OPEN SCIENCE - UZH2345be9a-3d67-4a55-8097-6885ec2… · OpenAIRE - Supporting Open Science in Europe Transparency in Data Sharing and Peer Review Christian Fuhrer, Main Library University

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OPEN SCIENCEResearch Data & Scientific Publishing: Future Developments

Introduction and Overview

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

OpenAIRE - Supporting Open Science in Europe

Transparency in Data Sharing and Peer Review

Christian Fuhrer, Main Library University of Zurich

André Hoffmann, Main Library University of Zurich and OpenAIREplus (EU FP7 Project)

Eva Amsen, Outreach Director for the Open Access Journal F1000Research

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Open Access Week 2013

Open Science

Research Data & Scientific Publishing: Future Developments

Open Access Week 2013, Christian Fuhrer 21.20.2013

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]

http://www.hbz.uzh.ch/

http://www.oai.uzh.ch/

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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

2 Open Access Week 2013, Christian Fuhrer 21.20.2013



http://www.openaire.eu/

http://f1000research.com/



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11.11.2013 Titel der Präsentation, Simon Allemann Seite 3

Introduction and Overview Christian Fuhrer

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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?

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Page 6 28.6.2012 Christian Gutknecht

Com

pact

Muo

n S

olen

oid

(CM

S),

Pho

to b

y M

urie

l

Loek Essers (2011). CERN pushes storage limits as it probes secrets of universe. In Computerworld. 11.7.2011 6

http://commons.wikimedia.org/wiki/File:Muon_Barrel.jpg?uselang=de

http://news.idg.no/cw/art.cfm?id=FF726AD5-1A64-6A71-CE987454D9028BDF

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Ser

ver

room

in C

ER

N. P

hoto

by

Flo

rian

Hirz

inge

r

Loek Essers (2011). CERN pushes storage limits as it probes secrets of universe. In Computerworld. 11.7.2011 7

http://de.wikipedia.org/w/index.php?title=Datei:CERN_Server_03.jpg&filetimestamp=20090312142836

http://de.wikipedia.org/w/index.php?title=Datei:CERN_Server_03.jpg&filetimestamp=20090312142836

http://news.idg.no/cw/art.cfm?id=FF726AD5-1A64-6A71-CE987454D9028BDF

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Long Tail

Number of research projects

Siz

e, c

ompl

exity

Open Access Week 2013, Christian Fuhrer 21.20.2013 8

All disciplines increasingly produce data Few projects produce large and complex data: BIG DATA Most projects produce «some» data: SMALL DATA

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Data Publication Pyramid EU Project ODE (Opportunities for Data Exchange)

Reilly, S. et al. (2011). Report on Integration of Data and Publications

• Data contained or explained in articles Publications with data

• Data and explanations as supplements to articles

Processed Data and Data

Representations

• Referenced data in data repositories or IT centers

Data Collections and Structured Databases

• Data on institute‘s or personal discs Raw Data and Data Sets


http://www.alliancepermanentaccess.org/wp-content/uploads/downloads/2011/11/ODE-ReportOnIntegrationOfDataAndPublications-exesummary_final.pdf




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How to publish data?

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Publishing research data like this…


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http://dx.doi.org/10.1038/msb.2012.9


http://dx.doi.org/10.1038/msb.2012.9

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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)

http://www.re3data.org/ DFG-Projekt (2012-2014)


http://www.re3data.org/

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Or not at all?

Manuscript

Publication

Library

Data Metadata

Private Files

Klump, Jens (2007). Semantic linking of data and journal publications in the STD-DOI project European GeoInformatics Workshop Edinburgh, 7 March 2007


http://www.esi.ac.uk/meetings/712/talks/3398

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Funder requirements

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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

Seite 16 Open Access Week 2013, Christian Fuhrer 21.20.2013

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„ − FP7 (2007-2013): Open Access Pilot, Mandate in «Special Clause 39» − Horizon 2020 (2014-2020; 80 Billion Euro): OA as general principle

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

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.

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Open Access and Open Data in the EU


http://ec.europa.eu/research/science-society/index.cfm?fuseaction=public.topic&id=1300

http://ec.europa.eu/research/press/2008/pdf/annex_1_new_clauses.pdf

http://europa.eu/rapid/pressReleasesAction.do?reference=IP/12/790&format=HTML&aged=0&language=EN&guiLanguage=en



http://albertopen.telegrafenberg.de/?p=678



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Funder Policy: National Science Foundation (US)

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

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.

„


http://www.nsf.gov/bfa/dias/policy/dmp.jsp

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University of Oxford: Policy on the Management of Research Data and Records

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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: […]

„


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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/


http://oa.mpg.de/lang/en-uk/berlin-prozess/berliner-erklarung/

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Who can help?

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http://www.admin.ox.ac.uk/rdm/




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13.12.2012 Kolloquium Medizinische Informatik, Christian Fuhrer http://libraries.mit.edu/guides/subjects/data-management/index.html



http://libraries.mit.edu/guides/subjects/data-management/index.html

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Supplemental Material in ZORA, citable using DOI

Zurich Open Repository and Archive, www.zora.uzh.ch, www.oai.uzh.ch

http://www.zora.uzh.ch/


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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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but hopefully a few

We won’t be able to answer all today

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11/11/2013 Page 1

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]


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11/11/2013 Open Access Week 2013, André Hoffmann Page 2

Table of Contents

– What is Open Science?

– Project OpenAIRE

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What is Open Science?

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by Greg Emmerich / CC-BY-SA-3.0

reusability reproducability

http://creativecommons.org/licenses/by-sa/3.0/

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Open Science


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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

http://creativecommons.org/licenses/by-sa/3.0/

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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 Silo

Data Silo

Data Silo

Data Silo

Data Silo

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Open Standards


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Project OpenAIRE

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Open Access Pilot


Deposit

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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


387 Publication Repositories (i.e. ZORA)

Open Access Journals

Data Repositories (Zenodo) Data Journals

Metad

ata/ U

sage d

ata

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http://www.openaire.eu

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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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From Pilot to Service: Zenodo


http://www.zenodo.org

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Human Network

Region 1 (North)

• Denmark • Finland • Iceland • Norway • Sweden

Region 2 (South)

• Cyprus • Greece • Italy • Malta • Portugal • Spain • Turkey

Region 3 (East)

• Bulgaria • Croatia • Czech

Republic • Estonia • Hungary • Latvia • Lithuania • Poland • Romania • Slovakia • Slovenia

Region 4 (West)

• Austria • Belgium • France • Germany • Ireland • Luxemburg • Netherlands • Switzerland • UK


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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/

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Open Access: Default Mode


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Questions?

André Hoffmann

[email protected]

www.openaire.eu

– @openaire_eu

– facebook.com/groups/openaire

– linkedin.com/groups/OpenAIRE-3893548

11/11/2013 Page 27 Open Access Week 2013, André Hoffmann

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Backup

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Concerns about Open Data

https://docs.google.com/document/d/1nDtHpnIDTY_G32EMJniXaOGBufjHCCk4VC9WGOf7jK4/edit





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www.data.gov


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www.data.gov


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OpenAIRE HUB

Visualize - Manage Enhanced Publications

Get support (NOADs)

Search & Browse

Curate & collaborate

Deposit Publications

& data

Research impact Citations, usage

statistics +++

Link Classify

De-duplicate Cite

Text Mine Zenodo

Data repositories Data Journals

ResearchID (ORCID, ..)

OpenDOAR

…

CRIS Systems

National funding

EC funding

Usage data Metadata on publications

Metadata on data

342 validated repositories

Publication repositories Open Access Journals

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http://www.dlib.indiana.edu/~jenlrile/metadatamap/seeingstandards.pdf

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

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

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

» BMC journals » BMJ Group journals » Elsevier journals » IOS Press journals » The Lancet journals » Nature-titled journals » PLoS journals » RSC journals » SAGE journals » Adv Clin Neurosci Rehabil » Bioinformatics » Cardiovasc Ther » Ecol Lett » Eur J Neurosci » F1000Research

» Int J Eat Disord » Int J Obstet Anesth » J Clin Invest » J Neurol » J Neurosci » J Pain » J Plant Ecol » Neurourol Urodyn » New Engl J Med » Proc Natl Acad Sci USA » PROTEOMICS J » Science

Respondents that would see the publication of data with a DOI and protocol information as potential prior publication: » Cell Press journals » Ann Oncol

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:

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

http://f1000.com/posters

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:

http://f1000r.es/zr

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

http://f1000.com/specialists

F1000RESEARCH

OPEN ACCESS WEEK OFFER:

OA2013

First paper free until 31 March 2014

ARTICLE PROCESSING CHARGES

Article type Detailed article type APC

Case Report Case report US $250

Short Article

single-result articles / data articles /

observation articles / articles based on

posters / correspondence /

commentaries

US $500

All other articles

includes research articles / methods

articles / protocols / opinions /

reviews incl. systematic reviews

US $1000

Regular Discounts • 50% discount on APCs for

referees (within 12 months after refereeing)

• 10% discount for subscribers (personal or via institute) to F1000Prime

• HINARI/AGORA waivers for low-income countries

Documents

OPEN SCIENCE - UZH2345be9a-3d67-4a55-8097-6885ec2… · OpenAIRE - Supporting Open Science in Europe Transparency in Data Sharing and Peer Review Christian Fuhrer, Main Library University