Publishing whole documents using an open XML standard format

What would be the best standard XML format for publishing whole documents (with semantic markup, but no presentational/formatting markup)?

1. OpenDocument (with embedded metadata)
2. NLM Journal Archiving and Interchange or Journal Publishing DTD
3. DocBook
4. Atom (with XHTML for content)
5. something else?

The documents would need to include section headings, figures, tables, footnotes, bibliography, etc.