Most menu actions referred in the following have keyboard shortcuts, and many are available from the toolbar. The keyboard shortcuts are found in the pull-down menus.

This is the main window from where you work with your databases. Below the menubar and the toolbar is a tabbed pane containing a panel for each of your currently open databases. When you select one of these panels, a table appears, listing all the database's entries, as well as a configurable selection of their fields.

• You decide which fields are shown in the table by checking the fields you want to see in the Preferences → Entry table dialog.

• Double-click a line of the table to edit the entry content. You can navigate the table with the arrow keys.

• Preferences → Entry table, but to more quickly change the order, click the header of a column to set it as the primary sort criterion, or reverse the sorting if it is already set. Another click will deselect the column as sorting criterion. Hold down Ctrl and click a column to add, reverse or remove it as a sub-criterion after the primary column. You can add an arbitrary number of sub-criteria, but only three levels will be stored for the next time you start JabRef.

• Adjust the width of each column by dragging the borders between their headers.

What function fulfills the biblatex source tab?

The biblatex source tab allows you to add and edit BibTeX entries by simply typing the desired content using correct BibTeX syntax. Advanced users may at times find this to be the speedier option. The required syntax is extensively described in "About BibTeX and its fields".

Additionally, here the data is shown "as is", which means special symbols that are usually supposed to be hidden or translated into readable form, may show regardless.

JabRef can optionally mark all new entries added or imported to a library with your username.

You can disable or enable this feature by entering Options → Preferences → General, and selecting/deselecting the line 'mark new entries with owner name'. You can also change the name used to mark entries. By default, your user name is used. Finally, if an entry with an existing field 'owner' is imported, the field is updated with your name if 'Overwrite' is checked.

The owner name is added in a field called 'owner', which by default is visible in the General fields tab in the entry editor.

JabRef supports following fields to jump to other entries.

Following fields are supported:

• cites - comma separated list of citation keys which are cited by this entry

• crossref - single entry which is cross referenced.

• related - comma separated list of citation keys which are in some kind related to this entry. The type of all relations can be specified by a single relatedtype (see https://github.com/plk/biblatex/issues/475#issuecomment-246931180). Note: biblatex prints this information if related is active at the biblatex package.

To use the crossref field, navigate to the general tab and insert the Crossref at the top.

To use cites and related, follow these steps:

1. Navigate to Bib(la)TeX source

2. Insert related = {citationkey},

3. Close the entry editor

4. Open the entry editor

5. Navigate to "Other fields"

6. There, you now see "related" with the possibilities to (i) navigate to the entry, (ii) add new related entries, (iii) remove related entries.

Notes

If you use crossref, JabRef will move these entries first in the bibliography as otherwise BibTeX cannot use the information of the cross-referenced fields. See also http://tex.stackexchange.com/a/148978/9075.

Please note that biblatex treats crossref differently than BibTeX.

Unsupported fields

• citedBy - this is the opposite of cites. Use cites instead.

• relations - this would introduce a complicated field similar to our save actions. A simple key/value is enough

• references - stores all references in plain text (PRVV plugin). Thus, we do not use it.

Further information

See https://github.com/koppor/jabref/issues/14 for the developer's discussion on the fields.

The entry editor opens from main window (table of entries). To open it 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 (see below). 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.

In this panel you can specify all relevant information on a single entry. The entry editor checks the type of your entry, and lists all the fields that are required, and the ones that are optional, for referring the entry with BibTeX. In addition, there are several fields termed General fields, that are common to all entry types.

You can fully customize which fields should be regarded as required and optional for each type of entry, and which fields appear in the General fields tabs. See Customizing entry types for more information about this.

For information about how the fields should be filled out, see BibTeX help.

The entry editor's panels

The entry editor contains six panels: Required fields, Optional fields, General, Abstract, Comments and Bib(la)TeX source, where General, Abstract and Comments can be customized (see Customizing general fields for details). Inside the three first panels, Tab and Shift + Tab are used to switch focus between the text fields.

Up to JabRef 4.1, the field was called "Review". The field name was changed to "Comments" as "Review" indicated some external reviews or some fundamental comments.

Switch panels by clicking on the tabs, or navigate to the panel to the left or right using the following key combinations: Ctrl + Tab or Ctrl + + switch to the tab to the right, and Ctrl + Shift + Tab or Ctrl + - switch to the tab to the left. You can also switch to the next or previous entry by pressing Ctrl + Shift + Down or Ctrl + Shift + Up, respectively, or by clicking the appropriate toolbar button.

BibTeX source (termed biblatex source in case of a biblatex library) shows how th entry will appear when the database is saved in BibTeX (or biblatex) format. If you wish, you can edit the source directly in this panel. When you move to a different panel, press Ctrl + S or close the entry editor, JabRef will try to parse the contents of the source panel. If there are problems, you will be notified, and given the option to edit your entry further, or to revert to the former contents.

Tip: If your database contains fields unknown to JabRef, these will be visible in the source panel.

Tip: the pdf and url fields support Drag and Drop operations. You can drop there an url from your browser. either a link to a pdf file (that JabRef can download for you) or you can keep the link.

Field consistency checking

When the contents of a field is changed, JabRef checks if the new contents are acceptable. For field types that are used by BibTeX, the contents are checked with respect to the use of the '#' character. The hash symbol is only to be used in pairs (except in escaped form, '\#'), wrapping the name of a BibTeX string that is referenced. Note that JabRef does not check if the referenced string actually exists (this is not trivial, since the BibTeX style you use can define an arbitrary set of strings unknown to JabRef).

If the contents are not accepted, the field will turn red, indicating an error. In this case the change will not be stored.

Handling of string constants

BibTeX supports string constants. One can define in the bibliography. JabRef offers editing of these strings via the String Editor.

For instance, if you see #jan# in the month field, the "real" BibTeX entry looks like month = jan. For more details, see Strings.

Word/name autocompletion

The entry editor offers autocompletion of words. In the File → Preferences → Autocomplete, you can enable or disable autocompletion, and choose for which fields autocompletion is active.

With autocompletion, JabRef records all words that appear in each of the chosen fields throughout your database. Whenever you write the beginning of one of these words, it will be suggested visually. To ignore the suggestion, simply write on. To accept the suggestion, either press Enter or use your arrow keys or other keys to remove the selection box around the suggested characters.

Note: the words considered for suggestion are only the ones appearing in the same field in entries of the same database as the one you are editing. There are many ways to realise this kind of feature, and if you feel it should have been implemented differently, we'd like to hear your suggestions!

Drag and drop behavior settings

The entry editor allows for file(s) to be dragged and dropped directly into the entry editor window. JabRef follows the default behavior of your operating system and uses Modifier keys to distinguish the drag and drop options. Copy means the entry editor will create a copy of the file in the current directory. The keyboard shortcuts needed to move, copy or link files are the following: Move means, the entry will move the file to the defined file directory, and rename the file according to the filename and file directory patterns. Link means the entry editor will create a link to the file. This creates a shortcut to the file and will not copy the file to the current directory.

• Move: Ctrl + Drag (Windows) or Option + Drag (MacOS/Linux)

• Copy: Shift + Drag (Windows) or Command + Drag (MacOS/Linux) or no key + Drag

• Link: Alt + Drag (Windows) or Command + Option + Drag (MacOS/Linux)

Copy citation key including citation command

Pressing Ctrl + K or the 'key' button causes the citation key for your entry including the surrounding to be copied to the clipboard.

Copy citation key

Pressing Ctrl + Shift + K causes the citation key for your entry to be copied to the clipboard.

Autogenerate citation key

Press Ctrl + G or the 'gen key' button (the magic wand) to autogenerate a citation key for your entry based on the contents of its required fields.

For more information on how JabRef generates citation keys, see Customizing the citation key generator.

Related Articles Tab

By selecting this Tab, we are sending the title of the selected paper to Mr. DLib.

Mr. DLib is a service that calculates recommendations for you based on this title. After a short loading time the recommendations are listed in the Related Articles Tab. For detailed information see Mr. DLibs help page. The following image shows the Related Articles Tab with recommendations to the selected item.

File Annotations Tab

JabRef can display the content of annotations in PDFs linked to an entry.

Mark or annotate something in a linked PDF.

In the entry editor, you can now select the tab "File annotations" and you will see the content you have highlighted or commented on in the PDF.

If you have multiple PDFs linked to the entry, you can select the document as well in the File Annotation tab.

JabRef can optionally set a field to contain the date an entry was added to the database.

Configuration

You can disable or enable this feature by entering File → Preferences → General, and selecting/deselecting the line 'Mark new entries with addition date'.

If an entry with a timestamp is pasted or imported, the field is updated with the current date if 'Overwrite' is checked. The value of the timestamp field will be updated upon changes in the entry if 'Update timestamp on modification' is checked.

By default, the date is added in a field called 'timestamp', which is visible in the General fields tab in the . You can alter the name of this field. The date format can also be customized (see below).

Usage

The timestamp field can be edited in the General fields tab of the . If you do not see these fields, enable them at or reset your preferences.

You can manually alter the value by typing in the date and time of your choice. Also, by clicking on the calendar icon located at the right end of the field, you can select the date you want in a calendar.

Formatting

The formatting of the time stamp is determined by a string containing designator words that indicate the position of the various parts of the date.

These are some of the available designator letters (examples are given in parentheses for Wednesday 14th of September 2005 at 5.45 PM):

• yy: year (05)

• yyyy: year (2005)

• MM: month (09)

• dd: day in month (14)

• HH: hour in day (17)

• mm: minute in hour (45)

These designators can be combined along with punctuation and whitespace. A couple of examples:

• yyyy.MM.dd gives 2005.09.14

• yy.MM.dd gives 05.09.14

• yyyy.MM.dd HH:mm gives 2005.09.14 17:45

The preferences for this feature are accessible via Library → Library properties → Content selectors and allows you to store often-used words or phrases. This creates the possibility to conveniently make use of them in the entry editor to fill in field content.

To add a new word by using the content selector in the entry editor, you can simply click into the text box for the field for which you configured the selectors. A drop down menu will appear and you can select the keyword of your choice. This mechanism is based on the autocompletion functionality in JabRef (File → Preferences → Autocompletion) . Therefore, you need to have autocompletion enabled in your preferences.

By default, the feature is enabled for the fields Journal, Author, Keywords and Publisher, but you can also add selectors to other fields.

The word selection is library-specific, and is saved along with your references in the .bib file.

BibTeX supports storing constant strings using @String {key = value}. JabRef supports managing them using Library → Edit string constants, which opens the String Editor. These values can be used in fields. For example, you can have:

@String { kopp = "Kopp, Oliver" }
@String { kubovy = "Kubovy, Jan" }
@String { et = " and " }

and then in some entry for example

@Misc{m1,
  author = kopp # et # kubovy,
}

or

@Misc{m2,
  author = kopp # " and " # kubovy,
}

In the JabRef field editor, the author has to be inserted as #kopp# #et# #kubovy# or #kopp# and #kubovy#.

Rendering of constants in JabRef's entry editor

Strings are rendered specially in the entry editor. This is especially important in the case of months. For instance, take the following BibTeX entry:

@Misc{m3,
  month = may,
}

In JabRef, the entry editor then displays #may#. In case the entry editor just displays may, this is written as follows:

@Misc{m4,
  month = {may},
}

In other words: The character # indicates something special in the entry editor.

JabRef's typed Strings

JabRef enhances the concept of Strings to add a type to those @Strings. The issue is how to preserve such type of a string in a BibTeX file. JabRef adds the type though prefixes:

• @String { aKopp = "Kopp, Oliver" } is a @String with the type author.

• @String { iMIT = "{Massachusetts Institute of Technology ({MIT})}" } is a @String with the type of institution.

• @String { anct = "Anecdote" } is a @String of type other.

• @String { lTOSCA = "Topology and Orchestration Specification for Cloud Applications" } is a @String of type other.

Then @Strings of type author should be used for author and editors fields only. @Strings of type institution should be used for institution and organization fields only. @Strings of type publisher should be used only for publisher fields. And finally @Strings of type other can be used anywhere.

It can also happen that you will have the same institution for more types:

• @String { aMIT = "{Massachusetts Institute of Technology ({MIT})}" } if the institution will appear as author or editor

• @String { iMIT = "{Massachusetts Institute of Technology ({MIT})}" } if the institution will appear as institution or organization

• @String { pMIT = "{Massachusetts Institute of Technology ({MIT}) press}" } if the institution will appear as publisher.

Even if the last example may appear contradicting the intention was to remove duplicity and unify the names of persons and institutions.

More examples

• \@String{aKahle = "Kahle, Brewster "} -> author

• \@String{aStallman = "Stallman, Richard"} -> author

• \@String{iMIT = "{Massachusetts Institute of Technology ({MIT})}" } -> institution

• \@String{pMIT = "{Massachusetts Institute of Technology ({MIT}) press}" } -> publisher

• \@String{anct = "Anecdote" } -> other

• \@String{eg = "for example" } -> other

• \@String{et = " and " } -> other

• \@String{lBigMac = "Big Mac" } -> other

Usage:

\@Misc {
  title       = "The GNU Project"
  author      = aStallman # et # aKahle
  institution = iMIT
  publisher   = pMIT
  note        = "Just " # eg
}

Further reading

See https://tex.stackexchange.com/questions/303467/bibliography-contents-journal-names-not-abbreviated-even-with-ieeeabrv/303489#303489 for a MWE for string constants.

This tool allows you to search for citations in LaTeX files.

In the user interface, a tab was added to the entry editor, the aesthetics have been improved, and the tool was renamed to Search for Citations in LaTeX files.

Overview

A new tab was added to the entry editor. It allows to search for citations to the active entry in the LaTeX file directory. It can be configured in the Library properties dialog.

See the image below to see how it works:

Key Features

The new tab

• A LaTeX Citations tab has been added to the entry editor.

• This tab can be disabled in the Entry editor preferences.

• A progress indicator appears while parsing.

• Current search is cancelled if another entry is selected.

• Parsed files are stored when the tool is run for the first time (to achieve better performance).

• The current search path is shown at the bottom, next to a button to set the LaTeX file directory.

• A user-friendly error logging and handling has also been implemented.

A custom user interface controller for listing citations

• The citations list view is the same for dialog tool and tab.

• The context of citations is shown instead of the whole line of text (which is shown as a tooltip).

• Absolute file path has been changed into a relative one, from the search path.

• New icons and styles for context, file path, and position (line and column) of a citation.

For linking attached files, see File links in JabRef.

JabRef lets you link documents on the web in the form of an URL or a DOI identifier.

Setting up external viewers

JabRef has to know which external viewers to use for web pages. These are by default set to values that probably make sense for your operating system, so there's a fair chance you don't have to change these values.

To change the external viewer settings, go to Options → Preferences → External programs.

Opening external links

There are several ways to open an external web page. In the entry editor, click on the icon "open" right of the text field to open the respective DOI or URL.

In the entry table you can select an entry and use the menu choice, keyboard shortcut or the right-click menu to open the file or web page. Finally, you can click on a URL or DOI icon.

By default the entry table will contain a singly column containing an indicator whether there is a DOI or a URL linked. You can remove the "Link identifiers" column in Options → Preferences → Entry table.

JabRef is is a program for working with BibTeX and biblatex databases. 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.

JabRef helps you work with your BibTeX libraries, but there are still rules to keep in mind when editing your entries, to ensure that your library is treated properly by the BibTeX program.

JabRef's conventions

Fields in the header of a bib file

JabRef stores the encoding of the file and (in case a shared SQL database is used) the ID of the shared library in the header of the bib file.

Encoding

% Encoding: <encoding>: States the encoding of a BibTeX file. E.g., % Encoding: UTF-8

Shared Id

To enable auto save, JabRef adds % DBID: <id> to the header. This helps JabRef identifying the SQL database where the file belongs. E.g., % DBID: 2mvhh73ge3hc5fosdsvuoa808t.

Standard BibTeX Format

An entry consists of entrytype, citekey, fields and field content. The BibTeX and Biblatex standards define a wide range of entrytypes and fields, which should give much leeway. Users that have further needs will be able to edit their entries and come up with custom entrytypes, fields and citekeys, as long as the syntax is honored.

Standard BibTeX fields

There is a lot of different fields in BibTeX, and some additional fields that you can set in JabRef.

The following fields are recognized by the default bibliography styles:

• bibtexkey A unique string used to refer to the entry in LaTeX documents. Note that when referencing an entry from LaTeX, the key must match case-sensitively with the reference string. Some characters should not be used in bibtexkey as they are not compatible or not recommended:

  { } ( ) , \ " - # ~ ^ : '

• address Usually the address of the publisher or other type of institution. For major publishing houses, you may omit the information entirely or give simply the city. For small publishers, on the other hand, you can help the reader by giving the complete address.

• annote An annotation. It is not used by the standard bibliography styles, but may be used by others that produce an annotated bibliography.

• author This field should contain the complete author list for your entry. The names are separated by the word and, even if there are more than two authors. Each name can be written in two equivalent forms:

  Donald E. Knuth or Knuth, Donald E.

  Eddie van Halen or van Halen, Eddie

  The second form should be used for authors with more than two names, to differentiate between middle names and last names.

• booktitle Title of a book, part of which is being cited. For book entries, use the title field instead.

• chapter A chapter (or section or whatever) number.

• crossref The library key of the entry being cross referenced.

• edition The edition of a book--for example, ``Second''. This should be an ordinal, and should have the first letter capitalized, as shown here; the standard styles convert to lower case when necessary.

• editor This field is analogue to the author field. If there is also an author field, then the editor field gives the editor of the book or collection in which the reference appears.

• howpublished How something strange has been published. The first word should be capitalized.

• institution The sponsoring institution of a technical report.

• journal The name of a journal or magazine. The name of a journal can be abbreviated using a "string". To define such string, use the string editor.

• key Used for alphabetizing, cross referencing, and creating a label when the ``author'' information is missing. This field should not be confused with the key that appears in the \cite command and at the beginning of the library entry.

• month The month in which the work was published or, for an unpublished work, in which it was written. You should use the standard three-letter abbreviation of the English names (jan, feb, mar, apr, may, jun, jul, aug, sep, oct, nov, dec).

• note Any additional information that can help the reader. The first word should be capitalized.

• number

  The number of a journal, magazine, technical report, or of a work in a series. An issue of a journal or magazine is usually identified by its volume and number; the organization that issues a technical report usually gives it a number; and sometimes books are given numbers in a named series.

• organization The organization that sponsors a conference or that publishes a manual.

• pages One or more page numbers or range of numbers, such as 42--111 or 7,41,73--97 or 43+ (which indicates page 43 and following pages). The standard styles convert a single dash (as in 7-33) to the double dash used in TeX to denote number ranges (as in 7--3).

• publisher The publisher's name.

• school The name of the academic institution where a thesis was written.

• series The name of a series or set of books. When citing an entire book, the title field gives its title and an optional series field gives the name of a series or multi-volume set in which the book is published.

• title The title of the work. The capitalization may depend on the bibliography style and on the language used. For words that have to be capitalized (such as a proper noun), enclose the word (or its first letter) in braces.

• type The type of a technical report - for example, "Research Note".

• volume The volume of a journal or multivolume book.

• year The year of publication or, for an unpublished work, the year it was written. Generally it should consist of four numerals, such as 1984, although the standard styles can handle any year whose last four nonpunctuation characters are numerals, such as "(about 1984)". This field is required for most entry types.

BibLaTeX fields

BibLaTeX defines more fields. It gets especially interesting in the context of date handling. See the BibLaTeX manual for detais.

• date The date of the publication. Can also include date ranges (e.g., 2014-04-07/2014-04-10).

Non-standard fields

BibTeX is extremely popular, and many people have used it to store information in non-standard fields. The information in these non-standard fields may be ignored by BibTeX.

Here is a list of some of the more common non-standard fields ("*" = not directly supported by JabRef):

• affiliation The authors affiliation.

• abstract An abstract of the work.

• doi The Digital Object Identifier, a permanent identifier given to documents.

• eid The Electronic identifier is for electronic journals that also appear in print. This number replaces the page number, and is used to find the article within the printed volume. Sometimes also called citation number.

• contents A table of contents

• copyright Copyright information.

• ISBN The International Standard Book Number.

• ISSN The International Standard Serial Number. Used to identify a journal.

• keywords Key words used for searching or possibly for annotation.

• language The language the document is in.

• location A location associated with the entry, such as the city in which a conference took place.

• LCCN The Library of Congress Control Number. I've also seen this as lib-congress.

• mrnumber The number of Mathematical Reviews.

• price The price of the document.

• size The physical dimensions of a work.

• URL The WWW Uniform Resource Locator that points to the item being referenced.

JabRef-specific fields

To help in managing your bibliography, and extend the features of BibTeX, JabRef defines some specific fields:

• External files

• General fields

• Owner

• Quality and grading

• Time stamp

Define your own fields

You can create new fields by editing (or creating) entry types.

Hints on fields

• Generally, you can use LaTeX commands inside of fields containing text. BibTeX will automatically format your reference lists, and those fields that are included in the lists will be (de)capitalized according to your bibliography style. To ensure that certain characters remain capitalized, enclose them in braces, like in the word {B}elgium.

• An institution name should be inside {} brackets.

  If the institution name also includes its abbreviation, this abbreviation should be also in {} brackets.

  For instance, {The Attributed Graph Grammar System ({AGG})}.

Further information resources

• Tame the BeaST - The B to X of BibTxX - long manual explaining the workings of BibTeX, the BibTeX format, and the available entry types with required and optional fields.

• BibTeX format according to Wikibook

• BibTeX format according to Wikipedia

• Reference documentation about BibTeX --> btxdoc.pdf

• BibTeX tips and FAQ --> btxFAQ.pdf

BibTeX files

• https://github.com/lvilnis/BibtexParser/tree/master/inputs

• https://github.com/environmentalinformatics-marburg/jabref

• http://www.math.uiuc.edu/K-theory/aux/K-theory.bib (large file > 6000 publications)

• http://mirrors.ircam.fr/pub/CTAN/biblio/bibtex/contrib/test/test.bib

BibLaTeX files

• http://mirrors.ctan.org/macros/latex/contrib/biblatex/bibtex/bib/biblatex/biblatex-examples.bib

• http://distrib-coffee.ipsl.jussieu.fr/pub/mirrors/ctan/macros/latex/contrib/biblatex/bibtex/bib/biblatex/biblatex-examples.bib

BibTeX and BibLaTeX files in the JabRef repository

• https://github.com/JabRef/jabref/tree/main/src/test/resources/testbib

Good references for the BibTeX "standard"

• http://texdoc.net/pkg/btxdoc

• http://maverick.inria.fr/~Xavier.Decoret/resources/xdkbibtex/bibtex_summary.html

BibLaTeX standard

• http://ftp.fau.de/ctan/macros/latex/contrib/biblatex/doc/biblatex.pdf

• https://github.com/plk/biblatex

BibTeX parsers

• https://github.com/ambs/Text-BibTeX

• https://github.com/lvilnis/BibtexParser

• https://github.com/sciunto-org/python-bibtexparser

• citation.js

Although JabRef is primarily a GUI based application, it offers several command line options that may be useful. JabRef can even perform file conversion operations without opening the graphical interface.

Basics

Windows:

Locate JabRef.bat, for example: JabRef-5.0-portable_windows\JabRef\runtime\bin\JabRef.bat

Linux:

JabRef-5.0-portable_linux/JabRef/lib/runtime/bin/JabRef.

macOS:

/Applications/JabRef.app/Contents/MacOS/JabRef\

Do not use JabRef\JabRef.exe or bin/JabRef

The following documentation is for Windows, but works equally well on Linux and macOS:

In some cases, you have to specify --console to ensure that output is written to the console.

You can always specify one or more Bib(la)TeX files to load by simply listing their filenames. Take care to specify all options before your list of file names. Ensure that the first file name is not misunderstood as being an argument for an option; this simply means that if a boolean option like -n or -l immediately precedes a file name, add the word true as an argument. For instance, the command line will correctly load the file original.bib, export it in to filetoexport.xml, and suppress the GUI:

The word true prevents the file name from being interpreted as an argument to the -n option.

Options

Help: -h

(or --help)

Displays a summary of the command line options, including the list of available import and export formats.

No-GUI mode: -n

(or --nogui)

Suppresses the JabRef window (i.e. no GUI - Graphic User Interface - is displayed).

It causes the program to exit immediately once the command line options have been processed. This option is useful for performing file conversion operations from the command line or a script.

Import file: -i filename[,import format]

(or --import filename[,import format] or --importToOpen filename[,import format])

Import or load the file filename.

If only the filename is specified (or if the filename is followed by a comma and a * character), JabRef will attempt to detect the file format automatically. This works for BibTeX files, and also for all files in a supported import format. If the filename is followed by a comma and the name of an import format, the given import filter will be used.

Use the -h option to get the list of available import formats.

If an export option is also specified, the import will always be processed first, and the imported or loaded file will be used by the export filter. If the GUI is not suppressed (using the -n option), any imported or loaded file will show up in the main window.

If --importToOpen is used, the content of the file will be imported into the opened tab.

Note: The -i option can be specified only once, and for one file only.

Export file: -o filename[,export format]

(or --output filename[,export format])

Export or save a file imported or loaded by the same command line.

If a file is imported using the -i option, that file will be exported. If no -i option is used, the last file specified (and successfully loaded) will be exported.

If only filename is specified, it will be exported in BibTeX format. If the filename is followed by a comma and an export format, the given export filter will be used.

A custom export filter can be used, and will be preferred if the export name matches both a custom and a standard export filter.

If the GUI is not suppressed (using the -n option), any export operation will be performed before the JabRef window is opened, and the imported database will show up in the window.

Note: The -o option can be specified only once, and for one file only.

Xmp export option

The first option is to export all entries, which are included in the entries.bib file to the specified export.xmp file. The second argument, separated by comma, is the type of exporter used by JabRef.

The second option is to export every entry in the entries.bib in a single .xmp file. Therefore, the file name is replaced by the keyword split without a file ending! JabRef generates individual .xmp files at the path location. The file name is a combination of the identifier provided by JabRef and the cite key of the entry.

Import BibTeX: -importBibtex

Import or load code directly from the BibTeX file. This only works for BibTeX files, and does not support files of other import formats. If it detects this command line option, the JabRef CLI will take in its following argument as a BibTeX string that represents the BibTeX article file being read in for import (usually a filename). JabRef then passes on this information to a helper function that will parse the BibTex string into entries and return the resulting BibTex entries to the JabRef CLI.

If the GUI is not suppressed (using the -n option), any imported or loaded BibTeX file will show up in the main window.

Note: The -importBibtex option can be specified only once, and for one file only.

Export matching entries: -m [field]searchTerm,outputFile:file[,exportFormat]

(or --exportMatches [field]searchTerm,outputFile:file[,exportFormat])

Save to a new file all the database entries matching the given search term.

If the filename is followed by a comma and an export format, the given export filter will be used. Otherwise, the default format html-table (with Abstract and BibTeX, provided by tablerefsabsbib) is used.

Note: In addition it is also possible to search for entries within a time frame such as Year=1989-2005 (instead of only searching for entries of a certain year as in Year=2005).

Note: Search terms containing blanks need to be bracketed by quotation marks, as in (author=bock or title|keywords="computer methods")and not(author=sager)

Write BibTexEntry as metadata to PDF: -w CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all

(or -writeMetadatatoPdf -w CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all)

Exports information stored in the database as Metadata to linked files. The metadata is stored as XMP metadata and as an embedded bib file. The entries can be selected by citekey. Individual pdfs can be selectec by the path to the pdf (either as given in the database or as an absolute or relative path to the pdf file itself). The keyword all may be specified to write metadata on all pdfs in the database.

Write BibTexEntry as XMP metadata to PDF: -writeXMPtoPdf CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all

As -writeMetadatatoPdf, but only write XMP metadata.

Write BibTexEntry as XMP metadata to PDF: -embeddMetadataInPdf CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all

As -writeMetadatatoPdf, but only embedd a bib file.

Fetch entries from Web: -f=FetcherName:QueryString

(or --fetch=FetcherName:QueryString)

Query a Web fetcher and import the entries.

Pass both the name of a fetcher and your search term or paper id (e.g. --fetch=Medline:cancer), and the given fetcher will be run. Some fetchers will still display a GUI window if they need feedback from you.

The fetchers listed in the Web search panel can be run from the command line. To get the list of available fetchers, run --fetch without parameters.

Subdatabase from .aux file: -a infile[.aux],outfile[.bib] base-BibTeX-file

(or --aux infile[.aux],outfile[.bib] base-BibTeX-file)

Extract a subdatabase from a .aux file:

When you compile a LaTeX document (e.g. infile.tex), an .aux file is created (infile.aux). Among other things, it contains the list of entries used in your document. JabRef can extract the references used from the base-BibTeX-file to a new .bib file (outfile.bib). This way, you will have a subdatabase containing only the entries used in the .tex file.

Set file links: -asfl

(or --automaticallySetFileLinks)

Automatically set file links.

Regenerate keys: -g

(or --generateCitationKeys)

Regenerate all keys for the entries of a Bib(la)TeX file.

Export preferences: -x filename

(or --prexp filename)

Export user preferences to an XML file. After exporting, JabRef will start normally.

Import preferences: -p filename

(or --primp filename)

Import user preferences from an XML file (exported using the -x option, or through the GUI). After importing, JabRef will start normally.

Reset preferences: -d key

(or --prdef key)

Reset preferences (key1, key2,..., or all).

No files at startup: -b

(or --blank)

Do not open any files at startup

Version: -v

(or --version)

Display the version number of JabRef.

Debug mode: --debug

Display output in the console: --console

Show info and error messages in the console.

Development

As developer, you pass arguments to the app using gradle's --app switch. Enclose the arguments in quotes. For instance --args="--debug" turns on debug mode.

You can then view the event log in JabRef as follows:

General

Since JabRef 5.2 it is possible to use custom themes. In Preferences > Appearance > Visual theme the themes in general can be changed. Themes are just files defining the look of the UI.

• Light Theme: The default theme is the light theme ().

• Dark Theme: There is an alternative dark theme () which is based on Base.css and just overwrites the colors.

• Custom Theme: In Preferences > Appearance > Visual theme > Custom theme there can be set a custom theme by simply selecting a custom CSS (based on Base.css or Dark.css), for instance:

You can find a collection of user contributed themes at .

Selection of Useful CSS selectors

Examples

Known bugs

JabRef can automatically toggle journal names between abbreviated and unabbreviated form, as long as the names are contained in one of your journal lists.

This feature can be configured under Options → Preferences → Manage journal abbreviations.

JabRef includes a fairly extensive build-in list of journal abbreviations. This list is a merge of all lists available at . However, this might still be incomplete (or outdated) for the purposes of some users. Thus, JabRef allows to add abbreviations in the form of a personal list or external lists.

Using the feature

Journal name conversion can be accessed either from within the entry editor, or from the Quality menu. In the entry editor you will find a button labeled Toggle abbreviation by the journal field. Clicking this button will cause the current journal name to be switched to the next of four modes:

• Full name, e.g. "Aquacultural Engineering"

• Default abbreviation, e.g. "Aquacult. Eng."

• Medline abbreviation, e.g. "Aquacult Eng"

• Shortest unique abbreviation, e.g. "AQEND6"

If the current journal name is not found in your journal lists, the field will not be modified.

To convert the journal names of many entries in bulk, you can select any number of entries, and choose Quality → Abbreviate journal names → DEFAULT, Quality → Abbreviate journal names → MEDLINE, Quality → Abbreviate journal names → SHORTEST UNIQUE, or Quality → Unabbreviate journal names. These three actions will abbreviate and unabbreviate the journal names of all selected entries for which the journal name could be found in your journal lists.

Setting up additional journal lists

In addition to the build-in journal list, you can have a personal list and external lists.

Any entry in your personal journal list will override an entry with the same full journal name in one of the external lists. Similarly, the external lists are given precedence in the order they are listed.

Your personal journal abbreviations list

Your personal journal list is managed on top of the Manage journal abbreviations window. To start building your personal journal abbreviations list, choose Add new list, and enter a filename. If you already have a file that you want to use as a starting point, use the Open existing list button. The table will update to show the contents of the list you have selected.

The table and the tool buttons in the upper right allow you to add, remove and edit journal entries. For each entry you must provide the full journal name, and the default abbreviation (e.g. "Aquacultural Engineering" and "Aquacult. Eng."). The last field, which contains the shortest unique abbreviation, is optional. Therefore, you can actually safely omit it. To edit an entry, double-click its row in the table.

Once you click Save changes, if you have selected a file, and the table contains at least one entry, the table contents will be stored to the selected file, and JabRef's list of journals will be updated.

External journal lists

You can link to a number of external lists. These links can be set up on top of the Manage journal abbreviations window. External lists are similar to the personal list. The Open existing list button allows you to select an existing file on your computer.

The two last fields are optional, and you can omit them. JabRef supports the third field, which contains the shortest unique abbreviation. The last field is not currently used; its intention is gives frequency (e.g., M for monthly). For instance:

Contributing an external journal list

XMP is a standard created by Adobe Systems for storing metadata (data about data) in files. A well known example for metadata are MP3 tags, which can be used to describe artist, album and song name of a MP3 file. Adding metadata to MP3 helps other people to identify the songs correctly independent of file-name and can provide means for software (MP3 players for instance) to sort and group songs.

With XMP support the JabRef team tries to bring the advantages of metadata to the world of reference managers. You can now choose to "Write XMP metadata to PDFs" in the Tools menu of JabRef, which will put all the Bib(la)TeX information into the PDFs. If you then email a PDF to a colleague, they can just drag the file into JabRef and all information that you entered will be available to them.

Usage

To use the XMP-feature in JabRef you can do the following:

• To import a single annotated PDF-file that contains XMP, select File → Import into... and then choose the filter "XMP-annotated PDF", or drag the file into the main view.

• To annotate all the PDFs in a given database, select Tools → Write XMP metadata to PDFs.

• To verify if it worked, you can open the PDF in Adobe Acrobat and select File → Document Properties → Additional Metadata → Advanced. In the tree to the right you should see an entry called "". Note: this works only with Adobe Acrobat, not with Adobe Reader. If you do not have Adobe Acrobat, you can use pdfinfo instead in order to see the XMP metadata. pdfinfo is part of and .

BibTeXMP Fileformat

JabRef builds on to encode bibliographic information. That information us embedded in the PDF using the XMP format. Dublin Core itself i) builds on RDF and ii) can be extended with own information. In case BibTeX data cannot be stored using native Dublin Core fields, new fields are used. Basically, all fields and values are turned into nodes of an XML document. Only authors and editors are stored as rdf:Seq-structures, so users of the data can skip the splitting on ands. All strings and crossrefs will be resolved in the data.

The following easy minimal schema is used:

• The citation key is stored as citationkey.

• The type of the BibTeX entry is stored as entrytype.

• author and editor are encoding as rdf:Seqs where the individual authors are represented as rdf:lis.

• All other fields are saved using their field-name as is.

The following is an example of the mapping

will be transformed into

Be aware of the following caveats if you are trying to parse BibTeXMP:

• In RDF attribute-value pairs can also be expressed as nodes and vice versa.

Related Links

Some links about XMP and annotating PDFs

What are .sav, .bak and .tmp files?

JabRef generates .sav, .bak and .tmp files while working.

• .bak stands for the automatic backup feature: Each 20 seconds, after a change to the library, the current state of the library is saved to a .bak file. JabRef keeps 10 older versions of a .bak file in the .

• .sav preserves the last state of the library after saving. Thus, one can go back one save command in the history. Used when writing the .bib file. Used for copying the .bib away before overwriting on save.

• .tmp is a temporary file with changes that are supposed to be written to the .bib file.

Rough outline of what's happening during a write to the .bib file: A .tmp will be written --> .bib copies to .sav --> .tmp copies to .bib --> .sav gets deleted --> 20 seconds later, a copy of the .bib file will be stored as.bak file in the user data dir.

How to ignore JabRef's .sav and .bak files in Git

By using the service, you can generate an appropriate .gitignore file by opening . A gitignore file specifies intentionally untracked files that Git should ignore. Files already tracked by Git are not affected; See for further details.

Automatic backup of current library edits

This functionality runs in the background while you are working on a bibliographic database. It makes a backup copy (the .bak file) and keeps that up-to-date on every user interaction. For instance, when you change a field the new value would get saved into the backup copy. Assuming that JabRef crashes while you are working on a BibTeX database. When you try again to open the file JabRef crashed with you will get the following dialog:

Now you have the possibility to restore and review your changes which would normally get lost.

Where can I find the backup files?

• Unix/Linux: /home/<username>/.local/share/org.jabref/jabref

• Windows: Windows 7/10: C:\Users\<Account>\AppData\org.jabref\jabref Alternatively, open the run dialogue by pressing Windows+R, then enter %APPDATA%\..\Local\org.jabref\jabref Windows XP: C:\Documents and Settings\<Account>\Application Data\Local Settings\org.jabref\jabref>

• Mac OS X: /Users/username/Library/Application Support/org.jabref/jabref

Automatic saving of the current library

JabRef offers automatic saving of the library. No need to click on File --> Save or pressing Ctrl+S anymore: The opened database are saved automatically without manual intervention.

In case the .bib file should automatically be saved on each change, you can direct JabRef to do so. This feature needs to be activated in the preferences:

This feature can be toggled and configured under Preferences → Network.

Note that activating this feature under Windows XP SP2 (and possibly other configurations) may prompt a message box stating that certain features of the program have been blocked by the Windows firewall. You can safely tell the firewall to keep blocking - the firewall will not interfere with remote operation of JabRef.

If listening for remote operation is enabled, JabRef will at startup attempt to start listening to a specific port. This means that other applications can send information to JabRef through this port. JabRef will only accept local connections, to avoid the risk of interference from outside.

Binding to this port makes it possible for a second JabRef instance to discover that the first one is running. In this case, unless specifically instructed to run in stand-alone mode, the second JabRef instance will pass its command line options through the port to the first JabRef instance, and then immediately quit.

The first JabRef instance will read the command line options, and perform the indicated actions, such as reading or importing a file, or importing a file to the currently shown database. If a file is imported using the command-line option --importToOpen, the imported entries will be added to the currently shown database. If no database is open, a new one will be created.

Based on the .aux file generated by LaTeX, JabRef can create a subdatabase containing only the cited entries.

This feature is available through Tools → New subdatabase based on AUX file.

The license of the JabRef software

The JabRef software is under the MIT License. In short, JabRef is free to use, even commercially. You can also redistribute and modify JabRef as long as you include the original copyright and license notice in any copy of the software/source.

The license of the JabRef documentation

The documentation of JabRef is under the Creative Commons Attribution 4.0 International License. In short, you can make a commercial use of it, distribute it, modify it and rename it. You must give credit, include copyright, and state changes. And you cannot sublicense it.

JabRef-compatible text editors

JabRef can push entries, i.e., insert \cite{key} commands, to the following text editors:

• Emacs

• LyX/Kile

• TeXstudio

• Texmaker

• Vim

• WinEdt

Additionally, JabRef can natively insert citations and format a bibliography in:

• OpenOffice Writer

• LibreOffice Writer

See OpenOffice/LibreOffice integration for details.

JabRef journal abbreviation lists

JabRef can help you refactor your reference list by automatically abbreviating or unabbreviating journal names, as explained in the dedicated help.

Although JabRef comes with a build-in list of journals, additional lists are available at https://abbrv.jabref.org.

Export filters and style files for LibreOffice

JabRef allows you to create custom export filters and style files for LibreOffice. This functionality and the installation procedure are described in the help file on Custom export filters. Some users have created export filters that can be useful to many others.

Export filters are collected at https://layouts.jabref.org. Style files for LibreOffice are available at https://jstyles.jabref.org.

Endnote export filter set

This improves author recognition and adds support for more fields to EndNote.

Homepage: https://github.com/JabRef/EndNode-JabRef-filters

Export-Filter Editor

Using this tool you can easily create a custom export filter for JabRef to build your own bibliography style. The tool itself supports:

• HTML Export Filter

• RTF Export Filter

• OpenOffice/ LibreOffice Style File

• Saving the filter for later refinements

Download the Export-Filter Editor

Additional tools

BibSync

BibSync is a tool to synchronize your paper library with a BibTeX file which might be most useful for Physicists and Mathematicians since it supports synchronization with DOI and arXiv.

Bibtex4word

Bibtex4Word is an add-in for Microsoft Word that allows the citation of references and the insertion of a bibliography into your document using your choice of formatting style. It is lightweight, transparent and does not mess up your documents.

Eratosthenes Reference Manager

Eratosthenes Reference Manager is a BibTeX-based bibliography manager for Android. It integrates with JabRef, supporting top-level groups and attached files/external links.

Available for Android 4.0 and up.

Unfortunately, this application is not available anymore from Google Play and must be build on your own from source.

Feinerleiser

Feinerleiser is a tool for improving the JabRef-LibreOffice integration when writing for the humanities. This tool can be run to finalize a document, providing citation features that are not supported by JabRef itself.

gitignore.io

This site offers to generate .gitignore files using common patterns for applications. For instance, you can use the keywords JabRef, Windows, Linux, macos, latex to generate a .gitignore for your daily tex work.

• Homepage: https://www.gitignore.io/

• .gitignore for JabRef and friends: https://www.gitignore.io/api/jabref%2Clatex%2Cwindows%2Clinux%2Cmacos

WinEdt's JabRef launcher

This WinEdt's package allows to launch the JabRef program from within WinEdt.

Download the WinEdt's JabRef launcher

JabRef LibreOffice Converter

A LibreOffice extension that converts JabRef references to plain text code and vice versa so that you can use your references with MS Office and other software.

Description and download of the extension

Enable debug log

Sometimes, it helps to ask JabRef to write some more debugging messages.

Use Backups

If you encounter any errors that are related to wrong, erroneous, corrupt or vanished data in your library file or simply unintended behavior that has unknown causes, the first thing that is advised to do, is to find and make use of your backups.

1. Navigate to your backup directory.

2. Find and select all backups files (the .bak files).

3. Copy the backup files to a safe, but different location. (Basically, create a backup of the backups. This step is very important, as each 20 seconds, after a change to the library, the current state of the library is saved to a .bak file, but JabRef at most stores 10 backup files and if you continue to work with your original library file (.bib), eventually JabRef will overwrite your old backup files)

4. Compare the backup file with the erroneous library. You can do this by editing your chosen backup file (via JabRef or file editor) in such a way that the modification date is newer than that of your erroneous library. Open the erroneous library and the backup merge dialogue should trigger, which allows you to see what has changed in the file. Alternatively, to achieve the same result, it is possible to use third party file versioning systems like Git or visual difference and merge tools like Meld or WinMerge.

If this method works: Great! If this method does not work with the first backup file: Try an older backup file If this method does not work with any backup file: Try the method of half splitting.

The method of half splitting

The method of half splitting (also referred to as halving) can be used to find certain faults in your library file, which are caused by erroneous syntax, file conversions or incompatible encodings/charsets. These faults may make it impossible for JabRef to correctly parse, read or import the library file. An easy way to look at the method of halving is to repeatedly ask yourself the following question, after having deleted a part of your library file: "Is the error in the first part or the last part of the entries?"

How it works:

1. Create a backup of your library file.

2. Open your library with the text-editor of your choice (For example, Notepad++).

3. Delete half of your entries.

4. Open your library with JabRef.

5. If your library now miraculously does not trigger the error, don't stop and leave. Instead, rinse and repeat and use the technique of halving on the junk of entries that you just deleted (hence the need for backups!). Use the technique of halving on THAT part of the library.

6. Repeat deleting entries until you can isolate the specific entry or entries that trigger errors.

7. Remove these entries with the error. Add all the other entries back. Open JabRef. Be happy :-)\

Example:

Half splitting a library with two entries:

How efficient is this method?

Halving as a process of elimination will quickly lead to results, as the following table illustrates:

Related Literature

If you want to find out more about this method, the following articles explain the method of halving in various contexts:

• https://ljackso.medium.com/half-splitting-applying-a-troubleshooting-technique-to-debugging-code-6a0578d1833c

• https://www.ecmweb.com/maintenance-repair-operations/article/20889049/the-beauty-of-halfsplitting

• https://www.techrepublic.com/article/secrets-of-a-super-geek-use-half-splitting-to-solve-difficult-problems/

Sometimes, one has a BibTeX/biblatex entry with abbreviated short names:

@Article{Eshuis_2015,
  author    = {R. Eshuis and A. Norta and O. Kopp and E. Pitkanen},
  journal   = {{IEEE} Transactions on Services Computing},
  title     = {Service Outsourcing with Process Views},
  year      = {2015},
  month     = {jan},
  number    = {1},
  pages     = {136--154},
  volume    = {8},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
}

Now, one wants to have the full first names. In case, there is a DOI available, this is as simple as the following steps:

1. Determine the DOI: Switch to the "General" tab and click on "Look up DOI"
2. Fetch BibTeX data from the DOI: Click on "Get BibTeX data from DOI"
3. A popup appears. Select which data you want to merge into the eixting entry
4. Now the first names are expanded:

JabRef supports the MS Office Bibliography XML format for exporting and importing.

Howto: Import from Microsoft Word

See

Entry Type Mappings

Some field names in the XML format differ from the field names in the BibTeX/BibLaTeX format and can therefore be not directly mapped between the formats. Therefore this help file provides a list of all field mappings.

Field mappings

The field mapping for import and export is mostly the same, but there are some differences, as not all field exists in both formats. Additionally, some fields have to be treated differently during import/export.

BibTeX/BibLaTeX only fields

The following fields are BibTeX/biblatex only fields, they have no representation in office XML. In the resulting XML file, they are represented with the prefix BIBTEX_

The XML field SourceType contains the associated entry type from the first table, while the original BibTeX/BibLaTex entrytype is preserved in the field BIBTEX_ENTRY.

MS-Bib only fields

The following fields are XML-only fields, they have no BibTeX/biblatex representation: In the resulting bib database they are represented with the prefix msbib-.

Special Export treatment

The following fields are treated as follows during export:

Special Import treatment

The following fields are treated as follows during import:

The Medline (txt) format can be used by a simple text document. Here, you have to write the field names at the beginning of each line. The Medline (xml) format is a XML document. The field name has to be written between < and >. For further information visit . Medline (txt) and Medline (xml) always take the type "article". RIS works similar to Medline (txt) with the difference that different fields are supported and the file extension is "ris".

In other sources, you might encounter "MedlinePlain" as a synonym for "Medline (txt)" and "Medline" as a synonym for "Medline (XML)".

Table with fields