1. 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
18 November 2018
ARL Ottawa 2006

2. 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

3. My Foundation (and Bias)
18 November 2018
ARL Ottawa 2006

4. 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

5. 18 November 2018
ARL Ottawa 2006

6. 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

7. 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

8. 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

9. 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

10. The Journal Thus Far
18 November 2018
ARL Ottawa 2006

11. 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

12. 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

13. 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

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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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
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

21. 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

22. 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