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Designing the Microbial Research Commons Proceedings of an International Symposium Paul F. Uhlir, Editor Board on Research Data and Information Policy and Global Affairs THE NATIONAL ACADEMIES PRESS Washington, D.C. www.nap.edu

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THE NATIONAL ACADEMIES PRESS 500 Fifth Street, N.W. Washington, DC 20001 NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance. This study was supported by the National Science Foundation under Grant No. OCI-082173 and by the Department of Energy Grant No. DE-SC0002579. This report was prepared as an account of work sponsored by an agency of the United States government. Neither the United States government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States government or any agency thereof. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the organizations or agencies that provided support for the project. International Standard Book Number-13: 978-0-309-21979-2 International Standard Book Number-10: 0-309-21979-5 Additional copies of this report are available from the National Academies Press, 500 Fifth Street, N.W., Lockbox 285, Washington, DC 20055; (800) 624-6242 or (202) 334-3313 (in the Washington metropolitan area); Internet, http://www.nap.edu. Copyright 2011 by the National Academy of Sciences. All rights reserved. Printed in the United States of America.

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The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Ralph J. Cicerone is president of the National Academy of Sciences. The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding engineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Charles M. Vest is president of the National Academy of Engineering. The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Harvey V. Fineberg is president of the Institute of Medicine. The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy’s purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Ralph J. Cicerone and Dr. Charles M. Vest are chair and vice chair, respectively, of the National Research Council. www.national-academies.org

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Steering Committee for Designing the Microbial Research Commons: An International Symposium Dr. Cathy Wu, Chair, Edward G. Jefferson Professor of Bioinformatics & Computational Biology Delaware Biotechnology Institute University of Delaware Michael Carroll, J.D. Professor American University, Washington College of Law Dr. Micah Krichevsky President Bionomics International Rockville, MD Dr. Michael Lesk (NAE) Professor School of Communication, Information and Library Sciences Rutgers University Dr. Stephen J. McCormack Chief Executive Officer IMI Devices Bonn, Germany Dr. James Staley Health Services University of Washington Dr. Larry Smarr (NAE) Director, California Institute for Telecommunications and Information Technology Professor, University of California San Diego National Academies Staff Paul F. Uhlir, Director, Board on Research Data and Information v

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Preface and Acknowledgments The opportunities to accelerate scientific discovery and resulting applications are made increasingly possible by technological breakthroughs and pioneering methods to process and integrate vast amounts of data, information, and raw materials. Microbial research, which is outgrowing its “small science” institutional structures, should consider building upon these opportunities in an attempt to develop a global microbial research commons to promote access to databases, literature, and materials through an open, digitally distributed network. However, the increasingly blurred line between basic and applied research confers potential economic value even upon research inputs that are far upstream. As a result, the research community is increasingly being forced to come to terms with commoditizing pressures within developed economies. These pressures restrict the conduct of public-sector research through strong intellectual property rights and related contractual restrictions on access to and use of materials, publications, and data. At the same time, restrictive policies in developing countries under the Convention on Biological Diversity complicate research uses of microbial materials held in public repositories ex-situ, and make it increasingly difficult to access the vast in-situ materials these countries control. These trends have led to a proliferation of diverse licensing strategies and techniques, which collectively have elevated the transaction costs and other barriers for even relatively simple cooperative research projects. There is, thus, a need to focus on the obstacles to upstream, non-commercial research and the solutions to them. An early step is development of a set of design principles that address the economic, legal, and institutional dimensions of the transformation of the existing research infrastructure into what could become a globally distributed and digitally integrated research commons. The goal of this redesigned “soft” infrastructure would be to better manage publicly funded research resources, without compromising downstream commercial applications and fruitful partnerships between the public and private sectors, or between developed and developing countries. Of course, a variety of responses is possible. Some are more conservative with respect to an understanding of the scientific “commons” as a common resource available on a non- discriminatory and non-commercial basis, whereas others may be based upon a pro-actively managed or regulated set of practices. These latter responses would compromise the conservative view in the interest of achieving greater patronage and participation of actors who have other motives and rationales for participation. A more detailed discussion of the “commons” concept is provided in the presentation by Paul David in Chapter 3 and Charlotte Hess in Chapter 25, as well as from various other perspectives of course throughout this volume. The Board on Research Data and Information held an International Symposium on Designing the Microbial Research Commons at the National Academy of Sciences in Washington, DC on 8-9 October 2009. Organized by a separately appointed Steering Committee, this symposium expanded on prior international discussions on the same topic at a conference in June 2008 in Ghent, Belgium (see: http://www.microbialcommons.ugent.be/). The October 2009 symposium addressed topics such as models to lower the transaction costs and support access to and use of microbiological materials and digital resources from the perspective of publicly funded research, public-private interactions, and developing country concerns. The overall goal vii

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of the symposium was to stimulate more research and implementation of improved legal and institutional models for publicly funded research in microbiology. The International Symposium on Designing the Microbial Research Commons focused on accomplishing the following tasks: 1. Delineate the research and applications opportunities from improved integration of microbial data, information, and materials and from enhanced collaboration within the global microbial community. 2. Identify the global challenges and barriers—the scientific, technical, institutional, legal, economic, and socio-cultural—that hinder the integration of microbial resources and the collaborative practice of scientific communities in the microbial commons. 3. Characterize the alternative legal and policy approaches developed and implemented by other research communities, such as common-use licensing for scientific data and information, standard-form material transfer agreements, open access publishing, and open data networks that could be applied successfully by the microbial research community. 4. Define the contributions of new information and communication technology (ICT) tools in building federated information infrastructures, such as ontologies, data and text mining, and web 2.0. 5. Discuss and evaluate the institutional design and governance principles of data and information sharing among information infrastructures, drawing upon and analyzing successful and failed case studies in the life sciences. 6. Identify the range of policy issues that need to be addressed for maximizing open access to materials, data and literature information in an integrated microbial research commons. The statements in this volume are those of the individual authors and do not necessarily represent the views of other workshop participants, the steering committee, or the National Academies. The symposium agenda is provided in Appendix A and the list of the meeting participants is presented in Appendix B. On behalf of the Board, we gratefully acknowledge the support for this project of the Department of Energy under grant number DE-SC0002579, and from the National Science Foundation under grant number OCI-0821873, as well as the core support it has received from the National Institutes of Health, the Defense Technical Information Center, the Institute of Museum and Library Services, the National Institute of Standards and Technology, and the Library of Congress. viii

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This volume has been reviewed in draft form by individuals chosen for their technical expertise, in accordance with procedures approved by the NRC’s Report Review Committee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published report as sound as possible and to ensure that the report meets institutional standards for quality. The review comments and draft manuscript remain confidential to protect the integrity of the process. We wish to thank the following individuals for their review of selected papers: Minna Allarakhia, University of Waterloo, Canada; Subbiah Arunachalam, Consultant; Nancy Connell, University of Medicine and Dentistry of New Jersey; Michael Carroll, American University; Melanie Dulong de Rosnay, Communia; Micah Krichevsky, Bionomics International; Michael Lesk, Rutgers University; Elinor Ostrom, Indiana University; James Staley, University of Washington, Seattle; and W. Edward Steinmueller, University of Sussex, UK. Although the reviewers listed above have provided constructive comments and suggestions, they were not asked to endorse the content of the individual papers. Responsibility for the final content of the papers rests with the individual authors. We would especially like to recognize the contributions of Daniel Cohen, on assignment to the National Academies from the U.S. Library of Congress, who assisted with the editing and the production of the manuscript. Subhash Kuvelker and Cheryl Levey of the Board staff also helped with the review process and the preparation of this volume. Finally, and not least, we would like to thank Fran Sharples, director of the Board on Life Sciences, for her assistance with the project. Cathy H. Wu Paul F. Uhlir Steering Committee Chair Project Director ix

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Contents 1. Introduction – Cathy Wu ................................................................................................................................. 1 2. Microbiology in the 21st Century – Joan W. Bennett .......................................................................... 3 3. Breaking Anti-Commons Constraints on Global Scientific Research: Some New Moves in “Legal Jujitsu” – Paul A. David .......................................................................................................................... 13 4. An Industry Perspective: Development of an MTA Harmonious with a Microbial Research Commons – Stephen J. McCormack .......................................................................................... 25 5. Developing Country Perspective: Microbial Research Commons Including Viruses – Ashok Kolaskar ....................................................................................................................................................... 31 6. A Compensatory Liability Regime to Promote the Exchange of Microbial Genetic Resources for Research and Benefit Sharing – Jerome H. Reichman .............................................. 43 7. The Agricultural Research Service Culture Collection: Germplasm Accessions and Research Programs – Cletus P. Kurtzman .................................................................................................. 55 8. American Type Culture Collection: A Model for Biological Materials Resource Management – Frank Simione ......................................................................................................................... 63 9. Contracting to Preserve Open Science: Lessons for a Microbial Research Commons – Peter Lee.................................................................................................................................................................... 69 10. Designing the Digital Commons in Microbiology—Moving from Restrictive Dissemination of Publicly Funded Knowledge to Open Knowledge Environments: A Case Study in Microbiology –Paul Uhlir ................................................................................................................. 77 11. The Web-Enabled Research Commons: Applications, Goals, and Trends – Thinh Nguyen ....................................................................................................................................................................................... 91 12. Comments on Designing the Microbial Research Commons: Digital Knowledge Resources –Katherine Strandburg ................................................................................................................. 97 13. Toward a Biomedical Research Commons: A View from the National Library of Medicine at the National Institutes of Health – Jerry Sheehan ........................................................ 103 14. Academic Publications –Fred A. Rainey ............................................................................................ 111 15. StrainInfo: Reducing Microbial Data Entropy – Peter Dawyndt............................................. 115 16. Research and Applications in Energy and Environment – Daniel Drell .............................. 121 17. Large Scale Microbial Ecology Cyberinfrastructure – Paul Gilna........................................... 123 18. Proposal for a Microbial Semi-Commons: Perspectives from the International Cooperative Biodiversity Groups – Flora Katz ....................................................................................... 129 19. The International Treaty on Plant Genetic Resources – Shakeel Bhatti ............................. 137 20. Microbial Commons: Governing Complex Knowledge Assets – Minna Allarakhia......... 145 21. Digital Research: Microbial Genomics – Nikos Kyrpides ........................................................... 151 xi

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22. Accessing Microbiological Data: A User’s Perspective – Mark Segal .................................... 161 23. The Microbial Commons: Journals and Professional Societies – Samuel Kaplan............ 165 24. Microbial Commons: Overview of the Governance Considerations—A Framework for Discussion – Tom Dedeurwaerdere ............................................................................................................ 169 25. Institutional Design and Governance in the Microbial Research Commons – Charlotte Hess ........................................................................................................................................................................... 177 26. International Developments: A Context for the Creation of a Microbiology Commons – Anita Eisenstadt ................................................................................................................................................... 185 27. Options for Governing the Microbial Commons – Michael Halewood ................................ 191 28. Access and Benefit Sharing under the CBD and Access to Materials for Research – Stefan Jungcurt ..................................................................................................................................................... 201 29. Closing Observations – Cathy Wu ........................................................................................................ 209 Appendix A – Microbial Commons Symposium Agenda..................................................................... 211 Appendix B – Microbial Commons Symposium Participants ........................................................... 215 xii