Scholarly Communication and Publishing

Definitions

What is 'Pubmed Central (PMC)'?

PubMed Central is the U.S. National Institutes of Health free digital archive of biomedical and life sciences journal literature. Much of the full-text content in PubMed Central is added by authors themselves or publishers.

What is 'PubMed'?

PubMed is the database of citations and abstracts to the biomedical and life sciences journal literature. The links in PubMed to the full-text literature are added by library staff. Much of that full-text content is provided by subscriptions paid for by the UW-Madison libraries.

What does 'embargo' mean?

The time period between when the manuscript in published and when it becomes publicly available in PubMed Central.

Does 'research report' include the progress reports and final wrap-up reports that we submit to NIH?

No. The research reports that are peer-reviewed and published in a journal must be submitted to PubMed Central. The progress reports that you send to NIH that include citations must have a PMCID reference number attached to those citations that represent articles that fall under the NIH policy.

Numbers: PMCID, NIHMSID, PMID, HHMIMSID

What is a PMCID?

A PMCID is a unique PubMed Central reference number, which is assigned to each full-text record made available in PubMed Central.

What is a NIHMSID?

Before the full-text record appears (while a manuscript is still in preparation), PubMed Central gives the submission a different number, the National Institutes of Health Manuscript Submission ID (NIHMSID). Either the PMCID or the NIHMSID may be used on a grant application or progress report to demonstrate compliance with the NIH Public Access Policy. The PMCID, when available, is preferred.

What is a PMID?

The PubMed ID (PMID) identifies a citation record (rather than full-text) in the PubMed database. It is not evidence of compliance with the NIH Public Access Policy, because it does not identify a full-text submission of any kind.

What is a HHMIMSID?

The Howard Hughes Medical Institute Manuscript Submission ID (HHMIMSID) is the identification number given to an HHMI manuscript when it is submitted to PubMed Central. It should not be used to indicate compliance with the NIH Public Access Policy.

Do I have to find PMCIDs for all the articles cited in a grant submission, or just my own?

You don’t need to find PMCIDs for all articles in an NIH grant application, proposal or progress report. You only need to apply the PMCID for those articles that fall under the guidelines of the NIH policy.

Can PMC associate a single paper with more than one grant number?

Yes. In fact, you are asked to identify all NIH grants that apply to the final peer-reviewed manuscript when a submission is made.

How do I find an article's PMCID?

Search PubMedCentral for the article; the PMCID will be on the right near the top of the article's page. The PMCID can also be found in the citation record in PubMed. Feel free to ask a librarian to help.

If I find an article in PubMed Central but it doesn't have a PMCID, what should I do?

The NIHMSID, or NIH Manuscript Submission Identification Number, is an acceptable substitute if no PMCID can be located (The PMCID is applied at the time of publication.). The NIHMSID is also near the top of the article's page in PubMed Central. If you can find neither, feel free to ask a librarian to help!

What do you do if the PMCID has not been assigned yet?

If you or a third party has submitted a final peer-reviewed manuscript to the NIH manuscript submission system, a NIHMSID will be applied to that submission immediately. Use the NIHMSID in citations until the PMCID is available.

Example: Cerrato, A., et al., Genetic interactions between Drosophila melanogaster menin and Jun/Fos. Developmental Biology 2006 Oct 1; 298(1): 59-70. NIHMSID: NIHMS44135

If your final peer-reviewed manuscript is submitted by a publisher, a PMCID may not be assigned until several weeks after publication. During this time, please indicate compliance with the policy by indicating "PMC Journal - In Process".

Example: Sala-Torra, O., et al., Connective tissue growth factor (CTGF) expression and outcome in adult patients with acute lymphoblastic leukemia. Blood. 2007 April 1; 109(7): 3080-3083. PMCID: PMC Journal - In Process

Is a PMCID the same as a PMID (PubMed record ID number)?

No. Grant applications, proposals and progress reports must include PMCID, or if that is not available, NIHMSID. A PMID is not an allowable substitute.

Can I use EndNote or RefWorks to format citations in my grant applications and progress reports?

Yes. See the EndNote and RefWorks instructions developed by the Libraries.

Submission Process

If I see a link to the full-text of my article in PubMed, does that mean I have complied with the NIH Public Access Policy?

A full-text link that appears in PubMed may go to material that is not free. Such a link is not evidence by itself of compliance with the NIH Public Access Policy. Your article must appear in PubMed Central for you to comply with the policy.

If the publisher submits an article on the PI's behalf, does the PI still have to approve the PMC-formatted version?

It depends on the version deposited and Journal's agreement with NIH:

(1) If your journal deposits the final published article in PubMed Central and allows NIH to make it available to the public within 12 months of publication, you do not have to do anything to fulfill the submission requirement of the NIH Public Access Policy.

(2) If the journal deposits the final published article in PubMed Central, but delays its release to the public for more than 12 months after publication, you will have to deposit a copy of your manuscript yourself.

(3) If the journal only deposits a copy of your final peer-reviewed manuscript via the NIH Manuscript Submission system, you will still have to sign on to the NIH Manuscript Submission system to review and approve release of the article to PubMed Central.

Can I use eRA Commons to do the submission?

If you are an author/grant recipient, yes. If you are a third-party submitter, you must login through the myNCBI system access to NIHMS.

How many publishers submit to PMC on behalf of authors?

About 400, though the number is rising. See the NIH list of journals that submit articles to PubMed Central.

Sometimes articles change between accepted manuscript submission and publication. If this happens, do I have to resubmit the article to PMC?

No. The system does not allow a duplicate submission to be entered. If there are significant changes made to an article in the copyediting phase by the publisher, the PI may still have an opportunity to suggest small corrections to the submission during the approval process. Ask your librarian for help if you have questions.

Some journals submit their articles to PMC, but they do not ask the authors for NIH grant numbers (only for the fact that the research was NIH-funded). What am I supposed to do to associate NIH grant numbers with those?

If the publisher submits the final published article, the grant number does not have to be associated with it, so there is no problem. However, if the journal publisher submits the final peer-reviewed manuscript, the grant numbers are supposed to be associated with it, too. The author or a third party can access the NIH Manuscript Submission System and link the publisher-submitted manuscript to the appropriate NIH grant/award number.

Would it be all right to wait for proofs to submit an article to PMC, in order to ensure that PMC reflects changes made during the publication process?

The policy requires that the manuscript is submitted upon acceptance for publication. Once the manuscript is submitted, the PI is required to approve the submission and has the opportunity at that later time to make needed corrections to the submitted document.

Can a document be associated with more than one NIH grant number?

Yes.

If a document is submitted and associated with only one NIH grant number, but it is later discovered that it should have been associated with additional grant(s), can the record be corrected to add the additional grant numbers?

Yes, it is possible for additional grant numbers to be applied to a manuscript that has already been submitted to the system. NIH wants submitted manuscripts to have all of the grant numbers indicated that apply to that research.

If research was funded by both an NIH research grant and an NIH training grant, must the training grant number be associated with the document?

NIH requires that each submission of a final peer-reviewed manuscript indicate all NIH grants numbers that resulted in the research behind the manuscript.

Is there any cost to submit other than time?

No, although some publishers are offering the service for a fee. The Libraries will submit your article without cost to you.

Who and What

If I am a collaborator or consultant on the grant, but not the PI, do I have to submit?

The PI is responsible for seeing that all articles resulting from their NIH funding are submitted, but any of the authors of an article can do the submission, or it can be done for them by a publisher or other third party. It is the PI’s responsibility to approve all of the submissions of articles resulting from their NIH funding also.

Must I add my prior publications to PMC?

The Public Access Policy does not require retrospective submission of articles published prior to the policy's taking effect. Depending on copyright agreement with your publisher, you may submit those publications to PMC that resulted from funding by NIH if you wish. The Libraries are prepared to help you do so.

Can I use the publisher's typeset PDF?

If the publisher permits; most  require the author’s final peer-reviewed manuscript.

What file formats may I submit to PMC?

Several, including Microsoft Word, Microsoft Excel, Microsoft PowerPoint, PDF, TIFF, JPG,and others.

Will PMC accept supplementary material? What if that material has not been peer-reviewed?

PMC does indeed accept supplementary material. Images and graphs that are part of the peer-reviewed article will appear on the article's page; other materials are linked to.

Please clarify the dates. Which publications do I have to submit to PMC?

Only those articles that are accepted for publication after April 7 2008 and are the result of grants that were active during the NIH FY08 (1 Oct 07 – 30 Sep 08) or signed on or after April 7, need to be submitted to PubMed Central. If it results from a grant signed 7 Apr 2008 or later, the policy applies. If the grant was active in FY08 but the article grew out of research conducted in an earlier grant year, the policy does not apply. However, authors are encouraged to submit such articles to PMC if the terms of their publication agreements permit.

As a PI should I change my procedure for tracking publications growing out of the grants I supervise?

You may want to. Some universities are setting up centralized systems to track these publications, but that is not something that is likely to work on this campus. It is possible that some departments may start tracking the publications of their PI’s and researchers depending on the size of the department. We will be interested in learning how different PIs end up handling this.

Does the NIH policy apply to grants covering training or infrastructure?

NIH's response, "The NIH Public Access Policy applies to all types of grants. The answer to your question depends on if the research reported in the paper arise from NIH direct funds." So, the NIH policy applies to all peer-reviewed articles that arise, in whole or in part, from direct costs (costs that can be specifically identified with a particular project or activity) funded by NIH.

Timing

What if I have a grant submission containing a citation for an article that is in PMC but still under review, or under publisher embargo?

PMC issues an interim number (NIHMSID, or NIH Manuscript Submission Identification Number) that can be used instead of the PMCID in grant submissions, applications, proposals, or progress reports if no PMCID is available.

If final publication is delayed, do we have to worry about setting the date of publication in PMC in order to respect a publisher's desired embargo period?

The embargo may be set for no more than 12 months in order to comply with the policy. Some publishers honor a shorter embargo period.

Do I have to track publication dates in order to respect a publisher's desired embargo period?

No. The NIH manuscript submission system will track the publication date and the submitted embargo period for you and will transfer files to PMC.

Some journals submit articles to PMC for authors, but they may not do so in a timely fashion. What should I do if delay by the publisher means that there is no PMCID or NIHMSID available for an article that I must cite in a grant application, proposal or progress report?

If your final peer-reviewed manuscript is submitted by a publisher, a PMCID may not be assigned until several weeks after publication. During this time, please indicate compliance with the policy by indicating "PMC Journal - In Process".

Example: Sala-Torra, O., et al., Connective tissue growth factor (CTGF) expression and outcome in adult patients with acute lymphoblastic leukemia. Blood. 2007 April 1; 109(7): 3080-3083. PMCID: PMC Journal - In Process

Publisher Relations

Are any publishers unwilling to publish (or prepared to reject) articles subject to this policy? Will they be amending their author instructions and copyright transfer agreements to help researchers comply with this policy? Will I have to withdraw an article from a journal that refuses to allow me to comply?

NIH recommends that "Authors should work with the publisher before any rights are transferred, to ensure that all conditions of the NIH Public Access Policy can be met." (FAQ #c4). If your publisher will not accept NIH mandated archiving, contact a member of our Scholarly Communications & Publishing Subgroup to work with your publisher.  We have not yet encountered a publisher that was unwilling to comply with the NIH policy. There have been some publishers that were unaware of the policy and changed their policy and workflow to accommodate the NIH policy.

How do I find out what publisher policies are?

Check SHERPA RoMEO and read your publication agreements. If information is not available on the SHERPA website, it is helpful to check the publisher’s website as well. The Libraries are prepared to help you interpret the language in your copyright agreement or help you located needed information about a publisher complying with public access policies such as NIH.

Does the Office of Research and Sponsored Programs handle or oversee copyright-transfer agreements I sign with publishers?

No. Reading these agreements and amending them if necessary is the authors' responsibility. If you need help, the Libraries are prepared to assist.

What is the difference between the NIH suggested language and the CIC author’s addendum?

The CIC author’s addendum is intended to be appended to any publication agreement, and does not specifically mention NIH. Given that NIH compliance is mandated by law, publishers may be more receptive to the NIH language. However, if the publisher agrees to the CIC addendum, the author will have the right to submit the article to PMC, in compliance with the mandate.

What about presentations at society meetings, where the society journal (e.g. Annals of Surgery) has right of first refusal on a paper?

NIH recommends that "Authors should work with the publisher before any rights are transferred, to ensure that all conditions of the NIH Public Access Policy can be met." (FAQ #c4)

What should I do if the publisher has a click-through online copyright transfer agreement that does not allow for modification?

We will try to find out NIH’s recommendation. In the meantime, our suggestion (but we aren’t lawyers!) is that you click on through but follow up immediately with an email stating that the permission you just gave is subject to the following language: [and append suggested NIH language]. Retain a copy of this email for your records.

Do I have to document in any way that my manuscript has in fact been peer-reviewed?

No; adding the journal name is sufficient.

Will usage statistics for PMC articles be sent to the publisher of the journal where the article is eventually published?

There are no plans to do this automatically, although such statistics can be provided to authors. Interested journal publishers may want to work with PMC to see if this can be done.

Can a publisher’s Open Access fee be charged to the grant that funded the research?

The NIH FAQ states: “Yes. The NIH will reimburse publication costs, including author fees, for grants and contracts on three conditions: (1) such costs incurred are actual, allowable, and reasonable to advance the objectives of the award; (2) costs are charged consistently regardless of the source of support; (3) all other applicable rules on allowability of costs are met.”

Using EndNote to Manage NIHMSID & PMCID Numbers

Note: Instructions written for Endnote X1, (Windows). Procedures may vary depending on EndNote version and operating system.

pdf version

Setting Up EndNote

Assigning NIHMSID and PMCID fields in the Journal Article REFERENCE TYPE.

1. Select Edit, then Preferences, then Reference Types
2. Click on Modify Reference Types.
3. Choose Journal Article reference type.
4. Scroll down to assign NIHMSID to Custom 6 field.
5. Assign PMCID to Custom 7 field.
   (Optional) Add PMCID and NIHMSID to other Reference Types.
6. Click OK to save the modified Journal Article reference type.
7. Click OK to save changes to preferences.
   

Downloading UW-Madison Libraries’ NIH-PMCID Output Style, modified PubMed Import Filter, and modified PubMed Connecton File

1. Download the following modified EndNote files from http://www.library.wisc.edu/endnote/filters-styles.html

• NIH-PMCID.ens - Save to your EndNote X1\Styles subdirectory.
• PubMed-PMCID.enf - Save to your EndNote X1\Filters subdirectory.
• PubMed-(PMCID)-connect.enz - Saveto your EndNote X1\Connections subdirectory.

Adding NIH Manuscript References to EndNote

1. When a manuscript is accepted, create a Journal Article record in EndNote. Add the NIHMSID number you received from the NIH Manuscript Submission System to your EndNote record. Include the prefix “NIHMS”.
   
2. Add the PMCID number with the prefix “PMC” to the record when it becomes available. The article receives its PMCID at the time it is indexed in the PubMed database.

Formatting Manuscript References for NIH Documents

1. Set EndNote to display records in the NIH-PMCID output style.
2. Select desired record(s) to insert into your NIH report or application.
3. Click on EDIT and then click on COPY FORMATTED.
   
4. PASTE citation(s) into your report or application.

Viewing PMCIDs in PubMed

1. Display PubMed records in AbstractPlus or MEDLINE formats.
   

Importing PubMed records into EndNote

In PubMed

1. Search PubMed for author’s name.
   Example: gustafson d*[author]
2. Select Medline from the Display drop down menu.
3. Select File from the Send To drop down menu. If prompted, select Save. Otherwise, use your browser's File and Save As.
4. Change the Save as Type choice to Text (*.txt).
5. Name your file and click on Save.

In EndNote

1. Open Endnote and choose the Library into which you want to import the citations.
2. Choose Import from the File drop down menu.
3. Click on Choose File at the Import Data File: box and find the file you just saved from PubMed.
4. Select PubMed-PMCID import filter at the Import Option: box.
5. Click on Import.

Searching PubMed from within EndNote via the Connection File

In EndNote

1. Click on TOOLS, then ONLINE SEARCH.
2. Select PubMed-(PMCID)-Connect.
3. Enter your search terms and click on SEARCH.
4. Select records
5. Click on COPY SELECTED TO and choose the destination library.

NIHMSIDs and PMCIDs will import into the proper fields.

Using RefWorks to Manage NIHMSID & PMCID Numbers

pdf version

Setting Up Your RefWorks Account

1. In RefWorks, assign NIHMSID to User 4 Field Name and PMCID to User 5 Field Name.
   • Log in to your RefWorks account.
   • Select Tools, then Customize.
   • Under User Field Options, assign NIHMSID to User 4 Field and PMCID to User 5 Field.
   • Click on SAVE.
     
2. Add NIH-PMCID in your output styles Favorites list.
   • Click on Access Output Style in the Output Style drop-down menu.
   • Select NIH-PMCID.
   • Click on Add to Favorites.
   • Click on Back to Previous Page.

Adding Manuscript References to RefWorks

1. When a manuscript is accepted, create a Journal Article record in RefWorks.
2. Select NIH-PMCID in the View fields used by drop down menu.
3. Select desired folder name in In Folder(s) drop down menu.
4. Add the NIHMSID number you received from the NIH Manuscript Submission System to the NIHMSID field. Include the prefix “NIHMS”.
5. Add the PMCID number with the prefix “PMC” to the PMCID field when it becomes available. The article receives its PMCID at the time the article is indexed in the PubMed database.
   

Formatting Manuscript References for NIH Documents

1. Click on Bibliography at the top of the screen.
2. Select NIH-PMCID from the Output Styles drop-down menu.
3. Click in the radio button to the left of Format Bibliography from a List of References.
4. Select desired format from the File Type to Create drop-down menu.
5. Click in the radio button next to References From: and click on the desired folder from the drop-down menu.
   Hint: To create a temporary list of references, select the references you want to add to your list and click on the Add to My List under the folder name.
6. Click Create Bibliography.

Viewing PMCIDs in PubMed

1. Display PubMed records in AbstractPlus or MEDLINE formats.
   

Importing PubMed records into RefWorks

In PubMed

1. Click in the box to the left of desired records
2. Select Medline from the Display drop down menu.
3. Select Text from the Send To drop-down menu on the right side of the screen.
4. Use the browser’s Edit and Select All to select all of the records.
5. Copy the records using Edit and Copy.

In RefWorks

1. Click on References and Import at the top of the screen.
2. Select NLM PubMed from the Import Filter/Data Source drop down menu.
3. Select PubMed from the Database drop-down menu.
4. Click in the radio button next to Import Data from the following Text.
5. Click in the box and Paste your records into the text box.
6. Click on Import.
   PMCIDs and NIHMSIDs are imported into the NOTES field.
   
7. For each imported record, click on EDIT, then Copy and Paste the PMCID and NIHMSID into the NIHMSID and PMCID fields.
   

Campus Library Policies & Questions

As more journal articles become available free via PMC, might the libraries charge for Library Express delivery of final articles published in journals not owned by campus libraries?

There has been no discussion of this possibility. While it is true that the libraries are allocating resources to help campus comply with this initiative, we are doing so because of its importance to our community of scholars and researchers.

Questions

Contact Julie Schneider, Ebling Library, with questions about the NIH public-access policy.