I would suggest that there is no good answer to this question, as much as we all would like there to be one. A "file format" can be defined by many things and can have a range of purposes. Even a new and (supposedly) clearly defined file format can be adapted, extended, appropriated or twisted over time as new software implementations add proprietary functionality, interpret ambiguous definitions in different ways or simply fail to support all aspects of a format. As a consequence it's impossible to come up with a concise definition. At best a file format is a somewhat fuzzy entity.
A file format might be defined by a file format specification, a reference implementation for an application that renders it or indeed any other software that saves out data in a particular way. In practice it can often be a somewhat unclear combination of all three.
A file format might be designed to capture and store data in a carefully ordered and organised manner. Or it might simply capture the state of a software application at a particular time (eg. early MS Word formats).
"Older versions of the PDF specification included an appendix called “Implementation Notes”, which describes at least some of the deviations from the specification for which Acrobat reader attempts to compensate. These notes do not comprise a part of the ISO PDF 32000-1:2008 document. Further, these notes, while helpful, beg the question as to what we are to consider authoritative with respect to PDF format instances: the specification, or the behavior of the Acrobat reader application."