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Publishing and literature data-integration

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Some thoughts on science publishing from a 2013 meeting on literature and data integration

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  • DOWNLOAD THIS BOOKS INTO AVAILABLE FORMAT (2019 Update) ......................................................................................................................... ......................................................................................................................... Download Full PDF EBOOK here { https://soo.gd/irt2 } ......................................................................................................................... Download Full EPUB Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download Full doc Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download PDF EBOOK here { https://soo.gd/irt2 } ......................................................................................................................... Download EPUB Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download doc Ebook here { https://soo.gd/irt2 } ......................................................................................................................... ......................................................................................................................... ................................................................................................................................... eBook is an electronic version of a traditional print book THIS can be read by using a personal computer or by using an eBook reader. (An eBook reader can be a software application for use on a computer such as Microsoft's free Reader application, or a book-sized computer THIS is used solely as a reading device such as Nuvomedia's Rocket eBook.) Users can purchase an eBook on diskette or CD, but the most popular method of getting an eBook is to purchase a downloadable file of the eBook (or other reading material) from a Web site (such as Barnes and Noble) to be read from the user's computer or reading device. Generally, an eBook can be downloaded in five minutes or less ......................................................................................................................... .............. Browse by Genre Available eBooks .............................................................................................................................. Art, Biography, Business, Chick Lit, Children's, Christian, Classics, Comics, Contemporary, Cookbooks, Manga, Memoir, Music, Mystery, Non Fiction, Paranormal, Philosophy, Poetry, Psychology, Religion, Romance, Science, Science Fiction, Self Help, Suspense, Spirituality, Sports, Thriller, Travel, Young Adult, Crime, Ebooks, Fantasy, Fiction, Graphic Novels, Historical Fiction, History, Horror, Humor And Comedy, ......................................................................................................................... ......................................................................................................................... .....BEST SELLER FOR EBOOK RECOMMEND............................................................. ......................................................................................................................... Blowout: Corrupted Democracy, Rogue State Russia, and the Richest, Most Destructive Industry on Earth,-- The Ride of a Lifetime: Lessons Learned from 15 Years as CEO of the Walt Disney Company,-- Call Sign Chaos: Learning to Lead,-- StrengthsFinder 2.0,-- Stillness Is the Key,-- She Said: Breaking the Sexual Harassment Story THIS Helped Ignite a Movement,-- Atomic Habits: An Easy & Proven Way to Build Good Habits & Break Bad Ones,-- Everything Is Figureoutable,-- What It Takes: Lessons in the Pursuit of Excellence,-- Rich Dad Poor Dad: What the Rich Teach Their Kids About Money THIS the Poor and Middle Class Do Not!,-- The Total Money Makeover: Classic Edition: A Proven Plan for Financial Fitness,-- Shut Up and Listen!: Hard Business Truths THIS Will Help You Succeed, ......................................................................................................................... .........................................................................................................................
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  • DOWNLOAD THIS BOOKS INTO AVAILABLE FORMAT (2019 Update) ......................................................................................................................... ......................................................................................................................... Download Full PDF EBOOK here { https://soo.gd/irt2 } ......................................................................................................................... Download Full EPUB Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download Full doc Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download PDF EBOOK here { https://soo.gd/irt2 } ......................................................................................................................... Download EPUB Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download doc Ebook here { https://soo.gd/irt2 } ......................................................................................................................... ......................................................................................................................... ................................................................................................................................... eBook is an electronic version of a traditional print book THIS can be read by using a personal computer or by using an eBook reader. (An eBook reader can be a software application for use on a computer such as Microsoft's free Reader application, or a book-sized computer THIS is used solely as a reading device such as Nuvomedia's Rocket eBook.) Users can purchase an eBook on diskette or CD, but the most popular method of getting an eBook is to purchase a downloadable file of the eBook (or other reading material) from a Web site (such as Barnes and Noble) to be read from the user's computer or reading device. Generally, an eBook can be downloaded in five minutes or less ......................................................................................................................... .............. Browse by Genre Available eBooks .............................................................................................................................. Art, Biography, Business, Chick Lit, Children's, Christian, Classics, Comics, Contemporary, Cookbooks, Manga, Memoir, Music, Mystery, Non Fiction, Paranormal, Philosophy, Poetry, Psychology, Religion, Romance, Science, Science Fiction, Self Help, Suspense, Spirituality, Sports, Thriller, Travel, Young Adult, Crime, Ebooks, Fantasy, Fiction, Graphic Novels, Historical Fiction, History, Horror, Humor And Comedy, ......................................................................................................................... ......................................................................................................................... .....BEST SELLER FOR EBOOK RECOMMEND............................................................. ......................................................................................................................... Blowout: Corrupted Democracy, Rogue State Russia, and the Richest, Most Destructive Industry on Earth,-- The Ride of a Lifetime: Lessons Learned from 15 Years as CEO of the Walt Disney Company,-- Call Sign Chaos: Learning to Lead,-- StrengthsFinder 2.0,-- Stillness Is the Key,-- She Said: Breaking the Sexual Harassment Story THIS Helped Ignite a Movement,-- Atomic Habits: An Easy & Proven Way to Build Good Habits & Break Bad Ones,-- Everything Is Figureoutable,-- What It Takes: Lessons in the Pursuit of Excellence,-- Rich Dad Poor Dad: What the Rich Teach Their Kids About Money THIS the Poor and Middle Class Do Not!,-- The Total Money Makeover: Classic Edition: A Proven Plan for Financial Fitness,-- Shut Up and Listen!: Hard Business Truths THIS Will Help You Succeed, ......................................................................................................................... .........................................................................................................................
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  • DOWNLOAD THIS BOOKS INTO AVAILABLE FORMAT (2019 Update) ......................................................................................................................... ......................................................................................................................... Download Full PDF EBOOK here { https://soo.gd/irt2 } ......................................................................................................................... Download Full EPUB Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download Full doc Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download PDF EBOOK here { https://soo.gd/irt2 } ......................................................................................................................... Download EPUB Ebook here { https://soo.gd/irt2 } ......................................................................................................................... Download doc Ebook here { https://soo.gd/irt2 } ......................................................................................................................... ......................................................................................................................... ................................................................................................................................... eBook is an electronic version of a traditional print book THIS can be read by using a personal computer or by using an eBook reader. (An eBook reader can be a software application for use on a computer such as Microsoft's free Reader application, or a book-sized computer THIS is used solely as a reading device such as Nuvomedia's Rocket eBook.) Users can purchase an eBook on diskette or CD, but the most popular method of getting an eBook is to purchase a downloadable file of the eBook (or other reading material) from a Web site (such as Barnes and Noble) to be read from the user's computer or reading device. Generally, an eBook can be downloaded in five minutes or less ......................................................................................................................... .............. Browse by Genre Available eBooks .............................................................................................................................. Art, Biography, Business, Chick Lit, Children's, Christian, Classics, Comics, Contemporary, Cookbooks, Manga, Memoir, Music, Mystery, Non Fiction, Paranormal, Philosophy, Poetry, Psychology, Religion, Romance, Science, Science Fiction, Self Help, Suspense, Spirituality, Sports, Thriller, Travel, Young Adult, Crime, Ebooks, Fantasy, Fiction, Graphic Novels, Historical Fiction, History, Horror, Humor And Comedy, ......................................................................................................................... ......................................................................................................................... .....BEST SELLER FOR EBOOK RECOMMEND............................................................. ......................................................................................................................... Blowout: Corrupted Democracy, Rogue State Russia, and the Richest, Most Destructive Industry on Earth,-- The Ride of a Lifetime: Lessons Learned from 15 Years as CEO of the Walt Disney Company,-- Call Sign Chaos: Learning to Lead,-- StrengthsFinder 2.0,-- Stillness Is the Key,-- She Said: Breaking the Sexual Harassment Story THIS Helped Ignite a Movement,-- Atomic Habits: An Easy & Proven Way to Build Good Habits & Break Bad Ones,-- Everything Is Figureoutable,-- What It Takes: Lessons in the Pursuit of Excellence,-- Rich Dad Poor Dad: What the Rich Teach Their Kids About Money THIS the Poor and Middle Class Do Not!,-- The Total Money Makeover: Classic Edition: A Proven Plan for Financial Fitness,-- Shut Up and Listen!: Hard Business Truths THIS Will Help You Succeed, ......................................................................................................................... .........................................................................................................................
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Publishing and literature data-integration

  1. 1. Scientific publishing bite-size to large-scale data dissemination Pedro Beltrao, EMBL-EBI @pedr0be| trao _ pbe| trao. bIogspot. com 3, ‘l V l’? EMBL-EBI i
  2. 2. How should Iiterature be integrated with data ? I don’t really have any answers. - I use data - I have an interest in scientific publishing. Maybe I can share some observations for discussion. EMBL-EBI
  3. 3. The pace of change in scientific publishing is unpredictable Thinking about how to incentivize change is as important as thinking about what to change EMBL-EBI
  4. 4. OK it is mostly slow Debate Do mie need a Unique Scientist ID for publications in biomedìcine? Andreas Bohne-Langi’ and Elke Lance Biomedica! Digita! Libraries 2005, 2: 1 doi:101186/1742-5581-2-1 Something as “simp| e” as a common user identifier as taken many years to get off the ground (ORCID). Publishers + grant agencies coming together without any (immediate) incentive to agree on an implementation. Making use ofthese existing groups (Crossref) should facilitate new developments. EiviIElLr-Eiîll à
  5. 5. but not always slow a «Gli EMBL-EBI
  6. 6. but not always slow EMIaLr-Eal È
  7. 7. but not always slow PI D5 P195 BIOLOGY MEDICINE PAÌHOGENS COMPUTAÎIONAI. BIOLOGY EMBL-EBI
  8. 8. PLOS One Will publish anything that is scientifically sound (they stili reject on the order of 30% apparently) limare- ‘nati îlpx 31mm Adria» x/
  9. 9. a very fast change WORLITS LARGEST JUURNAL By quickly expanding the size 01 its megziiournal PL0S ONE (Iefî). the Public Library of Science (PLOS) began lo see revenues exceed expenses {rom 2010 (righi). 40 40 777 I Ali PLOS iournals î Net FIÌVBHLJG E 35 I PLOS ONE 35 î Expenses g 3o 3o c u» g, 25 u) 25 _ D 8 20 C 70 >. g ' à i5 E‘ i5 E I0 10 è’ 5 5 4 0 0 2003 2005 2007 2009 2011 2013 2007 2008 2009 2010 2011 2012 Almost 35 thousand articles per year EMBL-EBI
  10. 10. ‘f’ The Greùtflvovar of the PLOS One clones o
  11. 11. We can do that too. .. at Ieast we hope we can SCIENTIFIC REPQRTS FiOOOResearch OPEN SCIENCE - OPEN DATA - OPEN PEER REVIEW EMIEILr-Eèll È
  12. 12. We can do it cheaper PeerJ EMBL-EBI
  13. 13. Oh yeah ? We can do it for free i <_>pen Q Biology 0 ACS Central Science EMBL-EBI
  14. 14. Publishers are hoping to cover a broad range of “perceived” impact Brand Power Expensive but attracts researchers Trickie down publishing “Catch-a| |” journals S58 Peer review “ne Pre-print blogs etc If tomorrow immediate open access is mandated, this structure works
  15. 15. Publishers are hoping to cover a broad range of “perceived” impact Brand Power Nature Expensive but attracts researchers Nature babie Trickie down publishing Nature Com « unications “Catch-a| |” journals S58 Scie tific Reports If tomorrow immediate open access is mandated, this structure works EMBL-EBI
  16. 16. The expanding roie of a scientific articie One large scale-study - White paper declaring intentions - Meta-data articie - Data articie - Database articie - New aigorithm articie - Interpretation articie EMBL-EBI
  17. 17. BMC MicroPub I wrote a satire blog post describing a new journal - ORCID and Twitter account to verify “scientists” - Atweet as a submission - 3 re-tweets as peer-review EMBL-EBI
  18. 18. BMC MicroPub’ Arfldes Krammer Lab «ÉIHHLaI- Latest model for our structure ofthe Naphthalene Lz-Dioxygenase bound to phenetole « iPÌFÌDÌÌIJLPÎÌDiIC‘ o Rflolv ti flùffifln! ‘Fìvhliîf *Mi. .. lstyeargrad éuzooicai Protocol stack: 10 weird tricks to solubilizeyour protein (1/11) K ‘ sapguuds ‘y The real deal at cheap prices ! ! I-itl, ‘ lîuxfi-cs I trae 00cm 0- Hewv u REMO-ci l ‘mmrvw- m un V for PROCEEDINGS of che Thlrd Annual ascoun Satellite Workshop on lvlmlvely Parallel Sequendng (RECOMB-seq 2013) o o . ‘.0 - o u o . .. ‘ma / x o . “una c; or. “ Scope BMC MicroPub i5 an open access. peer- revieived journai with a rei/ oiutionarv publishing system. it aims to bring ziil the science that fits a ÎWEEÎ tor fast easy access lo researchers output. Authors regisler Io the system with their tvailter account whith is Iinkec I0 un ORCID ID. Validated science ieeds are parsea ior contcnt anu lweets containing the ttmicropub mg will be considered a submission. Submissions that gets restweeted by al Ieast 3 aher iiAicroPub registered scientists is considereu lo be “peer- reviewed” and will be published. 1t is journai poiicy to publish work ueemeu by peer reviev/ ers to be a coherent aria sound ziddition lo scientific kntwuleuge ano lo put Iess emphzisis on interest Ieveis. prwided that the research constitutes a useîul contribution to the field, Amantea starai Submn I nuuuluink Regista Slot: up lor salde alata Conhd un ADVERTÎSÉHEIU ( Hoflndcentrai T's: Ouv- Mm; Puhhhr 32 miilion paga virws per monti: 5 million user sssiompa momh 1.5 million mgktmnls 390,000 tamburi‘ danna
  19. 19. Nano-publication movement exists A few peopie asked me when was BMC MicroPub going to be available to the public (i) Goto Nanopub. org to find out more EIKvAIEILr-EIEII à
  20. 20. The unbundiing of the scientific process À Deposited '_' _ / Manuscript T" , manuscript i ‘ j/ drafts ‘ÎÈV’ in a pre-print server /4——7 Deposited Î_ manuscript in Comments a re- rint . p p Peer-revlew Manuscript accepted for publication server Comments I Comments C°mm9ÙÎ5 peepreview Peeigreview Peer-revlew About 7 years ago I wrote about how it would be great to open/ expose the scientific process. Data items couid be combined and re-combined into articles that would be peer-reviewed openly. Now that I am getting my wish, I am not sure I want this anymore. It is becoming impossibie to navigate through this iandscape EIMIEILr-EIEII à
  21. 21. The expanding roie of a scientific articie The giorified “micro-pub| ication” press release or data items Severa‘ groups a few scientists working for working for a I had some free many years few years time EIIvAIEILr-EIEII à
  22. 22. Data in the Iiterature Several groups a few Sci . - __5_Q___-_uié e working for a I had some free many years few years time Several data-types are mandated to be deposited in established databases EIIvAIEILr-EIEII fi
  23. 23. Data in the Iiterature OK; Databases Several groups a few Sci I - _i_g__. __; ,g e working for a I had some free many years few years time Expert curation teams attemptto standardize and coiiect this knowiedge
  24. 24. Data in the Iiterature Several g “mp3 a few sci a ' - _ — e working for a I had some free many years few years time Databases Expert curation Re-using and integrating data from the Iiterature depends on these processes. We need them to scale. EllvlIElLr-EIEII à
  25. 25. Data in the Iiterature — heiping curators Deveioping tools to facilitate curation is probably where the biggest impact can be made. - Making articles more machine readabie at the point of publication (genes, interactions, reactions, Iocalizations, functions). Even ifthis adds work to authors. Take advantage of the intense competition among publishers to provide new services. - Articie prioritization (relative to fieids, to target bio functions, target proteins, etc). Also important for credit attribution and fiitering. - Gamification of curation — “Does this sentence describe the interaction between X and Y ? ” This can feed back as tools for authors or exposed for database users. EMBL-EBI
  26. 26. Literature in the data Science publishing is more than data - Context - Interpretation - Discussion - Vision of what is just out of reach This is mostly captured in review articles. This process might aiso not scale. Computer assisted synthesis might become highly relevant.
  27. 27. Look fonNard to some discussions flvllsiLr-EIEII È

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