Frequently Asked Questions (FAQs)

For questions and answers about the NIH Public Access Policy, please refer to the Public Access Frequently Asked Questions web page.

For All Users

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 for more details.

What funding agencies does NIHMS support?

Please see the Funders List.

When should a manuscript be submitted to NIHMS?

Please see your funder's public access policy for instructions specific to your paper. For example, the NIH Public Access Policy calls for the peer-reviewed, accepted manuscript to be deposited in NIHMS at the time of acceptance for publication.

What steps are involved in the NIHMS process?

Step Description
Step 1: Deposit Files Step 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.
Step 2: Initial Approval Step 2: Initial Approval
The Reviewer reviews the submission, confirms or adds associated funding, and either rejects or approves the material for processing in NIHMS.
Step 3: NIHMS Conversion Step 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. Processing time for this step is usually 2-3 weeks but may vary depending on the volume of submissions at a given time. An e-mail notification is sent to the Reviewer when the record is available for final review.
Step 4: Final Approval Step 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.
Step 5: PMCID Assigned Step 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?
Available in PMC The manuscript is made available in PMC following the publisher-required embargo period (if applicable).

How do I sign in to NIHMS?

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

NIH intramural researchers should use the NIH sign-in option. eRA Commons account holders (e.g., NIH extramural, VA researchers) should use the corresponding eRA Commons sign-in option. Non-NIH HHS intramural researchers should sign in through HHS AMS. HHMI investigators should sign in through the HHMI sign-in route.

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

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.

For illustrated sign-in instructions, see the Step-by-Step Tutorials page.

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

What is the relationship/difference between a Submitter, Reviewer, Reviewer (Pending), Verified Author, PI, and Watcher in NIHMS?

Each of these roles taken on by users of the NIHMS system is defined in the Glossary

What do statuses mean in NIHMS?

An NIHMS submission goes through various stages of processing. Statuses serve to indicate what action(s) are being taken or are needed. A complete list of statuses and their meanings is available in the Glossary under Status.

For Submitters

Who can submit manuscripts to NIHMS?

Manuscript files may be submitted to NIHMS by the author, the PI, the publisher, or other third party (i.e., anyone given access to the author's files, such as administrative personnel, graduate students, and librarians). Approval of the PDF Receipt and PMC-ready documents requires author review and authorization (see Reviewer).

How do I submit manuscripts to NIHMS?

To submit a manuscript to PMC via NIHMS, you will first need to sign in to NIHMS. (See How do I sign in to NIHMS? for sign-in information. Illustrated sign-in instructions are available on the Step-by-Step Tutorials page.) Once you are signed in, click the "Submit New Manuscript" button. The submission system will take you through the following steps:

1. Provide Title Information
You have the option to manually enter the journal and manuscript title information or find the corresponding citation in PubMed or in your My NCBI Bibliography.

2. Add Funding
Select all appropriate funding mechanisms (i.e., grants, contracts, intramural) from any of the participating agencies or organizations that supported the work.

3. Upload File(s)
Upload the manuscript material, including all figures, tables, supplemental files, and so on, as applicable.

4. Review the Uploaded File(s)
The submission system will generate a "receipt" in PDF format for the uploaded files. This PDF Receipt summarizes the information entered into the system and merges the manuscript's files into one viewable document. Any supplemental files are represented by placeholders at the end of the receipt. Review this document to ensure that the submission is complete.

An NIHMSID is automatically assigned to the record once files are provided.

5. Set Embargo and Reviewer
If an author on the paper, indicate the release date when the manuscript will be made publicly available in PubMed Central (PMC) and agree to the Submission Statement.

Otherwise, designate an author (i.e., Reviewer) to review the material, certify compliance with Submitter requirements, and send the submission to the Reviewer for approval (the Reviewer will receive an e-mail inviting him or her to review the material).

What files should I submit?

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.

Do I have to submit supplemental material?

Yes. Material that has been submitted to the accepting journal in support of the manuscript must be submitted, including online and electronic supplemental files containing figures, tables, text, and movies.

What file format should I use?

As noted above, all the files associated with the peer-reviewed, accepted manuscript must be submitted. Therefore, the NIHMS system supports a wide variety of file types (MS Word, Word Perfect, PDF, PowerPoint, Excel, etc.). As required by journals, high-resolution images (i.e., .pdf, .tiff, .jpg, .eps, .ai) should be submitted to ensure the best reproduction quality in PubMed Central. With the exception of supplementary materials, PMC will convert submitted images into standard file types.

What is the release delay or embargo period?

The release delay or embargo period is the interval between a manuscript's final publication date and when the NIHMS manuscript will appear publicly in PubMed Central (see the NIHMS Glossary for more information).

How do I find out if a manuscript has already been submitted?

Users can search for records in the NIHMS system by NIHMSID or PubMed ID. (Note: Records can be located by PubMed ID only if the record in NIHMS is matched to a PubMed record.) The Search box is located on the right-hand side of the Manuscript List page after signing in to the submission system.

If the record is associated with the account used to sign in to the system, the record details will be available. If the record is not associated with the account, the user can request access to the record (see How can I monitor a submission not associated with my account in NIHMS?).

For PIs and Authors

What is the language of the NIHMS submission statement to which I must agree?

The Submission Statement for NIHMS that must be approved by the Reviewer is as follows:

I am an author of this manuscript, and I am providing it to the National Institutes of Health (NIH) to make publicly available in PubMed Central [Embargo period] after its official date of publication in the journal.

I confirm that:

Publication and Copyright Agreements -- In any agreements that I have made with the journal, I have retained the right to deposit this version of the manuscript with PMC, so that it may be appropriately tagged and made available to the public on the PMC web site; or, I otherwise am legally authorized to deposit this manuscript for the purposes described.

Confidentiality -- The manuscript may contain confidential information that must not be publicly disclosed prior to publication of the paper in the named journal.

Peer Review -- The version I am depositing has been peer reviewed and accepted for publication and includes all modifications resulting from the peer review process.

Funding -- The manuscript is the result of research supported, in whole or in part, by direct costs funded by participating Funder(s).

Can publishers submit my paper to PubMed Central for me?

Publishers may submit manuscripts to NIHMS on behalf of authors. Check with the publisher to determine if they submit to NIHMS as a service to authors. Manuscripts submitted to NIHMS by publishers require two approvals by the author (see What steps are involved in the NIHMS process?).

Submissions and approvals in NIHMS are not required for articles published in PMC-participating journals.

Note: For non-PMC-participating journals, it is ultimately the responsibility of an author or PI to ensure that a manuscript is submitted in a timely manner to NIHMS in accordance with the funding agency’s public access policy.

When will a PMCID be assigned to my manuscript?

A PMCID is assigned when the following two criteria are met:

  1. The converted materials (i.e., the PMC-ready documents) have been approved by the Reviewer and
  2. The article has been matched to a PubMed record for one of the following:
      a. a final print publication date or
      b. an electronic publication date for a journal that is an electronic publication only or
      c. an electronic publication date for a journal where PubMed has not received the final print publication date within 6 months of the electronic publication date

How can I monitor a submission not associated with my account in NIHMS?

To monitor the progress of an NIHMS submission, your account needs to be associated with the record. You can associate your account with an NIHMS record by placing a Watch request:

  1. Sign in to NIHMS.
  2. Use the Search box on your Manuscript List page to locate the record you would like to monitor. You will need the corresponding PubMed ID (PMID) or NIHMSID to search NIHMS.
  3. If there is a record that corresponds to the ID you entered, you will be taken to the Manuscript Summary page, where you can view the current status of the record. Note: If the paper has not yet been matched to a PMID, the manuscript and journal titles will be hidden to protect confidentiality.
  4. To associate your account with the record, select the "Watch Manuscript" button in the lower right-hand corner of the Manuscript Summary page.
  5. On the next page, select "Confirm" to indicate that you would like to follow the progress of the record in the NIHMS system. Note: If the NIHMS record has not been matched to a PMID, you will be asked to provide manuscript and journal title information to verify your association with the paper.

Once you have confirmed that you would like to watch a record, a notification of your request will be sent to the current Reviewer assigned to the NIHMS record. If he/she does not object, you will be granted access in one week's time, at which point the record will appear in your Manuscript List.

How can I take over Reviewer responsibilities for a submission in NIHMS?

If a submission has become stalled in the NIHMS process due to inaction by the assigned Reviewer, another author or PI associated with the NIHMS record can request to take over Reviewer responsibilities:

  1. Sign in to NIHMS.
  2. On your Manuscript List page, click the Stalled tab to view the stalled records currently associated with your account.
  3. If the record is in a state that requires Reviewer action, a "claim" button will appear in the Status column and lower right-hand corner of the Manuscript Summary page (which is accessible by clicking on the manuscript title). Click the button to initiate your request.
  4. On the next page, select "Confirm" to indicate that you are an author (or PI) on the manuscript and would like to take over Reviewer responsibilities.

If the currently assigned Reviewer does not act on the submission within one week of your request, the manuscript will be moved to your attention in your Manuscript List to allow you to take action on the submission.

If you would like to take over Reviewer responsibilities for a record that is not stalled in the NIHMS process, please contact the Help Desk with your request.

How can I take over Reviewer responsibilities if I am not associated with a record in NIHMS?

Submit a request to Watch the NIHMS submission (see How can I monitor a submission not associated with my account in NIHMS?). Should your Watch request be approved and the NIHMS submission is stalled, you will then have the opportunity to submit a Claim request. Note: If you would like to take over Reviewer responsibilities for a record that is not stalled in the NIHMS process, please contact the Help Desk with your request.

What if I need to make corrections to the text of a manuscript in NIHMS?

Please note that the PDF Receipt is used only as the basis for generating PMC-ready documents. The PMC-ready documents will be made available to the Reviewer following conversion, at which time the Reviewer may request necessary text-level edits, as well as corrections to figure, table, and supplemental files (see What steps are involved in the NIHMS process?). Only the converted documents will appear in PubMed Central (the PDF Receipt will not), and no materials will be released without the final approval of the Reviewer.

Why hasn’t the submitter provided the final published version of the manuscript?

In observance of copyright restrictions, public access policies often call for the submission of the peer-reviewed, accepted manuscript. To use the final published version of the article, the explicit permission of the publisher is needed. Before contacting the publisher, please take into account that doing so will delay the processing of the manuscript in NIHMS, and the publisher can deny the request.

We understand that there are often changes made to a manuscript between the accepted and final versions. When the PMC-ready documents are available, the Reviewer will have an opportunity to request necessary text-level edits, as well as corrections to figure, table, and supplemental files (see What steps are involved in the NIHMS process?).

How do I associate funding with a submission?

Users are permitted only to add/remove funding to/from an NIHMS record prior to the initial approval of the PDF Receipt (see What steps are involved in the NIHMS process?).

Users should link only funding that directly supported the manuscript being submitted. If there are multiple funding sources that supported a manuscript and it is unclear which funding should be listed, users may link only their funding support and proceed. Please contact your institution’s Office of Sponsored Research for assistance determining which funding directly supported your project.

Intramural investigators who do not have support from a specific grant or project should use the generic project code for Official Duty to indicate general intramural program support.

For instructions on how to link grants to a publication while initiating a manuscript submission, please review pages 6 and 7 of the Deposit Files tutorial.

For instructions on how to link funding to an existing submission prior to the completion of the initial approval, please review the Associating Funding at Initial Approval tutorial.

The PI/awardee on the selected project will be notified that the association has been made and will have the option to request the grant be removed if it did not directly support the paper. Grant associations are also subject to staff review.

Please contact the Help Desk to edit funding associations for submissions beyond the initial approval stage.

Note: Grant PIs and their delegates can also use My NCBI’s My Bibliography feature to manage grant associations at any time. Please review the My NCBI Help page for instructions. Unfortunately, this option is not currently available for contracts and non-eRA grants.

For Publishers

What options does a publisher have for depositing papers in PubMed Central?

There are two main ways publishers may deposit papers in PubMed Central (PMC).

The first is that a journal can apply to be PMC participating. If a journal is “PMC participating,” it means the journal has met PMC’s scientific and technical standards, and the publisher has agreed to deposit final article XML directly in PMC at the time of publication without author involvement. Directions on how to initiate the PMC agreement process can be found on the PMC Add a Journal" page.

The second way a publisher may deposit papers in PMC is through NIHMS. In NIHMS, the publisher may deposit manuscripts usually as Word or PDF files and provides a name and contact e-mail address for an author. The author will be notified that he/she needs to approve the initial deposit and associate relevant funding with the NIHMS record (see the Funders List). NIHMS then converts the submitted files to XML, which is used to create PMC documents. Following file conversion, the author receives a second notification and must approve the PMC documents to complete the NIHMS process (see What steps are involved in the NIHMS process?).

Although there are no formal agreements made between NIHMS and publishers, there are a few questions publishers must adequately address before an NIHMS Publisher account can be issued. If you are interested in submitting manuscript files (not XML) to NIHMS, see How does a publisher submit manuscripts to NIHMS on behalf of authors?

How does a publisher submit manuscripts to NIHMS on behalf of authors?

Publishers may submit manuscripts to NIHMS using any of the following three methods:

  1. Submission via a My NCBI account
  2. Submission via an NIHMS Publisher account
  3. Submission via the NIHMS Publisher Bulk-Upload Pathway

Submission via a My NCBI account

Publishers may submit to NIHMS on behalf of authors using a My NCBI account. My NCBI accounts may be obtained by clicking on "Register for an NCBI account" here. Additional information on how to sign in to the NIHMS system can be found under How do I sign in to NIHMS? and How do I submit manuscripts via NIHMS?

Submission via an NIHMS Publisher account

Publisher accounts are typically established for only those institutions requiring a high volume of submissions to the NIHMS system for compliance with the NIH or participating funder's public access policy. Submitters from other institutions should establish a standard My NCBI account (see above) with which to submit manuscripts.

For publishers submitting a high volume of submissions to NIHMS, Publisher accounts have two advantages. Publishers may (a) set the release delay (i.e., embargo period) for each manuscript in accordance with their agreement with the authors and (b) opt to display (along with the NIHMS-prepared web version) their own PDF of the final published version of the article (rather than the NIHMS-prepared PDF) in PubMed Central

To request an NIHMS Publisher account, please contact the Help Desk with the following information:

  1. Number of NIH-funded articles your institution publishes annually
  2. Number of journals for which your institution will be submitting manuscripts
  3. A link to a website with the following information about your institution:
    • Names and addresses of the owners of the publishing company
    • Location (full address) of corporate office(s)
    • Editorial policies
    • Editorial and peer-review processes

Submission via the NIHMS Publisher Bulk-Upload Pathway

The NIHMS Publisher Bulk-Upload Pathway was developed to offer publishers a way to use in-house automated processes to organize and transmit multiple manuscript submissions to NIHMS. Manuscripts are submitted to the NIHMS system via FTP. Arrangements must be made with NCBI regarding the location on the FTP server to send manuscript bundles. For publishers that already FTP files to PubMed Central, you will use the login credentials currently used for PubMed Central deposits. An XML metadata file is transmitted with each manuscript bundle. For complete details regarding submissions via the Bulk-Upload Pathway, please refer to the documentation contained in the bulk-upload information package. Note: Publishers submitting via the NIHMS Publisher Bulk-Upload Pathway must still meet the same requirements as those submitting via an NIHMS Publisher account.

To make arrangements to submit via the NIHMS Publisher Bulk-Upload Pathway, please contact the Help Desk.

How does a publisher request removal of a manuscript that appears in PMC in conflict with the author's transfer of copyright to the journal?

Please send a removal request to the Help Desk that includes the citation of the manuscript to be removed, the PubMed ID of the manuscript, and its URL in PMC. Please also include relevant details of the author’s copyright transfer agreement for the manuscript.

What if I have questions not addressed in the For Publishers area of this FAQ?

Additional information that may also be helpful is available under For All NIHMS Users and For Submitters. If you find you require further assistance after reviewing those sections, please contact the Help Desk.