Research Objects,

SEEK4Science and

FAIRDOMProfessor Carole Goble CBE FREng FBCSThe University of Manchester, UKThe Software Sustainability Institute, UKcarole.goble@manchester.ac.uk

researchobject.org

Schloss Dagstuhl Seminar 16041 Reproducibility of Data-Oriented Experiments in e-Science, 25-29 January 2016

Metadata objects – not necessarily encapsulated!Platform Independent framework to Bundle, Port and Link(scattered) resources, related experiments, and hold context

ContainerPackaging: Zip files, Docker images, BagIt, …

Catalogues & Commons Platforms: FAIRDOM SEEK, STELAR eLab

ManifestMetadataDescribes the aggregated resources, theirannotations and their provenance

Manifest

Manifest Metadata

Manifest Construction• Identification – id, title, creator, status….• Aggregates – list of ids/links to resources• Annotations – list of annotations about resources

Manifest

Manifest Description• Checklists – what should be there• Provenance – where it came from• Versioning – its evolution• Dependencies – what else is needed

Manifest

Manifest Construction

Unique identifiers as

names for things.

doi, epic, orcid, purl, RII,

Identifiers.org

Mechanism of

aggregation to group

things together.

OAI-ORE

Metadata about those

things & how they relate

to each other.

W3C OADM

http://w3id.org/ro/

FAIR Manifest Descriptions: RO typesContent Annotation Profiles

Checklist

Pro

ven

ance

Versio

nin

g

Dependencies

NISO-JATS

Dublin Core

EFO ISA

SBML

JERM

Gamble, Goble, Klyne, ZhaoMIM: A Minimum Information Model vocabulary and framework for Scientific Linked Data,IEEE 8th Intl Conf on eScience , 2012

SED-ML

SBOLMIAPE

FAIRDOMHub Sys Bio Commons

https://doi.org/10.15490/seek.1.investigation.56

Aggregating Commons

Links into public resources

Integration with public

resources

Integration with

modelling tools

FAIRDOM Repositories

SOPs

models

dataLaunch local

executables

Integration with lab tools

Integration with lab

management systems

and local file stores

Direct Upload

BiVes

RO Unzip

• Reproducibility• Versioning• Systematic and

extensible meta-data collection

• Cross platform exchange

• Publishing

Living Snapshot

https://doi.org/10.15490/seek.1.investigation.56

https://dx.doi.org/10.1111/febs.13237

SEEK Demo

Video

Other Implementations

• COMBINE Archive +RO

• Workflows RO Bundle

• STELAR Asthma eLabs

• Data Publishing

• ATLAS LHC Experiments

using CDE, Docker, improved manifests for

people

Links

• Researchobject.org

• Fair-dom.org

• Seek4science.org