reproducible and citable data and models: an introduction

Introduction: What do we mean by citable data and reproducible models?

Carole Goble, Wolfgang Müller, Dagmar WaltemathFAIRDOM ConsortiumThe University of Manchester, UKcarole.goble@manchester.ac.uk

EraSysAPP Workshop Data Citation and Model Reproducibility, Rostock, 14-16 Sept 2015

“An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship. The actual scholarship is the complete software development environment, [the complete data] and the complete set of instructions which generated the figures.” David Donoho, “Wavelab and Reproducible

Research,” 1995

Reproducible Codes and Available Data

Why Unreproducible Research Happens

• Tainted resources• Black boxes• Poor Reporting• Unavailable

resources / results: data, software • Bad maths

• Sins of omission• Poor training,

sloppinesshttps://www.sciencenews.org/article/12-reasons-research-goes-wrong (adapted)

Ioannidis, Why Most Published Research Findings Are False, August 2005Joppa, et al, Troubling Trends in Scientific Software Use SCIENCE 340 May 2013

Scientific method• Impact factor mania• Pressure to publish• Broken peer review• Research never

reported• Disorganisation• Time pressures• Prep & curate

costs

Social environment

FAIR ReproducibilityFind, Access, Interoperate, Reuse

FAIR Publishing

Catalogues Data specific Public Archives

Commons & Cross Resource Infra Portable Packaging

STANDARDS

Standards

Packaging, Porting, Reusing

Bergman et al COMBINE archive and OMEX format: one file to share all information to reproduce a

modeling project, BMC Bioinformatics 2014, 15:369 

Citable Data

• Persistent Identifiers• Resolution• Citation attribution• Credit lists• Citation infrastructure• Snapshots and versioning• Link Data with Publications

submit articleand move on…

publish article

Research Environment

Publication Environment

Peer Review

• Find, Access, Interoperate, Reuse– Catalogues, Public Archives,

Licensing, Guidelines, Standards

– Packaging models and Data

• Data / Software Publishing– Link Data / Software and

Literature

• Credit and citation

submit articleand move on…

publish article

Research Environment

Publication Environment

Peer Review

Citing data in research articles: principles, implementation, challenges – and the benefits of changing our waysJohanna McEntyre (Mon)

Publishing data and code openly Tom Ingraham (Mon)

The FAIRDOM Commons for Systems Biology Carole Goble (Mon)

The OpenAIRE infrastructure and RDA Data Publishing Working Group: results and vision Paolo Manghi (Wed)

Data

submit articleand move on…

publish article

Research Environment

Publication Environment

Peer Review

Standards for reproducibility of model-based resultsDagmar Waltemath (Tues)

Reproducible model construction, validation and simulation Jacky Snoep (Tues)

Capturing the context – one small(ish) step for modellers, one giant leap for mankind Mihai Glont (Tues)

Archiving modeling results Finn Bacall, Stuart Owen, Martin Scharm (Weds)

Models

submit articleand move on…

publish article

Research Environment

Publication Environment

Peer Review

Hands On