Complying with the NIH Public Access Policy - Copyright Considerations and Options

On January 11, 2008, the National Institutes of Health ('NIH') adopted a revised Public Access Policy for peer-reviewed journal articles reporting research supported in whole or in part by NIH funds. Under the revised policy, the grantee shall ensure that a copy of the author's final manuscript, including any revisions made during the peer review process, be electronically submitted to the National Library of Medicine's PubMed Central ('PMC') archive and that the person submitting the manuscript will designate a time not later than 12 months after publication at which NIH may make the full text of the manuscript publicly accessible in PMC. NIH adopted this policy to implement a new statutory requirement under which: 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 publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law. This White Paper is written primarily for policymaking staff in universities and other institutional recipients of NIH support responsible for ensuring compliance with the Public Access Policy. The January 11, 2008, Public Access Policy imposes two new compliance mandates. First, the grantee must ensure proper manuscript submission. The version of the article to be submitted is the final version over which the author has control, which must include all revisions made after peer review. The statutory command directs that the manuscript be submitted to PMC 'upon acceptance for publication.' That is, the author's final manuscript should be submitted to PMC at the same time that it is sent to the publisher for final formatting and copy editing. Proper submission is a two-stage process. The electronic manuscript must first be submitted through a process that requires input of additional information concerning the article, the author(s), and the nature of NIH support for the research reported. NIH then formats the manuscript into a uniform, XML-based format used for PMC versions of articles. In the second stage of the submission process, NIH sends a notice to the Principal Investigator requesting that the PMC-formatted version be reviewed and approved. Only after such approval has grantee's manuscript submission obligation been satisfied. Second, the grantee also has a distinct obligation to grant NIH copyright permission to make the manuscript publicly accessible through PMC not later than 12 months after the date of publication. This obligation is connected to manuscript submission because the author, or the person submitting the manuscript on the author's behalf, must have the necessary rights under copyright at the time of submission to give NIH the copyright permission it requires. This White Paper explains and analyzes only the scope of the grantee's copyright-related obligations under the revised Public Access Policy and suggests six options for compliance with that aspect of the grantee's obligation. Time is of the essence for NIH grantees. As a practical matter, the grantee should have a compliance process in place no later than April 7, 2008. More specifically, the new Public Access Policy applies to any article accepted for publication on or after April 7, 2008 if the article arose under (1) an NIH Grant or Cooperative Agreement active in Fiscal Year 2008, (2) direct funding from an NIH Contract signed after April 7, 2008, (3) direct funding from the NIH Intramural Program, or (4) from an NIH employee. In addition, effective May 25, 2008, anyone submitting an application, proposal or progress report to the NIH must include the PMC reference number when citing articles arising from their NIH funded research. (This includes applications submitted to the NIH for the May 25, 2008 and subsequent due dates.) Conceptually, the compliance challenge that the Public Access Policy poses for grantees is easily described. The grantee must depend to some extent upon the author(s) to take the necessary actions to ensure that the grantee is in compliance with the Public Access Policy because the electronic manuscripts and the copyrights in those manuscripts are initially under the control of the author(s). As a result, any compliance option will require an explicit understanding between the author(s) and the grantee about how the manuscript and the copyright in the manuscript are managed. It is useful to conceptually keep separate the grantee's manuscript submission obligation from its copyright permission obligation because the compliance personnel concerned with manuscript management may differ from those responsible for overseeing the author's copyright management. With respect to copyright management, the grantee has the following six options: (1) rely on authors to manage copyright but also to request or to require that these authors take responsibility for amending publication agreements that call for transfer of too many rights to enable the author to grant NIH permission to make the manuscript publicly accessible ('the Public Access License'); (2) take a more active role in assisting authors in negotiating the scope of any copyright transfer to a publisher by (a) providing advice to authors concerning their negotiations or (b) by acting as the author's agent in such negotiations; (3) enter into a side agreement with NIH-funded authors that grants a non-exclusive copyright license to the grantee sufficient to grant NIH the Public Access License; (4) enter into a side agreement with NIH-funded authors that grants a non-exclusive copyright license to the grantee sufficient to grant NIH the Public Access License and also grants a license to the grantee to make certain uses of the article, including posting a copy in the grantee's publicly accessible digital archive or repository and authorizing the article to be used in connection with teaching by university faculty; (5) negotiate a more systematic and comprehensive agreement with the biomedical publishers to ensure either that the publisher has a binding obligation to submit the manuscript and to grant NIH permission to make the manuscript publicly accessible or that the author retains sufficient rights to do so; or (6) instruct NIH-funded authors to submit manuscripts only to journals with binding deposit agreements with NIH or to journals whose copyright agreements permit authors to retain sufficient rights to authorize NIH to make manuscripts publicly accessible.

Visible Volume: a Robust Measure for Protein Structure Characterization

We propose a new characterization of protein structure based on the natural tetrahedral geometry of the β carbon and a new geometric measure of structural similarity, called visible volume. In our model, the side-chains are replaced by an ideal tetrahedron, the orientation of which is fixed with respect to the backbone and corresponds to the preferred rotamer directions. Visible volume is a measure of the non-occluded empty space surrounding each residue position after the side-chains have been removed. It is a robust, parameter-free, locally-computed quantity that accounts for many of the spatial constraints that are of relevance to the corresponding position in the native structure. When computing visible volume, we ignore the nature of both the residue observed at each site and the ones surrounding it. We focus instead on the space that, together, these residues could occupy. By doing so, we are able to quantify a new kind of invariance beyond the apparent variations in protein families, namely, the conservation of the physical space available at structurally equivalent positions for side-chain packing. Corresponding positions in native structures are likely to be of interest in protein structure prediction, protein design, and homology modeling. Visible volume is related to the degree of exposure of a residue position and to the actual rotamers in native proteins. In this article, we discuss the properties of this new measure, namely, its robustness with respect to both crystallographic uncertainties and naturally occurring variations in atomic coordinates, and the remarkable fact that it is essentially independent of the choice of the parameters used in calculating it. We also show how visible volume can be used to align protein structures, to identify structurally equivalent positions that are conserved in a family of proteins, and to single out positions in a protein that are likely to be of biological interest. These properties qualify visible volume as a powerful tool in a variety of applications, from the detailed analysis of protein structure to homology modeling, protein structural alignment, and the definition of better scoring functions for threading purposes.