, or JabRef is still blocked after performing a search in the browser, you can also change your IP address manually or wait for some hours to get unblocked again.

GVK

Advanced search

You can simply enter words / names / years you want to search for, or you can specify search fields.

Supported fields are:

Year ranges are not supported. In case a year range is provided, it is ignored. Otherwise, GVK returns no results.

Notes

• queries can be combined with and. The use of and is optional, though.

• in many cases you can use the truncation sign ?

• spaces in person names are not supported yet. Please use the truncation sign ? after the first name for several given names. E.g. per Maas,jan?

Sample queries

• marx kapital

• author:grodke and title:db2

• author:"Maas,jan?"

IEEEXplore

INSPIRE

Query syntax

The following list shows some of the field indicators that can be used:

Jstor

It is possible to limit the search by adding a field name to the search, such as field:"text". The supported fields are:

• title: The title of the article

• author: an author of the article

• journal: journal title (sent as pt to Jstor)

• pt: publication title

MathSciNet

Medline/PubMed

The Medline syntax is completely different form the Lucene syntax. One cannot use fielded search there.

There are two ways of specifying which entries to download:

1. Enter one or more MEDLINE IDs (separated by comma/semicolon) in the text field.

Examples

• May \[au\] AND Anderson \[au\]

• Anderson RM \[au\] HIV \[ti\]

• Valleron \[au\] 1988:2000\[dp\] HIV \[ti\]

• Valleron \[au\] AND 1987:2000\[dp\] AND (AIDS \[ti\] OR HIV\[ti\])

• Anderson \[au\] AND Nature \[ta\]

• Population \[ta\]

SAO/NASA Astrophysics Data System

SearchAll

Semantic Scholar

Springer

zbMATH Open

Structured Search

You cannot use the same query syntax as in the one-line search at zbmath.org; you have to stick with the Apache Lucence syntax. This means that your query can be composed of several terms, combined by the logical operators AND and OR. Queries are case-insensitive. Further operators that can be used are NOT for logical negation, * for a right wildcard, " " for exact phrase matches, and parentheses ( ) to group terms. Optionally, it is possible to add a field name in the form field:text to limit the search results. The supported fields are:

Examples

From an ID to an entry

For other identifiers, choose Library → New entry, or click on the New entry button, or use the keyboard shortcut CTRL + N. In the lower part of the window, there are two boxes : "ID type" and "ID". In the field "ID type", you can select the desired identifier, e.g. "ISBN" (it works also for DOI). Then enter the identifier in the textbox below and press Enter. That will generate an entry based on the given ID (you can also click on "Generate"). The entry is added to your library and opened in the entry editor. In case an error occurs, a popup is shown.

Supported databases

Arxiv

Crossref

ID search is carried out using the DOI.

ISBN

DiVA

ID search is carried out using the DiVA id (diva2).

DOI

ID search is carried out using the DOI.

IACR eprints

ID search is carried out using the Cryptology ePrint ID.

Library of congress

MathSciNet

ID search is carried out using the MR number.

Medline/Pubmed

mEDRA

ID search is carried out using the DOI.

SAO/NASA ADS

Title

Based on the title of your publication, JabRef call Crossref, which return the corresponding DOI. Then JabRef fetches the reference based on this DOI.

To return a reference, the publication needs to have a DOI.

RFC

IETF (Internet Engineering Task Force) Datatracker is a database that "contains data about the documents, working groups, meetings, agendas, minutes, presentations, and more, of the IETF." It used to be available at https://datatracker.ietf.org/ (currently down).

ID search is carried out using the (Request for Comments number) (RFC) of the IETF database.

zbMATH Open

ID search is carried out using the Zbl number.

See also:

This feature is available through Lookup -> Search for unlinked local files.

The following description appeared first on .

Preparation: Adjust the JabRef key generation pattern to fit your needs

JabRef offers a BibTeX key generation and offers different patterns described at .

Link the PDFs to your bib library

In case you have numerous PDF files and want to convert them into new entries, JabRef can search automatically for the PDF files, let you select the relevant ones, and convert them into new entries.

1. Create or open a .bib library.

2. Go to Lookup -> Search for unlinked local files. (or press SHIFT + F7)
3. The "Search for unlinked local files" dialog opens.

4. Choose a start directory using the "Browse" button.

5. Click on "Search" / "Scan directory".

6. In "Select files", the files not yet contained in the library are shown.

7. Select the entries you are interested in. Note: the button Export selected files allows you to export the list of the selected files (a text file containing on each line one filename with its path)

8. Click on Import.

   The windows close and the entry table now contains the newly-imported entries.

9. The entry editor with the last imported entry is shown

10. You can now save the file and are finished.

11. Optional: Click on "General" to see the linked file

12. Optional: Click on "BibTeX source" to see the BibTeX source

13. Optional: You have to shrink it to see the entry in the entry table, enlarge the JabRef window and use the mouse at the upper border of the entry editor

14. Optional: Press Esc to show the entry preview

Further information

PDFs for which it works

Better filenames

This makes the filenames start with the bibtey key followed by the full title. In the concrete case, \bibtexkey only may be the better option as the described bibtey key already contains the title.

Mr.DLib

Related questions on stack overflow

Entry edition is done in the entry editor.

To open the entry editor for a specific entry, you can either:

• double-click on the entry in the table of entries

• select the entry and press Enter

• select the entry and go to the menu View → Open entry editor

• select the entry and press CTRL + E

Then you can modify the content of the entry. When done, click on the top left-hand corner of the entry editor or press ESC to close the entry editor and go back to the table of entries.

JabRef allows you to define and use your own importers, in very much the same way as the standard import filters are defined. An import filter is defined by one or more Java classes, which parse the contents of a file from an input stream and create BibTex entries. So with some basic Java programming, you can add an importer for your favorite source of references or register a new, improved version of an existing importer. Also, this allows you to add compiled custom importers that you might have obtained e.g. from GitHub without rebuilding JabRef (see "Sharing your work" below).

Custom importers take precedence over standard importers. This way, you can override existing importers for the Autodetect and Command Line features of JabRef. Custom importers are ordered by name.

Adding a custom import filter

Make sure, you have a compiled custom import filter (one or more .class files as described below) and the class files are in a directory structure according to their package structure. To add a new custom import filter, open the dialog box Options → Manage custom imports, and click Add from folder. A file chooser will appear, allowing you to select the classpath of your importer, i.e. the directory where the top folder of the package structure of your importer resides. In a second file chooser, you select your importer class file, which must be derived from ImportFormat. By clicking Select new ImportFormat Subclass, your new importer will appear in the list of custom import filters. All custom importers will appear in the File → Import → Custom Importers and File → Import and Append → Custom Importers submenus of the JabRef window.

Please note that if you move the class to another directory you will have to remove and re-add the importer. If you add a custom importer under a name that already exists, the existing importer will be replaced. Although in some cases it is possible to update an existing custom importer without restarting JabRef (when the importer is not on the classpath), we recommend restarting JabRef after updating a custom-importer. You can also register importers contained in a ZIP- or JAR-file, simply select the Zip- or Jar-archive, then the entry (class-file) that represents the new importer.

Creating an import filter

For examples and some helpful files on how to build your own importer, please check our download page.

A simple example

Let us assume that we want to import files of the following form:

1936;John Maynard Keynes;The General Theory of Employment, Interest and Money
2003;Boldrin & Levine;Case Against Intellectual Monopoly
2004;ROBERT HUNT AND JAMES BESSEN;The Software Patent Experiment

In your favorite IDE or text editor create a class derived from ImportFormat that implements methods getFormatName(), isRecognizedFormat and importEntries(). Here is an example:

import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import net.sf.jabref.logic.importer.Importer;
import net.sf.jabref.logic.importer.ParserResult;
import net.sf.jabref.logic.util.FileExtensions;
import net.sf.jabref.model.entry.BibEntry;
import net.sf.jabref.model.entry.BibtexEntryTypes;

public class SimpleCSVImporter extends Importer {

    @Override
    public String getName() {
        return "Simple CSV Importer";
    }

    @Override
    public FileExtensions getExtensions() {
        return FileExtensions.TXT;
    }

    @Override
    public String getDescription() {
        return "Imports CSV files, where every field is separated by a semicolon.";
    }

    @Override
    public boolean isRecognizedFormat(BufferedReader reader) {
        return true; // this is discouraged except for demonstration purposes
    }

    @Override
    public ParserResult importDatabase(BufferedReader input) throws IOException {
        List<BibEntry> bibitems = new ArrayList<>();

        String line = input.readLine();
        while (line != null) {
            if (!line.trim().isEmpty()) {
                String[] fields = line.split(";");
                BibEntry be = new BibEntry();
                be.setType(BibtexEntryTypes.TECHREPORT);
                be.setField("year", fields[0]);
                be.setField("author", fields[1]);
                be.setField("title", fields[2]);
                bibitems.add(be);
                line = input.readLine();
            }
        }
        return new ParserResult(bibitems);
    }
}

Note that the example is in the default package. Suppose you have saved it under /mypath/SimpleCSVImporter.java. Also, suppose the JabRef-2.0.jar is in the same folder as SimpleCSVImporter.java and Java is on your command path. Compile it using a JSDK 1.4 e.g. with

javac -classpath JabRef-2.0.jar SimpleCSVImporter.java

Now there should be a file /mypath/SimpleCSVImporter.class.

In JabRef, open Options → Manage custom imports and click Add from folder. Navigate to /mypath and click the Select ... button. Select the SimpleCSVImporter.class and click the Select ... button. Your importer should now appear in the list of custom importers under the name "Simple CSV Importer" and, after you click Close also in the File → Import → Custom Importers and File → Import and Append → Custom Importers submenus of the JabRef window.

Sharing your work

With custom importer files, it's fairly simple to share custom import formats between users. If you write an import filter for a format not supported by JabRef, or an improvement over an existing one, we encourage you to post your work on our GitHub page. We'd be happy to distribute a collection of submitted import files or to add to the selection of standard importers.

Groups allow structuring of bibliographic libraries in a tree-like way that is similar to organizing files on disk in directories and sub-directories. The two main differences are:

• While a file is always located in exactly one directory, an entry may be contained in more than one group.

• Groups may use certain criteria to dynamically define their content. New entries that match these criteria are automatically added to these groups. This feature is not available in common file systems, but in several Email clients (e.g. Thunderbird and Opera).

Selecting a group shows the entries contained in that group. Selecting multiple groups shows the entries contained in any group (union) or those entries common in all selected groups (intersection), depending on the current settings. All this is explained in detail below.

Groups interface and first steps

The group interface is shown in the side pane on the left of the screen. It can be toggled on or off by pressing Alt + 3 or by the menu View → Groups. The interface has several buttons, but most functions are accessed via a context menu (i.e. a right-click). Drag-and-drop is also supported.

Creating a group and adding entries to it

To create a group and manually assign entries to it, press the Add group button located at the bottom of the pane, enter a name for the group, then press (leaving all values at their defaults). Now select the entries to be assigned to the group, and drag-and-drop them to the group (or use Add selected entries to this group in the context menu of the group interface). Finally, select the group to see its content. Only the entries you just assigned to the group should be displayed in the entry table.

You can also automatically fill a group based on keywords. For this, you need to use a different type of groups.

When you have numerous groups, the one of interest can be displayed by typing its name in the ''Filter groups'' field located near the top of the group pane.

Display union or intersection of groups

Selecting one group shows the entries contained in that group (accounting for hierarchical settings).

When selecting several groups, you can intersect or unionize them: Union displays all the entries of the selected groups while Intersection displays all the entries shared among the selected groups.

For example, if you have a group for the author 'Smith' and another one for the author 'Doe', selecting the groups displays the entries that they co-authored if 'Intersection' is selected. If 'Union' is selected, the entries that at least one of them authored are displayed.

To test this, create two groups having some entries in common. Click the Intersection/Union button and make sure that Union is selected. Now select both groups. You should see all entries contained in any of the two groups. Click again on the Intersection/Union. This selects Intersection. Now you should see only those entries contained in both groups (which might be none at all if groups do not share entries, or exactly the same entries if both groups contain the same entries).

Group tree. Creating and removing groups

Just like directories, groups are structured like a tree, with the group All Entries at the root. By right-clicking on a group and selecting Add subgroup, you can add a subgroup to the selected group. The Add group button (at the bottom of the pane) lets you create a new subgroup of the group All Entries, regardless of the currently selected group(s). The context menu also allows removing groups and/or subgroups, and to sort subgroups alphabetically. Moving groups to a different location in the tree can be done by drag-and-drop.

Group dialog window

The properties of a group can be defined in the 'Edit group' dialog window (the same window is displayed when creating a new group). To modify the group properties, right-click on the group name in the group pane and select Edit group in the context menu.

Name

Defines the name of the group, as displayed in the group pane.

Description

A description of the group, to help you remember what it is about. This description is displayed when hovering the mouse over the group name.

Icon and color

An icon can be displayed in front of the group name. Choose your favorite icon among the ones available at https://materialdesignicons.com/, and enter its name of the field Icon (replacing any hyphens (-) with underscores (_)). The color of the icon can be set in the field Color.

Hierarchical context

The displayed entries depend on the hierarchical context of the group. When a group is selected, the displayed entries can be:

• independent of its supergroup and of its subgroups.

• a union between the entries of the group and of its subgroups.

• an intersection between the entries of the group and of its supergroup.

Independent group

By default, a group is independent of its position in the group's tree: When selected, the table of entries shows only the group's content (i.e. all of its entries).

Intersection between a group and its supergroup

For a group defined with a hierarchical context Intersection, only the entries contained in both the group and its supergroup are displayed when the group is selected.

This is especially relevant for groups based on keywords or search expression, where it is often useful to define a group that intersects its supergroup. For example, consider a supergroup containing entries with the keyword distribution and a subgroup containing entries with the keyword gauss. With the subgroup gauss defined as an intersection (of its supergroup), selecting the subgroup gauss displays entries that match both conditions, i.e. are concerned with Gaussian distributions. Note that entries that only belong to the subgroup gauss will not be shown, i.e. for an entry to be displayed when selecting gauss, it must be assigned to both the subgroup gauss and the supergroup distribution. By adding another intersection group for laplace to the supergroup distribution, the grouping can easily be extended to Laplace distributions.

Union between a group and its subgroups

The union of a group and its subgroups is the logical complement of the intersection: when defined as union, selecting the group displays both the group's own entries and its subgroups' entries.

For example, you can create a group for your references about music, and then subgroups about the music styles (classic, jazz, rock, etc.). By setting the group "Music" as union, when you subsequently add references to a subgroup, they will automatically appear in group "Music" as well (without additional action).

Nesting (sub)groups

You can populate your Group pane by configuring JabRef to use the bibtex source's keywords = {...}, by clicking the + icon and following the previous instructions. You can nest subgroups by using the right chevron > (see here). You achieve this by editing the keywords = {...}, bibtex field in the entry source by placing > between any two keywords where the left-hand keyword is the parent group and the right-hand keyword will be its sub-group. The library entry will be placed there. Note: when you select + to do this, the first delimiter must be the right chevron, and the second must be whichever field separator you have configured (by default a comma ,).

Mixing refining groups with including groups

If a refining group is a subgroup of a group that includes its subgroups -- the refining group's siblings --, these siblings are ignored when the refining group is selected.

Types of groups

JabRef has five types of groups:

• Explicit selection. The group contains entries that were assigned manually. It behaves like a directory on disk, and contains only those entries that you explicitly assigned to it.

• Searching for a keyword. The group contain entries in which a certain field (e.g. author) contains a certain keyword (e.g. Smith). This method does not require manual assignment of entries but uses information that is already present in the database.

• Free search expression. Similar to Searching for a keyword, but for several keywords in several fields.

• Specified keywords. This feature will gather all words found in a specific field of your choice, and create a group for each word.

  • Authors' last names. Groups can be generated for each author's last name.

• Cited entries. The group contains the entries cited in a LaTeX document, based on its .aux file.

Explicit selection

Groups based on explicit selection are populated only by manual assignment of entries.

After creating an explicit-selection group, you select the entries to be assigned to it and use either drag-and-drop or the context menu Add selected entries to this group of the group interface.

To remove entries from an explicit-selection group, select them and use the context menu Remove selected entries from this group of the group interface.

Searching for a keyword in a field

This method groups entries in which a specified field (e.g. author) contains a specified keyword (e.g. Smith). The mentioned example will group all entries referring to the author Smith.

The search can be case-sensitive or not (checkbox 'Case sensitive'). The search can either be done as a plain-text or a regular-expression search (checkbox 'Regular expression').

Obviously, this will work only for entries including the specified grouping field, and the quality of the grouping will depend on the content accuracy.

The content of the group is updated dynamically whenever the database changes: JabRef allows to manually assign/remove entries to/from the group by simply appending/removing the search term to/from the content of the grouping field. For example, if you add the keyword A to an entry, this entry will be added to the dedicated group automatically. This makes sense only for the keywords field or for self-defined fields, but obviously not for fields like author or year.

Using a free-form search expression

This is similar to the above, but rather than search for a single search term on a single field, a search expression syntax can be used. It supports logical operators (AND, OR, NOT) and allows searching multiple fields.

For example, the search expression keywords=regression and not keywords=linear groups entries concerned with non-linear regression.

The content of the group is updated dynamically whenever the database changes.

Specified keywords

With the group type "Specified keywords", you can quickly create a set of groups appropriate for your database. This feature will gather all words found in a specific field of your choice, and create a group for each word. This is useful for instance if your database contains suitable keywords for all entries. By auto-generating groups based on the keywords field, you should have a basic set of groups at no cost. If you have an entry with "keywords = {A, B}", then this group type creates subgroups "A" and "B" both containing the entry.

You can also specify characters to ignore, for instance, commas used between keywords. These will be treated as separators between words, and not part of them. This step is important for combined keywords such as laplace distribution to be recognized as a single semantic unit. (You cannot use this option to remove complete words. Instead, delete the unwanted groups manually after they were created automatically.)

The content of the group is updated dynamically whenever the database changes.

Using the cited entries of a LaTeX document

The group contains the entries cited in a LaTeX document, based on its '.aux' file. The .aux file has to be specified.

The content of the group is updated dynamically whenever the .aux file changes.

Group color bars in the entry table

To see easily to which groups an entry belongs to, the entry table has a column dedicated to groups. For each entry, a set of color bars is displayed. The number of bars and their colors depend on the groups to which the entry belongs to.

By hovering the mouse on this column, you can see the list of groups to which an entry belongs to.

The "groups" column is displayed by default. Using the menu File → Preferences, tab Entry table, you can:

• remove the "groups" column by clicking on the bin icon next to the item "Groups".

• add the "groups" column by selecting the "Groups" item in the drop-down menu, and clicking on the + button located to the right of the drop-down menu.

Groups and searching

When viewing the contents of selected group(s), a search can be performed within these contents using the regular search facility.

Preferences about groups

General preferences for groups can be accessed using File → Preferences, tab Groups.

View

When selecting multiple groups, you can choose to:

• display only entries belonging to all selected groups (intersection)

• display all entries belonging to one or more of the selected groups (union). This is the default option.

Automatically assign new entry to selected grouping

The checkbox "Automatically assign new entry go selected grouping" makes it possible to automatically assign new entries to selected groups. If checked (default), upon selection of one or more groups, all the new entries created will be assigned to the selected groups. This works both for entries created from the menu button or entries pasted from the clipboard. If unchecked, new entries are not assigned to groups automatically.

Display count of items in group

If checked (default), the number of entries in each group is displayed in the group name, at the right of the group pane.

Keyword separator

The character separating two keywords can be set in this field. The default keyword separator is a comma (,).

Groups in the library file

Groups are saved as a @COMMENT block in the .bib-file and are shared among all users (future versions of JabRef might support user-dependent groups).

Main Window of JabRef

Upon the first start of JabRef the main user interface is showing up the main elements are:

• Menu bar

• Icon bar (shortcuts for most frequently used features)

• Side bar (for groups and web search)

Creation of a new library

A "library" is the main file that saves all the information about your collection of references. The storage format of the file is text-based in the BibTeX standard (by default).

To create a new library, just select the "New library" menu item in the "File" menu:

The main screen is now showing an empty "entry table" we will now start to fill with some entries.

Adding of a new entry manually

To add a new entry select the menu bar entry "Library" -> "New entry", click on the icon in the icon bar, or just hit CTRL-N.

This opens a dialog where you can select the type of reference you want to store. By default all entry types defined by the BibTeX format are available:

For our running example we will select "Article".

After clicking on the "Article" button, the dialog closes and the so called "Entry Editor" is opened for the newly created entry:

The most important information about the references to be added can now be entered in the "Required Fields" tab. "Author", "Title", "Journal", and "Year" should be self-explanatory - however, a "citationkey", might not be familiar to you. Basically, the idea of the "citationkey" is coming from working with BibTeX, where it is necessary to have an unique identifier for each entry. This allows for referencing within a document you might be creating using the stored information in your library. Moreover, also within JabRef this "key" is used for example for cross-references to other related entries or to determine file names for full-text references.

The key usually follows a global pattern and can be easily created automatically by clicking on the "generate" button next to the field.

After entering some information, you can see on the right side of the entry editor a preview of the bibliographic data:

There are further possibilities to add entries to your library which are described in the section "Collect" of this documentation:

Enhancing the information

After creating the basic information the addition of all other bibliographical details is often cumbersome and error-prone. To ease this task, JabRef allows for an automatic completion of the bibliographic information by looking up the data in public databases. To use this feature just click on the "Update with bibliographic information from the web" button in the editor:

If additional information is found you will be asked in a dialog which information should be taken over:

Adding a full text document

Usually, you also want to attach a reference to the full-text of a reference. For this, you can use the "file" field in the "General" tab. Here you can either attach a file manually, search for an already existing local file matching the citationkey pattern, or trying to automatically download a matching full text from the web.

To test the automatic download of full texts you can click on the "Get full-text" icon next to the file field, or choose "Lookup" -> "Search full text documents online" from the menu. As soon as a full-text is found, the file will be stored in the local file directory and linked to the entry:

Finding more references in the web

If you want to search for other references, it is also possible to directly trigger a search in many of the most common bibliographic databases. To start a search just use the "Web Search" feature of JabRef: First select one of the existing data sources, enter a search term and click on "search":

The search results will be shown in an window where you can select all the search hits to be added to your library.

Next steps

After adding more and more entries, your library might be a bit too unstructured. In order to keep all you references organized JabRef is offering a lot of helpful features like grouping, consistency checks, etc.

You can find more information on this topics in the "Organize" section of the documentation:

If you want to start writing your own papers, articles or thesis, you might find some helpful information on how to use JabRef for citing your collected references from your library:

JabRef can be either installed (the preferred way) or be used as a portable application.

Installation instructions

To get the latest version, head to downloads.jabref.org, download the installer for your system (e.g., dmg files for MacOS and msi files for Windows), run them and follow the on-screen instructions.

Alternatively, on Windows, you can use the chocolatey package manager and execute choco install jabref to get the latest version. On Ubuntu, you can use snap install jabref to get the latest stable version from snapcraft.

Portable version

The portable version of JabRef is designed to be run from a USB stick (or similar) with no installation.

Download it from downloads.jabref.org. These are generic archive files (e.g., tar.gz files for Linux and MacOS, and zip files for Windows) which need to be extracted. Inside the archive files you will find the file needed to run JabRef:

• for Windows JabRef.exe.

• for Linux

  • either runbin/JabRef

  • or /lib/runtime/bin/JabRef.

• for Mac, this is the file JabRef.app.

Be sure to activate "Load and Save preferences from/to jabref.xml on start-up (memory stick mode)" in Options → Preferences → General. Also, if the Linux version of JabRef portable is put into a folder named bin, it will not start. Other names are fine, like apps.

Development version

If you want to take advantage of the latest features, you can use pre-built binaries crafted from the latest development branch. To use the prebuilt binaries, visit builds.jabref.org/main and download the packaged binaries (e.g., dmg files for MacOS and exe files for Windows), run them and follow the instructions.

If you want to try the development version in parallel with the stable version, we recommend to download the portable version (e.g. JabRef-X.Y.portable_windows.zip, JabRef-X.Y.portable_macos.tar.gz, or JabRef-X.Y.portable_linux.tar.gz) from builds.jabref.org/main to ensure that both versions do not conflict.

Troubleshooting

Building From Source

This method is mainly for package maintainers and users who would like to build the latest snapshots of JabRef directly from the source. If you want to setup JabRef for development, follow the instructions for setting up a workspace.

To build JabRef from source, you first need to have a working Java Development Kit (see above link for details) and Git installed on your system. After installing the two requirements, you open a terminal window (i.e., a command prompt) and type the following:

git clone --recurse-submodules --depth=10 https://github.com/JabRef/jabref
cd jabref
./gradlew assemble
./gradlew jlink

In a nutshell, you clone the latest snapshot of JabRef into jabref directory, change directory to jabref, initialize and update all the submodules (dependencies) of JabRef, assemble them to be built via JDK and finally build and link them together.

The output should be the build/image subdirectory that contains the JabRef binary with all of its Java dependencies. To start JabRef, you need to run bin/JabRef (in Linux and MacOS) or bin/JabRef.bat (in Windows) under build/image subdirectory.

Purpose

When you import new entries from a supported reference format or fetch entries directly from the Internet, the inspection window allows you to select the entries you want to keep, to avoid adding duplicated entries, and to perform some simple operations like generating citation keys for the entries or adding them to groups. If you are importing into an existing database, it is often easier to perform these operations before they are mixed in between the entries of your database.

The inspection window

Entries are first shown in the inspection window. Note that, if this takes too long (for example), you can click on the button Stop at the bottom of the window.

Once the entries displayed in the inspection window, none of them have been added to one of your databases yet.

By default, all the entries are selected for importation, as shown by the checked boxes in the Keep column. You can select/unselect an entry by clicking on these checkboxes. On the left panel, buttons allow you to Select all the entries for importation, or to Deselect all the entries.

A left-click on an entry (out of the check box and icons) let you choose it. It displays a preview of the entry below the entry table. As usual, you can choose several entries by using the Shift or the Ctrl keys. Then, pushing the button Delete on the left panel will remove the chosen entries from the table.

A right-click on an entry displays a drop-down menu which allows you to:

• delete the entry

• add the entry to a group

• link a local file to the entry

• download the file corresponding to the entry

• automatically set file links to the entry

• attach an URL to the entry

Duplicated entries

Potential duplicates are pointed out by an icon in the second column. A click on this icon allows you to check the similarities. A button on the left panel allows you to Deselect all duplicates (without inspection).

Citation key generation

On the left panel, if the box Generate keys is checked, keys will be automatically generated on import. You can also choose to generate the keys now by clicking on the button Generate now.

Import into the database

Once you are done with the entry selection, you can add these entries to your database by clicking on OK at the bottom of the window. Alternatively, you can Cancel the import.

One can add free text to an entry. This is possible in the "Comments" tab of JabRef.

There is the general "comments" field.

JabRef offers to separate comments from as well as user-specific comments field.

The following screenshots show the comments for the user koppor. As default, general comments are managed through the field comment. In addition, the field comment-koppor stores the comments of the user koppor.

Now, lets assume, the library (.bib File) is shared among different users. koppor closed the library and opened it later again. He sees that a user otheruser has written a comment:

Now, koppor desides, that he does not want to add any comments in JabRef, so he pushes the "Hide user comments" button. Then, JabRef does not display the comment field for koppor's user any more:

A bit later, koppor thinks, he wants to put comments again. To achieve that, he needs to navigate to File -> Preferences -> Entry editor. Then, he needs to add a checkmark to "Show user comment fields". then, he needs to press "Save" to save the preferences.

Then, JabRef's entry editor shows the field "Comment-koppor" again.

A set of 6 special fields allows you to tag your entries in order to rate read papers, indicate their relevance to your work, indicate that their quality has been assured, etc. Internally, each special field is stored in a separate BibTeX field.

This feature has to be activated in File → Preferences → Entry Table by checking the item Enable special fields.

The status of each special field can be displayed in the table of entries as dedicated columns.

Like any other field, the special field columns can be turned on and off individually in File → Preferences → Entry Table.

You can see the value of a special field by:

• clicking in the column.

• a right-click on an entry.

• the menu Edit.

Types of Fields

Relevance

An entry can be marked as relevant: a black-and-white star is displayed (in the first column of the image below).

Read status

The read status can be set to "No" (no symbol in the column), to "Skimmed" (an orange eye), or to "read" (a green eye).

Ranking

JabRef offers a rank from one to five yellow stars to rate your papers. By default, no rank is given.

Quality assured

An entry may be marked as quality assured (fourth column in the image below). For example, you can mark the entries for which a thorough check of the field contents has been done.

Priority

You can set the priority of an entry from low (red flag) to high (green flag). For example, you can use it to prioritize unread papers.

Printed

This field allows to state is the paper has been printed or not (sixth column in the image above).

Configuration of the storage mode in the library

How to find, sort, and clean entries

JabRef is designed to facilitate your workflow.

You can select a subset of entries using the . Within a library, you can organize your entries in a tree-like structure made of .

You can add information to an entry using the , but JabRef can also for you. And JabRef takes care of the (PDF, etc.)

Once your database starts to be large, some tidy-up may be needed. JabRef can , , , help you in .

Hence, your database is always clean and up-to-date.

The search bar is located in the icon bar.

To make the cursor jump to the search field, you can:

• Click in the search field.

• Press Ctrl + F.

Search history

To find the search history, you can right click in the search field. Only ten recent searches will be displayed in the sub-menu. You can find clear history button under your search history.

Search settings

At the right of the search text field, 2 buttons allow for selecting some settings:

• Regular expressions
• Case sensitivity

  • Whether or not the search query is case sensitive.

Simple search

In a normal search, the program searches your library for all occurrences of the words in your search string, once you entered it. Only entries containing all words will be considered matches. To search for sequences of words, enclose the sequences in double-quotes. For instance, the query progress "marine aquaculture" will match entries containing both the word "progress" and the phrase "marine aquaculture".

All entries that do not match are hidden, leaving for display the matching entries only.

To stop displaying the search results, just clear the search field, press Esc or click on the "Clear" (X) button.

Search using regular expressions

General syntax

Search within specific Fields

To search for entries whose author contains miller, enter: author = miller. The = sign is actually a shorthand for contains. Searching for an exact match is possible using matches or ==.

Search for terms containing spaces

If the search term contains spaces, enclose it in quotes. Do not use spaces in the field specification! E.g to search for entries with the title "image processing", type: title = "image processing"

Search using parentheses, and, or and not

To search for entries with the title or the keyword "image processing", type: title|keywords = "image processing". To search for entries without the title or the keyword "image processing", type: title|keywords != "image processing" It is also possible to chain search expressions. In general, you can use and, or, not, and parentheses as intuitively expected:

(author = miller or title|keywords = "image processing") and not author = brown and != author = blue

Regular Expression search and Field Types

The selection of field types to search (required, optional, all) is always overruled by the field specification in the search expression. If a field is not given, all fields are searched. For example, video and year == 1932 will search for entries with any field containing video and the field year being exactly 1932.

Pseudo fields

JabRef defines the following pseudo fields:

Advanced use of regular expressions

Regular expressions and casing

By default, regular expressions do not account for upper/lower casing. Hence, while the examples below are all in lower case, they match also upper- and mixed case strings.

If casing is important to your search, activate the case-sensitive button.

Searching for entries with an empty or missing field

• . means: any character

• + means: one or more times

author != .+ returns entries with empty or no author field.

• ^ means: the beginning of a line

• [a-zA-Z] means: a through z or A through Z, inclusive (range)

• $ means: the end of a line

• X{n} means: X, exactly n times

owner != ^[a-zA-Z]{3}$ returns empty and non-three-letter owners

Searching for a given word

• \b means: word boundary

• \B means: not a word boundary

keywords = \buv\b matches uv but not lluvia (it does match uv-b however)

author = \bblack\b matches black but neither blackwell nor blacker

author == black does not match john black, but author = \bblack\b does.

author = \bblack\B matches blackwell and blacker, but not black.

Searching with optional spelling

• ? means: none or one copy of the preceding character.

• {n,m} means: at least n, but not more than m copies of the preceding character.

• [ ] defines a character class

title =neighbou?r matches neighbour and neighbor, and also neighbours and neighbors, and neighbouring and neighboring, etc.

title = neighbou?rs?\b matches neighbour and neighbor, and also neighbours and neighbors, but neither neighbouring nor neighboring.

author = s[aá]nchez matches sanchez and sánchez.

abstract = model{1,2}ing matches modeling and modelling.

abstract = modell?ing also matches modeling and modelling.

year == 200[5-9]|201[0-1]​specifies the range of years 2005-2011 (200[5-9] specifies years 2005-2009;| means "or"; 201[0-1] specifies years 2010-2011).

author = (John|Doe)matches entries written by either John or Doe.

author = (John|Doe).+(John|Doe)matches entries written by both John or Doe.

Searching for strings with a special character (()[]{}\^-=$!|?*+.)

If a special character (i.e. ( ) [ ] { } \ ^ - = $ ! | ? * + . ) is included in your search string, it has to be escaped with a backslash, such as \} for }.

It means that to search for a string including a backslash, two consecutive backslashes (\\) have to be used: abstract = xori{\\c{c}}o matches xoriço.

Searching for strings with double quotation marks (")

The character " has a special meaning: it is used to group words into phrases for exact matches. So, if you search for a string that includes a double quotation, the double quotation character has to be replaced with the hexadecimal character 22 in ASCII table \x22.

Neither a simple backslash \", nor a double backslash \\" will work as an escape for ". Neither author = {\"o}quist with regular expression disabled, nor author = \{\\\"O\}quist with regular expression enabled, will find anything, even if the name {\"o}quist exists in the library.

Hence, to search for {\"o}quist as an author, you must input author = \{\\\x22o\}quist, with regular expressions enabled (Note: the \, {, _ and the } are escaped with a backslash; see above).

Greedy quantifiers

Reluctant quantifiers

Possessive quantifiers

The field "keywords"

Keywords can be added to your entries in a specific field. In the entry editor, the keywords field is displayed in the General tab. There, you can add new keywords to an entry by typing it in. If auto-completion is activated for the field keywords (File → Preferences → Entry editor), suggestions are given based on existing keywords.

By default, the keyword separator is a comma. It can be redefined in the preferences (File → Preferences → Groups).

Additionally, the values (relevance, priority, etc.) can be added to the keywords field automatically. This will allow you to group, sort, and search your library based on the special field values. See in File → Preferences → Entry table the item "Special fields" and select "Synchronize with keywords".

Management of keywords

Managing the keywords of specified entries

Select at least one entry and go to Edit → Manage keywords.

The keyword list is displayed in two modes:

• the keywords shared by ALL of the selected entries.

• the keywords appearing in ANY of the selected entries.

You can edit a keyword by double-clicking on it, or by clicking on the pencil icon. A keyword can be deleted by clicking on the minus icon.

List of often-used keywords

To fasten the addition of often-used keywords, JabRef can store the list of your preferred keywords.

Go to File → Manage content selectors.

Searching for entries based on keywords

Grouping entries based on keywords

JabRef is is a program for working with BibTeX and biblatex libraries. JabRef program uses no separate internal file format but directly works with BibTeX and biblatex. That means, your BibTeX/biblatex file is kept as is when opening in JabRef and saving again: You normally load and save your libraries directly in the BibTeX/biblatex.bib format. In addition, you can also import and export bibliography libraries in a number of other formats into JabRef.

The library mode can be changed in the library properties.

More information on BibTeX is available on our information page on BibTeX fields.

JabRef lets you link up your entries with files of any type stored on your system. Thereby, it uses the field file, which contains a list of linked files. Each entry can have an arbitrary number of file links, and each linked file can be opened quickly from JabRef. The fields url and doi are used as links to documents on the web in the form of a URL or a DOI identifier, respectively (see URL and DOI in JabRef).

In BibTeX/biblatex terms, the file links are stored as text in the field file. From within JabRef, however, they appear as an editable list of links accessed from the entry editor along with other fields.

Adding external links to an entry

If the "file" field is included in General fields, you can edit the list of external links for an entry in the Entry editor. The editor includes buttons for inserting, editing and removing links, as well as buttons for reordering the list of links.

Directories for files

JabRef offers the following directory settings:

1. File → Preferences → Linked files, item Main file directory.

One of these settings is required. Mostly the "Main file directory" is enough.

JabRef uses these 3 directories to search for the files: JabRef starts in the user-specific file directory, then the general file directory, and, finally, the main file directory​

JabRef enables setting a directory per database. When sharing a library across multiple persons, each user might have a different directory. Either, each user can set his directory in the "Main file directory". In case the group also shares papers and thus there are two directories (the private one and a group-shared one), one can set a directory within the library (the "General file directory"). In case a user has a different location of the shared folder (e.g., different paths on Linux and Windows), he can use the "User-specific file directory". This setting is persisted in the bib file in a way that it does not overwrite the setting of another user. For this, JabRef uses the username of the currently logged-in user (-<loginname> is used as a suffix in the jabref-meta field). So, both mary and aileen can set a different user-specific file directory.

If JabRef saves an attached file and my login name matches the name stored in the bib file, it chooses that directory. If no match is found, it uses the "General file directory" of the bib file. If that is not found, it uses the one configured at File → Preferences → Linked files.

In some settings, the bib file is stored in the same directory as the PDF files. Then, one ignores all the above directories and enable "Search and store files relative to library file location". In this case, JabRef starts searching for PDF files in the directory of the bib file. It is also possible to achieve this result by setting . as "General file directory" in the library properties.

Relative file directories obviously only work in the library properties for a bib file, e.g. a.bib Library → Library properties → General file directory → papers. Assume to have two bib files: a.bib and b.bib located in different directories: a.bib located at C:\a.bib and b.bib located at X:\b.bib. When I click on the + icon in the general Tab of file a.bib, the popup is opened in the directory C:\papers (assuming C:\papers exists).

Auto-linking files

If you have a file within or below one of your file directories with an extension matching one of the defined external file types, and a name starting with (or matching) an entry's citation key, the file can be auto-linked. JabRef will detect the file and display a "link-add" icon in the entry editor, at the left of the filename. Click on the "link-add" icon to link this file to the entry.

The rules for which file names can be auto-linked to a citation key can be set up in File → Preferences → Linked files, section Autolink files.

Filename format and file directory pattern

Files can be automatically renamed and organized in folders according to custom patterns. The pattern syntax follows the same as for the Customize the citation key generator. JabRef can rename files according to this pattern, either automatically or as part of a cleanup operation.

With file directory pattern, JabRef can automatically create subfolders and move the files into the directory based on the defined pattern. As an example, you have a single folder, e.g. papers for all your PDFs linked to their corresponding entry in JabRef. Now you want to arrange them according to defined groups. Let's say you have two groups, Automation and Biology, with a couple of entries. Now set the file directory pattern to: [groups:(unknown)]

If you now execute the cleanup action "Move files", JabRef will automatically move the files of the corresponding in the file directory to the subfolders papers/Automation and papers/Biology respectively.

Explanation: The expression in the brackets says: Create a subdirectory based on the field “groups” of the entry. If the field groups is not set or empty, use “unknown” as a fallback name for the directory. If you have one entry assigned to multiple groups, the directory will have the name “groupA, groupB”.

For an entry, if you want to download a file and link it to the entry, you can do this by clicking the Download button in the entry editor.

A dialog box will appear, prompting you to enter the URL. The file will be downloaded to your main file directory, named based on the entry's citation key, and finally linked from the entry.

Using Regular Expression Search for Auto-Linking

It is possible to have greater flexibility in the naming scheme by using regular expressions for the search. In most cases, it should not be necessary though to adapt the given default.

If you open the preferences (File → Preferences → Linked Files), you will find in the section Autolink files an option called "Use regular expression search". Checking this option will allow you to enter your own regular expression for search in the PDF directories.

The following syntax is understood:

• * - Search in all immediate subdirectories, excluding the current and any deeper subdirectories.

• ** - Search in all subdirectories recursively AND the current directory.

• . and .. - The current directory and the parent directory.

• [title] - All expressions in square brackets are replaced by their corresponding citation key pattern.

• [extension] - Is replaced by the file-extension of the field you are using.

• All other text is interpreted as a regular expression. But caution: You need to escape backslashes by putting two backslashes after each other to not confuse them with the path-separator.

The default for searches is **/.*[citationkey].*\\.[extension]. As you can see, this will search in all subdirectories of the extension-based directory (for instance in the PDF directory) for any file that has the correct extension and contains the citation key somewhere.

Opening external files

There are several ways to open an external file or web page. In the entry table, you can click on the PDF icon to open the PDF. In case there are multiple PDFs linked, always the first one is opened. You can also right-click on the line of the entry in the entry table and select "Open file". There is also a keyboard shortcut for this: In the default setting, this is F4, but it can also be customized.

To access any of an entry's links, click on the icon with the right mouse button (or Ctrl + Click on Mac OS X) to bring up a menu showing all links.

Setting up external file types

In general, there is no need to change the settings of external file types. So, this setting is for advanced users. See Manage external file types.

After selecting a set of entries, go to Edit → Manage field names and content, to set, append, rename and clear a field.

This dialog window is displayed:

Set the field name (by typing it in or using the drop-down menu), and select the action to be carried out. Additionally, a checkbox allows overwriting the existing field values.

The actions are:

• Set fields. Enter the field content to be used. For example, "Field name = owner" and "Set fields = Smith" adds the line "owner = {Smith}," to the entries. If the field "owner" is already present in an entry, it is not modified, except if "Overwrite existing field values" is checked.

• Append to fields. Enter the string to be appended at the end of the field content (if the field does not exist, it will be created). For example, "Field name = keywords" and "Add to fields = , programming" adds the keyword "programming" to the list of keywords.

• Rename field to. Enter the new name for this field. For example, "Field name = institution" and "Rename fields = school" renames the field "institution" into "school". The field content is not altered.​

• Clear fields. This removes the field from the entries. For example, set the "Field name" to "comments". If "Overwrite existing field values" is checked, all the fields "comments" (and their content) are removed. If it is not checked, only the empty fields "comments" are removed.

JabRef can look for duplicated entries inside a library.

This feature is accessible directly through Quality → Find duplicates. It is also used when importing new entries from a supported reference format or directly from the Internet.

Detection of potential duplicates is done by an edit distance algorithm. Extra weighting is put on the fields author, editor, title. and journal.

The differences between the two entries can be configured through the toolbox located at the top of the window. From the toolbox, you can choose to show or hide differences, choose how to display differences (Unified or Split) and you can also choose how to compare entries (by words or characters).

Show or Hide Differences

• Plain Text — This option hides the differences.

• Show Differences — This option shows the differences.

Choose Differences Display Mode

• Unified View — In this mode, differences are shown on the right side.

• Split View — In this mode, differences are shown on both sides, with deletions on the left side and additions and updates on the right side.

Choose Entries Comparison Method

• Highlight words — This option compares entries values in terms of words.

• Highlight characters — This option compares entries values in terms of characters. It divides both entry values into characters before comparing each character individually. This is perfect for comparing values with small differences (1 or 2 different characters).

From the toolbox's top-left corner, you also can choose to select all the left entry values by clicking Left or selecting all the right entry values by clicking Right. Be aware that selecting all entry values will select a value even when it is empty.

Selecting which entry to keep

You are offered to:

• Automatically remove exact duplicates. This button shows up if there are exact duplicates. Click it to stop showing other exact duplicates and have them removed automatically.

• Keep left — Keeps the left entry and removes the right entry.

• Keep right — Keeps the right entry and removes the left entry.

• Keep both — Keeps both entries. This usually means that you don't consider the entries to be duplicates.

• Keep merged — Keeps the merged entry only and removes the previous entries.

• Cancel — Closes the dialog and stops showing other duplicates.

JabRef can check the integrity of a library.

This feature is available through Quality → Check integrity.

JabRef can cleanup the entries of a library. To do a cleanup of the entries, go to Quality → Cleanup entries. Then select the actions to be carried out.

under the tableEnable field formatters. Then, under the table, you can select using 2 drop-down menus:

• an entry field (upon which the action will be applied).

• the type of action to be carried out (such as HTML to LaTeX, which converts HTML code to LaTeX code, as described in the window).​ See the list of formatting actions.

A click on the "circular arrow" icon enables a set of recommended formatting actions (the set of actions will depend on your database type: BibTeX or biblatex).

See also

Helpful groups

• Group for your own papers: author=YOURSELF

• Group for the papers of your team: author=YOURSELF and author=COLLEAGUE1 and author=COLLEAGUE2

Sort order

Library → Library properties.

Use integrity check often

Use Quality → Check integrity often to ensure that the quality of your library does not degrade.

Enable save actions

To ensure that your library stays consistent, specify your save actions in Library → Library properties.

JabRef can help you to merge entries of your library.

First, select the two entries to be merged. Then select the menu Quality → Merge entries. Alternatively, select the right-click menu Merge entries.

The Merge entries window will pop up:

Diff Highlighting

The differences between the two entries can be configured through the toolbox located at the top of the window. From the toolbox, you can choose to show or hide differences, choose how to display differences (Unified or Split) and you can also choose how to compare entries (by words or characters).

Show or Hide Differences

• Plain Text — This option hides the differences.

• Show Differences — This option shows the differences.

Choose Differences Display Mode

• Unified View — In this mode, differences are shown on the right side.

• Split View — In this mode, differences are shown on both sides, with deletions on the left side and additions and updates on the right side.

Choose Entries Comparison Method

• Highlight words — This option compares entries values in terms of words.

• Highlight characters — This option compares entries values in terms of characters. It divides both entry values into characters before comparing each character individually. This is perfect for comparing values with small differences (1 or 2 different characters).

From the toolbox's top-left corner, you also can choose to select all the left entry values by clicking Left or selecting all the right entry values by clicking Right. Be aware that selecting all entry values will select a value even when it is empty.

Select Both Field Values (AKA Merge Fields)

When merging entries, sometimes you want to select both values for a certain field. A common use case for this would be wanting the merged entry to have both the left and right entry groups. Now, you can simply click the merge button next to the groups label and we’ll take care of the rest. We’ll merge the left and right entry groups, keeping only one copy of any common group. And this works for more than just groups - you can also merge keywords, comments and files. So go ahead and give it a try - it’ll make your life a lot easier.

Open DOIs and URLs from The Merge Dialog

There are two buttons at the end of each field cell: one for copying the content of the field cell, and the other for opening links; at the moment, only URLs and DOIs can be opened.

Select or Edit Merged Entry Manually

For each field, you can select whether to choose the left entry value or the right one. You can do that by clicking on the given field cell. Once you did that, the merged entry will update its content to reflect the new change.

You can also edit the merged entry values manually. Doing so, will update the selected field cell if the left or right cell equals that value you typed.

Finally, after selecting which fields to keep, you can decide to Merge entries. Alternatively, you can press Cancel.

See also: Find duplicates

JabRef allows you to push any entries in your main window to an external editor through the push-to-external application feature. It works with Emacs, LyX/Kile, Texmaker, TeXstudio, Vim, and WInEdt.

To push as citation, first select the entries in your entry table that you would like to push. Then, either:

• go to Tools → Push entry to external application​

• Press CTRL + L

• Click on the dedicated button in the taskbar (left of the Generate citation key button)

By default the external editor used to push citations is TeXstudio. You can select another application in Options → Preferences → External programs. Under the Push applications section, click on the Application to push entries to field. This will cause a dropdown menu to appear, from which you are then able to select from a list of all the external editors you have configured.

You can configure the citation command at "Cite command". JabRef intelligently parses the value you gave here. In the example, the congiration \cite{key1,key2} means, that the cite command is \cite, the keys are enclosed by {...} and that multiple keys are separted by a comma (,). With that, you can even support Pandoc's Markdown citation syntax. Configure it with [@key1,@key2].

Once you have made your selection and click Save, the push-to-external application button icon will change to match that of the selected external editor application.

When you click on the push-to-external application button, JabRef will export your selected entries to an open LaTeX file in the selected external editor application. As an example, here is what happens when you export one entry to TexStudio.

As long as you continue using the same external editor application, clicking on the push-to-external application button for subsequent exports will just add new citations or extend an existing citation with additional entries. Following the example above, here is what happens when you export a second entry to TeXStudio on an existing citation, which is extended to include the new entry in your LaTeX document.

Hints on Emacs

There are the tools emacsclient and gnuclient. Both support GNU Emacs. Additionally, gnuclient supports XEmacs. As default configuration, JabRef uses emacsclient. JabRef passes -e as parameter, because JabRef adds the emacs command after the given parameters. For a discussion on the use of emacsclient, see a stackoferflow answer. The parameter -n (for --no-wait) is also passed, but that is not necessary.

On Windows, you can install emacs using choco install emacs. Then, start emacs. Afterwards, start the emacs daemon with following command:

C:\tools\emacs\bin\emacs.exe --daemon

If that does not work, hints are provided at https://emacs.stackexchange.com/q/35545/12933.

You can import your citations into a Microsoft Word document through JabRef's export feature. Please follow the steps below for instructions on how to export your JabRef sources into a Microsoft Word document.

1. Select the "File" tab in the upper lefthand corner of JabRef, hover over "Export", and select "Export selected entries". Be sure to save your file as a "MS Office 2007" file.

2. Open Microsoft Word and click on the "References" tab.

3. Select "Manage Sources", click "Browse", and locate the desired file. The file type should be an XML document.

   Mac OS users will not see a "Manage Sources" button. Mac users should follow these steps:

   a.) Copy the selected file to /Library/Containers/com.microsoft.word/Data/Library/Application Support/Microsoft/Office or alternatively to /Users/{username}/Library/Containers/com.microsoft.Word/Data/Library/Application Support/Microsoft/Office/ and name it Sources.xml

   b.) Restart Word

   c.) Select "References", and then select "Citations"

   d.) A sidebar will open on the right side of the window. Click the icon with three dots.

   e.) Click “Citation Sources Manager” from the drop down bar.

   f.) Copy over your citations from the masters list.

4. Click on "Bibliography" under the "References" tab to add your cited sources.

More discussion at https://tex.stackexchange.com/a/351452/9075. See https://www.youtube.com/watch?v=2PpLZTol9_o

For a detailed list of the fields which are exported in the Office 2007 XML format see the following page.

Usage

To use this feature you have to connect to a remote database. To do so you have to open File in the menu bar and then click the Connect to shared database item. The Connect to shared database dialog will open and you will have to fill in the shared's database connection settings. Under the field Database type you can choose between PostgreSQL (at least version 9.1), MySQL (at least 5.5, not recommended, because there is no live synchronization), and Oracle depending on your shared database. Then, you have to fill out the remaining fields with the according information. If you like you can save your password by clicking the Remember password? checkbox.

SSL configuration

Since version 5.0 JabRef supports secure SSL connection to the database. For PostgreSQL make sure the server supports SSL and you have correctly setup the . Then into a java readable format and import them into a (custom) keystore. For MySQL the procedure is similar. and for the java keystore. However, it has only been tested with PostgreSQL. Once the certificates are imported into the keystore, specify the path to the keystore file in the connection dialog and the password for accessing the keystore.

After connecting to your shared database, your main window should look like this:

JabRef will automatically detect your changes and push them to the shared side. JabRef will also constantly check if there is a newer version available. If you experience connection issues, you can pull changes from your shared database via the icon in the icon bar. If a newer version is available, JabRef will try to automatically merge the new version and your local copy. If this fails, the Update refused dialog will show up. You will then have to manually merge using the Update refused dialog. The dialog helps you by pointing out the differences, you then will have to choose if you want to keep your local version or update to the shared version. Confirm your merge by clicking on Merge entries.

The Update refused dialog can also take a different form, if the BibEntry you currently work on has been deleted on the shared side. You can choose to keep the BibEntry in the database by clicking Keep or update to the shared side and click Close.

If you experience a problem with your connection to your shared database, the Connection lost dialog will show up. You can choose to Reconnect, Work offline or Close database. Most of the time simply reconnecting will fix this problem, if that's not the case you will have to choose between Work offline or Close database. Pick Work offline if you want to make sure your changes are saved. If you think there is nothing to save just pick Close database. If you choose to work offline, JabRef will convert the shared database to a local .bib database. Since you are no longer working online, but instead on a local database, you will have to import your work via copy and paste into the shared database. However before you import it into the shared database, make sure to check if changes happened during your offline time. Otherwise you might override someone else's work.

Try it out

Context

This situation occurs when you try to open an SQL database which was created with JabRef version older than 3.6.

With release of the SQL database structure has changed. So all SQL databases with an pre-3.6 structure are no longer supported.

Migration

To migrate your pre-3.6 SQL database into new shared SQL database you have to follow these steps:

• Open JabRef and goto File -> Import from external SQL database

• Enter required data and click on Connect

• Choose the database which should be imported and press Import

• Save the database locally (File -> Save database)

• Goto: File -> Open shared database

• Enter required data and click on Connect

• Now goto File -> Import into current database

• Choose the file you saved locally and import it

JabRef allows you to send entries to third parties via email.

How to send as e-mail

1. Select one or multiple entries

2. Choose Tools → Send as email in the menu

This will open your default email application and automatically paste the entries in their raw BibTeX format. Once your correspondents have received the email, they will be able to directly copy and paste the entries into JabRef (or use them in other ways).

How to attach linked files of entries to your email

Once Send as email is pressed, JabRef will also automatically open the folder of attached files, as long as the option automatically open folders of attached files is enabled at File → Preferences → External programs → Sending of emails. Attaching these files to your email is possible by dragging and dropping the PDF files into your favorite email application.

JabRef allows you to define and use your own export filters, in the same way as the standard export filters are defined. An export filter is defined by one or more layout files, which with the help of a collection of built-in formatter routines specify the format of the exported files. Your layout files must be prepared in a text editor outside of JabRef.

The custom export format of JabRef is an alternative to the Citation Style Language, which is an XML-based format to describe bibliographic rendering.

Existing public files are collected at https://layouts.jabref.org.

Adding a custom export filter

The only requirement for a valid export filter is the existence of a file with the extension .layout. To add a new custom export filter, open the dialog box File → Preferences, go to the section Custom export formats, and click on Add. A new dialog box will appear, allowing you to specify a name for the export filter (which will appear as one of the choices in the File type dropdown menu of the file dialog when you use the File → Export menu choice in the JabRef window), the path to the .layout file, and the preferred file extension for the export filter (which will be the suggested extension in the file dialog when you use the export filter). Note that if you intend to use the custom export filter also for "Copy...->Export to Clipboard" in the maintable, the extension must be one of the following: txt, rtf, rdf, xml, html, htm, csv, or ris.

Creating the export filter

To see examples of how export filters are made, look for the package containing the layout files for the standard export filters on our download page.

Regarding tool support, there is the Export-Filter Editor for Jabref to quickly create export filters.

Layout files

Let us assume that we are creating an HTML export filter. While the export filter only needs to consist of a single .layout file, which in this case could be called html.layout, you may also want to add two files called html.begin.layout and html.end.layout. The former contains the header part of the output, and the latter the footer part. JabRef will look for these two files whenever the export filter is used, and if found, either of these will be copied verbatim to the output before or after the individual entries are written.

Note that these files must reside in the same directory as html.layout, and must be named by inserting .begin and .end, respectively. In our example export filter, these could look like the following:

html.begin.layout: <!DOCTYPE html><html> <body style="color:#275856; font-family: Arial, sans-serif;">

html.end.layout: </body></html>

The file html.layout provides the default template for exporting one single entry. If you want to use different templates for different entry types, you can do this by adding entry-specific .layout files. These must also reside in the same directory as the main layout file, and are named by inserting .entrytype into the name of the main layout file. The entry type name must be in all lowercase. In our example, we might want to add a template for book entries, and this would go into the file html.book.layout. For a PhD thesis we would add the file html.phdthesis.layout, and so on. These files are similar to the default layout file, except that they will only be used for entries of the matching type. Note that the default file can easily be made general enough to cover most entry types in most export filters.

The layout file format

Layout files are created using a simple markup format where commands are identified by a preceding backslash. All text not identified as part of a command will be copied verbatim to the output file.

Field commands

An arbitrary word preceded by a backslash, e.g. \author, \editor, \title or \year, will be interpreted as a reference to the corresponding field, which will be copied directly to the output.

Field formatters

Often there will be a need for some preprocessing of the field contents before output. This is done using a field formatter - a java class containing a single method that manipulates the contents of a field.

A formatter is used by inserting the \format command followed by the formatter name in square braces, and the field command in curly braces, e.g.:

\format[ToLowerCase]{\author}

You can also specify multiple formatters separated by commas. These will be called sequentially, from left to right, e.g.

\format[ToLowerCase,HTMLChars]{\author}

will cause the formatter ToLowerCase to be called first, and then HTMLChars will be called to format the result. You can list an arbitrary number of formatters in this way.

The argument to the formatters, withing the curly braces, does not have to be a field command. Instead, you can insert normal text, which will then be passed to the formatters instead of the contents of any field. This can be useful for some fomatters, e.g. the CurrentDate formatter (described below).

Some formatters take an extra argument, given in parentheses immediately after the formatter name. The argument can be enclosed in quotes, which is necessary if it includes the parenthesis characters. For instance, \format[Replace("\s,_")]{\journal} calls the Replace formatter with the argument \s,_ (which results in the "journal" field after replacing all whitespace by underscores).

See below for a list of built-in export formatters.

Conditional output

Some static output might only make sense if a specific field is set. For instance, say we want to follow the editor names with the text (Ed.). This can be done with the following text:

\format[HTMLChars,AuthorFirstFirst]{\editor} (Ed.)

However, if the editor field has not been set - it might not even make sense for the entry being exported - the (Ed.) would be left hanging. This can be prevented by instead using the \begin and \end commands:

\begin{editor} \format[HTMLChars,AuthorFirstFirst]{\editor} (Ed.) \end{editor}

The \begin and \end commands make sure the text in between is printed if and only if the field referred in the curly braces is defined for the entry being exported.

A conditional block can also be dependent on more than one field, and the content is only printed when simple boolean conditions are satisfied. Three boolean operators are provided:

• AND operator : &, &&

• OR operator : |, ||

• NOT operator : !

For example, to output text only if both year and month are set, use a block like the following: \begin{year&&month}Month: \format[HTMLChars]{\month}\end{year&&month} which will print "Month: " plus the contents of the month field, but only if also the year field is defined.

As an example for the usage of the NOT operator, consider the following: \begin{!year}\format[HTMLChars]{(no year)}\end{!year} Here, "no year" is printed as output text if no year field is defined.

Note: Use of the \begin and \end commands is a key to creating layout files that work well with a variety of entry types.

Grouped output

If you wish to separate your entries into groups based on a certain field, use the grouped output commands. Grouped output is very similar to conditional output, except that the text in between is printed only if the field referred in the curly braces has changed value.

For example, let's assume I wish to group by keyword. Before exporting the file, make sure you have sorted your entries based on keyword. Now use the following commands to group by keyword:

\begingroup{keywords}New Category: \format[HTMLChars]{\keywords} \endgroup{keywords}

Built-in export formatters

JabRef provides the following set of formatters:

• Authors : this formatter provides formatting options for the author and editor fields; for detailed information, see below. It deprecates a range of dedicated formatters provided in versions of JabRef prior to 2.7.

• CreateBibORDFAuthors : formats authors for according to the requirements of the Bibliographic Ontology (bibo).

• CreateDocBookAuthors : formats the author field in DocBook style.

• CreateDocBookEditors : formats the editor field in DocBook style.

• CurrentDate : outputs the current date. With no argument, this formatter outputs the current date and time in the format "yyyy.MM.dd hh:mm:ss z" (date, time and time zone). By giving a different format string as argument, the date format can be customized. For example \format[CurrentDate]{yyyy.MM.dd} will give the date only, e.g. 2005.11.30.

• DateFormatter : formats a date. With no argument, the date is given in ISO-format (yyyy-MM-dd), which is also the expected format of the input. The argument may contain yyyy, MM, and dd in any combination. For example \format[DateFormatter(MM/yyyy)]{\date} will output 07/2016 if the date field contains 2016-07-15.

• Default : takes a single argument, which serves as a default value. If the string to format is non-empty, it is output without changes. If it is empty, the default value is output. For instance, \format[Default(unknown)]{\year} will output the entry's year if set, and "unknown" if no year is set.

• DOIStrip : strips any prefixes from the DOI string.

• DOICheck : provides the full url for a DOI link.

• EntryTypeFormatter : camel case of entry types, so "inbook" -> "InBook".

• FileLink(filetype) : if no argument is given, this formatter outputs the first external file link encoded in the field. To work, the formatter must be supplied with the contents of the "file" field.

  This formatter takes the name of an external file type as an optional argument, specified in parentheses after the formatter name. For instance, \format[FileLink(pdf)]{\file} specifies pdf as an argument. When an argument is given, the formatter selects the first file link of the specified type. In the example, the path to the first PDF link will be output.

• FirstPage : returns the first page from the "pages" field, if set. For instance, if the pages field is set to "345-360" or "345--360", this formatter will return "345".

• FormatChars : This formatter converts LaTeX character sequences their equicalent unicode characters and removes other LaTeX commands without handling them.

• FormatPagesForHTML : replaces "--" with "-".

• FormatPagesForXML : replaces "--" with an XML en-dash.

• GetOpenOfficeType : returns the number used by the OpenOffice.org bibliography system (versions 1.x and 2.x) to denote the type of this entry.

• HTMLChars : replaces TeX-specific special characters (e.g. {\"{a}} or {\sigma}) with their HTML representations, and translates LaTeX commands \emph, \textit, \textbf, \texttt, \underline, \textsuperscript, \textsubscript, \sout into HTML equivalents.

• HTMLParagraphs : interprets two consecutive newlines (e.g. \n \n) as the beginning of a new paragraph and creates paragraph-html-tags accordingly.

• IfPlural : outputs its first argument if the input field looks like an author list with two or more names, or its second argument otherwise. E.g. \format[IfPlural(Eds.,Ed.)]{\editor} will output "Eds." if there is more than one editor, and "Ed." if there is only one.

• JournalAbbreviator : The given input text is abbreviated according to the journal abbreviation lists. If no abbreviation for input is found (e.g. not in list or already abbreviated), the input will be returned unmodified. For instance, when using \format[JournalAbbreviator]{\journal}, "Physical Review Letters" gets "Phys. Rev. Lett."

• LastPage : returns the last page from the "pages" field, if set. For instance, if the pages field is set to "345-360" or "345--360", this formatter will return "360".

• NoSpaceBetweenAbbreviations : LayoutFormatter that removes the space between abbreviated First names. Example: J. R. R. Tolkien becomes J.R.R. Tolkien.

• NotFoundFormatter : Formatter used to signal that a formatter hasn't been found. This can be used for graceful degradation if a layout uses an undefined format.

• Number : outputs the 1-based sequence number of the current entry in the current export. This formatter can be used to make a numbered list of entries. The sequence number depends on the current entry's place in the current sort order, not on the number of calls to this formatter.

• Ordinal : replaces numbers with ordinals so 1 is replaced with 1st etc.

• RemoveBrackets : removes all curly brackets "{" or "}".

• RemoveBracketsAddComma : removes all curly brackets "{" or "}". The closing curly bracket is replaced by a comma.

• RemoveLatexCommands : removes LaTeX commands like \em, \textbf, etc. If used together with HTMLChars or XMLChars, this formatter should be called last.

• RemoveTilde : replaces the tilde character used in LaTeX as a non-breakable space by a regular space. Useful in combination with the NameFormatter discussed in the next section.

• RemoveWhitespace : removes all whitespace characters.

• Replace(regexp,replacewith) : does a regular expression replacement. To use this formatter, a two-part argument must be given. The parts are separated by a comma. To indicate the comma character, use an escape sequence: ,

  The first part is the regular expression to search for. Remember that any commma character must be preceded by a backslash, and consequently a literal backslash must be written as a pair of backslashes. A description of Java regular expressions can be found at vogella's repository.

  The second part is the text to replace all matches with.

• RisAuthors : to be documented.

• RisKeywords : to be documented.

• RisMonth : to be documented.

• RTFChars : replaces TeX-specific special characters (e.g. {^a} or {"{o}}) with their RTF representations, and translates LaTeX commands \emph, \textit, \textbf into RTF equivalents.

• ShortMonth : formats the month field to use 3 letter BibTeX strings (jan, feb, mar, apr, ...).

• ToLowerCase : turns all characters into lower case.

• ToUpperCase : turns all characters into upper case.

• WrapContent : This formatter outputs the input value after adding a prefix and a postfix, as long as the input value is non-empty. If the input value is empty, an empty string is output (the prefix and postfix are not output in this case). The formatter requires an argument containing the prefix and postix separated by a comma. To include the comma character in either, use an escape sequence (,).

• WrapFileLinks : See below.

• XMLChars : replaces TeX-specific special characters (e.g. {^a} or {"{o}}) with their XML representations.

The Authors formatter

To accommodate for the numerous citation styles, the Authors formatter allows flexible control over the layout of the author list. The formatter takes a comma-separated list of options, by which the default values can be overridden. The following option/value pairs are currently available, where the default values are given in curly brackets.

AuthorSort = [ {FirstFirst} | LastFirst | LastFirstFirstFirst ] specifies the order in which the author names are formatted.

• FirstFirst : first names are followed by the surname.

• LastFirst : the authors' surnames are followed by their first names, separated by a comma.

• LastFirstFirstFirst : the first author is formatted as LastFirst, the subsequent authors as FirstFirst.

AuthorAbbr = [ FullName | LastName | {Initials} | InitialsNoSpace | FirstInitial | MiddleInitial ] specifies how the author names are abbreviated.

• FullName : shows full author names; first names are not abbreviated.

• LastName : show only surnames, first names are removed.

• Initials : all first names are abbreviated.

• InitialsNospace : as Initials, with any spaces between initials removed.

• FirstInitial : only first initial is shown.

• MiddleInitial : first name is shown, but all middle names are abbreviated.

AuthorPunc = [ {FullPunc} | NoPunc | NoComma | NoPeriod ] specifies the punctuation used in the author list when AuthorAbbr is used

• FullPunc : no changes are made to punctuation.

• NoPunc : all full stops and commas are removed from the author name.

• NoComma : all commas are removed from the author name.

• NoPeriod : all full stops are removed from the author name.

AuthorSep = [ {Comma} | And | Colon | Semicolon | Sep=<string> ] specifies the separator to be used between authors. Any separator can be specified, with the Sep=<string> option. Note that appropriate spaces need to be added around string.

AuthorLastSep = [ Comma | {And} | Colon | Semicolon | Amp | Oxford | LastSep=<string> ] specifies the last separator in the author list. Any separator can be specified, with the LastSep=<string> option. Note that appropriate spaces need to be added around string.

AuthorNumber = [ {inf} | <integer> ] specifies the number of authors that are printed. If the number of authors exceeds the maximum specified, the authorlist is replaced by the first author (or any number specified by AuthorNumberEtAl), followed by EtAlString.

AuthorNumberEtAl = [ {1} | <integer> ] specifies the number of authors that are printed if the total number of authors exceeds AuthorNumber. This argument can only be given after AuthorNumber has already been given.

EtAlString = [ { et al.} | EtAl=<string> ] specifies the string used to replace multiple authors. Any string can be given, using EtAl=<string>

If an option is unspecified, the default value (shown in curly brackets above) is used. Therefore, only layout options that differ from the defaults need to be specified. The order in which the options are defined is (mostly) irrelevant. So, for example,

\format[Authors(Initials,Oxford)]{\author}

is equivalent to

\format[Authors(Oxford,Initials)]{\author}

As mentioned, the order in which the options are specified is irrelevant. There is one possibility for ambiguity, and that is if both AuthorSep and AuthorLastSep are given. In that case, the first applicable value encountered would be for AuthorSep, and the second for AuthorLastSep. It is good practise to specify both when changing the default, to avoid ambiguity.

Examples

Given the following authors, "Joe James Doe and Mary Jane and Bruce Bar and Arthur Kay" ,the Authors formatter will give the following results:

Authors(), or equivalently, Authors(FirstFirst,Initials,FullPunc,Comma,And,inf,EtAl= et al.) J. J. Doe, M. Jane, B. Bar and A. Kay

Authors(LastFirstFirstFirst,MiddleInitial,Semicolon) Doe, Joe J.; Mary Jane; Bruce Bar and Arthur Kay

Authors(LastFirst,InitialsNoSpace,NoPunc,Oxford) Doe JJ, Jane M, Bar B, and Kay A

Authors(2,EtAl= and others) J. J. Doe and others

Most commonly available citation formats should be possible with this formatter. For even more advanced options, consider using the Custom Formatters detailed below.

The WrapFileLinks formatter

This formatter iterates over all file links, or all file links of a specified type, outputting a format string given as the first argument. The format string can contain a number of escape sequences indicating file link information to be inserted into the string.

This formatter can take an optional second argument specifying the name of a file type. If specified, the iteration will only include those files with a file type matching the given name (case-insensitively). If specified as an empty argument, all file links will be included.

After the second argument, pairs of additional arguments can be added in order to specify regular expression replacements to be done upon the inserted link information before insertion into the output string. A non-paired argument will be ignored. In order to specify replacements without filtering on file types, use an empty second argument.

The escape sequences for embedding information are as follows:

• \i : This inserts the iteration index (starting from 1), and can be useful if the output list of files should be enumerated.

• \p : This inserts the file path of the file link.

• \f : This inserts the name of the file link's type.

• \x : This inserts the file's extension, if any.

• \d : This inserts the file link's description, if any.

For instance, an entry could contain a file link to the file "/home/john/report.pdf" of the "PDF" type with description "John's final report". Using the WrapFileLinks formatter with the following argument:

\format[WrapFileLinks(\i. \d (\p))]{\file}

would give the following output:

1. John's final report (/home/john/report.pdf)

If the entry contained a second file link to the file "/home/john/draft.txt" of the "Text file" type with description 'An early "draft"', the output would be as follows:

1. John's final report (/home/john/report.pdf)

2. An early "draft" (/home/john/draft.txt)

If the formatter was called with a second argument, the list would be filtered. For instance:

\format[WrapFileLinks(\i. \d (\p),,text file)]{\file}

would show only the text file:

1. An early "draft" (/home/john/draft.txt)

If we wanted this output to be part of an XML styled output, the quotes in the file description could cause problems. Adding two additional arguments to translate the quotes into XML characters solves this:

\format[WrapFileLinks(\i. \d (\p),,text file,",")]{\file}

would give the following output:

1. An early "draft" (/home/john/draft.txt)

Additional pairs of replacements could be added.

Custom formatters

If none of the available formatters can do what you want to achieve, you can add your own by implementing the net.sf.jabref.export.layout.LayoutFormatter interface. If you insert your class into the net.sf.jabref.export.layout.format package, you can call the formatter by its class name only, like with the standard formatters. Otherwise, you must call the formatter by its fully qualified name (including package name). In any case, the formatter must be in your classpath when running JabRef.

Using Custom Name Formatters

From JabRef 2.2, it is possible to define custom name formatters using the BibTeX-sty-file syntax. This allows ultimate flexibility, but is a cumbersome to write

You can define your own formatter in the preference tab "Name Formatter" using the following format and then use it with the name given to it as any other formatter

<case1>@<range11>@<format>@<range12>@<format>@<range13>...@@ <case2>@<range21>@... and so on.

This format first splits the task to format a list of author into cases depending on how many authors there are (this is since some formats differ depending on how many authors there are). Each individual case is separated by @@ and contains instructions on how to format each author in the case. These instructions are separated by a @.

Cases are identified using integers (1, 2, 3, etc.) or the character * (matches any number of authors) and will tell the formatter to apply the following instructions if there are a number of less or equal of authors given.

Ranges are either <integer>..<integer>, <integer> or the character * using a 1 based index for indexing authors from the given list of authors. Integer indexes can be negative to denote them to start from the end of the list where -1 is the last author.

For instance with an authorlist of "Joe Doe and Mary Jane and Bruce Bar and Arthur Kay":

• 1..3 will affect Joe, Mary and Bruce

• 4..4 will affect Arthur

• * will affect all of them

• 2..-1 will affect Mary, Bruce and Arthur

The <format>-strings use the BibTeX formatter format:

The four letters v, f, l, j indicate the name parts von, first, last, jr which are used within curly braces. A single letter v, f, l, j indicates that the name should be abbreviated. If one of these letters or letter pairs is encountered JabRef will output all the respective names (possibly abbreviated), but the whole expression in curly braces is only printed if the name part exists.

For instance if the format is "{ll} {vv {von Part}} {ff}" and the names are "Mary Kay and John von Neumann", then JabRef will output "Kay Mary" (with two space between last and first) and "Neuman von von Part John".

I give two examples but would rather point you to the BibTeX documentation.

Small example: "{ll}, {f.}" will turn "Joe Doe" into "Doe, J."

Large example:

To turn:

"Joe Doe and Mary Jane and Bruce Bar and Arthur Kay"

into

"Doe, J., Jane, M., Bar, B. and Kay, A."

you would use

1@*@{ll}, {f}.@@2@1@{ll}, {f}.@2@ and {ll}, {f}.@@*@1..-3@{ll}, {f}., @-2@{ll}, {f}.@-1@ and {ll}, {f}.

The order of the exported entries can be set in File → Preferences, tab File, under the menu "Export sort order".

See also:

You can add an arbitrary number of tabs to the entry editor. These will be present for all entry types. To customize these tabs, go to Options → Preferences → Custom editor tabs.

You specify one tab on each line. The line should start with the name of the tab, followed by a colon (:), and the fields it should contain, separated by semicolons (;).

For example:

will give one tab named "General" containing the fields url, keywords, doi and pdf, and another tab named "Abstract" containing the fields abstract and annote.

It does not matter how you capitalise your field names. In the entry editor's tabs, normally fields' first letter is capitalised, i.e. abstract is represented as Abstract, KEYwords would be represented as Keywords (DOI, ISBN, URL are exceptions in that all letters are capitalised). In the bibtex code, all field names use lower case: KEYwords is keywords in the entry's bibtex code.

Introduction

This feature offers an interface for inserting citations and formatting a Bibliography in an OpenOffice or LibreOffice Writer document from JabRef.

Throughout this help document, whenever the name OpenOffice is used, it can be interchanged with LibreOffice.

Using the OpenOffice/LibreOffice interface

To communicate with OpenOffice, JabRef must first connect to a running OpenOffice instance. You need to start OpenOffice and enter your document before connecting from JabRef.

JabRef needs to know the location of your OpenOffice executable (soffice.exe on Windows, and soffice on other platforms), and the directory where several OpenOffice jar files reside. If you connect by clicking the Connect button, JabRef will try to automatically determine these locations. If this does not work, you need to connect using the Manual connect button, which will open a window asking you for the needed locations.

After the connection has been established, you can insert citations by selecting one or more entries in JabRef and using the Push to OpenOffice button in the dropdown menu of JabRef's toolbar, or by using the appropriate button in the OpenOffice panel in the side pane. This will insert citations for the selected entries at the current cursor position in the OpenOffice document, and update the bibliography to contain the full reference.

Note: JabRef does not use OpenOffice's built-in bibliography system, because of the limitations of that system. A document containing citations inserted from JabRef will not generally be compatible with other reference managers such as Bibus and Zotero.

Two different types of citations can be inserted - either a citation in parenthesis, "(Author 2007)", or an in-text citation, "Author (2007)". This distinction is only meaningful if author-year citations are used instead of numbered citations, but the distinction will be preserved if you switch between the two styles.

If you modify entries in JabRef after inserting their citations into OpenOffice, you will need to synchronize the bibliography. By default, Automatically sync bibliography when inserting citations is enabled. This can be disabled by clicking the Settings button and unchecking Automatically sync bibliography when inserting citations. The Sync OO bibliography button will update all entries of the bibliography, provided their citation keys have not been altered (JabRef encodes the citation key into the reference name for each citation to keep track of which citation key the original JabRef entry has).

The style file

To customize the citation style you need to select a style file, or use one of the default styles. The style defines the format of citations and the format of the bibliography. You can use standard JabRef export formatters to process fields before they are sent to OpenOffice. Through the style file, the intention is to give as much flexibility in citation styles as possible. You can switch style files at any time, and use the Update button to refresh your bibliography to follow the new style.

By clicking the Select style button you can bring up a window that allows selection of either the default style or an external style file. If you want to create a new style based on the default, you can click the View button to bring up the default style contents, which can be copied into a text editor and modified.

To choose an external style file, you have two options. Either you can choose a style file directly, or you can set a style file directory. If you do the latter, you will see a list of styles from that directory (and subdirectories), and can choose one from that list.

To edit an already loaded custom style file or to reload changes that you made to a style file, click on Select style to bring up the style selection window, then right-click the currently loaded file to bring up a menu that allows you to choose either "Edit" or "Reload".

CAUTION: Please take care that your style file is saved using UTF-8 for character encoding. If you use another character encoding (even other unicode encodings such as UTF-16 or UTF-32), JabRef will not be able to process your style file.

Here is an example style file:

(Note that the layout for each entry type must be constrained to a single line in the style file - above, the lines are broken up to improve readability.)

Global properties

The PROPERTIES section describes global properties for the bibliography. The following table describes the available properties:

Citation properties

The CITATION section describes the format of the citation markers inserted into the text.

The following table gives a brief description of all the available citation properties. Properties that are not given in the style file will keep their default value.

If numbered entries are used, the BracketBefore and BracketAfter properties are the most important - they define which characters the citation number is wrapped in. The citation is composed as follows: [BracketBefore][Number][BracketAfter] where [Number] is the number of the citation, determined according to the ordering of the bibliography and/or the position of the citation in the text. If a citation refers to several entries, these will be separated by the string given in the property CitationSeparator (for instance, if CitationSeparator=;, the citation could look like [2;4;6]). If two or more of the entries have a series of consecutive numbers, the numbers can be grouped (for instance [2-4] for 2, 3 and 4 or [2;5-7] for 2, 5, 6 and 7). The property GroupedNumbersSeparator (default -) determines which string separates the first and last of the grouped numbers. The integer property MinimumGroupingCount (default 3) determines what number of consecutive numbers is required before entries are grouped. If MinimumGroupingCount=3, the numbers 2 and 3 will not be grouped, while 2, 3, 4 will be. If MinimumGroupingCount=0, no grouping will be done regardless of the number of consecutive numbers.

If numbered entries are not used, author-year citations will be created based on the citation properties. A parenthesis citation is composed as follows: [BracketBefore][Author][YearSeparator][Year][BracketAfter] where [Author] is the result of looking up the field or fields given in the AuthorField property, and formatting a list of authors. The list can contain up to MaxAuthors names - if more are present, the list will be composed as the first author plus the text specified in the property EtAlString. If the property MaxAuthorsFirst is given, it overrides MaxAuthors the first time each citation appears in the text.

If several, slash-separated, fields are given in the AuthorField property, they will be looked up successively if the first field is empty for the given entry. In the example above, the "author" field will be used, but if empty, the "editor" field will be used as a backup.

The names in the author list will be separated by the text given by the AuthorSeparator property, except for the last two names, which will be separated by the text given by AuthorLastSeparator. If the property AuthorLastSeparatorInText is given, it overrides the former for citations of the in-text type. This makes it possible to get citations like (Olsen & Jensen, 2008) and Olsen and Jensen (2008) for the same style.

[Year] is the result of looking up the field or fields given in the [YearField] property.

An in-text citation is composed as follows: [Author][InTextYearSeparator][BracketBefore][Year][BracketAfter] where [Author] and [Year] are resolved in exactly the same way as for the parenthesis citations.

If two different cited sources have the same authors and publication year, and author-year citations are used, their markers will need modification in order to be distinguishable. This is done automatically by appending a letter after the year for each of the publications; 'a' for the first cited reference, 'b' for the next, and so on. For instance, if the author "Olsen" has two cited papers from 2005, the citation markers will be modified to (Olsen, 2005a) and (Olsen, 2005b). In the bibliography layout, the placement of the "uniquefier" letter is indicated explicitly by inserting the virtual field uniq.

If several entries that have been "uniquefied" are cited together, they will be grouped in the citation marker. For instance, of the two entries in the example above are cited together, the citation marker will be (Olsen, 2005a, b) rather than Olsen, 2005a; Olsen, 2005b). The grouped uniquefier letters (a and b in our example) will be separated by the string specified by the UniquefierSeparator property.

Author-year citations referring more than one entry will by default be sorted chronologically. If you wish them to be sorted alphabetically, the citation property MultiCiteChronological should be set to false..

Reference list layout

The LAYOUT section describes how the bibliography entry for each entry type in JabRef should appear. Each line should start with either the name of an entry type, or the word default, followed by a '='. The default layout will be used for all entry types for which an explicit layout hasn't been given.

If author-year citations are used, you have to explicitly specify the position of the "uniquefier" letter that is added to distinguish similar-looking citations. This is done by including a marker for the virtual field uniq, typically right after the year (as shown in the example style file). The uniq field is automatically set correctly for each entry before its reference text is laid out.

To indicate formatting in the bibliography, you can use the HTML-like tag pairs <b> </b>, <i> </i>,  and  to specify bold text, italic text, superscript and subscript, respectively.

If you are using numbered citations, the number for each entry will be automatically inserted at the start of each entry in the reference list. By default, the numbers will be enclosed in the same brackets defined for citations. The optional citation properties BracketBeforeInList and BracketAfterInList override BracketBefore and BracketAfter if set. These can be used if you want different types of brackets (or no brackets) in the reference list. Note that these need not be brackets as such - they can be any combination of characters.

Known issues

• Make sure to save your Writer document in OpenDocument format (odt). Saving to Word format will lose your reference marks.
• There is currently no support for footnote based citations.

• The cursor may be poorly positioned after inserting a citation.

• Copy-pasting the example style file directly from this page can give an unparseable file. To avoid this, instead download the example file from the link in the download section.

• Make sure that libreoffice-java-common is installed on Linux for LibreOffice 5, otherwise important libraries are missing.

• The snap version of LibreOffice and JabRef may cause connection issues. Try to use the *deb versions instead.

• Open Office 4 will only work running under a 32-bit Java JRE/JDK on Windows because there is no 64-bit version of OpenOffice yet.

Location

The Entry Preview is located inside the Entry Editor (except when navigated to the File annotations or {} biblatex source tab):

You can display the entry preview as a separate tab (see screenshot above) by checking the box Show preview as a tab in entry editor in the entry preview settings Options > Preferences > Entry preview > Current Preview (see screenshot below).

Layouts/Styles

The entry preview displays either the Customized Preview Style or a certain Citation Style. You can select the styles that should be available for display in Options → Preferences → Entry preview. In Available you find all styles selectable for display, in Selected all styles already selected for display:

You can switch between all selected styles (customized preview and citation styles) in the entry preview in the main window by pressing F9.

Display Mechanism

Modification of the Customized Preview Style

JabRef allows sharing both and . You can also .

To customize entry types, select the menu File → Preferences → Entry types.

When customizing an entry type, you both define how its entry editor should look, and what it takes for JabRef to consider an entry complete. You can both make changes to the existing entry types, and define new ones.

Using the entry customization dialog

The entry customization interface is divided into two areas. On the left side all entry types (including any custom types) are listed. If you select a type from the left side, the right area shows all fields for the selected entry.

Adding and removing entry types

The currently available entry types are listed in the left panel.

To add a new entry type, you must enter a name for it in the text field below the type list, and click Add. The new entry type will be added to the list, and selected for modification.

To remove a custom entry type, select it and click the trash icon. This operation is only available for custom entry types that are not merely modifications of standard types. It is not possible to remove a standard entry type.

Editing entry types

When an entry type is selected, the current required and optional fields are listed on the right. A radio button indicates and allows to change the field's type from required to optional and vice versa.

To add a new field, edit the text field below the list, or select a field name from the dropdown menu, then click Add. The chosen field name will be added at the end of the list.

To remove a field select it in the list and click the trash icon to remove it.

To change the order of the fields you can use drag and drop.

Either/or fields

Certain entry types have an either-or condition in their required fields. For instance, a book entry is complete with either the author or the editor field, or both. To indicate such a condition in a custom entry type, you should add a field named as the set of alternative fields separated by slashes, for instance author/editor indicates the condition mentioned above for the book entry type.

The pattern used in the auto generation of citation labels can be set for each of the standard entry types in File → Preferences, tab Citation key generator. A detailed description can be found in the .

Citation key patterns

The key pattern can contain any text you wish, in addition to field markers that indicate that a specific field of the entry should be inserted at that position of the key. A field marker generally consists of the field name (in upper case letters) enclosed in square braces, e.g., [TITLE]. If the field is undefined in an entry at the time of key generation, no text will be inserted by the field marker. A field enclosed in square braces can be further changed by appending one or more of the separated by :, e.g., [TITLE:abbr].

For an entry with the title An awesome paper on JabRef, the citation key pattern demo[TITLE:abbr] will provide the key demoAapoJ.

Special field markers

Several special field markers are offered, which extract only a specific part of a field. Feel free to suggest new special field markers.

Author-related field markers

• [auth]: The last name of the first author

• [authFirstFull]: Get the von part and last name of the first author

• [authForeIni]: The forename initial of the first author

• [auth.etal]: The last name of the first author, and the last name of the second author if there are two authors or .etal if there are more than two.

• [authEtAl]: The last name of the first author, and the last name of the second author if there are two authors or EtAl if there are more than two. This is similar to auth.etal. The difference is that the authors are not separated by . and in case of more than 2 authors EtAl instead of .etal is appended.

• [auth.auth.ea]: The last name of the first two authors, separated by .. If there are more than two authors, adds .ea.

• [authors]: The last name of all authors.

• [authorsN]: The last name of up to N authors. If there are more authors, EtAl is appended

• [authIniN]: The beginning of each author's last name, using at most N characters in total.

• [authN]: The first N characters of the first author's last name.

• [authN_M]: The first N characters of the Mth author's last name.

• [authorIni]: The first 5 characters of the first author's last name, and the last name initial of the remaining authors.

• [authshort]: The last name if one author is given; the first character of up to three authors' last names if more than one author is given. A plus character is added, if there are more than three authors

• [authorsAlpha]: Corresponds to the BibTeX style “alpha”,

  • One author: The first three letters of the last name

  • Two to four authors: The first letter of the last name of each author

  • More than four authors: The first letter of the first three authors' last name. A + is added at the end if it is not in the .

• [authorLast]: The last name of the last author.

• [authorLastForeIni]: The forename initial of the last author.