Zoos join ISIS to allow them to make use of animal records keeping software to manage their own animal collections. One of the requirements of joining ISIS is that every member's data must be submitted to ISIS at least every six months. ISIS then pool the data into a "global" dataset, and a small subset of that information is made available on the public area of the ISIS web site.
Most ISIS-member zoos maintain records for all of their animals, whether they be domestic species or not - plenty of zoos have children's zoo's with ponies, sheep, chickens etc. and most of these animals are individually identified, and therefore, individually accessioned into the ISIS software.
Hence, if a zoo has a group of guinea pigs in its children's area or petting zoo, they are usually entered into the records so the usual behavioural and medical data can be maintained.
Many zoos also have groups of animals that are bred for food - rabits, mice, rats, guinepigs etc. These are almost never entered into the records system, as keeping accurate records on them is a somewhat pointless excercise.