eLife and innovations for open sharing

Talk presented at APE 2013 in Berlin on 2013-01-30.

Transcript

1. Innovations for
   Open Sharing
   at eLife
   Ian Mulvany Head of Technology
   

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2. World-class backing
   • Supported by three of the world’s leading research funders
   • Effective research communication is a critical part of research
   • Editorially, eLife is entirely independent of the funders
   Ground-breaking science, selected by experts, published
   without delay, open for greater influence.
   

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3. v1
   3
   Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013
   

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4. v1
   3
   Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013
   Announcement
   

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5. v1
   3
   Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013
   Announcement
   EIC
   

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6. v1
   3
   Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013
   Announcement
   EIC
   Editorial Board
   

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7. v1
   3
   Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013
   Announcement
   EIC
   Editorial Board
   1st Submission
   

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8. v1
   3
   Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013
   Announcement
   EIC
   Editorial Board
   1st Submission
   1st Publication
   

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9. v1
   3
   Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013
   Announcement
   EIC
   Editorial Board
   1st Submission
   1st Publication
   Journal Platform
   

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10. v1
    3
    Jun 2011 Jul 2011 Nov 2011 Jun 2012 Oct 2012 Nov 2012 Jan 2013
    Announcement
    EIC
    Editorial Board
    1st Submission
    1st Publication
    Journal Platform
    60 Publications
    

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11. v1
    4
    elife.elifesciences.org
    

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12. v1
    4
    elife.elifesciences.org
    We launched in December 2012,
    this made us very happy :)
    

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13. v1
    5
    Build an
    Architecture
    of Attention
    image: flickr abustaca
    

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14. v1
    5
    Build an
    Architecture
    of Attention
    image: flickr abustaca
    In a world of OA abundance, this is what we
    think publishers should be doing for their authors.
    

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15. v1
    6
    Make content
    Promiscuous
    image: flickr tonicastillo
    

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16. v1
    6
    Make content
    Promiscuous
    image: flickr tonicastillo
    Do this, and give the work a chance to meet a reader
    that can use it.
    

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17. v1
    Social
    7
    Robots Humans
    and
    

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18. v1
    Social
    7
    Robots Humans
    and
    We do things to promote sharing that are aimed at
    both humans and robots.
    

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19. v1
    8
    CC-BY
    Being CC-BY works for both humans and robots - WIN!
    

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20. v1
    9
    Humans
    image: flickr matthewfield
    

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21. v1
    Media policy 2
    10
    Open
    Reviews
    By opening up the review letters, and author response,
    we hope that we can share the experience of peer
    review and help readers understand the decision
    criteria for the journal.
    

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22. v1
    11
    

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23. v1
    11
    

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24. v1
    12
    

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25. v1
    12
    

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26. v1
    13
    94 %
    Making the decision letter open is at the discretion of
    the author, 94% of our authors want to make this
    information open.
    

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27. v1
    14
    Digests
    Every paper gets a
    digest, the digest is a
    short summary
    written for a lay
    audience, with the
    aim of making the
    research more
    accessible to the
    wider public.
    

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28. Media Policy
    v1
    15
    - Authors: openly discuss and
    share your work whenever you
    have the chance
    - eLife: share openly, promote,
    foster understanding
    

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29. v1
    16
    No
    Inglefinger
    Our media policy is designed to
    get of of the way of the authors,
    and increase their ability to talk
    about their work.
    

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30. v1
    17
    By the end of October, we will have
    covered 122 studies from journals for
    our consumer service. Of those, 45
    were embargoed — but we didn’t hit
    the embargo on 12 of them, because
    we had better things to do, like cover
    more interesting studies that weren’t
    embargoed.
    - Ivan Oransky
    73%
    

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31. v1
    17
    By the end of October, we will have
    covered 122 studies from journals for
    our consumer service. Of those, 45
    were embargoed — but we didn’t hit
    the embargo on 12 of them, because
    we had better things to do, like cover
    more interesting studies that weren’t
    embargoed.
    - Ivan Oransky
    73%
    There is evidence to suggest
    that most reported science is not
    under an embargo in any case
    

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32. v1
    18
    Robots
    image: http://damhorst.de/hawkins/wp-content/uploads/2010/06/RobotArmy_Stehickdruff_schwarz.jpg
    

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33. v1
    19
    Strategy
    Peer review
    Traditional Venues
    This is how publishing usually
    works
    

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34. v1
    20
    Peer review
    Traditional Venues
    This is the system that we are building,
    API driven to increase the surface area of
    the content, and to deliver usage
    information to the authors
    

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35. v1
    20
    Peer review
    Traditional Venues
    This is the system that we are building,
    API driven to increase the surface area of
    the content, and to deliver usage
    information to the authors
    

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36. v1
    20
    Peer review
    Traditional Venues
    API
    Non-Traditional Venues
    This is the system that we are building,
    API driven to increase the surface area of
    the content, and to deliver usage
    information to the authors
    

    View Slide

37. v1
    20
    Peer review
    Traditional Venues
    API
    Non-Traditional Venues
    This is the system that we are building,
    API driven to increase the surface area of
    the content, and to deliver usage
    information to the authors
    

    View Slide

38. v1
    20
    Peer review
    Traditional Venues
    API
    Non-Traditional Venues
    This is the system that we are building,
    API driven to increase the surface area of
    the content, and to deliver usage
    information to the authors
    

    View Slide

39. v1
    20
    All Curated
    Peer review
    Traditional Venues
    API
    Non-Traditional Venues
    This is the system that we are building,
    API driven to increase the surface area of
    the content, and to deliver usage
    information to the authors
    

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40. v1
    21
    We wanted a robust API, that we could
    create quickly, we chose fluidinfo as a
    hosted service
    

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41. v1
    22
    fluidinfo allows the creation of openly writable
    objects with a fluid data model, we mapped our
    article XML into key - value pairs in fluidinfo
    

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42. v1
    23
    Every article has an API endpoint.
    

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43. v1
    23
    Every article has an API endpoint.
    

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44. v1
    24
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    "2013-01-23T17:35:03.582705", "value": "*For correspondence: darnelr@rockefeller.edu"}, "elifesciences.org/api_v1/article/award_group_funding_
    {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "Howard Hughes Medical Institute"}, "elifesciences.org/
    article/research_organism": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "Mouse"}, "elifesciences.or
    article/license_url": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "http://creativecommons.org/licen
    "elifesciences.org/api_v1/article/doi_url": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "http://dx.
    10.7554/eLife.00178"}, "elifesciences.org/api_v1/article/pub_date_timestamp": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:3
    "value": 1358812800}, "elifesciences.org/api_v1/article/components": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.5827
    ["http://dx.doi.org/10.7554/eLife.00178.001", "http://dx.doi.org/10.7554/eLife.00178.002", "http://dx.doi.org/10.7554/eLife.00178.003", "http:
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    dx.doi.org/10.7554/eLife.00178.031"]}, "elifesciences.org/api_v1/article/journal_title": {"username": "elifesciences.org", "updated-at":
    "2013-01-23T17:35:03.582705", "value": "eLife"}, "elifesciences.org/api_v1/article/keywords": {"username": "elifesciences.org", "updated-at":
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    "elifesciences.org/api_v1/article/authors": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": ["Taesun Eo
    Zhang", "Huidong Wang", "Kenneth Lay", "John Fak", "Jeffrey L Noebels", "Robert B Darnell"]}, "elifesciences.org/api_v1/article/award_group_aw
    {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "NS34389"}, "elifesciences.org/api_v1/article/accepted_
    {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": 29}, "elifesciences.org/api_v1/article/accepted_date_da
    {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "November 29, 2012"}, "elifesciences.org/api_v1/article
    article_institution": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value": "University of Toronto"}, "elifes
    api_v1/article/award_group_principle_award_recipient": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "value":
    Darnell"}, "elifesciences.org/api_v1/article/accepted_date_timestamp": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.58
    "value": 1354147200}, "elifesciences.org/api_v1/article/refs": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "
    ["Blainey PC van Oijen AM Banerjee A Verdine GL Xie XS. 2006. A base-excision DNA-repair protein finds intrahelical lesion bases by fast slidi
    with DNA. Proc Natl Acad Sci USA 103: 5752 \u2013 7.", "Boutz PL Stoilov P Li Q Lin CH Chawla G Ostrow K. 2007. A post-transcriptional regulat
    polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 21: 1636 \u2013 52.", "Brennan CM Steit
    HuR and mRNA stability. Cell Mol Life Sci 58: 266 \u2013 77.", "Buckanovich RJ Darnell RB. 1997. The neuronal RNA binding protein Nova-1 recog
    RNA targets in vitro and in vivo. Mol Cell Biol 17: 3194 \u2013 201.", "Buckanovich RJ Posner JB Darnell RB. 1993. Nova, the paraneoplastic Ri
    homologous to an RNA-binding protein and is specifically expressed in the developing motor system. Neuron 11: 657 \u2013 72.", "Chao JA Patsko
    Levy M Almo SC Singer RH. 2010. ZBP1 recognition of beta-actin zipcode induces RNA looping. Genes Dev 24: 148 \u2013 58.", "Cooper TA Wan L Dr
    2009. RNA and disease. Cell 136: 777 \u2013 93.", "Crittenden SL Bernstein DS Bachorik JL Thompson BE Gallegos M Petcherski AG. 2002. A conser
    binding protein controls germline stem cells in Caenorhabditis elegans. Nature 417: 660 \u2013 3.", "Darnell RB. 2004. Paraneoplastic neurolog
    windows into neuronal function and tumor immunity. Arch Neurol 61: 30 \u2013 2.", "Darnell RB. 2006. Developing global insight into RNA regula
    Spring Harb Symp Quant Biol 71: 321 \u2013 7.", "Darnell RB Posner JB. 2006. Paraneoplastic syndromes affecting the nervous system. Semin Onco
    \u2013 98.", "Darnell RB. 1996. Onconeural antigens and the paraneoplastic neurologic disorders: at the intersection of cancer, immunity, and
    Proc Natl Acad Sci USA 93: 4529 \u2013 36.", "Darnell RB. 2010. HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley In
    RNA 1: 266 \u2013 86.", "Darnell RB Posner JB. 2011. Paraneoplastic syndromes (contemporary neurology series). USA: Oxford University Press.",
    Sherman BT Hosack DA Yang J Gao W Lane HC. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.",
    Darnell RB. 2003. Nova regulates GABA(A) receptor gamma2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer. Mo
    23: 4687 \u2013 700.", "Dredge BK Stefani G Engelhard CC Darnell RB. 2005. Nova autoregulation reveals dual functions in neuronal splicing. EM
    \u2013 20.", "Dredge BK Jensen KB. 2011. NeuN/Rbfox3 nuclear and cytoplasmic isoforms differentially regulate alternative splicing and nonsens
    decay of Rbfox2. PLoS One 6: e21585.", "Eom T Antar LN Singer RH Bassell GJ. 2003. Localization of a beta-actin messenger ribonucleoprotein co
    zipcode-binding protein modulates the density of dendritic filopodia and filopodial synapses. J Neurosci 23: 10433 \u2013 44.", "Fabian MR Son
    Filipowicz W. 2010. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79: 351 \u2013 79.", "Gehman LT Stoilov P Magu
    A Lin CH Shiue L. 2011. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet 43: 706 \u2013 11
    10.1038/ng.841.", "Giorgi C Yeo GW Stone ME Katz DB Burge C Turrigiano G. 2007. The EJC factor eIF4AIII modulates synaptic strength and neuron
    expression. Cell 130: 179 \u2013 91.", "Goina E Skoko N Pagani F. 2008. Binding of DAZAP1 and hnRNPA1/A2 to an exonic splicing silencer in a n
    exon 18 mutant. Mol Cell Biol 28: 3850 \u2013 60.", "Goodrich JS Clouse KN Schupbach T. 2004. Hrb27C, Sqd and Otu cooperatively regulate gurke
    localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. Development 131: 1949 \u2013 58.", "Gu W Pan F Zhang H Bass
    This is what the response looks like
    

    View Slide

45. authors
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    "value": 1354147200}, "elifesciences.org/api_v1/article/refs": {"username": "elifesciences.org", "updated-at": "2013-01-23T17:35:03.582705", "
    ["Blainey PC van Oijen AM Banerjee A Verdine GL Xie XS. 2006. A base-excision DNA-repair protein finds intrahelical lesion bases by fast slidi
    with DNA. Proc Natl Acad Sci USA 103: 5752 \u2013 7.", "Boutz PL Stoilov P Li Q Lin CH Chawla G Ostrow K. 2007. A post-transcriptional regulat
    polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 21: 1636 \u2013 52.", "Brennan CM Steit
    HuR and mRNA stability. Cell Mol Life Sci 58: 266 \u2013 77.", "Buckanovich RJ Darnell RB. 1997. The neuronal RNA binding protein Nova-1 recog
    RNA targets in vitro and in vivo. Mol Cell Biol 17: 3194 \u2013 201.", "Buckanovich RJ Posner JB Darnell RB. 1993. Nova, the paraneoplastic Ri
    homologous to an RNA-binding protein and is specifically expressed in the developing motor system. Neuron 11: 657 \u2013 72.", "Chao JA Patsko
    Levy M Almo SC Singer RH. 2010. ZBP1 recognition of beta-actin zipcode induces RNA looping. Genes Dev 24: 148 \u2013 58.", "Cooper TA Wan L Dr
    2009. RNA and disease. Cell 136: 777 \u2013 93.", "Crittenden SL Bernstein DS Bachorik JL Thompson BE Gallegos M Petcherski AG. 2002. A conser
    binding protein controls germline stem cells in Caenorhabditis elegans. Nature 417: 660 \u2013 3.", "Darnell RB. 2004. Paraneoplastic neurolog
    windows into neuronal function and tumor immunity. Arch Neurol 61: 30 \u2013 2.", "Darnell RB. 2006. Developing global insight into RNA regula
    Spring Harb Symp Quant Biol 71: 321 \u2013 7.", "Darnell RB Posner JB. 2006. Paraneoplastic syndromes affecting the nervous system. Semin Onco
    \u2013 98.", "Darnell RB. 1996. Onconeural antigens and the paraneoplastic neurologic disorders: at the intersection of cancer, immunity, and
    Proc Natl Acad Sci USA 93: 4529 \u2013 36.", "Darnell RB. 2010. HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley In
    RNA 1: 266 \u2013 86.", "Darnell RB Posner JB. 2011. Paraneoplastic syndromes (contemporary neurology series). USA: Oxford University Press.",
    Sherman BT Hosack DA Yang J Gao W Lane HC. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.",
    Darnell RB. 2003. Nova regulates GABA(A) receptor gamma2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer. Mo
    23: 4687 \u2013 700.", "Dredge BK Stefani G Engelhard CC Darnell RB. 2005. Nova autoregulation reveals dual functions in neuronal splicing. EM
    \u2013 20.", "Dredge BK Jensen KB. 2011. NeuN/Rbfox3 nuclear and cytoplasmic isoforms differentially regulate alternative splicing and nonsens
    decay of Rbfox2. PLoS One 6: e21585.", "Eom T Antar LN Singer RH Bassell GJ. 2003. Localization of a beta-actin messenger ribonucleoprotein co
    zipcode-binding protein modulates the density of dendritic filopodia and filopodial synapses. J Neurosci 23: 10433 \u2013 44.", "Fabian MR Son
    Filipowicz W. 2010. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79: 351 \u2013 79.", "Gehman LT Stoilov P Magu
    A Lin CH Shiue L. 2011. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet 43: 706 \u2013 11
    10.1038/ng.841.", "Giorgi C Yeo GW Stone ME Katz DB Burge C Turrigiano G. 2007. The EJC factor eIF4AIII modulates synaptic strength and neuron
    expression. Cell 130: 179 \u2013 91.", "Goina E Skoko N Pagani F. 2008. Binding of DAZAP1 and hnRNPA1/A2 to an exonic splicing silencer in a n
    exon 18 mutant. Mol Cell Biol 28: 3850 \u2013 60.", "Goodrich JS Clouse KN Schupbach T. 2004. Hrb27C, Sqd and Otu cooperatively regulate gurke
    localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. Development 131: 1949 \u2013 58.", "Gu W Pan F Zhang H Bass
    v1
    25
    It has key value pairs, lots of them.
    

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46. authors
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    ["Blainey PC van Oijen AM Banerjee A Verdine GL Xie XS. 2006. A base-excision DNA-repair protein finds intrahelical lesion bases by fast slidi
    with DNA. Proc Natl Acad Sci USA 103: 5752 \u2013 7.", "Boutz PL Stoilov P Li Q Lin CH Chawla G Ostrow K. 2007. A post-transcriptional regulat
    polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 21: 1636 \u2013 52.", "Brennan CM Steit
    HuR and mRNA stability. Cell Mol Life Sci 58: 266 \u2013 77.", "Buckanovich RJ Darnell RB. 1997. The neuronal RNA binding protein Nova-1 recog
    RNA targets in vitro and in vivo. Mol Cell Biol 17: 3194 \u2013 201.", "Buckanovich RJ Posner JB Darnell RB. 1993. Nova, the paraneoplastic Ri
    homologous to an RNA-binding protein and is specifically expressed in the developing motor system. Neuron 11: 657 \u2013 72.", "Chao JA Patsko
    Levy M Almo SC Singer RH. 2010. ZBP1 recognition of beta-actin zipcode induces RNA looping. Genes Dev 24: 148 \u2013 58.", "Cooper TA Wan L Dr
    2009. RNA and disease. Cell 136: 777 \u2013 93.", "Crittenden SL Bernstein DS Bachorik JL Thompson BE Gallegos M Petcherski AG. 2002. A conser
    binding protein controls germline stem cells in Caenorhabditis elegans. Nature 417: 660 \u2013 3.", "Darnell RB. 2004. Paraneoplastic neurolog
    windows into neuronal function and tumor immunity. Arch Neurol 61: 30 \u2013 2.", "Darnell RB. 2006. Developing global insight into RNA regula
    Spring Harb Symp Quant Biol 71: 321 \u2013 7.", "Darnell RB Posner JB. 2006. Paraneoplastic syndromes affecting the nervous system. Semin Onco
    \u2013 98.", "Darnell RB. 1996. Onconeural antigens and the paraneoplastic neurologic disorders: at the intersection of cancer, immunity, and
    Proc Natl Acad Sci USA 93: 4529 \u2013 36.", "Darnell RB. 2010. HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley In
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    Darnell RB. 2003. Nova regulates GABA(A) receptor gamma2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer. Mo
    23: 4687 \u2013 700.", "Dredge BK Stefani G Engelhard CC Darnell RB. 2005. Nova autoregulation reveals dual functions in neuronal splicing. EM
    \u2013 20.", "Dredge BK Jensen KB. 2011. NeuN/Rbfox3 nuclear and cytoplasmic isoforms differentially regulate alternative splicing and nonsens
    decay of Rbfox2. PLoS One 6: e21585.", "Eom T Antar LN Singer RH Bassell GJ. 2003. Localization of a beta-actin messenger ribonucleoprotein co
    zipcode-binding protein modulates the density of dendritic filopodia and filopodial synapses. J Neurosci 23: 10433 \u2013 44.", "Fabian MR Son
    Filipowicz W. 2010. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79: 351 \u2013 79.", "Gehman LT Stoilov P Magu
    A Lin CH Shiue L. 2011. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet 43: 706 \u2013 11
    10.1038/ng.841.", "Giorgi C Yeo GW Stone ME Katz DB Burge C Turrigiano G. 2007. The EJC factor eIF4AIII modulates synaptic strength and neuron
    expression. Cell 130: 179 \u2013 91.", "Goina E Skoko N Pagani F. 2008. Binding of DAZAP1 and hnRNPA1/A2 to an exonic splicing silencer in a n
    exon 18 mutant. Mol Cell Biol 28: 3850 \u2013 60.", "Goodrich JS Clouse KN Schupbach T. 2004. Hrb27C, Sqd and Otu cooperatively regulate gurke
    localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. Development 131: 1949 \u2013 58.", "Gu W Pan F Zhang H Bass
    v1
    25
    authors:
    Taesun Eom", "Chaolin
    Zhang", "Huidong
    Wang", "Kenneth Lay",
    "John Fak", "Jeffrey
    L Noebels", "Robert B
    Darnell
    It has key value pairs, lots of them.
    

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47. v1
    26
    Some of our
    services are
    hooked up already,
    some are being
    done manually and
    some are under
    development.
    

    View Slide

48. v1
    26
    Some of our
    services are
    hooked up already,
    some are being
    done manually and
    some are under
    development.
    

    View Slide

49. v1
    26
    Some of our
    services are
    hooked up already,
    some are being
    done manually and
    some are under
    development.
    

    View Slide

50. v1
    26
    Some of our
    services are
    hooked up already,
    some are being
    done manually and
    some are under
    development.
    

    View Slide

51. v1
    27
    We will pull usage
    data back to our
    journal for the
    authors to see, via
    our writable API
    

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52. v1
    28
    https://github.com/
    elifesciences
    Our code is open,
    have a look, help
    us make it better.
    http://dev.elifesciences.org/
    

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53. If you have done any of
    these, let us know how it
    went.
    If you want to try any of
    these things, ask us about
    our experiences
    v1
    Conclusion
    

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54. v1
    30
    Follow us
    @eLife_sciences
    @IanMulvany
    

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55. Thank you!
    v1
    31
    APE 2013
    

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