There are four submission methods. Method A and B involve the final article as it appears in the journal (with the journal’s fonts, pagination, etc.). Method C and D involve the final peer-reviewed manuscript (without the journal’s fonts, etc.)
See additional information at the NIH Guide to Submission Methods.
NIH will delay processing of non-competing continuation grant awards if publications arising from that award are not in compliance with the NIH public access policy.
Some journals automatically deposit all NIH-funded final published articles into PMC without author involvement. Usually you will need to pay a fee to the journal for this service. A list of these journals is available at NIH: Determine Submission Method You will need to reply to emails from the NIH to verify accuracy of the submitted manuscript, illustrations, etc.
Most journals do NOT automatically submit your article to PMC for you. Some will do so on request for a fee. You can see the publishers who do this at: https://publicaccess.nih.gov/select_deposit_publishers.htm (Look at the column under “Method B.”) You will need to reply to emails from the NIH to verify accuracy of the submitted manuscript, illustrations, etc.
You deposit your final peer-reviewed manuscript in PMC yourself via the NIH Manuscript Submission System (NIHMS). NIHMS has different ways to upload depending on who you are. Choose “My NCBI” unless you work for the NIH or were funded by the HHMI. You will need the grant number(s), grantee, author names, the final peer-reviewed manuscript, and any supporting figures, tables, charts, graphics, and supplementary data that were submitted to the publisher. NIH will convert the files into standard PubMed format. You will need to reply to emails from the NIH to verify accuracy of the submitted manuscript, illustrations, etc.
Some publishers start the submission process for you, but require you to complete it. They deposit your final peer-reviewed manuscript for you and determine the number of months after publication when the article may be made publicly available in PMC. You are required to finish the submission process in NIHMS. You will need to reply to emails from the NIH to verify accuracy of the submitted manuscript, illustrations, etc.
When you submit your article, it will be assigned a temporary NIHMS number. When your article is published you will get a PMCID number (PubMed Central ID number). Only use the NIHMS number until the PMCID is available. After that the NIHMS number is invalid.
Be sure to make note of these numbers. You will need to include the relevant one in your grant’s progress reports, final reports, and future NIH applications and proposals. For detailed information, see Include PMCID in Citations.
Please note: The PMCID is not the same thing as the PMID number (PubMed ID number). The PMCID number appears on the article in both PubMed and PubMed Central. They are two different databases with very similar names. If you only have the PMID, you can find out the PMCID using the PMCID Converter.
For additional information, visit NIH Public Access Policy page from the TMC Library website.