Main Library
OPEN SCIENCE Research Data & Scientific Publishing: Future Developments
Introduction and Overview Christian Fuhrer, Main Library University of Zurich
OpenAIRE - Supporting Open Science in Europe André Hoffmann, Main Library University of Zurich and OpenAIREplus (EU FP7 Project)
Transparency in Data Sharing and Peer Review Eva Amsen, Outreach Director for the Open Access Journal F1000Research
Join the Discussion!
Monday, October 21, 2013 16:00 - 18:00
University of Zurich, Campus Irchel, Room Y 35 F 51 Winterthurerstrasse 190, 8057 Zürich Hauptbibliothek
Open Access Week 2013
Open Science
Research Data & Scientific Publishing: Future Developments
Main Library (Hauptbibliothek) University of Zurich Coordination Open Access Strickhofstrasse 35, CH-8057 Zürich Tel. +41 44 635 41 62 www.hbz.uzh.ch, www.oai.uzh.ch, [email protected]
21.20.2013 Open Access Week 2013, Christian Fuhrer 1
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Introduction and Overview Christian Fuhrer Main Library (Hauptbibliothek) University of Zurich, Open Access oai(at)hbz.uzh.ch, www.oai.uzh.ch
OpenAIRE - Supporting Open Science in Europe André Hoffmann Main Library (Hauptbibliothek) University of Zurich and OpenAIREplus (EU FP7 Project) oai(at)hbz.uzh.ch, www.oai.uzh.ch, www.openaire.eu
Transparency in Data Sharing and Peer Review Eva Amsen Outreach Director for the Open Access Journal F1000Research, Eva.Amsen(at)f1000.com, http://f1000research.com
21.20.2013 Open Access Week 2013, Christian Fuhrer 2 Hauptbibliothek
Introduction and Overview
Christian Fuhrer
11.11.2013 Titel der Präsentation, Simon Allemann Seite 3 Hauptbibliothek
Open Access: free access to and re-use of scholarly publications
Open Data: free access to and re-use of research data or other data (e.g. government)
Open Science: umbrella term of the movement to make scientific research, data and dissemination accessible to all levels of an inquiring society, amateur or professional.
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Which data?
11.11.2013 Titel der Präsentation, Simon Allemann Seite 5 Hauptbibliothek
Compact Muon Muon PhotoCompactSolenoidMuriel by (CMS),
Loek Essers28.6.2012 (2011). CERN pushesChristian storage Gutknecht limits as it probes secrets of universe. In Computerworld. 11.7.2011 Page 6 6 Hauptbibliothek
Serverroom inPhoto CERN. Florianby Hirzinger
Loek Essers (2011). CERN pushes storage limits as it probes secrets of universe. In Computerworld. 11.7.2011 7 Hauptbibliothek
All disciplines increasingly produce data
Few projects produce large and complex data:
BIG DATA
Most projects produce
complexity «some» data: SMALL DATA Size,
Long Tail
Number of research projects
21.20.2013 Open Access Week 2013, Christian Fuhrer 8 Hauptbibliothek Data Publication Pyramid EU Project ODE (Opportunities for Data Exchange)
Publications • Data contained or explained in articles with data
Processed Data • Data and explanations as supplements and Data to articles Representations
Data Collections and • Referenced data in data Structured Databases repositories or IT centers
• Data on institute‘s or Raw Data and Data Sets personal discs
Reilly, S. et al. (2011). Report on Integration of Data and Publications
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How to publish data?
11.11.2013 Titel der Präsentation, Simon Allemann Seite 10 Hauptbibliothek Publishing research data like this…
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http://dx.doi.org/10.1038/msb.2012.9
21.20.2013 Open Access Week 2013, Christian Fuhrer 12 Hauptbibliothek Or better like this...
Data repositories (150+), some examples: • GenBank (US) • Protein Data Bank (US) • Dryad (UK) • DANS: Data Archiving and Networked Services (NL) • ADS: Archaeology Data Service (UK) • GESIS Data Archive (DE) • FORS (CH)
DFG-Projekt (2012-2014) http://www.re3data.org/
21.20.2013 Open Access Week 2013, Christian Fuhrer 13 Hauptbibliothek Or not at all?
Library
Publication Private Files
Manuscript Data Metadata
Klump, Jens (2007). Semantic linking of data and journal publications in the STD-DOI project European GeoInformatics Workshop Edinburgh, 7 March 2007
21.20.2013 Open Access Week 2013, Christian Fuhrer 14 Hauptbibliothek
Funder requirements
11.11.2013 Titel der Präsentation, Simon Allemann Seite 15 Hauptbibliothek Funder requirements
− Those who pay for your (academic) research… − … want your important data to be disseminated as widely as possible − … want your data to be reproducible − … want you to manage your data well − … for your own impact and the impact of the funder − … for economic impact − … since society has paid the bill
− Funders have been communicating this more and more loudly for 2-3 years
21.20.2013 Open Access Week 2013, Christian Fuhrer Seite 16 Hauptbibliothek Open Access and Open Data in the EU
− FP7 (2007-2013): Open Access Pilot, Mandate in «Special Clause 39» − Horizon 2020 (2014-2020; 80 Billion Euro): OA as general principle
Scientific data: open access to research results will boost Europe's innovation capacity (Press release, Brussels, 17 July 2012)
„ − define open access to peer-reviewed publications as the general principle in Horizon 2020, either through open access publishing ('Gold' open access) or self-archiving ('Green' open access) − promote open access to research data (experimental results, observations and computer- generated information etc.) and set a pilot framework in Horizon 2020, […] − develop and support e-infrastructures to host and share scientific information (publications and data) which are interoperable on European and global level − help researchers to comply with open access obligations and promote a culture of sharing.
Goals: By 2016: 60% OA to publications in EU By 2020: 100% OA to publications in EU EU-commissioners Neelie Kroes (Digitale Agenda) and Maire Geoghegan-Quinn (Research, Innovation und Science) http://europa.eu/rapid/pressReleasesAction.do?reference=IP/12/790&format=HTML&aged=0&language=EN&guiLanguage=en http://albertopen.telegrafenberg.de/?p=678
21.20.2013 Open Access Week 2013, Christian Fuhrer Page 17 Hauptbibliothek Funder Policy: National Science Foundation (US)
Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or „ gathered in the course of work under NSF grants.
Proposals submitted or due on or after January 18, 2011, must include a supplementary document of no more than two pages labeled “Data Management Plan”. This supplementary document should describe how „ the proposal will conform to NSF policy on the dissemination and sharing of research results.
http://www.nsf.gov/bfa/dias/policy/dmp.jsp
21.20.2013 Open Access Week 2013, Christian Fuhrer 18 Hauptbibliothek
University of Oxford: Policy on the Management of Research Data and Records
1. The University of Oxford seeks to promote the highest standards in the management of research data and records as fundamental to both high quality research and academic integrity. […] „ 5. Research data and records should be: a. Accurate, complete, authentic and reliable; b. Identifiable, retrievable, and available when needed; c. Secure and safe; d. Kept in a manner that is compliant with legal obligations and, where applicable, the requirements of funding bodies and project-specific protocols approved under the University Policy on the Ethical Conduct of
Research Involving Human Participants and Personal Data.
e. Able to be made available to others in line with appropriate ethical, data sharing and open access principles.
10. The University is responsible for: […]
21.20.2013 Open Access Week 2013, Christian Fuhrer 19 Hauptbibliothek Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities
Open access contributions include original scientific research results, raw data and metadata, source „ materials, digital representations of pictorial and graphical materials and scholarly multimedia material.
Signed by the University of Zurich (2004), the Swiss National Science Foundation (2006) and many other institutions and funders
http://oa.mpg.de/lang/en-uk/berlin-prozess/berliner-erklarung/
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Who can help?
11.11.2013 Titel der Präsentation, Simon Allemann Seite 21 Hauptbibliothek
University of Oxford: Policy on the Management of Research Data and Records
http://www.admin.ox.ac.uk/rdm/
21.20.2013 Open Access Week 2013, Christian Fuhrer 22 Hauptbibliothek
University of Oxford: Policy on the Management of Research Data and Records
http://www.admin.ox.ac.uk/rdm/
13.12.2012 Kolloquium Medizinische Informatik,http://libraries.mit.edu/guides/subjects/data Christian Fuhrer -management/index.html23 Hauptbibliothek Supplemental Material in ZORA, citable using DOI
Zurich Open Repository and Archive, www.zora.uzh.ch, www.oai.uzh.ch Hauptbibliothek
So many (upcoming) questions regarding research data!
Storage Publication Funder expectations: data management, Open Data How can universities and libraries help? Novel possibilities of Open Access journals: data – peer review
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We won’t be able to answer all today
but hopefully a few
11.11.2013 Titel der Präsentation, Simon Allemann Seite 26 Main Library
OpenAIRE - Supporting Open Science in Europe
André Hoffmann Main Library (Hauptbibliothek) University of Zurich Coordination Digital Preservation Strickhofstrasse 35, CH-8057 Zürich Tel. +41 44 635 41 65 www.oai.uzh.ch [email protected]
11/11/2013 Page 1 Main Library Table of Contents
– What is Open Science? – Project OpenAIRE
11/11/2013 Open Access Week 2013, André Hoffmann Page 2 Main Library What is Open Science? Main Library
reusability reproducability
by Greg Emmerich / CC-BY-SA-3.0
11/11/2013 Open Access Week 2013, André Hoffmann Page 4 Main Library Open Science
11/11/2013 Open Access Week 2013, André Hoffmann Page 5 Main Library Drivers for Open Science
• new technologies (big data and IT infrastructure) • societal challenges (Human Genome Project - Bermuda Principles) • plagiarism or fraud • “data is the new oil”
by Junior Melo / CC-BY-SA-3.0
11/11/2013 Open Access Week 2013, André Hoffmann Page 6 Main Library Benefits
• Wider access and visibility • More collaboration (other scientists see results instantly and comment) • Faster development (innovation) • More transparency • Better reproducability • Better reusability
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«Stop hugging your data» Sir Tim Berners-Lee
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Data Silo
Data Data Silo Silo Data Silo
Data Data Silo Silo
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11/11/2013 Open Access Week 2013, André Hoffmann Page 10 Main Library Open Standards
11/11/2013 Open Access Week 2013, André Hoffmann Page 11 Main Library Project OpenAIRE Main Library Open Access Pilot Deposit
11/11/2013 Open Access Week 2013, André Hoffmann Page 13 Main Library Open Access Infrastructure for Research in Europe
Technical network • Building up the infrastructure • Linking publication and data Human network • Guidelines • Support (Helpdesk System)
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Infrastructure Open Access Journals 387 Publication Repositories (i.e. ZORA) Usage data Metadata/
Data Repositories (Zenodo) Data Journals
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http://www.openaire.eu
11/11/2013 Open Access Week 2013, André Hoffmann Page 17 Main Library OpenAIRE Beneficiaries
• Researchers & Project managers: One-step deposition of publications for local reporting and global dissemination • Researchers & Industry (especially SMEs) & Citizen scientists: One-stop shop for European open access research publications • Funding agencies & Research administrators: Comprehensive assessment of research impact
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Enhanced Publications
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11/11/2013 Open Access Week 2013, André Hoffmann Page 20 Main Library From Pilot to Service: Zenodo
http://www.zenodo.org
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11/11/2013 Open Access Week 2013, André Hoffmann Page 22 Main Library Human Network
Region 1 Region 2 Region 3 Region 4 (North) (South) (East) (West) • Denmark • Cyprus • Bulgaria • Austria • Finland • Greece • Croatia • Belgium • Iceland • Italy • Czech • France • Norway • Malta Republic • Germany • Sweden • Portugal • Estonia • Ireland • Spain • Hungary • Luxemburg • Turkey • Latvia • Netherlands • Lithuania • Switzerland • Poland • UK • Romania • Slovakia • Slovenia
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“A university is just a group of buildings gathered around a library.” Shelby Foote
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EU GrantsAccess is a joint information and counselling centre of the University of Zurich and ETH Zurich, the largest regional office of the Swiss Research Network Euresearch.
http://grantsaccess.ethz.ch/en/
11/11/2013 Open Access Week 2013, André Hoffmann Page 25 Main Library Open Access: Default Mode
11/11/2013 Open Access Week 2013, André Hoffmann Page 26 Main Library Questions?
André Hoffmann [email protected] www.openaire.eu
– @openaire_eu – facebook.com/groups/openaire – linkedin.com/groups/OpenAIRE-3893548
Open Access Week11/11/2013 2013, André Hoffmann Page 27 Main Library Backup Main Library Concerns about Open Data https://docs.google.com/document/d/1nDtHpnIDTY_G32EMJniXaOGBufjHC Ck4VC9WGOf7jK4/edit
11/11/2013 Open Access Week 2013, André Hoffmann Page 29 Main Library www.data.gov
11/11/2013 Open Access Week 2013, André Hoffmann Page 30 Main Library www.data.gov
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Visualize - Manage Get support Curate & collaborate Enhanced Publications (NOADs) Research impact Deposit Citations, usage Publications statistics & data Search & Browse +++
Link Classify
Text Mine Zenodo De-duplicate Cite OpenAIRE HUB
Metadata Usage data Metadata on publications on data CRIS 342 validated repositories Systems
EC funding ResearchID (ORCID, ..) OpenDOAR National Publication repositories Data repositories funding … Open Access Journals Data Journals
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http://www.dlib.indiana.edu/~jenlrile/metadatamap/seeingstandards.pdf
11/11/2013 Open Access Week 2013, André Hoffmann Page 33 TRANSPARENCY IN DATA SHARING AND PEER REVIEW
Eva Amsen, PhD Outreach Director, F1000Research
[email protected] http://f1000research.com @f1000Research INTRODUCTION WHAT IS F1000RESEARCH?
F1000Research is an open access journal for life scientists that accepts all scientifically sound articles, ranging from single findings, case reports, protocols, replications, and null or negative results to more traditional articles.
Key features:
• Publication within a week
• Transparent, post-publication peer review
• All data included
• Accepts non-traditional article types
WHAT IS F1000RESEARCH?
F1000Research has a prestigious international Advisory Panel of more than 200 of the most eminent names in biology and medicine, and over 1,100 expert Editorial Board members, including:
• Oliver Distler (Uni. Zurich) • Ben Schuler (Uni. Zurich) • Adrian Hehl (Uni. Zurich) • Christian Munz (Uni. Zurich) • Leo Eberl (Uni. Zurich) • Bruno Stieger (Uni. Hospital Zurich)
OPEN ACCESS Increase in open access publishing The Rise of Open Access Science 4 October 2013: Vol. 342 no. 6154 pp. 58-59
FROM OPEN ACCESS TO OPEN DATA THINK ABOUT DATA...
Not all scientific data have been published.
....why not? WHAT HAPPENS WHEN DATA ARE NOT PUBLIC
http://www.ted.com/talks/ben_goldacre_what_doctors_don_t_know_about_the_drugs_they_prescribe.html PUBLICATION BIAS
• Negative or null studies difficult to publish
• Refutation studies difficult to publish
• Replication studies difficult to publish
REPLICATION
http://www.bbc.co.uk/news/science-environment-15373071 PROBLEMS WITH DATA SHARING IN BIOMEDICAL LITERATURE
• Data not included with papers • Data behind a paywall • Data not licensed for re-use (legal issues) • Single data sets not published at all • Inconsistent requirements for data deposition • No (perceived) immediate benefit to individuals
DATA SHARING PLATFORMS
• Platforms to publish negative data • Journals that accept negative data • Preprint servers
• Platforms to deposit data • Structured repositories (for one type of data) e.g. GenBank, PDB • Unstructured repositories e.g. Institutional repositories, Figshare
DATA SHARING POLICIES
• Guidelines and standards to regulate and facilitate sharing formats e.g. Journals request MIAME format for microarray data, and PDB deposit for protein structures • Funding requirements • http://biosharing.org
A REGISTRY OF STANDARDS, DATABASES AND POLICIES
• A coherent, curated and searchable registry of standards for data sharing
Courtesy of Susanna Sansone BUT DATA ARE NOT BEING SHARED...
“A substantial proportion of original research papers published in high-impact journals are either not subject to any data availability policies, or do not adhere to the data availability instructions in their respective journals.”
“Journals should adopt more routinely policies for data sharing”
Alsheikh-Ali AA, Qureshi W, Al-Mallah MH, Ioannidis JPA (2011) Public Availability of Published Research Data in High-Impact Journals. PLoS ONE 6(9): e24357. doi:10.1371/journal.pone.0024357 F1000RESEARCH DATA SHARING POLICY
1. Include all data with publication • Data deposited in suitable data repositories, or via Figshare. • CC0 licence: reusable
2. Allow non-traditional publications • Data articles, short research papers, negative results...
DATA ARTICLE TRANSPARENCY: ALL DATA AVAILABLE
“One goal we had for publishing this Data article in F1000Research was to quickly share some of our ongoing behavioral datasets in order to encourage collaboration with others in the field.”
-Donald Cooper University of Colorado, Boulder JOURNAL POLICIES REGARDING DATASET PUBLICATION
Journals and publishers that have confirmed that they would not view publication of datasets with a DOI and associated protocol information as prior publication, if a more standard (analysis/conclusions) article based on the data was subsequently submitted to them: » BMC journals » Int J Eat Disord » BMJ Group journals » Int J Obstet Anesth » Elsevier journals » J Clin Invest » IOS Press journals » J Neurol » The Lancet journals » J Neurosci » Nature-titled journals » J Pain » PLoS journals » J Plant Ecol » RSC journals » Neurourol Urodyn » SAGE journals » New Engl J Med » Adv Clin Neurosci Rehabil » Proc Natl Acad Sci USA » Bioinformatics » PROTEOMICS J » Cardiovasc Ther » Science » Ecol Lett » Eur J Neurosci » F1000Research Respondents that would see the publication of data with a DOI and protocol information as potential prior publication: » Cell Press journals » Ann Oncol
F1000POSTERS
F1000Posters (http://f1000.com/posters) is a unique open access repository for posters and slide presentations in biology and medicine. This permanent, structured environment keeps researchers’ work visible long after a meeting has ended and maximizes the return on the time, effort and money invested in creating each presentation. • Free to access and free to deposit • Visibility for your research beyond scientific meetings • Enables peers to provide feedback on early work • Poster publication supported by many leading journals and publishers including Nature, PNAS, Elsevier, BMJ, Lancet, PLOS, BioMed Central, SAGE and others. See: http://f1000.com/posters/journalresponses F1000POSTERS F1000POSTERS FROM POSTER TO PAPER NEGATIVE RESULTS
“Taken together, these data suggest that reactive microglia in the nTS rely on different signaling mechanisms than those described in models of chronic pain..” OPEN PEER REVIEW The Rise of Open Access Science 4 October 2013: Vol. 342 no. 6154 pp. 58-59
THE PUBLICATION PROCESS
Most journals publish papers after they pass peer review. The peer review process can take months – sometimes years. After rejection, start over again with another journal. This delays publication.
PUBLICATION DELAY IS A PROBLEM
• Can be scooped during review process
• No recent published work to show for funding applications
• Lab members leave during revision process, and paper may never be published if the project is abandoned.
• Slows down research progress
• Frustrating...
THE PUBLICATION PROCESS
• F1000Research articles are published online after an in-house pre-refereeing check, on average, within 6 working days. • Peer review and revisions are carried out publicly. • Articles with sufficient positive referee reports are indexed in PubMed.
VERSIONS Different versions of the article are tracked REFEREE SCORES
• Approved
• Approved with reservations
• Not approved
Articles with sufficient positive evaluations are indexed in PubMed, Scopus, and Embase.
or
Minimal requirements for indexing
CITING F1000RESEARCH PAPERS • Citations to F1000Research papers point to a particular version. Example citation: Spence J, Titov N, Johnston L et al. (2013) Internet-delivered eye movement desensitization and reprocessing (iEMDR): an open trial [v2; ref status: indexed, http://f1000r.es/zr] F1000Research 2013, 2:79 (doi: 10.12688/f1000research.2-79.v2) • If a paper has been updated since it was cited, and readers land on an outdated version of an article, a pop-up message on the article page makes readers aware that there is a newer version:
REFEREE REPORTS ARE PUBLIC All referee names are visible.
Referee reports and other comments are visible to anyone. JOURNALS WITH TRANSPARENT PEER REVIEW 2012: F1000Research All reviewers named, all reports public. eLife Decision letter published with articles with author approval. Reviewers anonymous, but editor named. PeerJ Peer review history published with articles with author approval. Reviewers encouraged to sign report, and editor always named. GigaScience Pre-publication history published with articles, and reviewers named. (encouraged, opt-out)
2011 BMJ Open All reviewers named, all reports public
2010 EMBO journal Review process file published with articles. Reviewers anonymous, editor named.
2007 Frontiers journals Reviewers named, but reports not public
2006 Biology Direct Reviewer comments published, and reviewers named
2001 Atmospheric Chemistry and Physics Reviewers comments published on pre-publication discussion site. Reviewer names optional. 2000 Medical journals in the BMC series Pre-publication history published with articles, and reviewers named (encouraged).
BENEFITS OF TRANSPARENT REVIEW FOR AUTHORS AND READERS • Visible discussion between referees and authors (and editors) puts paper in context. • Referees are good at spotting broader significance of an article. • Shows the back story of a paper. (e.g. Why did it take 3 rounds of review? • Authors can demonstrate that their paper was reviewed by top people in their field. • Reduces bias amongst referees • Educational aspect of open peer review: • Open referee reports can serve as examples. • Demonstrates differences between reviewers USING OPEN REFEREE REPORTS AS EDUCATIONAL TOOL
http://bit.ly/OpenPeerReviewExamples BENEFITS FOR REVIEWERS
• Take credit for hard work
• Demonstrate experience as reviewer
• Shows reviewer’s informed opinion of the work as a peer in the field, and where they thought it could be improved. • Especially relevant in borderline cases, where an article just barely passed review.
GENERAL INFORMATION WHY PUBLISH WITH F1000RESEARCH?
•Speed of publication •Post-publication peer review means your article can be published within a week. •Transparent peer review reduces bias and improves quality of reviews •Revise or update your article after publication •Newer versions of the paper are linked to previous versions. •Help the wider scientific community by sharing data •Get credit for a wider range of work •Short research articles, data articles, observations, replications, refutations, or negative results are hard to publish elsewhere
F1000 SPECIALISTS
F1000 Specialists are official, local representatives for F1000 at their universities, hospitals and institutions.
To find out more and to apply visit http://f1000.com/specialists F1000RESEARCH
OPEN ACCESS WEEK OFFER:
OA2013
First paper free until 31 March 2014
ARTICLE PROCESSING CHARGES
Detailed article Article type APC Regular Discounts type Case Report Case report US $250 • 50% discount on APCs for single-result articles referees (within 12 months / data articles / after refereeing) observation articles • 10% discount for subscribers Short Article / articles based on US $500 (personal or via institute) to posters / F1000Prime correspondence / • HINARI/AGORA waivers for commentaries low-income countries includes research articles / methods articles / protocols / All other articles US $1000 opinions / reviews incl. systematic reviews