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Stony Brook University

NIH Public Access Policy: Using NIHMS

A Guide to the NIH Public Access Policy

NEWS!

Do you want to know how often your papers in PubMed Central are being accessed?

Read the NCBI Insights Article on how to view those stats.

Getting Help!

The Health Sciences Library offers free individual & group consultations on NIH Public Access Policy (NIHPAP) compliance.

Contact us to schedule an appointment:

  • telephone on campus 4-3099 | off campus (631) 444-3099
  • email
  • Chat click the 'Chat is Online' button on the top right of all Library pages.
  • SBU Answers the University Libraries knowledgebase; Ask a question, get an answer, or search our FAQ.

NIHMS HELP

The most common problem steps in this process are:

1. A journal or an author initiated the submission, but didn't complete entering the manuscript files. The submission is stalled at the manuscript upload stage. It gets a temporary NIHMSID but turns red (non-compliant) after 3 months.

2. The journal initiated the submission, but the corresponding author (according to the journal's records) doesn't respond to the email from the NIH asking him/her to approve the PDF Receipt. The corresponding author may have not noticed, forgotten, or moved away. The submission is stalled at the manuscript upload stage. It gets a temporary NIHMSID but turns red (non-compliant) after 3 months.

3. The corresponding author approves the PDF Receipt, but for some reason doesn't respond to the email to the email from the NIH asking him/her to approve the Final Web Version. The corresponding author may have not noticed, forgotten, or moved away. The submission is stalled at the manuscript upload stage. It gets a temporary NIHMSID but turns red (non-compliant) after 3 months.

Note that the responsibility for approving the PDF Receipt (and the Final Web Version) can be reassigned to another author upon request to the NIHMS HELP.

All problems with the NIHMS system can be reported to the NIHMS HELP. They usually respond within a business day.

The NIH Manuscript Submission System (NIHMS)

The NIHMS handles all submissions of peer-reviewed articles for inclusion in PubMed Central.

Remember that some publishers have direct agreements with the NIH and will handle the submission for you. Others will initiate the process, but you will have to log into NIHMS to complete the submission process. In yet other cases, you will have to do the entire submission yourself.

To access NIHMS go to http://nihms.nih.gov.

While several login routes are provided, it is strongly recommended to always use your eRA Commons/NIH login for NIHMS as well as My NCBI. Always use the same login consistently for NIHMS. Note that logins for CDC and HHMI researchers are also provided.

The NIH provides a step-by-step submission tutorial and a FAQ.

 

Submitting a Manuscript

1. Enter Basic  Information

After logging in, you will see a several tabs that allow you to see and manage the status of your already submitted manuscripts. If a manuscript requires immediate attention, it will display that for you. To start a new submission click on "Submit New Manuscript."

Step 1: Enter journal name and article title

There are three options:

  1. Enter it manually (only use this if your article is not in PubMed or in your My Bibliography)
  2. Lookup the article (in PubMed)
  3. Draw it from My NCBI Bibliography (This is usually the best option. Note that sometimes a manually-entered citation in My Bibliography may not sync right away to be available to select at this point.)

Step 2: Enter grant information (Add Funding)

At least one NIH grant award must be linked to the manuscript. The system provides a search by PI name or award ID #.

Step 3: Upload Manuscript Files

The full, final peer-reviewed manuscript (prior to journal formatting) must be submitted along with any figures, tables, or supplementary data. Make certain all files are correct and complete.

Note: if you submit the journal-formatted pdf, the NIH will convert it into a manuscript form. Only a publisher with an arrangement with the NIH can submit the journal-formatted pdf (usually Method A Publishers).

After you have submitted the files (or the journal has), you must check the files: The NIH automatically converts the submitted files into once contiguous, temporary pdf called a "PDF Receipt." Alternatively, if the journal did this part of the submission, the corresponding author will receive an email asking him/her to go in and approve the PDF Receipt.

Note: If your submission is initiated by a publisher (usually Method D Publishers), this is the first step where author responsibility kicks in. A submission can stall here if the author does not approve the PDF Receipt.

Step 4: Check Files: Confirming PDF Receipt

In this part of the process, you will review the PDF Receipt generated from Step 3, choose the reviewer for the rest of the submission process, and set the Embargo date.

First, check very carefully that the manuscript, any additional supporting documents, author and grant information are correct. 

Then Click on "Set Reviewer & Embargo."

If you are a delegate for an author or want another author to take over responsibility at this point, you can enter a new reviewer for the submission. Choose the responsible reviewer.

Enter the "Embargo period" post-publication as required by journal publisher. They are only allowed up to 12 months from date of publication, so it can't be more than that. For some journals, it may be shorter. Confirm it with the publisher.

You can choose to allow NIH Program Administrators to access the manuscript before the PMC release date. This may be helpful if you are submitting grant paperwork prior to that release date.

When everything is complete, Click on "Approve."

At this point, you must read the NIHMS author submission statement and indicate agreement if you have fullfilled the stated conditions.

Your NIHMSID will be assigned when this is done. The NIHMSID substitutes for the PMCID for 3 months.

Step 5: NIH Processing

The manuscript will be converted into XML - the standardized digital format used by PubMed Central - by the NIH staff. There is nothing the author needs to do during this process. It may take a few weeks.

Step 6: Approval of the converted manuscript (web version)

After XML conversion, the author must review the manuscript as it will appear in PubMed Central. The NIH will send an email to the responsible author/PI, as done earlier in Step 4. Corrections to the submission may be requested, if necessary, prior to final approval. 

Once the author/PI has received that email, he/she must log in to NIHMS, review the "final web version" of the submission (the version to be released on PubMed Central), and approve it. Note that this is another step at which article submissions can be stalled. Pay attention to emails from the NIH regarding NIHMS Submissions.

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.

After the author makes the final confirmation, the article will be publicly accessible through PubMed Central after the time-delay (embargo period) specified in Step 4.

The article is assigned a PMCID and is fully compliant at this point, regardless of the remaining length of the embargo period.

A graphical, step-by-step set of instructions for this process is provided at http://nihms.nih.gov/db/sub.cgi?page=stepbystep.