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:

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

ArXiv is a repository of scientific preprints in the fields of mathematics, physics, astronomy, computer science, quantitative biology, statistics, and quantitative finance (Wikipedia).

ID search is carried out using the ArXiv identifier.

Crossref

Crossref is an official Digital Object Identifier (DOI) Registration Agency of the International DOI Foundation.

ID search is carried out using the DOI.

ISBN

First, eBook.de's API is used to fetch bibliographic information based on the ISBN. If no entry is found, the JabRef tries OttoBib to get data.

ID search is carried out using the International Standard Book Number.

DiVA

DiVA (Digitala Vetenskapliga Arkivet) is a database with publications from about 40 Swedish universities and research institutions.

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

DOI

JabRef uses http://dx.doi.org/ (provided by http://crossref.org/) to convert the given DOI to a new entry.

ID search is carried out using the DOI.

IACR eprints

The International Association for Cryptologic Research maintains an eprint archive to which anyone can submit papers and technical reports. These eprints are given IDs based on the year of submission, e.g. the 10th submission in 2018 gets the ID "2018/10". To get the ID, you may want to use their web search form at https://eprint.iacr.org/search.html.

ID search is carried out using the Cryptology ePrint ID.

Library of congress

The Library of Congress is the research library that officially serves the United States Congress and is the de facto national library of the United States (wikipedia).

ID search is carried out using the Library of Congress Control Number (LCCN).

MathSciNet

MathSciNet is a searchable online bibliographic database. It contains all of the contents of the journal Mathematical Reviews (MR) since 1940 along with an extensive author database, links to other MR entries, citations, full journal entries, and links to original articles. It contains almost 3 million items and over 1.7 million links to original articles (Wikipedia).

ID search is carried out using the MR number.

Medline/Pubmed

Medline/Pubmed is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine, and health care. Medline also covers much of the literature in biology and biochemistry, as well as fields such as molecular evolution (Wikipedia).

ID search is carried out using the PubMed Unique Identifier (PMID).

Screenshot of new entry dialog

mEDRA

mEDRA is the multilingual European Registration Agency of DOI, the standard persistent identifier for any form of intellectual property on a digital network.

ID search is carried out using the DOI.

SAO/NASA ADS

SAO/NASA Astrophysics Data System is an online database of over eight million astronomy and physics papers from both peer reviewed and non-peer reviewed sources. Abstracts are available free online for almost all articles, and full scanned articles are available in Graphics Interchange Format (GIF) and Portable Document Format (PDF) for older articles (Wikipedia).

ID search is carried out using the ADS Bibcode.

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

zbMATH Open is an abstracting and reviewing service in pure and applied mathematics. Its database contains about 4 million bibliographic entries with reviews or abstracts currently drawn from about 3,000 journals and book series, and 180,000 books. The coverage starts in the 18th century and is complete from 1868 to the present by the integration of the "Jahrbuch über die Fortschritte der Mathematik" database (about).

ID search is carried out using the Zbl number.

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.

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.

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:

Entry edition is done in the .

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.

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.

- - -

JabRef offers an official browser extension. It automatically identifies and extracts bibliographic information on websites and sends them to JabRef with one click.

When you find an interesting article through Google Scholar, the arXiv or journal websites, this browser extension allows you to add those references to JabRef. Even links to accompanying PDFs are sent to JabRef, where those documents can easily be downloaded, renamed, and placed in the correct folder. .

Installation and Configuration

Normally, you simply install the extension from the browser store and are ready to go.

- - -

While Chrome extensions can work in Edge (and will install), JabRef is configured to work with the Edge extension in the Edge Browser, and the Chrome extension in the Chrome Browser. It will not work if they are mixed.

Usage

After the installation, you should be able to import bibliographic references into JabRef directly from your browser. Just visit a publisher site or some other website containing bibliographic information (for example, ) and click the JabRef symbol in the Firefox search bar (or press Alt+Shift+J). Once the JabRef browser extension has extracted the references and downloaded the associated PDF's, the import window of JabRef opens.

You might want to configure JabRef so that new entries are always imported in an already opened instance of JabRef. For this, activate "Listen to remote operation on port" under the "Network" tab of the JabRef Preferences.

Troubleshooting

In case you have Adblock Plus extension and Jabref extension doesn't work

1) Go to . 2) Deactivate AdBlock plus extension for the whole domain (zotero.org) by clicking on the Adblock plus extension button and sliding the corresponding slider to allow adds on the whole domain. 3) Close and reopen the browser in order to reload all the extension and their settings. 4) Verify the functioning of the Jabref extension by visiting a page you know is working to extract its bibliographic data (for example, ) by pressing the extension button or Alt + Shift + J.

In case you encounter problems in this procedure refer to issue #241 on GitHub for further help.

In case script jabrefHost.py doesn't work

Error message bad interpreter: /usr/bin/python3: no such file or directory means that python3 is not installed at the expected location. Run which python3 to see if python3 is installed elsewhere. Then copy that path at the first line of jabrefHost.py maintaining #! prefix.

In case PowerShell script JabRefHost.ps1 cannot be executed due to ExecutionPolicy

Manual Installation

Most JabRef installations include the necessary files, so test the extension before proceeding with the following instructions. However, sometimes, a manual installation is necessary (e.g. if you use the portable version of JabRef). In this case, please take the following steps:

Windows

3. Download the following files and copy them to the same directory as JabRef.exe
4. Make sure that the correct file name of the JabRef.bat file is specified in JabRefHost.ps1 under $jabRefExe.

5. Run the following command from the console (with the correct path to the jabref.json file):

   a. For Firefox support:

   b. For Chrome/Opera/Brave/Vivaldi and other chromium-based browser support:

   c. For Edge support:

   You may need to change the root HKEY_LOCAL_MACHINE to HKEY_CURRENT_USER if you don't have admin rights.

Linux

Deb, RPM or Portable

2. • • /usr/lib64/mozilla/native-messaging-hosts/org.jabref.jabref.json (and /usr/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json) to install with admin rights for all users

     • ~/.mozilla/native-messaging-hosts/org.jabref.jabref.json to install without admin rights for the current user

   • • /etc/opt/chrome/native-messaging-hosts/org.jabref.jabref.json to install with admin rights for all users

     • ~/.config/google-chrome/NativeMessagingHosts/org.jabref.jabref.json to install without admin rights for the current user
   • • /etc/chromium/native-messaging-hosts/org.jabref.jabref.json to install with admin rights for all users

     • ~/.config/chromium/NativeMessagingHosts/org.jabref.jabref.json to install without admin rights for the current user

   • • /etc/opt/edge/native-messaging-hosts/org.jabref.jabref.json to install with admin rights for all users

     • ~/.config/microsoft-edge/NativeMessagingHosts/org.jabref.jabref.json to install without admin rights for the current user

3. Open the file org.jabref.jabref.json with a text editor, and alter it so that its path variable matches the location of your jabrefHost.py file.

Snap

3. Connect the appropriate plug for the selected browser:

   • Firefox: snap connect jabref:hostfs-mozilla-native-messaging-jabref

   • Chrome: snap connect jabref:etc-opt-chrome-native-messaging-jabref

   • Chromium: snap connect jabref:etc-chromium-native-messaging-jabref

   • Edge: snap connect jabref:etc-opt-edge-native-messaging-jabref

Flatpak

Browser

If the browser is installed as a snap or flatpak there is an extra step to enable the extension.

With Firefox installed as a snap (default in Ubuntu):

• flatpak permission-set webextensions org.jabref.jabref snap.firefox yes

With Firefox installed as a flatpak:

• Enable the following permission (Note that this will partially disable confinement):

  • via terminal command: flatpak override --user --talk-name=org.freedesktop.Flatpak org.mozilla.firefox

  • via Flatseal app: add org.freedesktop.Flatpak to the Session Bus Talk section for org.mozilla.firefox

macOS

2. • • /Library/Application Support/Mozilla/NativeMessagingHosts/org.jabref.jabref.json to install with admin rights for all users

     • ~/Library/Application Support/Mozilla/NativeMessagingHosts/org.jabref.jabref.json to install without admin rights for the current user

   • • /Library/Google/Chrome/NativeMessagingHosts/org.jabref.jabref.json to install with admin rights for all users

     • ~/Library/Application Support/Google/Chrome/NativeMessagingHosts/org.jabref.jabref.json to install without admin rights for the current user
   • • /Library/Application Support/Chromium/NativeMessagingHosts/org.jabref.jabref.json to install with admin rights for all users

     • ~/Library/Application Support/Chromium/NativeMessagingHosts/org.jabref.jabref.json to install without admin rights for the current user

   • • /Library/Microsoft/Edge/NativeMessagingHosts/org.jabref.jabref.json to install with admin rights for all users

     • ~/Library/Application Support/Microsoft Edge {Channel_Name}/NativeMessagingHosts/org.jabref.jabref.json to install without admin rights for the current user

     The {Channel_Name} in Microsoft Edge {Channel_Name} must be one of the following values: Canary, Dev, Beta.

     When using the Stable release/channel, {Channel_Name} is not required.

3. Check that the Python script works. In Terminal run /Applications/JabRef.app/Contents/Resources/jabrefHost.py. If there are no errors the script is working properly. Stop the script by pressing Ctrl + D.

Local JabRef installs

org.jabref.jabref.json directs the browser extension to a python script in the JabRef app, which is set to the most common install path by default (/Applications/JabRef.app/Contents/Resources/jabrefHost.py). If you have installed JabRef somewhere else, most likely to your local applications folder (~/Applications/JabRef), then you will need to update this path to the correct location. For example, in local installs this would be /Users/USER/Applications/JabRef.app/Contents/Resources/jabrefHost.py, where USER is your username.

JabRef can fetch automatically additional information about your entries. It can even get the publication file!​

• To find identifiers (arxiv, DOI)_: select the entries and go to the menu Lookup → search document identifier online.​

• To find the DOI: open the entry editor, and in the General tab, click on the button Lookup DOI.

• To find the document related to an entry: select the entry and to the menu Lookup → search full text documents online.​

Be aware: The options above require your entry or entries to be filled with enough and correct bibliographic information. If the entry holds incomplete or inaccurate data, fetching the identifier or text document my fail.

Completing information based on DOI or ISBN

JabRef can help you complement your entries with bibliographic data, which is associated with their registered DOI or ISBN. This is a very reliable way of obtaining correct bibliographic information and is very much recommended.

The following features require your entry to have a DOI or ISBN and are disabled / greyed out otherwise.

• Option A) In the entry table, right-click on the entry to complement, and select the menu Get bibliographic data from DOI/ISBN/...

• Option B) Open the entry editor, and in the General tab, click on the button Get bibliographic data from DOI

Using any of the options opens the window Merge entries:

There it is possible to choose what is kept for each field: the left side, the right side, or the merged entry. By default, the original entry (left) is kept, and any fields not present in the original entry are obtained from the information collected from the DOI.

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

See also: Find duplicates, Merge entries

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 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 .

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

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 allows sharing both Bib(La)TeX library and SQL database. You can also export your library to a variety of formats.

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 certificates. Then convert the client certificates into a java readable format and import them into a (custom) keystore. For MySQL the procedure is similar. Setting up MySQL with SSL and converting the certificates 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

You can test the shared SQL database support by using https://www.freemysqlhosting.net for MySQL (not recommended) and https://www.elephantsql.com/ for PostgreSQL (recommended).

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

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

When sharing a Bib(la)TeX library, JabRef automatically recognizes a change in the bib file on disk and notifies the user of it. This works well on network drives.

Note: the use of a version control system (SVN, git, etc.) is recommended as this will allow for reverting changes.

To make the sharing of a Bib(la)TeX library easier, it is recommended to set specific library properties. In the menu Library → Library properties:

• Select UTF-8 as encoding.

• Define a General file directory, which will be used to store shared PDF (and other) files.

• Check Refuse to save the library before external changes have been reviewed.

• Define a sort order (year, author, title is recommended)..

• Check Enable save formatters, and defines these actions, to help enforcing a consistent format for the entries.

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 is highly customizable, allowing users to get the behaviour they expect.

The File → Preference menu command allows you to configure the JabRef interface, and to set the default features of your libraries. Features specific to a given library are configured in the Library menu. For example, while the default key patterns are set in File → Preferences → Citation key generator → Key patterns, key patterns specific to a library can be set in Library → Citation key patterns.

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:

NAME
Example style file for JabRef-OpenOffice integration.

JOURNALS
Journal name 1
Journal name 2

PROPERTIES
Title="References"
IsSortByPosition="false"
IsNumberEntries="false"
ReferenceParagraphFormat="Default"
ReferenceHeaderParagraphFormat="Heading 1"

CITATION
AuthorField="author/editor"
YearField="year"
MaxAuthors="3"
MaxAuthorsFirst="3"
AuthorSeparator=", "
AuthorLastSeparator=" & "
EtAlString=" et al."
ItalicEtAl="true"
YearSeparator=" "
InTextYearSeparator=" "
BracketBefore="["
BracketAfter="]"
BracketBeforeInList="["
BracketAfterInList="]"
CitationSeparator="; "
UniquefierSeparator=","
GroupedNumbersSeparator="-"
MinimumGroupingCount="3"
FormatCitations="false"
CitationCharacterFormat="Default"
MultiCiteChronological="false"
PageInfoSeparator="; "

LAYOUT
article=\format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\author}
(<b>\year\uniq</b>). <i>\title</i>, \journal \volume\begin{pages} :
\format[FormatPagesForHTML]{\pages}\end{pages}.

book=\format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\author}\begin{editor}
\format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\editor} (Ed.)\end{editor},
<b>\year\uniq</b>. <i>\title</i>. \publisher, \address.

incollection=\format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\author}
(<b>\year\uniq</b>). <i>\title</i>. In: \format[AuthorLastFirst,
AuthorAbbreviator,AuthorAndsReplacer]{\editor} (Ed.), <i>\booktitle</i>, \publisher.

inbook=\format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\author}
(<b>\year\uniq</b>). <i>\chapter</i>. In: \format[AuthorLastFirst,
AuthorAbbreviator,AuthorAndsReplacer]{\editor} (Ed.), <i>\title</i>, \publisher.

phdthesis=\format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\author}
(<b>\year\uniq</b>). <i>\title</i>, \school.

default=\format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\author}
(<b>\year\uniq</b>). <i>\title</i>, \journal \volume\begin{pages} :
\format[FormatPagesForHTML]{\pages}\end{pages}.

(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.)

Regarding tool support, there is the Export-Filter-Editor for Jabref to quickly create a style file.

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.

The remainder of each line defines the layout, with normal text and spaces appearing literally in the bibliography entry. Information from the entry is inserted by adding \field markers with the appropriate field name (e.g. \author for inserting the author names). Formatting information for the field can be included here, following JabRef's standard export layout syntax. Refer to JabRef's documentation on custom export filters for more information about which formatters are available and tooling hints.

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.

  • Otherwise, try to use the external tool JabRef LibreOffice Converter. This LibreOffice extension converts the reference marks to code that can be saved.

• 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.

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.

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 "http://purl.org/net/bibteXMP". 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 Xpdf tools and Poppler.

BibTeXMP Fileformat

JabRef builds on Dublin Core 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

@INPROCEEDINGS{CroAnnHow05,
  author = {Crowston, K. and Annabi, H. and Howison, J. and Masango, C.},
  title = {Effective work practices for floss development: A model and propositions},
  booktitle = {Hawaii International Conference On System Sciences (HICSS)},
  year = {2005},
  owner = {oezbek},
  timestamp = {2006.05.29},
  url = {http://james.howison.name/publications}
}

will be transformed into

<?xpacket begin="" id="W5M0MpCehiHzreSzNTczkc9d"?><x:xmpmeta xmlns:x="adobe:ns:meta/">
  <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
    <rdf:Description xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:about="">
      <dc:creator>
        <rdf:Seq>
          <rdf:li>K. Crowston</rdf:li>
          <rdf:li>H. Annabi</rdf:li>
          <rdf:li>J. Howison</rdf:li>
          <rdf:li>C. Masango</rdf:li>
        </rdf:Seq>
      </dc:creator>
      <dc:relation>
        <rdf:Bag>
          <rdf:li>bibtex/booktitle/Hawaii International Conference On System Sciences (HICSS)</rdf:li>
          <rdf:li>bibtex/citationkey/CroAnnHow05</rdf:li>
          <rdf:li>bibtex/file/:CroAnnHow05.pdf:PDF</rdf:li>
          <rdf:li>bibtex/owner/fdarboux</rdf:li>
          <rdf:li>bibtex/timestamp/2020-11-22</rdf:li>
          <rdf:li>bibtex/url/http://james.howison.name/publications</rdf:li>
        </rdf:Bag>
      </dc:relation>
      <dc:title>
        <rdf:Alt>
          <rdf:li xml:lang="x-default">Effective work practices for floss development: A model and propositions</rdf:li>
        </rdf:Alt>
      </dc:title>
      <dc:date>
        <rdf:Seq>
          <rdf:li>2005</rdf:li>
        </rdf:Seq>
      </dc:date>
      <dc:format>application/pdf</dc:format>
      <dc:type>
        <rdf:Bag>
          <rdf:li>InProceedings</rdf:li>
        </rdf:Bag>
      </dc:type>
    </rdf:Description>
  </rdf:RDF>
</x:xmpmeta><?xpacket end="w"?>

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

• Wikipedia article on XMP

• James Howison's blog "Themp---Managing Academic Papers like MP3s"

• Good thread on ArsTechnica discussing the management of PDFs.

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.

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:

C:\portable-apps\JabRef-5.0-portable_windows\JabRef\runtime\bin\JabRef.bat [OPTIONS] [BIBTEX_FILE]

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 docbook format to filetoexport.xml, and suppress the GUI:

C:\portable-apps\JabRef-5.0-portable_windows\JabRef\runtime\bin\JabRef.bat -o filetoexport.xml,docbook5 -n true original.bib

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

Options

• Help: -h

• No-GUI mode: -n

• Import file: -i filename[,import format]

• Export file: -o filename[,export format]

• Import BibTeX: -importBibtex

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

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

• Fetch entries from Web: -f=FetcherName:QueryString

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

• Set file links: -asfl

• Regenerate keys: -g

• Export preferences: -x filename

• Import preferences: -p filename

• Reset preferences: -d key

• No files at startup: -b

• Version: -v

• Debug mode: --debug

• Display output in the console: --console

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

XMP is an ISO standard for the creation, processing and interchange of standardized and custom metadata for digital documents and data sets.

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.

JabRef.bat -o path\export.xmp,xmp  path\entries.bib -n

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.

JabRef.bat -o path\split,xmp  path\entries.bib -n

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.

Information about to the search function is given in 'advanced search' documentation.

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

Show debug level messages. The log files are stored in an internal file. See FAQs for Windows, Linux, macOS depending on your OS where to find it.

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:

The license of the JabRef software

The JabRef software is under the . 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 . 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 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:

Q: After downloading and unzipping, OS X shows “JabRef Installer.app” cannot be opened because it is from an unidentified developer

A: Currently this is necessary, since our code signing infrastructure is not operational. Ctrl-click to open the downloaded .dmg file in Finder to install JabRef.

Q: After installing JabRef 5.9 on macOS ventura I get the error message: JabRef 5.9 is damaged and cannot be opened

A: Execute xattr -d com.apple.quarantine /Applications/JabRef.app

Because we could not get 5.9 notarized correctly from Apple this step is unfortuantely necessary.

Q: I am trying to install JabRef, but I am blocked by "JabRef Installer cannot be opened because it is from an unidentified developer."

A: To override that, Ctrl + Click instead, and choose "open", which gives the same warning but the possibility to override it. then you can install.

Q: Jabref slow/hangs on MacOS Sierra

A: This is a problem some users experience in JabRef 4.0 or later on MacOS Sierra. It seems this is a bug in the networking part of Java on MacOS. You can try to add localhost explicitly to /etc/hosts as described here.

Q: Some characters are not displayed in the main table (math characters or some upper-cased letter)

A: This might be a problem related to the font you are using. You can download some other font that supports mathematical alphanumeric symbols, for example, FreeSerif or Cambria Math. A list of fonts supporting Math Unicode blocks is available at http://www.fileformat.info/info/unicode/block/mathematical_alphanumeric_symbols/fontsupport.htm.

Q: Where can I find JabRef's log files?

A: It's in Users/.../Library/Logs/jabref/version.

We are really happy that you are interested in contributing to JabRef. Please take your time to look around here. We especially invite you to look into our community members page where members introduce themselves.

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

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

The following description appeared first on tex.stackexchange.com.

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

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

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

The importer based on the content has been written for IEEE and LNCS formatted papers. Other formats are not (yet) supported. In case a DOI is found on the first page, the DOI is used to generate the BibTeX information.

The next development step is to extract the title of the PDF, use the "Lookup DOI" and then the Get BibTeX data from DOI functionality from JabRef to fetch the BibTeX data.

We are also thinking about replacing the code completely by using another library. This is much effort and there is no timeline for that.

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

JabRef used to have support for Mr.DLib, which returned back a full BibTeX entry or a PDF. Due to unclear copyright situation of a used library, this service was removed. Further, Mr.DLib changes its focus and will provide literature recommendations. See the realted articles tab.

Related questions on stack overflow

• Extract titles from each page of a PDF?

• Zotero: Extract references from PDF and create new library items from them

• Is there an open source tool for producing bibtex entries from paper PDFs?

• Extracting information from PDFs of research papers

Introduction

JabRef comes with a set of translations into 20 different languages: Chinese (simplified), Danish, Dutch, English, Farsi, French, German, Greek, Indonesian, Italian, Japanese, Norwegian, Persian, Portuguese, Portuguese (Brazil), Russian, Spanish, Swedish, Tagalog, Turkish and Vietnamese.

If the JabRef interface already exists in your language, you can help improve it. Otherwise, you can start translating JabRef into your own language.

Improving an existing translation

We use the service of to keep our translations updated. It is a service directly running in the browser and one can quickly join and start translating.

• Visit to get started

• Select your preferred language, login, and click on JabRef_en.properties

• Choose the string you want to translate in the left panel (strings to be translated are listed first)

  and enter the translation in the central panel (suggestions are given at the bottom)

Translating JabRef into a new language

Crowdin offers to quickly add a new language. Please contact us so that we add a new language for you.

Testing the translation

Crowdin allows for downloading the current translation file:

Place the downloaded file in the path src/main/resources/l10n. Then, execute gradlew run in the root directory and JabRef should start.

For a new language to be available within JabRef, a corresponding line must be added in the Java class GUIGlobals (found in the directory /src/main/java/org/jabref/logic/l10n/Languages.java in the JabRef source code tree). The line is inserted in the static {} section where the map LANGUAGES is populated. The code must of course be recompiled after this modification.

Localization in JabRef code

File location

File format

Each entry is first given in English, then in the other language, with the two parts separated by an '=' character. For instance, a line can look like this in a German translation file:

Note that each space character is escaped (\) to make it a valid property key. The translation value does not need any escapes.

Some entries contain "variables" that are inserted at runtime by JabRef - this can for instance be a file name or a file type name:

A variable is denoted by %0, %1, %2 etc. In such entries, simply repeat the same notation in the translated version.

As we can see, there are several "special" characters: the percent sign and the equals sign, along with the colon character. If these characters are to be part of the actual text in an entry, they must be escaped in the English version, as with the colon in the following example:

The character encoding should be UTF-8. Please avoid Unicode escaping such as \u2302.

Is there any way to include JabRef in the start menu of Ubuntu?

Yes, there is. See for details.

JabRef does not start under Linux! What can I do?

JabRef 5.x

JabRef comes with a bundled JRE. There is no need to install Java separately. Thus, there should be no issues at start up.

JabRef 4.x

JabRef requires Java 8

Please follow the steps provided on our . JabRef 4.x does not run under Java 9 or newer. See

You might see the error message Error: Could not find or load main class org.jabref.JabRefMain. This means, you do not have support activated in your Java runtime environment. This typically happens if you use , where one needs to setup separately.

I am on Debian/Ubuntu and clicking on the JabRef icon works, but I cannot start JabRef from the command line. What is wrong?

You have several Java Virtual Machines installed, and under the command line the wrong one is chosen. Have a look at the previous question that tells you how to change the virtual machine used.

For Ubuntu you may also have a look at the .

Everything looks too big or too small. How can I change it to to a more reasonable size?

Where can I find JabRef's log files?

A: On Linux, the path to the log files is ~/.local/share/jabref/logs/$version/

Here is a quick start guide on how to improve help pages in the .

Prerequisite

The Jabref help pages are hosted at with integration to GitHub, which provides version control based on . In order to edit or create a JabRef help page, you need a GitHub account. You can sign up for free. If you already have an account, please make sure that you are signed in.

Editing Help Pages directly in the browser

The easiest way to fix small errors, or to add additional information, is to edit a help page directly in your browser, using the following steps.

1. Start editing

At the top of each help page, you can find the GitHub icon with "Edit on GitHub" link. Just click the link to show the source of the page.

This leads you to the GitHub page associated with the help page:

To actually edit the page, click on the pencil icon, as highlighted above.

2. Make your changes

The window to edit the page at GitHub looks like this:

In order to review your changes, click on the "Preview changes" tab:

3. Saving the changes

To save the changes, create a so-called "Commit" by scrolling down and pressing the "Propose File Change" button:

Please note: The message you provide here will be visible in the history of the help page, so please consider your change and provide a meaningful description of your changes.

As the last step, submit the changes you have made back to the JabRef team:

Just press the "Create Pull Request" button, and confirm the creation of the request on the next page.

Advanced editing

To edit more than one file at a time, add screenshots, and for other more advanced changes, we recommend that you checkout this repository locally and create a Pull Request of your changes using the standard git and GitHub workflow.

Tables

Q: I use JabRef in my work. Should I mention JabRef in my publications?

A: You are not obliged to cite JabRef, but we would greatly appreciate it if you do.

Q: Is JabRef free for private and corporate use?

A: Yes it is. JabRef is distributed under the MIT License, which .

Q: JabRef does not start. What should I do?

A: You can try resetting the settings. Depending on your operating system, you may need to pass the command line arguments -d all -n to JabRef.

(E.g. in Windows this means jabref-X.Y.exe -d all -n, where X.Y means the version number of JabRef. If this does not help, run regedit and delete the folder HKEY_CURRENT_USER\SOFTWARE\JavaSoft\Prefs\net\sf\jabref. Be careful with regedit, as you can easily corrupt the basic Windows configuration.)

Q: I have tried the latest version of JabRef. Since then, the library entries are no longer displayed in any old version. What should I do?

A: Don't panic. No data should be damaged in your bib library. Since version 5.0 the columns in the main entry table are stored differently internally. You can reset the preferences by command line. See above.

Q: I have a huge library. What can I do to mitigate performance issues?

A: Check your configuration. Disable some or all of following preferences:

• disable fulltext index (File → Preferences → Linked files → Fulltext Index → ...)

• disable time stamps (File → Preferences → General → Time Stamp → ...)

• disable field formatters (Library → Library Properties → Saving → Save actions → ...)

• disable autosave (File → Preferences → File → Saving → ...)

• disable count of items in group (File → Preferences → Groups → ...)

Any preference that has the potential to affect all your entries at once is worth inspecting.

Q: Are there any publications dealing with JabRef?

Q: Does JabRef support non-English languages or UTF8 in general?

A: Yes. In File → Preferences → General, set "Default Encoding" to UTF8 and select an alternative user interface language in "Language" if required.

Q: If I double click a BibTeX file in the file browser, JabRef always opens a new window. Can JabRef open the libraries in the same window just in a different tab?

A: In File → Preference → Single Instance, ensure that "Enforce single JabRef Instance (and allow remote operations) using port [6050]" is checked. Note that 6050 is the default port and can be changed if desired.

Q: I have a DOI/ISBN/ePrint/etc. Is it possible to create an entry directly out of this identifier?

Q: Why can't JabRef find any DOI/ISBN/ePrint/etc.?

Q: I miss a field translator, lastfollowedon, etc. How can I add such fields?

Q: How do I prevent JabRef from introducing line breaks in certain fields (such as “title”) when saving the .bib file?

A: Open File → Preferences. In the “File” panel, you will find an option called “Do not wrap the following fields when saving”. This option contains a semicolon-separated list of field names. Any field you add to this list will always be stored without introduction of line breaks.

Q: Is it possible to append entries from a BibTeX file, e.g. from my web browser to the currently opened library?

Q: How do I link external files with paths relative to my .bib file, so I can move my library along with its files to another directory?

Q: Can I use a bib-file specific PDF directory?

A: In Library → Library properties you can choose a library-specific directory in the field “General file directory”. If you want to set a directory only for you (so that other users should use the default directory), use the field “User-specific file directory”.

Q: How do I export my bibliography entries into a simple text file, so I can import them into a spreadsheet (in LibreOffice, OpenOffice, MS Office, etc.)?

A: Use File → Export. As “Filter” choose “OpenOffice/LibreOffice CSV”.

Q: How do I add and remove keywords of multiple entries?

Q: When linking a file, I cannot set the correct type. How do I add new types?

Q: When an organization is provided as author, my BibTeX style doesn't recognize it. For instance, why is “European Commission” converted to “Commission, E.”?

A: Use curly braces to tell BibTeX to keep your author field as-is: {European Commission}. In BibLaTeX, you can use label = {EC} to have EC05 as a label for a publication of the European Commission in the year 2005.

Q: Is there a FAQ on BibTeX?

Q: How do I export a subset of my library to BibTeX (or BibLaTeX) format?

A: Your JabRef library is already a file in Bib(La)TeX format. To export a specific subset of your library, select the entries to be exported and then choose File → Export → Save selected as plain BibTeX....

Q: I have the Bib(La)TeX code of a reference. How to add it to my library as a new entry?

A: Paste the Bib(la)Tex code of a reference into the table of entries, and JabRef will create the new corresponding entry.

Q: I have the PDF of a publication. How to make it a new entry of my library?

Q: I am looking at a publication in my web browser. How to make it a new entry of my library?

Q: I am missing the DOI of some of my publications. Can JabRef help?

A: JabRef can fetch the DOI for you: select the entries and go to Lookup → Search document identifier online → DOI.

Q: I am missing the PDF of some of my publications. Can JabRef help?​

A: JabRef can fetch the PDFs for you: select the entries and to Lookup → Search full text documents online.​

Q: How do I export a subset corresponding to my LaTeX file?

A: Upon compilation, LaTeX generates a file with the extension ".aux". This file contains the keys of the cited references (among other things). Using this AUX file, JabRef can extract the relevant entries. Choose the menu Tools → New sublibrary based on AUX file... , then select the AUX file.

Q: When I modify my library, I would like that JabRef performs entry cleaning automatically. How to do this?

Q: Search on Google scholar does not work anymore. Why?

Q: JabRef does not push to vim, although I have configured the right path and server name. What is going on?

A: You have to start vim with the option --servername (such as vim --servername MyVimServer). If you get the Unknown option argument message, it means your version of vim does not include the clientserver feature (you can check with vim --version). In such a case, you have to install another version of vim.

Q: My plugins stopped working. Why?

Q: In the preferences, I want to change the option XYZ. How to find it?

A: Enter XYZ in the search field located at the upper left-hand corner of the preference window.

Q: "Unable to monitor file changes. Please close files and processes and restart. You may encounter errors if you continue with this session."

Q: "I'm using JabRef with Linux (Gnome desktop version) and each time I want to see a pdf document in JabRef, the document viewer Evince is opened. I would prefer to open it with Okular."

A: JabRef opens the pdf document with the application Gnome has set by default: Evince. If you want JabRef to open another application (Okular or other), in your file explorer, right-click on whatever pdf file > properties > Open With > choose your application > Set as default at the bottom right corner. From now on, both when you double-click a pdf file in your file explorer or when you ask JabRef to open it via its document viewer, your chosen application will be used.

Q: How does JabRef support me in sharing my Bib(La)TeX libraries?

A: JabRef automatically recognizes a change in the bib file on disk and notifies the user of it. This is cool for network drives.

Q: How to do collaborative work on a library?

Q: Which network protocols and ports are used by JabRef?

A: JabRef uses https to connect to external catalogs to fetch bibliographic data. The concrete port used depends on the external service. Mostly, the standard port 443 is used. When connecting to a SQL database, the standard port for PostgreSQL and MySQL is used. JabRef offers a local interface used by the browser plugin. For that, JabRef uses a proprietary, text-based protocol offered on the configurable port 6050.

Q: My question is not answered here. What can I do?

Q: There is a mistake in this FAQ, a dead link, or I have written a better/new explanation for a question! What can I do?

See also:

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:

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 , and to perform some simple operations like generating citation keys for the entries or adding them to . 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

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.

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:

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

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

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.

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