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Threads

 Threads

My slides from iAnnotate 2013, describing how you might take the Encode Threads idea, and make a more general version.

Ian Mulvany

July 18, 2013
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  1. iannotate workshop, April 2013
    @ianmulvany head of technology - eLife
    Threads
    weaving together the scholarly literature, using an
    annotation based approach?
    image: flickr: vpickering
    Text

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  2. ✦ a storify for science?
    ✦ where the idea comes from?
    ✦ why is eLife interested?
    ✦ what we have done so far in this direction?
    ✦ what problems are there with the idea?
    ✦ what happens next?

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  3. ✦ how do you think it should be built?
    (what sucks about where we are heading?)
    ✦ what problems are we missing?
    ✦ would you be interested in helping?

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  4. Science sucks
    at getting
    better at
    doing science

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  5. image: flickr: designshard

    View full-size slide

  6. Advertising
    Ads
    Brand
    navigation
    brand
    join
    account
    Search
    navigation
    Jobs
    issue navigation
    Article
    info
    Jobs
    Personal
    related,
    pubmed
    crossref
    tools
    alerts
    email
    rights
    content

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  7. ✦ 5 TeraBases
    ✦ 1715 × Human Genome
    ✦ 3k experiments
    ✦ 410 authors on the main paper
    ✦ 6 high profile papers
    ✦ ~35 companion papers
    ENCODE
    http://encodeproject.org/ENCODE/

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  8. ✦ Interactive figures
    ✦ Virtual machine with the analysis
    ✦ Threads
    Encode innovations

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  9. BLOB
    PROVENANCE

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  10. image: flickr: sfslim

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  11. genomeinformatician.blogspot.com/

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  12. ✦ building the thread gives overview of the topic
    ✦ could give credit to the composer
    ✦ readers benefit from well constructed threads
    ✦ easier to create than review articles
    ✦ explicitly shows the upside of OA CONTENT
    ✦ would be great not to have to do it in word

    View full-size slide

  13. v1
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    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
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    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
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    Spring Harb Symp Quant Biol 71: 321 \u2013 7.", "Darnell RB Posner JB. 2006. Paraneoplastic syndromes affecting the nervous system. Semin Onco
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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
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    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
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    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

    View full-size slide

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    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
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    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
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    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
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    View full-size slide

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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
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    23: 4687 \u2013 700.", "Dredge BK Stefani G Engelhard CC Darnell RB. 2005. Nova autoregulation reveals dual functions in neuronal splicing. EM
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    authors:
    Taesun Eom", "Chaolin
    Zhang", "Huidong
    Wang", "Kenneth Lay",
    "John Fak", "Jeffrey
    L Noebels", "Robert B
    Darnell

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  16. dev.elifesciences.org

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  17. XML
    Converter
    node.js
    JSON Article
    Viewer

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  18. Indicies
    nodes
    annotations

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  19. http://elifesciences.github.io/articleviewer/#00005

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  20. Many still use paper
    Most use PDFs
    How do you get the of the researcher to care?
    How would you identify worthwhile threads
    How do you make it easy to use?
    What’s a sufficent volume of content?

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  21. XML is not uniform anyway :(
    No workflow tool will integrate, today
    DOI -> XML is not trivial
    Where are they stored?

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  22. Next steps
    ✦talk a bit more to the EBI
    ✦evaluate:
    ✦ how cheaply could we build it
    ✦ can we prove that it would be useful to people

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  23. ✦ how do you think it should be built?
    (what sucks about where we are heading?)
    ✦ what problems are we missing?
    ✦ would you be interested in helping?

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  24. flickr:
    OZinOH
    Journal of Open Research Software - JORS

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