Federal legislation is now in effect which mandates that researchers funded by NIH grants awarded April 2008 or after must submit an electronic version of final, peer-reviewed articles within 12 months of publication.

It takes only about 10 minutes to submit a manuscript. It is our recommendation that the submissions are made by authors who are responsible for the final revisions of the manuscript(s) and who have access to NIH grant numbers.

Below is information about the policy and links to the submission system.

The NIH Public Access Policy implements Division G, Title II, Section 218 of PL 110-161 (Consolidated Appropriations Act, 2008). The law states:

The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicy available no later than 12 months after the offical date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

You are not required to submit manuscripts for work that was funded by grants or awards given prior to NIH Fiscal Year (FY) 2008--which began October 2007--although you may do so if you choose and if you own rights to the material. Compliance is connected to current NIH funding as of FY2008, and the date of acceptance of the publication.

Here are the requirements for periods covered by the mandate:

• Manuscript generated by NIH FY2008 (or after) grant and accepted for publication on or after April 7, 2008
• Manuscript generated by a continuing NIH grant that is active in FY 2008 (or after) and accepted for publication on or after April 7, 2008
• Manuscript generated by NIH contract awarded after April 7, 2008

If you are publishing a manuscript based on NIH-grant-funded data collected during the mandated period you must comply, even if the publication is made long after the grant has expired.

Return to top

It is important to address copyright issues before submitting a manuscript to the NIH Public Access Manuscript Submission system (NIHMS).

• If you have signed a contract with a publisher transferring rights to your manuscript to them, you will have to obtain permission to submit your manuscript to NIH for public access.
• Authors are urged by NIH to avoid signing such agreements, since they will not allow the author to comply with the policy.
• The NIH provides sample language to request in future copyright agreements with journal publishers:

"Journal acknowledges that Author retains the right to provide a copy of the final manuscript to the NIH upon acceptance for Journal publication, for public archiving in PubMed Central as soon as possible but no later than 12 months after publication by Journal."

• If an author has submitted a manuscript to the NIH Public Access system that is copyrighted to a journal, journals may request to have the material removed from the Public Access system.

For other information on copyright issues, please consult the NIH FAQ page copyright section.

Please be aware that these are suggestions and guidelines as recommended by the NIH policy pages. They are not intended to be interpreted as legal counsel.

Return to top

Here are the links to the submission system and helpful pages from the NIH:

• Submit your manuscripts at the NIHMS submission page
• There are also excellent submission tutorials located the NIHMS site
• The home page for the Public Access policy is a good starting place to read the policy and to link to other helpful pages
• The NIH maintains a comprehensive FAQ page for the NIH Public Access policy

  Return to top

Before you begin the submission process, check to see if the journal you are publishing with is one of the PubMed Central journals that will submit the manuscript for you.

You can find a list of PubMed Central (PMC) journals at the NIH submission policy site.

If you publish with one of these journals, you will still have to assign a grant reporting reference to the manuscript through the NIHMS system. This can only be done by a principal investigator (P.I.) thorugh the eRA link to NIHMS submission. Please refer to the grants reporting section of this guide for more information.

Return to top

If the journal does not submit to PubMed Central for authors, these authors must self-submit. If multiple PIs are involved, one should be designated as corresponding and submitting author.

Before submission authors need to determine any stipulations journals may have placed on submission by authors. These stipulations can be found on the publisher's copyright agreement form or on the publisher's web pages for submission. Some considerations and stipulations are:

• Embargo period (may not be longer than 12 months as mandated by NIH)
  • This embargo period usually begins after the journal publication itself, not after electronic submission of pre-print ahead of publication in indexes such as MEDLINE.
• Including a link to the journal's publisher
• Including the DOI (digital object identifier) of the final version
• Version to submit to PMC: final peer-reviewed version or final journal-formatted version
• Link to the final formatted version on the journal's website
• Including a statement specified by the publisher
• Including the full final citation of the published work

Return to top

Below are some step-by-step instructions on submission to the NIHMS system:

From the NIHMS submission page: (http://www.nihms.nih.gov/)

• Log in to the NIHMS System through the link in the upper right corner of the submission page
• Select the proper category for your submssion type:
  • You need an eRA commons profile to submit as a P.I.
  • You need a myNCBI account to submit on behalf of someone else. A pop-up window will prompt you to log in to your myNCBI account. If you do not have one, you can register for one at this time. There is no fee for creating a myNCBI account.

• After logging in via the proper channel, click the button labeled "Submit New Manuscript"

What info do you need to begin?

• The name of the journal
• The manuscript title
• Grant number - Because this information is needed, it is recommended that someone familiar with the work submit the manuscript. This is usually either the principal investigator or first author of the paper. Note: If the work is funded by several grants, they may be entered in a single submission.
• All the files necessary: What formats of file should you submit?
  
  • Use the final, peer-reviewed and edited version
  • This will usually be the double-spaced document format you use to submit for review.
  • Do NOT use the journal-formatted "reprint" PDF, unless the journal allows you to submit the formatted version
  • Your manuscript can be a Word document or any format that is required by the journal to which you submitted.
  • Include any and all figures, tables, etc. They can be either embedded in the manuscript or included as separate files, but they must be submitted.
• Use the links supplied on the NIHMS starting page to help answer your questions about file formats.

Hit the "Continue" button on each submission page to proceed through the submission process. You will be prompted to supply all the necessary information. If you wish to discontinue the process, you may hit the "Cancel Submission" button on the lower left of each page.

NLM Skill Kit: NIH Manuscript Submission System

NIH Public Access Submission Process

Return to top

If you get a message stating "Please use Grants Reporting to assign your grants to the article", this means that you have tried to submit a manuscript for a journal that belongs to the PubMed Central submission group, and they will do it for you. If you receive this message, go to the upper right corner of your submission page, and click on the "Grants Reporting" link:

Note: you must be signed in to eRA Commons as the principal investigator to do Grants Reporting or to see this link. You cannot do Grants Reporting if you are using the myNCBI submission process to submit for someone else.

Return to top

After a manuscript is submitted, the PI will receive up to two e-mails from the NIHMS prompting approval of the submission. At this point, PIs will be prompted to create an eRA Commons account if one is not already in existence.

Submission approval includes verification of the manuscript and grant award. This is the point at which publisher-stipulated embargo periods may also be added, if the manuscript has been submitted by a third party. Final review of the web version before PMC posting is the final step of the approval process.

NIHMS sends reminder e-mails to the PI if the initial requests for approval are overlooked. Authors should be aware that submission of the manuscript is not sufficient for compliance with the NIH mandate: Approval of the manuscript is necessary for full compliance.

If Publisher submits manuscripts for authors
PI will receive two e-mails from NIHMS:

1. Approve PDF Receipt : PI is asked to review the PDF, confirm that it is the correct manuscript and enter grant information. NIHMS will then convert the PDF to a web-suitable version.
2. Approve Web Version : PI is prompted to do a final review of the web-formatted version to be posted to PMC.

If PI submits
PI will receive only one e-mail from NIHMS:

1. Approve Web Version : PI is prompted to do a final review of the web-formatted version to be posted to PMC.

If third party submits on behalf of PI
PI will receive two e-mails from NIHMS:

1. Approve PDF Receipt : PI is asked to review the PDF, confirm that it is the correct manuscript, enter grant information and assign any publisher-stipulated embargo period (maximum of 12 months allowable by mandate). NIHMS will then convert the PDF to a web-suitable version.
2. Approve Web Version : PI is prompted to do a final review of the web-formatted version to be posted to PMC.

Return to top

Here are some of the links that are found throughout this document, plus some handy tools and resources from the NIH.

NIH Resources

• Revised Policy on Enhancing Public Access to Archived Publications Resulting from NIH-Funded Research (NOT-OD-08-033)
• Reminder Concerning Grantee Compliance with Public Access Policy and Related NIH Monitoring Activities (NOT-OD-08-119)
• Overview of the NIH Public Access Policy
• NIH Submission Methods
• NIH Grants Search Tool
• NIH Public Access Policy Frequently Asked Questions
• NIH PubMed Central (PMC) Journal List
• PubMed Central
• PMID : PMCID Converter

NIHMS Resources

• NIHMS Home Page and Log-In
• NIHMS Tutorials for Submitters
• NIHMS Video Tutorial: Submitting an Article to PubMed Central (for PIs/Authors who self-submit)
• NIHMS Video Tutorial: Approving Submission of an Article to PubMed Central (for PIs/Authors who need to approve a submission made by a publisher or third party)
• NIHMS Help Desk
• Skill Kit: NIH Manuscript Submission System - Get the Help You Need

Return to top

These instructions will demonstrate the procedure for modifying the PubMed (NLM) import filter to include the PMCID, then how to display it in citations by modifying output style.

There are several steps that must be done to put the PMCID in the proper place in EndNote references. First, the EndNote Preferences need to be modified. To do this, open your EndNote program (with or without an EndNote Library). Click on Edit then click on Preferences. A new window will open labeled EndNote Preferences.

From the list on the left, click on Reference Types. The right panel of the window will change to the default selection, Journal Article. If the Default Reference Type is NOT Journal Article, then use the drop down arrow to select Journal Article.

Next click on the button Modify Reference Types.

A new window will open. Scroll down until the column on the left has Custom 1, Custom 2, Custom 3, etc. visible. Place your arrow pointer in the column next to Custom 1, which in most cases will be blank. Type PMC in this space. That will become the new label in the EndNote record. Then, click the OK button at the bottom.

Modifying the PubMed(NLM) Import Filter

EndNote has an import filter for PubMed called PubMed (NLM). This is the file you want to modify to add the PMCID to your EndNote records. To preserve the integrity of the original file, you will want to rename this file. Choose a name such as "PubMed with PMCID (NLM)". To do this, click on Edit and hover the pointer over Import Filters.  If you have used the PubMed(NLM) filter to import references recently, it should be one of the choices on the right. If not, then select Open Filter Manager and from the list of import filter choices, select PubMed (NLM) and then rename it: Go to File/Save As and then rename the file to PubMed with PMCID (NLM). The name in the window should now be the name you used to Save As. This is the file you want to modify, NOT the original PubMed (NLM) file.  Click on Edit and go down to Import Filters. A selection of options will appear. Your new PubMed with PMCID (NLM) should be one of the options. If not, then select Open Filter Manager and from the list of import filters, select PubMed with PMCID (NLM) and click on the Edit button. A new window will open with the editing choices on the left and a display window on the right.

Modifying this file is much like modifying the reference types in the EndNote preferences.

Click on Templates in the left column and a two column window will display in the right hand side. You are going to add the PMC field from the PubMed MEDLINE record display in the Tag column and PMC in the Field(s) column.

Position your cursor in the box after {IGNORE} (later updates of EndNote have Notes in this field) next to the PL tag and press . This should give you an empty row between the PL and the PMID tags. Under the Tag column, type PMC ? (Note: there is a space between the C and the dash) and then press to position your cursor in the Field(s) column and type PMC. Close the window and, when prompted, save the changes you have made.

Note added September 2009:  If you have a newer version of EndNote (X2 and above), the PubMed(NLM) import filter may already have a field for PMC in it.  Verify this by opening the import filter for PubMed(NLM) as described above, click on Templates in the left column of the window, select Journal Article, and scroll down the page to see if the PMC - field is already in the listing.  If it is, there may be an {IGNORE} field in this line.  Just delete the {IGNORE} and type PMC in this field.  Close and save the filter manager.

Modifying the Output Style(s)

Note added September 2009:  EndNote has a style called NIH.  Whenever possible, use this style for grant submissions and annual reports to the NIH.  This style follows the guidelines specified by the NIH, and includes the PMCID in the correct location at the end of citations of articles that have been assigned a PMCID. If you don't wish to use this style, follow the instructions below.

The last step is to modify an output style to display the PMCID at the end of the citation. You can pick whatever output style(s) you wish, the process is the same. The Numbered style is used as an example for this guide.

After selecting the style you wish to edit, be sure to rename the file like you did with the Import Filter.  When you have the file selected, just do File/SAVE AS and give it a new name (this guide used Numbered with PMCID). It is also a good idea to fill in the Based On part of the display in the right hand window to include the name of the EndNote style you are modifying.

With the new file now selected, click on the Templates item under Bibliography. The first choice in the window under Reference Types on the right hand display will be Journal Article. For our purposes, the PMC field will be added to the end of the Journal Article type.

Place the cursor at the end of the Journal Article record which, in this example, is right after the period (.).  Press the space bar and then type: `PMCID:` PMC. Include the grave accent ( ` ) diacritical mark (located to the left of the "1" key on your keyboard) on either side of `PMCID:` Now, the journal type should look like this:

Author, Title. Journal, Year|. Volume|(Issue)|: p. Pages|. `PMCID:` PMC

You may not have all of the fields in your record that are in this example. This varies by the style you choose. Just add `PMCID:` PMC to the end of the string that is there.  Then close the window and save the changes.

• You will use your new import filter when importing references from PubMed to yourEndNote libraries
• You can use your new Output style in your bibliography in NIH grant applications, proposals and progress reports after May 25 when citing your work accepted for publication after April 7, 2008.

PLEASE NOTE: This only works for the EndNote program that is loaded on your computer.  THIS DOES NOT WORK FOR ENDNOTE WEB.

 

EndNote FAQ on the PMCID: http://www.endnote.com/support/faqs/import/faq15.asp

EndNote Assistance is available at Galter Health Sciences Library:
Galter Library Education Team
312-503-8109

Adapted from document originally created by Lee Vucovich of the University of Alabama, Lister Hill Library.

Return to top

Ask the Biosciences Librarian Pamela Shaw for assistance.

Pamela Shaw, Biosciences Librarian
Pamela's Liaison Page
312-503-8689

Return to top

This page last updated Oct 8, 2009.