Prompted by Tweets in response to this Grauniad Higher Ed piece:
If “research” being published is primarily human readable text, then nothing wrong with PDF provided saved in a text-searchable form – how you save it matters. (And purists would say LATEX is a better format which keeps text separate from formatting – but formatted viewers have less wide-spread adoption than Adobe products. And being locked against casual editing, or open to annotation and comment are all widely available features with PDF.)
If what is being published really is structured – or benefits from being structured – where the organisation and formatting of content is really part of the information being published, then an XML document with (say) RDF-Schema (for structure) and style-sheets (for presentation) is the most future-proof way to go. Turns documents into databases without building the database first.
This is a common issue for all information publishing in all businesses, not just academic research.