Frequently Asked Questions about the NIHMS System, My NCBI, & My Bibliography
Q: What is the NIH Manuscript Submission System (NIHMS)
A: The NIH developed the NIHMS system to support the submission of peer-reviewed manuscripts to PubMed Central or PMC. Authors, PIs, and even publishers can use the system to deposit manuscripts.
Q: What is the Author Manuscript?
A: The author manuscript is the version of a paper that has been peer reviewed and accepted for publication by the journal. This manuscript should include all changes made during the peer review process but is not the version that is formatted in the journal’s published style.
Q: How can I determine if the manuscript needs to be submitted?
A: The start date of the policy is April, 2008, so any article after that date qualifies and must be a manuscript resulting from NIH funding – in full or in part. Have one about which you are unsure? Get advice from NIH at
Q: What if I submit a manuscript and the publisher submits a manuscript?
A: The NIHMS system will catch that and choose the publisher’s version over the author version. If you are uncertain if the journal will submit a PDF or manuscript, see this web page for a list of journals and what they have agreed to do. https://publicaccess.nih.gov/submit_process_journals.htm
Q: How Do I know if the publisher will submit the manuscript or the final version?
A: You can look up the journal on the NIH website and determine if the publisher will do it or if the PI (or you) will need to do it. https://publicaccess.nih.gov/submit_process_journals.htm
Q: What are the best practices for NIHMS Methods C & D (The ones you & the PI will use)
A: 1) You can enter the citation of a paper into My Bibliography as a forthcoming paper as soon as it is accepted by the publisher. 2) For compliance, a manuscript must be linked to the NIH award and 3) PIs (or authors) must approve the PMC-ready version once they are converted. Gather a few other tips at:
Q: Can I see how the submission system works?
A: Yes you can. NIH has created several tutorials about the NIHMS system – from depositing files to initial approval to final approval – for either the author (or PI) or for delegates.
Q: Which funders use the NIHMS system?
A: The National Institutes of Health, of course, but 10 others including the Veteran’s Administration (VA), Howard Hughes Medical Institute (HHMI), Food & Drug Administration (FDA), and the Centers for Disease Control & Prevention (CDC). For the full list, see https://www.nihms.nih.gov/db/sub.cgi?page=funders
Q: How are the NIHMS system and PMC related?
A: NIHMS system is how authors can get their manuscripts into PMC – the starting point. PMC is the archive or repository – the end point.
Q: When is a PMCID given?
A: From start to finish, it usually takes about 6 weeks to generate a PMCID, and is given after the final approval by the author or PI.
Q: Do I see anything in PMC before the embargo period is complete?
A: You can see the citation details in PMC before the full-text is available. You may need to use a search filter for “include embargoed articles” but that is easy to find on the PMC search page.
Q: What is the difference between a PMCID & a PMID?
A: It is more than just a “C.” PMC is the full text archive of NIH funded research and PubMed is a citation database that includes the Medline database. PMC citations show up in PubMed, but most PubMed citations cannot be found in PMC
Q: Do I need to have my own NCBI account?
A: Your PI can set you up as a delegate so that you can work on their account and this is what the NIH information suggests. However, in reality, many AAs simply use their PIs account to help manage compliance.
Q: How is My Bibliography populated?
A: It can be populated by 1) finding the article citations in PubMed and adding it from there, or 2) you can search from within My Bibliography for specific authors. 3) You can manually enter citations into My Bibliography. Another option, particularly helpful for a very long list of citations or for ones not in PubMed is 4) the upload a file option. The file in this last option must be a specific file type – either MEDLINE or RIS will work (these are common to citation management programs).
Q: How does My Bibliography work with progress reports?
A: For some reports, the citation list is pulled from My Bibliography, and only items from there will be available for the report. Keeping My Bibliography updated is the best way to ensure new citations can be part of the progress reports.
Q: What if I have more questions about PMC?
A: The online PMC FAQ can help you troubleshoot those odd circumstances.
Q: What if I have more questions about My Bibliography?
A: The online My Bibliography FAQ will have some great advice for you.
Q: What local (UC San Deigo resources are available?
A: Both the Library & Research Service Core have online resources, and both Jill and Karen are available to meet with you (see emails in footer).