Research Data & Scientific Publishing: Future Developments. Christian Fuhrer, Main Library University of Zurich

Transcription

1 Main Library OPEN SCIENCE Research Data & Scientific Publishing: Future Developments Introduction and Overview Join the Discussion! 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 Monday, October 21, :00-18:00 University of Zurich, Campus Irchel, Room Y 35 F 51 Winterthurerstrasse 190, 8057 Zürich

2 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 Open Access Week 2013, Christian Fuhrer 1

3 Hauptbibliothek Introduction and Overview Christian Fuhrer Main Library (Hauptbibliothek) University of Zurich, Open Access oai(at)hbz.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, Transparency in Data Sharing and Peer Review Eva Amsen Outreach Director for the Open Access Journal F1000Research, Eva.Amsen(at)f1000.com, Open Access Week 2013, Christian Fuhrer 2

4 Hauptbibliothek Introduction and Overview Christian Fuhrer Titel der Präsentation, Simon Allemann Seite 3

5 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 Open Access Week 2013, Christian Fuhrer 4

6 Hauptbibliothek Which data? Titel der Präsentation, Simon Allemann Seite 5

7 Hauptbibliothek Compact Muon Solenoid (CMS), Photo by Muriel Loek Essers (2011). CERN pushes Christian storage Gutknecht limits as it probes secrets of universe. In Computerworld Page 6 6

8 Hauptbibliothek Server room in CERN. Photo by Florian Hirzinger Loek Essers (2011). CERN pushes storage limits as it probes secrets of universe. In Computerworld

9 Hauptbibliothek All disciplines increasingly produce data Size, complexity Few projects produce large and complex data: BIG DATA Most projects produce «some» data: SMALL DATA Long Tail Number of research projects Open Access Week 2013, Christian Fuhrer 8

10 Hauptbibliothek Data Publication Pyramid EU Project ODE (Opportunities for Data Exchange) Publications with data Data contained or explained in articles Processed Data and Data Representations Data and explanations as supplements to articles Data Collections and Structured Databases Referenced data in data repositories or IT centers Raw Data and Data Sets Data on institute s or personal discs Reilly, S. et al. (2011). Report on Integration of Data and Publications Open Access Week 2013, Christian Fuhrer 9

11 Hauptbibliothek How to publish data? Titel der Präsentation, Simon Allemann Seite 10

12 Hauptbibliothek Publishing research data like this Open Access Week 2013, Christian Fuhrer 11

13 Hauptbibliothek Open Access Week 2013, Christian Fuhrer 12

14 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 ( ) Open Access Week 2013, Christian Fuhrer 13

15 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 Open Access Week 2013, Christian Fuhrer 14

16 Hauptbibliothek Funder requirements Titel der Präsentation, Simon Allemann Seite 15

17 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 Open Access Week 2013, Christian Fuhrer Seite 16

18 Hauptbibliothek Open Access and Open Data in the EU FP7 ( ): Open Access Pilot, Mandate in «Special Clause 39» Horizon 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 computergenerated 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) Open Access Week 2013, Christian Fuhrer Page 17

19 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 Open Access Week 2013, Christian Fuhrer 18

20 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: [ ] Open Access Week 2013, Christian Fuhrer 19

21 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 Open Access Week 2013, Christian Fuhrer 20

22 Hauptbibliothek Who can help? Titel der Präsentation, Simon Allemann Seite 21

23 Hauptbibliothek University of Oxford: Policy on the Management of Research Data and Records Open Access Week 2013, Christian Fuhrer 22

24 Hauptbibliothek University of Oxford: Policy on the Management of Research Data and Records Kolloquium Medizinische Informatik, Christian Fuhrer 23

25 Hauptbibliothek Supplemental Material in ZORA, citable using DOI Zurich Open Repository and Archive,

26 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 Titel der Präsentation, Simon Allemann Seite 25

27 Hauptbibliothek We won t be able to answer all today but hopefully a few Titel der Präsentation, Simon Allemann Seite 26

28 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 andre.hoffmann@hbz.uzh.ch 11/11/2013 Page 1

29 Main Library Table of Contents What is Open Science? Project OpenAIRE 11/11/2013 Open Access Week 2013, André Hoffmann Page 2

30 Main Library What is Open Science?

31 Main Library reusability reproducability by Greg Emmerich / CC-BY-SA /11/2013 Open Access Week 2013, André Hoffmann Page 4

32 Main Library Open Science 11/11/2013 Open Access Week 2013, André Hoffmann Page 5

33 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 /11/2013 Open Access Week 2013, André Hoffmann Page 6

34 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 11/11/2013 Open Access Week 2013, André Hoffmann Page 7

35 Main Library «Stop hugging your data» Sir Tim Berners-Lee 11/11/2013 Open Access Week 2013, André Hoffmann Page 8

36 Main Library Data Silo Data Silo Data Silo Data Silo Data Silo Data Silo 11/11/2013 Open Access Week 2013, André Hoffmann Page 9

37 Main Library 11/11/2013 Open Access Week 2013, André Hoffmann Page 10

38 Main Library Open Standards 11/11/2013 Open Access Week 2013, André Hoffmann Page 11

39 Main Library Project OpenAIRE

40 Main Library Open Access Pilot Deposit 11/11/2013 Open Access Week 2013, André Hoffmann Page 13

41 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) 11/11/2013 Open Access Week 2013, André Hoffmann Page 14

42 Main Library Infrastructure 387 Publication Repositories (i.e. ZORA) Open Access Journals Metadata/ Usage data Data Repositories (Zenodo) Data Journals 11/11/2013 Open Access Week 2013, André Hoffmann Page 15

43 Main Library 11/11/2013 Open Access Week 2013, André Hoffmann Page 16

44 Main Library 11/11/2013 Open Access Week 2013, André Hoffmann Page 17

45 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 11/11/2013 Open Access Week 2013, André Hoffmann Page 18

46 Main Library Enhanced Publications 11/11/2013 Open Access Week 2013, André Hoffmann Page 19

47 Main Library 11/11/2013 Open Access Week 2013, André Hoffmann Page 20

48 Main Library From Pilot to Service: Zenodo 11/11/2013 Open Access Week 2013, André Hoffmann Page 21

49 Main Library 11/11/2013 Open Access Week 2013, André Hoffmann Page 22

50 Main Library Human Network Region 1 (North) Region 2 (South) Region 3 (East) Region 4 (West) Denmark Finland Iceland Norway Sweden Cyprus Greece Italy Malta Portugal Spain Turkey Bulgaria Croatia Czech Republic Estonia Hungary Latvia Lithuania Poland Romania Slovakia Slovenia Austria Belgium France Germany Ireland Luxemburg Netherlands Switzerland UK 11/11/2013 Open Access Week 2013, André Hoffmann Page 23

51 Main Library A university is just a group of buildings gathered around a library. Shelby Foote 11/11/2013 Open Access Week 2013, André Hoffmann Page 24

52 Main Library 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. 11/11/2013 Open Access Week 2013, André Hoffmann Page 25

53 Main Library Open Access: Default Mode 11/11/2013 Open Access Week 2013, André Hoffmann Page 26

54 Main Library Questions? André Hoffmann facebook.com/groups/openaire linkedin.com/groups/openaire Open Access Week 11/11/ , André Hoffmann Page 27

55 Main Library Backup

56 Main Library Concerns about Open Data Ck4VC9WGOf7jK4/edit 11/11/2013 Open Access Week 2013, André Hoffmann Page 29

57 Main Library 11/11/2013 Open Access Week 2013, André Hoffmann Page 30

58 Main Library 11/11/2013 Open Access Week 2013, André Hoffmann Page 31

59 Main Library Get support (NOADs) Deposit Publications & data Visualize - Manage Enhanced Publications Search & Browse Curate & collaborate Research impact Citations, usage statistics +++ Link Classify OpenAIRE HUB De-duplicate Text Mine Cite Zenodo Metadata on publications Usage data 342 validated repositories CRIS Systems Metadata on data EC funding ResearchID (ORCID,..) Publication repositories Open Access Journals National funding OpenDOAR Data repositories Data Journals 11/11/2013 Open Access Week 2013, André Hoffmann Page 32

60 Main Library 11/11/2013 Open Access Week 2013, André Hoffmann Page 33

61 TRANSPARENCY IN DATA SHARING AND PEER REVIEW Eva Amsen, PhD Outreach Director, F1000Research

62 INTRODUCTION

63 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

64 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)

65 OPEN ACCESS

66 Increase in open access publishing

67 The Rise of Open Access Science 4 October 2013: Vol. 342 no pp

68 FROM OPEN ACCESS TO OPEN DATA

69 THINK ABOUT DATA... Not all scientific data have been published....why not?

70 WHAT HAPPENS WHEN DATA ARE NOT PUBLIC

71 PUBLICATION BIAS Negative or null studies difficult to publish Refutation studies difficult to publish Replication studies difficult to publish

72 REPLICATION

73 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

74 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

75 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

76 A REGISTRY OF STANDARDS, DATABASES AND POLICIES A coherent, curated and searchable registry of standards for data sharing Courtesy of Susanna Sansone

77 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): e doi: /journal.pone

78 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...

79 DATA ARTICLE

80 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

81 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» 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

82 F1000POSTERS F1000Posters ( 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:

83 F1000POSTERS

84 F1000POSTERS

85 FROM POSTER TO PAPER

86 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..

87 OPEN PEER REVIEW

88 The Rise of Open Access Science 4 October 2013: Vol. 342 no pp

89

90 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.

91 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...

92 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.

93 VERSIONS Different versions of the article are tracked

94 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

95

96 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, F1000Research 2013, 2:79 (doi: /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:

97 REFEREE REPORTS ARE PUBLIC All referee names are visible. Referee reports and other comments are visible to anyone.

98 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 2010 EMBO journal 2007 Frontiers journals 2006 Biology Direct All reviewers named, all reports public Review process file published with articles. Reviewers anonymous, editor named. Reviewers named, but reports not public Reviewer comments published, and reviewers named 2001 Atmospheric Chemistry and Physics Reviewers comments published on pre-publication discussion site. Reviewer names optional Medical journals in the BMC series Pre-publication history published with articles, and reviewers named (encouraged).

99 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

100 USING OPEN REFEREE REPORTS AS EDUCATIONAL TOOL

101 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.

102 GENERAL INFORMATION

103 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

104 F1000 SPECIALISTS F1000 Specialists are official, local representatives for F1000 at their universities, hospitals and institutions. To find out more and to apply visit

105 F1000RESEARCH OPEN ACCESS WEEK OFFER: OA2013 First paper free until 31 March 2014

106

107 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 includes research articles / methods articles / protocols / All other articles opinions / US $1000 reviews incl. systematic reviews 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