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Open (and Big) Data – the next challenge

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Open (and Big) Data – the next challenge Beyond dead trees: are publishers the problem or solution? Scott Edmunds OASPA Asia, 2nd June 2013 @gigascience


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Harnessing Data-Driven Intelligence Using networking power of the internet to tackle problems Can ask new questions & find hidden patterns & connections Build on each others efforts quicker & more efficiently More collaborations across more disciplines Harness wisdom of the crowds: crowdsourcing, citizen science, crowdfunding Enables: Enabled by: Removing silos, open licenses, transparency, immediacy


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Dead trees not fit for purpose 1812 1665 1869


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The problems with publishing Scholarly articles are merely advertisement of scholarship . The actual scholarly artefacts, i.e. the data and computational methods, which support the scholarship, remain largely inaccessible --- Jon B. Buckheit and David L. Donoho, WaveLab and reproducible research, 1995 Lack of transparency, lack of credit for anything other than “regular” dead tree publication. If there is interest in data, only to monetise & re-silo Traditional publishing policies and practices a hindrance


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Things holding us back: Disincentives to share or communicate: Ingelfinger*! Embargoes, anti preprint & early data release policies Page/method/citation limits Disincentives to remix Open source approaches = plagiarism? Disincentives to release more quickly/more granularly “Salami Slicing” First 2 years of citation data the only currency “Faddism” v long term use or reproducibility. Publication bias. * T-Shirts available from Graham Steel / http://www.zazzle.co.uk/steelgraham


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The consequences: growing replication gap Ioannidis et al., (2009). Repeatability of published microarray gene expression analyses. Nature Genetics 41: 14 Ioannidis JPA (2005) Why Most Published Research Findings Are False. PLoS Med 2(8) Out of 18 microarray papers, results from 10 could not be reproduced


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Consequences: increasing number of retractions >15X increase in last decade Strong correlation of “retraction index” with higher impact factor 1. Science publishing: The trouble with retractions http://www.nature.com/news/2011/111005/full/478026a.html 2. Retracted Science and the Retraction Index ? http://iai.asm.org/content/79/10/3855.abstract?


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Consequences: growing replication gap Ioannidis et al., 2009. Repeatability of published microarray gene expression analyses. Nature Genetics 41: 14 Science publishing: The trouble with retractions http://www.nature.com/news/2011/111005/full/478026a.html Bjorn Brembs: Open Access and the looming crisis in science https://theconversation.com/open-access-and-the-looming-crisis-in-science-14950 More retractions: >15X increase in last decade At current % > by 2045 as many papers published as retracted Insufficient methods


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“Faked research is endemic in China” Global perceptions of Chinese Research Million RMB rewards for high IF publications = ? 475, 267 (2011) New Scientist, 17th Nov 2012: http://www.newscientist.com/article/mg21628910.300-fraud-fighter-faked-research-is-endemic-in-china.html Nature, 29th September 2010: http://www.nature.com/news/2010/100929/full/467511a.html Science, 29th November 2013: http://www.sciencemag.org/content/342/6162/1035.full Nature 20th July 2011: http://www.nature.com/news/2011/110720/full/475267a.html


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“Faked research is endemic in China” Global perceptions of Chinese Research Million RMB rewards for high IF publications = ? 475, 267 (2011) New Scientist, 17th Nov 2012: http://www.newscientist.com/article/mg21628910.300-fraud-fighter-faked-research-is-endemic-in-china.html Nature, 29th September 2010: http://www.nature.com/news/2010/100929/full/467511a.html Science, 29th November 2013: http://www.sciencemag.org/content/342/6162/1035.full Nature 20th July 2011: http://www.nature.com/news/2011/110720/full/475267a.html “Wide distribution of information is key to scientific progress, yet traditionally, Chinese scientists have not systematically released data or research findings, even after publication.“ “There have been widespread complaints from scientists inside and outside China about this lack of transparency. ” “Usually incomplete and unsystematic, [what little supporting data released] are of little value to researchers and there is evidence that this drives down a paper's citation numbers.”


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Issues not just in China… …to publish protocols BEFORE analysis …better access to supporting data …more transparent & accountable review …to publish replication studies Need:


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Data Software Review Re-use… = Credit } Credit where credit is overdue: “One option would be to provide researchers who release data to public repositories with a means of accreditation.” “An ability to search the literature for all online papers that used a particular data set would enable appropriate attribution for those who share. “ Nature Biotechnology 27, 579 (2009) New incentives/credit


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GigaSolution: deconstructing the paper www.gigadb.org www.gigasciencejournal.com Utilizes big-data infrastructure and expertise from: Combines and integrates: Open-access journal Data Publishing Platform Data Analysis Platform


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Rewarding open data


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Validation checks Fail – submitter is provided error report Pass – dataset is uploaded to GigaDB. Submission Workflow Curator makes dataset public (can be set as future date if required) DataCite XML file Excel submission file Submitter logs in to GigaDB website and uploads Excel submission GigaDB DOI assigned Files Submitter provides files by ftp or Aspera XML is generated and registered with DataCite Curator Review Curator contacts submitter with DOI citation and to arrange file transfer (and resolve any other questions/issues). DOI 10.5524/100003 Genomic data from the crab-eating macaque/cynomolgus monkey (Macaca fascicularis) (2011) Public GigaDB dataset See: http://database.oxfordjournals.org/content/2014/bau018.abstract


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10-100x faster download than FTP Provide curation & integration with other DBs


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IRRI GALAXY Beneficiaries of this open data?


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IRRI GALAXY Beneficiaries of this open data? Rice 3K project: 3,000 rice genomes, 13.4TB public data


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NO New Article types v Species Description <2012


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NO Collaborations with Pensoft & PLOS Cyber-centipedes & virtual worms


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SOURCE USER NARRATIVE DATA PUBLISHER EXTERNAL DATABASES ARRAYEXPRESS Morphbank DATA PRODUCTION CURATION/ INTEGRATION Genomics Barcoding Imaging microCT Video (SOCIAL) MEDIA


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NO “Cyber-type” description 2013


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New & more transparent peer-review: open review BMC Series Medical Journals


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Reward open & transparent review End reviewer 3 Downfall parody videos, now!


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New & more transparent peer-review: pre-prints


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Real-time open-review = paper in arXiv + blogged reviews Reward open & transparent review http://tmblr.co/ZzXdssfOMJfy www.gigasciencejournal.com/content/2/1/10


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Real-time open-review = paper in arXiv + blogged reviews Reward open & transparent review


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Readers are interested in open review Next step to link to ORCID


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Cloud solutions? Reward better handling of metadata… Novel tools/formats for data interoperability/handling.


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Rewarding and aiding reproducibility OMERO: providing access to imaging data…


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Implement workflows in a community-accepted format http://galaxyproject.org Rewarding and aiding reproducibility


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galaxy.cbiit.cuhk.edu.hk


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Visualizations & DOIs for workflows


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How are we supporting data reproducibility? Data sets Analyses Linked to Linked to DOI DOI Open-Paper Open-Review DOI:10.1186/2047-217X-1-18 >23,000 accesses Open-Code 7 reviewers tested data in ftp server & named reports published DOI:10.5524/100044 Open-Pipelines Open-Workflows DOI:10.5524/100038 Open-Data 78GB CC0 data Code in sourceforge under GPLv3: http://soapdenovo2.sourceforge.net/ >20,000 downloads Enabled code to being picked apart by bloggers in wiki http://homolog.us/wiki/index.php?title=SOAPdenovo2


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7 referees downloaded & tested data, then signed reports Reward open & transparent review


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Post publication: bloggers pull apart code/reviews in blogs + wiki: SOAPdenov2 wiki: http://homolog.us/wiki1/index.php?title=SOAPdenovo2 Homologus blogs: http://www.homolog.us/blogs/category/soapdenovo/ Reward open & transparent review


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SOAPdenovo2 workflows implemented in galaxy.cbiit.cuhk.edu.hk


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SOAPdenovo2 workflows implemented in galaxy.cbiit.cuhk.edu.hk Implemented entire workflow in our Galaxy server, inc.: 3 pre-processing steps 4 SOAPdenovo modules 1 post processing steps Evaluation and visualization tools Also will be available to download by >36K Galaxy users in


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SOAPdenovo2 S. aureus pipeline


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Taking a microscope to peer review


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The SOAPdenovo2 Case study Subject to and test with 3 models: Data Method/Experimental protocol Findings Types of resources in an RO ISA-TAB/ISA2OWL Nanopublication Wfdesc/ISA-TAB/ISA2OWL Models to describe each resource type


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Lessons learned: Most published research findings are false. Or at least have errors. On a semantic level (via nanopublications) discovered 4 minor errors in text (interpretation not data) Is possible to push button(s) & recreate a result from a paper Reproducibility is COSTLY. How much are you willing to spend? Much easier to do this before rather than after publication


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“Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal


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“Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal


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“Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal


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Image Source: http://commons.wikimedia.org/wiki/File:System-Mechanic-California.jpg “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal


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Give us data, papers & pipelines* Help us make it happen! scott@gigasciencejournal.com editorial@gigasciencejournal.com database@gigasciencejournal.com Contact us: * APC’s currently generously covered by BGI until 2015 www.gigasciencejournal.com


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Ruibang Luo (BGI/HKU) Shaoguang Liang (BGI-SZ) Tin-Lap Lee (CUHK) Qiong Luo (HKUST) Senghong Wang (HKUST) Yan Zhou (HKUST) Thanks to: @gigascience facebook.com/GigaScience blogs.biomedcentral.com/gigablog/ Peter Li Huayan Gao Chris Hunter Jesse Si Zhe Nicole Nogoy Laurie Goodman Amye Kenall (BMC) Marco Roos (LUMC) Mark Thompson (LUMC) Jun Zhao (Lancaster) Susanna Sansone (Oxford) Philippe Rocca-Serra (Oxford) Alejandra Gonzalez-Beltran (Oxford) www.gigadb.org galaxy.cbiit.cuhk.edu.hk www.gigasciencejournal.com CBIIT Funding from: Our collaborators: team: Case study:


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