How to find, sort, and clean entries

Import and export of bibliographic information using online bibliographic databases

Import and export of bibliographic information using identifiers (such as a DOI)

JabRef can check the integrity of a database.

This feature is available through Quality → Check integrity....

Import and export of bibliographic information

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

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

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

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

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

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

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

This feature is available through Edit → Set/clear/rename fields.

This feature allows you to store a selection of often-used words or phrases that you use often in your database. By default it is enabled for the fields Journal, Author, Keywords and Publisher, but you can also add selectors to other fields, in the upper part of the Manage dialog (menu Options -→ Manage content selectors).

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

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

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

To fetch entries from arXiv, choose Search → Web search, and the search interface will appear in the side pane. Select ArXiv.org in the dropdown menu. Enter the words of your query, and press Enter or the Fetch button.

The results are displayed in the . In case an error occurs, it is shown in a popup.

is a public search engine for scientific and academic papers primarily with a focus on computer and information science. However, CiteSeerX has been expanding into other scholarly domains such as economics, physics and others ().

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

The results are displayed in the . In case an error occurs, it is shown in a popup.

is a computer science bibliography website listing more than 3.1 million journal articles, conference papers, and other publications on computer science ().

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

The results are displayed in the . In case an error occurs, it is shown in a popup.

(aka Springer Science+Business Media) is a global publishing company that publishes books, e-books and peer-reviewed journals in science, technical and medical publishing. Springer also hosts a number of scientific databases, including SpringerLink, Springer Protocols, and SpringerImages ().

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

The results are displayed in the . In case an error occurs, it is shown in a popup.

is a reviewing service providing reviews and abstracts for articles in pure and applied mathematics ().

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

Then, the results are displayed in the . In case an error occurs, it is shown in a popup.

To use this feature, choose BibTeX → New entry.... In the lower part, there is the box "ID-based entry generator". In the field "ID type", you can select "Title". The field "ID" is focused. Enter the title here and press Enter to generate an entry based on the title. You can also click on "Generate". Then, (provided by ) is used to determine the DOI and convert the determined DOI to a BibTeX entry. The found entry is opened in an entry editor. In case an error occurs, a popup is shown. In case no DOI could be determined, no entry is created.

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).

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

Then, the results are displayed in the import inspection window. In case an error occurs, it is shown in a popup.

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).

To fetch entries from SAO/NASA Astrophysics Data System, choose Search → Web search, and the search interface will appear in the side pane. Select SAO/NASA Astrophysics Data System in the dropdown menu. To start a search, enter the words of your query, and press Enter or the Fetch button.

Then, the results are displayed in the import inspection window. In case an error occurs, it is shown in a popup.

Apart from fetching entries by using a full search, it is also possible to directly create a BibTeX entry using the BibTeX → New Entry dialog. More details are described at ADS-to-BibTeX.

DOAJ (Directory of Open Access Journals) is a database covering more than 10000 open access journals covering all areas of science, technology, medicine, social science and humanities (Wikipedia).

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

The results are displayed in the import inspection window. In case an error occurs, it is shown in a popup.

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

• title: The title of the article

• doi: The DOI of the article

• issn: The ISSN of the journal

• publisher: The publisher of the journal

• abstract: The abstract of the article

IEEEXplore is a scholarly research database that indexes, abstracts, and provides full-text for articles and papers on computer science, electrical engineering and electronics. IEEEXplore comprises over 180 journals, over 1,400 conference proceedings, more than 3,800 technical standards, over 1,800 eBooks and over 400 educational courses (Wikipedia)

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

By checking the Include abstracts checkbox, you may opt to download the abstracts along with the cite information for each entry. This will NOT cause more network queries.

The results are displayed in the import inspection window. In case an error occurs, it is shown in a popup.

Notes

• The search is done in guest mode, which means that a maximum of 100 results will be returned.

• The option to download BibTeX citations directly from IEEEXplore is not working yet.

• Please email Oscar Gustafsson ogib73@gmail.com or Aaron Chen nextAaron@gmail.com for any suggestions.

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 create a new entry form an IACR eprint ID, choose BibTeX → New entry.... In the lower part, there is the box "ID-based entry generator". In the field "ID type", "IACR" should be already selected. The field "ID" is focused. Enter the eprints' ID here and press Enter to generate an entry based on the Id. You can also click on "Generate". The new entry is opened in an entry editor. In case an error occurs, a popup is shown.

To get the ID, you may want to use their web search form at https://eprint.iacr.org/search.html.

This feature is available through Quality → Synchronize file links....

This feature is available through Search → Replace string....

This feature is available through Options → Manage external file types.

Sharing libraries.

FAQs on JabRef

This feature is available through Options → Manage protected terms.

JabRef can be configured in various ways.

This feature is available through Options → Customize key bindings.

You can reset the key bindings to default by pressing the "Default" button. This is especially useful when upgrading from a JabRef version before 3.8.2.

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

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

For example:

General:url;keywords;doi;pdf
Abstract:abstract;annote

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

For linking attached files, see File links in JabRef.

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

Setting up external viewers

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

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

Opening external links

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

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

By default the entry table will contain a singly column containing an indicator whether there is a DOI or a URL linked. You can disable any of these in Options → Preferences → Entry table columns.

Special fields offer the functionality

• rate read papers

• mark papers as relevant for the work

• mark BibTeX entries as quality assured, and

• prioritize unread papers.

The main difference from the marked entry is that the rated entry is not floating by default and only highlight the number column. Thus, an entry may be both marked and rated.

Each special field may be turned on and off in the settings.

The aim is to add a functionality to set a range of “positive” ratings. JabRef offers a rank from one to five stars to rate papers.

An entry may be marked as relevant.

An entry may be marked as quality assured. The intention is to mark BibTeX entries, where a thorough checking of the field contents has been done.

One may prioritize entries from prio3 (low) to prio1 (high). The main intention is to prioritize unread papers.

Internally, each special field is stored in a separate BibTeX field. If “Write values of special fields as separate fields to BibTeX” is active, these fields are also written when the database is saved. JabRef also offers synchronizing the fields with keywords. This is enabled by the setting “Synchronize with keywords”. If this setting is active, then each change in a special field is reflected in the keyword field. Vice versa, each change in a keyword also leads to a change in the special field. Additionally, when loading a the database or pasting a new entry, the keywords are used to set the special field values.

The ACM Portal includes two databases (Wikipedia):

• the ACM Digital Library is a text collection of every article published by the Association for Computing Machinery, including over 60 years of archives

  from articles, magazines and conference proceedings.

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

To fetch entries from ACM, choose Search → Web search, and the search interface will appear in the side pane. Select ACM portal in the dropdown menu. You may choose which database to search and you may opt to download the abstracts along with the cite information for each entry, by checking the Include abstracts checkbox. To start a search, enter the words of your query, and press Enter or the Fetch button.

Frequent connections to ACM Portal may get your IP banned for hours. To avoid this, JabRef will display a preview (for each search) of the first page of entries returned by the server. You can then choose which entries to download.

Then, the results are displayed in the .

Helpful groups

• Group for your own papers: author=YOURSELF

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

See Groups for more information on grouping.

Sort order

Sort your entries with the bibtexkey on save (can be set in the database properties). This makes finding an entry easier in a large file.

Use Quality -> Integrity Check often to ensure that the quality of your database does not degrade. See for more information.

Specify your save actions (can be set in the database properties). This ensures that your BibTeX file will look more consistent.

See for more information.

Opened from main window by double-clicking anywhere on the line of the entry, or selecting the entry and pressing Enter or Ctrl + D. The panel is closed by pressing Esc._

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

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

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

The entry editor's panels

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

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

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

The BibTeX source panel shows how the entry will appear when the database is saved in BibTeX format. If you wish, you can edit the BibTeX source directly in this panel. When you move to a different panel, press Ctrl + S or close the entry editor, JabRef will try to parse the contents of the source panel. If there are problems, you will be notified, and given the option to edit your entry further, or to revert to the former contents. If Show source by default is checked in the General options tab of the Preferences dialog, the source panel will be the one shown each time you open the entry editor. If you prefer editing the source rather than using the other four panels, you should check this option.

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

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

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

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

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

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

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

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

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

The entry editor allows for file(s) to be dragged and dropped directly into the entry editor window. There are three different types of behaviors that govern how the files are handled, and the user can set which behavior they would like the entry editor to use in the Entry editor tab of the Preferences dialog. These behaviors are the following: copy, link, move.

If the copy option is selected as the drag and drop behavior, the entry editor will create a copy of the file in the current directory. While this option is selected, the keyboard shortcuts needed to move, copy or link files are the following:

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

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

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

If the link option is selected as the drag and drop behavior, the entry editor will create a link of the file. This creates a shortcut to the file and will not copy the file to the current directory. While this option is selected, the keyboard shortcuts needed to move, copy or link files are the following:

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

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

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

If the move option (shown as Copy, rename and link file) is selected as the drag and drop behavior, the entry editor will move the file to the current directory by copying the file to the current location, renaming the copy, and linking it to the original file. While this option is selected, the keyboard shortcuts needed to move, copy or link files are the following:

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

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

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

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

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

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

For more information on how JabRef generates BibTeX keys, see .

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

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

Description of Google Scholar

Google Scholar is a freely accessible database that indexes the full text or metadata of scholarly literature across an array of publishing formats and disciplines. Google Scholar index includes most peer-reviewed online academic journals and books, conference papers, theses and dissertations, preprints, abstracts, technical reports, and other scholarly literature, including court opinions and patents (Wikipedia).

Usage

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

Traffic limitations

Google scholar can block "automated" crawls which generate too much traffic in a short time. Normally, the results are displayed in the import inspection window. In case an error occurs, it is shown in a popup.

However, after too much crawls JabRef --- or more precisely: your IP address --- could be blocked. 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.

Thus, the Google Scholar fetcher is not the best way to obtain lots of entries at the same time. If you are using Mozilla Firefox, the JabRef Plugin "JabFox" might be an alternative to download the BibTeX data directly from the browser. You can find the PlugIn here: .

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

To use this feature, choose BibTeX → New entry.... In the lower part, there is the box "ID-based entry generator". In the field "ID type", "DiVA" can be selected (see screenshot below). Select the field "ID" and enter the DiVA here (e.g., diva2:260746) and press Enter to generate an entry based on the Id. You can also click on "Generate". The found entry is opened in an entry editor. In case an error occurs, a popup is shown.

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."

To use this feature, choose BibTeX → New entry.... In the lower part, there is the box "ID-based entry generator". In the field "ID type", "RFC" can be selected (see screenshot below). Select the field "ID" and enter the RFC here, with or without the "rfc" prefix (e.g. 1954, rfc1954) and press Enter to generate an entry based on the Id. You can also click on "Generate". The found entry is opened in an entry editor. In case an error occurs, a popup is shown.

JabRef can cleanup the entries of a database. To do a cleanup of the entries, go to Quality → Cleanup entries.

In the lower part, you can choose "Run field formatter", where you can choose different Save Actions. Dependent on the database mode, "Recommended for BibTeX" or "Recommended for BibLaTeX". When pressing this button, the recommended cleanups for the respective mode is called.

JabRef generates .sav and .bak files while working. .sav is the automatic backup feature: Each 15 seconds, the current state of the library is saved. .bak preserves the last state of the library after saving. Thus, one can go back one save command in the history.

By using the service, you can generate an appropriate .gitignore file by opening .

In addition to .bak and to

JabRef supports following fields to jump to other entries.

Following fields are supported:

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

• crossref

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

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

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

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

The timestamp field can be edited in the

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

and then in some entry for example

or

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

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

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 a cross-platform application that works on Windows, Linux and Mac OS X. It is available free of charge and is actively developed. JabRef supports you in every step of your research work.

• across many online scientific catalogues like , CrossRef, Google Scholar, IEEEXplore, INSPIRE-HEP, Medline PubMed, MathSciNet, Springer, arXiv, and zbMATH

JabRef can help you complement your entries from their DOI.

Open the , and in the General tab, click on the button Get BibTeX data from DOI. Obviously, this feature is available only if your entry already has a DOI.

The Merge entry with DOI information window will pop-up.

The fields of the original entry and of the information gathered from the DOI are displayed side-by-side on the upper part of the window.

The differences between the two sides can be emphasized through the drop-down menu located at the upper right-hand corner of the window. Five ways of displaying the differences are offered:

, the GBV Union Catalogue, is a multimaterial bibliographic database of seven German federal states. It covers 41.5 million records of books, conference proceedings, periodicals, dissertations, microfilms and electronic resources.

To fetch entries from GVK, choose Search → Web search, and the search interface will appear in the side pane. Select GVK (Gemeinsamer Verbundkatalog) in the dropdown menu. To start a search, enter the words of your query, and press Enter or the Fetch button.

The results are displayed in the . In case an error occurs, it is shown in a popup.

You can simply enter words / names / years you want to search for, or you can specify search keys. Supported keys are:

JabRef can look for duplicated entries inside a database.

This feature is accessible directly through Quality → Find duplicates. It is also used when 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.

When two potential duplicates are found, their fields are displayed side-by-side.

The differences between the two entries can be emphasized through the drop-down menu located at the upper right-hand corner of the window. Five ways of displaying the differences are offered:

is an open access digital library for the field of high energy physics ().

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

The results are displayed in the . In case an error occurs, it is shown in a popup.

The INSPIRE-HEP search function merely passes your search queries onto the INSPIRE-HEP web search, so you should build your queries in the same way, except omitting the find or fin command. This help page will only give a brief introduction to the search queries. More extensive help on searching INSPIRE-HEP can be found on the page .

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 ().

To use this feature, choose BibTeX → New entry.... In the lower part, there is the box "ID-based entry generator". In the field "ID type", "Medline" can be selected (see screenshot below). Select the field "ID" and enter the Medline ID here (e.g., 27934767) and press Enter to generate an entry based on the Id. You can also click on "Generate". The found entry is opened in an entry editor. In case an error occurs, a popup is shown.

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.

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

• Download and install

JabRef allows you to push any entries in your main window to an external editor through the push-to-external application feature. You would need to first select the entries in your entry table that you would like to export before using the feature. Once you have done so, go to the tools submenu and click on the push-to-external application button to the left of the Generate BibTeX keys button. By default the external editor used to push exports is TeXStudio.

On MacOS:

On Windows:

JabRef also allows you to change the external editor application you would like to push your exports to. To do so, first go to Options → Preferences → External programs. Under the Push applications section click on the Application to push entries to field. This will cause a dropdown menu to appear, from which you are then able to select from a list of all the external editors you have configured.

To use this feature, choose BibTeX → New entry.... In the lower part, there is the box "ID-based entry generator". In the field "ID type", you can select "ISBN". The field "ID" is focused. Enter the ISBN here and press Enter to generate an entry based on the Id. You can also click on "Generate". Then, API is used to convert an ISBN to a BibTeX entry. If no entry is found, the fetcher tries to find an entry. The found entry is opened in an entry editor. In case an error occurs, a popup is shown.

Some fetched entries contain a url field. This field points to the URL of the book at the respective online book store. In case you buy the book using the link, the service provider (ebook.de) receive a commission to fund the service.

This help applies for older versions of JabRef. From JabRef 3.6 onwards, is supported

JabRef is capable of exporting the contents of the BibTeX database, along with groups information, to an external MySQL or PostgreSQL database.

You just need to be sure you have an user/password with full privileges on a MySQL or PostgreSQL server.

1. Choose File → Export to external SQL database, or click the corresponding button on the toolbar.

JabRef allows to share both Bib(La)TeX database and .

When sharing a Bib(La)TeX database, 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 database easier, it is recommended to set specific database properties. In the menu File -> database properties:

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 ().

To use this feature, choose BibTeX → New entry.... In the lower part, there is the box "ID-based entry generator". In the field "ID type", "SAO/NASA Astrophysics Data System" can be selected (see screenshot below). Select the field "ID" and enter the SAO/NASA Astrophysics Data System ID here (e.g., 2013Sci...339..671W) and press Enter to generate an entry based on the Id. You can also click on "Generate". The found entry is opened in an entry editor. In case an error occurs, a popup is shown.

To customize entry types, select the menu Options → Customize entry types.

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

Note that no modifications you make in this dialog will be stored until you click Apply. If you click Cancel or simply close the dialog, unapplied changes will be lost.

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

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

To use this feature, choose BibTeX → New entry.... In the lower part, there is the box "ID-based entry generator". In the field "ID type", "DOI" should be already selected. The field "ID" is focused. Enter the DOI here and press Enter to generate an entry based on the Id. You can also click on "Generate". Then, (provided by ) is used to convert the given DOI to a BibTeX entry. The found entry is opened in an entry editor. In case an error occurs, a popup is shown.

The entry preview is created using the same mechanism as used by the facility. When previewed, an entry is processed using one of the two alternative layouts (you can switch between the two layouts by pressing F9) to produce HTML code which is displayed by the preview panel. To modify the appearance and contents of the preview you need to edit the preview layouts using the syntax described in the help file on .

is an open database with over 20 million free scholarly articles harvested from over 50,000 journals and open-access repositories around the globe. Sources for these articles include repositories run by renowned universities, governments, and scholarly societies. Unpaywall is integrated into thousands of existing search engines, library platforms, and information products, making articles easy to find, track, and use for your scholarly communication needs.

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.

The results are displayed in the . In case an error occurs, it is shown in a popup.

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.

If you use version control, a few advices are given for a smoother sharing of a bib file.

In addition, we have many open issues dealing with collaboration.

Q: How to do collaborative work on a library?

A: You can either choose to use an SQL database or to share a bib file.

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

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

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

Using the feature

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

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

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

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

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

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

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

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

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

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

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

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

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

External lists can be found at . These data files are in CSV format (using semicolons as separators):

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

We want to expand both the build-in list and the selection of smaller lists, so if you have set up a representative list for your own subject area, we would appreciate it if you share your list via or by dropping a note on .

MEDLINE 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).

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

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.

2. Enter a set of names and/or words to search for. You can use the operators and and or and parentheses to refine your search expression. See for full description.

   Examples:

   • May \[au\] AND Anderson \[au\]

In both cases, press Enter or the Fetch button. If you use a text search, you will be prompted with the number of entries found, and given a choice of how many to download.

Then, the results are displayed in the . In case an error occurs, it is shown in a popup.

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

JabRef is not intended to be a tool for mass download of citations. The purpose of the WebFetchers (such as the Medline Fetcher) is to simplify download of single, or at least few entries without using the browser. That means, one tries to import the bibliographic information of already known publications in a simple way.

However, it is still possible to import hundreds or even thousands of entries from medline using the export functionality of the database itself. Perfom the search query you like, and then choose the "Send to" → "File" export (choose Medline or XML as format):

The downloaded file can then be imported using JabRefs "File" → "Import into current/new database" feature. Note: depending on the number the import might require some - or quite a lot of time. It was tried in 2016 with an exported XML file of 130MB an over 11000 found entries, which required more than 10 minutes of import.

Apart from fetching entries by using a full search it is also possible to directly create a BibTeX entry using the BibTeX → New Entry dialog. More details are described at .

JabRef can help you merging entries of your database.

First, select the two entries to be merged. Then select the menu Quality → Merge entries.... The Merge entries window will pop-up.

Parallel display of the entries' fields

The fields of the two entries are displayed side-by-side on the upper part of the window.

The differences between the two entries can be emphasized through the drop-down menu located at the upper right-hand corner of the window. Five ways of displaying the differences are offered:

• plain text: as is, no emphasis

• show diff - word: differences are shown in the right entry. Full words are struck out in red if they are removed from the left entry or underlined in blue if they are added to the right entry.

• show diff - character: differences are shown in the right entry. Individual characters are struck out in red or underlined in blue as above.

• show symmetric diff - word: differences are shown on both sides. Words are underlined and displayed in color.

• show symmetric diff - character: differences are shown on both sides. Characters are underlined and displayed in color.

In the central column, a radio button allows you to select which side to keep for each field: the left side, the right side, or none. By default, the left entry is kept, and any fields not present in the left entry are obtained from the right entry.

Based upon your selection, the merged entry is shown, both as a preview (on the left) and as source code (on the right).

If you right-click on the preview, you can Print entry preview or Copy preview.

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

See also:

Import inspection window

Purpose

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

The inspection window

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

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

By default, all the entries are selected for importation, as shown by the checked boxes in the Keep column. You can select/unselect an entry by clicking on these check boxes. 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 an 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

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

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.

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.

Export from JabRef

JabRef can export databases to EndNote-readable files. To use this feature, choose File → Export, choose the file type Endnote (txt) and then specify the name of the export file.

Import to EndNote

The default EndNote Import filter does not handle multiple authors or editors properly. There are two options to work around this:

1. Use the built-in filter and fix the file later. To open up the file in EndNote, create a new database or open an old database in EndNote. Then select File → Import, click on Choose File, then highlight the exported file and click Choose. Click on Import Options and select EndNote Import. Click Import to start the import. After import, select Edit→ Change Text. Change Any Field to Author. Enter " and " into the search field (without quotes). enter a return character into the change field (Option + Enter on Mac OS X, Ctrl + Enter on Windows XP). Click Change. Repeat with the Secondary Author field.

2. Install the EndNote Import from JabRef filter in the EndNote Extras. Follow the instructions in Advanced Use below. To open up the file in EndNote, create a new database or open an old database in EndNote. Then select File → Import, click on Choose File, then highlight the exported file and click Choose. Click on Import Options and select EndNote Import from JabRef (if it does not appear, select Other filters. If it still doesn't appear, it was not correctly installed.) Click Import to start the import.

The EndNote Export filter maps BibTeX entrytypes to EndNote reference types as follows:

By default, the export filter assumes that entries in the author or editor fields in brackets are corporate authors and replaces the brackets with a trailing comma. However, this means that entries that include LaTeX code in brackets will be assumed to be corporate authors and therefore will be improperly formatted.

For better interoperability between EndNote and JabRef, download the EndNote filter set from the Resources page of JabRef's web page.

JabRef is able to support collaborative work using a shared SQL database. This feature is available since JabRef 3.6.

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.

You can test the shared SQL database support by using for MySQL (not recommended) and for PostgreSQL (recommended).

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

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

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

1. Determine the DOI: Switch to the "General" tab and click on "Look up DOI"

2. Fetch BibTeX data from the DOI: Click on "Get BibTeX data from DOI"

3. A popup appears. Select which data you want to merge into the eixting entry

4. Now the first names are expaned:

Strings can be edited by BibTeX → Edit strings or pressing a button in the toolbar.

Strings are the BibTeX equivalent to constants in a programming language. Each string is defined with a unique name and a content. Elsewhere in the database, the name can be used to represent the content.

For instance, if many entries are from a journal with an abbreviation that may be hard to remember, such as 'J. Theor. Biol.' (Journal of Theoretical Biology), a string named JTB could be defined to represent the journal's name. Instead of repeating the exact journal name in each entry, the characters '#JTB#' (without quotes) are put into the journal field of each, ensuring the journal name is written identically each time.

A string reference can appear anywhere in a field, always by enclosing the string's name in a pair of '#' characters. This syntax is specific for JabRef, and differs slightly from the BibTeX notation that is produced when you save your database. Strings can by default be used for all standard BibTeX fields, and in Preferences → General → File you can opt to enable strings for non-standard fields as well. In the latter case you can specify a set of fields that are excepted from string resolving, and here it is recommended to include the 'url' field and other fields that may need to contain the '#' character and that may be processed by BibTeX/LaTeX.

A string may in the same way be referred in the content of another string, provided the referred string is defined before the referring one.

While the order of strings in your BibTeX file is important in some cases, you do not have to worry about this when using JabRef. The strings will be displayed in alphabetical order in the string editor, and stored in the same order, except when a different ordering is required by BibTeX.

For a complete description of string syntax, see the .

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

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

Overview

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

See the image below to see how it works:

Key Features

The new tab

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

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

• A progress indicator appears while parsing.

• Current search is cancelled if another entry is selected.

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

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

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

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

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

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

Field formatting can be tidied up when saving the database. That ensures your entries to have consistent formatting. If you check Enable save actions in the Database Properties, the list of actions can be configured.

Each action is defined by:

• 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).

Dependent on the database mode, "Recommended for BibTeX" or "Recommended for BibLaTeX". When pressing this button, the recommended cleanups for the respective mode is called.

Add braces encapsulating the complete field content. For instance

gets

However, this procedure is not recommended. It is better to use the "Protect Terms" functionality. See also .

Clears the field completely.

Escape underscores

Converts HTML code to LaTeX code.

Converts HTML code to Unicode.

Cleans up LaTeX code.

Normalizes the date to ISO date format. Format date string to yyyy-mm-dd or yyyy-mm. Keeps the existing String if it does not match one of the following formats:

• "M/y" (covers 9/15, 9/2015, and 09/2015)

• "MMMM (dd), yyyy" (covers September 1, 2015 and September, 2015)

• "yyyy-MM-dd" (covers 2009-1-15)

Normalizes the en dashes.

• Replace “-” with “--”.

Normalize month to BibTeX standard abbreviation.

Normalizes lists of persons to the BibTeX standard. This separates authors by "and"s with first names after last name separated by a commma; first names are not abbreviated.

• "John Smith" ⇒ "Smith, John"

• "John Smith and Black Brown, Peter" ⇒ "Smith, John and Black Brown, Peter"

• "John von Neumann and John Smith and Black Brown, Peter" ⇒ "von Neumann, John and Smith, John and Black Brown, Peter".

Normalize pages to BibTeX standard. Format page numbers, separated either by commas or double-hyphens. Converts the range number format to page_number--page_number. Removes unwanted literals except letters, numbers and -+ signs. Keeps the existing String if the resulting field does not match the expected Regex.

Converts ordinals to LaTeX superscripts, e.g. 1st, 2nd or 3rd. Will replace ordinal numbers even if they are semantically wrong, e.g. 21rd

• 1st Conf. Cloud Computing -> 1\textsuperscript{st} Conf. Cloud Computing

Removes braces encapsulating the complete field content.

Removes all hyphenated line breaks in the field content.

Removes all line breaks in the field content.

Shortens DOI to more human readable form using .

Converts Unicode characters to LaTeX encoding.

Converts units to LaTeX formatting. This includes:

• Add braces around the unit to keep case.

• Replace hyphen with non-break hyphen

• Replace space with a hard space

Changes the first letter of all words to capital case and the remaining letters to lower case.

Changes all letters to lower case.

Adds {} brackets around acronyms, month names and countries to preserve their case.

Capitalize the first word, changes other words to lower case.

Capitalize all words, but converts articles, prepositions, and conjunctions to lower case.

Changes all letters to upper case.

Shortens lists of persons if there are more than 2 persons to "et al.".

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. Thereby, 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:

JabRef thereby used the service offered by . This servce was shut down in 2019. The following explanations are only for historical interest.

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

2. Select an entry type. Select "InProceedings", this works in the most cases

After step 4 from above, you can manually assign the types to each text.

• Select the text

• Double click on the type at the right side at "Available BibTeX fields"

After you finished, you can press "Accept".

Each database can have specific properties that can be modified through File → Database properties) or by right clicking on the tab of the database and choosing "Database properties". These specific properties override the generic properties defined in Options → Preferences.

The database-specific properties are stored in the database itself. This way, when moving the database to another computer, these properties are preserved. In most of cases these are stored in the bib-file database using text blocks starting with @Comment{jabref-meta: .

Database encoding

This setting determines which character encoding JabRef will use when writing this database to disk. Changing this setting will override the setting made in Preferences dialog for this database. JabRef specifies the encoding near the top of the bib file, in order to be able to use the correct encoding next time you open the file.

The dropdown menu allows to select one encoding. UTF-8 is highly recommended.

In your database, files (PDF, etc.) can be linked to an entry. The list of these files are stored in the file field of the entry. The location of these files has to be specified.

For your database, you can define a General file directory and a User-specific file directory. These settings override the main file directory defined in the Preferences dialog.

The General file directory is a common path for all the users of a shared database. The User-specific file directory allows each user to have its own file directory for the database. If defined, it overrides the General file directory.

JabRef stores the name of the current system alongside the User-specific file directory. This assumes that each user of the database has a different system name. For example, when using the computer laptop, the entry in the bib file is @Comment{jabref-meta: fileDirectory-jabref-laptop:\somedir;}

Relative directories can be specified. This means that the location of the files will be interpreted relative to the location of the bib file. Simply setting a directory to "." (without quotes) means that the files should reside in the same directory as the bib file.

Note: the legacy PDF/PS links (i.e. the pdf and ps fields, which were used in JabRef versions prior to 2.3), should in current versions be replaced by general file links. This can be done using Quality → Cleanup entries... and enabling Upgrade external PDF/PS links to use the 'file' field.

When saving the database, the order of the entries will be preserved if Save entries in their original order is selected. Alternatively, by selecting Save entries ordered as specified, you can choose to sort the entries using three criteria. For each criterion, you can type-in the field to be used and select the order.

Note: Entries containing a crossref field will always be placed prior to the other entries. This is a necessary preliminary for BibTeX to be able to determine the correct referenced values. (See: , p. 26)

While you edit a shared database, another user may be editing it too. By default, saving the database will overwrite changes done by others (although a warning message about the changes will be displayed).

To avoid discarding changes involuntarily, and hence to allow a smooth collaborative work, you can choose to Refuse to save the database before external changes have been reviewed. This setting lets you enforce reviewing of external changes before the database can be saved: users will only be able to save the database after any external changes have been reviewed and either merged or rejected.

Note: this is not a security feature, merely a way to prevent users from overwriting other users' changes inadvertently. This feature does not protect your database against malicious users.

Field formatting can be tidied up when saving the database. That ensures your entries to have consistent formatting. If you check Enable save actions, the list of actions can be configured.

For more information see .

Note that some properties are not available for shared as they are not handled like a .bib file. The following properties are not available:

• Database encoding (always UTF-8)

• Save sort order

• Database protection

This feature is available through Quality → Find unlinked files....

The following description appeared first on .

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

1. Create or open a .bib file.

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.

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

Firefox - Chrome - Edge - Vivaldi

JabRef has 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. A wide range of publisher sites, library catalogs and databases are supported.

Installation and Configuration

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

- - -

Sometimes, a manual installation is necessary (e.g. if you use the portable version of JabRef). In this case, please take the following steps:

1. Make sure you have at least installed.

2. Install the JabRef browser extension: , ,

3. On Windows 7, please .

1. Download and install the Debian package of

2. Install the JabRef browser extension: , ,

3. Download and put it into

1. Install the snap package of

2. Install the JabRef browser extension: , ,

3. Connect the appropriate plug for the selected browser:

1. Download and install the DMG package of .

2. Install the JabRef browser extension: , ,

3. Download and put it into

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 "Remote operation" under the Advanced tab in the JabRef Preferences.

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.

I am not a programmer

I would like to improve the help page. What are the steps?

Please use the "Edit on GitHub" link at the upper right corner. Then, follow GitHub's guide to edit files in other user's repository.

I would like to help translating JabRef to another language. How do I get started?

We encourage you to read about translating the JabRef user interface.

I want to keep Wikipedia pages up-to-date

JabRef improves -- and Wikipedia pages should keep up!

Simply click on "Edit" (top right-hand tab).

Currently existing pages are:

• Deutsch:

• English:

• Español:

• Français:

• Italiano:

• Русский:

• Portuguese:

• Svenska:

• Українська:

• 中文:

If there is no page for you own language, you can easily create one.

Donations keeps us going! You can use Paypal, Flattr, or bank transfers. Your institution/company can contribute too, through bank transfer for example. All details are provided at .

Our team consists of volunteers. To provide better support, we are currently trying to get a funded developer on board. Please consider donating money!

Please head to to learn about our current efforts to measure and improve code quality.

We collect small issues at . In case you do not find something suitable, you are invited to get in touch with us. Comment at the issue, check the or join our . For the brave, we also collect issues at .

After finding something, please check our for detailed information and further links.

Look at the discussions in our forum at . Find an interesting topic, discuss it and start contributing.

You can talk to the core developers of JabRef in the .

XMP is a standard created by Adobe Systems for storing metadata (data about data) in files. An 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 in the General Tab of JabRef, which will put all the BibTeX information into the PDF. If you then email this PDF to a colleague she can just drag the file into JabRef and all information that you entered will be available to her.

Usage

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

• To import a single annotated PDF-file that contains XMP you can select "File → Import into... → XMP-annotated PDF" or drag the file into the main view.

• To write the bibliographic information to the associated PDF do the following: Double click the entry in the main view, go to the "General" tab and click on "Write XMP".

• If you want to annotate all the PDFs in a given database you can select "Tools → Write XMP for database"

• 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 "". This works only with Adobe Acrobat, not with Adobe Reader.

• If you don't have Adobe Acrobat, you can use pdfinfo instead in order to see the XMP metadata. pdfinfo is part of and .

XMP uses a subset of the Resource Description Framework (RDF) to store data. For JabRef a new metadata format is used which maps very closely to BibTeX. 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 'and's. All strings and crossrefs will be resolved in the data.

The following easy minimal schema is used:

• The BibTeX-key is stored as bibtexkey.

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

• author

The following is an example of the mapping

will be transformed into

Beware of the following caveats if you trying to parse BibTeXMP:

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

Some links about XMP and annotating PDFs

Introduction

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

For each language, there is the file JabRef_xx.properties (xx denotes the country code for the language). It contains all translations in a key/value format. In the JabRef source code tree, the property files reside in the /src/main/resources/l10n directory.

Improving an existing translation

We use the service of Crowdin to keep our translations updated. It is a service directly running in the browser and one can quickly join and start translating. Please visit https://translate.jabref.org/ to get started.

Translating JabRef into a new language

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

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 esacpes.

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.

To test your translation you must be able to compile the source tree after making your additions. This requires you to install the . Ensure that you use the most recent version.

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 testing a crowdin-contributed translation without having to compile JabRef, one has to wait until the translation is incorporated into the current source code of JabRef.

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.

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

Yes, there is. See http://askubuntu.com/a/721387/196423 for details.

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

JabRef 5.x

JabRef 5.x requires Java 13 (It is included in the native builds)

JabRef 4.x

JabRef requires Java 8

Please follow the steps provided on our installation page. JabRef 4.x does not run under Java 9 or newer. See https://github.com/JabRef/jabref/issues/2594

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

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 .

As far as we know, JabRef is not yet running on these free JVMs, due of our dependencies. However, JabRef is reported to run nicely on the runtime, which is based on the built with to fill in missing classes. Some issues have been encountered with the look and feel (see issues and ). Please let us know if newer versions give different results. If you have an idea or the expertise to make JabRef work under Classpath, let us know.

In the background, JabRef uses . Applications using JavaFX can be scaled via java -Dglass.gtk.uiScale=1.5 -jar <application>.jar. If you have installed JabRef via a package manager, you probably don't have a .jar file but a binary file. In this case, you need to find your JabRef.cfg in your installation folder (possibly located at /opt/JabRef/lib/app/JabRef.cfg) and add in the section [JavaOptions] the line -Dglass.gtk.uiScale=1.5. Then, restart JabRef. Try finding a value that is suitable for you. On high resolution displays, values around 1.5 seem to be reasonable.

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

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

Here is a quick start guide of how to improve the help page.

Our help pages are hosted at with an 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.

The easiest way to fix small errors or to add additional information is to edit a JabRef help page directly in your browser:

At the top of each help page you can find the GitHub icon. Just click here to show the source of the page.

This leads you to GitHub:

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.

Locate JabRef.bat (Windows) or JabRef (Linux, Mac OS). In the partable versions, this is JabRef-5.0-portable_windows\JabRef\runtime\bin\JabRef.bat and JabRef-5.0-portable_linux\JabRef\lib\runtime\bin\JabRef.

Do not use JabRef\JabRef.exe or

The search bar is located between the icon bar and the database tabs.

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

• click in the search field.

• select the menu Search → Search.

Groups allow to structure a BibTeX database in a tree-like way that is similar to organizing files on disk in directories and subdirectories. The two main differences are:

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

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

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