Many organizations and services that ingest JATS documents (including libraries, database services, service providers such as web hosts, and tool vendors) provide guidelines on how they want JATS to be structured for their ingest. Some require particular versions and/or impose business rules in addition to the validity to the JATS schemas, for example, that all tables and figures must be referenced from within the text.

Guidelines can be quite elaborate. For example, the PubMed Central Tagging Guidelines [PMC Guidelines 2021], includes comprehensive text explanations, tagged examples, and an online style checker that confirms whether an XML file conforms to PMC Style as defined in the PMC XML Tagging Guidelines.