Philip Bourne University of California San Diego pbourne@ucsd.edu Realizing the Power of On-line Publishing in Copyright and Creativity in International Scholarship Philip Bourne University of California San Diego pbourne@ucsd.edu 18 November 2018 ARL Ottawa 2006

My Agenda Copyright - describe the process and motivation for a humble scientist (me) to establish an open access journal in partnership with an international society Creativity – with the above as a foundation describe one approach we are taking to establish new modes of scientific dissemination Ask the question – what is the libraries role in all of this? 18 November 2018 ARL Ottawa 2006

My Foundation (and Bias) http://www.wwpdb.org/ 18 November 2018 ARL Ottawa 2006

Public Library of Science Founded 2000 3 wild and crazy guys (scientists) – very significant following Early success – impact factor of 13.9 for PLoS Biology Open access business model promising but not guaranteed Harold Varmus Patrick O. Brown Harold Varmus, Pat Brown and Mike Eisen established the Public Library of Science, initially as a sort of pressure group whose aim was to force publishers to change their ways. Michael B. Eisen 18 November 2018 ARL Ottawa 2006

18 November 2018 ARL Ottawa 2006

Drivers – Scientific Conscience “Faced with the option of submitting to an open-access or closed-access journal, we now wonder whether it is ethical for us to opt for closed access on the grounds of impact factor or preferred specialist audience.” -- Costello and Osrin in The Lancet 18 November 2018 ARL Ottawa 2006

Drivers - Open Access (in order of an author’s priorities) All published materials available on-line free to all Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s) Copyright remains with the author Specifically, our aim is to achieve open access to the literature, whereby journal articles are freely available immediately upon publication their use is unrestricted, so that readers can download, print off, reanalyse, extract data and so on authors retain the copyright, and specifically the right to be appropriately cited papers are also deposited separately from the publisher in a public online archive (PMC) 18 November 2018 ARL Ottawa 2006

The International Society for Computational Biology Young society of 2000 members FASEB Member Main activates: Conferences, journals, education, SIG’s, regional meetings, Web portal 18 November 2018 ARL Ottawa 2006

Pushes the science of the society in new directions Polarized as to whether to adopt an open access journal (loss of revenue, previous association with OUP) Pushes the science of the society in new directions Result – Action outweighs talk PLoS Computational Biology published in partnership with the Society 18 November 2018 ARL Ottawa 2006

The Journal Thus Far 18 November 2018 ARL Ottawa 2006

But the best is yet to come…. A medium in which to try new modes of dissemination To explain this consider the following scenario 18 November 2018 ARL Ottawa 2006

Consider the day when… Prior to leaving for the home GS syncs her IPOL with the latest papers delivered overnight by the journal via RSS feed. On the bus she reviews the stream, selecting a paper close to her interest in HIV-1 proteases. The data shows apparent anomalies with her own work. By the time the bus stops she has recomputed the results, proven the anomaly and written a rebuttal and sent it to the journal 18 November 2018 ARL Ottawa 2006

Science Fiction? Five years ago Yes… Today No… Five years ago the idea of downloading data on a bus would have been absurd – not today Five years ago an IPOL would be absurd -not today Journals are providing RSS feeds today Why should the way we do science not change in the next five years? 18 November 2018 ARL Ottawa 2006

I would argue that the major step needed has already been made and that the implications are clear 18 November 2018 ARL Ottawa 2006

Signs of Change…… Some societies are adopting open access NIH supportive Hybrid Journals – PNAS, Springer, Oxford University Press, Blackwell, Company of Biologists Funders allowing payment of open access publication charges as part of research costs – Wellcome Trust, HHMI, Research Councils UK, DDCF Universities providing guidelines and incentives for authors 18 November 2018 ARL Ottawa 2006

Where Are We Today? Full text increasingly on-line and potentially usable Traditional publishers have used the internet as a distribution medium, but the power of the medium has yet to be realized Data increasingly on-line but not integrated with the publication derived from it …. 18 November 2018 ARL Ottawa 2006

P.E. Bourne 2005 (Editorial) PLoS Comp. Biol. 1(3) e34 This Seems Silly.. I Would Contest That in Many Ways A Journal and a Database are Very Similar P.E. Bourne 2005 (Editorial) PLoS Comp. Biol. 1(3) e34 18 November 2018 ARL Ottawa 2006

So What is Needed to Make Our Scenario a Reality? Seamless integration between papers reporting results and the data used to compute those results – public repositories of data and knowledge must become integrated in ways not possible today 18 November 2018 ARL Ottawa 2006

Can it Happen? The data repositories have been available for a long time With open access the knowledge repositories are available – its more that just abstracts If the perception of the difference between data and knowledge is lowered The technologies are there 18 November 2018 ARL Ottawa 2006

BioLit: Tools for New Modes of Scientific Dissemination The Knowledge and Data Cycle 0. Full text of PLoS papers stored in a database 4. The composite view has links to pertinent blocks of literature text and back to the PDB Biolit integrates biological literature and biological databases and includes: A database of journal text Authoring tools to facilitate database storage of journal text Tools to make static tables and figures interactive Biolit is being developed using the Protein Databank (PDB) and the corpus of all PLoS journals as a prototype BioLit is funded by the NSF DBI 0544575 For further information see “Will a Biological Database be Different from a Biological Journal?” P.E. Bourne (2005) 1(3) e34 4. 1. 3. A composite view of journal and database content results 1. A link brings up figures from the paper 3. 2. 2. Clicking the paper figure retrieves data from the PDB which is analyzed 18 November 2018 ARL Ottawa 2006

What Might be Possible With BioLit? New knowledge discovery through data mining New understanding about how knowledge is transferred – knowledge bubbles Comprehension is made easier The traditional paper is just one view of the science Knowledge is disseminated in different ways ….. 18 November 2018 ARL Ottawa 2006

What is the Role of the University Library in this New Medium? Should the library become an on-line open access publisher? Should the library become the archivist for institutional data and knowledge? Should the library become the integrator in the digital medium? 18 November 2018 ARL Ottawa 2006