NIH recommends that authors inform the journal when submitting an article for publication that it is subject to the NIH Public Access Policy. For instance, Duke University offers authors language for a submission letter [DOC].
Some journals already grant digital archiving rights to authors in their standard agreements, but currently most do not. While the situation will probably change over time, authors are responsible for taking whatever actions are necessary to retain the right to deposit. See Retaining Rights.
Authors or someone in their organization (e.g., an assistant or a librarian) can log on to NIHMS to submit a copy of the accepted peer-reviewed manuscript and associated files (e.g., word processing file plus figures). Label the manuscript with the correct author names, grant number, etc. as directed.
The principal investigator will subsequently be asked by NIH to approve the submission and affirm that copyright allows deposit to PubMed Central. NIH will convert the deposited files into a standard PubMed Central format and e-mail the author to review the formatted manuscript to make any necessary corrections and approve its public availability in PubMed Central after any delay period specified during submission.
Authors can publish their articles in a journal that submits articles to PubMed Central for public availability within 12 months of publication. Many journal publishers embargo public access via PubMed Central for the maximum allowable period (12 months).
Some publishers offer special deposit services to NIH-funded authors. They might submit copies of manuscripts or final published articles to NIH. While the author does not need to go through the deposit process, the investigator will be contacted to review and approve any submitted manuscript. Publishers may charge a fee for a deposit service or may combine it with other fee-based services such as immediate open access to the article on the publisher’s Web site.