The Authors Alliance has written a set of questions and answers to what they anticipate can be some problems that will arise when authors are negotiating their publishing contracts with journals.
They acknowledge that it will take some time to discover what issues will arise, but they offer some very good advice for several different situations that may occur, and they include some links and language from publishers and resources that are very helpful.
This guidance can be found at The NIH Public Access Policy: Q&A for Authors.
The Authors Alliance recommends that authors:
Communication among coauthors is essential while preparing the manuscript for publication. The NIH has three statements authors should include in the manuscript to indicate they are NIH funded and must have the right to deposit manuscripts to PubMed Central:
If you are not preparing the manuscript yourself for submission to the journal, make sure the first author/corresponding author has included these statements, as well as all NIH award numbers which supported your work.
If you are preparing the manuscript for submission to the journal, extend the same courtesy to your coauthors: ask them if they were NIH funded for their roles and ask them to supply you with award numbers.
Communication with the journal upon submission of the manuscript for review and publication can be more complicated.
The submitting / corresponding author should: