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On May 2, 2005, The National Institutes of Health (NIH) Public Access Policy went into effect for NIH-funded researchers to submit their final, peer-reviewed manuscripts—only those that have been accepted for publication—to PubMed Central (PMC).
To facilitate this submission process, the NIH developed the NIH Manuscript Submission System (NIHMS) as a way to manage your manuscript submissions.
Your manuscript can be submitted in a wide range of electronic word-processing formats. Additional files, such as figures, tables, or supplementary information, should also be included with your manuscript submission. You do not need to format your manuscript beyond the requirements of the journal that has accepted your article.
This user’s guide gives you step-by-step instructions on how to submit and approve manuscripts so that they may be placed in PMC for permanent archiving.
If you find that you have additional questions or would like to submit comments regarding the NIHMS System, please contact the NIHMS Help Desk.
From http://www.nihms.nih.gov/, there are several ways for a submitter to log in to the NIHMS System.
To begin, look for the yellow box at the right side of the screen and click on “Log in”.
The best log in route to use depends upon the submitter’s occupation:
eRA Commons – for NIH extramural principal investigators, grantees, or applicants
NIH – for NIH intramural scientists and NIH staff
WT – for Wellcome Trust grantees and staff
Publisher – for publishers
My NCBI – for others
Note: Use the same login option for all visits to the NIHMS System to avoid creating duplicate accounts. If separate logins are created by a single user, not all of the user’s submissions will be consolidated but will be distributed among the different login accounts, thus creating confusion.
eRA Commons – for NIH extramural PIs, grantees, or applicants
The NIH eRA Commons is a Web-based system for NIH extramural grantee organizations, grantees, and the public to receive and transmit information electronically. To be able to use the NIH eRA Commons route, you must be registered as a user. Contact your Office of Sponsored Programs or Office of Clinical Research representative for information about registering for an eRA Commons account.
NIH – for NIH intramural scientists and NIH staff
The NIH Login may be accessed and used only for authorized Government business by intramural personnel. If you are employed by NIH, this is the place to log in to the NIHMS System.
WT – for Wellcome Trust grantees and staff
Researchers who received funds from Wellcome Trust should use this system to log in to the NIHMS System.
My NCBI – for others
Anyone can register for an account through My NCBI, including members of the public. This system is not recommended for NIH extramural PIs, grantees, and applicants (who should use eRA Commons) or for NIH intramural scientists (who should use the NIH login). My NCBI should be used only by those submitting a manuscript on behalf of the PI. For instance, if the PI wants a colleague or assistant to submit a manuscript but does not want the submitter using a personal account login and password, the manuscript should be submitted via a My NCBI account.
A publisher submitting the published version of articles to the NIHMS System should log in using the system designed specifically for publishers to use. The publisher log in process is quick, and easy for multiple submissions. To obtain a publisher login account, please contact the NIHMS Help Desk.
Researchers who received funds from Wellcome Trust should use this log in route to access the NIHMS System.
Provide bibliographic information, Wellcome Trust grant information, NIH Intramural grant or project information, and all manuscript files.
Step 1: Log in to the NIHMS System using one of the appropriate methods listed in the Log in to NIHMS System section. The first screen is the Manuscript List, which shows the manuscripts that need your attention, are in the submission process, are awaiting release to PMC, or have been released to PMC.
Step 2: Next to the yellow arrow that says Start Here, click on the button Submit New Manuscript. The next screen is the Submission Overview, which details the steps to take to submit a manuscript and provides answers to frequently asked questions.
Step 3: Click the “Continue” button.
Review a PDF version of your manuscript to ensure that we received all of the content.
Review and approve the Web version of your manuscript for use in PubMed Central (PMC).
Here you must enter the name of the journal in which the accepted manuscript will be published. Just by typing in a few letters, a drop-down list of journals indexed in PubMed1 will appear for you to choose from. You can also type in the name of the journal manually.
Next, type in the title of the manuscript. At this point, you can Save & Exit, Cancel Submission, or move on to Step 2 by clicking on the Next: Grant Info button.
Here you enter the grant information required for the submission. Each manuscript submitted must be assigned at least one grant, project number, or other source of NIH funding. You can enter the grant or project number or the first and last name of the PI.
When you click the Add button, if the NIHMS System finds a match, it will appear on the screen. Sometimes the NIHMS System will find several matches, depending on how the information is entered, and you can choose the correct grant from a list.
When you are finished entering all of the grant information and want to continue with the submission, click on the Upload Files button.
Here you will find information on what files to include (please do include supplements and videos, if any), the list of acceptable formats, and how to label each file uploaded. There are three things you must enter to upload a file:
Type of file (i.e., text, figure, supplement, etc.)
Label of file (i.e., supplemental video 3, figure 1)
Name of file – automatically filled in when the user clicks Browse to access his or her computer and designate a file for uploading
You can keep adding files as needed by clicking the purple Add another file link. When you are finished collecting the files, click the Upload Files button. A window will pop up to show the progress of the upload.
When all files have been successfully uploaded, you will see a new screen.
Here you have a chance to review all the information just entered for this submission.
This is the final part of the submission process. However, if the person submitting the manuscript at this time is not the PI but instead a Submitter (or PI proxy), he or she will not be able to move to the final step. Only the PI can view and approve the submitted manuscript (see the following section).
When the PI logs in to the NIHMS System, or if the PI is in the system submitting a manuscript, he or she will see the final screen.
Review: Click on the highlighted PDF file and view it before approving it. Be sure all of the pieces of the manuscript are there, including supplemental files and/or videos (a mention of these types of files will appear on a mostly blank page at the end of the PDF receipt).
Set Delay: Set the release delay of the manuscript to PMC (up to 12 months). If you are not sure about your publisher’s policy about release (embargo) dates, contact the publisher before setting this delay.
Approve: Click on the green Approve button.
Submission Statement: read the statement and click either Agree or Disagree (clicking Disagree will place the submission on hold).
Submission is now complete and in the hands of the NIHMS System staff. The process of preparing the manuscript for PMC takes from 1 to 2 weeks, depending on the manuscript. When the Web version (PMC version) of the manuscript is available for review, the PI will be notified via email.
After the submitted manuscript has been processed and prepared for PubMed Central (PMC), an email will be sent to the Corresponding PI. The email will include a link that will take the PI directly into the NIHMS System so that he or she can view and approve the Web version (both HTML and PDF) of the manuscript.
It is important for the PI to view both the HTML and PDF formats and either approve both for posting on PMC (see Approve Web Version) or request corrections (see Request Corrections).
The PI must click on the URL in the notification email received, or if that is not available, read how to log in to the NIHMS System.
Once in the system, you will see the Manuscript List screen. The manuscript(s) you need to view and approve are listed at the top, below the section Manuscripts That Require Your Attention.
A Manuscript Status alert will appear next to the manuscript title that says Waiting for PI approval of final Web version of manuscript.
Click on the hyperlinked manuscript title to access the Web version. This screen is called the Review and Approve screen.
In the next screen, you will see the link PMC-ready Manuscript highlighted in yellow with an arrow pointing to it. Click on this highlighted link to access the Web version of your manuscript. (The other hyperlinked file to the right of the highlighted Web version link, Original Submission, is the original submission PDF, which is for your reference only).
A new screen will appear showing the Web version of the manuscript. You will see the HTML first with the NIH Public Access logo at the top. Check carefully for errors and/or missing data.
In the upper part of the left frame, click on PDF to access the PDF version.
When you are finished viewing the Web version, close the screen. You will not be logging out of the NIHMS System by closing this screen because it is a separate screen from the NIHMS System.
You will return to the Review and Approve screen.
Click the green Approve button or click the blue Request Corrections button (see the next section).
Note: Visual guides are available on the NIHMS System website that provide instructions on how to view and approve the Web version. See Approve WEB Version eRA PI if you are logging in using eRA Commons or use Approve WEB Version NIH PI if you are logging in as an NIH employee.
If you notice a formatting error or critical textual error in the Web version of the manuscript, please submit a request for corrections. Please note that only errors or omissions that impact the scientific accuracy of your article are eligible for correction. Please report all corrections at one time.
Follow the same instructions listed above in the Approve Web Version section to view the Web version of your manuscript. Then, after returning to the Review and Approve screen, click on the blue button Request Corrections. (Also see the visual guide Request Corrections on the NIHMS System website).
In the text boxes, describe the required changes and where they are located:
Click on the yellow hyperlink Manuscript with paragraph numbering to view your manuscript. This version will have all sections and paragraphs numbered.
Use the numbering (if applicable) to describe the location of the error (e.g., P3, P27, S7, Title, Figure 2, References, Footnotes).
Describe all required changes in detail.
Click the purple link Add another Request for Corrections if you need to add more text boxes to report corrections.
Note: Only errors or omissions that impact the scientific accuracy of your article are eligible for correction.
When you are ready to send the list of corrections, click the green Send button. The NIHMS System staff will be notified and sent your list of corrections. If the corrections are minor, the manuscript may be available for your review again in a few days. However, if the corrections are extensive or complex, the manuscript may need to be reprocessed, which can take from 1 to 2 weeks, depending on the corrections. The PI will be notified when the Web version is available for his or her review.
1 PubMed (PM) indexes abstracts only. PMC archives full-text research articles and is linked to PubMed. Manuscripts submitted to the NIHMS system will be prepared for archiving on PMC as well as indexed in PubMed.
