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: .
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: Tame the BeaST, 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 Save Actions.
Note that some properties are not available for shared SQL databases 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