As per your own comment (but to give an actual example), if you need to increase a transaction time-out you can use an annotation on the method of whichever class defines your transactional boundary (usually a "facade" implmentation).
For example, using org.springframework.transaction.annotation.Transactional
@Transactional(timeout = 600) // value is in secondsIt sounds like you need this for a one-off data conversion task rather than day-to-day production code so increasing the time-out is probably justifiable. Otherwise it would be worth considering batching the processing into smaller chunks and making each one a unique transaction which is expected to complete within the default time-out for your system.