The NIH has a number of resources further explaining their policy and processes:
There are four ways to submit your paper, depending on what journal it is being published in:
A. Publish in a journal in this list and no author involvement is required. Journals deposit all final published articles in PubMed Central: http://publicaccess.nih.gov/submit_process_journals.htm
B. Request that a publisher deposit your final published article for you. Publishers in this list will deposit your final published paper, at your request (and often for a fee): http://publicaccess.nih.gov/select_deposit_publishers.htm
C. Deposit the final peer-reviewed manuscript yourself via NIH Manuscript Submission System (NIHMS). Information required includes: journal name, manuscript title, grant numbers (or first and last name of PI), manuscript files. Log-in from here: http://www.nihms.nih.gov/
D. Complete the submission process for final peer-reviewed manuscripts deposited by the publisher (follow all steps for self-submission following article deposit):https://publicaccess.nih.gov/Method D Publishers
More information on journal policies can be found here.
See NIHMS General Faq (http://www.nihms.nih.gov/faq.html#questions)
Manuscripts may be entered by any author or any person delegated by the author. However, the author must perform the final approval in Step 5 before the manuscript is published in PubMed Central. Final responsibility for completing the process rests with the author.
Note that while the author is responsible for submission of any article, it is the PI who will be held responsible by NIH for lack of compliance of articles funded by their specific grant award.
Step 1: Log in to NIHMS
The NIHMS system accepts submissions from:
You should use the same login for all subsequent visits!
For those with NIH awards, the eRA account is created by the Proposals team in DSR. Anyone needing an account can use the request form at: http://apps.research.ufl.edu/research/nihera/register.cfm.
Step 2: Enter Basic Information
After logging in, begin submission by
Step 3: Upload manuscript
Provide basic information about the manuscript and contact information, then upload the manuscript file(s). The system will generate a PDF receipt that summarizes the entered information and merges the manuscript's files into one viewable document. Confirm that the manuscript and any additional supporting documents are correct. Your NIHMSID will be assigned when this is done.
When self-submitting, the final peer-reviewed manuscript should be submitted, unless the journal publisher has given permission to submit the final published article. Your manuscript should include full text and figures and all edits & modifications from peer review, but does not need to include layout and formatting made by the journal for the final published article version.
Step 4: Submission agreement and processing
An email will be sent to the corresponding author to approve the PDF and choose the release date when the manuscript will be made publicly available on PMC: up to a 12 months delay (embargo period) from journal publication date is allowed by the policy. Once you have approved and selected the release date, the manuscript will be converted into XML - the standardized digital format used by PubMed Central.
Step 5: Approval of the converted manuscript (web version)
After XML conversion, the author must review the manuscript as it will appear in PubMed Central. Corrections may be requested, if necessary, prior to final approval. After the author makes the final confirmation, the article will be publicly accessible through PubMed Central after the time-delay specified by the author.
Final author approval confirms authority/right to publish this version of the manuscript in PubMedCentral, that peer-review has been conducted appropriately and all resulting edits included, and that the manuscript was supported at least in part by NIH funding.