The database is backed up nightly, producing a time stamped archive that can be retrieved back to 2007. The backups are Postgres dump files (back to 2018; prior to 2018 backup files are stored for an Informix database) that can easily be loaded into a new Postgres / Informix instance.
In addition to database backup files, ZFIN versions the software by release name: release-<ID>. The software lives in GitHub.
ZFIN also provides download files (user facing) that are generated nightly. They are time stamped back to 2012.