Nencki Institute of Experimental Biology, 24.06.2016

1. Open access
to publications and data
Marta Hoffman-Sommer
Open Science Platform, ICM, University of Warsaw

2. “Open science is the idea that scientific knowledge of all kinds should
be openly shared as early as is practical in the discovery process.”
Michael Nielsen

3. Open science
Open access to publications
Open data
Open source
Open educational
resources
Open peer review
Open notebook
science
Citizen science

4. European Commission (2013):
„Open access can be defined as the practice of providing on-line access to
scientificinformation that is free of charge to the end-user and that is re-usable.
In the context of research and innovation, 'scientific information' can refer to
(i) peer-reviewed scientific research articles (published in scholarly journals)
or
(ii) research data (data underlying publications, curated data and/or raw data).”
Guidelines on Open Access to Scientific Publications and Research Data
in Horizon 2020. Version 16 December 2013.

5. What are the benefits of open publications and data?
 open publications and data reach a broader audience – they have more impact
 people from outside of the academic community can use them – teachers, students,
doctors, entrepreneurs, non-governmental organizations
 researchers representing far away scientific disciplines have access – facilitates
interdisciplinary studies
 open data can be used in novel, unexpected ways, and included in larger datasets
 archiving – safe long-term storage of digital copies of files
 faster scholarly communication – research moves faster, there is less duplication of
results, less competitiveness, more cooperation, also international cooperation
 easier to identify cases of scientific misconduct or fraud, and to check reproducibility
 the use of open licenses allows text and data mining

6. Scientific information
Articles and books
KTHBiblioteket,CC-BY-SA
https://www.flickr.com/photos/kthbiblioteket/4472640423/
Research data

7. „By ’open access’ to [peer-reviewed research literature], we mean its free
availability on the public internet, permitting any users to read, download, copy,
distribute, print, search, or link to the full texts of these articles, crawl them for
indexing, pass them as data to software, or use them for any other lawful purpose,
without financial, legal, or technical barriers
other than those inseparable from gaining access to the internet itself.
The only constraint on reproduction and distribution, and the only role for
copyright in this domain, should be to
give authors control over the integrity of their work and the right to be properly
acknowledged and cited.”
Budapest Open Access Initiative (BOAI), 2002

8. 1. Open repositories
The author makes the publication available through self-archiving – parallel to
its publication in any kind of research journal
2. Open access journals
The publisher makes the publication available directly from the journal’s site.

9. Open access to publications
Gold road:
Open journals and books
Green road:
Open repositories

10. Open access journals
An OA journal grants access to the full texts of all papers it publishes,
e.g. through its own website.
PLOS – Public Library of Science
https://www.plos.org/
BMC – BioMed Central
https://www.biomedcentral.com
eLife
https://elifesciences.org/

11. https://doaj.org/
…and a lot more:

12. Financing of scientific journals
Author
Publisher
Reader
subscription
Author
Publisher
Reader
APC
Author
Publisher
Reader
Other
institution
External
funding
Subscription
journals
OA journal
APC-based
OA journal
non-APC-based
APC – article processing charge

13. Financing of scientific journals
Author
Publisher
Reader
subscription
Author
Publisher
Reader
APC
Author
Publisher
Reader
External
institution
subsidy
Subscription
journals
OA journal
APC-based
OA journal
non-APC-based
APC – article processing charge

14. Open access journal publishers
PLOS – Public Library of Science
non-profit publisher
author-pays APC model
https://www.plos.org/
BMC – BioMed Central
for-profit publisher
(Springer Nature)
author-pays APC model
https://www.biomedcentral.com
eLife
non-profit publisher
non-APC model
funded by: HHMI, Max-Planck Soc.,
Wellcome Trust
https://elifesciences.org/

15. Hybrid journals
Author
Publisher
Reader
subscription
Subscription
journals
Author
Publisher
Reader
APC
OA article
APC-based
The whole journal stays
behind a paywall,
but individual articles
are open on the
website
upon payment of APC
Hybrid journal:
double-dipping

16. Publication repositories
An OA repository is where the author makes the publication
available, through self-archiving
– parallel to its publication in any chosen research journal.

17. Publication repositories
Institutional – run by a university, research institute, granting agency –
they collect the whole research output of the institution in one place.
Disciplinary – accepts deposits from researchers affiliated with any
institution, as long as they fit in the topic.

18. Institutional repositories
DASH – Digital Access to Scholarship at Harvard
https://dash.harvard.edu/
AMUR – Adam Mickiewicz University Repository
https://repozytorium.amu.edu.pl/
PubMed Central – run by the NIH (National Institutes of Health)

19. Disciplinary repositories
SSRN – Social Sciences Research Network
www.ssrn.com
arXiv – Physics, Mathematics, Computer Science,
Quantitative Biology, Quantitative Finance and
Statistics
http://arxiv.org/

20. What about papers that don’t have a suitable
institutional nor disciplinary repository?

21. General repositories
(catch-all)
CeON Repository – publication repository,
run by ICM University of Warsaw
https://depot.ceon.pl/
Zenodo – publication and data repository,
run at CERN, funded by the EC
https://zenodo.org/
Figshare – publication and data repository,
run by a private company
https://figshare.com/

22. http://www.opendoar.org/

23. Financing of open repositories
Author
Repository
Reader
Institution
open
repository
(e.g. university, research institute, consortium
of institutions, granting agency, government, …)

24. closed-access
journal
Author
Publisher
Reader
subskrypcja
Author
Publisher
Reader
APC
open-access
journal
APC-based
Author
Repository
Reader
Other
institution
open
repository
Green OADiamond (platinum)
OA
Gold OA
Subscription
model
Open access funding models
Author
Publisher
Reader
Other
institution
subsidy
open-access
journal
non-APC-based

25. How to deposit your paper in a repository?
• Choose a repository
• Do you have the rights necessary to disseminate the paper?
• Deposit your paper: enter the metadata required by the repository
and upload your file

26. Scientific information
Articles and books
KTHBiblioteket,CC-BY-SA
https://www.flickr.com/photos/kthbiblioteket/4472640423/
Research data

27. „Research data is data that is collected, observed, or created,
for purposes of analysis to produce original research results.”
Definitions of research data
„…the recorded factual material commonly accepted in the
scientific community as necessary to validate research findings.”

28. Numerical data
Text documents, lab notes
Questionnaires, responses, transcripts
Audiotapes, videotapes
Photographs, films
Artifacts, specimens, samples
Models, algorithms, scripts
Simulation results
Methodologies and workflows
Examples of research data:

29. Numerical data
Text documents, lab notes
Questionnaires, responses, transcripts
Audiotapes, videotapes
Photographs, films
Artifacts, specimens, samples
Models, algorithms, scripts
Simulation results
Methodologies and workflows
Examples of research data
The focus [in the context of open access] is on research data
that is available in digital form.

30. “Open data and content can be freely used,
modified, and shared by anyone for any purpose.”
Open Knowledge Foundation
The Open Definition:
What is open data?

31. Major sources of open data
Public data Research data

32. Research data archives / repositories
1. Secure long-term storage – trusted archive or repository
2. Stable location – stable digital identifier, e.g. DOI (digital
object identifier)
3. Visibility – well known among interested researchers,
well visible in search engines

33. Digital research data repositories
• specialized
• disciplinary
• institutional
• general (catch-all)

34. Specialized data repositories
Berman,Kleywegt,Nakamura,Markley(2012)
http://dx.doi.org/10.1016/j.str.2012.01.010
Protein Data Bank
– since 1971
Oxford Text Archive
– since 1976
GenBank
– since 1982
http://www.ncbi.nlm.nih.gov/ge
nbank/statistics

35. Disciplinary repositories
Data underlying research papers
in biology Social sciences and humanities data

36. Institutional repositories
University data repository
Data repository run by one of the
Research Councils UK:
Natural Environment Research Council

37. General data repositories
National research data repository:
Netherlands
National research data repository:
Poland
General repository:
publications and data
General repository:
publications and data

38. re3data.org

39. • Articles describing data (data descriptors)
• The data itself is deposited in a repository
• Some journals also allow you to attach your data as Supplementary Material
Data journals
 This is an addition to the repository system, not an alternative

40. Should all data be open? No.
But data existence should always be open:
• Allows discovery & negotiation on use
• Avoids pointless replication
Slide adapted from Kevin Ashley, DCC, CC-BY
Privacy protection (human subjects!)
National security issues
Interference with commercialization plans
Ethical issues, protection of endangered species, ...

41. How to deposit your data in a repository?
• Choose a repository
• Do you have the rights necessary to disseminate the data?
• Deposit your data: enter the metadata required by the repository and
upload your file(s)
Preparing sensible metadata and documentation and
organizing your files may take time!

43. Mandate on open access to publications in H2020
Under Horizon 2020, each beneficiary must ensure open access to all peer-
reviewed scientific publications relating to its results.
In order to comply with this requirement, beneficiaries must, at the very least,
ensure that their publications, if any, can be read online, downloaded and printed.
However, as any additional rights such as the right to copy, distribute, search, link,
crawl, and mine increase the utility of the accessible publication, beneficiaries
should make every effort to provide for as many of them as possible.

44. Open research data pilot in H2020
„Participating projects are required to deposit the research data described
above, preferably into a research data repository.
As far as possible, projects must then take measures to enable for third
parties to access, mine, exploit, reproduce and disseminate (free of
charge for any user) this research data.
One straightforward and effective way of doing this is to attach a Creative
Commons Licence (CC-BY or CC0 tool) to the data deposited.”

45. Open research data pilot in H2020
Projects may opt-out, but…
„The use of a detailed data management plan covering individual datasets is
required for funded projects participating in the Open Research Data Pilot.”

46. Thank you for your attention
Contact:
m.hoffman-sommer@icm.edu.pl