Guide for My Bibliography and Compliance


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  • While this is yet another federal mandate- called the NIH Public Access Policy and places a real compliance burden on research institutions, there are benefits and reasons for its new policy that will hopefully have a positive impact on all of us and on science and medicine in general.
    Help scientists access more literature
    Address constantly increasing journal subscription prices – placing burdens on libraries and institutions
    Help taxpayers – Scientists given gov’t grants; scientists provide journal content free; and their institutions/libraries then have to pay for access to their own content
    Also to preserve the system to some degree and help publishers –
    Embargo period
    Manuscript – not final published paper that is submitted.
    Compliance – is very important to preserve our funding
  • Dissemination of this work is greatly advanced by the NIH PA policy – both for scientists, as this quote indicates is so essential, and for the general public, who are supporting this work with their tax dollars and therefore by that token, do have rights to access it.
  • Here’s what I’ll be covering:
    Compliance is important in order to preserve our NIH funding!!
    EndNote demo for those who are interested +
  • This is the law that passed at the end of last year as part of the nation’s appropriations legislation.
    The law directed the NIH to adopt a policy – which they did –including these essentials:
    Final peer-reviewed manuscript– final edited copy, not in the publisher’s format yet.
    Submit to PMC upon acceptance for publication – meaning as soon as possible following acceptance – to comply, we should try to follow this as closely as possible.
    Designate when (up to 12 mos. after publication) it be made publicly available = embargo period
    Consistent with copyright law – should comply with publisher copyright transfer agreement. (more on that coming).
  • Reviews are included only if they are peer-reviewed, which is not normally the case.
  • NCBI= National Center for Biotechnology Information
  • PubMed –
    You can link out from it to PMC or to a journal site to obtain the full text article
    Each article in PubMed has a PMID; only the articles in PMC have a PMCID
  • Submission method: A,B,C, or D
    Version – final published copy; or final peer-reviewed manuscript
    Who will submit? Author or intermediary; or publisher
    When? Should be submitted upon approval for publication
    Who will approve the submission? Usually the corresponding author
    When will the paper be made public on PMC? This is the embargo period.
  • Determine Applicability -- Does the policy apply to your paper? Is it peer-reviewed and did you use NIH funding? Was it accepted on or after April 7, 2008?
    Address Copyright - Ensure publishing agreement allows paper posting to PMC
    -- via the Library -- or
    -- ensure Publisher does it --
    3. Cite PMCID number in grants
  • Most copyright agreements now allow posting; Corresponding authors need to take charge of this, -- or any author, if he’s NIH funded and no other collaborating author is.
    NIH says you should not publish in a journal that doesn’t allow posting – not really an issue any more.
    Some journals do the posting for you. – either final paper (no further action required by you); or manuscript version (you must complete approvals!)
  • Link to our website-
    Show main page first;
    Also have links to posting policies, alphabetical by journal title -Show color-coded list.
    Links to other sites that list policies
    Links to FAQ’s
    journals list next;– “Cancer” J Biol Chem Cancer Research
    Submission request form next
  • The 4 methods (A –D) vary on two dimensions:
    The format of the paper submitted: either the final published paper (Methods A and B) or the final peer-reviewed manuscript (Methods C and D),
    Who does the submission: Either the publisher (Methods A, and B – by author arrangement), or the author or his intermediary (Method C) or in Method D – the publisher begins the process, but the author must approve the submissions in order to finalize the process..
    Method A: The list of journals approved to do this submission is on the Public Access Policy website and on our website – and some are incorporated into our Deposit/No Deposit list
    The final publishers version is what is deposited here – Authors just need to await the PMCID no. which will appear in PubMed and PMC once the process is complete.
  • Some publishers have an arrangement with NIH to deposit individual final published articles in PubMed Central (PMC) on a case-by-case basis.  These journals do not automatically deposit every NIH-funded paper in PMC.  Rather, the author can choose to arrange with the journal for the deposit of a specific article; this usually involves choosing the journal’s fee-based open access option for publishing that article. 
    The publisher programs that have this arrangement with NIH are:
    ACS AuthorChoice
    APA Open Access
    BMJ Unlocked
    IUCr Open Access
    Portland Press Opt2Pay
    SAGE Open
    Society for Endocrinology Open Access
    Springer Open Choice
    Taylor & Francis iOpenAccess
    Wiley-Blackwell Online Open
  • Institutions and investigators are responsible for ensuring that manuscripts are submitted upon acceptance for publication
  • Show submission request form to submit
    Submission request form next
  • Complete;hit “Send” and Lydia or another library staff member will receive your request.
    You will receive a confirmation email requesting that you send your final peer-reviewed manuscript and and associated figures in one or separate files, depending on how they are formatted.
  • You will need to indicate this on the email you get once a paper is submitted on your behalf
    The corresponding author will receive two emails and will need to approve each in order for the process to be completed.
    Often indicated on author agreement. Look for the embargo period.
    Is time period– AFTER publication- NOT after submission -- this is around the time when PMCID no. is assigned.
    Some journals allow immediate full text access; some have a number of months after publication– If the embargo period is beyond 12 mos., it doesn’t comply with the mandate.
    The publisher designates the embargo period; it’s usually 12 months. If you can’t locate it, the library will help with this too..
  • Make sure you indicate to the publisher that you are NIH funded – and need them to submit your papter!
    Institutions and investigators are responsible for ensuring that manuscripts are submitted upon acceptance for publication.
  • – There is one Elsevier journal that is an exception to this rule: Journal of Urology!!
    This is the manuscript only (not the final article); that’s why you still have to go in and approve it!– VERY IMPORTANT to complete this step, in order to obtain the PMCID no.
    Elsevier functions this way. These are listed in red on our list.
    You may have to notify them that you are an NIH grantee and then you will need to go into the NIH MS system and approve the web version of your manuscript.
    You will receive two separate emails requesting approval of your manuscript. You must respond to these!
    Emails go to the investigator – not the AA; he/she may forward them to you.
  • Temp no. first. = NIHMS no. – Get this no. to Use in grant citations until PMCID (permanent no. is assigned)- around the time of publication- YOUR PI MAY BE THE ONE TO GET THIS.
    First, Lydia will need to review the PDF just to make sure it looks like everything is there. The author will also be emailed twice to review the pdf and or web format and give approval to the posting.– NIHMS no. is part of this mailing
    You will also be emailed to logon to the eGrants system and approve the web formatted version of the article. That completes the process and I believe you will then need to seek the PMCID no. in PubMed or PMC. – which should appear shortly after the process is completed, as soon as there is a record for the reference in PubMed
    At some point you are asked for the embargo period – try to get this right!
  • Probably beginning in August – you won’t be able to use the NIHMS no. if an article is more than 3 mos. Old.
    PMCID no. assigned usually around the time the article is published.
    (However, we seem to have quite a few articles floating around without PMCIDs!) We will need them for the Core Grant renewal, so we’re workikng on this. If you have any without them, please pursue!!!
  • The NIH hook:
    You must do this, so don’t wait until grant time to recognize that you don’t have the required number and then come to the library for posting, although, if you do, we will do it for you.
    Liz will show you how to do this in EndNote
    In August, they will likely enact a 3-month limit on the use of the NIHMS ID –So, 3 mos. sfter the publication date of an article, it will need to have a PMCID. An NIHMS will no longer be acceptable to demonstrate compliance.
  • Locate PMCID no. in PubMed on the Abstracts – at bottom right. – as opposed to the PMID number.
    The PMCID is posted in PubMed as soon as an article has been successfully processed by PMC, which usually occurs around the time of publication
    Library can locate it for you
    Show PubMed search and limit to PMC
    See also link back to full text in PMC.
  • The PMCID and the temp no. will also at the top of the abstract (HTML version) in PMC – This is the PDF version.
    Ask the library to locate it if you need it.
    Journals submitting for you submit the final published version, not this manuscript version.
  • Use if you have a legit reason to not have a PMCID or NIHMS.
    Keep checking PubMed or PMC for the PMCID no.
    NO NIH funding used?
    Second list is for those with Open Choice, individual article agreements!!!
  • Make sure the copyright transfer agreement allows posting the article to a repository like PubMed Central
    4. Labels on citations in grants, progress reports, biosketches are required.
    Make sure you follow up on each paper that falls under the policy- to get those PMCIDs!
  • Final peer-reviewed manuscript is the version to submit in Methods C and D– when either the author (or his intermediary) or the publisher (not on the approved PMC “list”) does the submission.
    This is the version with all of the changes made, so that the publisher says “OK, I’m going to publish that.”.
    The final published article includes the stylistic and formatting changes and edits done by the publisher.. The NIH expects the author to ensure that the manuscript version has the same scientific content as the final published article. The look may different, but the facts should be the same.(per Neil Thakur’s MLA video webcast, 2009 MLA Annual Meeting)
    In Methods A and B, when the publisher from the approved list submits, or because the author paid a publishef for an Open Choice option,it’s the final published article that is submitted.
  • Corresponding author may not have responded to NIH email to approve the paper; or he perhaps never gave you the NIHMSID .
    The publisher should have the NIHMSID as soon as it does the submission
    If the publisher is not cooperating, the institution must address this with the publisher (See Thakur advice).
  • Liz will show this – It works with the NIH style.
  • See “Contact Us” on NIH PA homepage
  • Guide for My Bibliography and Compliance

    1. 1. NIH Public Access Policy- Update Karen M. Albert, MLS, AHIP Senior Director, Education & Information Services July, 2009
    2. 2. “…“…publication is the lifeblood in the career of a workingpublication is the lifeblood in the career of a working scientist. Publication is the means by which anscientist. Publication is the means by which an investigator tells his or her colleagues, the world ininvestigator tells his or her colleagues, the world in general, and posterity about what he or she hasgeneral, and posterity about what he or she has found in the course of doing experiments…”found in the course of doing experiments…” Harold Varmus ,Harold Varmus , The Art and Politics of Science (2009), pg247
    3. 3. Outline and Objectives  Presentation outline:  Brief policy overview  How to comply-Library support  Typical problems – solutions  Answer questions  Objectives:  Gain a basic understanding of the policy and how to comply  Learn how the Library can help
    4. 4. NIH Public Access Policy Rationale  Signed into law December 2007  Formerly a recommendation, now a requirement  Pressure to make results of tax-payer funded research accessible to the public  “To ensure that the public has access to the published results of NIH-funded research to help advance science and improve human health.”
    5. 5. The Law -- NIH Public Access Policy Requires all investigators funded by the NIH to submit or have submitted for them to . . . PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication. . . in a manner consistent with copyright law. --Responsibility of the grantee to ensure articles are submitted
    6. 6. Policy Applies to Any Final Manuscript that ….  Is peer-reviewed, and  Accepted for publication in a journal on or after April 7, 2008, and  Arises from:  Direct funding from an NIH grant or cooperative agreement, or  Direct funding from an NIH contract signed on or after April 7, 2008  Does NOT apply to non-peer-reviewed materials such as letters, editorials or book chapters
    7. 7. U.S. Government Initiative: PubMed Central (PMC)  Free digital archive of biomedical & life sciences journal literature  Developed & managed by NIH/NLM/NCBI  Publishers deposit electronic content  Content available immediately or after a specified embargo period  Voluntary participation by publishers was low
    8. 8.
    9. 9. PubMed vs. PubMed Central  PubMed Central (PMC)  Digital archive of full-text, peer-reviewed journal papers  Each paper indexed with a PMCID  Series of numbers preceded by ‘PMC’  Content is publicly accessible and integrated with other databases  PubMed:  Provides access to citations from biomedical literature.  Includes 17 million+ citations from MEDLINE and other life sciences journals.  Science journals for biomedical articles back to the 1950s  Links to full text articles and other scientific resources.  Each citation indexed with a PMID
    10. 10. Points to consider in complying  Which submission method will be used?  What version of the paper will be made available on PMC?  Who will submit the paper?  When will it be submitted?   Who will approve the submission?  When will the paper be made public on PMC?
    11. 11. How to Comply Step 1-Address copyright Before signing a copyright transfer agreement, make sure the publisher permits deposit of the article in PubMed Central (via NIHMS System)
    12. 12. How to Comply Step 2- Check Library website for journal/publisher policies – Some journals post for you! See Journal Deposit/No Deposit List
    13. 13. Journals List Library website:
    14. 14. How to Comply Step 3 - Submit article to NIH - 4 Methods: Method A: Publish in a journal on this list that deposits all NIH-funded final published articles in PMC without author involvement - Examples:
    15. 15. How to Comply Method B: Make arrangements to have a publisher on this list deposit a specific final published article in PubMed Central. This is generally an “Open Choice”- author-pays model- which costs $$$
    16. 16. How to Comply Method C: Deposit the final peer-reviewed manuscript in PMC yourself via the NIH Manuscript System ( NIHMS) The Library will do this for you! Email:
    17. 17. Submission form Library website:
    18. 18. Library’s submission request form
    19. 19. The number of months after publication that the full-text manuscript can be made freely available in PubMed Central. -- usually 12 months -- Journal Embargo Period
    20. 20. Author approval still required  NIHMS emails corresponding author to approve manuscript  Can be done only by authors who log into NIHMS with an eRA Commons Account or NIH Account.  NIHMS emails author again to approve PMC-formatted manuscript for public display  After specified delay period, NIHMS automatically sends article to PMC for public posting
    21. 21. How to comply- Publisher submits -- Author Approves Method D: Complete the submission process for a final peer-reviewed manuscript that the publisher has deposited in the NIHMS. 
    22. 22. Publisher submission Some publishers (like Elsevier) submit final manuscripts to PMC on behalf of authors.-- You still have to approve the manuscript via the NIH Manuscript Submission system
    23. 23. Publishers that submit, but require PI approval  Elsevier (except for J Urology)  Taylor and Francis  Wiley-Blackwell  Oxford U. Press  Nature – some journals  MaryAnn Liebert  Lippincott Williams and Wilkins
    24. 24. Method D – Process Details  Publishers submit the manuscript to NIHMS  NIHMS emails the corresponding author  Author must approve the manuscript  Author receives NIHMS number  NIHMS emails corresponding author again  Author approves PMC-formatted version for public display  Once the process is complete, NIHMS emails all authors the citation and PMCID no.  After specified delay period, NIHMS automatically sends article to PMC for public posting
    25. 25. One of the Two approval steps
    26. 26. How to Comply Step 4 - Demonstrate Compliance  Cite NIHMS (temporary number)  Cite PMCID (permanent number)  Provide reason article does not fall under the policy
    27. 27. How to Comply: Cite PMCID number In all grant applications, renewals, progress reports or biosketches  List the PubMed Central reference number (PMCID) at end of journal citation.  If a PMCID number is not yet available, include the NIH Manuscript Submission system reference number (NIHMS ID) instead.  See “Citation Methods” Web page at Example: Varmus H, Klausner R, Zerhouni E, Acharya T, Daar A, Singer P. 2003. PUBLIC HEALTH: Grand Challenges in Global Health. Science 302(5644): 398–399. PMCID: PMC243493
    28. 28. Locating PMCID’s PubMed: Abstract or Abstract Plus Format
    29. 29. PubMed Central (PMC)- formatted article
    30. 30. PMID to PMCID Converter Use this link to find PMCID numbersUse this link to find PMCID numbers when you have the PMID number:when you have the PMID number:
    31. 31. NIH Grantee Compliance Reminder- Acceptable Explanations  Explanations to use for lack of required #’s:  “Paper accepted prior to April 7, 2008”  “Paper was not peer-reviewed”  “PMC Journal – In Process” Papers from journals that submit final published version directly to PMC on behalf of authors NOTE: Use only for Methods A or B journals FAQ:
    32. 32. Summary of Steps Step 1 -- Address Copyright Step 2 -- Identify Journal Submission Policy Step 3 -- Submit article to NIH (via Methods A, B, C or D)  Method A: Journal submits final article of PMC  Method B: Author-pays an Open Choice fee; Journal submits final article to PMC  Method C: Library submits; Author approves  Method D- Publisher submits; Author approves Step 4 -- Demonstrate compliance  PMCID  NIHMS  Other wording
    33. 33. Problems/Questions: Which version should be submitted? Final peer-reviewed manuscript: The Investigator's final manuscript of a peer-reviewed paper accepted for journal publication, including all modifications from the peer review process. Final published article: The journal’s authoritative copy of the paper, including all modifications from the publishing peer review process, copyediting and stylistic edits, and formatting changes.
    34. 34. Problem with publisher submission  Where is my manuscript’s NIHMSID?  Three sources of information:  Ask the corresponding author- See Library’s sample letter  Ask the Publisher  Ask the NIHMS Help Desk at:  If no response, ask Library for help
    35. 35. Configuring EndNote  To configure EndNote to include the PubMed Central ID (PMCID):  See Library’s EndNote page -- scroll to bottom or link here:  Contact the Library for help, if needed
    36. 36. Points to Remember  Act on accepted papers promptly  Follow up on all eligible papers to obtain PMCIDs  Email or call the Library for help: or x2711  See NIH Public Access Homepage: