scott edmunds, recon 2015: beyond dead trees, publishing digital research objects
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0000-0001-6444-1436
@SCEdmunds
[email protected] Edmunds
Beyond dEad trees
publishing digital research objects
Need to move beyond 350 year old incentive systems
Buckheit & Donoho: Scholarly articles are merely advertisement of scholarship. The actual scholarly artifacts, i.e. the data and computational methods, which support the scholarship, remain largely inaccessible.
JIFBAIT Network
more
GWASGWAS
JIFBAIT NEWS
Arsenic Life forms, will they take over the planet?
By Melba Ketchum, PhD
Which Overhyped, Unreproducible Experiment Are You?
Want rapid citations for 2 years only? Carry out this quiz.
You got: STAP CellsOf course dipping cells in coffee will make them pluripotent. Even if the research gets discredited, it’ll still get 100’s of citations in two years.
The end result….Attempts to “game the peer-review system on an industrial scale”
1. dx.doi.org/10.1087/201102032. http://www.scientificamerican.com/article/for-sale-your-name-here-in-a-prestigious-science-journal/3. http://www.scmp.com/comment/insight-opinion/article/1758662/china-must-restructure-its-academic-inc
entives-curb-research
Companies offering authorship of papers made to order by “paper mills”. Meta-analyses, network analysis & more.
Guaranteed publication in JIF journal, often using fake referees, ID theft, etc.
Consequences: increasing number of retractions>15X increase in last decade
At current % > by 2045 as many papers published as retracted
1. Science publishing: The trouble with retractions http://www.nature.com/news/2011/111005/full/478026a.html 2. Bjorn Brembs: Open Access and the looming crisis in science https://theconversation.com/open-access-and-the-looming-crisis-in-science-14950
STAP paper demonstrates problems:
Nature Editorial, 2nd July 2014:
“We have concluded that we and the referees could not have detected the problems that fatally undermined the papers. The referees’ rigorous reports quite rightly took on trust what was presented in the papers.”
http://www.nature.com/news/stap-retracted-1.15488
STAP paper demonstrates problems:
…to publish protocols BEFORE analysis…better access to supporting data…more transparent & accountable review
…to publish replication studies
Need:
• Review• Data• Software• Models• Pipelines• 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
GigaSolution: deconstructing the paper
www.gigadb.orgwww.gigasciencejournal.com
Utilizes big-data infrastructure and expertise from:
Combines and integrates (with DOIs):Open-access journal
Data Publishing Platform
Data Analysis Platform
Open Review Platform
Things we need to reward
1. Reward Open Data
Data Publishing: nothing new…
Data & Metadata Collection/Experiments
Analysis/Hypothesis/Analysis
Conclusions
+ Area of Interest/Question
1839
1859
20 Yrs.
Data Publishing: Can be Life or Death
Climate change, global hunger, pollution, cancer, disease outbreaks…
http://www.nature.com/news/data-sharing-make-outbreak-research-open-access-1.16966
To maximize its utility to the research community and aid those fighting the current epidemic, genomic data is released here into the public domain under a CC0 license. Until the publication of research papers on the assembly and whole-genome analysis of this isolate we would ask you to cite this dataset as:
Li, D; Xi, F; Zhao, M; Liang, Y; Chen, W; Cao, S; Xu, R; Wang, G; Wang, J; Zhang, Z; Li, Y; Cui, Y; Chang, C; Cui, C; Luo, Y; Qin, J; Li, S; Li, J; Peng, Y; Pu, F; Sun, Y; Chen,Y; Zong, Y; Ma, X; Yang, X; Cen, Z; Zhao, X; Chen, F; Yin, X; Song,Y ; Rohde, H; Li, Y; Wang, J; Wang, J and the Escherichia coli O104:H4 TY-2482 isolate genome sequencing consortium (2011) Genomic data from Escherichia coli O104:H4 isolate TY-2482. BGI Shenzhen. doi:10.5524/100001 http://dx.doi.org/10.5524/100001
Our first DOI:
To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to Genomic Data from the 2011 E. coli outbreak. This work is published from: China.
Downstream consequences:
“Last summer, biologist Andrew Kasarskis was eager to help decipher the genetic origin of the Escherichia coli strain that infected roughly 4,000 people in Germany between May and July. But he knew it that might take days for the lawyers at his company — Pacific Biosciences — to parse the agreements governing how his team could use data collected on the strain. Luckily, one team had released its data under a Creative Commons licence that allowed free use of the data, allowing Kasarskis and his colleagues to join the international research effort and publish their work without wasting time on legal wrangling.”
1. Citations (~300) 2. Therapeutics (primers, antimicrobials) 3. Platform Comparisons
4. Example for faster & more open science
1.3 The power of intelligently open dataThe benefits of intelligently open data were powerfully illustrated by events following an outbreak of a severe gastro-intestinal infection in Hamburg in Germany in May 2011. This spread through several European countries and the US, affecting about 4000 people and resulting in over 50 deaths. All tested positive for an unusual and little-known Shiga-toxin–producing E. coli bacterium. The strain was initially analysed by scientists at BGI-Shenzhen in China, working together with those in Hamburg, and three days later a draft genome was released under an open data licence. This generated interest from bioinformaticians on four continents. 24 hours after the release of the genome it had been assembled. Within a week two dozen reports had been filed on an open-source site dedicated to the analysis of the strain. These analyses provided crucial information about the strain’s virulence and resistance genes – how it spreads and which antibiotics are effective against it. They produced results in time to help contain the outbreak. By July 2011, scientists published papers based on this work. By opening up their early sequencing results to international collaboration, researchers in Hamburg produced results that were quickly tested by a wide range of experts, used to produce new knowledge and ultimately to control a public health emergency.
second
1. http://www.gigasciencejournal.com/content/3/1/222. http://minotour.nottingham.ac.uk/ 3. https://github.com/lexnederbragt/INF-BIOx121_fall2014_de_novo_assembly
1st Nanopore MinION E. Coli genome released via GigaDB 10th September 2014 (>125GB)
Data Note peer reviewed & published 20th October1
Immediately used for teaching materials2 & real-time tools3
second
Real time sequencing era needs real time publication!
• First nanopore clinical amplicon sequencing paper (& data) published March 2015
• Can determine virus/bacteria strains in hours
• Already in use tackling Ebola in West Africa
• “Living internet of things”
http://www.gigasciencejournal.com/content/4/1/12
IRRI GALAXYRice 3K project: 3,000 rice genomes, 13.4TB public data
Feed The World With (Big) Data
OMERO: providing access to imaging data
Already used by JCB.
View, filter, measure raw images with direct links from journal article.
See all image data, not just cherry picked examples.
Download and reprocess.
Need for better handling of imaging data
The alternative...
...look but don't touch
Need for better handling of imaging data
2. Reward Open DataExecutable
Methods
Answer
Metadata
softwareAnalysis
(Pipelines)
Workflows/Environments
Idea
Study
Rewarding the
DOI, etc.Publication
Publication
Publication
Data
Software
https://github.com/gigascience
Transparent
Open & able to build upon
Taking citeable snapshots
@jeejkang
gigagalaxy.net
WorkflowsReward Sharing of Workflows
Visualisations & DOIs for workflows
http://www.gigasciencejournal.com/series/Galaxy 29
Facilitate reproducibility, reuse & sharing & publish outputs of: Knitr, Sweave, Jupyter/iPython Notebook, etc.
Open DocumentsReward Open/Dynamic Workbooks
E.g.
http://www.gigasciencejournal.com/content/3/1/3
E.g.
http://www.gigasciencejournal.com/content/3/1/3
E.g.
http://www.gigasciencejournal.com/content/3/1/3
Reviewer (Christophe Pouzat): “It took me a couple of hours to get the data, the few custom developed routines, the “vignette” and to REPRODUCE EXACTLY the analysis presented in the manuscript. With few more hours, I was able to modify the authors’ code to change their Fig. 4. In addition to making the presented research trustworthy, the reproducible research paradigm definitely makes the reviewer’s job much more fun!
http://www.gigasciencejournal.com/content/3/1/23http://www.gigasciencejournal.com/content/4/1/19
Virtual Machines
• Downloadable as virtual harddisk/available as Amazon Machine Image
• Experimenting & reviewing container (docker) submissions
Taking a microscope to the publication process
http://biorxiv.org/content/early/2014/12/08/011973
Lessons Learned• Is possible to push button(s) & recreate a result from
a paper
• Most published research findings are false. Or at least have errors
• Reproducibility is COSTLY. How much are you willing to spend?
• Much easier to do this before rather than after publication
The cost of staying with the status quo?
• Ioannidis estimate that 85% of research resources are wasted.
• ~US$28B year unnecessarily spent on preclinical research in US.
• Each retraction estimated to cost $400,000.http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001747http://elifesciences.org/content/3/e02956http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002165
Death to the Publication. Long live the Research Object!
Manifesto for a reproducible publisher:
The era of the 1665-style publication is over
Reward replication not advertising
Credit FAIR data, not JIF-bait narrative
Granularity ≠ salami slicing. Ingelfinger is the enemy
We need a recognizable mark/badge/score(s) for replication
Separate category in ORCID for actually usable things
?
Ruibang Luo (BGI/HKU)Shaoguang Liang (BGI-SZ)Tin-Lap Lee (CUHK)Qiong Luo (HKUST)Senghong Wang (HKUST)Yan Zhou (HKUST)
Thanks to:
@gigasciencefacebook.com/GigaScienceblogs.biomedcentral.com/gigablog/
Peter LiChris HunterJesse Si ZheRob DavidsonNicole NogoyLaurie GoodmanAmye Kenall (BMC)
Marco Roos (LUMC)Mark Thompson (LUMC)Jun Zhao (Lancaster)Susanna Sansone (Oxford)Philippe Rocca-Serra (Oxford) Alejandra Gonzalez-Beltran (Oxford)
www.gigadb.orggigagalaxy.net
www.gigasciencejournal.com
CBIITFunding from:
Our collaborators:team: (Case study)
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