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NIH Manuscript Submission Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-.

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NIH Manuscript Submission Help [Internet].

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Navigating the NIHMS Process

Created: ; Last Update: October 19, 2016.

What Is NIHMS?

The National Institutes of Health (NIH) developed the NIH Manuscript Submission (NIHMS) system to facilitate the submission of peer-reviewed manuscripts for inclusion in PubMed Central (PMC) in support of the NIH Public Access Policy. Since its inception in 2005, NIHMS has expanded to support the public access policies of other organizations and government agencies (see the Funders List). The NIHMS system allows users such as authors, principal investigators, and publishers to supply material for conversion to XML documents in a format that can be ingested by PMC. Depositing a manuscript in NIHMS for inclusion in PMC is a multi-step process, requiring an author to approve the deposited files and associated funding before conversion and the PMC-ready version after conversion.

Manuscripts can be submitted in a wide range of electronic formats. All the files associated with the peer-reviewed, accepted manuscript need to be submitted to NIHMS before the conversion process can begin, including all parts referenced or called out in the text, such as the following:

  • Title page with author and affiliation information
  • Main text of the manuscript (Note: Manuscript files may contain embedded figures and tables.)
  • References
  • Figures
  • Tables
  • Appendices
  • Supplementary files (online, electronic, etc.)

Note: Failure to provide the title page, text, and references, in addition to all referenced tables, figures, appendices, and supplemental materials, may delay processing of the submission for inclusion in PubMed Central.

This user guide provides help tools and other information about the NIHMS process. If you have additional questions or would like to submit comments regarding the NIHMS system, please contact the NIHMS Help Desk at vog.hin.mln.ibcn@pleh-smhin.

Signing in to the NIHMS System

NIHMS currently supports seven account types: NIH, eRA Commons, HHS AMS, NASA, NIST, My NCBI, and HHMI.

NIH intramural researchers should use the NIH sign-in option. eRA Commons account holders (e.g., NIH, CDC, AHRQ, and FDA extramural; VA researchers) should use the corresponding eRA Commons sign-in option. Non-NIH HHS intramural researchers should sign in through HHS AMS. NASA, NIST, and HHMI researchers should sign in through their respective sign-in routes.

My NCBI users and users without any of the above accounts can sign in through the My NCBI route.

Note: Accounts are not automatically linked or aliased, so users are encouraged to choose one account and use that for all subsequent visits. If a user cannot remember whether or not he/she has an account or which account was previously used to process a submission, please use the “Request e-mail reminder” feature in the sign-in box on the homepage or contact the Help Desk at

Publisher accounts are available for publishers interested in submitting manuscripts on behalf of authors to NIHMS. Additional publisher options are discussed in the For Publishers area of the NIHMS FAQ.

Illustrated sign-in instructions are available on the NIHMS Step-by-Step Tutorials page.

Overview of the NIHMS Process

There are five steps involved in the NIHMS process:

Image users-Image001.jpgStep 1: Deposit Files
A manuscript may be submitted by the author, the PI, the publisher, or another third party. Third-party submitters must designate an author or PI to serve as the Reviewer for an NIHMS submission. In these cases, the Reviewer will receive notification of the deposit via e-mail.
Image users-Image002.jpgStep 2: Initial Approval
The Reviewer reviews the submission, confirms or adds associated funding, and either rejects or approves the material for processing in NIHMS.
Image users-Image003.jpgStep 3: NIHMS Conversion
NIHMS staff reviews the approved files for completeness, and complete submissions are converted to archival XML. The PMC-ready documents (Web and PDF versions) are checked to ensure they accurately reflect the submitted files. An e-mail notification is sent to the Reviewer when the record is available for final review.
Image users-Image004.jpgStep 4: Final Approval
The Reviewer reviews the PMC-ready documents (Web and PDF versions) and either requests corrections or approves them for inclusion in PMC. Final Approval is required to complete manuscript processing in NIHMS.
Image users-Image005.jpgStep 5: PMCID Assigned
A PMCID is assigned when Final Approval is complete and the manuscript is matched to a PubMed record with complete citation information. For details, see When will a PMCID be assigned to my manuscript? in the NIHMS FAQ.
Image users-Image006.jpgManuscript is made available in PMC following the publisher-required embargo period (if applicable).

Submission Tutorials

The following submission tutorials (including PDFs of each) are available on the NIHMS Step-by-Step Tutorials page.

Submission Help for Authors/PIs

Deposit Files: Instructions for authors and PIs submitting a manuscript.

Initial Approval: Instructions for authors and PIs who have been notified via e-mail that a submission has been initiated on their behalf.

Final Approval: Instructions for authors and PIs who have been notified via e-mail that the PMC-ready version of their manuscript is ready for final review.

Submission Help for Non-Authors/Non-PIs

Deposit Files: Instructions for a third party (e.g., assistant, librarian, publisher) starting a submission on behalf of an author or PI.

Tip: Most pages of the NIHMS system display help information on the right-hand side of the screen to guide users through the submission and approval processes.

Statuses in NIHMS

As an NIHMS submission goes through various stages of processing, its status serves to indicate what action(s) is being taken or is needed. A complete list of statuses and their meanings is available in the NIHMS Glossary under Status.

Bookshelf ID: NBK3846


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