transparent publishing & open science - how to share ... · transparent publishing & open...
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Transparent Publishing & Open Science -how to share reproducible data
Transparent Peer ReviewOpen Data & Structured MethodsPreprintsTransparent Metrics
Reproducibility Crisis
Scientific Integrity
Broken Peer Review?
Research Assessment (DORA etc.)
NamesReports
Reports + Names
Open Peer Review Reportsscientific discourse & accountability
• Signed Decision Letters• Author rebuttals• Dates• Cross-referee discussion• Author Preconsultation• No confidential comments• Named co-referees• Optional: >97% adoption
Peer Review
EMBO Transparent Process open whole editorial process to authors & readers
structured referee reports
• Accountability• 3 orthogonal expert views on dataset• Training• Referee Credit
• Technical / Editorial / Further reaching
• html; DOIs• summaries• add to preprint version• referee credit (ORCID, CrossRef, Publons)
Are researchers adequately trained in peer review?
Strongly agree Agree
Neutral Disagree
Strongly disagree Don't know
next
Letter‘We, the undersigned journals, recognise the benefits of transparency in the peer review process. Therefore, we enable or undertake to enable the publication of all of the content of peer review, but not necessarilythe names of reviewers (this is also called open peer review reports)
and author responses alongside final, published articles…..’
one set of instructions
+commitment
Figure
Source Data
Raw Data
A new layer in papers: Source Data
Source Data• Minimally Processed Data• Replicates
Source Data
‘I’m a great believer in seeing all the data – this is an important lever for transparency‘
Michael Farthing, founder COPE
• Archive • Replicates• Reanalysis• Reuse• Discourage manipulation
Data Packagesfigure + metadata = nodal point for science communication
metadataRDF
source dataCSV
figureJPEG
manifestXML
descriptioninterpretation
HTML
authorshipHTML
methods
HTML
codePY
citationHTML
Small molecules
Genes
Proteins
Cellular components Cell types
Tissues
Organisms
Smart Figure Knowledge graph Specific dataData-oriented search
AI powered Data Search
• Integration with Data Repositories (Biostudies)• Figure level authorship• methods >< data links
Reproducible Methods & Data availabilityReagents & Tools Table (materials, reagents, models, software; source & identifiers)Protocols (written & video)
Preprints – dissemination before QCEncourage posting:• Clear Guidelines• Extended scooping protection• Journal to preprint (bioRxiv) submission facility:
350 co-submission posts (Jan-Sept 2018, across EMBO Press)
• [adding referee comments]
A concerned author (20/8/2018)’The decision not to consider the work … now leaves … us subject to being scooped...prevent submissions falling into the apparently predatory trap BioRxiv in the future.
Reproducibility Crisis
Scientific Integrity
Broken Peer Review?
Research Assessment (DORA etc.)
Broadly adopted journal standardsFunder MandatesResourcing (NB: PlanS)