Scholarly Publishing in Biomed - Recently Updated Pages

Definitions to Know

corl — Mon, 16 Jan 2012 03:26:07 CST

AF, or Author’s final: This is the peer-reviewed author’s final version of the manuscript prior to publication. It may be in the form of a PDF from the publisher (with markings) or in the form of multiple edited files that were last modified by the author. For our purposes, we are interested in obtaining the multiple files from the author that make up the author’s final. We will then convert this into a PDF to be routed through the IPS.

NIHMS system: NIH Manuscript Submission System, the NIH’s vehicle to process grant and manuscript matching, route manuscripts for approval and prepare them for inclusion into PubMed Central.

PubMed Central: PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.

Embargo: a period during which access to published information is not allowed to certain types of users, i.e. non-subscribers.handbags for sale.

SHERPA/RoMEO: A database of publisher copyright and self-archiving policies. Records of publishers and journals contain summaries of permissions that are normally given as part of each publisher's copyright transfer agreement.

Journal and Publisher Information

glenn030 — Mon, 07 Apr 2008 13:11:23 CDT

Compliant with NIH Policy

These journal publishers automatically submit the published version of the NIH-funded articles to PubMed Central. This is a terrific service, because it eliminates the need for the use of NIH Manuscript submission system and subsequent approvals of versions prior to release on PMC.

Fully compliant: Articles available within 12 months

Compliance Statement not Available

These journal publishers do not permit authors to submit versions of articles to online archives. Exceptions, or permission, must be negotiated on an individual basis.

Lippincott, Williams & Wilkins

Infectious Diseases titles from this publisher
Biological Sciences titles from this publisher

Update: Publisher policies for at least one title, AIDS, specify that the publisher will deposit articles on behalf of the author.
? How can authors secure rights to comply with the NIH Policy? Learn about author addendums.

Find Policies

Sherpa/RoMEO is a database of publisher's copyright and archiving policies, complete with links to publisher and journal policy pages.

Sherpa/RoMEO

All journals that contribute content to PubMed Central are listed here. Embargo dates vary.
All PMC Journals (varying embargo dates)

? How can authors include the specific text that publishers mention in their policies? Learn about publisher disclaimers.

Selected Journal Policies

Top journals for SBRI Authors

AIDS (Lippincott Williams & Wilkins)	Author/institution must submit author's final
Eukaryotic Cell	Automatically submitted (publisher submits published version)
Infection and Immunity	Automatically submitted (publisher submits published version)
International Journal for Parasitology	Publisher submits author's final
Journal of Clinical Microbiology	Automatically submitted (publisher submits published version)
Journal of Gastroenterology and Hepatology	Author/institution must submit author's final
Journal of Immunology -Bethesda	Author/institution must submit author's final
Journal of Infectious Diseases (University of Chicago)	Author/institution must submit author's final
Journal of Virology	Automatically submitted (publisher submits published version)
Microbiology (Kluwer/Springer)	Author/institution must submit author's final
Molecular and Biochemical Parasitology	Publisher submits author's final
Molecular and Cellular Proteomics (MCP)	Author/institution must submit author's final
Molecular Microbiology	Author/institution must submit author's final
Nature -London-	Author/institution must submit author's final
PLoS Medicine	Automatically submitted (publisher submits published version)
PNAS (Proceedings of the National Academy of Sciences of the United States of America)	Automatically submitted (publisher submits published version)
RNA	Automatically submitted (publisher submits published version)
Science	Author/institution must submit author's final
Virology -New York	Publisher submits author's final

Citing the PMC ID

glenn030 — Thu, 27 Mar 2008 19:27:20 CDT

If a PubMed Central reference number is not yet available, include the NIH Manuscript Submission system reference number (NIHMS ID) instead.[1]

From a PubMed Search

Within a PMC record

[1] NIH PUblic Access Policy Frequently Asked Questions. Accessed March 19,2 008. http://publicaccess.nih.gov/FAQ.htm#c6

Scholarly Publishing in Biomedical Research Science and the NIH Public Access Policy

glenn030 — Thu, 27 Mar 2008 19:05:53 CDT

This wiki is intended to provide introductory guidance for two parties:

authors who are NIH-funded and publishing in the biomedical researcher field
scientific support staff, librarians, and grants officers who support and track the scholarly publication activities of research scientists

The Seattle Biomedical Research Institute has created a SharePoint-based system to track publications and evaluate whether submission to PubMed Central by the author (or support staff) is necessary. Read a brief overview of the system.

I am interested to learn of other systems that handle the routing and evaluation of articles. Please add descriptions of your systems on the Compliance Solutions page.

NIH Manuscript Submission System	Journal and Publisher Information
Public Access Policy Information	Citing the PMC ID
Definitions to Know	Compliance Solutions

This wiki was created for the Medical Library Association course Web 2.0 101: Introduction to Second Generation Web Tools.

Compliance Solutions

glenn030 — Wed, 19 Mar 2008 15:49:30 CDT

Has your institution created a system to manage compliance with the NIH Public Access Policy? Share it here.

History of the IPS

glenn030 — Wed, 19 Mar 2008 15:10:25 CDT

The Seattle Biomedical Research Institute's Institute Publications System, or IPS, was created in order to facilitate the submission of manuscripts for grant citation review and to address compliance with the NIH Public Access Policy. Our local system is described below (simplified). What is not described is faculty education in areas of compliance, author rights, and subjective decision making pertaining to where to publish articles

As of April 2008, the NIH will require PIs to contribute a copy of the author’s final manuscript to PubMed Central and later cite manuscripts by their PubMed Central ID number in progress reports and subsequent communications (including applications for funds) to the NIH. Given that PIs will not be the primary submitter of items to PubMed Central, including the correct grant number at publication is crucial. It is one key identifier that the NIH uses to match grant progress. It is also an indexed field for searching articles in PubMed.

The IPS brings together the conditions around grant citation approval, PubMed Central submission need, submission roles, and accountability for various steps in the process. Certain staff can track process through the IPS. Grant staff is the designated approvers of the grant citation, but the approval process includes notification for others who should know about requested changes. PIs are notified of processes, but only at critical times, like when a determination has been made about who will submit an article to PMC (publisher or SBRI). This system is available for use by all SBRI authors who receive NIH funding directly. For authors who are supported by NIH funds from a PI, the PI receiving the grant will be referenced throughout the IPS. A record of all transactions pertaining to the review and submission of the manuscript are contained within the IPS.

Authors (or designated scientific support staff) submit articles (at the time of acceptance for publication) to the [local] Institute Publications System. The system then determines which conditions apply to the article based on the funder and journal of publication. The article is routed to the grants office for grant citation confirmation. Approval and change requests are stored. Next, scientific support staff look up publisher policies as needed, create disclaimer pages, and upload items to the NIH Manuscript Submission system for deposit into PubMed Central. Once the embargo period has passed or a PubMed Central ID number is entered in the record, the item's status changes to Available in PubMed Central. As a final step, the IPS provides content for populating SBRI's institutional repository, E-prints. After submission status is known and a PMC ID number is entered, the item is routed for import to E-prints.

Seattle Biomedical Research Institute is a growing organization. We currently have nineteen principal investigators who publish up to 100 articles per year. We were able to build a beta system in a short period of time because we have quick access to administration, grants officers, legal counsel, support staff, information technology staff, and a librarian.

NIH Manuscript Submission System

glenn030 — Wed, 19 Mar 2008 14:20:01 CDT

The NIH Manuscript Submission System is NIH’s vehicle to process grant and manuscript matching, route manuscripts for approval and prepare them for inclusion into PubMed Central.

To familiarize yourself with the system:

Create an NCBI account if you do not already have one (for third-party submitters)..
Create a test submission to the NIHMS system. (Log in at right. Choose to cancel prior to confirming your PDF receipt.)
Review PMC sample articles: Author submits author's final and Publisher submits author's final.

Policy Information

glenn030 — Wed, 19 Mar 2008 14:18:51 CDT

"The NIH Public Access Policy ensures that the public has access to the published results of NIH funded research. It requires scientists to submit journal articles that arise from NIH funds to the digital archive PubMed Central (http://www.pubmedcentral.nih.gov/). The Policy requires that these articles be accessible to the public on PubMed Central to help advance science and improve human health."

Overview, how to comply, and inportant dates
Frequently Asked Questions
Training (created by NIH). The Public Access Training slideshow is highly recommended.

Publisher Disclaimer

glenn030 — Wed, 19 Mar 2008 13:54:35 CDT

Several publishers require that authors include brief statements referencing publisher versions, publisher home pages, or other rights conditions when submitting an article to PMC. For example:

The link must be accompanied by the following text: “The original publication is available at www.springerlink.com”.
The definitive version of this article is available at….
This is the author’s version of a peer-reviewed manuscript. It has not been quality-checked by XYZ’s publishers…
This is the author’s final version.

If you are submitting a manuscript (whether you are the PI or a third party) and must include any disclaimer text from the publisher, you can type out their disclaimer, save it as a separate document called “Publisher Disclaimer,” then submit it with the uploaded manuscript. Use the manuscript label box. Be sure to make the actual manuscript "1" and the disclaimer "2."

Author Addenda

glenn030 — Wed, 19 Mar 2008 13:50:16 CDT

Unless addressed in the transfer agreement, the publisher may forbid an author to do the following:

Post the work to the author's own web site, an institutional repository, or a subject-based repository.
Copy the work for distribution to students.
Use the work as the basis for future articles or other works.
Give permission for the work to be used in a course at the author's institution.
Grant permission to faculty and students at other universities to use the material.

An author's addendum is a standardized legal instrument that modifies the publisher's agreement and allows the author to keep key rights. The addenda usually spells out what rights the author does or does not have in several key areas:

The extent of the author's ability to continue to use the copyrighted work even after the transfer of copyright to a publisher, including the ability of the author to make copies of the work or prepare new works based on the copyrighted work.
The author's ability to authorize others to use the work.
Whether and when the author's institution can make any use of the work.
Whether and when the author's funding agency can make use of the work.
When and under what circumstances, if any, people at other institutions can use the work.
What legal protections are available to the author.[1]

Addenda For Use
An addendum may be generated automatically online at the Science Commons, SPARC and MIT Author Addendum: http://scholars.sciencecommons.org/. Simply enter information about the author and publication to generate a PDF which may be submitted to the publisher.

[1] Hirtle, Peter B. “Author Addenda: An Examination of Five Alternatives,” D-Lib Magazine, November 2006. http://www.dlib.org/dlib/november06/hirtle/11hirtle.html