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

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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)