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Sharinghigh-quality andwell-organizedscientific data and information
Jeffery Loo
SHARINGHIGH-QUALITY andWELL-ORGANIZEDSCIENTIFIC INFORMATION
SHARINGHIGH-QUALITY andWELL-ORGANIZEDSCIENTIFIC INFORMATION
Alzheimer’s Disease   Globally in 2006, 26.6 million patients By 2050, predicted to affect 1 in 85 people
•2003 collaboration - NIH, FDA, drug companies, universities, and non-profitgroups    •result = wealth of new diagnostics a...
• share all data publicly, online, freely• https://ida.loni.ucla.edu/services/Menu/  IdaData.jsp?project=ADNI
“Companies were caught in a prisoner’sdilemma,” said Dr. Jason Karlawish, anAlzheimer’s researcher at the University ofPen...
Sharing is good, butthere are some barriers        Let’s focus on journals Historically, limited distribution with     pub...
Journal sticker shock    http://www.library.ucsf.edu/help/scholpub/stickershock
Journal cost effectivenesshttp://www.journalprices.com/
a paradigm for sharing                                     Open access                         free and online access to s...
Providing Open Access        Green OA                                         Gold OA       self-archiving                ...
3. How can librarians support OA 1. What are the advantages?                                             benefits?         ...
OA advantagesFunding agency requirement                            Sustainable financial    NIH Public Access              ...
Supporting OA• Advocacy• Referal to OA options and venues • SHERPA/RoMEO, http://    www.sherpa.ac.uk/romeo/ • DOAJ, http:...
Addressing challenges• http://www.biomedcentral.com/openaccess/  inquiry/myths.pdf
SHARINGHIGH-QUALITY andWELL-ORGANIZEDSCIENTIFIC INFORMATION
The interesting case            of Dr. Jacques              Venveniste•   a tale of peer review    •   evaluating the qual...
Cinchona    Samuel Hahnemann• Homeopathy• let like be cured by like
• prepare remedies by serial dilution
systematic reviews failed todemonstrate effectivenessLinde, K; Scholz, M; Ramirez, G; Clausius, N; Melchart, D; Jonas, WB ...
• water memory• water retains a “memory” of substances
antibody   white blood cells
editorial - suspend judgment
successful results   but then ...
Peer review is important•   determines quality•   an author can do everything right methodologically, but still be    wron...
Complications with peer        review•   timeliness•   immense effort/workload•   lack transparency•   objectivity•   disj...
Dilemma for discussion•   What if a journal publication had 100 publications that    appeared methodologically sound, but ...
Mind map of your   responses
PLoS Journals• a model for responding to peer review  challenges• “Article-level metrics” • transparent details on the use...
PLoS One demohttp://dx.doi.org/10.1371/journal.pmed.0050201
3 principles for high-quality•   Crowdsourcing    •   taking tasks traditionally performed by        specific individuals a...
3 principles for high-quality•   Automated metrics    •   easy to generate    •   quick identification    •   connections t...
3 principles for high-quality•   Transparency of reviews and usage statistics    •   historical record    •   permit curre...
SHARINGHIGH-QUALITY andWELL-ORGANIZEDSCIENTIFIC INFORMATION
Fostering well-organized          data• If study data are shared, readers may  evaluate the quality of study• encourage sc...
Data management           literacyhttps://sites.google.com/site/managescientificdata/
Assigning permanentidentifiers to digital files• This helps researchers to find your work
One option is a DOI• Unique identification number for your file• Looks like this • 10.1126/science.331.6018.692• Find the fil...
How does it find the digital          file?• DOIs have metadata• move the file, update location details for  DOI
EZID Demo•   DOI and ARK generation service from UC3, California Digital Library,    University of California•   http://n2...
Summary  haiku            be open and have          quality and tidiness -           share info this way
Summary  haiku                 be open and have               quality and tidiness -                share info this way  S...
Sharing high-quality and well-organized scientific data and information
Sharing high-quality and well-organized scientific data and information
Sharing high-quality and well-organized scientific data and information
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Sharing high-quality and well-organized scientific data and information

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  • \n
  • Who am I?\nLibrarian @ Chemistry\nMLIS @ UBC\nNLM Associate Fellowship\nMSc Chemoinformatics\nPhD UNC-Chapel Hill - people want to use their mobile phones for health care services\n10 years ago - cynicism - amazed where a library degree can take you\nharvard article - focus on your strengths\n
  • why this topic?\nsharing = good --> kindergarten, fundamental value of libraries\nhigh-quality --> good to have nice things\nwell-organized --> hard to live in a mess\nscientific information --> do what you like\n
  • A story demonstrate > sharing is good\n
  • A.D. Is a form of dementia - with cognitive and functional impairments\nsymptoms can include confusion, irritability and aggression, mood swings, trouble with language, and long-term memory loss. \nGradually, bodily functions are lost, ultimately leading to death\n
  • 2003 - NIH, FDA, drug companies, universities, and non-profit groups\nunprecedented collaboration --> identify biological markers of Alzheimer’s - DNA sequence that causes disease or is associated with susceptibility to disease\nresult = wealth of new diagnostics and drugs\n\n
  • key to success - share all data, publicly available immediately to anyone with Internet access\neveryone gets a big picture of A.D.\nrealized that better off working together than individually --> develop a common data set\nit’s like I divide a cake recipe, each party needs the other’s info to make the cake\n\n
  • no one owns data = worrisome, others can profit or mis-use\nbut companies would profit from developments from greater knowledge\n
  • Sharing information - more knowledge to work from and the problem space becomes smaller - sharing the burden\n\n
  • let’s focus on traditional journal articles\nhistorically, sharing is tough\npublishers held copyright, limited distribution\nwhile free for authors to publish, readers/libraries paid for access\nexpensive subscriptions and licenses --> show chart, sticker shock\n
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  • music analogy\n instead of scholarly publications, think music\n Gratis OA = listening to music on the radio\n Libre OA = taking a recording, sampling\n
  • self-archive\n pre-print - draft not yet published, penultimate copy\n post-print = final version of record\n
  • What are the advantages of OA publishing for journal articles?\ndisadvantages?\nBased on the above, what could librarians do to support OA and mitigate challenges\n
  • Requirement by funding agencies\n NIH public Access = research received NIH funding, then papers need to be in PubMed Central within 12 months of publication\nMaximize impact = easier access may mean greater citations to the work\nshift costs from library subscriptions to potentially more sustainable sharing models\nreturn on investment of public funds for research\n
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  • students can review this document\n\n
  • More sharing > more info available > don’t want flood of bad info\n
  • typically in journal publications - reviewers are identified, they read, and write recommendations/raise issues\nauthor responds and make revisions\n
  • homeopathy = form of alternative medicine\nnot giving my opinion, just the facts\nprinciple of homeopathy - let like be cured by like - ingesting cinchona bark induces malaria-like symptoms, therefore cinchona as cure\n\n
  • prepare remedies by serial dilution\ndilute the medicine to a low dilution - guessing strong concentrations may make you sick\ndiluted until almost none of the original substance remains\n\n
  • systematic review failed to demonstrate effectiveness\n^ a b c d Linde, K; Scholz, M; Ramirez, G; Clausius, N; Melchart, D; Jonas, WB (1999), "Impact of Study Quality on Outcome in Placebo-Controlled Trials of Homeopathy", Journal of Clinical Epidemiology 52 (7): 631–6,doi:10.1016/S0895-4356(99)00048-7, PMID 10391656\n^ Cucherat, M; Haugh, MC; Gooch, M; Boissel, JP (2000), "Evidence of clinical efficacy of homeopathy. A meta-analysis of clinical trials. HMRAG. Homeopathic Medicines Research Advisory Group", European journal of clinical pharmacology 56 (1): 27–33, PMID 10853874\n^ Mathie, R (2003), "The research evidence base for homeopathy: a fresh assessment of the literature", Homeopathy 92 (2): 84–91,doi:10.1016/S1475-4916(03)00006-7, PMID 12725250\n^ a b c d Caulfield, Timothy; Debow, Suzanne (2005), "A systematic review of how homeopathy is represented in conventional and CAM peer reviewed journals", BMC Complementary and Alternative Medicine 5: 12,doi:10.1186/1472-6882-5-12, PMC 1177924, PMID 15955254\n\n
  • contemporary homeopaths propose the mechanism behind homeopathy = water memory\nclaimed ability of water to retain a "memory" of substances previously dissolved \nNo scientific evidence supports this claim.[1][2]\nThe concept was proposed by Jacques Benveniste\n\n
  • experiment whereby his research team diluted a solution of human antibodies so that nearly not a single molecule remained\nadded this solution to human basophils (type of white blood cells) and found there was a biological response as though you added the original antibody\n\n
  • submitted a paper to Nature, prominent science journal\neditors found no methodological flaws, but felt it outside of known laws of science\nconcern = if publish, lend credibility\n\n
  • published - Nature, 333, 1988\neditorial - suspend judgement\neditor Maddox demanded experiment re-run under supervision of what was termed as “ghostbusters” - Maddox, magician and paranormal researcher James Randi, physicist and freelance debunker at NIH Walter Stewart\n\n
  • redid experiments, successful results - videotaped, photographed it\ndid a blinded study, researchers did not know what was in a tube, they did not have results\nNature did a follow up in a later issue, no substantial evidence\n\n
  • Benveniste was outraged "Salem witchhunts or McCarthy-like prosecutions."\ncomplained that the magician was doing magic tricks to distract the technicians\n1997 - paper that water memory effect  could be transmitted over phone lines - digital biology\n\n
  • this case - important points about peer review\npeer review is important\ndetermines quality - author can do everything correct, methodologically, but still be wrong\nprevent misinformation\n
  • complications\nslow timing -- timeliness\nimmense effort/workload\nlack transparency - they said/they said, not disclosed\nobjectivity\ndisjointed responses - what if you only read the first article only\n
  • consider the opposite\nis it worth fighting - or can we accept\n
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  • Article usage statistics\nCitations from the scholarly literature\nSocial bookmarks\nComments\nNotes\nBlog posts\nRatings\n
  • crowdsourcing --> farm hand analogy\n
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  • \n
  • More sharing of high quality information --> well-organized so you can find\n
  • Focus on data\nIf the data behind research is shared, opportunity to evaluate the quality --> IRS audit\nWant scientists to share their data for this reason\nBut needs to be well-organized\n
  • Librarians have role - help scientists to generate well-organized, well-formed data - so that it can be shared easily\nEmerging area - align with information literacy\nBerkeley - instructional program - demo website\n\n
  • Related to information organization is assigning permanent identifiers\n
  • \n
  • DOIs have metadata associated with it, including location details\nWhen a file is moved, the author can update location details in a DOIs metadata\nin this way DOIs are more stable links to your file\n
  • \n
  • summarize succinctly - haiku\n\n
  • Transcript of "Sharing high-quality and well-organized scientific data and information"

    1. 1. Sharinghigh-quality andwell-organizedscientific data and information
    2. 2. Jeffery Loo
    3. 3. SHARINGHIGH-QUALITY andWELL-ORGANIZEDSCIENTIFIC INFORMATION
    4. 4. SHARINGHIGH-QUALITY andWELL-ORGANIZEDSCIENTIFIC INFORMATION
    5. 5. Alzheimer’s Disease Globally in 2006, 26.6 million patients By 2050, predicted to affect 1 in 85 people
    6. 6. •2003 collaboration - NIH, FDA, drug companies, universities, and non-profitgroups •result = wealth of new diagnostics and drugs
    7. 7. • share all data publicly, online, freely• https://ida.loni.ucla.edu/services/Menu/ IdaData.jsp?project=ADNI
    8. 8. “Companies were caught in a prisoner’sdilemma,” said Dr. Jason Karlawish, anAlzheimer’s researcher at the University ofPennsylvania. “They all wanted to movethe field forward, but no one wantedto take the risks of doing it.”“This one makes sense. The development ofreliable and valid measures of Alzheimer’sdisease requires such large science with suchlimited returns on the investmentthat it was in no one company’sinterest to pursue it.”
    9. 9. Sharing is good, butthere are some barriers Let’s focus on journals Historically, limited distribution with publishers holding copyright
    10. 10. Journal sticker shock http://www.library.ucsf.edu/help/scholpub/stickershock
    11. 11. Journal cost effectivenesshttp://www.journalprices.com/
    12. 12. a paradigm for sharing Open access free and online access to scholarly publications typically journal articles, increasingly books/monographs Gratis OA Libre OA free and online access free, online access + additional usage rights which may include share - copy, distribute, transmit remix - adapt the work make commercial use of work
    13. 13. Providing Open Access Green OA Gold OA self-archiving publishingpost online a version of the scholarly publish in an OA journalwork for free public use with immediate free access on publisher website1. put in an institutional repository(DSpace, DRUM) generally, authors pay an article processing fee to publish2. central repository (PubMedCentral, ArXiv)3. OA website (personal home page, OA Hybridadding a Creative Commons License) journal journal PLoS some articles are open access (if BMC author selects OA option), some articles are not
    14. 14. 3. How can librarians support OA 1. What are the advantages? benefits? 4. How can librarians mitigate2. What are the disadvantages? OA challenges?
    15. 15. OA advantagesFunding agency requirement Sustainable financial NIH Public Access model for libraries (?) Return on research funding investment Maximize impact http://opcit.eprints.org/oacitation-biblio.html
    16. 16. Supporting OA• Advocacy• Referal to OA options and venues • SHERPA/RoMEO, http:// www.sherpa.ac.uk/romeo/ • DOAJ, http://www.doaj.org/• Fund and support OA
    17. 17. Addressing challenges• http://www.biomedcentral.com/openaccess/ inquiry/myths.pdf
    18. 18. SHARINGHIGH-QUALITY andWELL-ORGANIZEDSCIENTIFIC INFORMATION
    19. 19. The interesting case of Dr. Jacques Venveniste• a tale of peer review • evaluating the quality/suitability of a scholarly work by qualified individuals within the relevant field
    20. 20. Cinchona Samuel Hahnemann• Homeopathy• let like be cured by like
    21. 21. • prepare remedies by serial dilution
    22. 22. systematic reviews failed todemonstrate effectivenessLinde, K; Scholz, M; Ramirez, G; Clausius, N; Melchart, D; Jonas, WB (1999), "Impact of Study Quality on Outcome in Placebo-Controlled Trials of Homeopathy", Journal of ClinicalEpidemiology 52 (7): 631–6,doi:10.1016/S0895-4356(99)00048-7, PMID 10391656Cucherat, M; Haugh, MC; Gooch, M; Boissel, JP (2000), "Evidence of clinical efficacy of homeopathy. A meta-analysis of clinical trials. HMRAG. Homeopathic Medicines ResearchAdvisory Group", European journal of clinical pharmacology 56 (1): 27–33, PMID 10853874Mathie, R (2003), "The research evidence base for homeopathy: a fresh assessment of the literature", Homeopathy 92 (2): 84–91,doi:10.1016/S1475-4916(03)00006-7, PMID12725250Caulfield, Timothy; Debow, Suzanne (2005), "A systematic review of how homeopathy is represented in conventional and CAM peer reviewed journals", BMC Complementary andAlternative Medicine 5: 12,doi:10.1186/1472-6882-5-12, PMC 1177924, PMID 15955254
    23. 23. • water memory• water retains a “memory” of substances
    24. 24. antibody white blood cells
    25. 25. editorial - suspend judgment
    26. 26. successful results but then ...
    27. 27. Peer review is important• determines quality• an author can do everything right methodologically, but still be wrong• prevents misinformation
    28. 28. Complications with peer review• timeliness• immense effort/workload• lack transparency• objectivity• disjointed responses
    29. 29. Dilemma for discussion• What if a journal publication had 100 publications that appeared methodologically sound, but the results are surprising/unexpected/contradictory and requires intensive review to assess quality.• What could be done differently so peer review is easier? • Think of the complications/concerns of peer review: timeliness, immense effort/workload, lack transparency, objectivity, disjointed responses • Propose changes, techniques, approaches, solutions
    30. 30. Mind map of your responses
    31. 31. PLoS Journals• a model for responding to peer review challenges• “Article-level metrics” • transparent details on the use and reach of the article • academic community may rate a publication and leave a comment
    32. 32. PLoS One demohttp://dx.doi.org/10.1371/journal.pmed.0050201
    33. 33. 3 principles for high-quality• Crowdsourcing • taking tasks traditionally performed by specific individuals and distributing the work to a group of people or community (crowd) via an open call • reduce the workload
    34. 34. 3 principles for high-quality• Automated metrics • easy to generate • quick identification • connections to other publications and tools
    35. 35. 3 principles for high-quality• Transparency of reviews and usage statistics • historical record • permit current opinion on a historical work • see what others have to say -- sometimes this is best information to guide decision-making
    36. 36. SHARINGHIGH-QUALITY andWELL-ORGANIZEDSCIENTIFIC INFORMATION
    37. 37. Fostering well-organized data• If study data are shared, readers may evaluate the quality of study• encourage scientists to share well- organized data
    38. 38. Data management literacyhttps://sites.google.com/site/managescientificdata/
    39. 39. Assigning permanentidentifiers to digital files• This helps researchers to find your work
    40. 40. One option is a DOI• Unique identification number for your file• Looks like this • 10.1126/science.331.6018.692• Find the file in a web browser by appending DOI to http://dx.doi.org/
    41. 41. How does it find the digital file?• DOIs have metadata• move the file, update location details for DOI
    42. 42. EZID Demo• DOI and ARK generation service from UC3, California Digital Library, University of California• http://n2t.net/ezid • click help tab • create DOI • add URL • templates • save all changes • demo doi resolution• API - programmatically generate DOI • role for metadata librarian
    43. 43. Summary haiku be open and have quality and tidiness - share info this way
    44. 44. Summary haiku be open and have quality and tidiness - share info this way SHARING >> open access HIGH-QUALITY >> peer review, alternative metrics WELL-ORGANIZED >> data management literacy SCIENTIFIC INFORMATION
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