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NIH Public Access Compliance: How Do I Make This Paper Compliant?

This LibGuide will walk users through issues of compliance with the NIH

Depositing a Publication in the NIH Manuscript Submission System

Step 1: Collect & Prepare Files for Submission

If you are depositing a publication in the NIH Manuscript Submission system, you will need to make sure you have all the documents for your submission.

It is important to note: You cannot submit the final, published version of the manuscript because of copyright. Therefore, you will need to track down the following documents:
  • The Author's Accepted Manuscript
    • This is the version of the manuscript that was submitted after peer review but before the publisher's formatting, copyediting, and typesetting. 
    • Make sure that the manuscript also has any titles and captions for Tables and Figures. 
    • Again, you cannot submit the final version of the publication due to copyright so it is essential that you track down this version of the manuscript. 
  • All Tables & Figures (Including Supplementary Tables & Figures)
    • You will be asked to submit Tables and Figures as separate files. 
    • Make sure that the versions of the Tables and Figures that you are submitting match the versions referenced in the manuscript. For example, make sure that if Figure 1 A-D are referenced, that the version you are submitting has parts A-D. 
  • Any Additional Supplementary Information
    • You will also need to upload any supplementary documents associated with the publication even if they are not mentioned in the text. 
Professional Tip: To be incredibly thorough, it helps to compare the documents that you are submitting to the final, published manuscript to make sure that you have all of the figures, tables, and supplementary information/materials. 

A note on file formats: the Manuscript Submission System supports a wide variety of file formats when submitting documents.

  • Manuscripts are often submitted as MS Word or PDF documents but other file formats (WordPerfect, PowerPoint, Excel, etc.) are also accepted. LaTeX text files are not accepted, but you can knit the entire publication together in a software like Overleaf or R Studio and submit a single PDF in this case (if you do this, make sure all of the components of the publication are included in the final PDF). 
  • High resolution images (.pdf, .tiff, .jpg, .eps, .ai) should be submitted for best quality. ChemDraw files are not accepted and will need to be converted to another format

Step 2: Navigate to the NIH Manuscript Submission System & Prepare to Submit

  • Go to the NIHMS System home page:
  • Login using the same credentials that you use to login to eRA Commons and My NCBI.
  • Click the "Submit New Manuscript" button on the right side of the page.

Step 3: Deposit Files & Submit Manuscript

  • You have the option to populate the information from a data source or to enter it manually. You should try to populate using a source first. 
  • If you are not able to populate the information from a source (like PubMed), then you can manually enter the title and the journal of the publication. 
  • Once you have populated or entered this information, click "Next". 
  • Note: if you need additional guidance or support as you go through the submission process, you can click on the human icon which will give you a walkthrough of the submission system. 
  • If you are an author: click the "Search Funding" button to find the NIH grant(s) that you wish to associate with this publication. 
  • If you are a submitter/delegate: click "Next" without associating funding, the author/PI can do this step when they review the initial submission. 
  • An important note: it is a process to unlink/disassociate funding with a publication once it has been associated. Therefore, be absolutely sure that you wish to associate a specific grant with a publication. 

  • Upload the Manuscript document under the Manuscript section
  • Upload any Figures and Tables in their respective sections. 
  • If there are videos associated with the publication, upload these. 
  • If there are supplementary materials, make sure to upload all of these as well. 
  • A note on labels: you will be asked to label each of the documents as you upload them. Label them the same way that they are referenced in the manuscript text. For example: "Figure 1". 
  • Double check to make sure all of the documents are there. 
  • Check the box to certify that all the documents are present. 
  • Click "Next".

Reviewer and Release Delay (Embargo)
  • If you are an author: the reviewer will be "Self", and you will need to specify if there is a publication embargo. You can check your publishing agreement or with the publisher of the journal to see if there is an embargo. 

  • If you are a submitter: change the drop down box to "Enter name and email manually", and enter the name and email of the author that will be reviewing the submission. They will be asked to specify if there is an embargo. 

  • Once you have entered the information, click either "Next" or "Send to Reviewer". 

Step 4: Approval & Processing

  • If you are an author: after submission, the documents will be uploaded and be processed for conversion to PubMed. You will be notified when the Final Version of the manuscript is ready for review and approval. 
  • If you are a submitter: the designated author will get an email asking them to associate funding and review the submission. Once they have done this, it will go to conversion. After conversion, the reviewing author will be asked to approve the final version. 
  • You can always check back to see the status of the submission in the portal. 
  • If there are issues with documents, the NIHMS Helpdesk will email you detailed information about what is incorrect with the submission to be fixed. You can always reach out to the author of this guide at any stage in the process for support. 

Note: The NIH Manuscript Submission Reference Number (NIHMSID) is a temporary identifier to be used only until the PubMed Central Reference Number (PMCID) has been assigned. A NIHMSID can be used on an RPPR to demonstrate compliance if it is within 90 days of the publication date. If it is after 90 days, the publication will appear as non-compliant until it is given a PubMed Central ID. See this NIH Notice for more information.

  • Once you submit a publication into the NIH Manuscript Submission system, you can update the corresponding "My Bibliography" with the NIHMSID. You can do this by navigating to "My Bibliography", clicking "Edit Status" next to the citation, and adding the NIHMSID in the correct box. Then click "Save".